diff --git a/CMakeLists.txt b/CMakeLists.txt index 461343e..a3eebd4 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -9,7 +9,10 @@ find_package(ZLIB REQUIRED) find_package(BZip2 REQUIRED) find_package(LibLZMA REQUIRED) find_package(CURL REQUIRED) -find_package(Git REQUIRED) + +if(NOT APPLE) + find_package(OpenSSL REQUIRED) +endif() include(ExternalProject) set(installDir ${CMAKE_CURRENT_BINARY_DIR}/install) @@ -17,43 +20,41 @@ set(installDir ${CMAKE_CURRENT_BINARY_DIR}/install) ExternalProject_Add(htslib BUILD_IN_SOURCE YES - GIT_REPOSITORY "https://github.com/samtools/htslib.git" - GIT_TAG "1.10.2" - UPDATE_COMMAND "" - CONFIGURE_COMMAND "" - BUILD_COMMAND $(MAKE) - INSTALL_COMMAND $(MAKE) install prefix=${installDir} - LOG_DOWNLOAD YES + URL https://github.com/samtools/htslib/releases/download/1.10.2/htslib-1.10.2.tar.bz2 + CONFIGURE_COMMAND ./configure --prefix=${installDir} --enable-libcurl --enable-s3 + BUILD_COMMAND $(MAKE) lib-static ) -# Setup user config to force same c++ compiler in boost -if((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") OR (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")) - set(BOOST_UCONFIG "${CMAKE_BINARY_DIR}/user-config.jam") - if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU") - file(WRITE "${BOOST_UCONFIG}" "using gcc : : \"${CMAKE_CXX_COMPILER}\" ;\n") - elseif(CMAKE_CXX_COMPILER_ID STREQUAL "Clang") - file(WRITE "${BOOST_UCONFIG}" "using clang : : \"${CMAKE_CXX_COMPILER}\" ;\n") - set(B2_OPTIONS ${B2_OPTIONS} "toolset=clang") - endif() - set(BOOST_PATCH_COMMAND ${CMAKE_COMMAND} -E copy ${BOOST_UCONFIG} tools/build/src/user-config.jam) +# Setup boost user config so that it uses the same c++ compiler as other components: +if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU") + set (BOOST_COMPILER_TAG "gcc") +elseif(CMAKE_CXX_COMPILER_ID STREQUAL "Clang") + set (BOOST_COMPILER_TAG "clang") + set(B2_OPTIONS ${B2_OPTIONS} "toolset=clang") +elseif(CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang") + set (BOOST_COMPILER_TAG "darwin") + set(B2_OPTIONS ${B2_OPTIONS} "toolset=clang") +endif() + +if (BOOST_COMPILER_TAG) + set(BOOST_UCONFIG "${CMAKE_BINARY_DIR}/user-config.jam") + file(WRITE "${BOOST_UCONFIG}" "using ${BOOST_COMPILER_TAG} : : \"${CMAKE_CXX_COMPILER}\" ;\n") + set(BOOST_PATCH_COMMAND ${CMAKE_COMMAND} -E copy ${BOOST_UCONFIG} tools/build/src/user-config.jam) endif() ExternalProject_Add(Boost BUILD_IN_SOURCE YES URL https://boostorg.jfrog.io/artifactory/main/release/1.73.0/source/boost_1_73_0.tar.bz2 - UPDATE_COMMAND "" PATCH_COMMAND ${BOOST_PATCH_COMMAND} - CONFIGURE_COMMAND ./bootstrap.sh --prefix=${installDir}/lib - BUILD_COMMAND ./b2 install -j8 --prefix=${installDir} --with-filesystem --with-system --with-program_options link=static ${B2_OPTIONS} + CONFIGURE_COMMAND ./bootstrap.sh --prefix=${installDir} + BUILD_COMMAND ./b2 install -j8 --with-filesystem --with-system --with-program_options link=static ${B2_OPTIONS} INSTALL_COMMAND "" ) ExternalProject_Add(spdlog - GIT_REPOSITORY "https://github.com/gabime/spdlog.git" - GIT_TAG "v1.6.1" - UPDATE_COMMAND "" + URL https://github.com/gabime/spdlog/archive/refs/tags/v1.6.1.tar.gz CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=${installDir} -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER} @@ -61,20 +62,16 @@ ExternalProject_Add(spdlog ExternalProject_Add(googletest - GIT_REPOSITORY "https://github.com/google/googletest.git" - GIT_TAG "release-1.10.0" - UPDATE_COMMAND "" + URL https://github.com/google/googletest/archive/refs/tags/release-1.10.0.tar.gz CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=${installDir} -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER} ) -# CMAKE_CXX_STANDARD is required for OS X 10.15 +# CMAKE_CXX_STANDARD is required for macOS 10.15 ExternalProject_Add(abseil - GIT_REPOSITORY "https://github.com/abseil/abseil-cpp" - GIT_TAG "20210324.2" - UPDATE_COMMAND "" + URL https://github.com/abseil/abseil-cpp/archive/refs/tags/20210324.2.tar.gz CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=${installDir} -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER} -DCMAKE_CXX_STANDARD=11 @@ -88,7 +85,6 @@ ExternalProject_Add(ehunter TEST_COMMAND "ctest" CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=${installDir} -DCMAKE_PREFIX_PATH:PATH=${installDir} - -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} ${CMAKE_SOURCE_DIR}/ehunter ) diff --git a/docs/02_Installation.md b/docs/02_Installation.md index 6d9ec49..62cfe21 100644 --- a/docs/02_Installation.md +++ b/docs/02_Installation.md @@ -9,16 +9,17 @@ build the program from source follow the instructions below. Prerequisites: - - A recent version of [GCC](https://gcc.gnu.org/) or + - A recent version of [gcc](https://gcc.gnu.org/) or [clang](http://clang.llvm.org/) compiler supporting the C++11 standard + - The minimum gcc version is 5.1 - [CMake](https://cmake.org/) version 3.13.0 or above - - Additional development libraries, which depend on the operating system: - - Centos7 - - `yum install bzip2-devel libcurl-devel libstdc++-static xz-devel zlib-devel` + - Additional development packages, which depend on the operating system: + - Centos8 + - `bzip2-devel libcurl-devel libstdc++-static openssl-devel xz-devel zlib-devel` - Ubuntu 20.04 - - `apt install zlib1g libbz2-dev liblzma-dev libcurl4-openssl-dev` + - `libbz2-dev libcurl4-openssl-dev liblzma-dev libssl-dev zlib1g-dev ` - macOS 10.15 - - `brew install xz` + - `xz` (from homebrew) If the above prerequisites are satisfied, you are ready to build the program. Note that during the build procedure, cmake will diff --git a/docs/03_Usage.md b/docs/03_Usage.md index c872cbf..9279086 100644 --- a/docs/03_Usage.md +++ b/docs/03_Usage.md @@ -1,9 +1,11 @@ # Usage -Expansion Hunter requires an indexed BAM or a CRAM file containing aligned reads -from a PCR-free WGS sample, a FASTA file with a reference genome assembly (which -must be the same as the one used to align the reads), and a [variant catalog -file](04_VariantCatalogFiles.md). +Expansion Hunter requires the following inputs: +1. A BAM or a CRAM file containing aligned reads from a PCR-free WGS sample. + 1. The BAM or CRAM file must be sorted and indexed if using the seeking [analysis mode](#analysis-modes). + 2. The BAM or CRAM file may be a local filesystem path or [URL](#url-support). +4. A FASTA file with a reference genome assembly (which must be the same as the one used to align the reads) +5. A [variant catalog file](04_VariantCatalogFiles.md). Expansion Hunter outputs a VCF file and a JSON file with variant genotypes and other useful information along with a BAMlet containing alignments of reads that @@ -12,8 +14,8 @@ are largely equivalent, but the JSON file may be easier to parse programmatically. Here is a template with the names of the required parameters. ```bash -ExpansionHunter --reads \ - --reference \ +ExpansionHunter --reads \ + --reference \ --variant-catalog \ --output-prefix ``` @@ -26,6 +28,16 @@ optional arguments. * `--sex ` Specifies sex of the sample; can be either `male` or `female` (default). This parameter only affects repeats on sex chromosomes. +* `--threads ` Specifies how many threads to can be used accelerate analysis + of large variant catalogs. Set to 1 by default. Typically seeking mode can + benefit from relatively high thread counts, while for streaming mode + there is limited benefit beyond about 16 threads. + +* `--min-locus-coverage ` Specifies minimum read coverage depth at loci + on diploid chromosomes required to attempt genotyping. Automatically reduced + to half for loci on haploid chromosomes. The locus will be skipped if the + coverage falls below this value. Set to 10 by default. + * `--region-extension-length ` Specifies how far from on/off-target regions to search for informative reads. Set to 1000 by default. @@ -33,14 +45,17 @@ optional arguments. `streaming`. The default mode is `seeking`. See further description of analysis modes below. -* `--threads ` Specifies how many threads to can be used accelerate analysis - of large variant catalogs. Set to 1 by default. Typically seeking mode can - benefit from relatively high thread counts, while for streaming mode - there is limited benefit beyond about 16 threads. Note that the full list of program options with brief explanations can be obtained by running `ExpansionHunter --help`. +### URL support + +The aligned reads input BAM or CRAM file may be a local filesystem path or URL. +Supported protocols for URL input include ftp, https and s3. S3 bucket access +can be configured using the URL syntax and environment variables supported by +samtools/htslib. + ### Analysis modes #### Seeking mode diff --git a/docs/05_OutputJsonFiles.md b/docs/05_OutputJsonFiles.md index 8dbd815..bb4e370 100644 --- a/docs/05_OutputJsonFiles.md +++ b/docs/05_OutputJsonFiles.md @@ -5,6 +5,7 @@ parameters (`SampleParameters` field) and analysis results summarized by locus (`LocusResults` field). The locus results contain these fields * `AlleleCount` The expected number of alleles at the locus * `Coverage` Estimated read coverage at the locus + * `FragmentLength` The fragment size estimated from read pairs fully contained in either the left or right flank of the repeat region * `LocusId` Locus identifier * `ReadLength` Mean read length at the locus * `Variants` Genotypes and other information describing each variant diff --git a/ehunter/CMakeLists.txt b/ehunter/CMakeLists.txt index de31781..7135a99 100644 --- a/ehunter/CMakeLists.txt +++ b/ehunter/CMakeLists.txt @@ -1,5 +1,5 @@ cmake_minimum_required(VERSION 3.13) -project(ExpansionHunter LANGUAGES C CXX) +project(ExpansionHunter LANGUAGES CXX) set(CMAKE_CXX_STANDARD 11) set(CMAKE_CXX_STANDARD_REQUIRED ON) @@ -29,10 +29,14 @@ find_package(Threads REQUIRED) find_package(spdlog REQUIRED) find_package(absl REQUIRED) +if (NOT APPLE) + find_package(OpenSSL REQUIRED) +endif () + find_library(htslib libhts.a) find_library(htslib hts) -add_subdirectory(thirdparty/graph-tools-master-f421f4c) +add_subdirectory(thirdparty/graph-tools-master-0cd9399) add_library(ExpansionHunterLib alignment/AlignmentClassifier.hh alignment/AlignmentClassifier.cpp @@ -95,8 +99,8 @@ add_library(ExpansionHunterLib set(CTPL_INCLUDE_DIRS thirdparty/ctpl/ctpl-0.0.2) -target_include_directories(ExpansionHunterLib PUBLIC - ${CMAKE_SOURCE_DIR} +target_include_directories(ExpansionHunterLib PUBLIC ${CMAKE_SOURCE_DIR}) +target_include_directories(ExpansionHunterLib SYSTEM PUBLIC ${Boost_INCLUDE_DIRS} ${LIBLZMA_INCLUDE_DIRS} ${CURL_INCLUDE_DIRS} @@ -104,10 +108,9 @@ target_include_directories(ExpansionHunterLib PUBLIC ) # Set static linking of gcc standard libraries to simplify binary distribution -if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU") +if (CMAKE_CXX_COMPILER_ID STREQUAL "GNU") set(STATIC_FLAGS -static-libgcc -static-libstdc++) -endif() - +endif () target_link_libraries(ExpansionHunterLib PUBLIC ${STATIC_FLAGS} @@ -122,6 +125,11 @@ target_link_libraries(ExpansionHunterLib PUBLIC spdlog::spdlog absl::flat_hash_set) +if (NOT APPLE) + target_link_libraries(ExpansionHunterLib PUBLIC + OpenSSL::Crypto) +endif () + add_executable(ExpansionHunter app/ExpansionHunter.cpp ) @@ -148,6 +156,7 @@ add_executable(UnitTests tests/RegionGraphTest.cpp tests/RepeatAnalyzerTest.cpp tests/RepeatGenotypeTest.cpp + tests/RFC1MotifAnalysisUtilTest.cpp tests/SmallVariantGenotyperTest.cpp tests/SoftclippingAlignerTest.cpp tests/StrAlignTest.cpp diff --git a/ehunter/core/Common.cpp b/ehunter/core/Common.cpp index 6c3b711..cc7a588 100644 --- a/ehunter/core/Common.cpp +++ b/ehunter/core/Common.cpp @@ -23,6 +23,8 @@ #include "core/Common.hh" +#include + using std::string; namespace ehunter @@ -97,4 +99,10 @@ std::ostream& operator<<(std::ostream& out, NumericInterval numericInterval) return out; } +bool isURL(const std::string& path) +{ + static const std::regex url_regex(".*?://.*"); + return std::regex_match(path, url_regex); +} + } diff --git a/ehunter/core/Common.hh b/ehunter/core/Common.hh index 649cac2..b06e8d9 100644 --- a/ehunter/core/Common.hh +++ b/ehunter/core/Common.hh @@ -115,4 +115,10 @@ std::ostream& operator<<(std::ostream& out, ReadType readType); std::ostream& operator<<(std::ostream& out, AlleleCount alleleCount); std::ostream& operator<<(std::ostream& out, NumericInterval numericInterval); +/// \brief Returns true if the path refers to a URL instead of a local file +/// +/// This does not test if the URL is well formed +/// +bool isURL(const std::string& path); + } diff --git a/ehunter/core/LocusStats.cpp b/ehunter/core/LocusStats.cpp index dcdd729..6c5c351 100644 --- a/ehunter/core/LocusStats.cpp +++ b/ehunter/core/LocusStats.cpp @@ -61,10 +61,7 @@ void LocusStatsCalculator::inspect(const GraphAlignment& readAlign, const GraphA recordFragLen(readAlign, mateAlign); } -void LocusStatsCalculator::inspectRead(const GraphAlignment& readAlign) -{ - recordReadLen(readAlign); -} +void LocusStatsCalculator::inspectRead(const GraphAlignment& readAlign) { recordReadLen(readAlign); } static AlleleCount determineExpectedAlleleCount(ChromType chromType, Sex sex) { diff --git a/ehunter/core/Parameters.hh b/ehunter/core/Parameters.hh index 1a7a4f4..3a487e3 100644 --- a/ehunter/core/Parameters.hh +++ b/ehunter/core/Parameters.hh @@ -113,10 +113,11 @@ class HeuristicParameters { public: HeuristicParameters( - int regionExtensionLength, int qualityCutoffForGoodBaseCall, bool skipUnaligned, + int regionExtensionLength, int minLocusCoverage, int qualityCutoffForGoodBaseCall, bool skipUnaligned, const graphtools::AlignerType alignerType, int kmerLenForAlignment = 14, int paddingLength = 10, int seedAffixTrimLength = 14, int orientationPredictorKmerLen = 10, int orientationPredictorMinKmerCount = 3) : regionExtensionLength_(regionExtensionLength) + , minLocusCoverage_(minLocusCoverage) , qualityCutoffForGoodBaseCall_(qualityCutoffForGoodBaseCall) , skipUnaligned_(skipUnaligned) , alignerType_(std::move(alignerType)) @@ -129,6 +130,7 @@ public: } int regionExtensionLength() const { return regionExtensionLength_; } + int minLocusCoverage() const { return minLocusCoverage_; } int qualityCutoffForGoodBaseCall() const { return qualityCutoffForGoodBaseCall_; } bool skipUnaligned() const { return skipUnaligned_; } graphtools::AlignerType alignerType() const { return alignerType_; } @@ -140,6 +142,7 @@ public: private: int regionExtensionLength_; + int minLocusCoverage_; int qualityCutoffForGoodBaseCall_; bool skipUnaligned_; graphtools::AlignerType alignerType_; @@ -153,12 +156,16 @@ private: // Per-locus parameters (settable from variant catalog) controlling genotyping struct GenotyperParameters { + GenotyperParameters(int minLocusCoverage) + : minLocusCoverage(minLocusCoverage) + { + } // Base error rate assumed in SNV key-allele genotyping model double errorRate = 0.02; // Threshold to call SNV key-allele confidently present / absent double likelihoodRatioThreshold = 10000; // Minimal estimated locus coverage (depth) to attempt genotyping - double minLocusCoverage = 10; + double minLocusCoverage; // Minimal number of reads spanning a variant breakpoint int minBreakpointSpanningReads = 5; }; diff --git a/ehunter/genotyping/AlignMatrix.cpp b/ehunter/genotyping/AlignMatrix.cpp index 6c40fb1..b90f1a7 100644 --- a/ehunter/genotyping/AlignMatrix.cpp +++ b/ehunter/genotyping/AlignMatrix.cpp @@ -126,36 +126,32 @@ std::ostream& operator<<(std::ostream& out, const AlignMatrix& matrix) std::iota(alignIndexes.begin(), alignIndexes.end(), 0); // Sort alignIndexes to canonicalize the alignmatrix output - std::sort( - alignIndexes.begin(), alignIndexes.end(), - [&alignsByRead](const unsigned ai, const unsigned bi) -> bool + std::sort(alignIndexes.begin(), alignIndexes.end(), [&alignsByRead](const unsigned ai, const unsigned bi) -> bool { + const auto& a(alignsByRead[ai]); + const auto& b(alignsByRead[bi]); + if (a.size() < b.size()) { - const auto& a(alignsByRead[ai]); - const auto& b(alignsByRead[bi]); - if (a.size() < b.size()) + return true; + } + if (b.size() < a.size()) + { + return false; + } + for (unsigned i(0); i < a.size(); ++i) + { + if (a[i] < b[i]) { return true; } - if (b.size() < a.size()) + if (b[i] < a[i]) { return false; } - for (unsigned i(0); i < a.size(); ++i) - { - if (a[i] < b[i]) - { - return true; - } - if (b[i] < a[i]) - { - return false; - } - } - return false; - }); + } + return false; + }); - auto dumpStrAlign = [&out](const StrAlign& align) - { + auto dumpStrAlign = [&out](const StrAlign& align) { out << "("; switch (align.type()) { diff --git a/ehunter/io/BamletWriter.hh b/ehunter/io/BamletWriter.hh index a510033..614634d 100644 --- a/ehunter/io/BamletWriter.hh +++ b/ehunter/io/BamletWriter.hh @@ -46,7 +46,7 @@ namespace ehunter { /// Supports multiple threads calling the write() method on the same object. To make this more efficient for high -/// thread counts, this object creates its own asynchronous write thread to prevent calling threads from blocking on +/// thread counts, this object creates its own asynchronous write thread to prevent calling threads from blocking /// on the final bam record write operation. /// class BamletWriter : public graphtools::AlignmentWriter, private boost::noncopyable diff --git a/ehunter/io/CatalogLoading.cpp b/ehunter/io/CatalogLoading.cpp index c4c609f..cfcce73 100644 --- a/ehunter/io/CatalogLoading.cpp +++ b/ehunter/io/CatalogLoading.cpp @@ -128,6 +128,8 @@ static vector generateIds(const std::string& locusId, const Json& varian return variantIds; } +/// \brief Translate a single locus from the catalog file json structure into an intermediate locus configuration +/// static LocusDescriptionFromUser loadUserDescription(Json& locusJson, const ReferenceContigInfo& contigInfo) { LocusDescriptionFromUser userDescription; @@ -199,6 +201,28 @@ static LocusDescriptionFromUser loadUserDescription(Json& locusJson, const Refer userDescription.minLocusCoverage = locusJson["MinimalLocusCoverage"].get(); } + static const std::string rfc1MotifAnalysisKey("RFC1MotifAnalysis"); + if (checkIfFieldExists(locusJson, rfc1MotifAnalysisKey)) + { + const Json& record(locusJson[rfc1MotifAnalysisKey]); + if (record.type() == Json::value_t::boolean) + { + userDescription.useRFC1MotifAnalysis = record.get(); + } + else if (record.type() == Json::value_t::object) + { + userDescription.useRFC1MotifAnalysis = true; + } + else + { + std::stringstream out; + out << record; + throw std::logic_error( + "Key '" + rfc1MotifAnalysisKey + + "' must have either a boolean or object value type, observed value is '" + out.str() + "'"); + } + } + return userDescription; } diff --git a/ehunter/io/JsonWriter.cpp b/ehunter/io/JsonWriter.cpp index b728f2b..bbcda4c 100644 --- a/ehunter/io/JsonWriter.cpp +++ b/ehunter/io/JsonWriter.cpp @@ -143,6 +143,15 @@ void VariantJsonWriter::visit(const RepeatFindings* repeatFindingsPtr) record_["Genotype"] = encodeGenotype(*repeatFindings.optionalGenotype()); record_["GenotypeConfidenceInterval"] = streamToString(*repeatFindings.optionalGenotype()); } + + const auto rfc1Status(repeatFindings.getRFC1Status()); + if (rfc1Status) + { + nlohmann::json rfc1Results; + rfc1Results["Call"] = label(rfc1Status->call); + rfc1Results["Description"] = rfc1Status->description; + record_["RFC1MotifAnalysis"] = rfc1Results; + } } void VariantJsonWriter::visit(const SmallVariantFindings* smallVariantFindingsPtr) diff --git a/ehunter/io/LocusSpecDecoding.cpp b/ehunter/io/LocusSpecDecoding.cpp index f82db27..888538f 100644 --- a/ehunter/io/LocusSpecDecoding.cpp +++ b/ehunter/io/LocusSpecDecoding.cpp @@ -284,7 +284,7 @@ LocusSpecification decodeLocusSpecification( NodeToRegionAssociation referenceRegionsOfGraphNodes = associateNodesWithReferenceRegions(blueprint, locusGraph, completeReferenceRegions); - GenotyperParameters parameters; + GenotyperParameters parameters(heuristicParams.minLocusCoverage()); if (userDescription.errorRate) { parameters.errorRate = *userDescription.errorRate; @@ -300,7 +300,7 @@ LocusSpecification decodeLocusSpecification( LocusSpecification locusSpec( userDescription.locusId, chromType, std::move(targetReadExtractionRegions), std::move(locusGraph), - std::move(referenceRegionsOfGraphNodes), std::move(parameters)); + std::move(referenceRegionsOfGraphNodes), std::move(parameters), userDescription.useRFC1MotifAnalysis); locusSpec.setOfftargetReadExtractionRegions(userDescription.offtargetRegions); int variantIndex = 0; @@ -365,6 +365,17 @@ void assertValidity(const LocusDescriptionFromUser& userDescription) "Locus " + userDescription.locusId + " must specify variant types for " + to_string(numVariants) + " variants"); } + + if (userDescription.useRFC1MotifAnalysis) + { + if ((numVariants != 1) or (userDescription.variantTypesFromUser[0] != VariantTypeFromUser::kCommonRepeat)) + { + throw std::runtime_error( + "Locus " + userDescription.locusId + + " has option 'useRFC1MotifAnalysis' enabled, which requires that" + " exactly one variant of type 'Repeat' is defined."); + } + } } } diff --git a/ehunter/io/LocusSpecDecoding.hh b/ehunter/io/LocusSpecDecoding.hh index 896a01b..8ea8a3f 100644 --- a/ehunter/io/LocusSpecDecoding.hh +++ b/ehunter/io/LocusSpecDecoding.hh @@ -45,6 +45,8 @@ enum class VariantTypeFromUser struct LocusDescriptionFromUser { std::string locusId; + + /// Regular expression defining the structure of the locus std::string locusStructure; std::vector variantIds; std::vector referenceRegions; @@ -54,6 +56,9 @@ struct LocusDescriptionFromUser boost::optional errorRate; boost::optional likelihoodRatioThreshold; boost::optional minLocusCoverage; + + /// If true, turn on additional motif processing for a repeat + bool useRFC1MotifAnalysis = false; }; void assertValidity(const LocusDescriptionFromUser& userDescription); diff --git a/ehunter/io/ParameterLoading.cpp b/ehunter/io/ParameterLoading.cpp index e79ccf8..6087605 100644 --- a/ehunter/io/ParameterLoading.cpp +++ b/ehunter/io/ParameterLoading.cpp @@ -58,6 +58,7 @@ struct UserParameters // Heuristic parameters string alignerType; int regionExtensionLength; + double minLocusCoverage = 10.0; int qualityCutoffForGoodBaseCall = 20; bool skipUnaligned; @@ -76,21 +77,23 @@ boost::optional tryParsingUserParameters(int argc, char** argv) basicOptions.add_options() ("help,h", "Print help message") ("version,v", "Print version number") - ("reads", po::value(¶ms.htsFilePath)->required(), "BAM/CRAM file with aligned reads") - ("reference", po::value(¶ms.referencePath)->required(), "FASTA file with reference genome") + ("reads", po::value(¶ms.htsFilePath)->required(), "aligned reads BAM/CRAM file/URL") + ("reference", po::value(¶ms.referencePath)->required(), "reference genome FASTA file") ("variant-catalog", po::value(¶ms.catalogPath)->required(), "JSON file with variants to genotype") ("output-prefix", po::value(¶ms.outputPrefix)->required(), "Prefix for the output files") - ("region-extension-length", po::value(¶ms.regionExtensionLength)->default_value(1000), "How far from on/off-target regions to search for informative reads") ("sex", po::value(¶ms.sampleSexEncoding)->default_value("female"), "Sex of the sample; must be either male or female") - ("log-level", po::value(¶ms.logLevel)->default_value("info"), "trace, debug, info, warn, or error"); + ; // clang-format on // clang-format off po::options_description advancedOptions("Advanced options"); advancedOptions.add_options() - ("aligner,a", po::value(¶ms.alignerType)->default_value("dag-aligner"), "Specify which aligner to use (dag-aligner or path-aligner)") - ("analysis-mode,m", po::value(¶ms.analysisMode)->default_value("seeking"), "Specify which analysis workflow to use (seeking or streaming)") - ("threads,n", po::value(¶ms.threadCount)->default_value(1), "Number of threads to use") + ("region-extension-length", po::value(¶ms.regionExtensionLength)->default_value(1000), "How far from on/off-target regions to search for informative reads") + ("min-locus-coverage", po::value(¶ms.minLocusCoverage)->default_value(10.0), "Minimum read coverage depth for diploid loci (set to half for loci on haploid chromosomes)") + ("aligner", po::value(¶ms.alignerType)->default_value("dag-aligner"), "Graph aligner to use (dag-aligner or path-aligner)") + ("analysis-mode", po::value(¶ms.analysisMode)->default_value("seeking"), "Analysis workflow to use (seeking or streaming)") + ("threads", po::value(¶ms.threadCount)->default_value(1), "Number of threads to use") + ("log-level", po::value(¶ms.logLevel)->default_value("info"), "trace, debug, info, warn, or error") ; // clang-format on @@ -182,10 +185,13 @@ void assertValidity(const UserParameters& userParameters) } // Validate input file paths - assertPathToExistingFile(userParameters.htsFilePath); - if (userParameters.analysisMode != "streaming") + if (not isURL(userParameters.htsFilePath)) { - assertIndexExists(userParameters.htsFilePath); + assertPathToExistingFile(userParameters.htsFilePath); + if (userParameters.analysisMode != "streaming") + { + assertIndexExists(userParameters.htsFilePath); + } } assertPathToExistingFile(userParameters.referencePath); assertPathToExistingFile(userParameters.catalogPath); @@ -320,8 +326,8 @@ boost::optional tryLoadingProgramParameters(int argc, char** OutputPaths outputPaths(vcfPath, jsonPath, bamletPath); SampleParameters sampleParameters = decodeSampleParameters(userParams); HeuristicParameters heuristicParameters( - userParams.regionExtensionLength, userParams.qualityCutoffForGoodBaseCall, userParams.skipUnaligned, - decodeAlignerType(userParams.alignerType)); + userParams.regionExtensionLength, userParams.minLocusCoverage, userParams.qualityCutoffForGoodBaseCall, + userParams.skipUnaligned, decodeAlignerType(userParams.alignerType)); LogLevel logLevel; try diff --git a/ehunter/locus/CMakeLists.txt b/ehunter/locus/CMakeLists.txt index 59b80cb..ebdea5f 100644 --- a/ehunter/locus/CMakeLists.txt +++ b/ehunter/locus/CMakeLists.txt @@ -1,5 +1,6 @@ target_sources(ExpansionHunterLib # Requires CMake 3.13 or later PRIVATE + AlignmentBuffer.hh AlignmentBuffer.cpp IrrPairFinder.hh IrrPairFinder.cpp LocusAligner.hh LocusAligner.cpp LocusAnalyzer.hh LocusAnalyzer.cpp @@ -7,6 +8,9 @@ target_sources(ExpansionHunterLib # Requires CMake 3.13 or later LocusFindings.hh LocusFindings.cpp LocusSpecification.hh LocusSpecification.cpp RepeatAnalyzer.hh RepeatAnalyzer.cpp + RFC1MotifAnalysis.hh RFC1MotifAnalysis.cpp + RFC1MotifAnalysisUtil.hh RFC1MotifAnalysisUtil.cpp + RFC1Status.hh SmallVariantAnalyzer.hh SmallVariantAnalyzer.cpp VariantAnalyzer.hh VariantAnalyzer.cpp VariantFindings.hh VariantFindings.cpp @@ -18,4 +22,4 @@ target_sources(UnitTests # Requires CMake 3.13 or later IrrPairFinderTest.cpp LocusAlignerTest.cpp LocusAnalyzerTest.cpp - ) \ No newline at end of file + ) diff --git a/ehunter/locus/LocusAligner.cpp b/ehunter/locus/LocusAligner.cpp index cb9995e..4062ca6 100644 --- a/ehunter/locus/LocusAligner.cpp +++ b/ehunter/locus/LocusAligner.cpp @@ -30,11 +30,13 @@ namespace locus { LocusAligner::LocusAligner( - std::string locusId, GraphPtr graph, const HeuristicParameters& params, AlignWriterPtr writer) + std::string locusId, GraphPtr graph, const HeuristicParameters& params, AlignmentWriterPtr writer, + AlignmentBufferPtr buffer) : locusId_(std::move(locusId)) , aligner_(graph, params.kmerLenForAlignment(), params.paddingLength(), params.seedAffixTrimLength()) , orientationPredictor_(graph, params.orientationPredictorKmerLen(), params.orientationPredictorMinKmerCount()) , writer_(std::move(writer)) + , alignmentBuffer_(std::move(buffer)) { } @@ -55,6 +57,13 @@ LocusAligner::AlignedPair LocusAligner::align(Read& read, Read* mate, graphtools if (readAlign && mateAlign) { + // Optionally buffer reads for specialized caller extensions: + if (alignmentBuffer_) + { + alignmentBuffer_->testAndPushRead(read.sequence(), read.isReversed(), *readAlign); + } + + // Output realigned reads to bam: writer_->write( locusId_, read.fragmentId(), read.sequence(), read.isFirstMate(), read.isReversed(), read.isReversed(), *readAlign); diff --git a/ehunter/locus/LocusAligner.hh b/ehunter/locus/LocusAligner.hh index 295b8df..954cde8 100644 --- a/ehunter/locus/LocusAligner.hh +++ b/ehunter/locus/LocusAligner.hh @@ -28,6 +28,7 @@ #include "alignment/OrientationPredictor.hh" #include "core/Parameters.hh" #include "core/Read.hh" +#include "locus/AlignmentBuffer.hh" #include "graphalign/GappedAligner.hh" #include "graphio/AlignmentWriter.hh" @@ -44,9 +45,16 @@ public: using Align = graphtools::GraphAlignment; using OptionalAlign = boost::optional; using AlignedPair = std::pair; - using AlignWriterPtr = std::shared_ptr; + using AlignmentWriterPtr = std::shared_ptr; + using AlignmentBufferPtr = std::shared_ptr; - LocusAligner(std::string locusId, GraphPtr graph, const HeuristicParameters& params, AlignWriterPtr writer); + /// + /// \param[in] buffer Buffer to store all locus reads for downstream analysis. This is only needed in specialized + /// calling scenarios. Buffering is skipped with this is null. + /// + LocusAligner( + std::string locusId, GraphPtr graph, const HeuristicParameters& params, AlignmentWriterPtr writer, + AlignmentBufferPtr buffer); /// \param[in,out] alignerSelector A per-thread alignment workspace which mutates during alignment /// @@ -58,8 +66,9 @@ private: std::string locusId_; graphtools::GappedGraphAligner aligner_; OrientationPredictor orientationPredictor_; - AlignWriterPtr writer_; + AlignmentWriterPtr writer_; + AlignmentBufferPtr alignmentBuffer_; }; } -} \ No newline at end of file +} diff --git a/ehunter/locus/LocusAlignerTest.cpp b/ehunter/locus/LocusAlignerTest.cpp index f7982dc..1d5334a 100644 --- a/ehunter/locus/LocusAlignerTest.cpp +++ b/ehunter/locus/LocusAlignerTest.cpp @@ -39,9 +39,9 @@ using graphtools::GraphAlignment; LocusAligner makeStrAligner(graphtools::Graph* graph) { - HeuristicParameters params(1000, 20, true, graphtools::AlignerType::DAG_ALIGNER, 4, 0, 0, 4, 1); + HeuristicParameters params(1000, 10, 20, true, graphtools::AlignerType::DAG_ALIGNER, 4, 0, 0, 4, 1); auto writer = std::make_shared(); - return { "str", graph, params, writer }; + return { "str", graph, params, writer, {} }; } TEST(AligningReads, ReadPairFromSameStrand_Aligned) diff --git a/ehunter/locus/LocusAnalyzer.cpp b/ehunter/locus/LocusAnalyzer.cpp index 4549cd6..bd60c33 100644 --- a/ehunter/locus/LocusAnalyzer.cpp +++ b/ehunter/locus/LocusAnalyzer.cpp @@ -24,6 +24,7 @@ #include #include "locus/LocusAligner.hh" +#include "locus/RFC1MotifAnalysis.hh" #include "locus/RepeatAnalyzer.hh" #include "locus/SmallVariantAnalyzer.hh" @@ -42,7 +43,8 @@ namespace locus LocusAnalyzer::LocusAnalyzer(LocusSpecification locusSpec, const HeuristicParameters& params, AlignWriterPtr writer) : locusSpec_(std::move(locusSpec)) - , aligner_(locusSpec_.locusId(), &locusSpec_.regionGraph(), params, std::move(writer)) + , alignmentBuffer_(locusSpec_.useRFC1MotifAnalysis() ? std::make_shared() : nullptr) + , aligner_(locusSpec_.locusId(), &locusSpec_.regionGraph(), params, std::move(writer), alignmentBuffer_) , statsCalc_(locusSpec_.typeOfChromLocusLocatedOn(), locusSpec_.regionGraph()) { for (const auto& variantSpec : locusSpec_.variantSpecs()) @@ -114,10 +116,12 @@ void LocusAnalyzer::processOntargetMates(Read& read, Read* mate, graphtools::Ali } else { - if (alignedPair.first) { + if (alignedPair.first) + { statsCalc_.inspectRead(*alignedPair.first); } - if (alignedPair.second) { + if (alignedPair.second) + { statsCalc_.inspectRead(*alignedPair.second); } } @@ -167,6 +171,13 @@ LocusFindings LocusAnalyzer::analyze(Sex sampleSex, boost::optional geno locusFindings.findingsForEachVariant.emplace(variantId, std::move(variantFindingsPtr)); } + // Run RFC1 caller if required for this locus: + if (locusSpec().useRFC1MotifAnalysis()) + { + assert(alignmentBuffer_); + runRFC1MotifAnalysis(*alignmentBuffer_, locusFindings); + } + return locusFindings; } @@ -196,4 +207,4 @@ void LocusAnalyzer::runVariantAnalysis( } } -} \ No newline at end of file +} diff --git a/ehunter/locus/LocusAnalyzer.hh b/ehunter/locus/LocusAnalyzer.hh index 13b7102..d4f630b 100644 --- a/ehunter/locus/LocusAnalyzer.hh +++ b/ehunter/locus/LocusAnalyzer.hh @@ -33,6 +33,7 @@ #include "core/GenomicRegion.hh" #include "core/LocusStats.hh" #include "core/Read.hh" +#include "locus/AlignmentBuffer.hh" #include "locus/IrrPairFinder.hh" #include "locus/LocusAligner.hh" #include "locus/LocusFindings.hh" @@ -83,6 +84,10 @@ private: void runVariantAnalysis(const Read& read, const Align& readAlign, const Read& mate, const Align& mateAlign); LocusSpecification locusSpec_; + + // Read alignments are optionally buffered for custom additional analysis at certain loci + std::shared_ptr alignmentBuffer_; + LocusAligner aligner_; LocusStatsCalculator statsCalc_; boost::optional irrPairFinder_; diff --git a/ehunter/locus/LocusAnalyzerTest.cpp b/ehunter/locus/LocusAnalyzerTest.cpp index 891cf7c..3ceb24a 100644 --- a/ehunter/locus/LocusAnalyzerTest.cpp +++ b/ehunter/locus/LocusAnalyzerTest.cpp @@ -38,8 +38,10 @@ LocusSpecification buildStrSpec(const std::string& structure) vector referenceRegions = { GenomicRegion(1, 1, 2) }; NodeToRegionAssociation dummyAssociation; - GenotyperParameters params; - LocusSpecification locusSpec("region", ChromType::kAutosome, referenceRegions, graph, dummyAssociation, params); + GenotyperParameters params(10); + const bool useRFC1MotifAnalysis(false); + LocusSpecification locusSpec( + "region", ChromType::kAutosome, referenceRegions, graph, dummyAssociation, params, useRFC1MotifAnalysis); VariantClassification classification(VariantType::kRepeat, VariantSubtype::kCommonRepeat); locusSpec.addVariantSpecification("repeat", classification, GenomicRegion(1, 1, 2), { 1 }, 1); return locusSpec; @@ -49,7 +51,7 @@ TEST(CreatingLocusAnalyzer, TypicalParameters_Created) { auto locusSpec = buildStrSpec("ATTCGA(C)*ATGTCG"); - HeuristicParameters heuristicParams(1000, 20, true, AlignerType::DAG_ALIGNER, 4, 1, 5, 4, 1); + HeuristicParameters heuristicParams(1000, 10, 20, true, AlignerType::DAG_ALIGNER, 4, 1, 5, 4, 1); auto writer = std::make_shared(); graphtools::AlignerSelector selector(heuristicParams.alignerType()); diff --git a/ehunter/locus/LocusSpecification.cpp b/ehunter/locus/LocusSpecification.cpp index d14cc34..7344c73 100644 --- a/ehunter/locus/LocusSpecification.cpp +++ b/ehunter/locus/LocusSpecification.cpp @@ -54,13 +54,15 @@ namespace ehunter { LocusSpecification::LocusSpecification( RegionId locusId, ChromType typeOfChromLocusLocatedOn, std::vector targetReadExtractionRegions, - graphtools::Graph regionGraph, NodeToRegionAssociation referenceRegions, GenotyperParameters genotyperParams) + graphtools::Graph regionGraph, NodeToRegionAssociation referenceRegions, GenotyperParameters genotyperParams, + const bool useRFC1MotifAnalysis) : locusId_(std::move(locusId)) , typeOfChromLocusLocatedOn_(typeOfChromLocusLocatedOn) , targetReadExtractionRegions_(std::move(targetReadExtractionRegions)) , regionGraph_(std::move(regionGraph)) , referenceRegions_(std::move(referenceRegions)) , parameters_(std::move(genotyperParams)) + , useRFC1MotifAnalysis_(useRFC1MotifAnalysis) { } diff --git a/ehunter/locus/LocusSpecification.hh b/ehunter/locus/LocusSpecification.hh index c3029ca..3215636 100644 --- a/ehunter/locus/LocusSpecification.hh +++ b/ehunter/locus/LocusSpecification.hh @@ -50,7 +50,8 @@ class LocusSpecification public: LocusSpecification( RegionId locusId, ChromType typeOfChromLocusLocatedOn, std::vector targetReadExtractionRegions, - graphtools::Graph regionGraph, NodeToRegionAssociation referenceRegions, GenotyperParameters genotyperParams); + graphtools::Graph regionGraph, NodeToRegionAssociation referenceRegions, GenotyperParameters genotyperParams, + bool useRFC1MotifAnalysis); const RegionId& locusId() const { return locusId_; } ChromType typeOfChromLocusLocatedOn() const { return typeOfChromLocusLocatedOn_; } @@ -83,6 +84,8 @@ public: bool requiresGenomeWideDepth() const; + bool useRFC1MotifAnalysis() const { return useRFC1MotifAnalysis_; } + private: std::string locusId_; ChromType typeOfChromLocusLocatedOn_; @@ -92,6 +95,7 @@ private: std::vector variantSpecs_; NodeToRegionAssociation referenceRegions_; GenotyperParameters parameters_; + bool useRFC1MotifAnalysis_; }; using RegionCatalog = std::vector; diff --git a/ehunter/locus/RepeatAnalyzer.cpp b/ehunter/locus/RepeatAnalyzer.cpp index 4a23de0..73c90f5 100644 --- a/ehunter/locus/RepeatAnalyzer.cpp +++ b/ehunter/locus/RepeatAnalyzer.cpp @@ -21,6 +21,8 @@ #include "locus/RepeatAnalyzer.hh" +#include + // clang-format off // Note that spdlog.h must be included before ostr.h #include "spdlog/spdlog.h" @@ -31,13 +33,13 @@ #include "graphutils/SequenceOperations.hh" #include "alignment/AlignmentFilters.hh" -#include "alignment/OperationsOnAlignments.hh" #include "genotyping/AlignMatrixFiltering.hh" #include "genotyping/StrGenotyper.hh" namespace ehunter { +using boost::make_unique; using boost::optional; using graphtools::GraphAlignment; using graphtools::NodeId; @@ -59,48 +61,41 @@ void RepeatAnalyzer::processMates( unique_ptr RepeatAnalyzer::analyze(const LocusStats& stats) { - optional repeatGenotype = boost::none; + if (isLowDepth(stats)) + { + return make_unique( + CountTable(), CountTable(), CountTable(), stats.alleleCount(), boost::none, GenotypeFilter::kLowDepth); + } + auto genotypeFilter = GenotypeFilter(); - CountTable countsOfSpanningReads; - CountTable countsOfFlankingReads; - CountTable countsOfInrepeatReads; - if (stats.meanReadLength() == 0 || stats.depth() < genotyperParams_.minLocusCoverage) + const int minBreakpointSpanningReads = stats.alleleCount() == AlleleCount::kTwo + ? genotyperParams_.minBreakpointSpanningReads + : (genotyperParams_.minBreakpointSpanningReads / 2); + + GraphVariantAlignmentStats alignmentStats = alignmentStatsCalculator_.getStats(); + if (alignmentStats.numReadsSpanningRightBreakpoint() < minBreakpointSpanningReads + || alignmentStats.numReadsSpanningLeftBreakpoint() < minBreakpointSpanningReads) { genotypeFilter = genotypeFilter | GenotypeFilter::kLowDepth; } - else + + if (countOfInrepeatReadPairs_) { - // const double haplotypeDepth = stats.alleleCount() == AlleleCount::kTwo ? stats.depth() / 2 : stats.depth(); - const int minBreakpointSpanningReads = stats.alleleCount() == AlleleCount::kTwo - ? genotyperParams_.minBreakpointSpanningReads - : (genotyperParams_.minBreakpointSpanningReads / 2); - - GraphVariantAlignmentStats alignmentStats = alignmentStatsCalculator_.getStats(); - if (alignmentStats.numReadsSpanningRightBreakpoint() < minBreakpointSpanningReads - || alignmentStats.numReadsSpanningLeftBreakpoint() < minBreakpointSpanningReads) - { - genotypeFilter = genotypeFilter | GenotypeFilter::kLowDepth; - } - - if (countOfInrepeatReadPairs_) - { - const int maxMotifsInRead = std::ceil(stats.meanReadLength() / static_cast(repeatUnit_.length())); - strgt::addIrrPairsIfPossibleExpansion(maxMotifsInRead, alignMatrix_, countOfInrepeatReadPairs_); - } - - countsOfSpanningReads = countAligns(StrAlign::Type::kSpanning, alignMatrix_); - countsOfFlankingReads = countAligns(StrAlign::Type::kFlanking, alignMatrix_); - countsOfInrepeatReads = countAligns(StrAlign::Type::kInRepeat, alignMatrix_); - - repeatGenotype = strgt::genotype( - stats.alleleCount(), repeatUnit_.length(), stats.meanReadLength(), stats.medianFragLength(), alignMatrix_); + const int maxMotifsInRead = std::ceil(stats.meanReadLength() / static_cast(repeatUnit_.length())); + strgt::addIrrPairsIfPossibleExpansion(maxMotifsInRead, alignMatrix_, countOfInrepeatReadPairs_); } - unique_ptr variantFindingsPtr(new RepeatFindings( - countsOfSpanningReads, countsOfFlankingReads, countsOfInrepeatReads, stats.alleleCount(), repeatGenotype, - genotypeFilter)); - return variantFindingsPtr; + auto countsOfSpanningReads = countAligns(StrAlign::Type::kSpanning, alignMatrix_); + auto countsOfFlankingReads = countAligns(StrAlign::Type::kFlanking, alignMatrix_); + auto countsOfInrepeatReads = countAligns(StrAlign::Type::kInRepeat, alignMatrix_); + + auto genotype = strgt::genotype( + stats.alleleCount(), repeatUnit_.length(), stats.meanReadLength(), stats.medianFragLength(), alignMatrix_); + + return make_unique( + countsOfSpanningReads, countsOfFlankingReads, countsOfInrepeatReads, stats.alleleCount(), genotype, + genotypeFilter); } } diff --git a/ehunter/locus/SmallVariantAnalyzer.cpp b/ehunter/locus/SmallVariantAnalyzer.cpp index b034c56..effa49e 100644 --- a/ehunter/locus/SmallVariantAnalyzer.cpp +++ b/ehunter/locus/SmallVariantAnalyzer.cpp @@ -24,7 +24,9 @@ #include #include +#include +using boost::make_unique; using boost::optional; using graphtools::NodeId; using std::string; @@ -64,73 +66,67 @@ int SmallVariantAnalyzer::countReadsSupportingNode(graphtools::NodeId nodeId) co std::unique_ptr SmallVariantAnalyzer::analyze(const LocusStats& stats) { - optional genotype = boost::none; - auto genotypeFilter = GenotypeFilter(); - - int refNodeSupport = 0; - int altNodeSupport = 0; + if (isLowDepth(stats)) + { + auto refStatus = AlleleCheckSummary(AlleleStatus::kUncertain, 0); + auto altStatus = AlleleCheckSummary(AlleleStatus::kUncertain, 0); + return make_unique( + 0, 0, refStatus, altStatus, stats.alleleCount(), boost::none, GenotypeFilter::kLowDepth); + } - AlleleCheckSummary refAlleleStatus(AlleleStatus::kUncertain, 0); - AlleleCheckSummary altAlleleStatus(AlleleStatus::kUncertain, 0); + NodeId refNode = optionalRefNode_ ? *optionalRefNode_ : ClassifierOfAlignmentsToVariant::kInvalidNodeId; + NodeId altNode = ClassifierOfAlignmentsToVariant::kInvalidNodeId; - if (stats.meanReadLength() == 0 || stats.depth() < genotyperParams_.minLocusCoverage) + switch (variantSubtype_) { - genotypeFilter = genotypeFilter | GenotypeFilter::kLowDepth; + case VariantSubtype::kInsertion: + altNode = nodeIds_.front(); + break; + case VariantSubtype::kDeletion: + altNode = ClassifierOfAlignmentsToVariant::kInvalidNodeId; + break; + case VariantSubtype::kSwap: + altNode = (refNode == nodeIds_.front()) ? nodeIds_.back() : nodeIds_.front(); + break; + case VariantSubtype::kSMN: + if (refNode != nodeIds_.front()) + throw std::logic_error("Invalid SMN specification"); + altNode = nodeIds_.back(); + break; + default: + std::ostringstream encoding; + encoding << variantSubtype_; + throw std::logic_error("Invalid small variant subtype: " + encoding.str()); } - else + + int refNodeSupport = countReadsSupportingNode(refNode); + int altNodeSupport = countReadsSupportingNode(altNode); + + const double haplotypeDepth = stats.alleleCount() == AlleleCount::kTwo ? stats.depth() / 2 : stats.depth(); + const int minBreakpointSpanningReads = stats.alleleCount() == AlleleCount::kTwo + ? genotyperParams_.minBreakpointSpanningReads + : (genotyperParams_.minBreakpointSpanningReads / 2); + + SmallVariantGenotyper smallVariantGenotyper(haplotypeDepth, stats.alleleCount()); + auto genotype = smallVariantGenotyper.genotype(refNodeSupport, altNodeSupport); + + auto refAlleleStatus = allelePresenceChecker_.check(haplotypeDepth, refNodeSupport, altNodeSupport); + auto altAlleleStatus = allelePresenceChecker_.check(haplotypeDepth, altNodeSupport, refNodeSupport); + + GraphVariantAlignmentStats alignmentStats = alignmentStatsCalculator_.getStats(); + const bool insufficientBreakpointCoverage + = alignmentStats.numReadsSpanningLeftBreakpoint() < minBreakpointSpanningReads + || alignmentStats.numReadsSpanningRightBreakpoint() < minBreakpointSpanningReads; + + auto genotypeFilter = GenotypeFilter(); + if ((variantSubtype_ != VariantSubtype::kSMN) && insufficientBreakpointCoverage) { - NodeId refNode = optionalRefNode_ ? *optionalRefNode_ : ClassifierOfAlignmentsToVariant::kInvalidNodeId; - NodeId altNode = ClassifierOfAlignmentsToVariant::kInvalidNodeId; - - switch (variantSubtype_) - { - case VariantSubtype::kInsertion: - altNode = nodeIds_.front(); - break; - case VariantSubtype::kDeletion: - altNode = ClassifierOfAlignmentsToVariant::kInvalidNodeId; - break; - case VariantSubtype::kSwap: - altNode = (refNode == nodeIds_.front()) ? nodeIds_.back() : nodeIds_.front(); - break; - case VariantSubtype::kSMN: - if (refNode != nodeIds_.front()) - throw std::logic_error("Invalid SMN specification"); - altNode = nodeIds_.back(); - break; - default: - std::ostringstream encoding; - encoding << variantSubtype_; - throw std::logic_error("Invalid small variant subtype: " + encoding.str()); - } - - refNodeSupport = countReadsSupportingNode(refNode); - altNodeSupport = countReadsSupportingNode(altNode); - - const double haplotypeDepth = stats.alleleCount() == AlleleCount::kTwo ? stats.depth() / 2 : stats.depth(); - const int minBreakpointSpanningReads = stats.alleleCount() == AlleleCount::kTwo - ? genotyperParams_.minBreakpointSpanningReads - : (genotyperParams_.minBreakpointSpanningReads / 2); - - SmallVariantGenotyper smallVariantGenotyper(haplotypeDepth, stats.alleleCount()); - genotype = smallVariantGenotyper.genotype(refNodeSupport, altNodeSupport); - - refAlleleStatus = allelePresenceChecker_.check(haplotypeDepth, refNodeSupport, altNodeSupport); - altAlleleStatus = allelePresenceChecker_.check(haplotypeDepth, altNodeSupport, refNodeSupport); - - GraphVariantAlignmentStats alignmentStats = alignmentStatsCalculator_.getStats(); - const bool insufficientBreakpointCoverage - = alignmentStats.numReadsSpanningLeftBreakpoint() < minBreakpointSpanningReads - || alignmentStats.numReadsSpanningRightBreakpoint() < minBreakpointSpanningReads; - if ((variantSubtype_ != VariantSubtype::kSMN) && insufficientBreakpointCoverage) - { - genotypeFilter = genotypeFilter | GenotypeFilter::kLowDepth; - } + genotypeFilter = genotypeFilter | GenotypeFilter::kLowDepth; } - return std::unique_ptr(new SmallVariantFindings( + return make_unique( refNodeSupport, altNodeSupport, refAlleleStatus, altAlleleStatus, stats.alleleCount(), genotype, - genotypeFilter)); + genotypeFilter); } } diff --git a/ehunter/locus/VariantAnalyzer.cpp b/ehunter/locus/VariantAnalyzer.cpp index 292fa34..ba1993b 100644 --- a/ehunter/locus/VariantAnalyzer.cpp +++ b/ehunter/locus/VariantAnalyzer.cpp @@ -20,3 +20,8 @@ // #include "locus/VariantAnalyzer.hh" +bool ehunter::VariantAnalyzer::isLowDepth(const LocusStats& stats) const +{ + const double diploidCoverage = stats.alleleCount() == AlleleCount::kTwo ? stats.depth() : 2 * stats.depth(); + return (stats.meanReadLength() == 0 || diploidCoverage < genotyperParams_.minLocusCoverage); +} diff --git a/ehunter/locus/VariantAnalyzer.hh b/ehunter/locus/VariantAnalyzer.hh index 0765aa1..c539395 100644 --- a/ehunter/locus/VariantAnalyzer.hh +++ b/ehunter/locus/VariantAnalyzer.hh @@ -56,6 +56,7 @@ public: const graphtools::GraphAlignment& mateAlignment) = 0; + bool isLowDepth(const LocusStats& stats) const; virtual std::unique_ptr analyze(const LocusStats& stats) = 0; const std::string& variantId() const { return variantId_; } diff --git a/ehunter/locus/VariantFindings.hh b/ehunter/locus/VariantFindings.hh index cec3d39..7077c9e 100644 --- a/ehunter/locus/VariantFindings.hh +++ b/ehunter/locus/VariantFindings.hh @@ -30,6 +30,7 @@ #include "genotyping/AlleleChecker.hh" #include "genotyping/RepeatGenotype.hh" #include "genotyping/SmallVariantGenotype.hh" +#include "locus/RFC1Status.hh" namespace ehunter { @@ -85,6 +86,10 @@ public: const boost::optional& optionalGenotype() const { return optionalGenotype_; } GenotypeFilter genotypeFilter() const { return genotypeFilter_; } + void setRFC1Status(const RFC1Status& rfc1Status) { rfc1Status_ = rfc1Status; } + + boost::optional getRFC1Status() const { return rfc1Status_; } + bool operator==(const RepeatFindings& other) const { return countsOfSpanningReads_ == other.countsOfSpanningReads_ @@ -99,6 +104,7 @@ private: AlleleCount alleleCount_; boost::optional optionalGenotype_; GenotypeFilter genotypeFilter_; + boost::optional rfc1Status_; }; class SmallVariantFindings : public VariantFindings diff --git a/ehunter/sample/HtsSeekingSampleAnalysis.cpp b/ehunter/sample/HtsSeekingSampleAnalysis.cpp index 6f2a73e..b7da1d6 100644 --- a/ehunter/sample/HtsSeekingSampleAnalysis.cpp +++ b/ehunter/sample/HtsSeekingSampleAnalysis.cpp @@ -334,6 +334,18 @@ SampleFindings htsSeekingSampleAnalysis( const InputPaths& inputPaths, Sex sampleSex, const HeuristicParameters& heuristicParams, const int threadCount, const RegionCatalog& regionCatalog, locus::AlignWriterPtr alignmentWriter) { + if (ehunter::isURL(inputPaths.htsFile())) + { + // For URL input paths, the index needs to be downloaded in advance if seeking mode is using multiple threads. + // This is needed because htslib has no protection against the race condition created by multiple threads + // independently downloading this index to the same file path. + // + if (threadCount > 1) + { + (void)HtsFileSeeker(inputPaths.htsFile(), inputPaths.reference()); + } + } + LocusThreadSharedData locusThreadSharedData; std::vector locusThreadLocalDataPool(threadCount); diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/CMakeLists.txt b/ehunter/thirdparty/graph-tools-master-f421f4c/CMakeLists.txt deleted file mode 100644 index f45b519..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/CMakeLists.txt +++ /dev/null @@ -1,63 +0,0 @@ -cmake_minimum_required(VERSION 3.5.0) - -project(graphtools CXX) - -set(CMAKE_EXPORT_COMPILE_COMMANDS ON) - -set(CMAKE_CXX_STANDARD 11) -set(CMAKE_CXX_STANDARD_REQUIRED ON) -set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake") - -set(BUILD_TESTS OFF CACHE BOOL "Should unit tests be built") - -set(USE_ASAN OFF CACHE BOOL "Use clang address sanitizer") -set(USE_MSAN OFF CACHE BOOL "Use clang memory sanitizer") - -set(CMAKE_EXPORT_COMPILE_COMMANDS ON) -set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -D_DEBUG") - -if (CMAKE_SYSTEM_PROCESSOR MATCHES "^x86_64$") - if (NOT GRAPHTOOLS_AVX2) - set(GRAPHTOOLS_VECTORIZATION "-msse4.2") - else (NOT GRAPHTOOLS_AVX2) - set(GRAPHTOOLS_VECTORIZATION "-mavx2") - endif (NOT GRAPHTOOLS_AVX2) -endif (CMAKE_SYSTEM_PROCESSOR MATCHES "^x86_64$") - -if (CMAKE_CXX_COMPILER_ID STREQUAL "GNU") - set(GRAPHTOOLS_CXX_OPTIMIZATION_FLAGS "${GRAPHTOOLS_VECTORIZATION} -O2 -ftree-vectorize -finline-functions -fpredictive-commoning -fgcse-after-reload -funswitch-loops -ftree-slp-vectorize -fvect-cost-model -fipa-cp-clone -ftree-phiprop") -endif () - -SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${GRAPHTOOLS_CXX_OPTIMIZATION_FLAGS} -Wall -Werror -pedantic -Wsign-compare -Wno-missing-braces -Wno-deprecated-copy -Wno-unknown-warning-option") - -if (USE_ASAN) - SET(CLANG_ASAN "-O1 -g -fsanitize=address -fno-omit-frame-pointer") - SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CLANG_ASAN}") - SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${CLANG_ASAN}") - SET(BUILD_TESTS ON) -endif () - -if (USE_MSAN) - SET(CLANG_MSAN "-O1 -g -fsanitize=memory -fno-omit-frame-pointer") - SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CLANG_MSAN}") - SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${CLANG_MSAN}") - SET(BUILD_TESTS ON) -endif () - -#find_package(Threads REQUIRED) -find_package(Boost 1.5 COMPONENTS program_options filesystem system REQUIRED) - -file(GLOB SOURCES "src/graphalign/*.cpp" "src/graphalign/*/*.cpp" "src/graphcore/*.cpp" "src/graphutils/*.cpp" "src/graphio/*.cpp") -add_library(graphtools ${SOURCES}) -target_include_directories(graphtools PUBLIC "include") -target_include_directories(graphtools PUBLIC "external/include") -target_include_directories(graphtools PUBLIC "external/sparsepp/sparsepp-e40d7a0") -target_link_libraries(graphtools Boost::boost) -target_compile_features(graphtools PRIVATE cxx_range_for) - -if (BUILD_TESTS) - enable_testing() - # Download and unpack googletest at configure time - include(GetGoogleTest) - add_subdirectory(tests) -endif (BUILD_TESTS) diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/Dockerfile b/ehunter/thirdparty/graph-tools-master-f421f4c/Dockerfile deleted file mode 100644 index 25f52d1..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/Dockerfile +++ /dev/null @@ -1,33 +0,0 @@ -FROM ubuntu:16.04 - -RUN apt-get -qq update && apt-get install -yq \ - wget curl software-properties-common && \ - wget -O llvm.key https://apt.llvm.org/llvm-snapshot.gpg.key && apt-key add llvm.key && rm -f llvm.key - -RUN apt-add-repository "deb http://apt.llvm.org/xenial/ llvm-toolchain-xenial-5.0 main" - -RUN apt-get -qq update && apt-get install -yq \ - build-essential \ - cmake \ - zlib1g-dev \ - libbz2-dev \ - valgrind \ - cppcheck \ - clang-5.0 \ - clang-format-5.0 \ - clang-tidy-5.0 \ - libboost-all-dev \ - && \ - apt-get clean -y && \ - rm -rf /var/lib/apt/lists/* - -RUN update-alternatives --install /usr/bin/clang++ clang++ /usr/bin/clang++-5.0 1000 && \ - update-alternatives --install /usr/bin/clang clang /usr/bin/clang-5.0 1000 && \ - update-alternatives --config clang && \ - update-alternatives --config clang++ - -RUN apt-get -qq update && apt-get install -yq \ - git \ - && \ - apt-get clean -y && \ - rm -rf /var/lib/apt/lists/* diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/LICENSE.txt b/ehunter/thirdparty/graph-tools-master-f421f4c/LICENSE.txt deleted file mode 100644 index d645695..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/LICENSE.txt +++ /dev/null @@ -1,202 +0,0 @@ - - Apache License - Version 2.0, January 2004 - http://www.apache.org/licenses/ - - TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION - - 1. 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We also recommend that a - file or class name and description of purpose be included on the - same "printed page" as the copyright notice for easier - identification within third-party archives. - - Copyright [yyyy] [name of copyright owner] - - Licensed under the Apache License, Version 2.0 (the "License"); - you may not use this file except in compliance with the License. - You may obtain a copy of the License at - - http://www.apache.org/licenses/LICENSE-2.0 - - Unless required by applicable law or agreed to in writing, software - distributed under the License is distributed on an "AS IS" BASIS, - WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - See the License for the specific language governing permissions and - limitations under the License. diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/README.md b/ehunter/thirdparty/graph-tools-master-f421f4c/README.md deleted file mode 100644 index 15ea265..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/README.md +++ /dev/null @@ -1,29 +0,0 @@ -# A library for working with sequence graphs - -## Introduction - -Graph-tools library aims to provide data models and methods for working with sequence graphs and alignments to them. - -See docs/development.md for build instructions - -## Contents - -### Graph definition -- A data model for graphs in memory and as JSON: [graphs.md](docs/graphs.md) - - The graphs are DAGs, with the addition of support for self-loops on individual nodes -- Paths through graphs to define sequences, e.g. for alignments: [paths.md](docs/paths.md) -- Path Families, subsets of edges of the graph, to define haplotypes: [path_families.md](docs/path_families.md) -- Graph-to-reference mappings: Translating positions in the graph to positions in a linear reference (e.g. genome) -- Nucleotide sequence definition:[query_and_reference_sequences.md](docs/query_and_reference_sequences.md) - - Extended alphabet for degenerate bases and base quality - -### Alignment -- Methods to perform both gapped and gapless alignment of sequences to graphs, -- A rich set of heuristics for filtering alignments. - -### GraphIO -The separate GraphIO library contains methods to read and write - - Graphs from JSON - - (Linear) Reference sequences from fasta - - Graph-alignments from BAM -It depends on htslib. \ No newline at end of file diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/RELEASES.md b/ehunter/thirdparty/graph-tools-master-f421f4c/RELEASES.md deleted file mode 100644 index bbd71c0..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/RELEASES.md +++ /dev/null @@ -1,42 +0,0 @@ -# Graph-Tools Release Notes / Change Log - -## Version 0.3.0 -| Date Y-m-d | Ticket | Description | -|------------|---------|----------------------------------------------------------------------| -| 2018-07-13 | GT-536 | Add output of graph alignments as (unmapped) BAM records | -| 2018-06-28 | GT-526 | Simple mapping of graph positions to a linear reference | -| 2018-06-26 | GT-502 | Change path coordinate system from closed to half open | - -## Version 0.2.0 -| Date Y-m-d | Ticket | Description | -|------------|---------|----------------------------------------------------------------------| -| 2018-06-26 | GT-512 | Add support for reading and writing graphs from JSON | -| 2018-06-26 | GT-505 | Add functions to reconstruct path families from paths and graphs | -| 2018-06-21 | GT-524 | Add GraphIO library | -| 2018-05-31 | GT-482 | projectAlignmentOntoGraph fix when alignments don't cover entire path| -| 2018-05-24 | GT-470 | Add function to generate paths from path families + documentation | -| 2018-05-22 | GT-458 | Fix bugs in gapped aliner and alignment comparison | -| 2018-05-20 | GT-442 | Document definitions of query and reference sequences | -| 2018-05-10 | GT-445 | Add functions for exact match extension of paths | -| 2018-05-08 | GT-416 | Add projection of graph to linear reference coordinates | -| 2018-05-04 | GT-457 | Provide a common interface for graph aligners | -| 2018-05-03 | GT-444 | Remove sequences from all alignment objects | - -## Version 0.1.1 - -| Date Y-m-d | Ticket | Description | -|------------|---------|----------------------------------------------------------------------| -| 2018-04-26 | GT-453 | Add Path Families | - -## Version 0.1.0 - -| Date Y-m-d | Ticket | Description | -|------------|---------|----------------------------------------------------------------------| -| 2018-04-16 | GT-438 | Add feature to disable graph sequence expansion | -| 2018-04-09 | GT-431 | Faster reference sequence expansion | -| 2018-04-05 | GT-397 | Add gapped alignment | -| 2018-03-29 | GT-353 | Integration issues / function ports from paragraph-tools | - -## Version 0.0.1 - -Initial release. diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/cmake/GetGoogleTest.cmake b/ehunter/thirdparty/graph-tools-master-f421f4c/cmake/GetGoogleTest.cmake deleted file mode 100644 index aded63a..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/cmake/GetGoogleTest.cmake +++ /dev/null @@ -1,44 +0,0 @@ -######################### Google Test ############################ -# Download and unpack googletest at configure time - -FILE(WRITE "${CMAKE_BINARY_DIR}/external/googletest-build/CMakeLists.txt" "\ -cmake_minimum_required(VERSION 2.8.12) -project(googletest-build NONE) -include(ExternalProject) -ExternalProject_Add(googletest - # GIT_REPOSITORY https://github.com/google/googletest.git - # GIT_TAG release-1.8.0 - URL \"${CMAKE_SOURCE_DIR}/external/googletest-release-1.10.0.tar.gz\" - URL_HASH MD5=ecd1fa65e7de707cd5c00bdac56022cd - SOURCE_DIR \"${CMAKE_BINARY_DIR}/external/googletest-src\" - BINARY_DIR \"${CMAKE_BINARY_DIR}/external/googletest-build\" - CONFIGURE_COMMAND \"\" - BUILD_COMMAND \"\" - INSTALL_COMMAND \"\" - TEST_COMMAND \"\" - )" -) - -execute_process(COMMAND ${CMAKE_COMMAND} -G "${CMAKE_GENERATOR}" . - RESULT_VARIABLE result - WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/external/googletest-build ) -if(result) - message(FATAL_ERROR "CMake step for googletest failed: ${result}") -endif() -execute_process(COMMAND ${CMAKE_COMMAND} --build . - RESULT_VARIABLE result - WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/external/googletest-build ) -if(result) - message(FATAL_ERROR "Build step for googletest failed: ${result}") -endif() - -# Add googletest directly to our build. This defines -# the gtest and gtest_main targets. -add_subdirectory(${CMAKE_BINARY_DIR}/external/googletest-src - ${CMAKE_BINARY_DIR}/external/googletest-build) -#add_subdirectory(${CMAKE_BINARY_DIR}/external/googletest-src/googletest -# ${CMAKE_BINARY_DIR}/external/googletest-build-test) -#add_subdirectory(${CMAKE_BINARY_DIR}/external/googletest-src/googlemock -# ${CMAKE_BINARY_DIR}/external/googletest-build-mock) - -################################################################## \ No newline at end of file diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/docs/alignment.md b/ehunter/thirdparty/graph-tools-master-f421f4c/docs/alignment.md deleted file mode 100644 index 5275500..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/docs/alignment.md +++ /dev/null @@ -1,37 +0,0 @@ -# Graph alignment - -## Alignment methods - -## Alignment representation - -## BAM Output - -Graph-tools supports outputting alignments in BAM format (through `graphIO/BamWriter`). -Currently this does not produce full BAM alignments, but rather 'unaligned' BAM records -that are placed at the right start position in the (linear) reference genome and include -the actual alignment against the alignment encoded as a string in a custom tag. - -For this to work a projection of the graph onto a linear reference genome is needed (class `GraphReferenceMapping`). -This assigns a reference coordinate interval to graph nodes and hence allows projecting positions (and paths) in the graph to -positions in the linear reference that the BAM is based on. - -### BAM encoding for graph alignments - -The BAM record for read `R` with graph-alignment `g`: - * Qname, Seq, Qual describe the read (matching fastq input) - * Chromosome and Position are set to the first projected reference position of the graph-alignment path (`g.path`) - 1. Find first node `n` in `g.path` that has a reference mapping - 2. Set the BAM read position to the projected position of the first base of `n` + the offset of `g.path` in `n`. - * Mate Chrom and Position undefined - * Read is `unmapped`: No mapQ, CIGAR - * Flags - * read paired, first/second in pair, failedQC: Set according to fastq/input BAM - * read unmapped and mate unmapped is set - * read reverse strand is set depending on mapping to graph in forward or reverse direction - * all other flags are unset - * The actual graph alignment is encoded in custom tags - * XG: string - Graph CIGAR - * Combination of Alignment path and CIGAR against each node. - * E.g. 0[Ref start: 2, 2M]1[Ref start: 0, 1M]3[Ref start: 0, 3M] - * Alignment starts at position 2 on node 0 with 2 matches - * Continues at Node1 with 1 match and node3 with 3 matches diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/docs/development.md b/ehunter/thirdparty/graph-tools-master-f421f4c/docs/development.md deleted file mode 100644 index d3c894e..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/docs/development.md +++ /dev/null @@ -1,31 +0,0 @@ -# Building - -The following is required to build graph-tools library from source: - -- A C++ 11 compliant compiler (tested with GCC 6.3.0), -- CMake 3.5.0 or above. -- BOOST 1.5 or above - -To build the library, perform the standard out-of-source CMake build. The unit -tests are not built by default. To build the unit tests, pass `-DBUILD_TESTS=ON` -to CMake. - -To also build the included graphIO library, pass `-DBUILD_GRAPHIO=ON` to CMake. -In that case htslib is required. By default htslib is downloaded from github and build during the CMake configure step. Alternatively -set $HTSLIB_INSTALL_PATH to the path (install prefix) of an already installed htslib. -GraphIO also includes a (header-only) version of the nlohmann/json library. - -## Incorporating the library into other CMake projects - -Copy graph-tools to the source tree of your project. Assuming that the library -was placed in `thirdparty/graph-tools` directory in the project's root, add -`add_subdirectory(thirdparty/graph-tools)` and -`target_link_libraries( graphtools)` to your CMakeLists.txt file. - -# Code standards -C++ code should follow the [c++ core guidelines](https://github.com/isocpp/CppCoreGuidelines/blob/master/CppCoreGuidelines.md). -Code has to pass cppcheck; see [docker-cppcheck.sh](/src/sh/docker-cppcheck.sh) for details. - -## Style guide -Naming of identifiers should match the surrounding code. -Formatting should (exactly) match the output of clang-format 5.0.1; see [format-everything.sh](/src/sh/format-everything.sh) for details. diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/docs/graph.md b/ehunter/thirdparty/graph-tools-master-f421f4c/docs/graph.md deleted file mode 100644 index 213af08..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/docs/graph.md +++ /dev/null @@ -1,53 +0,0 @@ -# Graph model - -## Definitions -The sequence graph is made up of nodes and directed edges. Each node holds a (non-empty) sequence. Edges connect -nodes and do not hold sequences themselves. A path is a sequence of nodes, where each node is connected to its successor with a directed edge. A path defines a sequence in the graph. - -## Graph class -### Files -- `include/graphcore/Graph.hh` -- `tests` - - `GraphOperationsTest.cpp` - - `GraphCoordinatesTest.cpp` - -The graph class holds nodes, edges and edge labels (used for path families). -Nodes are simple structs with a name and sequence. Within a graph each node has a unique NodeID, numbered from 0 to -graph.numNodes. -Edges are defined as pairs of NodeIDs and are stored directly within the graph using a node adjacency list. -Every edge can optionally be labeled with one or more labels. - -Graphs are allowed to contain self-loops (edges from a node to itself). Excluding self-loop edges the graph has to be a DAG. A path -may pass through such an loop-edge multiple times, defining a repeated sequence. - -## Paths -See [path](paths.md) and [path family](path_families.md) documentation. - -## Reference Mapping -A graph reference mapping (`include/Graphcore/GraphReferenceMapping.hh`) is used to define a projection of the graph onto linear reference genome coordinates. A subset of nodes -are assigned one (or possibly multiple) reference intervals. For reference nodes this would be the interval their sequence comes from -for alt. allele nodes the 'replaced' reference sequence (or position of insertion). - -These reference mappings can be stored in JSON, either together with the graph or separately. They are used to generate BAM output of alignments. - -## JSON model -Graphs can be serialized in JSON. The format is -- "nodes": array of node objects containing - - "name": string (required; not-empty) - Unique name for this node - - "sequence": string; not-empty - Nucleotide sequence of this node - - [Extended alphabet](query_and_reference_sequences.md) - - Either "sequence" or "reference" is required - - "reference": string - Region in the reference genome - - Sets the sequence of the node to match the reference region if no explicit "sequence" is given - - Region is given as a 0-based half-open interval (:-) - - Also defines this reference region as the mapping position of the node for GraphReferenceMapping -- "edges": array of edge objects containing - - "from": string - name of the start node - - "to": string - name of the end node - - "labels": array of string - edge labels applied to this edge -- "paths": array of path objects (optional) containing - - path_id: string - name of the path - - nodes: array of string - name of nodes in the path (in order) -- "graph_id": string (optional) - name for the graph -- "reference_genome": string - path to a fasta file with the reference genome sequence - - required if using "reference" sequences in node definitions diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/docs/path_families.md b/ehunter/thirdparty/graph-tools-master-f421f4c/docs/path_families.md deleted file mode 100644 index 92b69e1..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/docs/path_families.md +++ /dev/null @@ -1,102 +0,0 @@ -# Path Families - -## Files - -* [include/graphcore/PathFamily.hh](/include/graphcore/PathFamily.hh) -* [src/graphcore/PathFamily.hh](/src/graphcore/PathFamily.cpp) -* [tests/PathFamilyTest.cpp](/tests/PathFamilyTest.cpp) - -## Definitions - -If enumerating all [paths](paths.md) in a set becomes impractical, -we can define a set of paths implicitly by a set of edges. -We call sets of paths defined in this way *path families*. -We construct a path family from -a set of edges *F = \{ f1, f2, ... fl \}*. -A path *P* is in the path family *F* iff. at least one node in *P* -is connected via an edge in *F* and for any node *pn* in *P* -both of these conditions hold: - -* No incoming edge into *pn* exists in *F* or edge *(pn-1, pn)* is in *F*. -* No outgoing edge from *pn* exists in *F* or edge *(pn, pn+1)* is in *F*. - -Informally, a path family F consists of paths that enter and exit nodes -only through edges in F when such edges exist. -A path does not have to cover the entire path family -(either all nodes or all edges), but may start in the middle or -enter/exit through any edge into a node that has no incoming/outgoing -edges in *F*. - -In graph-tools, path families can be created as follows: - -```c++ -Graph G = makeDeletionGraph("TTT", "AT", "CCCCC"); -PathFamily family(&G); -// family of all possible alleles -family.addEdge(0, 1); -family.addEdge(1, 2); -family.addEdge(0, 2); -``` - -The primary operation provided by path families is a query -operation which tells us whether a given path is contained in -a path family: - -```c++ -Path path(&graph, 0, { 0, 1, 2 }, 0); -assert( family.containsPath(path) ); -``` - -We can also test if a path family includes another family: - -```c++ -PathFamily family2(&G); -family2.addEdge(0, 1); -family2.addEdge(1, 2); - -assert( family.includes(family2) ); -assert( !family2.includes(family) ); -``` -# Path Family Operations - -## Files - -* [include/graphcore/PathFamilyOperations.hh](/include/graphcore/PathFamilyOperations.hh) -* [src/graphcore/PathFamilyOperations.cpp](/src/graphcore/PathFamilyOperations.cpp) -* [tests/PathFamilyOperationsTest.cpp](/tests/PathFamilyOperationsTest.cpp) - -## Operations - -### Generate path segments in a family -```c++ -list getPathSegmentsForFamily(PathFamily const& family); -``` - -This function generates a set of maximum-length path segments for a family, -where each path that is the result of merging two path segments -is also contained in the path family. - -### Enumerate path combinations in a family - -```c++ -bool enumeratePathCombinationsInFamily( - PathFamily const& family, list const& segments, std::list* paths, size_t maxPaths); -``` - -Given a set of path segments from a family, this function -performs restricted enumeration of all paths that can be -obtained by merging path segments. - -### Generate a set of maximal paths - -```c++ -bool getMaximalPathsForFamily( - PathFamily const& family, list* paths, size_t maxPaths); -``` - -This function combines segment generation and path enumeration into a -single function call: - -* It generates all path segments for a path family. -* It then enumerates all (or a maximum number of ) merged paths from - these segments. diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/docs/paths.md b/ehunter/thirdparty/graph-tools-master-f421f4c/docs/paths.md deleted file mode 100644 index 3f8068f..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/docs/paths.md +++ /dev/null @@ -1,110 +0,0 @@ -# Paths - -## Files - -* [include/graphcore/Path.hh](/include/graphcore/Path.hh) -* [src/graphcore/Path.cpp](/src/graphcore/Path.cpp) -* [tests/PathTest.cpp](/tests/PathTest.cpp) - -## Definitions - -A path *P* in a graph *G* of length *k* is given by - -* a list of nodes *{ ni for i = 1 ... k }* -* a start position on *n1* -* an end position on *nk* - -In order path *P* to be valid in *G*, we require - -* all nodes in *P* must be present in *G*, -* for all *i* in *1 ... k - 1*, *G* must have an edge - *(ni, ni+1)*, -* the start and end position must be valid given the - node sequence lengths of *n1* and *nk*. - -In graph-tools, paths can be created as follows: - -```c++ -Graph G = makeDeletionGraph("TTT", "AT", "CCCCC"); -Path P1(&G, 1, { 0, 1, 2 }, 1)); -Path P2(&G, 1, { 0, 2 }, 2)); -``` - -Path objects can be used to determine the sequence generated by -a path: - -```c++ -assert( P1.seq() == "TTATCC" ); -assert( P2.seq() == "TTCCC" ); -``` - -We can also generate human-readable encodings for paths: - -```c++ -assert( "(0@1)-(1)-(2@1)" == P1.encode() ); -assert( "(0@1)-(2@2)" == P2.encode() ); -``` - -Here, the start and end positions are encoded as *nodeId@position*. - -Other functions provided by paths include: - -* functions to test / quantify a path's overlap with a single node. -* `getDistanceFromPathStart()`: Given node *nj* and offset *o*, calculate the distance from the start of the path to position - *nj@o* if *nj* is contained in the path. -* `shrink*()` / `extend*()` / `shift*()` / `remove*()`: various modifier functions for shrinking and expanding paths at the ends. - -# Path Operations - -## Files - -* [include/graphcore/PathOperations.hh](/include/graphcore/PathOperations.hh) -* [src/graphcore/PathOperations.cpp](/src/graphcore/PathOperations.cpp) -* [tests/PathOperationsTest.cpp](/tests/PathOperationsTest.cpp) - -## Operations - -### Path Extension (`extendPath*`) - -We provide a set of functions to enumerate the possible paths generated -by extending a given path by a number of bases to the left or right. - -Furthermore, paths can also be extended while they uniquely match a given -query sequence (`extendPath*Matching*` functions). This is useful to -produce sets of maximal unique matches of a sequence on a graph from -a seed. - -### Sequence Decomposition (`splitSequenceByPath`) - -```c++ -vector splitSequenceByPath(const Path& path, const string& sequence); -``` - -This function is useful to map a sequence of the same length of a path onto -that path. It returns a list of sequences that correspond to the substring -of the input sequence mapped onto each node in the path. - -### Path Overlap and Merging - -We provide various operations to check if the union of two -paths will produce valid paths also (`checkIfPathsAdjacent`, -`checkPathPrefixSuffixOverlap`). - -If the union of two paths is a valid path, `mergePaths` can be -used to produce this union path. - -The `greedyMerge` and `exhaustiveMerge` function -aim to reduce redundancy in a set of paths by merging paths in a set -if they are compatible in the way described above. Exhaustively -merging paths can take a long time since this function attempts -to merge all possible path prefixes with all possible suffixes, -greedy merging will pick only one prefix / suffix combination. - -### Path Intersections - -```c++ -list intersectPaths(Path const& p1, Path const& p2); -``` - -This returns a set of all longest paths that are subpaths -of both p1 and p2. \ No newline at end of file diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/docs/query_and_reference_sequences.md b/ehunter/thirdparty/graph-tools-master-f421f4c/docs/query_and_reference_sequences.md deleted file mode 100644 index b9982c8..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/docs/query_and_reference_sequences.md +++ /dev/null @@ -1,53 +0,0 @@ -# Query and reference sequences - -## Introduction - -A large part of the GraphTools library is concerned with alignment of query sequences (typically short reads) to a -reference represented by a sequence graph. This section explains the distinction between query sequences and reference -sequences that make up graphs. - -A **query sequence** must consist of characters representing core nucleotides A, C, G, T and a missing nucleotide symbol -N. The uppercase and lowercase core nucleotide characters correspond to high and low quality base calls respectively. - -Here is an example of a query sequence with many low quality base calls. - -```C++ -CCGACCACGCCCCGGCCCCcGCCCCGGCCCCcaGCGcgCGaCcCCtGaGgTcccGgGctTGCcaCaGgCcggcGgtGttTCCCcCCttgttttTTtCtg -``` - -A **reference sequence** -- a sequence of a node in a graph -- must consist of characters representing cores nucleotides -(A, C, G, T) or degenerate nucleotides (that correspond to multiple nucleotides). The following table lists the -degenerate nucleotides as defined by the International Union of Pure and Applied Chemistry. - -| Degenerate nucleotide | Corresponding core nucleotides | -|-----------------------|--------------------------------| -| R | A, G | -| Y | C, T | -| K | G, T | -| M | A, C | -| S | C, G | -| W | A, T | -| B | C, G, T | -| D | A, G, T | -| H | A, C, T | -| V | A, C, G | -| N | A, C, G, T | - -Here is an example of a reference sequence representing a trinucleotide repeat consisting of 12 Alanine codons. - -```C++ -GCNGCNGCNGCNGCNGCNGCNGCNGCNGCNGCNGCN -``` - -## Matching query and reference sequences - -The rules for matching the characters of query and reference sequences are given in the table above. Additionally, we -require that the missing nucleotide character N in the query sequences does not match any other characters. (Note the -distinction with reference N that matches A, C, G, and T.) - -To accommodate the needs of the existing clients of the GraphTools library, we allow query Ns within alignments to be a -part of mismatch operations or "missing nucleotide" operations. See the section on -[representation of alignments](representation_of_alignments.md) for more details. - -The basic machinery for matching query and reference sequences is provided in `BaseMatching.*` and -`SequenceOperations.*` files inside `graphutils`. diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/external/googletest-release-1.10.0.tar.gz b/ehunter/thirdparty/graph-tools-master-f421f4c/external/googletest-release-1.10.0.tar.gz deleted file mode 100644 index ab10868..0000000 Binary files a/ehunter/thirdparty/graph-tools-master-f421f4c/external/googletest-release-1.10.0.tar.gz and /dev/null differ diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/external/include/nlohmann/json.hpp b/ehunter/thirdparty/graph-tools-master-f421f4c/external/include/nlohmann/json.hpp deleted file mode 100644 index a70aaf8..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/external/include/nlohmann/json.hpp +++ /dev/null @@ -1,25447 +0,0 @@ -/* - __ _____ _____ _____ - __| | __| | | | JSON for Modern C++ -| | |__ | | | | | | version 3.9.1 -|_____|_____|_____|_|___| https://github.com/nlohmann/json - -Licensed under the MIT License . -SPDX-License-Identifier: MIT -Copyright (c) 2013-2019 Niels Lohmann . - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE. -*/ - -#ifndef INCLUDE_NLOHMANN_JSON_HPP_ -#define INCLUDE_NLOHMANN_JSON_HPP_ - -#define NLOHMANN_JSON_VERSION_MAJOR 3 -#define NLOHMANN_JSON_VERSION_MINOR 9 -#define NLOHMANN_JSON_VERSION_PATCH 1 - -#include // all_of, find, for_each -#include // nullptr_t, ptrdiff_t, size_t -#include // hash, less -#include // initializer_list -#include // istream, ostream -#include // random_access_iterator_tag -#include // unique_ptr -#include // accumulate -#include // string, stoi, to_string -#include // declval, forward, move, pair, swap -#include // vector - -// #include - - -#include - -// #include - - -#include // transform -#include // array -#include // forward_list -#include // inserter, front_inserter, end -#include // map -#include // string -#include // tuple, make_tuple -#include // is_arithmetic, is_same, is_enum, underlying_type, is_convertible -#include // unordered_map -#include // pair, declval -#include // valarray - -// #include - - -#include // exception -#include // runtime_error -#include // to_string - -// #include - - -#include // size_t - -namespace nlohmann -{ -namespace detail -{ -/// struct to capture the start position of the current token -struct position_t -{ - /// the total number of characters read - std::size_t chars_read_total = 0; - /// the number of characters read in the current line - std::size_t chars_read_current_line = 0; - /// the number of lines read - std::size_t lines_read = 0; - - /// conversion to size_t to preserve SAX interface - constexpr operator size_t() const - { - return chars_read_total; - } -}; - -} // namespace detail -} // namespace nlohmann - -// #include - - -#include // pair -// #include -/* Hedley - https://nemequ.github.io/hedley - * Created by Evan Nemerson - * - * To the extent possible under law, the author(s) have dedicated all - * copyright and related and neighboring rights to this software to - * the public domain worldwide. This software is distributed without - * any warranty. - * - * For details, see . - * SPDX-License-Identifier: CC0-1.0 - */ - -#if !defined(JSON_HEDLEY_VERSION) || (JSON_HEDLEY_VERSION < 13) -#if defined(JSON_HEDLEY_VERSION) - #undef JSON_HEDLEY_VERSION -#endif -#define JSON_HEDLEY_VERSION 13 - -#if defined(JSON_HEDLEY_STRINGIFY_EX) - #undef JSON_HEDLEY_STRINGIFY_EX -#endif -#define JSON_HEDLEY_STRINGIFY_EX(x) #x - -#if defined(JSON_HEDLEY_STRINGIFY) - #undef JSON_HEDLEY_STRINGIFY -#endif -#define JSON_HEDLEY_STRINGIFY(x) JSON_HEDLEY_STRINGIFY_EX(x) - -#if defined(JSON_HEDLEY_CONCAT_EX) - #undef JSON_HEDLEY_CONCAT_EX -#endif -#define JSON_HEDLEY_CONCAT_EX(a,b) a##b - -#if defined(JSON_HEDLEY_CONCAT) - #undef JSON_HEDLEY_CONCAT -#endif -#define JSON_HEDLEY_CONCAT(a,b) JSON_HEDLEY_CONCAT_EX(a,b) - -#if defined(JSON_HEDLEY_CONCAT3_EX) - #undef JSON_HEDLEY_CONCAT3_EX -#endif -#define JSON_HEDLEY_CONCAT3_EX(a,b,c) a##b##c - -#if defined(JSON_HEDLEY_CONCAT3) - #undef JSON_HEDLEY_CONCAT3 -#endif -#define JSON_HEDLEY_CONCAT3(a,b,c) JSON_HEDLEY_CONCAT3_EX(a,b,c) - -#if defined(JSON_HEDLEY_VERSION_ENCODE) - #undef JSON_HEDLEY_VERSION_ENCODE -#endif -#define JSON_HEDLEY_VERSION_ENCODE(major,minor,revision) (((major) * 1000000) + ((minor) * 1000) + (revision)) - -#if defined(JSON_HEDLEY_VERSION_DECODE_MAJOR) - #undef JSON_HEDLEY_VERSION_DECODE_MAJOR -#endif -#define JSON_HEDLEY_VERSION_DECODE_MAJOR(version) ((version) / 1000000) - -#if defined(JSON_HEDLEY_VERSION_DECODE_MINOR) - #undef JSON_HEDLEY_VERSION_DECODE_MINOR -#endif -#define JSON_HEDLEY_VERSION_DECODE_MINOR(version) (((version) % 1000000) / 1000) - -#if defined(JSON_HEDLEY_VERSION_DECODE_REVISION) - #undef JSON_HEDLEY_VERSION_DECODE_REVISION -#endif -#define JSON_HEDLEY_VERSION_DECODE_REVISION(version) ((version) % 1000) - -#if defined(JSON_HEDLEY_GNUC_VERSION) - #undef JSON_HEDLEY_GNUC_VERSION -#endif -#if defined(__GNUC__) && defined(__GNUC_PATCHLEVEL__) - #define JSON_HEDLEY_GNUC_VERSION JSON_HEDLEY_VERSION_ENCODE(__GNUC__, __GNUC_MINOR__, __GNUC_PATCHLEVEL__) -#elif defined(__GNUC__) - #define JSON_HEDLEY_GNUC_VERSION JSON_HEDLEY_VERSION_ENCODE(__GNUC__, __GNUC_MINOR__, 0) -#endif - -#if defined(JSON_HEDLEY_GNUC_VERSION_CHECK) - #undef JSON_HEDLEY_GNUC_VERSION_CHECK -#endif -#if defined(JSON_HEDLEY_GNUC_VERSION) - #define JSON_HEDLEY_GNUC_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_GNUC_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) -#else - #define JSON_HEDLEY_GNUC_VERSION_CHECK(major,minor,patch) (0) -#endif - -#if defined(JSON_HEDLEY_MSVC_VERSION) - #undef JSON_HEDLEY_MSVC_VERSION -#endif -#if defined(_MSC_FULL_VER) && (_MSC_FULL_VER >= 140000000) - #define JSON_HEDLEY_MSVC_VERSION JSON_HEDLEY_VERSION_ENCODE(_MSC_FULL_VER / 10000000, (_MSC_FULL_VER % 10000000) / 100000, (_MSC_FULL_VER % 100000) / 100) -#elif defined(_MSC_FULL_VER) - #define JSON_HEDLEY_MSVC_VERSION JSON_HEDLEY_VERSION_ENCODE(_MSC_FULL_VER / 1000000, (_MSC_FULL_VER % 1000000) / 10000, (_MSC_FULL_VER % 10000) / 10) -#elif defined(_MSC_VER) - #define JSON_HEDLEY_MSVC_VERSION JSON_HEDLEY_VERSION_ENCODE(_MSC_VER / 100, _MSC_VER % 100, 0) -#endif - 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#undef JSON_HEDLEY_SUNPRO_VERSION -#endif -#if defined(__SUNPRO_C) && (__SUNPRO_C > 0x1000) - #define JSON_HEDLEY_SUNPRO_VERSION JSON_HEDLEY_VERSION_ENCODE((((__SUNPRO_C >> 16) & 0xf) * 10) + ((__SUNPRO_C >> 12) & 0xf), (((__SUNPRO_C >> 8) & 0xf) * 10) + ((__SUNPRO_C >> 4) & 0xf), (__SUNPRO_C & 0xf) * 10) -#elif defined(__SUNPRO_C) - #define JSON_HEDLEY_SUNPRO_VERSION JSON_HEDLEY_VERSION_ENCODE((__SUNPRO_C >> 8) & 0xf, (__SUNPRO_C >> 4) & 0xf, (__SUNPRO_C) & 0xf) -#elif defined(__SUNPRO_CC) && (__SUNPRO_CC > 0x1000) - #define JSON_HEDLEY_SUNPRO_VERSION JSON_HEDLEY_VERSION_ENCODE((((__SUNPRO_CC >> 16) & 0xf) * 10) + ((__SUNPRO_CC >> 12) & 0xf), (((__SUNPRO_CC >> 8) & 0xf) * 10) + ((__SUNPRO_CC >> 4) & 0xf), (__SUNPRO_CC & 0xf) * 10) -#elif defined(__SUNPRO_CC) - #define JSON_HEDLEY_SUNPRO_VERSION JSON_HEDLEY_VERSION_ENCODE((__SUNPRO_CC >> 8) & 0xf, (__SUNPRO_CC >> 4) & 0xf, (__SUNPRO_CC) & 0xf) -#endif - -#if defined(JSON_HEDLEY_SUNPRO_VERSION_CHECK) - #undef JSON_HEDLEY_SUNPRO_VERSION_CHECK -#endif -#if defined(JSON_HEDLEY_SUNPRO_VERSION) - #define JSON_HEDLEY_SUNPRO_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_SUNPRO_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) -#else - #define JSON_HEDLEY_SUNPRO_VERSION_CHECK(major,minor,patch) (0) -#endif - -#if defined(JSON_HEDLEY_EMSCRIPTEN_VERSION) - #undef JSON_HEDLEY_EMSCRIPTEN_VERSION -#endif -#if defined(__EMSCRIPTEN__) - #define JSON_HEDLEY_EMSCRIPTEN_VERSION JSON_HEDLEY_VERSION_ENCODE(__EMSCRIPTEN_major__, __EMSCRIPTEN_minor__, __EMSCRIPTEN_tiny__) -#endif - -#if defined(JSON_HEDLEY_EMSCRIPTEN_VERSION_CHECK) - #undef JSON_HEDLEY_EMSCRIPTEN_VERSION_CHECK -#endif -#if defined(JSON_HEDLEY_EMSCRIPTEN_VERSION) - #define JSON_HEDLEY_EMSCRIPTEN_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_EMSCRIPTEN_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) -#else - #define JSON_HEDLEY_EMSCRIPTEN_VERSION_CHECK(major,minor,patch) (0) -#endif - -#if defined(JSON_HEDLEY_ARM_VERSION) - #undef JSON_HEDLEY_ARM_VERSION -#endif -#if defined(__CC_ARM) && defined(__ARMCOMPILER_VERSION) - #define JSON_HEDLEY_ARM_VERSION JSON_HEDLEY_VERSION_ENCODE(__ARMCOMPILER_VERSION / 1000000, (__ARMCOMPILER_VERSION % 1000000) / 10000, (__ARMCOMPILER_VERSION % 10000) / 100) -#elif defined(__CC_ARM) && defined(__ARMCC_VERSION) - #define JSON_HEDLEY_ARM_VERSION JSON_HEDLEY_VERSION_ENCODE(__ARMCC_VERSION / 1000000, (__ARMCC_VERSION % 1000000) / 10000, (__ARMCC_VERSION % 10000) / 100) -#endif - -#if defined(JSON_HEDLEY_ARM_VERSION_CHECK) - #undef JSON_HEDLEY_ARM_VERSION_CHECK -#endif -#if defined(JSON_HEDLEY_ARM_VERSION) - #define JSON_HEDLEY_ARM_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_ARM_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) -#else - #define JSON_HEDLEY_ARM_VERSION_CHECK(major,minor,patch) (0) -#endif - -#if defined(JSON_HEDLEY_IBM_VERSION) - #undef JSON_HEDLEY_IBM_VERSION -#endif -#if defined(__ibmxl__) - #define JSON_HEDLEY_IBM_VERSION JSON_HEDLEY_VERSION_ENCODE(__ibmxl_version__, __ibmxl_release__, __ibmxl_modification__) -#elif defined(__xlC__) && defined(__xlC_ver__) - #define JSON_HEDLEY_IBM_VERSION JSON_HEDLEY_VERSION_ENCODE(__xlC__ >> 8, __xlC__ & 0xff, (__xlC_ver__ >> 8) & 0xff) -#elif defined(__xlC__) - #define JSON_HEDLEY_IBM_VERSION JSON_HEDLEY_VERSION_ENCODE(__xlC__ >> 8, __xlC__ & 0xff, 0) -#endif - -#if defined(JSON_HEDLEY_IBM_VERSION_CHECK) - #undef JSON_HEDLEY_IBM_VERSION_CHECK -#endif -#if defined(JSON_HEDLEY_IBM_VERSION) - #define JSON_HEDLEY_IBM_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_IBM_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) -#else - #define JSON_HEDLEY_IBM_VERSION_CHECK(major,minor,patch) (0) -#endif - -#if defined(JSON_HEDLEY_TI_VERSION) - #undef JSON_HEDLEY_TI_VERSION -#endif -#if \ - defined(__TI_COMPILER_VERSION__) && \ - ( \ - defined(__TMS470__) || defined(__TI_ARM__) || \ - defined(__MSP430__) || \ - defined(__TMS320C2000__) \ - ) -#if (__TI_COMPILER_VERSION__ >= 16000000) - #define JSON_HEDLEY_TI_VERSION JSON_HEDLEY_VERSION_ENCODE(__TI_COMPILER_VERSION__ / 1000000, (__TI_COMPILER_VERSION__ % 1000000) / 1000, (__TI_COMPILER_VERSION__ % 1000)) -#endif -#endif - -#if defined(JSON_HEDLEY_TI_VERSION_CHECK) - #undef JSON_HEDLEY_TI_VERSION_CHECK -#endif -#if defined(JSON_HEDLEY_TI_VERSION) - #define JSON_HEDLEY_TI_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_TI_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) -#else - #define JSON_HEDLEY_TI_VERSION_CHECK(major,minor,patch) (0) -#endif - -#if defined(JSON_HEDLEY_TI_CL2000_VERSION) - #undef JSON_HEDLEY_TI_CL2000_VERSION -#endif -#if defined(__TI_COMPILER_VERSION__) && defined(__TMS320C2000__) - #define JSON_HEDLEY_TI_CL2000_VERSION JSON_HEDLEY_VERSION_ENCODE(__TI_COMPILER_VERSION__ / 1000000, (__TI_COMPILER_VERSION__ % 1000000) / 1000, (__TI_COMPILER_VERSION__ % 1000)) -#endif - -#if defined(JSON_HEDLEY_TI_CL2000_VERSION_CHECK) - #undef JSON_HEDLEY_TI_CL2000_VERSION_CHECK -#endif -#if defined(JSON_HEDLEY_TI_CL2000_VERSION) - #define JSON_HEDLEY_TI_CL2000_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_TI_CL2000_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) -#else - #define JSON_HEDLEY_TI_CL2000_VERSION_CHECK(major,minor,patch) (0) -#endif - -#if defined(JSON_HEDLEY_TI_CL430_VERSION) - #undef JSON_HEDLEY_TI_CL430_VERSION -#endif -#if defined(__TI_COMPILER_VERSION__) && defined(__MSP430__) - #define JSON_HEDLEY_TI_CL430_VERSION JSON_HEDLEY_VERSION_ENCODE(__TI_COMPILER_VERSION__ / 1000000, (__TI_COMPILER_VERSION__ % 1000000) / 1000, (__TI_COMPILER_VERSION__ % 1000)) -#endif - -#if defined(JSON_HEDLEY_TI_CL430_VERSION_CHECK) - #undef JSON_HEDLEY_TI_CL430_VERSION_CHECK -#endif -#if defined(JSON_HEDLEY_TI_CL430_VERSION) - #define JSON_HEDLEY_TI_CL430_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_TI_CL430_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) -#else - #define JSON_HEDLEY_TI_CL430_VERSION_CHECK(major,minor,patch) (0) -#endif - -#if defined(JSON_HEDLEY_TI_ARMCL_VERSION) - #undef JSON_HEDLEY_TI_ARMCL_VERSION -#endif -#if defined(__TI_COMPILER_VERSION__) && (defined(__TMS470__) || defined(__TI_ARM__)) - #define JSON_HEDLEY_TI_ARMCL_VERSION JSON_HEDLEY_VERSION_ENCODE(__TI_COMPILER_VERSION__ / 1000000, (__TI_COMPILER_VERSION__ % 1000000) / 1000, (__TI_COMPILER_VERSION__ % 1000)) -#endif - -#if defined(JSON_HEDLEY_TI_ARMCL_VERSION_CHECK) - #undef JSON_HEDLEY_TI_ARMCL_VERSION_CHECK -#endif -#if defined(JSON_HEDLEY_TI_ARMCL_VERSION) - #define JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_TI_ARMCL_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) -#else - #define JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(major,minor,patch) (0) -#endif - -#if defined(JSON_HEDLEY_TI_CL6X_VERSION) - #undef JSON_HEDLEY_TI_CL6X_VERSION -#endif -#if defined(__TI_COMPILER_VERSION__) && defined(__TMS320C6X__) - #define JSON_HEDLEY_TI_CL6X_VERSION JSON_HEDLEY_VERSION_ENCODE(__TI_COMPILER_VERSION__ / 1000000, (__TI_COMPILER_VERSION__ % 1000000) / 1000, (__TI_COMPILER_VERSION__ % 1000)) -#endif - -#if defined(JSON_HEDLEY_TI_CL6X_VERSION_CHECK) - #undef JSON_HEDLEY_TI_CL6X_VERSION_CHECK -#endif -#if defined(JSON_HEDLEY_TI_CL6X_VERSION) - #define JSON_HEDLEY_TI_CL6X_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_TI_CL6X_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) -#else - #define JSON_HEDLEY_TI_CL6X_VERSION_CHECK(major,minor,patch) (0) -#endif - -#if defined(JSON_HEDLEY_TI_CL7X_VERSION) - #undef JSON_HEDLEY_TI_CL7X_VERSION -#endif -#if defined(__TI_COMPILER_VERSION__) && defined(__C7000__) - #define JSON_HEDLEY_TI_CL7X_VERSION JSON_HEDLEY_VERSION_ENCODE(__TI_COMPILER_VERSION__ / 1000000, (__TI_COMPILER_VERSION__ % 1000000) / 1000, (__TI_COMPILER_VERSION__ % 1000)) -#endif - -#if defined(JSON_HEDLEY_TI_CL7X_VERSION_CHECK) - #undef JSON_HEDLEY_TI_CL7X_VERSION_CHECK -#endif -#if defined(JSON_HEDLEY_TI_CL7X_VERSION) - #define JSON_HEDLEY_TI_CL7X_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_TI_CL7X_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) -#else - #define JSON_HEDLEY_TI_CL7X_VERSION_CHECK(major,minor,patch) (0) -#endif - -#if defined(JSON_HEDLEY_TI_CLPRU_VERSION) - #undef JSON_HEDLEY_TI_CLPRU_VERSION -#endif -#if defined(__TI_COMPILER_VERSION__) && defined(__PRU__) - #define JSON_HEDLEY_TI_CLPRU_VERSION JSON_HEDLEY_VERSION_ENCODE(__TI_COMPILER_VERSION__ / 1000000, (__TI_COMPILER_VERSION__ % 1000000) / 1000, (__TI_COMPILER_VERSION__ % 1000)) -#endif - -#if defined(JSON_HEDLEY_TI_CLPRU_VERSION_CHECK) - #undef JSON_HEDLEY_TI_CLPRU_VERSION_CHECK -#endif -#if defined(JSON_HEDLEY_TI_CLPRU_VERSION) - #define JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_TI_CLPRU_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) -#else - #define JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(major,minor,patch) (0) -#endif - -#if defined(JSON_HEDLEY_CRAY_VERSION) - #undef JSON_HEDLEY_CRAY_VERSION -#endif -#if defined(_CRAYC) - #if defined(_RELEASE_PATCHLEVEL) - #define JSON_HEDLEY_CRAY_VERSION JSON_HEDLEY_VERSION_ENCODE(_RELEASE_MAJOR, _RELEASE_MINOR, _RELEASE_PATCHLEVEL) - #else - #define JSON_HEDLEY_CRAY_VERSION JSON_HEDLEY_VERSION_ENCODE(_RELEASE_MAJOR, _RELEASE_MINOR, 0) - #endif -#endif - -#if defined(JSON_HEDLEY_CRAY_VERSION_CHECK) - #undef JSON_HEDLEY_CRAY_VERSION_CHECK -#endif -#if defined(JSON_HEDLEY_CRAY_VERSION) - #define JSON_HEDLEY_CRAY_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_CRAY_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) -#else - #define JSON_HEDLEY_CRAY_VERSION_CHECK(major,minor,patch) (0) -#endif - -#if defined(JSON_HEDLEY_IAR_VERSION) - #undef JSON_HEDLEY_IAR_VERSION -#endif -#if defined(__IAR_SYSTEMS_ICC__) - #if __VER__ > 1000 - #define JSON_HEDLEY_IAR_VERSION JSON_HEDLEY_VERSION_ENCODE((__VER__ / 1000000), ((__VER__ / 1000) % 1000), (__VER__ % 1000)) - #else - #define JSON_HEDLEY_IAR_VERSION JSON_HEDLEY_VERSION_ENCODE(VER / 100, __VER__ % 100, 0) - #endif -#endif - -#if defined(JSON_HEDLEY_IAR_VERSION_CHECK) - #undef JSON_HEDLEY_IAR_VERSION_CHECK -#endif -#if defined(JSON_HEDLEY_IAR_VERSION) - #define JSON_HEDLEY_IAR_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_IAR_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) -#else - #define JSON_HEDLEY_IAR_VERSION_CHECK(major,minor,patch) (0) -#endif - -#if defined(JSON_HEDLEY_TINYC_VERSION) - #undef JSON_HEDLEY_TINYC_VERSION -#endif -#if defined(__TINYC__) - #define JSON_HEDLEY_TINYC_VERSION JSON_HEDLEY_VERSION_ENCODE(__TINYC__ / 1000, (__TINYC__ / 100) % 10, __TINYC__ % 100) -#endif - -#if defined(JSON_HEDLEY_TINYC_VERSION_CHECK) - #undef JSON_HEDLEY_TINYC_VERSION_CHECK -#endif -#if defined(JSON_HEDLEY_TINYC_VERSION) - #define JSON_HEDLEY_TINYC_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_TINYC_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) -#else - #define JSON_HEDLEY_TINYC_VERSION_CHECK(major,minor,patch) (0) -#endif - -#if defined(JSON_HEDLEY_DMC_VERSION) - #undef JSON_HEDLEY_DMC_VERSION -#endif -#if defined(__DMC__) - #define JSON_HEDLEY_DMC_VERSION JSON_HEDLEY_VERSION_ENCODE(__DMC__ >> 8, (__DMC__ >> 4) & 0xf, __DMC__ & 0xf) -#endif - -#if defined(JSON_HEDLEY_DMC_VERSION_CHECK) - #undef JSON_HEDLEY_DMC_VERSION_CHECK -#endif -#if defined(JSON_HEDLEY_DMC_VERSION) - #define JSON_HEDLEY_DMC_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_DMC_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) -#else - #define JSON_HEDLEY_DMC_VERSION_CHECK(major,minor,patch) (0) -#endif - -#if defined(JSON_HEDLEY_COMPCERT_VERSION) - #undef JSON_HEDLEY_COMPCERT_VERSION -#endif -#if defined(__COMPCERT_VERSION__) - #define JSON_HEDLEY_COMPCERT_VERSION JSON_HEDLEY_VERSION_ENCODE(__COMPCERT_VERSION__ / 10000, (__COMPCERT_VERSION__ / 100) % 100, __COMPCERT_VERSION__ % 100) -#endif - -#if defined(JSON_HEDLEY_COMPCERT_VERSION_CHECK) - #undef JSON_HEDLEY_COMPCERT_VERSION_CHECK -#endif -#if defined(JSON_HEDLEY_COMPCERT_VERSION) - #define JSON_HEDLEY_COMPCERT_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_COMPCERT_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) -#else - #define JSON_HEDLEY_COMPCERT_VERSION_CHECK(major,minor,patch) (0) -#endif - -#if defined(JSON_HEDLEY_PELLES_VERSION) - #undef JSON_HEDLEY_PELLES_VERSION -#endif -#if defined(__POCC__) - #define JSON_HEDLEY_PELLES_VERSION JSON_HEDLEY_VERSION_ENCODE(__POCC__ / 100, __POCC__ % 100, 0) -#endif - -#if defined(JSON_HEDLEY_PELLES_VERSION_CHECK) - #undef JSON_HEDLEY_PELLES_VERSION_CHECK -#endif -#if defined(JSON_HEDLEY_PELLES_VERSION) - #define JSON_HEDLEY_PELLES_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_PELLES_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) -#else - #define JSON_HEDLEY_PELLES_VERSION_CHECK(major,minor,patch) (0) -#endif - -#if defined(JSON_HEDLEY_GCC_VERSION) - #undef JSON_HEDLEY_GCC_VERSION -#endif -#if \ - defined(JSON_HEDLEY_GNUC_VERSION) && \ - !defined(__clang__) && \ - !defined(JSON_HEDLEY_INTEL_VERSION) && \ - !defined(JSON_HEDLEY_PGI_VERSION) && \ - !defined(JSON_HEDLEY_ARM_VERSION) && \ - !defined(JSON_HEDLEY_TI_VERSION) && \ - !defined(JSON_HEDLEY_TI_ARMCL_VERSION) && \ - !defined(JSON_HEDLEY_TI_CL430_VERSION) && \ - !defined(JSON_HEDLEY_TI_CL2000_VERSION) && \ - !defined(JSON_HEDLEY_TI_CL6X_VERSION) && \ - !defined(JSON_HEDLEY_TI_CL7X_VERSION) && \ - !defined(JSON_HEDLEY_TI_CLPRU_VERSION) && \ - !defined(__COMPCERT__) - #define JSON_HEDLEY_GCC_VERSION JSON_HEDLEY_GNUC_VERSION -#endif - -#if defined(JSON_HEDLEY_GCC_VERSION_CHECK) - #undef JSON_HEDLEY_GCC_VERSION_CHECK -#endif -#if defined(JSON_HEDLEY_GCC_VERSION) - #define JSON_HEDLEY_GCC_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_GCC_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) -#else - #define JSON_HEDLEY_GCC_VERSION_CHECK(major,minor,patch) (0) -#endif - -#if defined(JSON_HEDLEY_HAS_ATTRIBUTE) - #undef JSON_HEDLEY_HAS_ATTRIBUTE -#endif -#if defined(__has_attribute) - #define JSON_HEDLEY_HAS_ATTRIBUTE(attribute) __has_attribute(attribute) -#else - #define JSON_HEDLEY_HAS_ATTRIBUTE(attribute) (0) -#endif - -#if defined(JSON_HEDLEY_GNUC_HAS_ATTRIBUTE) - #undef JSON_HEDLEY_GNUC_HAS_ATTRIBUTE -#endif -#if defined(__has_attribute) - #define JSON_HEDLEY_GNUC_HAS_ATTRIBUTE(attribute,major,minor,patch) __has_attribute(attribute) -#else - #define JSON_HEDLEY_GNUC_HAS_ATTRIBUTE(attribute,major,minor,patch) JSON_HEDLEY_GNUC_VERSION_CHECK(major,minor,patch) -#endif - -#if defined(JSON_HEDLEY_GCC_HAS_ATTRIBUTE) - #undef JSON_HEDLEY_GCC_HAS_ATTRIBUTE -#endif -#if defined(__has_attribute) - #define JSON_HEDLEY_GCC_HAS_ATTRIBUTE(attribute,major,minor,patch) __has_attribute(attribute) -#else - #define JSON_HEDLEY_GCC_HAS_ATTRIBUTE(attribute,major,minor,patch) JSON_HEDLEY_GCC_VERSION_CHECK(major,minor,patch) -#endif - -#if defined(JSON_HEDLEY_HAS_CPP_ATTRIBUTE) - #undef JSON_HEDLEY_HAS_CPP_ATTRIBUTE -#endif -#if \ - defined(__has_cpp_attribute) && \ - defined(__cplusplus) && \ - (!defined(JSON_HEDLEY_SUNPRO_VERSION) || JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,15,0)) - #define JSON_HEDLEY_HAS_CPP_ATTRIBUTE(attribute) __has_cpp_attribute(attribute) -#else - #define JSON_HEDLEY_HAS_CPP_ATTRIBUTE(attribute) (0) -#endif - -#if defined(JSON_HEDLEY_HAS_CPP_ATTRIBUTE_NS) - #undef JSON_HEDLEY_HAS_CPP_ATTRIBUTE_NS -#endif -#if !defined(__cplusplus) || !defined(__has_cpp_attribute) - #define JSON_HEDLEY_HAS_CPP_ATTRIBUTE_NS(ns,attribute) (0) -#elif \ - !defined(JSON_HEDLEY_PGI_VERSION) && \ - !defined(JSON_HEDLEY_IAR_VERSION) && \ - (!defined(JSON_HEDLEY_SUNPRO_VERSION) || JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,15,0)) && \ - (!defined(JSON_HEDLEY_MSVC_VERSION) || JSON_HEDLEY_MSVC_VERSION_CHECK(19,20,0)) - #define JSON_HEDLEY_HAS_CPP_ATTRIBUTE_NS(ns,attribute) JSON_HEDLEY_HAS_CPP_ATTRIBUTE(ns::attribute) -#else - #define JSON_HEDLEY_HAS_CPP_ATTRIBUTE_NS(ns,attribute) (0) -#endif - -#if defined(JSON_HEDLEY_GNUC_HAS_CPP_ATTRIBUTE) - #undef JSON_HEDLEY_GNUC_HAS_CPP_ATTRIBUTE -#endif -#if defined(__has_cpp_attribute) && defined(__cplusplus) - #define JSON_HEDLEY_GNUC_HAS_CPP_ATTRIBUTE(attribute,major,minor,patch) __has_cpp_attribute(attribute) -#else - #define JSON_HEDLEY_GNUC_HAS_CPP_ATTRIBUTE(attribute,major,minor,patch) JSON_HEDLEY_GNUC_VERSION_CHECK(major,minor,patch) -#endif - -#if defined(JSON_HEDLEY_GCC_HAS_CPP_ATTRIBUTE) - #undef JSON_HEDLEY_GCC_HAS_CPP_ATTRIBUTE -#endif -#if defined(__has_cpp_attribute) && defined(__cplusplus) - #define JSON_HEDLEY_GCC_HAS_CPP_ATTRIBUTE(attribute,major,minor,patch) __has_cpp_attribute(attribute) -#else - #define JSON_HEDLEY_GCC_HAS_CPP_ATTRIBUTE(attribute,major,minor,patch) JSON_HEDLEY_GCC_VERSION_CHECK(major,minor,patch) -#endif - -#if defined(JSON_HEDLEY_HAS_BUILTIN) - #undef JSON_HEDLEY_HAS_BUILTIN -#endif -#if defined(__has_builtin) - #define JSON_HEDLEY_HAS_BUILTIN(builtin) __has_builtin(builtin) -#else - #define JSON_HEDLEY_HAS_BUILTIN(builtin) (0) -#endif - -#if defined(JSON_HEDLEY_GNUC_HAS_BUILTIN) - #undef JSON_HEDLEY_GNUC_HAS_BUILTIN -#endif -#if defined(__has_builtin) - #define JSON_HEDLEY_GNUC_HAS_BUILTIN(builtin,major,minor,patch) __has_builtin(builtin) -#else - #define JSON_HEDLEY_GNUC_HAS_BUILTIN(builtin,major,minor,patch) JSON_HEDLEY_GNUC_VERSION_CHECK(major,minor,patch) -#endif - -#if defined(JSON_HEDLEY_GCC_HAS_BUILTIN) - #undef JSON_HEDLEY_GCC_HAS_BUILTIN -#endif -#if defined(__has_builtin) - #define JSON_HEDLEY_GCC_HAS_BUILTIN(builtin,major,minor,patch) __has_builtin(builtin) -#else - #define JSON_HEDLEY_GCC_HAS_BUILTIN(builtin,major,minor,patch) JSON_HEDLEY_GCC_VERSION_CHECK(major,minor,patch) -#endif - -#if defined(JSON_HEDLEY_HAS_FEATURE) - #undef JSON_HEDLEY_HAS_FEATURE -#endif -#if defined(__has_feature) - #define JSON_HEDLEY_HAS_FEATURE(feature) __has_feature(feature) -#else - #define JSON_HEDLEY_HAS_FEATURE(feature) (0) -#endif - -#if defined(JSON_HEDLEY_GNUC_HAS_FEATURE) - #undef JSON_HEDLEY_GNUC_HAS_FEATURE -#endif -#if defined(__has_feature) - #define JSON_HEDLEY_GNUC_HAS_FEATURE(feature,major,minor,patch) __has_feature(feature) -#else - #define JSON_HEDLEY_GNUC_HAS_FEATURE(feature,major,minor,patch) JSON_HEDLEY_GNUC_VERSION_CHECK(major,minor,patch) -#endif - -#if defined(JSON_HEDLEY_GCC_HAS_FEATURE) - #undef JSON_HEDLEY_GCC_HAS_FEATURE -#endif -#if defined(__has_feature) - #define JSON_HEDLEY_GCC_HAS_FEATURE(feature,major,minor,patch) __has_feature(feature) -#else - #define JSON_HEDLEY_GCC_HAS_FEATURE(feature,major,minor,patch) JSON_HEDLEY_GCC_VERSION_CHECK(major,minor,patch) -#endif - -#if defined(JSON_HEDLEY_HAS_EXTENSION) - #undef JSON_HEDLEY_HAS_EXTENSION -#endif -#if defined(__has_extension) - #define JSON_HEDLEY_HAS_EXTENSION(extension) __has_extension(extension) -#else - #define JSON_HEDLEY_HAS_EXTENSION(extension) (0) -#endif - -#if defined(JSON_HEDLEY_GNUC_HAS_EXTENSION) - #undef JSON_HEDLEY_GNUC_HAS_EXTENSION -#endif -#if defined(__has_extension) - #define JSON_HEDLEY_GNUC_HAS_EXTENSION(extension,major,minor,patch) __has_extension(extension) -#else - #define JSON_HEDLEY_GNUC_HAS_EXTENSION(extension,major,minor,patch) JSON_HEDLEY_GNUC_VERSION_CHECK(major,minor,patch) -#endif - -#if defined(JSON_HEDLEY_GCC_HAS_EXTENSION) - #undef JSON_HEDLEY_GCC_HAS_EXTENSION -#endif -#if defined(__has_extension) - #define JSON_HEDLEY_GCC_HAS_EXTENSION(extension,major,minor,patch) __has_extension(extension) -#else - #define JSON_HEDLEY_GCC_HAS_EXTENSION(extension,major,minor,patch) JSON_HEDLEY_GCC_VERSION_CHECK(major,minor,patch) -#endif - -#if defined(JSON_HEDLEY_HAS_DECLSPEC_ATTRIBUTE) - #undef JSON_HEDLEY_HAS_DECLSPEC_ATTRIBUTE -#endif -#if defined(__has_declspec_attribute) - #define JSON_HEDLEY_HAS_DECLSPEC_ATTRIBUTE(attribute) __has_declspec_attribute(attribute) -#else - #define JSON_HEDLEY_HAS_DECLSPEC_ATTRIBUTE(attribute) (0) -#endif - -#if defined(JSON_HEDLEY_GNUC_HAS_DECLSPEC_ATTRIBUTE) - #undef JSON_HEDLEY_GNUC_HAS_DECLSPEC_ATTRIBUTE -#endif -#if defined(__has_declspec_attribute) - #define JSON_HEDLEY_GNUC_HAS_DECLSPEC_ATTRIBUTE(attribute,major,minor,patch) __has_declspec_attribute(attribute) -#else - #define JSON_HEDLEY_GNUC_HAS_DECLSPEC_ATTRIBUTE(attribute,major,minor,patch) JSON_HEDLEY_GNUC_VERSION_CHECK(major,minor,patch) -#endif - -#if defined(JSON_HEDLEY_GCC_HAS_DECLSPEC_ATTRIBUTE) - #undef JSON_HEDLEY_GCC_HAS_DECLSPEC_ATTRIBUTE -#endif -#if defined(__has_declspec_attribute) - #define JSON_HEDLEY_GCC_HAS_DECLSPEC_ATTRIBUTE(attribute,major,minor,patch) __has_declspec_attribute(attribute) -#else - #define JSON_HEDLEY_GCC_HAS_DECLSPEC_ATTRIBUTE(attribute,major,minor,patch) JSON_HEDLEY_GCC_VERSION_CHECK(major,minor,patch) -#endif - -#if defined(JSON_HEDLEY_HAS_WARNING) - #undef JSON_HEDLEY_HAS_WARNING -#endif -#if defined(__has_warning) - #define JSON_HEDLEY_HAS_WARNING(warning) __has_warning(warning) -#else - #define JSON_HEDLEY_HAS_WARNING(warning) (0) -#endif - -#if defined(JSON_HEDLEY_GNUC_HAS_WARNING) - #undef JSON_HEDLEY_GNUC_HAS_WARNING -#endif -#if defined(__has_warning) - #define JSON_HEDLEY_GNUC_HAS_WARNING(warning,major,minor,patch) __has_warning(warning) -#else - #define JSON_HEDLEY_GNUC_HAS_WARNING(warning,major,minor,patch) JSON_HEDLEY_GNUC_VERSION_CHECK(major,minor,patch) -#endif - -#if defined(JSON_HEDLEY_GCC_HAS_WARNING) - #undef JSON_HEDLEY_GCC_HAS_WARNING -#endif -#if defined(__has_warning) - #define JSON_HEDLEY_GCC_HAS_WARNING(warning,major,minor,patch) __has_warning(warning) -#else - #define JSON_HEDLEY_GCC_HAS_WARNING(warning,major,minor,patch) JSON_HEDLEY_GCC_VERSION_CHECK(major,minor,patch) -#endif - -/* JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_ is for - HEDLEY INTERNAL USE ONLY. API subject to change without notice. */ -#if defined(JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_) - #undef JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_ -#endif -#if defined(__cplusplus) -# if JSON_HEDLEY_HAS_WARNING("-Wc++98-compat") -# if JSON_HEDLEY_HAS_WARNING("-Wc++17-extensions") -# define JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_(xpr) \ - JSON_HEDLEY_DIAGNOSTIC_PUSH \ - _Pragma("clang diagnostic ignored \"-Wc++98-compat\"") \ - _Pragma("clang diagnostic ignored \"-Wc++17-extensions\"") \ - xpr \ - JSON_HEDLEY_DIAGNOSTIC_POP -# else -# define JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_(xpr) \ - JSON_HEDLEY_DIAGNOSTIC_PUSH \ - _Pragma("clang diagnostic ignored \"-Wc++98-compat\"") \ - xpr \ - JSON_HEDLEY_DIAGNOSTIC_POP -# endif -# endif -#endif -#if !defined(JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_) - #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_(x) x -#endif - -#if defined(JSON_HEDLEY_CONST_CAST) - #undef JSON_HEDLEY_CONST_CAST -#endif -#if defined(__cplusplus) -# define JSON_HEDLEY_CONST_CAST(T, expr) (const_cast(expr)) -#elif \ - JSON_HEDLEY_HAS_WARNING("-Wcast-qual") || \ - JSON_HEDLEY_GCC_VERSION_CHECK(4,6,0) || \ - JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) -# define JSON_HEDLEY_CONST_CAST(T, expr) (__extension__ ({ \ - JSON_HEDLEY_DIAGNOSTIC_PUSH \ - JSON_HEDLEY_DIAGNOSTIC_DISABLE_CAST_QUAL \ - ((T) (expr)); \ - JSON_HEDLEY_DIAGNOSTIC_POP \ - })) -#else -# define JSON_HEDLEY_CONST_CAST(T, expr) ((T) (expr)) -#endif - -#if defined(JSON_HEDLEY_REINTERPRET_CAST) - #undef JSON_HEDLEY_REINTERPRET_CAST -#endif -#if defined(__cplusplus) - #define JSON_HEDLEY_REINTERPRET_CAST(T, expr) (reinterpret_cast(expr)) -#else - #define JSON_HEDLEY_REINTERPRET_CAST(T, expr) ((T) (expr)) -#endif - -#if defined(JSON_HEDLEY_STATIC_CAST) - #undef JSON_HEDLEY_STATIC_CAST -#endif -#if defined(__cplusplus) - #define JSON_HEDLEY_STATIC_CAST(T, expr) (static_cast(expr)) -#else - #define JSON_HEDLEY_STATIC_CAST(T, expr) ((T) (expr)) -#endif - -#if defined(JSON_HEDLEY_CPP_CAST) - #undef JSON_HEDLEY_CPP_CAST -#endif -#if defined(__cplusplus) -# if JSON_HEDLEY_HAS_WARNING("-Wold-style-cast") -# define JSON_HEDLEY_CPP_CAST(T, expr) \ - JSON_HEDLEY_DIAGNOSTIC_PUSH \ - _Pragma("clang diagnostic ignored \"-Wold-style-cast\"") \ - ((T) (expr)) \ - JSON_HEDLEY_DIAGNOSTIC_POP -# elif JSON_HEDLEY_IAR_VERSION_CHECK(8,3,0) -# define JSON_HEDLEY_CPP_CAST(T, expr) \ - JSON_HEDLEY_DIAGNOSTIC_PUSH \ - _Pragma("diag_suppress=Pe137") \ - JSON_HEDLEY_DIAGNOSTIC_POP \ -# else -# define JSON_HEDLEY_CPP_CAST(T, expr) ((T) (expr)) -# endif -#else -# define JSON_HEDLEY_CPP_CAST(T, expr) (expr) -#endif - -#if \ - (defined(__STDC_VERSION__) && (__STDC_VERSION__ >= 199901L)) || \ - defined(__clang__) || \ - JSON_HEDLEY_GCC_VERSION_CHECK(3,0,0) || \ - JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ - JSON_HEDLEY_IAR_VERSION_CHECK(8,0,0) || \ - JSON_HEDLEY_PGI_VERSION_CHECK(18,4,0) || \ - JSON_HEDLEY_ARM_VERSION_CHECK(4,1,0) || \ - JSON_HEDLEY_TI_VERSION_CHECK(15,12,0) || \ - JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(4,7,0) || \ - JSON_HEDLEY_TI_CL430_VERSION_CHECK(2,0,1) || \ - JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,1,0) || \ - JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,0,0) || \ - JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ - JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(2,1,0) || \ - JSON_HEDLEY_CRAY_VERSION_CHECK(5,0,0) || \ - JSON_HEDLEY_TINYC_VERSION_CHECK(0,9,17) || \ - JSON_HEDLEY_SUNPRO_VERSION_CHECK(8,0,0) || \ - (JSON_HEDLEY_IBM_VERSION_CHECK(10,1,0) && defined(__C99_PRAGMA_OPERATOR)) - #define JSON_HEDLEY_PRAGMA(value) _Pragma(#value) -#elif JSON_HEDLEY_MSVC_VERSION_CHECK(15,0,0) - #define JSON_HEDLEY_PRAGMA(value) __pragma(value) -#else - #define JSON_HEDLEY_PRAGMA(value) -#endif - -#if defined(JSON_HEDLEY_DIAGNOSTIC_PUSH) - #undef JSON_HEDLEY_DIAGNOSTIC_PUSH -#endif -#if defined(JSON_HEDLEY_DIAGNOSTIC_POP) - #undef JSON_HEDLEY_DIAGNOSTIC_POP -#endif -#if defined(__clang__) - #define JSON_HEDLEY_DIAGNOSTIC_PUSH _Pragma("clang diagnostic push") - #define JSON_HEDLEY_DIAGNOSTIC_POP _Pragma("clang diagnostic pop") -#elif JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) - #define JSON_HEDLEY_DIAGNOSTIC_PUSH _Pragma("warning(push)") - #define JSON_HEDLEY_DIAGNOSTIC_POP _Pragma("warning(pop)") -#elif JSON_HEDLEY_GCC_VERSION_CHECK(4,6,0) - #define JSON_HEDLEY_DIAGNOSTIC_PUSH _Pragma("GCC diagnostic push") - #define JSON_HEDLEY_DIAGNOSTIC_POP _Pragma("GCC diagnostic pop") -#elif JSON_HEDLEY_MSVC_VERSION_CHECK(15,0,0) - #define JSON_HEDLEY_DIAGNOSTIC_PUSH __pragma(warning(push)) - #define JSON_HEDLEY_DIAGNOSTIC_POP __pragma(warning(pop)) -#elif JSON_HEDLEY_ARM_VERSION_CHECK(5,6,0) - #define JSON_HEDLEY_DIAGNOSTIC_PUSH _Pragma("push") - #define JSON_HEDLEY_DIAGNOSTIC_POP _Pragma("pop") -#elif \ - JSON_HEDLEY_TI_VERSION_CHECK(15,12,0) || \ - JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(5,2,0) || \ - JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,4,0) || \ - JSON_HEDLEY_TI_CL6X_VERSION_CHECK(8,1,0) || \ - JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ - JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(2,1,0) - #define JSON_HEDLEY_DIAGNOSTIC_PUSH _Pragma("diag_push") - #define JSON_HEDLEY_DIAGNOSTIC_POP _Pragma("diag_pop") -#elif JSON_HEDLEY_PELLES_VERSION_CHECK(2,90,0) - #define JSON_HEDLEY_DIAGNOSTIC_PUSH _Pragma("warning(push)") - #define JSON_HEDLEY_DIAGNOSTIC_POP _Pragma("warning(pop)") -#else - #define JSON_HEDLEY_DIAGNOSTIC_PUSH - #define JSON_HEDLEY_DIAGNOSTIC_POP -#endif - -#if defined(JSON_HEDLEY_DIAGNOSTIC_DISABLE_DEPRECATED) - #undef JSON_HEDLEY_DIAGNOSTIC_DISABLE_DEPRECATED -#endif -#if JSON_HEDLEY_HAS_WARNING("-Wdeprecated-declarations") - #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_DEPRECATED _Pragma("clang diagnostic ignored \"-Wdeprecated-declarations\"") -#elif JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) - #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_DEPRECATED _Pragma("warning(disable:1478 1786)") -#elif JSON_HEDLEY_PGI_VERSION_CHECK(17,10,0) - #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_DEPRECATED _Pragma("diag_suppress 1215,1444") -#elif JSON_HEDLEY_GCC_VERSION_CHECK(4,3,0) - #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_DEPRECATED _Pragma("GCC diagnostic ignored \"-Wdeprecated-declarations\"") -#elif JSON_HEDLEY_MSVC_VERSION_CHECK(15,0,0) - #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_DEPRECATED __pragma(warning(disable:4996)) -#elif \ - JSON_HEDLEY_TI_VERSION_CHECK(15,12,0) || \ - (JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(4,8,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(5,2,0) || \ - (JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,4,0) || \ - (JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,3,0) || \ - (JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,2,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,5,0) || \ - JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ - JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(2,1,0) - #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_DEPRECATED _Pragma("diag_suppress 1291,1718") -#elif JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,13,0) && !defined(__cplusplus) - #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_DEPRECATED _Pragma("error_messages(off,E_DEPRECATED_ATT,E_DEPRECATED_ATT_MESS)") -#elif JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,13,0) && defined(__cplusplus) - #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_DEPRECATED _Pragma("error_messages(off,symdeprecated,symdeprecated2)") -#elif JSON_HEDLEY_IAR_VERSION_CHECK(8,0,0) - #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_DEPRECATED _Pragma("diag_suppress=Pe1444,Pe1215") -#elif JSON_HEDLEY_PELLES_VERSION_CHECK(2,90,0) - #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_DEPRECATED _Pragma("warn(disable:2241)") -#else - #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_DEPRECATED -#endif - -#if defined(JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_PRAGMAS) - #undef JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_PRAGMAS -#endif -#if JSON_HEDLEY_HAS_WARNING("-Wunknown-pragmas") - #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_PRAGMAS _Pragma("clang diagnostic ignored \"-Wunknown-pragmas\"") -#elif JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) - #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_PRAGMAS _Pragma("warning(disable:161)") -#elif JSON_HEDLEY_PGI_VERSION_CHECK(17,10,0) - #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_PRAGMAS _Pragma("diag_suppress 1675") -#elif JSON_HEDLEY_GCC_VERSION_CHECK(4,3,0) - #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_PRAGMAS _Pragma("GCC diagnostic ignored \"-Wunknown-pragmas\"") -#elif JSON_HEDLEY_MSVC_VERSION_CHECK(15,0,0) - #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_PRAGMAS __pragma(warning(disable:4068)) -#elif \ - JSON_HEDLEY_TI_VERSION_CHECK(16,9,0) || \ - JSON_HEDLEY_TI_CL6X_VERSION_CHECK(8,0,0) || \ - JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ - JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(2,3,0) - #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_PRAGMAS _Pragma("diag_suppress 163") -#elif JSON_HEDLEY_TI_CL6X_VERSION_CHECK(8,0,0) - #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_PRAGMAS _Pragma("diag_suppress 163") -#elif JSON_HEDLEY_IAR_VERSION_CHECK(8,0,0) - #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_PRAGMAS _Pragma("diag_suppress=Pe161") -#else - #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_PRAGMAS -#endif - -#if defined(JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_CPP_ATTRIBUTES) - #undef JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_CPP_ATTRIBUTES -#endif -#if JSON_HEDLEY_HAS_WARNING("-Wunknown-attributes") - #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_CPP_ATTRIBUTES _Pragma("clang diagnostic ignored \"-Wunknown-attributes\"") -#elif JSON_HEDLEY_GCC_VERSION_CHECK(4,6,0) - #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_CPP_ATTRIBUTES _Pragma("GCC diagnostic ignored \"-Wdeprecated-declarations\"") -#elif JSON_HEDLEY_INTEL_VERSION_CHECK(17,0,0) - #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_CPP_ATTRIBUTES _Pragma("warning(disable:1292)") -#elif JSON_HEDLEY_MSVC_VERSION_CHECK(19,0,0) - #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_CPP_ATTRIBUTES __pragma(warning(disable:5030)) -#elif JSON_HEDLEY_PGI_VERSION_CHECK(17,10,0) - #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_CPP_ATTRIBUTES _Pragma("diag_suppress 1097") -#elif JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,14,0) && defined(__cplusplus) - #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_CPP_ATTRIBUTES _Pragma("error_messages(off,attrskipunsup)") -#elif \ - JSON_HEDLEY_TI_VERSION_CHECK(18,1,0) || \ - JSON_HEDLEY_TI_CL6X_VERSION_CHECK(8,3,0) || \ - JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) - #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_CPP_ATTRIBUTES _Pragma("diag_suppress 1173") -#elif JSON_HEDLEY_IAR_VERSION_CHECK(8,0,0) - #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_CPP_ATTRIBUTES _Pragma("diag_suppress=Pe1097") -#else - #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_CPP_ATTRIBUTES -#endif - -#if defined(JSON_HEDLEY_DIAGNOSTIC_DISABLE_CAST_QUAL) - #undef JSON_HEDLEY_DIAGNOSTIC_DISABLE_CAST_QUAL -#endif -#if JSON_HEDLEY_HAS_WARNING("-Wcast-qual") - #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_CAST_QUAL _Pragma("clang diagnostic ignored \"-Wcast-qual\"") -#elif JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) - #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_CAST_QUAL _Pragma("warning(disable:2203 2331)") -#elif JSON_HEDLEY_GCC_VERSION_CHECK(3,0,0) - #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_CAST_QUAL _Pragma("GCC diagnostic ignored \"-Wcast-qual\"") -#else - #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_CAST_QUAL -#endif - -#if defined(JSON_HEDLEY_DEPRECATED) - #undef JSON_HEDLEY_DEPRECATED -#endif -#if defined(JSON_HEDLEY_DEPRECATED_FOR) - #undef JSON_HEDLEY_DEPRECATED_FOR -#endif -#if JSON_HEDLEY_MSVC_VERSION_CHECK(14,0,0) - #define JSON_HEDLEY_DEPRECATED(since) __declspec(deprecated("Since " # since)) - #define JSON_HEDLEY_DEPRECATED_FOR(since, replacement) __declspec(deprecated("Since " #since "; use " #replacement)) -#elif defined(__cplusplus) && (__cplusplus >= 201402L) - #define JSON_HEDLEY_DEPRECATED(since) JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_([[deprecated("Since " #since)]]) - #define JSON_HEDLEY_DEPRECATED_FOR(since, replacement) JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_([[deprecated("Since " #since "; use " #replacement)]]) -#elif \ - JSON_HEDLEY_HAS_EXTENSION(attribute_deprecated_with_message) || \ - JSON_HEDLEY_GCC_VERSION_CHECK(4,5,0) || \ - JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ - JSON_HEDLEY_ARM_VERSION_CHECK(5,6,0) || \ - JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,13,0) || \ - JSON_HEDLEY_PGI_VERSION_CHECK(17,10,0) || \ - JSON_HEDLEY_TI_VERSION_CHECK(18,1,0) || \ - JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(18,1,0) || \ - JSON_HEDLEY_TI_CL6X_VERSION_CHECK(8,3,0) || \ - JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ - JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(2,3,0) - #define JSON_HEDLEY_DEPRECATED(since) __attribute__((__deprecated__("Since " #since))) - #define JSON_HEDLEY_DEPRECATED_FOR(since, replacement) __attribute__((__deprecated__("Since " #since "; use " #replacement))) -#elif \ - JSON_HEDLEY_HAS_ATTRIBUTE(deprecated) || \ - JSON_HEDLEY_GCC_VERSION_CHECK(3,1,0) || \ - JSON_HEDLEY_ARM_VERSION_CHECK(4,1,0) || \ - JSON_HEDLEY_TI_VERSION_CHECK(15,12,0) || \ - (JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(4,8,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(5,2,0) || \ - (JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,4,0) || \ - (JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,3,0) || \ - (JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,2,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,5,0) || \ - JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ - JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(2,1,0) - #define JSON_HEDLEY_DEPRECATED(since) __attribute__((__deprecated__)) - #define JSON_HEDLEY_DEPRECATED_FOR(since, replacement) __attribute__((__deprecated__)) -#elif \ - JSON_HEDLEY_MSVC_VERSION_CHECK(13,10,0) || \ - JSON_HEDLEY_PELLES_VERSION_CHECK(6,50,0) - #define JSON_HEDLEY_DEPRECATED(since) __declspec(deprecated) - #define JSON_HEDLEY_DEPRECATED_FOR(since, replacement) __declspec(deprecated) -#elif JSON_HEDLEY_IAR_VERSION_CHECK(8,0,0) - #define JSON_HEDLEY_DEPRECATED(since) _Pragma("deprecated") - #define JSON_HEDLEY_DEPRECATED_FOR(since, replacement) _Pragma("deprecated") -#else - #define JSON_HEDLEY_DEPRECATED(since) - #define JSON_HEDLEY_DEPRECATED_FOR(since, replacement) -#endif - -#if defined(JSON_HEDLEY_UNAVAILABLE) - #undef JSON_HEDLEY_UNAVAILABLE -#endif -#if \ - JSON_HEDLEY_HAS_ATTRIBUTE(warning) || \ - JSON_HEDLEY_GCC_VERSION_CHECK(4,3,0) || \ - JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) - #define JSON_HEDLEY_UNAVAILABLE(available_since) __attribute__((__warning__("Not available until " #available_since))) -#else - #define JSON_HEDLEY_UNAVAILABLE(available_since) -#endif - -#if defined(JSON_HEDLEY_WARN_UNUSED_RESULT) - #undef JSON_HEDLEY_WARN_UNUSED_RESULT -#endif -#if defined(JSON_HEDLEY_WARN_UNUSED_RESULT_MSG) - #undef JSON_HEDLEY_WARN_UNUSED_RESULT_MSG -#endif -#if (JSON_HEDLEY_HAS_CPP_ATTRIBUTE(nodiscard) >= 201907L) - #define JSON_HEDLEY_WARN_UNUSED_RESULT JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_([[nodiscard]]) - #define JSON_HEDLEY_WARN_UNUSED_RESULT_MSG(msg) JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_([[nodiscard(msg)]]) -#elif JSON_HEDLEY_HAS_CPP_ATTRIBUTE(nodiscard) - #define JSON_HEDLEY_WARN_UNUSED_RESULT JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_([[nodiscard]]) - #define JSON_HEDLEY_WARN_UNUSED_RESULT_MSG(msg) JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_([[nodiscard]]) -#elif \ - JSON_HEDLEY_HAS_ATTRIBUTE(warn_unused_result) || \ - JSON_HEDLEY_GCC_VERSION_CHECK(3,4,0) || \ - JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ - JSON_HEDLEY_TI_VERSION_CHECK(15,12,0) || \ - (JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(4,8,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(5,2,0) || \ - (JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,4,0) || \ - (JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,3,0) || \ - (JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,2,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,5,0) || \ - JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ - JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(2,1,0) || \ - (JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,15,0) && defined(__cplusplus)) || \ - JSON_HEDLEY_PGI_VERSION_CHECK(17,10,0) - #define JSON_HEDLEY_WARN_UNUSED_RESULT __attribute__((__warn_unused_result__)) - #define JSON_HEDLEY_WARN_UNUSED_RESULT_MSG(msg) __attribute__((__warn_unused_result__)) -#elif defined(_Check_return_) /* SAL */ - #define JSON_HEDLEY_WARN_UNUSED_RESULT _Check_return_ - #define JSON_HEDLEY_WARN_UNUSED_RESULT_MSG(msg) _Check_return_ -#else - #define JSON_HEDLEY_WARN_UNUSED_RESULT - #define JSON_HEDLEY_WARN_UNUSED_RESULT_MSG(msg) -#endif - -#if defined(JSON_HEDLEY_SENTINEL) - #undef JSON_HEDLEY_SENTINEL -#endif -#if \ - JSON_HEDLEY_HAS_ATTRIBUTE(sentinel) || \ - JSON_HEDLEY_GCC_VERSION_CHECK(4,0,0) || \ - JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ - JSON_HEDLEY_ARM_VERSION_CHECK(5,4,0) - #define JSON_HEDLEY_SENTINEL(position) __attribute__((__sentinel__(position))) -#else - #define JSON_HEDLEY_SENTINEL(position) -#endif - -#if defined(JSON_HEDLEY_NO_RETURN) - #undef JSON_HEDLEY_NO_RETURN -#endif -#if JSON_HEDLEY_IAR_VERSION_CHECK(8,0,0) - #define JSON_HEDLEY_NO_RETURN __noreturn -#elif JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) - #define JSON_HEDLEY_NO_RETURN __attribute__((__noreturn__)) -#elif defined(__STDC_VERSION__) && __STDC_VERSION__ >= 201112L - #define JSON_HEDLEY_NO_RETURN _Noreturn -#elif defined(__cplusplus) && (__cplusplus >= 201103L) - #define JSON_HEDLEY_NO_RETURN JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_([[noreturn]]) -#elif \ - JSON_HEDLEY_HAS_ATTRIBUTE(noreturn) || \ - JSON_HEDLEY_GCC_VERSION_CHECK(3,2,0) || \ - JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,11,0) || \ - JSON_HEDLEY_ARM_VERSION_CHECK(4,1,0) || \ - JSON_HEDLEY_IBM_VERSION_CHECK(10,1,0) || \ - JSON_HEDLEY_TI_VERSION_CHECK(15,12,0) || \ - (JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(4,8,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(5,2,0) || \ - (JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,4,0) || \ - (JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,3,0) || \ - (JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,2,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,5,0) || \ - JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ - JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(2,1,0) - #define JSON_HEDLEY_NO_RETURN __attribute__((__noreturn__)) -#elif JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,10,0) - #define JSON_HEDLEY_NO_RETURN _Pragma("does_not_return") -#elif JSON_HEDLEY_MSVC_VERSION_CHECK(13,10,0) - #define JSON_HEDLEY_NO_RETURN __declspec(noreturn) -#elif JSON_HEDLEY_TI_CL6X_VERSION_CHECK(6,0,0) && defined(__cplusplus) - #define JSON_HEDLEY_NO_RETURN _Pragma("FUNC_NEVER_RETURNS;") -#elif JSON_HEDLEY_COMPCERT_VERSION_CHECK(3,2,0) - #define JSON_HEDLEY_NO_RETURN __attribute((noreturn)) -#elif JSON_HEDLEY_PELLES_VERSION_CHECK(9,0,0) - #define JSON_HEDLEY_NO_RETURN __declspec(noreturn) -#else - #define JSON_HEDLEY_NO_RETURN -#endif - -#if defined(JSON_HEDLEY_NO_ESCAPE) - #undef JSON_HEDLEY_NO_ESCAPE -#endif -#if JSON_HEDLEY_HAS_ATTRIBUTE(noescape) - #define JSON_HEDLEY_NO_ESCAPE __attribute__((__noescape__)) -#else - #define JSON_HEDLEY_NO_ESCAPE -#endif - -#if defined(JSON_HEDLEY_UNREACHABLE) - #undef JSON_HEDLEY_UNREACHABLE -#endif -#if defined(JSON_HEDLEY_UNREACHABLE_RETURN) - #undef JSON_HEDLEY_UNREACHABLE_RETURN -#endif -#if defined(JSON_HEDLEY_ASSUME) - #undef JSON_HEDLEY_ASSUME -#endif -#if \ - JSON_HEDLEY_MSVC_VERSION_CHECK(13,10,0) || \ - JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) - #define JSON_HEDLEY_ASSUME(expr) __assume(expr) -#elif JSON_HEDLEY_HAS_BUILTIN(__builtin_assume) - #define JSON_HEDLEY_ASSUME(expr) __builtin_assume(expr) -#elif \ - JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,2,0) || \ - JSON_HEDLEY_TI_CL6X_VERSION_CHECK(4,0,0) - #if defined(__cplusplus) - #define JSON_HEDLEY_ASSUME(expr) std::_nassert(expr) - #else - #define JSON_HEDLEY_ASSUME(expr) _nassert(expr) - #endif -#endif -#if \ - (JSON_HEDLEY_HAS_BUILTIN(__builtin_unreachable) && (!defined(JSON_HEDLEY_ARM_VERSION))) || \ - JSON_HEDLEY_GCC_VERSION_CHECK(4,5,0) || \ - JSON_HEDLEY_PGI_VERSION_CHECK(18,10,0) || \ - JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ - JSON_HEDLEY_IBM_VERSION_CHECK(13,1,5) - #define JSON_HEDLEY_UNREACHABLE() __builtin_unreachable() -#elif defined(JSON_HEDLEY_ASSUME) - #define JSON_HEDLEY_UNREACHABLE() JSON_HEDLEY_ASSUME(0) -#endif -#if !defined(JSON_HEDLEY_ASSUME) - #if defined(JSON_HEDLEY_UNREACHABLE) - #define JSON_HEDLEY_ASSUME(expr) JSON_HEDLEY_STATIC_CAST(void, ((expr) ? 1 : (JSON_HEDLEY_UNREACHABLE(), 1))) - #else - #define JSON_HEDLEY_ASSUME(expr) JSON_HEDLEY_STATIC_CAST(void, expr) - #endif -#endif -#if defined(JSON_HEDLEY_UNREACHABLE) - #if \ - JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,2,0) || \ - JSON_HEDLEY_TI_CL6X_VERSION_CHECK(4,0,0) - #define JSON_HEDLEY_UNREACHABLE_RETURN(value) return (JSON_HEDLEY_STATIC_CAST(void, JSON_HEDLEY_ASSUME(0)), (value)) - #else - #define JSON_HEDLEY_UNREACHABLE_RETURN(value) JSON_HEDLEY_UNREACHABLE() - #endif -#else - #define JSON_HEDLEY_UNREACHABLE_RETURN(value) return (value) -#endif -#if !defined(JSON_HEDLEY_UNREACHABLE) - #define JSON_HEDLEY_UNREACHABLE() JSON_HEDLEY_ASSUME(0) -#endif - -JSON_HEDLEY_DIAGNOSTIC_PUSH -#if JSON_HEDLEY_HAS_WARNING("-Wpedantic") - #pragma clang diagnostic ignored "-Wpedantic" -#endif -#if JSON_HEDLEY_HAS_WARNING("-Wc++98-compat-pedantic") && defined(__cplusplus) - #pragma clang diagnostic ignored "-Wc++98-compat-pedantic" -#endif -#if JSON_HEDLEY_GCC_HAS_WARNING("-Wvariadic-macros",4,0,0) - #if defined(__clang__) - #pragma clang diagnostic ignored "-Wvariadic-macros" - #elif defined(JSON_HEDLEY_GCC_VERSION) - #pragma GCC diagnostic ignored "-Wvariadic-macros" - #endif -#endif -#if defined(JSON_HEDLEY_NON_NULL) - #undef JSON_HEDLEY_NON_NULL -#endif -#if \ - JSON_HEDLEY_HAS_ATTRIBUTE(nonnull) || \ - JSON_HEDLEY_GCC_VERSION_CHECK(3,3,0) || \ - JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ - JSON_HEDLEY_ARM_VERSION_CHECK(4,1,0) - #define JSON_HEDLEY_NON_NULL(...) __attribute__((__nonnull__(__VA_ARGS__))) -#else - #define JSON_HEDLEY_NON_NULL(...) -#endif -JSON_HEDLEY_DIAGNOSTIC_POP - -#if defined(JSON_HEDLEY_PRINTF_FORMAT) - #undef JSON_HEDLEY_PRINTF_FORMAT -#endif -#if defined(__MINGW32__) && JSON_HEDLEY_GCC_HAS_ATTRIBUTE(format,4,4,0) && !defined(__USE_MINGW_ANSI_STDIO) - #define JSON_HEDLEY_PRINTF_FORMAT(string_idx,first_to_check) __attribute__((__format__(ms_printf, string_idx, first_to_check))) -#elif defined(__MINGW32__) && JSON_HEDLEY_GCC_HAS_ATTRIBUTE(format,4,4,0) && defined(__USE_MINGW_ANSI_STDIO) - #define JSON_HEDLEY_PRINTF_FORMAT(string_idx,first_to_check) __attribute__((__format__(gnu_printf, string_idx, first_to_check))) -#elif \ - JSON_HEDLEY_HAS_ATTRIBUTE(format) || \ - JSON_HEDLEY_GCC_VERSION_CHECK(3,1,0) || \ - JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ - JSON_HEDLEY_ARM_VERSION_CHECK(5,6,0) || \ - JSON_HEDLEY_IBM_VERSION_CHECK(10,1,0) || \ - JSON_HEDLEY_TI_VERSION_CHECK(15,12,0) || \ - (JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(4,8,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(5,2,0) || \ - (JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,4,0) || \ - (JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,3,0) || \ - (JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,2,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,5,0) || \ - JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ - JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(2,1,0) - #define JSON_HEDLEY_PRINTF_FORMAT(string_idx,first_to_check) __attribute__((__format__(__printf__, string_idx, first_to_check))) -#elif JSON_HEDLEY_PELLES_VERSION_CHECK(6,0,0) - #define JSON_HEDLEY_PRINTF_FORMAT(string_idx,first_to_check) __declspec(vaformat(printf,string_idx,first_to_check)) -#else - #define JSON_HEDLEY_PRINTF_FORMAT(string_idx,first_to_check) -#endif - -#if defined(JSON_HEDLEY_CONSTEXPR) - #undef JSON_HEDLEY_CONSTEXPR -#endif -#if defined(__cplusplus) - #if __cplusplus >= 201103L - #define JSON_HEDLEY_CONSTEXPR JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_(constexpr) - #endif -#endif -#if !defined(JSON_HEDLEY_CONSTEXPR) - #define JSON_HEDLEY_CONSTEXPR -#endif - -#if defined(JSON_HEDLEY_PREDICT) - #undef JSON_HEDLEY_PREDICT -#endif -#if defined(JSON_HEDLEY_LIKELY) - #undef JSON_HEDLEY_LIKELY -#endif -#if defined(JSON_HEDLEY_UNLIKELY) - #undef JSON_HEDLEY_UNLIKELY -#endif -#if defined(JSON_HEDLEY_UNPREDICTABLE) - #undef JSON_HEDLEY_UNPREDICTABLE -#endif -#if JSON_HEDLEY_HAS_BUILTIN(__builtin_unpredictable) - #define JSON_HEDLEY_UNPREDICTABLE(expr) __builtin_unpredictable((expr)) -#endif -#if \ - JSON_HEDLEY_HAS_BUILTIN(__builtin_expect_with_probability) || \ - JSON_HEDLEY_GCC_VERSION_CHECK(9,0,0) -# define JSON_HEDLEY_PREDICT(expr, value, probability) __builtin_expect_with_probability( (expr), (value), (probability)) -# define JSON_HEDLEY_PREDICT_TRUE(expr, probability) __builtin_expect_with_probability(!!(expr), 1 , (probability)) -# define JSON_HEDLEY_PREDICT_FALSE(expr, probability) __builtin_expect_with_probability(!!(expr), 0 , (probability)) -# define JSON_HEDLEY_LIKELY(expr) __builtin_expect (!!(expr), 1 ) -# define JSON_HEDLEY_UNLIKELY(expr) __builtin_expect (!!(expr), 0 ) -#elif \ - JSON_HEDLEY_HAS_BUILTIN(__builtin_expect) || \ - JSON_HEDLEY_GCC_VERSION_CHECK(3,0,0) || \ - JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ - (JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,15,0) && defined(__cplusplus)) || \ - JSON_HEDLEY_ARM_VERSION_CHECK(4,1,0) || \ - JSON_HEDLEY_IBM_VERSION_CHECK(10,1,0) || \ - JSON_HEDLEY_TI_VERSION_CHECK(15,12,0) || \ - JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(4,7,0) || \ - JSON_HEDLEY_TI_CL430_VERSION_CHECK(3,1,0) || \ - JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,1,0) || \ - JSON_HEDLEY_TI_CL6X_VERSION_CHECK(6,1,0) || \ - JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ - JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(2,1,0) || \ - JSON_HEDLEY_TINYC_VERSION_CHECK(0,9,27) || \ - JSON_HEDLEY_CRAY_VERSION_CHECK(8,1,0) -# define JSON_HEDLEY_PREDICT(expr, expected, probability) \ - (((probability) >= 0.9) ? __builtin_expect((expr), (expected)) : (JSON_HEDLEY_STATIC_CAST(void, expected), (expr))) -# define JSON_HEDLEY_PREDICT_TRUE(expr, probability) \ - (__extension__ ({ \ - double hedley_probability_ = (probability); \ - ((hedley_probability_ >= 0.9) ? __builtin_expect(!!(expr), 1) : ((hedley_probability_ <= 0.1) ? __builtin_expect(!!(expr), 0) : !!(expr))); \ - })) -# define JSON_HEDLEY_PREDICT_FALSE(expr, probability) \ - (__extension__ ({ \ - double hedley_probability_ = (probability); \ - ((hedley_probability_ >= 0.9) ? __builtin_expect(!!(expr), 0) : ((hedley_probability_ <= 0.1) ? __builtin_expect(!!(expr), 1) : !!(expr))); \ - })) -# define JSON_HEDLEY_LIKELY(expr) __builtin_expect(!!(expr), 1) -# define JSON_HEDLEY_UNLIKELY(expr) __builtin_expect(!!(expr), 0) -#else -# define JSON_HEDLEY_PREDICT(expr, expected, probability) (JSON_HEDLEY_STATIC_CAST(void, expected), (expr)) -# define JSON_HEDLEY_PREDICT_TRUE(expr, probability) (!!(expr)) -# define JSON_HEDLEY_PREDICT_FALSE(expr, probability) (!!(expr)) -# define JSON_HEDLEY_LIKELY(expr) (!!(expr)) -# define JSON_HEDLEY_UNLIKELY(expr) (!!(expr)) -#endif -#if !defined(JSON_HEDLEY_UNPREDICTABLE) - #define JSON_HEDLEY_UNPREDICTABLE(expr) JSON_HEDLEY_PREDICT(expr, 1, 0.5) -#endif - -#if defined(JSON_HEDLEY_MALLOC) - #undef JSON_HEDLEY_MALLOC -#endif -#if \ - JSON_HEDLEY_HAS_ATTRIBUTE(malloc) || \ - JSON_HEDLEY_GCC_VERSION_CHECK(3,1,0) || \ - JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ - JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,11,0) || \ - JSON_HEDLEY_ARM_VERSION_CHECK(4,1,0) || \ - JSON_HEDLEY_IBM_VERSION_CHECK(12,1,0) || \ - JSON_HEDLEY_TI_VERSION_CHECK(15,12,0) || \ - (JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(4,8,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(5,2,0) || \ - (JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,4,0) || \ - (JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,3,0) || \ - (JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,2,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,5,0) || \ - JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ - JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(2,1,0) - #define JSON_HEDLEY_MALLOC __attribute__((__malloc__)) -#elif JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,10,0) - #define JSON_HEDLEY_MALLOC _Pragma("returns_new_memory") -#elif JSON_HEDLEY_MSVC_VERSION_CHECK(14, 0, 0) - #define JSON_HEDLEY_MALLOC __declspec(restrict) -#else - #define JSON_HEDLEY_MALLOC -#endif - -#if defined(JSON_HEDLEY_PURE) - #undef JSON_HEDLEY_PURE -#endif -#if \ - JSON_HEDLEY_HAS_ATTRIBUTE(pure) || \ - JSON_HEDLEY_GCC_VERSION_CHECK(2,96,0) || \ - JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ - JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,11,0) || \ - JSON_HEDLEY_ARM_VERSION_CHECK(4,1,0) || \ - JSON_HEDLEY_IBM_VERSION_CHECK(10,1,0) || \ - JSON_HEDLEY_TI_VERSION_CHECK(15,12,0) || \ - (JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(4,8,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(5,2,0) || \ - (JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,4,0) || \ - (JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,3,0) || \ - (JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,2,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,5,0) || \ - JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ - JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(2,1,0) || \ - JSON_HEDLEY_PGI_VERSION_CHECK(17,10,0) -# define JSON_HEDLEY_PURE __attribute__((__pure__)) -#elif JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,10,0) -# define JSON_HEDLEY_PURE _Pragma("does_not_write_global_data") -#elif defined(__cplusplus) && \ - ( \ - JSON_HEDLEY_TI_CL430_VERSION_CHECK(2,0,1) || \ - JSON_HEDLEY_TI_CL6X_VERSION_CHECK(4,0,0) || \ - JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) \ - ) -# define JSON_HEDLEY_PURE _Pragma("FUNC_IS_PURE;") -#else -# define JSON_HEDLEY_PURE -#endif - -#if defined(JSON_HEDLEY_CONST) - #undef JSON_HEDLEY_CONST -#endif -#if \ - JSON_HEDLEY_HAS_ATTRIBUTE(const) || \ - JSON_HEDLEY_GCC_VERSION_CHECK(2,5,0) || \ - JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ - JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,11,0) || \ - JSON_HEDLEY_ARM_VERSION_CHECK(4,1,0) || \ - JSON_HEDLEY_IBM_VERSION_CHECK(10,1,0) || \ - JSON_HEDLEY_TI_VERSION_CHECK(15,12,0) || \ - (JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(4,8,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(5,2,0) || \ - (JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,4,0) || \ - (JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,3,0) || \ - (JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,2,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,5,0) || \ - JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ - JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(2,1,0) || \ - JSON_HEDLEY_PGI_VERSION_CHECK(17,10,0) - #define JSON_HEDLEY_CONST __attribute__((__const__)) -#elif \ - JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,10,0) - #define JSON_HEDLEY_CONST _Pragma("no_side_effect") -#else - #define JSON_HEDLEY_CONST JSON_HEDLEY_PURE -#endif - -#if defined(JSON_HEDLEY_RESTRICT) - #undef JSON_HEDLEY_RESTRICT -#endif -#if defined(__STDC_VERSION__) && (__STDC_VERSION__ >= 199901L) && !defined(__cplusplus) - #define JSON_HEDLEY_RESTRICT restrict -#elif \ - JSON_HEDLEY_GCC_VERSION_CHECK(3,1,0) || \ - JSON_HEDLEY_MSVC_VERSION_CHECK(14,0,0) || \ - JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ - JSON_HEDLEY_ARM_VERSION_CHECK(4,1,0) || \ - JSON_HEDLEY_IBM_VERSION_CHECK(10,1,0) || \ - JSON_HEDLEY_PGI_VERSION_CHECK(17,10,0) || \ - JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,3,0) || \ - JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,2,4) || \ - JSON_HEDLEY_TI_CL6X_VERSION_CHECK(8,1,0) || \ - JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ - (JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,14,0) && defined(__cplusplus)) || \ - JSON_HEDLEY_IAR_VERSION_CHECK(8,0,0) || \ - defined(__clang__) - #define JSON_HEDLEY_RESTRICT __restrict -#elif JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,3,0) && !defined(__cplusplus) - #define JSON_HEDLEY_RESTRICT _Restrict -#else - #define JSON_HEDLEY_RESTRICT -#endif - -#if defined(JSON_HEDLEY_INLINE) - #undef JSON_HEDLEY_INLINE -#endif -#if \ - (defined(__STDC_VERSION__) && (__STDC_VERSION__ >= 199901L)) || \ - (defined(__cplusplus) && (__cplusplus >= 199711L)) - #define JSON_HEDLEY_INLINE inline -#elif \ - defined(JSON_HEDLEY_GCC_VERSION) || \ - JSON_HEDLEY_ARM_VERSION_CHECK(6,2,0) - #define JSON_HEDLEY_INLINE __inline__ -#elif \ - JSON_HEDLEY_MSVC_VERSION_CHECK(12,0,0) || \ - JSON_HEDLEY_ARM_VERSION_CHECK(4,1,0) || \ - JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(5,1,0) || \ - JSON_HEDLEY_TI_CL430_VERSION_CHECK(3,1,0) || \ - JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,2,0) || \ - JSON_HEDLEY_TI_CL6X_VERSION_CHECK(8,0,0) || \ - JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ - JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(2,1,0) - #define JSON_HEDLEY_INLINE __inline -#else - #define JSON_HEDLEY_INLINE -#endif - -#if defined(JSON_HEDLEY_ALWAYS_INLINE) - #undef JSON_HEDLEY_ALWAYS_INLINE -#endif -#if \ - JSON_HEDLEY_HAS_ATTRIBUTE(always_inline) || \ - JSON_HEDLEY_GCC_VERSION_CHECK(4,0,0) || \ - JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ - JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,11,0) || \ - JSON_HEDLEY_ARM_VERSION_CHECK(4,1,0) || \ - JSON_HEDLEY_IBM_VERSION_CHECK(10,1,0) || \ - JSON_HEDLEY_TI_VERSION_CHECK(15,12,0) || \ - (JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(4,8,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(5,2,0) || \ - (JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,4,0) || \ - (JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,3,0) || \ - (JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,2,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,5,0) || \ - JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ - JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(2,1,0) -# define JSON_HEDLEY_ALWAYS_INLINE __attribute__((__always_inline__)) JSON_HEDLEY_INLINE -#elif JSON_HEDLEY_MSVC_VERSION_CHECK(12,0,0) -# define JSON_HEDLEY_ALWAYS_INLINE __forceinline -#elif defined(__cplusplus) && \ - ( \ - JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(5,2,0) || \ - JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,3,0) || \ - JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,4,0) || \ - JSON_HEDLEY_TI_CL6X_VERSION_CHECK(6,1,0) || \ - JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ - JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(2,1,0) \ - ) -# define JSON_HEDLEY_ALWAYS_INLINE _Pragma("FUNC_ALWAYS_INLINE;") -#elif JSON_HEDLEY_IAR_VERSION_CHECK(8,0,0) -# define JSON_HEDLEY_ALWAYS_INLINE _Pragma("inline=forced") -#else -# define JSON_HEDLEY_ALWAYS_INLINE JSON_HEDLEY_INLINE -#endif - -#if defined(JSON_HEDLEY_NEVER_INLINE) - #undef JSON_HEDLEY_NEVER_INLINE -#endif -#if \ - JSON_HEDLEY_HAS_ATTRIBUTE(noinline) || \ - JSON_HEDLEY_GCC_VERSION_CHECK(4,0,0) || \ - JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ - JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,11,0) || \ - JSON_HEDLEY_ARM_VERSION_CHECK(4,1,0) || \ - JSON_HEDLEY_IBM_VERSION_CHECK(10,1,0) || \ - JSON_HEDLEY_TI_VERSION_CHECK(15,12,0) || \ - (JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(4,8,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(5,2,0) || \ - (JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,4,0) || \ - (JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,3,0) || \ - (JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,2,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,5,0) || \ - JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ - JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(2,1,0) - #define JSON_HEDLEY_NEVER_INLINE __attribute__((__noinline__)) -#elif JSON_HEDLEY_MSVC_VERSION_CHECK(13,10,0) - #define JSON_HEDLEY_NEVER_INLINE __declspec(noinline) -#elif JSON_HEDLEY_PGI_VERSION_CHECK(10,2,0) - #define JSON_HEDLEY_NEVER_INLINE _Pragma("noinline") -#elif JSON_HEDLEY_TI_CL6X_VERSION_CHECK(6,0,0) && defined(__cplusplus) - #define JSON_HEDLEY_NEVER_INLINE _Pragma("FUNC_CANNOT_INLINE;") -#elif JSON_HEDLEY_IAR_VERSION_CHECK(8,0,0) - #define JSON_HEDLEY_NEVER_INLINE _Pragma("inline=never") -#elif JSON_HEDLEY_COMPCERT_VERSION_CHECK(3,2,0) - #define JSON_HEDLEY_NEVER_INLINE __attribute((noinline)) -#elif JSON_HEDLEY_PELLES_VERSION_CHECK(9,0,0) - #define JSON_HEDLEY_NEVER_INLINE __declspec(noinline) -#else - #define JSON_HEDLEY_NEVER_INLINE -#endif - -#if defined(JSON_HEDLEY_PRIVATE) - #undef JSON_HEDLEY_PRIVATE -#endif -#if defined(JSON_HEDLEY_PUBLIC) - #undef JSON_HEDLEY_PUBLIC -#endif -#if defined(JSON_HEDLEY_IMPORT) - #undef JSON_HEDLEY_IMPORT -#endif -#if defined(_WIN32) || defined(__CYGWIN__) -# define JSON_HEDLEY_PRIVATE -# define JSON_HEDLEY_PUBLIC __declspec(dllexport) -# define JSON_HEDLEY_IMPORT __declspec(dllimport) -#else -# if \ - JSON_HEDLEY_HAS_ATTRIBUTE(visibility) || \ - JSON_HEDLEY_GCC_VERSION_CHECK(3,3,0) || \ - JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,11,0) || \ - JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ - JSON_HEDLEY_ARM_VERSION_CHECK(4,1,0) || \ - JSON_HEDLEY_IBM_VERSION_CHECK(13,1,0) || \ - ( \ - defined(__TI_EABI__) && \ - ( \ - (JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,2,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ - JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,5,0) \ - ) \ - ) -# define JSON_HEDLEY_PRIVATE __attribute__((__visibility__("hidden"))) -# define JSON_HEDLEY_PUBLIC __attribute__((__visibility__("default"))) -# else -# define JSON_HEDLEY_PRIVATE -# define JSON_HEDLEY_PUBLIC -# endif -# define JSON_HEDLEY_IMPORT extern -#endif - -#if defined(JSON_HEDLEY_NO_THROW) - #undef JSON_HEDLEY_NO_THROW -#endif -#if \ - JSON_HEDLEY_HAS_ATTRIBUTE(nothrow) || \ - JSON_HEDLEY_GCC_VERSION_CHECK(3,3,0) || \ - JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) - #define JSON_HEDLEY_NO_THROW __attribute__((__nothrow__)) -#elif \ - JSON_HEDLEY_MSVC_VERSION_CHECK(13,1,0) || \ - JSON_HEDLEY_ARM_VERSION_CHECK(4,1,0) - #define JSON_HEDLEY_NO_THROW __declspec(nothrow) -#else - #define JSON_HEDLEY_NO_THROW -#endif - -#if defined(JSON_HEDLEY_FALL_THROUGH) - #undef JSON_HEDLEY_FALL_THROUGH -#endif -#if \ - JSON_HEDLEY_HAS_ATTRIBUTE(fallthrough) || \ - JSON_HEDLEY_GCC_VERSION_CHECK(7,0,0) - #define JSON_HEDLEY_FALL_THROUGH __attribute__((__fallthrough__)) -#elif JSON_HEDLEY_HAS_CPP_ATTRIBUTE_NS(clang,fallthrough) - #define JSON_HEDLEY_FALL_THROUGH JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_([[clang::fallthrough]]) -#elif JSON_HEDLEY_HAS_CPP_ATTRIBUTE(fallthrough) - #define JSON_HEDLEY_FALL_THROUGH JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_([[fallthrough]]) -#elif defined(__fallthrough) /* SAL */ - #define JSON_HEDLEY_FALL_THROUGH __fallthrough -#else - #define JSON_HEDLEY_FALL_THROUGH -#endif - -#if defined(JSON_HEDLEY_RETURNS_NON_NULL) - #undef JSON_HEDLEY_RETURNS_NON_NULL -#endif -#if \ - JSON_HEDLEY_HAS_ATTRIBUTE(returns_nonnull) || \ - JSON_HEDLEY_GCC_VERSION_CHECK(4,9,0) - #define JSON_HEDLEY_RETURNS_NON_NULL __attribute__((__returns_nonnull__)) -#elif defined(_Ret_notnull_) /* SAL */ - #define JSON_HEDLEY_RETURNS_NON_NULL _Ret_notnull_ -#else - #define JSON_HEDLEY_RETURNS_NON_NULL -#endif - -#if defined(JSON_HEDLEY_ARRAY_PARAM) - #undef JSON_HEDLEY_ARRAY_PARAM -#endif -#if \ - defined(__STDC_VERSION__) && (__STDC_VERSION__ >= 199901L) && \ - !defined(__STDC_NO_VLA__) && \ - !defined(__cplusplus) && \ - !defined(JSON_HEDLEY_PGI_VERSION) && \ - !defined(JSON_HEDLEY_TINYC_VERSION) - #define JSON_HEDLEY_ARRAY_PARAM(name) (name) -#else - #define JSON_HEDLEY_ARRAY_PARAM(name) -#endif - -#if defined(JSON_HEDLEY_IS_CONSTANT) - #undef JSON_HEDLEY_IS_CONSTANT -#endif -#if defined(JSON_HEDLEY_REQUIRE_CONSTEXPR) - #undef JSON_HEDLEY_REQUIRE_CONSTEXPR -#endif -/* JSON_HEDLEY_IS_CONSTEXPR_ is for - HEDLEY INTERNAL USE ONLY. API subject to change without notice. */ -#if defined(JSON_HEDLEY_IS_CONSTEXPR_) - #undef JSON_HEDLEY_IS_CONSTEXPR_ -#endif -#if \ - JSON_HEDLEY_HAS_BUILTIN(__builtin_constant_p) || \ - JSON_HEDLEY_GCC_VERSION_CHECK(3,4,0) || \ - JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ - JSON_HEDLEY_TINYC_VERSION_CHECK(0,9,19) || \ - JSON_HEDLEY_ARM_VERSION_CHECK(4,1,0) || \ - JSON_HEDLEY_IBM_VERSION_CHECK(13,1,0) || \ - JSON_HEDLEY_TI_CL6X_VERSION_CHECK(6,1,0) || \ - (JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,10,0) && !defined(__cplusplus)) || \ - JSON_HEDLEY_CRAY_VERSION_CHECK(8,1,0) - #define JSON_HEDLEY_IS_CONSTANT(expr) __builtin_constant_p(expr) -#endif -#if !defined(__cplusplus) -# if \ - JSON_HEDLEY_HAS_BUILTIN(__builtin_types_compatible_p) || \ - JSON_HEDLEY_GCC_VERSION_CHECK(3,4,0) || \ - JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ - JSON_HEDLEY_IBM_VERSION_CHECK(13,1,0) || \ - JSON_HEDLEY_CRAY_VERSION_CHECK(8,1,0) || \ - JSON_HEDLEY_ARM_VERSION_CHECK(5,4,0) || \ - JSON_HEDLEY_TINYC_VERSION_CHECK(0,9,24) -#if defined(__INTPTR_TYPE__) - #define JSON_HEDLEY_IS_CONSTEXPR_(expr) __builtin_types_compatible_p(__typeof__((1 ? (void*) ((__INTPTR_TYPE__) ((expr) * 0)) : (int*) 0)), int*) -#else - #include - #define JSON_HEDLEY_IS_CONSTEXPR_(expr) __builtin_types_compatible_p(__typeof__((1 ? (void*) ((intptr_t) ((expr) * 0)) : (int*) 0)), int*) -#endif -# elif \ - ( \ - defined(__STDC_VERSION__) && (__STDC_VERSION__ >= 201112L) && \ - !defined(JSON_HEDLEY_SUNPRO_VERSION) && \ - !defined(JSON_HEDLEY_PGI_VERSION) && \ - !defined(JSON_HEDLEY_IAR_VERSION)) || \ - JSON_HEDLEY_HAS_EXTENSION(c_generic_selections) || \ - JSON_HEDLEY_GCC_VERSION_CHECK(4,9,0) || \ - JSON_HEDLEY_INTEL_VERSION_CHECK(17,0,0) || \ - JSON_HEDLEY_IBM_VERSION_CHECK(12,1,0) || \ - JSON_HEDLEY_ARM_VERSION_CHECK(5,3,0) -#if defined(__INTPTR_TYPE__) - #define JSON_HEDLEY_IS_CONSTEXPR_(expr) _Generic((1 ? (void*) ((__INTPTR_TYPE__) ((expr) * 0)) : (int*) 0), int*: 1, void*: 0) -#else - #include - #define JSON_HEDLEY_IS_CONSTEXPR_(expr) _Generic((1 ? (void*) ((intptr_t) * 0) : (int*) 0), int*: 1, void*: 0) -#endif -# elif \ - defined(JSON_HEDLEY_GCC_VERSION) || \ - defined(JSON_HEDLEY_INTEL_VERSION) || \ - defined(JSON_HEDLEY_TINYC_VERSION) || \ - defined(JSON_HEDLEY_TI_ARMCL_VERSION) || \ - JSON_HEDLEY_TI_CL430_VERSION_CHECK(18,12,0) || \ - defined(JSON_HEDLEY_TI_CL2000_VERSION) || \ - defined(JSON_HEDLEY_TI_CL6X_VERSION) || \ - defined(JSON_HEDLEY_TI_CL7X_VERSION) || \ - defined(JSON_HEDLEY_TI_CLPRU_VERSION) || \ - defined(__clang__) -# define JSON_HEDLEY_IS_CONSTEXPR_(expr) ( \ - sizeof(void) != \ - sizeof(*( \ - 1 ? \ - ((void*) ((expr) * 0L) ) : \ -((struct { char v[sizeof(void) * 2]; } *) 1) \ - ) \ - ) \ - ) -# endif -#endif -#if defined(JSON_HEDLEY_IS_CONSTEXPR_) - #if !defined(JSON_HEDLEY_IS_CONSTANT) - #define JSON_HEDLEY_IS_CONSTANT(expr) JSON_HEDLEY_IS_CONSTEXPR_(expr) - #endif - #define JSON_HEDLEY_REQUIRE_CONSTEXPR(expr) (JSON_HEDLEY_IS_CONSTEXPR_(expr) ? (expr) : (-1)) -#else - #if !defined(JSON_HEDLEY_IS_CONSTANT) - #define JSON_HEDLEY_IS_CONSTANT(expr) (0) - #endif - #define JSON_HEDLEY_REQUIRE_CONSTEXPR(expr) (expr) -#endif - -#if defined(JSON_HEDLEY_BEGIN_C_DECLS) - #undef JSON_HEDLEY_BEGIN_C_DECLS -#endif -#if defined(JSON_HEDLEY_END_C_DECLS) - #undef JSON_HEDLEY_END_C_DECLS -#endif -#if defined(JSON_HEDLEY_C_DECL) - #undef JSON_HEDLEY_C_DECL -#endif -#if defined(__cplusplus) - #define JSON_HEDLEY_BEGIN_C_DECLS extern "C" { - #define JSON_HEDLEY_END_C_DECLS } - #define JSON_HEDLEY_C_DECL extern "C" -#else - #define JSON_HEDLEY_BEGIN_C_DECLS - #define JSON_HEDLEY_END_C_DECLS - #define JSON_HEDLEY_C_DECL -#endif - -#if defined(JSON_HEDLEY_STATIC_ASSERT) - #undef JSON_HEDLEY_STATIC_ASSERT -#endif -#if \ - !defined(__cplusplus) && ( \ - (defined(__STDC_VERSION__) && (__STDC_VERSION__ >= 201112L)) || \ - JSON_HEDLEY_HAS_FEATURE(c_static_assert) || \ - JSON_HEDLEY_GCC_VERSION_CHECK(6,0,0) || \ - JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ - defined(_Static_assert) \ - ) -# define JSON_HEDLEY_STATIC_ASSERT(expr, message) _Static_assert(expr, message) -#elif \ - (defined(__cplusplus) && (__cplusplus >= 201103L)) || \ - JSON_HEDLEY_MSVC_VERSION_CHECK(16,0,0) -# define JSON_HEDLEY_STATIC_ASSERT(expr, message) JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_(static_assert(expr, message)) -#else -# define JSON_HEDLEY_STATIC_ASSERT(expr, message) -#endif - -#if defined(JSON_HEDLEY_NULL) - #undef JSON_HEDLEY_NULL -#endif -#if defined(__cplusplus) - #if __cplusplus >= 201103L - #define JSON_HEDLEY_NULL JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_(nullptr) - #elif defined(NULL) - #define JSON_HEDLEY_NULL NULL - #else - #define JSON_HEDLEY_NULL JSON_HEDLEY_STATIC_CAST(void*, 0) - #endif -#elif defined(NULL) - #define JSON_HEDLEY_NULL NULL -#else - #define JSON_HEDLEY_NULL ((void*) 0) -#endif - -#if defined(JSON_HEDLEY_MESSAGE) - #undef JSON_HEDLEY_MESSAGE -#endif -#if JSON_HEDLEY_HAS_WARNING("-Wunknown-pragmas") -# define JSON_HEDLEY_MESSAGE(msg) \ - JSON_HEDLEY_DIAGNOSTIC_PUSH \ - JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_PRAGMAS \ - JSON_HEDLEY_PRAGMA(message msg) \ - JSON_HEDLEY_DIAGNOSTIC_POP -#elif \ - JSON_HEDLEY_GCC_VERSION_CHECK(4,4,0) || \ - JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) -# define JSON_HEDLEY_MESSAGE(msg) JSON_HEDLEY_PRAGMA(message msg) -#elif JSON_HEDLEY_CRAY_VERSION_CHECK(5,0,0) -# define JSON_HEDLEY_MESSAGE(msg) JSON_HEDLEY_PRAGMA(_CRI message msg) -#elif JSON_HEDLEY_IAR_VERSION_CHECK(8,0,0) -# define JSON_HEDLEY_MESSAGE(msg) JSON_HEDLEY_PRAGMA(message(msg)) -#elif JSON_HEDLEY_PELLES_VERSION_CHECK(2,0,0) -# define JSON_HEDLEY_MESSAGE(msg) JSON_HEDLEY_PRAGMA(message(msg)) -#else -# define JSON_HEDLEY_MESSAGE(msg) -#endif - -#if defined(JSON_HEDLEY_WARNING) - #undef JSON_HEDLEY_WARNING -#endif -#if JSON_HEDLEY_HAS_WARNING("-Wunknown-pragmas") -# define JSON_HEDLEY_WARNING(msg) \ - JSON_HEDLEY_DIAGNOSTIC_PUSH \ - JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_PRAGMAS \ - JSON_HEDLEY_PRAGMA(clang warning msg) \ - JSON_HEDLEY_DIAGNOSTIC_POP -#elif \ - JSON_HEDLEY_GCC_VERSION_CHECK(4,8,0) || \ - JSON_HEDLEY_PGI_VERSION_CHECK(18,4,0) || \ - JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) -# define JSON_HEDLEY_WARNING(msg) JSON_HEDLEY_PRAGMA(GCC warning msg) -#elif JSON_HEDLEY_MSVC_VERSION_CHECK(15,0,0) -# define JSON_HEDLEY_WARNING(msg) JSON_HEDLEY_PRAGMA(message(msg)) -#else -# define JSON_HEDLEY_WARNING(msg) JSON_HEDLEY_MESSAGE(msg) -#endif - -#if defined(JSON_HEDLEY_REQUIRE) - #undef JSON_HEDLEY_REQUIRE -#endif -#if defined(JSON_HEDLEY_REQUIRE_MSG) - #undef JSON_HEDLEY_REQUIRE_MSG -#endif -#if JSON_HEDLEY_HAS_ATTRIBUTE(diagnose_if) -# if JSON_HEDLEY_HAS_WARNING("-Wgcc-compat") -# define JSON_HEDLEY_REQUIRE(expr) \ - JSON_HEDLEY_DIAGNOSTIC_PUSH \ - _Pragma("clang diagnostic ignored \"-Wgcc-compat\"") \ - __attribute__((diagnose_if(!(expr), #expr, "error"))) \ - JSON_HEDLEY_DIAGNOSTIC_POP -# define JSON_HEDLEY_REQUIRE_MSG(expr,msg) \ - JSON_HEDLEY_DIAGNOSTIC_PUSH \ - _Pragma("clang diagnostic ignored \"-Wgcc-compat\"") \ - __attribute__((diagnose_if(!(expr), msg, "error"))) \ - JSON_HEDLEY_DIAGNOSTIC_POP -# else -# define JSON_HEDLEY_REQUIRE(expr) __attribute__((diagnose_if(!(expr), #expr, "error"))) -# define JSON_HEDLEY_REQUIRE_MSG(expr,msg) __attribute__((diagnose_if(!(expr), msg, "error"))) -# endif -#else -# define JSON_HEDLEY_REQUIRE(expr) -# define JSON_HEDLEY_REQUIRE_MSG(expr,msg) -#endif - -#if defined(JSON_HEDLEY_FLAGS) - #undef JSON_HEDLEY_FLAGS -#endif -#if JSON_HEDLEY_HAS_ATTRIBUTE(flag_enum) - #define JSON_HEDLEY_FLAGS __attribute__((__flag_enum__)) -#endif - -#if defined(JSON_HEDLEY_FLAGS_CAST) - #undef JSON_HEDLEY_FLAGS_CAST -#endif -#if JSON_HEDLEY_INTEL_VERSION_CHECK(19,0,0) -# define JSON_HEDLEY_FLAGS_CAST(T, expr) (__extension__ ({ \ - JSON_HEDLEY_DIAGNOSTIC_PUSH \ - _Pragma("warning(disable:188)") \ - ((T) (expr)); \ - JSON_HEDLEY_DIAGNOSTIC_POP \ - })) -#else -# define JSON_HEDLEY_FLAGS_CAST(T, expr) JSON_HEDLEY_STATIC_CAST(T, expr) -#endif - -#if defined(JSON_HEDLEY_EMPTY_BASES) - #undef JSON_HEDLEY_EMPTY_BASES -#endif -#if JSON_HEDLEY_MSVC_VERSION_CHECK(19,0,23918) && !JSON_HEDLEY_MSVC_VERSION_CHECK(20,0,0) - #define JSON_HEDLEY_EMPTY_BASES __declspec(empty_bases) -#else - #define JSON_HEDLEY_EMPTY_BASES -#endif - -/* Remaining macros are deprecated. */ - -#if defined(JSON_HEDLEY_GCC_NOT_CLANG_VERSION_CHECK) - #undef JSON_HEDLEY_GCC_NOT_CLANG_VERSION_CHECK -#endif -#if defined(__clang__) - #define JSON_HEDLEY_GCC_NOT_CLANG_VERSION_CHECK(major,minor,patch) (0) -#else - #define JSON_HEDLEY_GCC_NOT_CLANG_VERSION_CHECK(major,minor,patch) JSON_HEDLEY_GCC_VERSION_CHECK(major,minor,patch) -#endif - -#if defined(JSON_HEDLEY_CLANG_HAS_ATTRIBUTE) - #undef JSON_HEDLEY_CLANG_HAS_ATTRIBUTE -#endif -#define JSON_HEDLEY_CLANG_HAS_ATTRIBUTE(attribute) JSON_HEDLEY_HAS_ATTRIBUTE(attribute) - -#if defined(JSON_HEDLEY_CLANG_HAS_CPP_ATTRIBUTE) - #undef JSON_HEDLEY_CLANG_HAS_CPP_ATTRIBUTE -#endif -#define JSON_HEDLEY_CLANG_HAS_CPP_ATTRIBUTE(attribute) JSON_HEDLEY_HAS_CPP_ATTRIBUTE(attribute) - -#if defined(JSON_HEDLEY_CLANG_HAS_BUILTIN) - #undef JSON_HEDLEY_CLANG_HAS_BUILTIN -#endif -#define JSON_HEDLEY_CLANG_HAS_BUILTIN(builtin) JSON_HEDLEY_HAS_BUILTIN(builtin) - -#if defined(JSON_HEDLEY_CLANG_HAS_FEATURE) - #undef JSON_HEDLEY_CLANG_HAS_FEATURE -#endif -#define JSON_HEDLEY_CLANG_HAS_FEATURE(feature) JSON_HEDLEY_HAS_FEATURE(feature) - -#if defined(JSON_HEDLEY_CLANG_HAS_EXTENSION) - #undef JSON_HEDLEY_CLANG_HAS_EXTENSION -#endif -#define JSON_HEDLEY_CLANG_HAS_EXTENSION(extension) JSON_HEDLEY_HAS_EXTENSION(extension) - -#if defined(JSON_HEDLEY_CLANG_HAS_DECLSPEC_DECLSPEC_ATTRIBUTE) - #undef JSON_HEDLEY_CLANG_HAS_DECLSPEC_DECLSPEC_ATTRIBUTE -#endif -#define JSON_HEDLEY_CLANG_HAS_DECLSPEC_ATTRIBUTE(attribute) JSON_HEDLEY_HAS_DECLSPEC_ATTRIBUTE(attribute) - -#if defined(JSON_HEDLEY_CLANG_HAS_WARNING) - #undef JSON_HEDLEY_CLANG_HAS_WARNING -#endif -#define JSON_HEDLEY_CLANG_HAS_WARNING(warning) JSON_HEDLEY_HAS_WARNING(warning) - -#endif /* !defined(JSON_HEDLEY_VERSION) || (JSON_HEDLEY_VERSION < X) */ - - -// This file contains all internal macro definitions -// You MUST include macro_unscope.hpp at the end of json.hpp to undef all of them - -// exclude unsupported compilers -#if !defined(JSON_SKIP_UNSUPPORTED_COMPILER_CHECK) - #if defined(__clang__) - #if (__clang_major__ * 10000 + __clang_minor__ * 100 + __clang_patchlevel__) < 30400 - #error "unsupported Clang version - see https://github.com/nlohmann/json#supported-compilers" - #endif - #elif defined(__GNUC__) && !(defined(__ICC) || defined(__INTEL_COMPILER)) - #if (__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__) < 40800 - #error "unsupported GCC version - see https://github.com/nlohmann/json#supported-compilers" - #endif - #endif -#endif - -// C++ language standard detection -#if (defined(__cplusplus) && __cplusplus >= 202002L) || (defined(_MSVC_LANG) && _MSVC_LANG >= 202002L) - #define JSON_HAS_CPP_20 - #define JSON_HAS_CPP_17 - #define JSON_HAS_CPP_14 -#elif (defined(__cplusplus) && __cplusplus >= 201703L) || (defined(_HAS_CXX17) && _HAS_CXX17 == 1) // fix for issue #464 - #define JSON_HAS_CPP_17 - #define JSON_HAS_CPP_14 -#elif (defined(__cplusplus) && __cplusplus >= 201402L) || (defined(_HAS_CXX14) && _HAS_CXX14 == 1) - #define JSON_HAS_CPP_14 -#endif - -// disable float-equal warnings on GCC/clang -#if defined(__clang__) || defined(__GNUC__) || defined(__GNUG__) - #pragma GCC diagnostic push - #pragma GCC diagnostic ignored "-Wfloat-equal" -#endif - -// disable documentation warnings on clang -#if defined(__clang__) - #pragma GCC diagnostic push - #pragma GCC diagnostic ignored "-Wdocumentation" -#endif - -// allow to disable exceptions -#if (defined(__cpp_exceptions) || defined(__EXCEPTIONS) || defined(_CPPUNWIND)) && !defined(JSON_NOEXCEPTION) - #define JSON_THROW(exception) throw exception - #define JSON_TRY try - #define JSON_CATCH(exception) catch(exception) - #define JSON_INTERNAL_CATCH(exception) catch(exception) -#else - #include - #define JSON_THROW(exception) std::abort() - #define JSON_TRY if(true) - #define JSON_CATCH(exception) if(false) - #define JSON_INTERNAL_CATCH(exception) if(false) -#endif - -// override exception macros -#if defined(JSON_THROW_USER) - #undef JSON_THROW - #define JSON_THROW JSON_THROW_USER -#endif -#if defined(JSON_TRY_USER) - #undef JSON_TRY - #define JSON_TRY JSON_TRY_USER -#endif -#if defined(JSON_CATCH_USER) - #undef JSON_CATCH - #define JSON_CATCH JSON_CATCH_USER - #undef JSON_INTERNAL_CATCH - #define JSON_INTERNAL_CATCH JSON_CATCH_USER -#endif -#if defined(JSON_INTERNAL_CATCH_USER) - #undef JSON_INTERNAL_CATCH - #define JSON_INTERNAL_CATCH JSON_INTERNAL_CATCH_USER -#endif - -// allow to override assert -#if !defined(JSON_ASSERT) - #include // assert - #define JSON_ASSERT(x) assert(x) -#endif - -/*! -@brief macro to briefly define a mapping between an enum and JSON -@def NLOHMANN_JSON_SERIALIZE_ENUM -@since version 3.4.0 -*/ -#define NLOHMANN_JSON_SERIALIZE_ENUM(ENUM_TYPE, ...) \ - template \ - inline void to_json(BasicJsonType& j, const ENUM_TYPE& e) \ - { \ - static_assert(std::is_enum::value, #ENUM_TYPE " must be an enum!"); \ - static const std::pair m[] = __VA_ARGS__; \ - auto it = std::find_if(std::begin(m), std::end(m), \ - [e](const std::pair& ej_pair) -> bool \ - { \ - return ej_pair.first == e; \ - }); \ - j = ((it != std::end(m)) ? it : std::begin(m))->second; \ - } \ - template \ - inline void from_json(const BasicJsonType& j, ENUM_TYPE& e) \ - { \ - static_assert(std::is_enum::value, #ENUM_TYPE " must be an enum!"); \ - static const std::pair m[] = __VA_ARGS__; \ - auto it = std::find_if(std::begin(m), std::end(m), \ - [&j](const std::pair& ej_pair) -> bool \ - { \ - return ej_pair.second == j; \ - }); \ - e = ((it != std::end(m)) ? it : std::begin(m))->first; \ - } - -// Ugly macros to avoid uglier copy-paste when specializing basic_json. They -// may be removed in the future once the class is split. - -#define NLOHMANN_BASIC_JSON_TPL_DECLARATION \ - template class ObjectType, \ - template class ArrayType, \ - class StringType, class BooleanType, class NumberIntegerType, \ - class NumberUnsignedType, class NumberFloatType, \ - template class AllocatorType, \ - template class JSONSerializer, \ - class BinaryType> - -#define NLOHMANN_BASIC_JSON_TPL \ - basic_json - -// Macros to simplify conversion from/to types - -#define NLOHMANN_JSON_EXPAND( x ) x -#define NLOHMANN_JSON_GET_MACRO(_1, _2, _3, _4, _5, _6, _7, _8, _9, _10, _11, _12, _13, _14, _15, _16, _17, _18, _19, _20, _21, _22, _23, _24, _25, _26, _27, _28, _29, _30, _31, _32, _33, _34, _35, _36, _37, _38, _39, _40, _41, _42, _43, _44, _45, _46, _47, _48, _49, _50, _51, _52, _53, _54, _55, _56, _57, _58, _59, _60, _61, _62, _63, _64, NAME,...) NAME -#define NLOHMANN_JSON_PASTE(...) NLOHMANN_JSON_EXPAND(NLOHMANN_JSON_GET_MACRO(__VA_ARGS__, \ - NLOHMANN_JSON_PASTE64, \ - NLOHMANN_JSON_PASTE63, \ - NLOHMANN_JSON_PASTE62, \ - NLOHMANN_JSON_PASTE61, \ - NLOHMANN_JSON_PASTE60, \ - NLOHMANN_JSON_PASTE59, \ - NLOHMANN_JSON_PASTE58, \ - NLOHMANN_JSON_PASTE57, \ - NLOHMANN_JSON_PASTE56, \ - NLOHMANN_JSON_PASTE55, \ - NLOHMANN_JSON_PASTE54, \ - NLOHMANN_JSON_PASTE53, \ - NLOHMANN_JSON_PASTE52, \ - NLOHMANN_JSON_PASTE51, \ - NLOHMANN_JSON_PASTE50, \ - NLOHMANN_JSON_PASTE49, \ - NLOHMANN_JSON_PASTE48, \ - NLOHMANN_JSON_PASTE47, \ - NLOHMANN_JSON_PASTE46, \ - NLOHMANN_JSON_PASTE45, \ - NLOHMANN_JSON_PASTE44, \ - NLOHMANN_JSON_PASTE43, \ - NLOHMANN_JSON_PASTE42, \ - NLOHMANN_JSON_PASTE41, \ - NLOHMANN_JSON_PASTE40, \ - NLOHMANN_JSON_PASTE39, \ - NLOHMANN_JSON_PASTE38, \ - NLOHMANN_JSON_PASTE37, \ - NLOHMANN_JSON_PASTE36, \ - NLOHMANN_JSON_PASTE35, \ - NLOHMANN_JSON_PASTE34, \ - NLOHMANN_JSON_PASTE33, \ - NLOHMANN_JSON_PASTE32, \ - NLOHMANN_JSON_PASTE31, \ - NLOHMANN_JSON_PASTE30, \ - NLOHMANN_JSON_PASTE29, \ - NLOHMANN_JSON_PASTE28, \ - NLOHMANN_JSON_PASTE27, \ - NLOHMANN_JSON_PASTE26, \ - NLOHMANN_JSON_PASTE25, \ - NLOHMANN_JSON_PASTE24, \ - NLOHMANN_JSON_PASTE23, \ - NLOHMANN_JSON_PASTE22, \ - NLOHMANN_JSON_PASTE21, \ - NLOHMANN_JSON_PASTE20, \ - NLOHMANN_JSON_PASTE19, \ - NLOHMANN_JSON_PASTE18, \ - NLOHMANN_JSON_PASTE17, \ - NLOHMANN_JSON_PASTE16, \ - NLOHMANN_JSON_PASTE15, \ - NLOHMANN_JSON_PASTE14, \ - NLOHMANN_JSON_PASTE13, \ - NLOHMANN_JSON_PASTE12, \ - NLOHMANN_JSON_PASTE11, \ - NLOHMANN_JSON_PASTE10, \ - NLOHMANN_JSON_PASTE9, \ - NLOHMANN_JSON_PASTE8, \ - NLOHMANN_JSON_PASTE7, \ - NLOHMANN_JSON_PASTE6, \ - NLOHMANN_JSON_PASTE5, \ - NLOHMANN_JSON_PASTE4, \ - NLOHMANN_JSON_PASTE3, \ - NLOHMANN_JSON_PASTE2, \ - NLOHMANN_JSON_PASTE1)(__VA_ARGS__)) -#define NLOHMANN_JSON_PASTE2(func, v1) func(v1) -#define NLOHMANN_JSON_PASTE3(func, v1, v2) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE2(func, v2) -#define NLOHMANN_JSON_PASTE4(func, v1, v2, v3) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE3(func, v2, v3) -#define NLOHMANN_JSON_PASTE5(func, v1, v2, v3, v4) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE4(func, v2, v3, v4) -#define NLOHMANN_JSON_PASTE6(func, v1, v2, v3, v4, v5) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE5(func, v2, v3, v4, v5) -#define NLOHMANN_JSON_PASTE7(func, v1, v2, v3, v4, v5, v6) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE6(func, v2, v3, v4, v5, v6) -#define NLOHMANN_JSON_PASTE8(func, v1, v2, v3, v4, v5, v6, v7) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE7(func, v2, v3, v4, v5, v6, v7) -#define NLOHMANN_JSON_PASTE9(func, v1, v2, v3, v4, v5, v6, v7, v8) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE8(func, v2, v3, v4, v5, v6, v7, v8) -#define NLOHMANN_JSON_PASTE10(func, v1, v2, v3, v4, v5, v6, v7, v8, v9) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE9(func, v2, v3, v4, v5, v6, v7, v8, v9) -#define NLOHMANN_JSON_PASTE11(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE10(func, v2, v3, v4, v5, v6, v7, v8, v9, v10) -#define NLOHMANN_JSON_PASTE12(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE11(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11) -#define NLOHMANN_JSON_PASTE13(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE12(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12) -#define NLOHMANN_JSON_PASTE14(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE13(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13) -#define NLOHMANN_JSON_PASTE15(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE14(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14) -#define NLOHMANN_JSON_PASTE16(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE15(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15) -#define NLOHMANN_JSON_PASTE17(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE16(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16) -#define NLOHMANN_JSON_PASTE18(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE17(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17) -#define NLOHMANN_JSON_PASTE19(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE18(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18) -#define NLOHMANN_JSON_PASTE20(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE19(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19) -#define NLOHMANN_JSON_PASTE21(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE20(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20) -#define NLOHMANN_JSON_PASTE22(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE21(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21) -#define NLOHMANN_JSON_PASTE23(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE22(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22) -#define NLOHMANN_JSON_PASTE24(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE23(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23) -#define NLOHMANN_JSON_PASTE25(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE24(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24) -#define NLOHMANN_JSON_PASTE26(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE25(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25) -#define NLOHMANN_JSON_PASTE27(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE26(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26) -#define NLOHMANN_JSON_PASTE28(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE27(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27) -#define NLOHMANN_JSON_PASTE29(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE28(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28) -#define NLOHMANN_JSON_PASTE30(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE29(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29) -#define NLOHMANN_JSON_PASTE31(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE30(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30) -#define NLOHMANN_JSON_PASTE32(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE31(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31) -#define NLOHMANN_JSON_PASTE33(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE32(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32) -#define NLOHMANN_JSON_PASTE34(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE33(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33) -#define NLOHMANN_JSON_PASTE35(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE34(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34) -#define NLOHMANN_JSON_PASTE36(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE35(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35) -#define NLOHMANN_JSON_PASTE37(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE36(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36) -#define NLOHMANN_JSON_PASTE38(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE37(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37) -#define NLOHMANN_JSON_PASTE39(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE38(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38) -#define NLOHMANN_JSON_PASTE40(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE39(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39) -#define NLOHMANN_JSON_PASTE41(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE40(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40) -#define NLOHMANN_JSON_PASTE42(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE41(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41) -#define NLOHMANN_JSON_PASTE43(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE42(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42) -#define NLOHMANN_JSON_PASTE44(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE43(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43) -#define NLOHMANN_JSON_PASTE45(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE44(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44) -#define NLOHMANN_JSON_PASTE46(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE45(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45) -#define NLOHMANN_JSON_PASTE47(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE46(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46) -#define NLOHMANN_JSON_PASTE48(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE47(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47) -#define NLOHMANN_JSON_PASTE49(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE48(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48) -#define NLOHMANN_JSON_PASTE50(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE49(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49) -#define NLOHMANN_JSON_PASTE51(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE50(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50) -#define NLOHMANN_JSON_PASTE52(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE51(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51) -#define NLOHMANN_JSON_PASTE53(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE52(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52) -#define NLOHMANN_JSON_PASTE54(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE53(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53) -#define NLOHMANN_JSON_PASTE55(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE54(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54) -#define NLOHMANN_JSON_PASTE56(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE55(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55) -#define NLOHMANN_JSON_PASTE57(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55, v56) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE56(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55, v56) -#define NLOHMANN_JSON_PASTE58(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55, v56, v57) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE57(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55, v56, v57) -#define NLOHMANN_JSON_PASTE59(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55, v56, v57, v58) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE58(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55, v56, v57, v58) -#define NLOHMANN_JSON_PASTE60(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55, v56, v57, v58, v59) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE59(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55, v56, v57, v58, v59) -#define NLOHMANN_JSON_PASTE61(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55, v56, v57, v58, v59, v60) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE60(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55, v56, v57, v58, v59, v60) -#define NLOHMANN_JSON_PASTE62(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55, v56, v57, v58, v59, v60, v61) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE61(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55, v56, v57, v58, v59, v60, v61) -#define NLOHMANN_JSON_PASTE63(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55, v56, v57, v58, v59, v60, v61, v62) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE62(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55, v56, v57, v58, v59, v60, v61, v62) -#define NLOHMANN_JSON_PASTE64(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55, v56, v57, v58, v59, v60, v61, v62, v63) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE63(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55, v56, v57, v58, v59, v60, v61, v62, v63) - -#define NLOHMANN_JSON_TO(v1) nlohmann_json_j[#v1] = nlohmann_json_t.v1; -#define NLOHMANN_JSON_FROM(v1) nlohmann_json_j.at(#v1).get_to(nlohmann_json_t.v1); - -/*! -@brief macro -@def NLOHMANN_DEFINE_TYPE_INTRUSIVE -@since version 3.9.0 -*/ -#define NLOHMANN_DEFINE_TYPE_INTRUSIVE(Type, ...) \ - friend void to_json(nlohmann::json& nlohmann_json_j, const Type& nlohmann_json_t) { NLOHMANN_JSON_EXPAND(NLOHMANN_JSON_PASTE(NLOHMANN_JSON_TO, __VA_ARGS__)) } \ - friend void from_json(const nlohmann::json& nlohmann_json_j, Type& nlohmann_json_t) { NLOHMANN_JSON_EXPAND(NLOHMANN_JSON_PASTE(NLOHMANN_JSON_FROM, __VA_ARGS__)) } - -/*! -@brief macro -@def NLOHMANN_DEFINE_TYPE_NON_INTRUSIVE -@since version 3.9.0 -*/ -#define NLOHMANN_DEFINE_TYPE_NON_INTRUSIVE(Type, ...) \ - inline void to_json(nlohmann::json& nlohmann_json_j, const Type& nlohmann_json_t) { NLOHMANN_JSON_EXPAND(NLOHMANN_JSON_PASTE(NLOHMANN_JSON_TO, __VA_ARGS__)) } \ - inline void from_json(const nlohmann::json& nlohmann_json_j, Type& nlohmann_json_t) { NLOHMANN_JSON_EXPAND(NLOHMANN_JSON_PASTE(NLOHMANN_JSON_FROM, __VA_ARGS__)) } - -#ifndef JSON_USE_IMPLICIT_CONVERSIONS - #define JSON_USE_IMPLICIT_CONVERSIONS 1 -#endif - -#if JSON_USE_IMPLICIT_CONVERSIONS - #define JSON_EXPLICIT -#else - #define JSON_EXPLICIT explicit -#endif - - -namespace nlohmann -{ -namespace detail -{ -//////////////// -// exceptions // -//////////////// - -/*! -@brief general exception of the @ref basic_json class - -This class is an extension of `std::exception` objects with a member @a id for -exception ids. It is used as the base class for all exceptions thrown by the -@ref basic_json class. This class can hence be used as "wildcard" to catch -exceptions. - -Subclasses: -- @ref parse_error for exceptions indicating a parse error -- @ref invalid_iterator for exceptions indicating errors with iterators -- @ref type_error for exceptions indicating executing a member function with - a wrong type -- @ref out_of_range for exceptions indicating access out of the defined range -- @ref other_error for exceptions indicating other library errors - -@internal -@note To have nothrow-copy-constructible exceptions, we internally use - `std::runtime_error` which can cope with arbitrary-length error messages. - Intermediate strings are built with static functions and then passed to - the actual constructor. -@endinternal - -@liveexample{The following code shows how arbitrary library exceptions can be -caught.,exception} - -@since version 3.0.0 -*/ -class exception : public std::exception -{ - public: - /// returns the explanatory string - JSON_HEDLEY_RETURNS_NON_NULL - const char* what() const noexcept override - { - return m.what(); - } - - /// the id of the exception - const int id; - - protected: - JSON_HEDLEY_NON_NULL(3) - exception(int id_, const char* what_arg) : id(id_), m(what_arg) {} - - static std::string name(const std::string& ename, int id_) - { - return "[json.exception." + ename + "." + std::to_string(id_) + "] "; - } - - private: - /// an exception object as storage for error messages - std::runtime_error m; -}; - -/*! -@brief exception indicating a parse error - -This exception is thrown by the library when a parse error occurs. Parse errors -can occur during the deserialization of JSON text, CBOR, MessagePack, as well -as when using JSON Patch. - -Member @a byte holds the byte index of the last read character in the input -file. - -Exceptions have ids 1xx. - -name / id | example message | description ------------------------------- | --------------- | ------------------------- -json.exception.parse_error.101 | parse error at 2: unexpected end of input; expected string literal | This error indicates a syntax error while deserializing a JSON text. The error message describes that an unexpected token (character) was encountered, and the member @a byte indicates the error position. -json.exception.parse_error.102 | parse error at 14: missing or wrong low surrogate | JSON uses the `\uxxxx` format to describe Unicode characters. Code points above above 0xFFFF are split into two `\uxxxx` entries ("surrogate pairs"). This error indicates that the surrogate pair is incomplete or contains an invalid code point. -json.exception.parse_error.103 | parse error: code points above 0x10FFFF are invalid | Unicode supports code points up to 0x10FFFF. Code points above 0x10FFFF are invalid. -json.exception.parse_error.104 | parse error: JSON patch must be an array of objects | [RFC 6902](https://tools.ietf.org/html/rfc6902) requires a JSON Patch document to be a JSON document that represents an array of objects. -json.exception.parse_error.105 | parse error: operation must have string member 'op' | An operation of a JSON Patch document must contain exactly one "op" member, whose value indicates the operation to perform. Its value must be one of "add", "remove", "replace", "move", "copy", or "test"; other values are errors. -json.exception.parse_error.106 | parse error: array index '01' must not begin with '0' | An array index in a JSON Pointer ([RFC 6901](https://tools.ietf.org/html/rfc6901)) may be `0` or any number without a leading `0`. -json.exception.parse_error.107 | parse error: JSON pointer must be empty or begin with '/' - was: 'foo' | A JSON Pointer must be a Unicode string containing a sequence of zero or more reference tokens, each prefixed by a `/` character. -json.exception.parse_error.108 | parse error: escape character '~' must be followed with '0' or '1' | In a JSON Pointer, only `~0` and `~1` are valid escape sequences. -json.exception.parse_error.109 | parse error: array index 'one' is not a number | A JSON Pointer array index must be a number. -json.exception.parse_error.110 | parse error at 1: cannot read 2 bytes from vector | When parsing CBOR or MessagePack, the byte vector ends before the complete value has been read. -json.exception.parse_error.112 | parse error at 1: error reading CBOR; last byte: 0xF8 | Not all types of CBOR or MessagePack are supported. This exception occurs if an unsupported byte was read. -json.exception.parse_error.113 | parse error at 2: expected a CBOR string; last byte: 0x98 | While parsing a map key, a value that is not a string has been read. -json.exception.parse_error.114 | parse error: Unsupported BSON record type 0x0F | The parsing of the corresponding BSON record type is not implemented (yet). -json.exception.parse_error.115 | parse error at byte 5: syntax error while parsing UBJSON high-precision number: invalid number text: 1A | A UBJSON high-precision number could not be parsed. - -@note For an input with n bytes, 1 is the index of the first character and n+1 - is the index of the terminating null byte or the end of file. This also - holds true when reading a byte vector (CBOR or MessagePack). - -@liveexample{The following code shows how a `parse_error` exception can be -caught.,parse_error} - -@sa - @ref exception for the base class of the library exceptions -@sa - @ref invalid_iterator for exceptions indicating errors with iterators -@sa - @ref type_error for exceptions indicating executing a member function with - a wrong type -@sa - @ref out_of_range for exceptions indicating access out of the defined range -@sa - @ref other_error for exceptions indicating other library errors - -@since version 3.0.0 -*/ -class parse_error : public exception -{ - public: - /*! - @brief create a parse error exception - @param[in] id_ the id of the exception - @param[in] pos the position where the error occurred (or with - chars_read_total=0 if the position cannot be - determined) - @param[in] what_arg the explanatory string - @return parse_error object - */ - static parse_error create(int id_, const position_t& pos, const std::string& what_arg) - { - std::string w = exception::name("parse_error", id_) + "parse error" + - position_string(pos) + ": " + what_arg; - return parse_error(id_, pos.chars_read_total, w.c_str()); - } - - static parse_error create(int id_, std::size_t byte_, const std::string& what_arg) - { - std::string w = exception::name("parse_error", id_) + "parse error" + - (byte_ != 0 ? (" at byte " + std::to_string(byte_)) : "") + - ": " + what_arg; - return parse_error(id_, byte_, w.c_str()); - } - - /*! - @brief byte index of the parse error - - The byte index of the last read character in the input file. - - @note For an input with n bytes, 1 is the index of the first character and - n+1 is the index of the terminating null byte or the end of file. - This also holds true when reading a byte vector (CBOR or MessagePack). - */ - const std::size_t byte; - - private: - parse_error(int id_, std::size_t byte_, const char* what_arg) - : exception(id_, what_arg), byte(byte_) {} - - static std::string position_string(const position_t& pos) - { - return " at line " + std::to_string(pos.lines_read + 1) + - ", column " + std::to_string(pos.chars_read_current_line); - } -}; - -/*! -@brief exception indicating errors with iterators - -This exception is thrown if iterators passed to a library function do not match -the expected semantics. - -Exceptions have ids 2xx. - -name / id | example message | description ------------------------------------ | --------------- | ------------------------- -json.exception.invalid_iterator.201 | iterators are not compatible | The iterators passed to constructor @ref basic_json(InputIT first, InputIT last) are not compatible, meaning they do not belong to the same container. Therefore, the range (@a first, @a last) is invalid. -json.exception.invalid_iterator.202 | iterator does not fit current value | In an erase or insert function, the passed iterator @a pos does not belong to the JSON value for which the function was called. It hence does not define a valid position for the deletion/insertion. -json.exception.invalid_iterator.203 | iterators do not fit current value | Either iterator passed to function @ref erase(IteratorType first, IteratorType last) does not belong to the JSON value from which values shall be erased. It hence does not define a valid range to delete values from. -json.exception.invalid_iterator.204 | iterators out of range | When an iterator range for a primitive type (number, boolean, or string) is passed to a constructor or an erase function, this range has to be exactly (@ref begin(), @ref end()), because this is the only way the single stored value is expressed. All other ranges are invalid. -json.exception.invalid_iterator.205 | iterator out of range | When an iterator for a primitive type (number, boolean, or string) is passed to an erase function, the iterator has to be the @ref begin() iterator, because it is the only way to address the stored value. All other iterators are invalid. -json.exception.invalid_iterator.206 | cannot construct with iterators from null | The iterators passed to constructor @ref basic_json(InputIT first, InputIT last) belong to a JSON null value and hence to not define a valid range. -json.exception.invalid_iterator.207 | cannot use key() for non-object iterators | The key() member function can only be used on iterators belonging to a JSON object, because other types do not have a concept of a key. -json.exception.invalid_iterator.208 | cannot use operator[] for object iterators | The operator[] to specify a concrete offset cannot be used on iterators belonging to a JSON object, because JSON objects are unordered. -json.exception.invalid_iterator.209 | cannot use offsets with object iterators | The offset operators (+, -, +=, -=) cannot be used on iterators belonging to a JSON object, because JSON objects are unordered. -json.exception.invalid_iterator.210 | iterators do not fit | The iterator range passed to the insert function are not compatible, meaning they do not belong to the same container. Therefore, the range (@a first, @a last) is invalid. -json.exception.invalid_iterator.211 | passed iterators may not belong to container | The iterator range passed to the insert function must not be a subrange of the container to insert to. -json.exception.invalid_iterator.212 | cannot compare iterators of different containers | When two iterators are compared, they must belong to the same container. -json.exception.invalid_iterator.213 | cannot compare order of object iterators | The order of object iterators cannot be compared, because JSON objects are unordered. -json.exception.invalid_iterator.214 | cannot get value | Cannot get value for iterator: Either the iterator belongs to a null value or it is an iterator to a primitive type (number, boolean, or string), but the iterator is different to @ref begin(). - -@liveexample{The following code shows how an `invalid_iterator` exception can be -caught.,invalid_iterator} - -@sa - @ref exception for the base class of the library exceptions -@sa - @ref parse_error for exceptions indicating a parse error -@sa - @ref type_error for exceptions indicating executing a member function with - a wrong type -@sa - @ref out_of_range for exceptions indicating access out of the defined range -@sa - @ref other_error for exceptions indicating other library errors - -@since version 3.0.0 -*/ -class invalid_iterator : public exception -{ - public: - static invalid_iterator create(int id_, const std::string& what_arg) - { - std::string w = exception::name("invalid_iterator", id_) + what_arg; - return invalid_iterator(id_, w.c_str()); - } - - private: - JSON_HEDLEY_NON_NULL(3) - invalid_iterator(int id_, const char* what_arg) - : exception(id_, what_arg) {} -}; - -/*! -@brief exception indicating executing a member function with a wrong type - -This exception is thrown in case of a type error; that is, a library function is -executed on a JSON value whose type does not match the expected semantics. - -Exceptions have ids 3xx. - -name / id | example message | description ------------------------------ | --------------- | ------------------------- -json.exception.type_error.301 | cannot create object from initializer list | To create an object from an initializer list, the initializer list must consist only of a list of pairs whose first element is a string. When this constraint is violated, an array is created instead. -json.exception.type_error.302 | type must be object, but is array | During implicit or explicit value conversion, the JSON type must be compatible to the target type. For instance, a JSON string can only be converted into string types, but not into numbers or boolean types. -json.exception.type_error.303 | incompatible ReferenceType for get_ref, actual type is object | To retrieve a reference to a value stored in a @ref basic_json object with @ref get_ref, the type of the reference must match the value type. For instance, for a JSON array, the @a ReferenceType must be @ref array_t &. -json.exception.type_error.304 | cannot use at() with string | The @ref at() member functions can only be executed for certain JSON types. -json.exception.type_error.305 | cannot use operator[] with string | The @ref operator[] member functions can only be executed for certain JSON types. -json.exception.type_error.306 | cannot use value() with string | The @ref value() member functions can only be executed for certain JSON types. -json.exception.type_error.307 | cannot use erase() with string | The @ref erase() member functions can only be executed for certain JSON types. -json.exception.type_error.308 | cannot use push_back() with string | The @ref push_back() and @ref operator+= member functions can only be executed for certain JSON types. -json.exception.type_error.309 | cannot use insert() with | The @ref insert() member functions can only be executed for certain JSON types. -json.exception.type_error.310 | cannot use swap() with number | The @ref swap() member functions can only be executed for certain JSON types. -json.exception.type_error.311 | cannot use emplace_back() with string | The @ref emplace_back() member function can only be executed for certain JSON types. -json.exception.type_error.312 | cannot use update() with string | The @ref update() member functions can only be executed for certain JSON types. -json.exception.type_error.313 | invalid value to unflatten | The @ref unflatten function converts an object whose keys are JSON Pointers back into an arbitrary nested JSON value. The JSON Pointers must not overlap, because then the resulting value would not be well defined. -json.exception.type_error.314 | only objects can be unflattened | The @ref unflatten function only works for an object whose keys are JSON Pointers. -json.exception.type_error.315 | values in object must be primitive | The @ref unflatten function only works for an object whose keys are JSON Pointers and whose values are primitive. -json.exception.type_error.316 | invalid UTF-8 byte at index 10: 0x7E | The @ref dump function only works with UTF-8 encoded strings; that is, if you assign a `std::string` to a JSON value, make sure it is UTF-8 encoded. | -json.exception.type_error.317 | JSON value cannot be serialized to requested format | The dynamic type of the object cannot be represented in the requested serialization format (e.g. a raw `true` or `null` JSON object cannot be serialized to BSON) | - -@liveexample{The following code shows how a `type_error` exception can be -caught.,type_error} - -@sa - @ref exception for the base class of the library exceptions -@sa - @ref parse_error for exceptions indicating a parse error -@sa - @ref invalid_iterator for exceptions indicating errors with iterators -@sa - @ref out_of_range for exceptions indicating access out of the defined range -@sa - @ref other_error for exceptions indicating other library errors - -@since version 3.0.0 -*/ -class type_error : public exception -{ - public: - static type_error create(int id_, const std::string& what_arg) - { - std::string w = exception::name("type_error", id_) + what_arg; - return type_error(id_, w.c_str()); - } - - private: - JSON_HEDLEY_NON_NULL(3) - type_error(int id_, const char* what_arg) : exception(id_, what_arg) {} -}; - -/*! -@brief exception indicating access out of the defined range - -This exception is thrown in case a library function is called on an input -parameter that exceeds the expected range, for instance in case of array -indices or nonexisting object keys. - -Exceptions have ids 4xx. - -name / id | example message | description -------------------------------- | --------------- | ------------------------- -json.exception.out_of_range.401 | array index 3 is out of range | The provided array index @a i is larger than @a size-1. -json.exception.out_of_range.402 | array index '-' (3) is out of range | The special array index `-` in a JSON Pointer never describes a valid element of the array, but the index past the end. That is, it can only be used to add elements at this position, but not to read it. -json.exception.out_of_range.403 | key 'foo' not found | The provided key was not found in the JSON object. -json.exception.out_of_range.404 | unresolved reference token 'foo' | A reference token in a JSON Pointer could not be resolved. -json.exception.out_of_range.405 | JSON pointer has no parent | The JSON Patch operations 'remove' and 'add' can not be applied to the root element of the JSON value. -json.exception.out_of_range.406 | number overflow parsing '10E1000' | A parsed number could not be stored as without changing it to NaN or INF. -json.exception.out_of_range.407 | number overflow serializing '9223372036854775808' | UBJSON and BSON only support integer numbers up to 9223372036854775807. (until version 3.8.0) | -json.exception.out_of_range.408 | excessive array size: 8658170730974374167 | The size (following `#`) of an UBJSON array or object exceeds the maximal capacity. | -json.exception.out_of_range.409 | BSON key cannot contain code point U+0000 (at byte 2) | Key identifiers to be serialized to BSON cannot contain code point U+0000, since the key is stored as zero-terminated c-string | - -@liveexample{The following code shows how an `out_of_range` exception can be -caught.,out_of_range} - -@sa - @ref exception for the base class of the library exceptions -@sa - @ref parse_error for exceptions indicating a parse error -@sa - @ref invalid_iterator for exceptions indicating errors with iterators -@sa - @ref type_error for exceptions indicating executing a member function with - a wrong type -@sa - @ref other_error for exceptions indicating other library errors - -@since version 3.0.0 -*/ -class out_of_range : public exception -{ - public: - static out_of_range create(int id_, const std::string& what_arg) - { - std::string w = exception::name("out_of_range", id_) + what_arg; - return out_of_range(id_, w.c_str()); - } - - private: - JSON_HEDLEY_NON_NULL(3) - out_of_range(int id_, const char* what_arg) : exception(id_, what_arg) {} -}; - -/*! -@brief exception indicating other library errors - -This exception is thrown in case of errors that cannot be classified with the -other exception types. - -Exceptions have ids 5xx. - -name / id | example message | description ------------------------------- | --------------- | ------------------------- -json.exception.other_error.501 | unsuccessful: {"op":"test","path":"/baz", "value":"bar"} | A JSON Patch operation 'test' failed. The unsuccessful operation is also printed. - -@sa - @ref exception for the base class of the library exceptions -@sa - @ref parse_error for exceptions indicating a parse error -@sa - @ref invalid_iterator for exceptions indicating errors with iterators -@sa - @ref type_error for exceptions indicating executing a member function with - a wrong type -@sa - @ref out_of_range for exceptions indicating access out of the defined range - -@liveexample{The following code shows how an `other_error` exception can be -caught.,other_error} - -@since version 3.0.0 -*/ -class other_error : public exception -{ - public: - static other_error create(int id_, const std::string& what_arg) - { - std::string w = exception::name("other_error", id_) + what_arg; - return other_error(id_, w.c_str()); - } - - private: - JSON_HEDLEY_NON_NULL(3) - other_error(int id_, const char* what_arg) : exception(id_, what_arg) {} -}; -} // namespace detail -} // namespace nlohmann - -// #include - -// #include - - -#include // size_t -#include // conditional, enable_if, false_type, integral_constant, is_constructible, is_integral, is_same, remove_cv, remove_reference, true_type - -namespace nlohmann -{ -namespace detail -{ -// alias templates to reduce boilerplate -template -using enable_if_t = typename std::enable_if::type; - -template -using uncvref_t = typename std::remove_cv::type>::type; - -// implementation of C++14 index_sequence and affiliates -// source: https://stackoverflow.com/a/32223343 -template -struct index_sequence -{ - using type = index_sequence; - using value_type = std::size_t; - static constexpr std::size_t size() noexcept - { - return sizeof...(Ints); - } -}; - -template -struct merge_and_renumber; - -template -struct merge_and_renumber, index_sequence> - : index_sequence < I1..., (sizeof...(I1) + I2)... > {}; - -template -struct make_index_sequence - : merge_and_renumber < typename make_index_sequence < N / 2 >::type, - typename make_index_sequence < N - N / 2 >::type > {}; - -template<> struct make_index_sequence<0> : index_sequence<> {}; -template<> struct make_index_sequence<1> : index_sequence<0> {}; - -template -using index_sequence_for = make_index_sequence; - -// dispatch utility (taken from ranges-v3) -template struct priority_tag : priority_tag < N - 1 > {}; -template<> struct priority_tag<0> {}; - -// taken from ranges-v3 -template -struct static_const -{ - static constexpr T value{}; -}; - -template -constexpr T static_const::value; -} // namespace detail -} // namespace nlohmann - -// #include - - -#include // numeric_limits -#include // false_type, is_constructible, is_integral, is_same, true_type -#include // declval - -// #include - - -#include // random_access_iterator_tag - -// #include - - -namespace nlohmann -{ -namespace detail -{ -template struct make_void -{ - using type = void; -}; -template using void_t = typename make_void::type; -} // namespace detail -} // namespace nlohmann - -// #include - - -namespace nlohmann -{ -namespace detail -{ -template -struct iterator_types {}; - -template -struct iterator_types < - It, - void_t> -{ - using difference_type = typename It::difference_type; - using value_type = typename It::value_type; - using pointer = typename It::pointer; - using reference = typename It::reference; - using iterator_category = typename It::iterator_category; -}; - -// This is required as some compilers implement std::iterator_traits in a way that -// doesn't work with SFINAE. See https://github.com/nlohmann/json/issues/1341. -template -struct iterator_traits -{ -}; - -template -struct iterator_traits < T, enable_if_t < !std::is_pointer::value >> - : iterator_types -{ -}; - -template -struct iterator_traits::value>> -{ - using iterator_category = std::random_access_iterator_tag; - using value_type = T; - using difference_type = ptrdiff_t; - using pointer = T*; - using reference = T&; -}; -} // namespace detail -} // namespace nlohmann - -// #include - -// #include - -// #include - - -#include - -// #include - - -// https://en.cppreference.com/w/cpp/experimental/is_detected -namespace nlohmann -{ -namespace detail -{ -struct nonesuch -{ - nonesuch() = delete; - ~nonesuch() = delete; - nonesuch(nonesuch const&) = delete; - nonesuch(nonesuch const&&) = delete; - void operator=(nonesuch const&) = delete; - void operator=(nonesuch&&) = delete; -}; - -template class Op, - class... Args> -struct detector -{ - using value_t = std::false_type; - using type = Default; -}; - -template class Op, class... Args> -struct detector>, Op, Args...> -{ - using value_t = std::true_type; - using type = Op; -}; - -template class Op, class... Args> -using is_detected = typename detector::value_t; - -template class Op, class... Args> -using detected_t = typename detector::type; - -template class Op, class... Args> -using detected_or = detector; - -template class Op, class... Args> -using detected_or_t = typename detected_or::type; - -template class Op, class... Args> -using is_detected_exact = std::is_same>; - -template class Op, class... Args> -using is_detected_convertible = - std::is_convertible, To>; -} // namespace detail -} // namespace nlohmann - -// #include -#ifndef INCLUDE_NLOHMANN_JSON_FWD_HPP_ -#define INCLUDE_NLOHMANN_JSON_FWD_HPP_ - -#include // int64_t, uint64_t -#include // map -#include // allocator -#include // string -#include // vector - -/*! -@brief namespace for Niels Lohmann -@see https://github.com/nlohmann -@since version 1.0.0 -*/ -namespace nlohmann -{ -/*! -@brief default JSONSerializer template argument - -This serializer ignores the template arguments and uses ADL -([argument-dependent lookup](https://en.cppreference.com/w/cpp/language/adl)) -for serialization. -*/ -template -struct adl_serializer; - -template class ObjectType = - std::map, - template class ArrayType = std::vector, - class StringType = std::string, class BooleanType = bool, - class NumberIntegerType = std::int64_t, - class NumberUnsignedType = std::uint64_t, - class NumberFloatType = double, - template class AllocatorType = std::allocator, - template class JSONSerializer = - adl_serializer, - class BinaryType = std::vector> -class basic_json; - -/*! -@brief JSON Pointer - -A JSON pointer defines a string syntax for identifying a specific value -within a JSON document. It can be used with functions `at` and -`operator[]`. Furthermore, JSON pointers are the base for JSON patches. - -@sa [RFC 6901](https://tools.ietf.org/html/rfc6901) - -@since version 2.0.0 -*/ -template -class json_pointer; - -/*! -@brief default JSON class - -This type is the default specialization of the @ref basic_json class which -uses the standard template types. - -@since version 1.0.0 -*/ -using json = basic_json<>; - -template -struct ordered_map; - -/*! -@brief ordered JSON class - -This type preserves the insertion order of object keys. - -@since version 3.9.0 -*/ -using ordered_json = basic_json; - -} // namespace nlohmann - -#endif // INCLUDE_NLOHMANN_JSON_FWD_HPP_ - - -namespace nlohmann -{ -/*! -@brief detail namespace with internal helper functions - -This namespace collects functions that should not be exposed, -implementations of some @ref basic_json methods, and meta-programming helpers. - -@since version 2.1.0 -*/ -namespace detail -{ -///////////// -// helpers // -///////////// - -// Note to maintainers: -// -// Every trait in this file expects a non CV-qualified type. -// The only exceptions are in the 'aliases for detected' section -// (i.e. those of the form: decltype(T::member_function(std::declval()))) -// -// In this case, T has to be properly CV-qualified to constraint the function arguments -// (e.g. to_json(BasicJsonType&, const T&)) - -template struct is_basic_json : std::false_type {}; - -NLOHMANN_BASIC_JSON_TPL_DECLARATION -struct is_basic_json : std::true_type {}; - -////////////////////// -// json_ref helpers // -////////////////////// - -template -class json_ref; - -template -struct is_json_ref : std::false_type {}; - -template -struct is_json_ref> : std::true_type {}; - -////////////////////////// -// aliases for detected // -////////////////////////// - -template -using mapped_type_t = typename T::mapped_type; - -template -using key_type_t = typename T::key_type; - -template -using value_type_t = typename T::value_type; - -template -using difference_type_t = typename T::difference_type; - -template -using pointer_t = typename T::pointer; - -template -using reference_t = typename T::reference; - -template -using iterator_category_t = typename T::iterator_category; - -template -using iterator_t = typename T::iterator; - -template -using to_json_function = decltype(T::to_json(std::declval()...)); - -template -using from_json_function = decltype(T::from_json(std::declval()...)); - -template -using get_template_function = decltype(std::declval().template get()); - -// trait checking if JSONSerializer::from_json(json const&, udt&) exists -template -struct has_from_json : std::false_type {}; - -// trait checking if j.get is valid -// use this trait instead of std::is_constructible or std::is_convertible, -// both rely on, or make use of implicit conversions, and thus fail when T -// has several constructors/operator= (see https://github.com/nlohmann/json/issues/958) -template -struct is_getable -{ - static constexpr bool value = is_detected::value; -}; - -template -struct has_from_json < BasicJsonType, T, - enable_if_t < !is_basic_json::value >> -{ - using serializer = typename BasicJsonType::template json_serializer; - - static constexpr bool value = - is_detected_exact::value; -}; - -// This trait checks if JSONSerializer::from_json(json const&) exists -// this overload is used for non-default-constructible user-defined-types -template -struct has_non_default_from_json : std::false_type {}; - -template -struct has_non_default_from_json < BasicJsonType, T, enable_if_t < !is_basic_json::value >> -{ - using serializer = typename BasicJsonType::template json_serializer; - - static constexpr bool value = - is_detected_exact::value; -}; - -// This trait checks if BasicJsonType::json_serializer::to_json exists -// Do not evaluate the trait when T is a basic_json type, to avoid template instantiation infinite recursion. -template -struct has_to_json : std::false_type {}; - -template -struct has_to_json < BasicJsonType, T, enable_if_t < !is_basic_json::value >> -{ - using serializer = typename BasicJsonType::template json_serializer; - - static constexpr bool value = - is_detected_exact::value; -}; - - -/////////////////// -// is_ functions // -/////////////////// - -template -struct is_iterator_traits : std::false_type {}; - -template -struct is_iterator_traits> -{ - private: - using traits = iterator_traits; - - public: - static constexpr auto value = - is_detected::value && - is_detected::value && - is_detected::value && - is_detected::value && - is_detected::value; -}; - -// source: https://stackoverflow.com/a/37193089/4116453 - -template -struct is_complete_type : std::false_type {}; - -template -struct is_complete_type : std::true_type {}; - -template -struct is_compatible_object_type_impl : std::false_type {}; - -template -struct is_compatible_object_type_impl < - BasicJsonType, CompatibleObjectType, - enable_if_t < is_detected::value&& - is_detected::value >> -{ - - using object_t = typename BasicJsonType::object_t; - - // macOS's is_constructible does not play well with nonesuch... - static constexpr bool value = - std::is_constructible::value && - std::is_constructible::value; -}; - -template -struct is_compatible_object_type - : is_compatible_object_type_impl {}; - -template -struct is_constructible_object_type_impl : std::false_type {}; - -template -struct is_constructible_object_type_impl < - BasicJsonType, ConstructibleObjectType, - enable_if_t < is_detected::value&& - is_detected::value >> -{ - using object_t = typename BasicJsonType::object_t; - - static constexpr bool value = - (std::is_default_constructible::value && - (std::is_move_assignable::value || - std::is_copy_assignable::value) && - (std::is_constructible::value && - std::is_same < - typename object_t::mapped_type, - typename ConstructibleObjectType::mapped_type >::value)) || - (has_from_json::value || - has_non_default_from_json < - BasicJsonType, - typename ConstructibleObjectType::mapped_type >::value); -}; - -template -struct is_constructible_object_type - : is_constructible_object_type_impl {}; - -template -struct is_compatible_string_type_impl : std::false_type {}; - -template -struct is_compatible_string_type_impl < - BasicJsonType, CompatibleStringType, - enable_if_t::value >> -{ - static constexpr auto value = - std::is_constructible::value; -}; - -template -struct is_compatible_string_type - : is_compatible_string_type_impl {}; - -template -struct is_constructible_string_type_impl : std::false_type {}; - -template -struct is_constructible_string_type_impl < - BasicJsonType, ConstructibleStringType, - enable_if_t::value >> -{ - static constexpr auto value = - std::is_constructible::value; -}; - -template -struct is_constructible_string_type - : is_constructible_string_type_impl {}; - -template -struct is_compatible_array_type_impl : std::false_type {}; - -template -struct is_compatible_array_type_impl < - BasicJsonType, CompatibleArrayType, - enable_if_t < is_detected::value&& - is_detected::value&& -// This is needed because json_reverse_iterator has a ::iterator type... -// Therefore it is detected as a CompatibleArrayType. -// The real fix would be to have an Iterable concept. - !is_iterator_traits < - iterator_traits>::value >> -{ - static constexpr bool value = - std::is_constructible::value; -}; - -template -struct is_compatible_array_type - : is_compatible_array_type_impl {}; - -template -struct is_constructible_array_type_impl : std::false_type {}; - -template -struct is_constructible_array_type_impl < - BasicJsonType, ConstructibleArrayType, - enable_if_t::value >> - : std::true_type {}; - -template -struct is_constructible_array_type_impl < - BasicJsonType, ConstructibleArrayType, - enable_if_t < !std::is_same::value&& - std::is_default_constructible::value&& -(std::is_move_assignable::value || - std::is_copy_assignable::value)&& -is_detected::value&& -is_detected::value&& -is_complete_type < -detected_t>::value >> -{ - static constexpr bool value = - // This is needed because json_reverse_iterator has a ::iterator type, - // furthermore, std::back_insert_iterator (and other iterators) have a - // base class `iterator`... Therefore it is detected as a - // ConstructibleArrayType. The real fix would be to have an Iterable - // concept. - !is_iterator_traits>::value && - - (std::is_same::value || - has_from_json::value || - has_non_default_from_json < - BasicJsonType, typename ConstructibleArrayType::value_type >::value); -}; - -template -struct is_constructible_array_type - : is_constructible_array_type_impl {}; - -template -struct is_compatible_integer_type_impl : std::false_type {}; - -template -struct is_compatible_integer_type_impl < - RealIntegerType, CompatibleNumberIntegerType, - enable_if_t < std::is_integral::value&& - std::is_integral::value&& - !std::is_same::value >> -{ - // is there an assert somewhere on overflows? - using RealLimits = std::numeric_limits; - using CompatibleLimits = std::numeric_limits; - - static constexpr auto value = - std::is_constructible::value && - CompatibleLimits::is_integer && - RealLimits::is_signed == CompatibleLimits::is_signed; -}; - -template -struct is_compatible_integer_type - : is_compatible_integer_type_impl {}; - -template -struct is_compatible_type_impl: std::false_type {}; - -template -struct is_compatible_type_impl < - BasicJsonType, CompatibleType, - enable_if_t::value >> -{ - static constexpr bool value = - has_to_json::value; -}; - -template -struct is_compatible_type - : is_compatible_type_impl {}; - -// https://en.cppreference.com/w/cpp/types/conjunction -template struct conjunction : std::true_type { }; -template struct conjunction : B1 { }; -template -struct conjunction -: std::conditional, B1>::type {}; - -template -struct is_constructible_tuple : std::false_type {}; - -template -struct is_constructible_tuple> : conjunction...> {}; -} // namespace detail -} // namespace nlohmann - -// #include - - -#include // array -#include // size_t -#include // uint8_t -#include // string - -namespace nlohmann -{ -namespace detail -{ -/////////////////////////// -// JSON type enumeration // -/////////////////////////// - -/*! -@brief the JSON type enumeration - -This enumeration collects the different JSON types. It is internally used to -distinguish the stored values, and the functions @ref basic_json::is_null(), -@ref basic_json::is_object(), @ref basic_json::is_array(), -@ref basic_json::is_string(), @ref basic_json::is_boolean(), -@ref basic_json::is_number() (with @ref basic_json::is_number_integer(), -@ref basic_json::is_number_unsigned(), and @ref basic_json::is_number_float()), -@ref basic_json::is_discarded(), @ref basic_json::is_primitive(), and -@ref basic_json::is_structured() rely on it. - -@note There are three enumeration entries (number_integer, number_unsigned, and -number_float), because the library distinguishes these three types for numbers: -@ref basic_json::number_unsigned_t is used for unsigned integers, -@ref basic_json::number_integer_t is used for signed integers, and -@ref basic_json::number_float_t is used for floating-point numbers or to -approximate integers which do not fit in the limits of their respective type. - -@sa @ref basic_json::basic_json(const value_t value_type) -- create a JSON -value with the default value for a given type - -@since version 1.0.0 -*/ -enum class value_t : std::uint8_t -{ - null, ///< null value - object, ///< object (unordered set of name/value pairs) - array, ///< array (ordered collection of values) - string, ///< string value - boolean, ///< boolean value - number_integer, ///< number value (signed integer) - number_unsigned, ///< number value (unsigned integer) - number_float, ///< number value (floating-point) - binary, ///< binary array (ordered collection of bytes) - discarded ///< discarded by the parser callback function -}; - -/*! -@brief comparison operator for JSON types - -Returns an ordering that is similar to Python: -- order: null < boolean < number < object < array < string < binary -- furthermore, each type is not smaller than itself -- discarded values are not comparable -- binary is represented as a b"" string in python and directly comparable to a - string; however, making a binary array directly comparable with a string would - be surprising behavior in a JSON file. - -@since version 1.0.0 -*/ -inline bool operator<(const value_t lhs, const value_t rhs) noexcept -{ - static constexpr std::array order = {{ - 0 /* null */, 3 /* object */, 4 /* array */, 5 /* string */, - 1 /* boolean */, 2 /* integer */, 2 /* unsigned */, 2 /* float */, - 6 /* binary */ - } - }; - - const auto l_index = static_cast(lhs); - const auto r_index = static_cast(rhs); - return l_index < order.size() && r_index < order.size() && order[l_index] < order[r_index]; -} -} // namespace detail -} // namespace nlohmann - - -namespace nlohmann -{ -namespace detail -{ -template -void from_json(const BasicJsonType& j, typename std::nullptr_t& n) -{ - if (JSON_HEDLEY_UNLIKELY(!j.is_null())) - { - JSON_THROW(type_error::create(302, "type must be null, but is " + std::string(j.type_name()))); - } - n = nullptr; -} - -// overloads for basic_json template parameters -template < typename BasicJsonType, typename ArithmeticType, - enable_if_t < std::is_arithmetic::value&& - !std::is_same::value, - int > = 0 > -void get_arithmetic_value(const BasicJsonType& j, ArithmeticType& val) -{ - switch (static_cast(j)) - { - case value_t::number_unsigned: - { - val = static_cast(*j.template get_ptr()); - break; - } - case value_t::number_integer: - { - val = static_cast(*j.template get_ptr()); - break; - } - case value_t::number_float: - { - val = static_cast(*j.template get_ptr()); - break; - } - - default: - JSON_THROW(type_error::create(302, "type must be number, but is " + std::string(j.type_name()))); - } -} - -template -void from_json(const BasicJsonType& j, typename BasicJsonType::boolean_t& b) -{ - if (JSON_HEDLEY_UNLIKELY(!j.is_boolean())) - { - JSON_THROW(type_error::create(302, "type must be boolean, but is " + std::string(j.type_name()))); - } - b = *j.template get_ptr(); -} - -template -void from_json(const BasicJsonType& j, typename BasicJsonType::string_t& s) -{ - if (JSON_HEDLEY_UNLIKELY(!j.is_string())) - { - JSON_THROW(type_error::create(302, "type must be string, but is " + std::string(j.type_name()))); - } - s = *j.template get_ptr(); -} - -template < - typename BasicJsonType, typename ConstructibleStringType, - enable_if_t < - is_constructible_string_type::value&& - !std::is_same::value, - int > = 0 > -void from_json(const BasicJsonType& j, ConstructibleStringType& s) -{ - if (JSON_HEDLEY_UNLIKELY(!j.is_string())) - { - JSON_THROW(type_error::create(302, "type must be string, but is " + std::string(j.type_name()))); - } - - s = *j.template get_ptr(); -} - -template -void from_json(const BasicJsonType& j, typename BasicJsonType::number_float_t& val) -{ - get_arithmetic_value(j, val); -} - -template -void from_json(const BasicJsonType& j, typename BasicJsonType::number_unsigned_t& val) -{ - get_arithmetic_value(j, val); -} - -template -void from_json(const BasicJsonType& j, typename BasicJsonType::number_integer_t& val) -{ - get_arithmetic_value(j, val); -} - -template::value, int> = 0> -void from_json(const BasicJsonType& j, EnumType& e) -{ - typename std::underlying_type::type val; - get_arithmetic_value(j, val); - e = static_cast(val); -} - -// forward_list doesn't have an insert method -template::value, int> = 0> -void from_json(const BasicJsonType& j, std::forward_list& l) -{ - if (JSON_HEDLEY_UNLIKELY(!j.is_array())) - { - JSON_THROW(type_error::create(302, "type must be array, but is " + std::string(j.type_name()))); - } - l.clear(); - std::transform(j.rbegin(), j.rend(), - std::front_inserter(l), [](const BasicJsonType & i) - { - return i.template get(); - }); -} - -// valarray doesn't have an insert method -template::value, int> = 0> -void from_json(const BasicJsonType& j, std::valarray& l) -{ - if (JSON_HEDLEY_UNLIKELY(!j.is_array())) - { - JSON_THROW(type_error::create(302, "type must be array, but is " + std::string(j.type_name()))); - } - l.resize(j.size()); - std::transform(j.begin(), j.end(), std::begin(l), - [](const BasicJsonType & elem) - { - return elem.template get(); - }); -} - -template -auto from_json(const BasicJsonType& j, T (&arr)[N]) --> decltype(j.template get(), void()) -{ - for (std::size_t i = 0; i < N; ++i) - { - arr[i] = j.at(i).template get(); - } -} - -template -void from_json_array_impl(const BasicJsonType& j, typename BasicJsonType::array_t& arr, priority_tag<3> /*unused*/) -{ - arr = *j.template get_ptr(); -} - -template -auto from_json_array_impl(const BasicJsonType& j, std::array& arr, - priority_tag<2> /*unused*/) --> decltype(j.template get(), void()) -{ - for (std::size_t i = 0; i < N; ++i) - { - arr[i] = j.at(i).template get(); - } -} - -template -auto from_json_array_impl(const BasicJsonType& j, ConstructibleArrayType& arr, priority_tag<1> /*unused*/) --> decltype( - arr.reserve(std::declval()), - j.template get(), - void()) -{ - using std::end; - - ConstructibleArrayType ret; - ret.reserve(j.size()); - std::transform(j.begin(), j.end(), - std::inserter(ret, end(ret)), [](const BasicJsonType & i) - { - // get() returns *this, this won't call a from_json - // method when value_type is BasicJsonType - return i.template get(); - }); - arr = std::move(ret); -} - -template -void from_json_array_impl(const BasicJsonType& j, ConstructibleArrayType& arr, - priority_tag<0> /*unused*/) -{ - using std::end; - - ConstructibleArrayType ret; - std::transform( - j.begin(), j.end(), std::inserter(ret, end(ret)), - [](const BasicJsonType & i) - { - // get() returns *this, this won't call a from_json - // method when value_type is BasicJsonType - return i.template get(); - }); - arr = std::move(ret); -} - -template < typename BasicJsonType, typename ConstructibleArrayType, - enable_if_t < - is_constructible_array_type::value&& - !is_constructible_object_type::value&& - !is_constructible_string_type::value&& - !std::is_same::value&& - !is_basic_json::value, - int > = 0 > -auto from_json(const BasicJsonType& j, ConstructibleArrayType& arr) --> decltype(from_json_array_impl(j, arr, priority_tag<3> {}), -j.template get(), -void()) -{ - if (JSON_HEDLEY_UNLIKELY(!j.is_array())) - { - JSON_THROW(type_error::create(302, "type must be array, but is " + - std::string(j.type_name()))); - } - - from_json_array_impl(j, arr, priority_tag<3> {}); -} - -template -void from_json(const BasicJsonType& j, typename BasicJsonType::binary_t& bin) -{ - if (JSON_HEDLEY_UNLIKELY(!j.is_binary())) - { - JSON_THROW(type_error::create(302, "type must be binary, but is " + std::string(j.type_name()))); - } - - bin = *j.template get_ptr(); -} - -template::value, int> = 0> -void from_json(const BasicJsonType& j, ConstructibleObjectType& obj) -{ - if (JSON_HEDLEY_UNLIKELY(!j.is_object())) - { - JSON_THROW(type_error::create(302, "type must be object, but is " + std::string(j.type_name()))); - } - - ConstructibleObjectType ret; - auto inner_object = j.template get_ptr(); - using value_type = typename ConstructibleObjectType::value_type; - std::transform( - inner_object->begin(), inner_object->end(), - std::inserter(ret, ret.begin()), - [](typename BasicJsonType::object_t::value_type const & p) - { - return value_type(p.first, p.second.template get()); - }); - obj = std::move(ret); -} - -// overload for arithmetic types, not chosen for basic_json template arguments -// (BooleanType, etc..); note: Is it really necessary to provide explicit -// overloads for boolean_t etc. in case of a custom BooleanType which is not -// an arithmetic type? -template < typename BasicJsonType, typename ArithmeticType, - enable_if_t < - std::is_arithmetic::value&& - !std::is_same::value&& - !std::is_same::value&& - !std::is_same::value&& - !std::is_same::value, - int > = 0 > -void from_json(const BasicJsonType& j, ArithmeticType& val) -{ - switch (static_cast(j)) - { - case value_t::number_unsigned: - { - val = static_cast(*j.template get_ptr()); - break; - } - case value_t::number_integer: - { - val = static_cast(*j.template get_ptr()); - break; - } - case value_t::number_float: - { - val = static_cast(*j.template get_ptr()); - break; - } - case value_t::boolean: - { - val = static_cast(*j.template get_ptr()); - break; - } - - default: - JSON_THROW(type_error::create(302, "type must be number, but is " + std::string(j.type_name()))); - } -} - -template -void from_json(const BasicJsonType& j, std::pair& p) -{ - p = {j.at(0).template get(), j.at(1).template get()}; -} - -template -void from_json_tuple_impl(const BasicJsonType& j, Tuple& t, index_sequence /*unused*/) -{ - t = std::make_tuple(j.at(Idx).template get::type>()...); -} - -template -void from_json(const BasicJsonType& j, std::tuple& t) -{ - from_json_tuple_impl(j, t, index_sequence_for {}); -} - -template < typename BasicJsonType, typename Key, typename Value, typename Compare, typename Allocator, - typename = enable_if_t < !std::is_constructible < - typename BasicJsonType::string_t, Key >::value >> -void from_json(const BasicJsonType& j, std::map& m) -{ - if (JSON_HEDLEY_UNLIKELY(!j.is_array())) - { - JSON_THROW(type_error::create(302, "type must be array, but is " + std::string(j.type_name()))); - } - m.clear(); - for (const auto& p : j) - { - if (JSON_HEDLEY_UNLIKELY(!p.is_array())) - { - JSON_THROW(type_error::create(302, "type must be array, but is " + std::string(p.type_name()))); - } - m.emplace(p.at(0).template get(), p.at(1).template get()); - } -} - -template < typename BasicJsonType, typename Key, typename Value, typename Hash, typename KeyEqual, typename Allocator, - typename = enable_if_t < !std::is_constructible < - typename BasicJsonType::string_t, Key >::value >> -void from_json(const BasicJsonType& j, std::unordered_map& m) -{ - if (JSON_HEDLEY_UNLIKELY(!j.is_array())) - { - JSON_THROW(type_error::create(302, "type must be array, but is " + std::string(j.type_name()))); - } - m.clear(); - for (const auto& p : j) - { - if (JSON_HEDLEY_UNLIKELY(!p.is_array())) - { - JSON_THROW(type_error::create(302, "type must be array, but is " + std::string(p.type_name()))); - } - m.emplace(p.at(0).template get(), p.at(1).template get()); - } -} - -struct from_json_fn -{ - template - auto operator()(const BasicJsonType& j, T& val) const - noexcept(noexcept(from_json(j, val))) - -> decltype(from_json(j, val), void()) - { - return from_json(j, val); - } -}; -} // namespace detail - -/// namespace to hold default `from_json` function -/// to see why this is required: -/// http://www.open-std.org/jtc1/sc22/wg21/docs/papers/2015/n4381.html -namespace -{ -constexpr const auto& from_json = detail::static_const::value; -} // namespace -} // namespace nlohmann - -// #include - - -#include // copy -#include // begin, end -#include // string -#include // tuple, get -#include // is_same, is_constructible, is_floating_point, is_enum, underlying_type -#include // move, forward, declval, pair -#include // valarray -#include // vector - -// #include - - -#include // size_t -#include // input_iterator_tag -#include // string, to_string -#include // tuple_size, get, tuple_element - -// #include - -// #include - - -namespace nlohmann -{ -namespace detail -{ -template -void int_to_string( string_type& target, std::size_t value ) -{ - // For ADL - using std::to_string; - target = to_string(value); -} -template class iteration_proxy_value -{ - public: - using difference_type = std::ptrdiff_t; - using value_type = iteration_proxy_value; - using pointer = value_type * ; - using reference = value_type & ; - using iterator_category = std::input_iterator_tag; - using string_type = typename std::remove_cv< typename std::remove_reference().key() ) >::type >::type; - - private: - /// the iterator - IteratorType anchor; - /// an index for arrays (used to create key names) - std::size_t array_index = 0; - /// last stringified array index - mutable std::size_t array_index_last = 0; - /// a string representation of the array index - mutable string_type array_index_str = "0"; - /// an empty string (to return a reference for primitive values) - const string_type empty_str = ""; - - public: - explicit iteration_proxy_value(IteratorType it) noexcept : anchor(it) {} - - /// dereference operator (needed for range-based for) - iteration_proxy_value& operator*() - { - return *this; - } - - /// increment operator (needed for range-based for) - iteration_proxy_value& operator++() - { - ++anchor; - ++array_index; - - return *this; - } - - /// equality operator (needed for InputIterator) - bool operator==(const iteration_proxy_value& o) const - { - return anchor == o.anchor; - } - - /// inequality operator (needed for range-based for) - bool operator!=(const iteration_proxy_value& o) const - { - return anchor != o.anchor; - } - - /// return key of the iterator - const string_type& key() const - { - JSON_ASSERT(anchor.m_object != nullptr); - - switch (anchor.m_object->type()) - { - // use integer array index as key - case value_t::array: - { - if (array_index != array_index_last) - { - int_to_string( array_index_str, array_index ); - array_index_last = array_index; - } - return array_index_str; - } - - // use key from the object - case value_t::object: - return anchor.key(); - - // use an empty key for all primitive types - default: - return empty_str; - } - } - - /// return value of the iterator - typename IteratorType::reference value() const - { - return anchor.value(); - } -}; - -/// proxy class for the items() function -template class iteration_proxy -{ - private: - /// the container to iterate - typename IteratorType::reference container; - - public: - /// construct iteration proxy from a container - explicit iteration_proxy(typename IteratorType::reference cont) noexcept - : container(cont) {} - - /// return iterator begin (needed for range-based for) - iteration_proxy_value begin() noexcept - { - return iteration_proxy_value(container.begin()); - } - - /// return iterator end (needed for range-based for) - iteration_proxy_value end() noexcept - { - return iteration_proxy_value(container.end()); - } -}; -// Structured Bindings Support -// For further reference see https://blog.tartanllama.xyz/structured-bindings/ -// And see https://github.com/nlohmann/json/pull/1391 -template = 0> -auto get(const nlohmann::detail::iteration_proxy_value& i) -> decltype(i.key()) -{ - return i.key(); -} -// Structured Bindings Support -// For further reference see https://blog.tartanllama.xyz/structured-bindings/ -// And see https://github.com/nlohmann/json/pull/1391 -template = 0> -auto get(const nlohmann::detail::iteration_proxy_value& i) -> decltype(i.value()) -{ - return i.value(); -} -} // namespace detail -} // namespace nlohmann - -// The Addition to the STD Namespace is required to add -// Structured Bindings Support to the iteration_proxy_value class -// For further reference see https://blog.tartanllama.xyz/structured-bindings/ -// And see https://github.com/nlohmann/json/pull/1391 -namespace std -{ -#if defined(__clang__) - // Fix: https://github.com/nlohmann/json/issues/1401 - #pragma clang diagnostic push - #pragma clang diagnostic ignored "-Wmismatched-tags" -#endif -template -class tuple_size<::nlohmann::detail::iteration_proxy_value> - : public std::integral_constant {}; - -template -class tuple_element> -{ - public: - using type = decltype( - get(std::declval < - ::nlohmann::detail::iteration_proxy_value> ())); -}; -#if defined(__clang__) - #pragma clang diagnostic pop -#endif -} // namespace std - -// #include - -// #include - -// #include - - -namespace nlohmann -{ -namespace detail -{ -////////////////// -// constructors // -////////////////// - -template struct external_constructor; - -template<> -struct external_constructor -{ - template - static void construct(BasicJsonType& j, typename BasicJsonType::boolean_t b) noexcept - { - j.m_type = value_t::boolean; - j.m_value = b; - j.assert_invariant(); - } -}; - -template<> -struct external_constructor -{ - template - static void construct(BasicJsonType& j, const typename BasicJsonType::string_t& s) - { - j.m_type = value_t::string; - j.m_value = s; - j.assert_invariant(); - } - - template - static void construct(BasicJsonType& j, typename BasicJsonType::string_t&& s) - { - j.m_type = value_t::string; - j.m_value = std::move(s); - j.assert_invariant(); - } - - template < typename BasicJsonType, typename CompatibleStringType, - enable_if_t < !std::is_same::value, - int > = 0 > - static void construct(BasicJsonType& j, const CompatibleStringType& str) - { - j.m_type = value_t::string; - j.m_value.string = j.template create(str); - j.assert_invariant(); - } -}; - -template<> -struct external_constructor -{ - template - static void construct(BasicJsonType& j, const typename BasicJsonType::binary_t& b) - { - j.m_type = value_t::binary; - typename BasicJsonType::binary_t value{b}; - j.m_value = value; - j.assert_invariant(); - } - - template - static void construct(BasicJsonType& j, typename BasicJsonType::binary_t&& b) - { - j.m_type = value_t::binary; - typename BasicJsonType::binary_t value{std::move(b)}; - j.m_value = value; - j.assert_invariant(); - } -}; - -template<> -struct external_constructor -{ - template - static void construct(BasicJsonType& j, typename BasicJsonType::number_float_t val) noexcept - { - j.m_type = value_t::number_float; - j.m_value = val; - j.assert_invariant(); - } -}; - -template<> -struct external_constructor -{ - template - static void construct(BasicJsonType& j, typename BasicJsonType::number_unsigned_t val) noexcept - { - j.m_type = value_t::number_unsigned; - j.m_value = val; - j.assert_invariant(); - } -}; - -template<> -struct external_constructor -{ - template - static void construct(BasicJsonType& j, typename BasicJsonType::number_integer_t val) noexcept - { - j.m_type = value_t::number_integer; - j.m_value = val; - j.assert_invariant(); - } -}; - -template<> -struct external_constructor -{ - template - static void construct(BasicJsonType& j, const typename BasicJsonType::array_t& arr) - { - j.m_type = value_t::array; - j.m_value = arr; - j.assert_invariant(); - } - - template - static void construct(BasicJsonType& j, typename BasicJsonType::array_t&& arr) - { - j.m_type = value_t::array; - j.m_value = std::move(arr); - j.assert_invariant(); - } - - template < typename BasicJsonType, typename CompatibleArrayType, - enable_if_t < !std::is_same::value, - int > = 0 > - static void construct(BasicJsonType& j, const CompatibleArrayType& arr) - { - using std::begin; - using std::end; - j.m_type = value_t::array; - j.m_value.array = j.template create(begin(arr), end(arr)); - j.assert_invariant(); - } - - template - static void construct(BasicJsonType& j, const std::vector& arr) - { - j.m_type = value_t::array; - j.m_value = value_t::array; - j.m_value.array->reserve(arr.size()); - for (const bool x : arr) - { - j.m_value.array->push_back(x); - } - j.assert_invariant(); - } - - template::value, int> = 0> - static void construct(BasicJsonType& j, const std::valarray& arr) - { - j.m_type = value_t::array; - j.m_value = value_t::array; - j.m_value.array->resize(arr.size()); - if (arr.size() > 0) - { - std::copy(std::begin(arr), std::end(arr), j.m_value.array->begin()); - } - j.assert_invariant(); - } -}; - -template<> -struct external_constructor -{ - template - static void construct(BasicJsonType& j, const typename BasicJsonType::object_t& obj) - { - j.m_type = value_t::object; - j.m_value = obj; - j.assert_invariant(); - } - - template - static void construct(BasicJsonType& j, typename BasicJsonType::object_t&& obj) - { - j.m_type = value_t::object; - j.m_value = std::move(obj); - j.assert_invariant(); - } - - template < typename BasicJsonType, typename CompatibleObjectType, - enable_if_t < !std::is_same::value, int > = 0 > - static void construct(BasicJsonType& j, const CompatibleObjectType& obj) - { - using std::begin; - using std::end; - - j.m_type = value_t::object; - j.m_value.object = j.template create(begin(obj), end(obj)); - j.assert_invariant(); - } -}; - -///////////// -// to_json // -///////////// - -template::value, int> = 0> -void to_json(BasicJsonType& j, T b) noexcept -{ - external_constructor::construct(j, b); -} - -template::value, int> = 0> -void to_json(BasicJsonType& j, const CompatibleString& s) -{ - external_constructor::construct(j, s); -} - -template -void to_json(BasicJsonType& j, typename BasicJsonType::string_t&& s) -{ - external_constructor::construct(j, std::move(s)); -} - -template::value, int> = 0> -void to_json(BasicJsonType& j, FloatType val) noexcept -{ - external_constructor::construct(j, static_cast(val)); -} - -template::value, int> = 0> -void to_json(BasicJsonType& j, CompatibleNumberUnsignedType val) noexcept -{ - external_constructor::construct(j, static_cast(val)); -} - -template::value, int> = 0> -void to_json(BasicJsonType& j, CompatibleNumberIntegerType val) noexcept -{ - external_constructor::construct(j, static_cast(val)); -} - -template::value, int> = 0> -void to_json(BasicJsonType& j, EnumType e) noexcept -{ - using underlying_type = typename std::underlying_type::type; - external_constructor::construct(j, static_cast(e)); -} - -template -void to_json(BasicJsonType& j, const std::vector& e) -{ - external_constructor::construct(j, e); -} - -template < typename BasicJsonType, typename CompatibleArrayType, - enable_if_t < is_compatible_array_type::value&& - !is_compatible_object_type::value&& - !is_compatible_string_type::value&& - !std::is_same::value&& - !is_basic_json::value, - int > = 0 > -void to_json(BasicJsonType& j, const CompatibleArrayType& arr) -{ - external_constructor::construct(j, arr); -} - -template -void to_json(BasicJsonType& j, const typename BasicJsonType::binary_t& bin) -{ - external_constructor::construct(j, bin); -} - -template::value, int> = 0> -void to_json(BasicJsonType& j, const std::valarray& arr) -{ - external_constructor::construct(j, std::move(arr)); -} - -template -void to_json(BasicJsonType& j, typename BasicJsonType::array_t&& arr) -{ - external_constructor::construct(j, std::move(arr)); -} - -template < typename BasicJsonType, typename CompatibleObjectType, - enable_if_t < is_compatible_object_type::value&& !is_basic_json::value, int > = 0 > -void to_json(BasicJsonType& j, const CompatibleObjectType& obj) -{ - external_constructor::construct(j, obj); -} - -template -void to_json(BasicJsonType& j, typename BasicJsonType::object_t&& obj) -{ - external_constructor::construct(j, std::move(obj)); -} - -template < - typename BasicJsonType, typename T, std::size_t N, - enable_if_t < !std::is_constructible::value, - int > = 0 > -void to_json(BasicJsonType& j, const T(&arr)[N]) -{ - external_constructor::construct(j, arr); -} - -template < typename BasicJsonType, typename T1, typename T2, enable_if_t < std::is_constructible::value&& std::is_constructible::value, int > = 0 > -void to_json(BasicJsonType& j, const std::pair& p) -{ - j = { p.first, p.second }; -} - -// for https://github.com/nlohmann/json/pull/1134 -template>::value, int> = 0> -void to_json(BasicJsonType& j, const T& b) -{ - j = { {b.key(), b.value()} }; -} - -template -void to_json_tuple_impl(BasicJsonType& j, const Tuple& t, index_sequence /*unused*/) -{ - j = { std::get(t)... }; -} - -template::value, int > = 0> -void to_json(BasicJsonType& j, const T& t) -{ - to_json_tuple_impl(j, t, make_index_sequence::value> {}); -} - -struct to_json_fn -{ - template - auto operator()(BasicJsonType& j, T&& val) const noexcept(noexcept(to_json(j, std::forward(val)))) - -> decltype(to_json(j, std::forward(val)), void()) - { - return to_json(j, std::forward(val)); - } -}; -} // namespace detail - -/// namespace to hold default `to_json` function -namespace -{ -constexpr const auto& to_json = detail::static_const::value; -} // namespace -} // namespace nlohmann - - -namespace nlohmann -{ - -template -struct adl_serializer -{ - /*! - @brief convert a JSON value to any value type - - This function is usually called by the `get()` function of the - @ref basic_json class (either explicit or via conversion operators). - - @param[in] j JSON value to read from - @param[in,out] val value to write to - */ - template - static auto from_json(BasicJsonType&& j, ValueType& val) noexcept( - noexcept(::nlohmann::from_json(std::forward(j), val))) - -> decltype(::nlohmann::from_json(std::forward(j), val), void()) - { - ::nlohmann::from_json(std::forward(j), val); - } - - /*! - @brief convert any value type to a JSON value - - This function is usually called by the constructors of the @ref basic_json - class. - - @param[in,out] j JSON value to write to - @param[in] val value to read from - */ - template - static auto to_json(BasicJsonType& j, ValueType&& val) noexcept( - noexcept(::nlohmann::to_json(j, std::forward(val)))) - -> decltype(::nlohmann::to_json(j, std::forward(val)), void()) - { - ::nlohmann::to_json(j, std::forward(val)); - } -}; - -} // namespace nlohmann - -// #include - - -#include // uint8_t -#include // tie -#include // move - -namespace nlohmann -{ - -/*! -@brief an internal type for a backed binary type - -This type extends the template parameter @a BinaryType provided to `basic_json` -with a subtype used by BSON and MessagePack. This type exists so that the user -does not have to specify a type themselves with a specific naming scheme in -order to override the binary type. - -@tparam BinaryType container to store bytes (`std::vector` by - default) - -@since version 3.8.0 -*/ -template -class byte_container_with_subtype : public BinaryType -{ - public: - /// the type of the underlying container - using container_type = BinaryType; - - byte_container_with_subtype() noexcept(noexcept(container_type())) - : container_type() - {} - - byte_container_with_subtype(const container_type& b) noexcept(noexcept(container_type(b))) - : container_type(b) - {} - - byte_container_with_subtype(container_type&& b) noexcept(noexcept(container_type(std::move(b)))) - : container_type(std::move(b)) - {} - - byte_container_with_subtype(const container_type& b, std::uint8_t subtype) noexcept(noexcept(container_type(b))) - : container_type(b) - , m_subtype(subtype) - , m_has_subtype(true) - {} - - byte_container_with_subtype(container_type&& b, std::uint8_t subtype) noexcept(noexcept(container_type(std::move(b)))) - : container_type(std::move(b)) - , m_subtype(subtype) - , m_has_subtype(true) - {} - - bool operator==(const byte_container_with_subtype& rhs) const - { - return std::tie(static_cast(*this), m_subtype, m_has_subtype) == - std::tie(static_cast(rhs), rhs.m_subtype, rhs.m_has_subtype); - } - - bool operator!=(const byte_container_with_subtype& rhs) const - { - return !(rhs == *this); - } - - /*! - @brief sets the binary subtype - - Sets the binary subtype of the value, also flags a binary JSON value as - having a subtype, which has implications for serialization. - - @complexity Constant. - - @exceptionsafety No-throw guarantee: this member function never throws - exceptions. - - @sa @ref subtype() -- return the binary subtype - @sa @ref clear_subtype() -- clears the binary subtype - @sa @ref has_subtype() -- returns whether or not the binary value has a - subtype - - @since version 3.8.0 - */ - void set_subtype(std::uint8_t subtype) noexcept - { - m_subtype = subtype; - m_has_subtype = true; - } - - /*! - @brief return the binary subtype - - Returns the numerical subtype of the value if it has a subtype. If it does - not have a subtype, this function will return size_t(-1) as a sentinel - value. - - @return the numerical subtype of the binary value - - @complexity Constant. - - @exceptionsafety No-throw guarantee: this member function never throws - exceptions. - - @sa @ref set_subtype() -- sets the binary subtype - @sa @ref clear_subtype() -- clears the binary subtype - @sa @ref has_subtype() -- returns whether or not the binary value has a - subtype - - @since version 3.8.0 - */ - constexpr std::uint8_t subtype() const noexcept - { - return m_subtype; - } - - /*! - @brief return whether the value has a subtype - - @return whether the value has a subtype - - @complexity Constant. - - @exceptionsafety No-throw guarantee: this member function never throws - exceptions. - - @sa @ref subtype() -- return the binary subtype - @sa @ref set_subtype() -- sets the binary subtype - @sa @ref clear_subtype() -- clears the binary subtype - - @since version 3.8.0 - */ - constexpr bool has_subtype() const noexcept - { - return m_has_subtype; - } - - /*! - @brief clears the binary subtype - - Clears the binary subtype and flags the value as not having a subtype, which - has implications for serialization; for instance MessagePack will prefer the - bin family over the ext family. - - @complexity Constant. - - @exceptionsafety No-throw guarantee: this member function never throws - exceptions. - - @sa @ref subtype() -- return the binary subtype - @sa @ref set_subtype() -- sets the binary subtype - @sa @ref has_subtype() -- returns whether or not the binary value has a - subtype - - @since version 3.8.0 - */ - void clear_subtype() noexcept - { - m_subtype = 0; - m_has_subtype = false; - } - - private: - std::uint8_t m_subtype = 0; - bool m_has_subtype = false; -}; - -} // namespace nlohmann - -// #include - -// #include - -// #include - -// #include - - -#include // size_t, uint8_t -#include // hash - -namespace nlohmann -{ -namespace detail -{ - -// boost::hash_combine -inline std::size_t combine(std::size_t seed, std::size_t h) noexcept -{ - seed ^= h + 0x9e3779b9 + (seed << 6U) + (seed >> 2U); - return seed; -} - -/*! -@brief hash a JSON value - -The hash function tries to rely on std::hash where possible. Furthermore, the -type of the JSON value is taken into account to have different hash values for -null, 0, 0U, and false, etc. - -@tparam BasicJsonType basic_json specialization -@param j JSON value to hash -@return hash value of j -*/ -template -std::size_t hash(const BasicJsonType& j) -{ - using string_t = typename BasicJsonType::string_t; - using number_integer_t = typename BasicJsonType::number_integer_t; - using number_unsigned_t = typename BasicJsonType::number_unsigned_t; - using number_float_t = typename BasicJsonType::number_float_t; - - const auto type = static_cast(j.type()); - switch (j.type()) - { - case BasicJsonType::value_t::null: - case BasicJsonType::value_t::discarded: - { - return combine(type, 0); - } - - case BasicJsonType::value_t::object: - { - auto seed = combine(type, j.size()); - for (const auto& element : j.items()) - { - const auto h = std::hash {}(element.key()); - seed = combine(seed, h); - seed = combine(seed, hash(element.value())); - } - return seed; - } - - case BasicJsonType::value_t::array: - { - auto seed = combine(type, j.size()); - for (const auto& element : j) - { - seed = combine(seed, hash(element)); - } - return seed; - } - - case BasicJsonType::value_t::string: - { - const auto h = std::hash {}(j.template get_ref()); - return combine(type, h); - } - - case BasicJsonType::value_t::boolean: - { - const auto h = std::hash {}(j.template get()); - return combine(type, h); - } - - case BasicJsonType::value_t::number_integer: - { - const auto h = std::hash {}(j.template get()); - return combine(type, h); - } - - case nlohmann::detail::value_t::number_unsigned: - { - const auto h = std::hash {}(j.template get()); - return combine(type, h); - } - - case nlohmann::detail::value_t::number_float: - { - const auto h = std::hash {}(j.template get()); - return combine(type, h); - } - - case nlohmann::detail::value_t::binary: - { - auto seed = combine(type, j.get_binary().size()); - const auto h = std::hash {}(j.get_binary().has_subtype()); - seed = combine(seed, h); - seed = combine(seed, j.get_binary().subtype()); - for (const auto byte : j.get_binary()) - { - seed = combine(seed, std::hash {}(byte)); - } - return seed; - } - - default: // LCOV_EXCL_LINE - JSON_ASSERT(false); // LCOV_EXCL_LINE - } -} - -} // namespace detail -} // namespace nlohmann - -// #include - - -#include // generate_n -#include // array -#include // ldexp -#include // size_t -#include // uint8_t, uint16_t, uint32_t, uint64_t -#include // snprintf -#include // memcpy -#include // back_inserter -#include // numeric_limits -#include // char_traits, string -#include // make_pair, move - -// #include - -// #include - - -#include // array -#include // size_t -#include //FILE * -#include // strlen -#include // istream -#include // begin, end, iterator_traits, random_access_iterator_tag, distance, next -#include // shared_ptr, make_shared, addressof -#include // accumulate -#include // string, char_traits -#include // enable_if, is_base_of, is_pointer, is_integral, remove_pointer -#include // pair, declval - -// #include - -// #include - - -namespace nlohmann -{ -namespace detail -{ -/// the supported input formats -enum class input_format_t { json, cbor, msgpack, ubjson, bson }; - -//////////////////// -// input adapters // -//////////////////// - -/*! -Input adapter for stdio file access. This adapter read only 1 byte and do not use any - buffer. This adapter is a very low level adapter. -*/ -class file_input_adapter -{ - public: - using char_type = char; - - JSON_HEDLEY_NON_NULL(2) - explicit file_input_adapter(std::FILE* f) noexcept - : m_file(f) - {} - - // make class move-only - file_input_adapter(const file_input_adapter&) = delete; - file_input_adapter(file_input_adapter&&) = default; - file_input_adapter& operator=(const file_input_adapter&) = delete; - file_input_adapter& operator=(file_input_adapter&&) = delete; - - std::char_traits::int_type get_character() noexcept - { - return std::fgetc(m_file); - } - - private: - /// the file pointer to read from - std::FILE* m_file; -}; - - -/*! -Input adapter for a (caching) istream. Ignores a UFT Byte Order Mark at -beginning of input. Does not support changing the underlying std::streambuf -in mid-input. Maintains underlying std::istream and std::streambuf to support -subsequent use of standard std::istream operations to process any input -characters following those used in parsing the JSON input. Clears the -std::istream flags; any input errors (e.g., EOF) will be detected by the first -subsequent call for input from the std::istream. -*/ -class input_stream_adapter -{ - public: - using char_type = char; - - ~input_stream_adapter() - { - // clear stream flags; we use underlying streambuf I/O, do not - // maintain ifstream flags, except eof - if (is != nullptr) - { - is->clear(is->rdstate() & std::ios::eofbit); - } - } - - explicit input_stream_adapter(std::istream& i) - : is(&i), sb(i.rdbuf()) - {} - - // delete because of pointer members - input_stream_adapter(const input_stream_adapter&) = delete; - input_stream_adapter& operator=(input_stream_adapter&) = delete; - input_stream_adapter& operator=(input_stream_adapter&& rhs) = delete; - - input_stream_adapter(input_stream_adapter&& rhs) noexcept : is(rhs.is), sb(rhs.sb) - { - rhs.is = nullptr; - rhs.sb = nullptr; - } - - // std::istream/std::streambuf use std::char_traits::to_int_type, to - // ensure that std::char_traits::eof() and the character 0xFF do not - // end up as the same value, eg. 0xFFFFFFFF. - std::char_traits::int_type get_character() - { - auto res = sb->sbumpc(); - // set eof manually, as we don't use the istream interface. - if (JSON_HEDLEY_UNLIKELY(res == EOF)) - { - is->clear(is->rdstate() | std::ios::eofbit); - } - return res; - } - - private: - /// the associated input stream - std::istream* is = nullptr; - std::streambuf* sb = nullptr; -}; - -// General-purpose iterator-based adapter. It might not be as fast as -// theoretically possible for some containers, but it is extremely versatile. -template -class iterator_input_adapter -{ - public: - using char_type = typename std::iterator_traits::value_type; - - iterator_input_adapter(IteratorType first, IteratorType last) - : current(std::move(first)), end(std::move(last)) {} - - typename std::char_traits::int_type get_character() - { - if (JSON_HEDLEY_LIKELY(current != end)) - { - auto result = std::char_traits::to_int_type(*current); - std::advance(current, 1); - return result; - } - else - { - return std::char_traits::eof(); - } - } - - private: - IteratorType current; - IteratorType end; - - template - friend struct wide_string_input_helper; - - bool empty() const - { - return current == end; - } - -}; - - -template -struct wide_string_input_helper; - -template -struct wide_string_input_helper -{ - // UTF-32 - static void fill_buffer(BaseInputAdapter& input, - std::array::int_type, 4>& utf8_bytes, - size_t& utf8_bytes_index, - size_t& utf8_bytes_filled) - { - utf8_bytes_index = 0; - - if (JSON_HEDLEY_UNLIKELY(input.empty())) - { - utf8_bytes[0] = std::char_traits::eof(); - utf8_bytes_filled = 1; - } - else - { - // get the current character - const auto wc = input.get_character(); - - // UTF-32 to UTF-8 encoding - if (wc < 0x80) - { - utf8_bytes[0] = static_cast::int_type>(wc); - utf8_bytes_filled = 1; - } - else if (wc <= 0x7FF) - { - utf8_bytes[0] = static_cast::int_type>(0xC0u | ((static_cast(wc) >> 6u) & 0x1Fu)); - utf8_bytes[1] = static_cast::int_type>(0x80u | (static_cast(wc) & 0x3Fu)); - utf8_bytes_filled = 2; - } - else if (wc <= 0xFFFF) - { - utf8_bytes[0] = static_cast::int_type>(0xE0u | ((static_cast(wc) >> 12u) & 0x0Fu)); - utf8_bytes[1] = static_cast::int_type>(0x80u | ((static_cast(wc) >> 6u) & 0x3Fu)); - utf8_bytes[2] = static_cast::int_type>(0x80u | (static_cast(wc) & 0x3Fu)); - utf8_bytes_filled = 3; - } - else if (wc <= 0x10FFFF) - { - utf8_bytes[0] = static_cast::int_type>(0xF0u | ((static_cast(wc) >> 18u) & 0x07u)); - utf8_bytes[1] = static_cast::int_type>(0x80u | ((static_cast(wc) >> 12u) & 0x3Fu)); - utf8_bytes[2] = static_cast::int_type>(0x80u | ((static_cast(wc) >> 6u) & 0x3Fu)); - utf8_bytes[3] = static_cast::int_type>(0x80u | (static_cast(wc) & 0x3Fu)); - utf8_bytes_filled = 4; - } - else - { - // unknown character - utf8_bytes[0] = static_cast::int_type>(wc); - utf8_bytes_filled = 1; - } - } - } -}; - -template -struct wide_string_input_helper -{ - // UTF-16 - static void fill_buffer(BaseInputAdapter& input, - std::array::int_type, 4>& utf8_bytes, - size_t& utf8_bytes_index, - size_t& utf8_bytes_filled) - { - utf8_bytes_index = 0; - - if (JSON_HEDLEY_UNLIKELY(input.empty())) - { - utf8_bytes[0] = std::char_traits::eof(); - utf8_bytes_filled = 1; - } - else - { - // get the current character - const auto wc = input.get_character(); - - // UTF-16 to UTF-8 encoding - if (wc < 0x80) - { - utf8_bytes[0] = static_cast::int_type>(wc); - utf8_bytes_filled = 1; - } - else if (wc <= 0x7FF) - { - utf8_bytes[0] = static_cast::int_type>(0xC0u | ((static_cast(wc) >> 6u))); - utf8_bytes[1] = static_cast::int_type>(0x80u | (static_cast(wc) & 0x3Fu)); - utf8_bytes_filled = 2; - } - else if (0xD800 > wc || wc >= 0xE000) - { - utf8_bytes[0] = static_cast::int_type>(0xE0u | ((static_cast(wc) >> 12u))); - utf8_bytes[1] = static_cast::int_type>(0x80u | ((static_cast(wc) >> 6u) & 0x3Fu)); - utf8_bytes[2] = static_cast::int_type>(0x80u | (static_cast(wc) & 0x3Fu)); - utf8_bytes_filled = 3; - } - else - { - if (JSON_HEDLEY_UNLIKELY(!input.empty())) - { - const auto wc2 = static_cast(input.get_character()); - const auto charcode = 0x10000u + (((static_cast(wc) & 0x3FFu) << 10u) | (wc2 & 0x3FFu)); - utf8_bytes[0] = static_cast::int_type>(0xF0u | (charcode >> 18u)); - utf8_bytes[1] = static_cast::int_type>(0x80u | ((charcode >> 12u) & 0x3Fu)); - utf8_bytes[2] = static_cast::int_type>(0x80u | ((charcode >> 6u) & 0x3Fu)); - utf8_bytes[3] = static_cast::int_type>(0x80u | (charcode & 0x3Fu)); - utf8_bytes_filled = 4; - } - else - { - utf8_bytes[0] = static_cast::int_type>(wc); - utf8_bytes_filled = 1; - } - } - } - } -}; - -// Wraps another input apdater to convert wide character types into individual bytes. -template -class wide_string_input_adapter -{ - public: - using char_type = char; - - wide_string_input_adapter(BaseInputAdapter base) - : base_adapter(base) {} - - typename std::char_traits::int_type get_character() noexcept - { - // check if buffer needs to be filled - if (utf8_bytes_index == utf8_bytes_filled) - { - fill_buffer(); - - JSON_ASSERT(utf8_bytes_filled > 0); - JSON_ASSERT(utf8_bytes_index == 0); - } - - // use buffer - JSON_ASSERT(utf8_bytes_filled > 0); - JSON_ASSERT(utf8_bytes_index < utf8_bytes_filled); - return utf8_bytes[utf8_bytes_index++]; - } - - private: - BaseInputAdapter base_adapter; - - template - void fill_buffer() - { - wide_string_input_helper::fill_buffer(base_adapter, utf8_bytes, utf8_bytes_index, utf8_bytes_filled); - } - - /// a buffer for UTF-8 bytes - std::array::int_type, 4> utf8_bytes = {{0, 0, 0, 0}}; - - /// index to the utf8_codes array for the next valid byte - std::size_t utf8_bytes_index = 0; - /// number of valid bytes in the utf8_codes array - std::size_t utf8_bytes_filled = 0; -}; - - -template -struct iterator_input_adapter_factory -{ - using iterator_type = IteratorType; - using char_type = typename std::iterator_traits::value_type; - using adapter_type = iterator_input_adapter; - - static adapter_type create(IteratorType first, IteratorType last) - { - return adapter_type(std::move(first), std::move(last)); - } -}; - -template -struct is_iterator_of_multibyte -{ - using value_type = typename std::iterator_traits::value_type; - enum - { - value = sizeof(value_type) > 1 - }; -}; - -template -struct iterator_input_adapter_factory::value>> -{ - using iterator_type = IteratorType; - using char_type = typename std::iterator_traits::value_type; - using base_adapter_type = iterator_input_adapter; - using adapter_type = wide_string_input_adapter; - - static adapter_type create(IteratorType first, IteratorType last) - { - return adapter_type(base_adapter_type(std::move(first), std::move(last))); - } -}; - -// General purpose iterator-based input -template -typename iterator_input_adapter_factory::adapter_type input_adapter(IteratorType first, IteratorType last) -{ - using factory_type = iterator_input_adapter_factory; - return factory_type::create(first, last); -} - -// Convenience shorthand from container to iterator -template -auto input_adapter(const ContainerType& container) -> decltype(input_adapter(begin(container), end(container))) -{ - // Enable ADL - using std::begin; - using std::end; - - return input_adapter(begin(container), end(container)); -} - -// Special cases with fast paths -inline file_input_adapter input_adapter(std::FILE* file) -{ - return file_input_adapter(file); -} - -inline input_stream_adapter input_adapter(std::istream& stream) -{ - return input_stream_adapter(stream); -} - -inline input_stream_adapter input_adapter(std::istream&& stream) -{ - return input_stream_adapter(stream); -} - -using contiguous_bytes_input_adapter = decltype(input_adapter(std::declval(), std::declval())); - -// Null-delimited strings, and the like. -template < typename CharT, - typename std::enable_if < - std::is_pointer::value&& - !std::is_array::value&& - std::is_integral::type>::value&& - sizeof(typename std::remove_pointer::type) == 1, - int >::type = 0 > -contiguous_bytes_input_adapter input_adapter(CharT b) -{ - auto length = std::strlen(reinterpret_cast(b)); - const auto* ptr = reinterpret_cast(b); - return input_adapter(ptr, ptr + length); -} - -template -auto input_adapter(T (&array)[N]) -> decltype(input_adapter(array, array + N)) -{ - return input_adapter(array, array + N); -} - -// This class only handles inputs of input_buffer_adapter type. -// It's required so that expressions like {ptr, len} can be implicitely casted -// to the correct adapter. -class span_input_adapter -{ - public: - template < typename CharT, - typename std::enable_if < - std::is_pointer::value&& - std::is_integral::type>::value&& - sizeof(typename std::remove_pointer::type) == 1, - int >::type = 0 > - span_input_adapter(CharT b, std::size_t l) - : ia(reinterpret_cast(b), reinterpret_cast(b) + l) {} - - template::iterator_category, std::random_access_iterator_tag>::value, - int>::type = 0> - span_input_adapter(IteratorType first, IteratorType last) - : ia(input_adapter(first, last)) {} - - contiguous_bytes_input_adapter&& get() - { - return std::move(ia); - } - - private: - contiguous_bytes_input_adapter ia; -}; -} // namespace detail -} // namespace nlohmann - -// #include - - -#include -#include // string -#include // move -#include // vector - -// #include - -// #include - - -namespace nlohmann -{ - -/*! -@brief SAX interface - -This class describes the SAX interface used by @ref nlohmann::json::sax_parse. -Each function is called in different situations while the input is parsed. The -boolean return value informs the parser whether to continue processing the -input. -*/ -template -struct json_sax -{ - using number_integer_t = typename BasicJsonType::number_integer_t; - using number_unsigned_t = typename BasicJsonType::number_unsigned_t; - using number_float_t = typename BasicJsonType::number_float_t; - using string_t = typename BasicJsonType::string_t; - using binary_t = typename BasicJsonType::binary_t; - - /*! - @brief a null value was read - @return whether parsing should proceed - */ - virtual bool null() = 0; - - /*! - @brief a boolean value was read - @param[in] val boolean value - @return whether parsing should proceed - */ - virtual bool boolean(bool val) = 0; - - /*! - @brief an integer number was read - @param[in] val integer value - @return whether parsing should proceed - */ - virtual bool number_integer(number_integer_t val) = 0; - - /*! - @brief an unsigned integer number was read - @param[in] val unsigned integer value - @return whether parsing should proceed - */ - virtual bool number_unsigned(number_unsigned_t val) = 0; - - /*! - @brief an floating-point number was read - @param[in] val floating-point value - @param[in] s raw token value - @return whether parsing should proceed - */ - virtual bool number_float(number_float_t val, const string_t& s) = 0; - - /*! - @brief a string was read - @param[in] val string value - @return whether parsing should proceed - @note It is safe to move the passed string. - */ - virtual bool string(string_t& val) = 0; - - /*! - @brief a binary string was read - @param[in] val binary value - @return whether parsing should proceed - @note It is safe to move the passed binary. - */ - virtual bool binary(binary_t& val) = 0; - - /*! - @brief the beginning of an object was read - @param[in] elements number of object elements or -1 if unknown - @return whether parsing should proceed - @note binary formats may report the number of elements - */ - virtual bool start_object(std::size_t elements) = 0; - - /*! - @brief an object key was read - @param[in] val object key - @return whether parsing should proceed - @note It is safe to move the passed string. - */ - virtual bool key(string_t& val) = 0; - - /*! - @brief the end of an object was read - @return whether parsing should proceed - */ - virtual bool end_object() = 0; - - /*! - @brief the beginning of an array was read - @param[in] elements number of array elements or -1 if unknown - @return whether parsing should proceed - @note binary formats may report the number of elements - */ - virtual bool start_array(std::size_t elements) = 0; - - /*! - @brief the end of an array was read - @return whether parsing should proceed - */ - virtual bool end_array() = 0; - - /*! - @brief a parse error occurred - @param[in] position the position in the input where the error occurs - @param[in] last_token the last read token - @param[in] ex an exception object describing the error - @return whether parsing should proceed (must return false) - */ - virtual bool parse_error(std::size_t position, - const std::string& last_token, - const detail::exception& ex) = 0; - - virtual ~json_sax() = default; -}; - - -namespace detail -{ -/*! -@brief SAX implementation to create a JSON value from SAX events - -This class implements the @ref json_sax interface and processes the SAX events -to create a JSON value which makes it basically a DOM parser. The structure or -hierarchy of the JSON value is managed by the stack `ref_stack` which contains -a pointer to the respective array or object for each recursion depth. - -After successful parsing, the value that is passed by reference to the -constructor contains the parsed value. - -@tparam BasicJsonType the JSON type -*/ -template -class json_sax_dom_parser -{ - public: - using number_integer_t = typename BasicJsonType::number_integer_t; - using number_unsigned_t = typename BasicJsonType::number_unsigned_t; - using number_float_t = typename BasicJsonType::number_float_t; - using string_t = typename BasicJsonType::string_t; - using binary_t = typename BasicJsonType::binary_t; - - /*! - @param[in, out] r reference to a JSON value that is manipulated while - parsing - @param[in] allow_exceptions_ whether parse errors yield exceptions - */ - explicit json_sax_dom_parser(BasicJsonType& r, const bool allow_exceptions_ = true) - : root(r), allow_exceptions(allow_exceptions_) - {} - - // make class move-only - json_sax_dom_parser(const json_sax_dom_parser&) = delete; - json_sax_dom_parser(json_sax_dom_parser&&) = default; - json_sax_dom_parser& operator=(const json_sax_dom_parser&) = delete; - json_sax_dom_parser& operator=(json_sax_dom_parser&&) = default; - ~json_sax_dom_parser() = default; - - bool null() - { - handle_value(nullptr); - return true; - } - - bool boolean(bool val) - { - handle_value(val); - return true; - } - - bool number_integer(number_integer_t val) - { - handle_value(val); - return true; - } - - bool number_unsigned(number_unsigned_t val) - { - handle_value(val); - return true; - } - - bool number_float(number_float_t val, const string_t& /*unused*/) - { - handle_value(val); - return true; - } - - bool string(string_t& val) - { - handle_value(val); - return true; - } - - bool binary(binary_t& val) - { - handle_value(std::move(val)); - return true; - } - - bool start_object(std::size_t len) - { - ref_stack.push_back(handle_value(BasicJsonType::value_t::object)); - - if (JSON_HEDLEY_UNLIKELY(len != std::size_t(-1) && len > ref_stack.back()->max_size())) - { - JSON_THROW(out_of_range::create(408, - "excessive object size: " + std::to_string(len))); - } - - return true; - } - - bool key(string_t& val) - { - // add null at given key and store the reference for later - object_element = &(ref_stack.back()->m_value.object->operator[](val)); - return true; - } - - bool end_object() - { - ref_stack.pop_back(); - return true; - } - - bool start_array(std::size_t len) - { - ref_stack.push_back(handle_value(BasicJsonType::value_t::array)); - - if (JSON_HEDLEY_UNLIKELY(len != std::size_t(-1) && len > ref_stack.back()->max_size())) - { - JSON_THROW(out_of_range::create(408, - "excessive array size: " + std::to_string(len))); - } - - return true; - } - - bool end_array() - { - ref_stack.pop_back(); - return true; - } - - template - bool parse_error(std::size_t /*unused*/, const std::string& /*unused*/, - const Exception& ex) - { - errored = true; - static_cast(ex); - if (allow_exceptions) - { - JSON_THROW(ex); - } - return false; - } - - constexpr bool is_errored() const - { - return errored; - } - - private: - /*! - @invariant If the ref stack is empty, then the passed value will be the new - root. - @invariant If the ref stack contains a value, then it is an array or an - object to which we can add elements - */ - template - JSON_HEDLEY_RETURNS_NON_NULL - BasicJsonType* handle_value(Value&& v) - { - if (ref_stack.empty()) - { - root = BasicJsonType(std::forward(v)); - return &root; - } - - JSON_ASSERT(ref_stack.back()->is_array() || ref_stack.back()->is_object()); - - if (ref_stack.back()->is_array()) - { - ref_stack.back()->m_value.array->emplace_back(std::forward(v)); - return &(ref_stack.back()->m_value.array->back()); - } - - JSON_ASSERT(ref_stack.back()->is_object()); - JSON_ASSERT(object_element); - *object_element = BasicJsonType(std::forward(v)); - return object_element; - } - - /// the parsed JSON value - BasicJsonType& root; - /// stack to model hierarchy of values - std::vector ref_stack {}; - /// helper to hold the reference for the next object element - BasicJsonType* object_element = nullptr; - /// whether a syntax error occurred - bool errored = false; - /// whether to throw exceptions in case of errors - const bool allow_exceptions = true; -}; - -template -class json_sax_dom_callback_parser -{ - public: - using number_integer_t = typename BasicJsonType::number_integer_t; - using number_unsigned_t = typename BasicJsonType::number_unsigned_t; - using number_float_t = typename BasicJsonType::number_float_t; - using string_t = typename BasicJsonType::string_t; - using binary_t = typename BasicJsonType::binary_t; - using parser_callback_t = typename BasicJsonType::parser_callback_t; - using parse_event_t = typename BasicJsonType::parse_event_t; - - json_sax_dom_callback_parser(BasicJsonType& r, - const parser_callback_t cb, - const bool allow_exceptions_ = true) - : root(r), callback(cb), allow_exceptions(allow_exceptions_) - { - keep_stack.push_back(true); - } - - // make class move-only - json_sax_dom_callback_parser(const json_sax_dom_callback_parser&) = delete; - json_sax_dom_callback_parser(json_sax_dom_callback_parser&&) = default; - json_sax_dom_callback_parser& operator=(const json_sax_dom_callback_parser&) = delete; - json_sax_dom_callback_parser& operator=(json_sax_dom_callback_parser&&) = default; - ~json_sax_dom_callback_parser() = default; - - bool null() - { - handle_value(nullptr); - return true; - } - - bool boolean(bool val) - { - handle_value(val); - return true; - } - - bool number_integer(number_integer_t val) - { - handle_value(val); - return true; - } - - bool number_unsigned(number_unsigned_t val) - { - handle_value(val); - return true; - } - - bool number_float(number_float_t val, const string_t& /*unused*/) - { - handle_value(val); - return true; - } - - bool string(string_t& val) - { - handle_value(val); - return true; - } - - bool binary(binary_t& val) - { - handle_value(std::move(val)); - return true; - } - - bool start_object(std::size_t len) - { - // check callback for object start - const bool keep = callback(static_cast(ref_stack.size()), parse_event_t::object_start, discarded); - keep_stack.push_back(keep); - - auto val = handle_value(BasicJsonType::value_t::object, true); - ref_stack.push_back(val.second); - - // check object limit - if (ref_stack.back() && JSON_HEDLEY_UNLIKELY(len != std::size_t(-1) && len > ref_stack.back()->max_size())) - { - JSON_THROW(out_of_range::create(408, "excessive object size: " + std::to_string(len))); - } - - return true; - } - - bool key(string_t& val) - { - BasicJsonType k = BasicJsonType(val); - - // check callback for key - const bool keep = callback(static_cast(ref_stack.size()), parse_event_t::key, k); - key_keep_stack.push_back(keep); - - // add discarded value at given key and store the reference for later - if (keep && ref_stack.back()) - { - object_element = &(ref_stack.back()->m_value.object->operator[](val) = discarded); - } - - return true; - } - - bool end_object() - { - if (ref_stack.back() && !callback(static_cast(ref_stack.size()) - 1, parse_event_t::object_end, *ref_stack.back())) - { - // discard object - *ref_stack.back() = discarded; - } - - JSON_ASSERT(!ref_stack.empty()); - JSON_ASSERT(!keep_stack.empty()); - ref_stack.pop_back(); - keep_stack.pop_back(); - - if (!ref_stack.empty() && ref_stack.back() && ref_stack.back()->is_structured()) - { - // remove discarded value - for (auto it = ref_stack.back()->begin(); it != ref_stack.back()->end(); ++it) - { - if (it->is_discarded()) - { - ref_stack.back()->erase(it); - break; - } - } - } - - return true; - } - - bool start_array(std::size_t len) - { - const bool keep = callback(static_cast(ref_stack.size()), parse_event_t::array_start, discarded); - keep_stack.push_back(keep); - - auto val = handle_value(BasicJsonType::value_t::array, true); - ref_stack.push_back(val.second); - - // check array limit - if (ref_stack.back() && JSON_HEDLEY_UNLIKELY(len != std::size_t(-1) && len > ref_stack.back()->max_size())) - { - JSON_THROW(out_of_range::create(408, "excessive array size: " + std::to_string(len))); - } - - return true; - } - - bool end_array() - { - bool keep = true; - - if (ref_stack.back()) - { - keep = callback(static_cast(ref_stack.size()) - 1, parse_event_t::array_end, *ref_stack.back()); - if (!keep) - { - // discard array - *ref_stack.back() = discarded; - } - } - - JSON_ASSERT(!ref_stack.empty()); - JSON_ASSERT(!keep_stack.empty()); - ref_stack.pop_back(); - keep_stack.pop_back(); - - // remove discarded value - if (!keep && !ref_stack.empty() && ref_stack.back()->is_array()) - { - ref_stack.back()->m_value.array->pop_back(); - } - - return true; - } - - template - bool parse_error(std::size_t /*unused*/, const std::string& /*unused*/, - const Exception& ex) - { - errored = true; - static_cast(ex); - if (allow_exceptions) - { - JSON_THROW(ex); - } - return false; - } - - constexpr bool is_errored() const - { - return errored; - } - - private: - /*! - @param[in] v value to add to the JSON value we build during parsing - @param[in] skip_callback whether we should skip calling the callback - function; this is required after start_array() and - start_object() SAX events, because otherwise we would call the - callback function with an empty array or object, respectively. - - @invariant If the ref stack is empty, then the passed value will be the new - root. - @invariant If the ref stack contains a value, then it is an array or an - object to which we can add elements - - @return pair of boolean (whether value should be kept) and pointer (to the - passed value in the ref_stack hierarchy; nullptr if not kept) - */ - template - std::pair handle_value(Value&& v, const bool skip_callback = false) - { - JSON_ASSERT(!keep_stack.empty()); - - // do not handle this value if we know it would be added to a discarded - // container - if (!keep_stack.back()) - { - return {false, nullptr}; - } - - // create value - auto value = BasicJsonType(std::forward(v)); - - // check callback - const bool keep = skip_callback || callback(static_cast(ref_stack.size()), parse_event_t::value, value); - - // do not handle this value if we just learnt it shall be discarded - if (!keep) - { - return {false, nullptr}; - } - - if (ref_stack.empty()) - { - root = std::move(value); - return {true, &root}; - } - - // skip this value if we already decided to skip the parent - // (https://github.com/nlohmann/json/issues/971#issuecomment-413678360) - if (!ref_stack.back()) - { - return {false, nullptr}; - } - - // we now only expect arrays and objects - JSON_ASSERT(ref_stack.back()->is_array() || ref_stack.back()->is_object()); - - // array - if (ref_stack.back()->is_array()) - { - ref_stack.back()->m_value.array->push_back(std::move(value)); - return {true, &(ref_stack.back()->m_value.array->back())}; - } - - // object - JSON_ASSERT(ref_stack.back()->is_object()); - // check if we should store an element for the current key - JSON_ASSERT(!key_keep_stack.empty()); - const bool store_element = key_keep_stack.back(); - key_keep_stack.pop_back(); - - if (!store_element) - { - return {false, nullptr}; - } - - JSON_ASSERT(object_element); - *object_element = std::move(value); - return {true, object_element}; - } - - /// the parsed JSON value - BasicJsonType& root; - /// stack to model hierarchy of values - std::vector ref_stack {}; - /// stack to manage which values to keep - std::vector keep_stack {}; - /// stack to manage which object keys to keep - std::vector key_keep_stack {}; - /// helper to hold the reference for the next object element - BasicJsonType* object_element = nullptr; - /// whether a syntax error occurred - bool errored = false; - /// callback function - const parser_callback_t callback = nullptr; - /// whether to throw exceptions in case of errors - const bool allow_exceptions = true; - /// a discarded value for the callback - BasicJsonType discarded = BasicJsonType::value_t::discarded; -}; - -template -class json_sax_acceptor -{ - public: - using number_integer_t = typename BasicJsonType::number_integer_t; - using number_unsigned_t = typename BasicJsonType::number_unsigned_t; - using number_float_t = typename BasicJsonType::number_float_t; - using string_t = typename BasicJsonType::string_t; - using binary_t = typename BasicJsonType::binary_t; - - bool null() - { - return true; - } - - bool boolean(bool /*unused*/) - { - return true; - } - - bool number_integer(number_integer_t /*unused*/) - { - return true; - } - - bool number_unsigned(number_unsigned_t /*unused*/) - { - return true; - } - - bool number_float(number_float_t /*unused*/, const string_t& /*unused*/) - { - return true; - } - - bool string(string_t& /*unused*/) - { - return true; - } - - bool binary(binary_t& /*unused*/) - { - return true; - } - - bool start_object(std::size_t /*unused*/ = std::size_t(-1)) - { - return true; - } - - bool key(string_t& /*unused*/) - { - return true; - } - - bool end_object() - { - return true; - } - - bool start_array(std::size_t /*unused*/ = std::size_t(-1)) - { - return true; - } - - bool end_array() - { - return true; - } - - bool parse_error(std::size_t /*unused*/, const std::string& /*unused*/, const detail::exception& /*unused*/) - { - return false; - } -}; -} // namespace detail - -} // namespace nlohmann - -// #include - - -#include // array -#include // localeconv -#include // size_t -#include // snprintf -#include // strtof, strtod, strtold, strtoll, strtoull -#include // initializer_list -#include // char_traits, string -#include // move -#include // vector - -// #include - -// #include - -// #include - - -namespace nlohmann -{ -namespace detail -{ -/////////// -// lexer // -/////////// - -template -class lexer_base -{ - public: - /// token types for the parser - enum class token_type - { - uninitialized, ///< indicating the scanner is uninitialized - literal_true, ///< the `true` literal - literal_false, ///< the `false` literal - literal_null, ///< the `null` literal - value_string, ///< a string -- use get_string() for actual value - value_unsigned, ///< an unsigned integer -- use get_number_unsigned() for actual value - value_integer, ///< a signed integer -- use get_number_integer() for actual value - value_float, ///< an floating point number -- use get_number_float() for actual value - begin_array, ///< the character for array begin `[` - begin_object, ///< the character for object begin `{` - end_array, ///< the character for array end `]` - end_object, ///< the character for object end `}` - name_separator, ///< the name separator `:` - value_separator, ///< the value separator `,` - parse_error, ///< indicating a parse error - end_of_input, ///< indicating the end of the input buffer - literal_or_value ///< a literal or the begin of a value (only for diagnostics) - }; - - /// return name of values of type token_type (only used for errors) - JSON_HEDLEY_RETURNS_NON_NULL - JSON_HEDLEY_CONST - static const char* token_type_name(const token_type t) noexcept - { - switch (t) - { - case token_type::uninitialized: - return ""; - case token_type::literal_true: - return "true literal"; - case token_type::literal_false: - return "false literal"; - case token_type::literal_null: - return "null literal"; - case token_type::value_string: - return "string literal"; - case token_type::value_unsigned: - case token_type::value_integer: - case token_type::value_float: - return "number literal"; - case token_type::begin_array: - return "'['"; - case token_type::begin_object: - return "'{'"; - case token_type::end_array: - return "']'"; - case token_type::end_object: - return "'}'"; - case token_type::name_separator: - return "':'"; - case token_type::value_separator: - return "','"; - case token_type::parse_error: - return ""; - case token_type::end_of_input: - return "end of input"; - case token_type::literal_or_value: - return "'[', '{', or a literal"; - // LCOV_EXCL_START - default: // catch non-enum values - return "unknown token"; - // LCOV_EXCL_STOP - } - } -}; -/*! -@brief lexical analysis - -This class organizes the lexical analysis during JSON deserialization. -*/ -template -class lexer : public lexer_base -{ - using number_integer_t = typename BasicJsonType::number_integer_t; - using number_unsigned_t = typename BasicJsonType::number_unsigned_t; - using number_float_t = typename BasicJsonType::number_float_t; - using string_t = typename BasicJsonType::string_t; - using char_type = typename InputAdapterType::char_type; - using char_int_type = typename std::char_traits::int_type; - - public: - using token_type = typename lexer_base::token_type; - - explicit lexer(InputAdapterType&& adapter, bool ignore_comments_ = false) - : ia(std::move(adapter)) - , ignore_comments(ignore_comments_) - , decimal_point_char(static_cast(get_decimal_point())) - {} - - // delete because of pointer members - lexer(const lexer&) = delete; - lexer(lexer&&) = default; - lexer& operator=(lexer&) = delete; - lexer& operator=(lexer&&) = default; - ~lexer() = default; - - private: - ///////////////////// - // locales - ///////////////////// - - /// return the locale-dependent decimal point - JSON_HEDLEY_PURE - static char get_decimal_point() noexcept - { - const auto* loc = localeconv(); - JSON_ASSERT(loc != nullptr); - return (loc->decimal_point == nullptr) ? '.' : *(loc->decimal_point); - } - - ///////////////////// - // scan functions - ///////////////////// - - /*! - @brief get codepoint from 4 hex characters following `\u` - - For input "\u c1 c2 c3 c4" the codepoint is: - (c1 * 0x1000) + (c2 * 0x0100) + (c3 * 0x0010) + c4 - = (c1 << 12) + (c2 << 8) + (c3 << 4) + (c4 << 0) - - Furthermore, the possible characters '0'..'9', 'A'..'F', and 'a'..'f' - must be converted to the integers 0x0..0x9, 0xA..0xF, 0xA..0xF, resp. The - conversion is done by subtracting the offset (0x30, 0x37, and 0x57) - between the ASCII value of the character and the desired integer value. - - @return codepoint (0x0000..0xFFFF) or -1 in case of an error (e.g. EOF or - non-hex character) - */ - int get_codepoint() - { - // this function only makes sense after reading `\u` - JSON_ASSERT(current == 'u'); - int codepoint = 0; - - const auto factors = { 12u, 8u, 4u, 0u }; - for (const auto factor : factors) - { - get(); - - if (current >= '0' && current <= '9') - { - codepoint += static_cast((static_cast(current) - 0x30u) << factor); - } - else if (current >= 'A' && current <= 'F') - { - codepoint += static_cast((static_cast(current) - 0x37u) << factor); - } - else if (current >= 'a' && current <= 'f') - { - codepoint += static_cast((static_cast(current) - 0x57u) << factor); - } - else - { - return -1; - } - } - - JSON_ASSERT(0x0000 <= codepoint && codepoint <= 0xFFFF); - return codepoint; - } - - /*! - @brief check if the next byte(s) are inside a given range - - Adds the current byte and, for each passed range, reads a new byte and - checks if it is inside the range. If a violation was detected, set up an - error message and return false. Otherwise, return true. - - @param[in] ranges list of integers; interpreted as list of pairs of - inclusive lower and upper bound, respectively - - @pre The passed list @a ranges must have 2, 4, or 6 elements; that is, - 1, 2, or 3 pairs. This precondition is enforced by an assertion. - - @return true if and only if no range violation was detected - */ - bool next_byte_in_range(std::initializer_list ranges) - { - JSON_ASSERT(ranges.size() == 2 || ranges.size() == 4 || ranges.size() == 6); - add(current); - - for (auto range = ranges.begin(); range != ranges.end(); ++range) - { - get(); - if (JSON_HEDLEY_LIKELY(*range <= current && current <= *(++range))) - { - add(current); - } - else - { - error_message = "invalid string: ill-formed UTF-8 byte"; - return false; - } - } - - return true; - } - - /*! - @brief scan a string literal - - This function scans a string according to Sect. 7 of RFC 7159. While - scanning, bytes are escaped and copied into buffer token_buffer. Then the - function returns successfully, token_buffer is *not* null-terminated (as it - may contain \0 bytes), and token_buffer.size() is the number of bytes in the - string. - - @return token_type::value_string if string could be successfully scanned, - token_type::parse_error otherwise - - @note In case of errors, variable error_message contains a textual - description. - */ - token_type scan_string() - { - // reset token_buffer (ignore opening quote) - reset(); - - // we entered the function by reading an open quote - JSON_ASSERT(current == '\"'); - - while (true) - { - // get next character - switch (get()) - { - // end of file while parsing string - case std::char_traits::eof(): - { - error_message = "invalid string: missing closing quote"; - return token_type::parse_error; - } - - // closing quote - case '\"': - { - return token_type::value_string; - } - - // escapes - case '\\': - { - switch (get()) - { - // quotation mark - case '\"': - add('\"'); - break; - // reverse solidus - case '\\': - add('\\'); - break; - // solidus - case '/': - add('/'); - break; - // backspace - case 'b': - add('\b'); - break; - // form feed - case 'f': - add('\f'); - break; - // line feed - case 'n': - add('\n'); - break; - // carriage return - case 'r': - add('\r'); - break; - // tab - case 't': - add('\t'); - break; - - // unicode escapes - case 'u': - { - const int codepoint1 = get_codepoint(); - int codepoint = codepoint1; // start with codepoint1 - - if (JSON_HEDLEY_UNLIKELY(codepoint1 == -1)) - { - error_message = "invalid string: '\\u' must be followed by 4 hex digits"; - return token_type::parse_error; - } - - // check if code point is a high surrogate - if (0xD800 <= codepoint1 && codepoint1 <= 0xDBFF) - { - // expect next \uxxxx entry - if (JSON_HEDLEY_LIKELY(get() == '\\' && get() == 'u')) - { - const int codepoint2 = get_codepoint(); - - if (JSON_HEDLEY_UNLIKELY(codepoint2 == -1)) - { - error_message = "invalid string: '\\u' must be followed by 4 hex digits"; - return token_type::parse_error; - } - - // check if codepoint2 is a low surrogate - if (JSON_HEDLEY_LIKELY(0xDC00 <= codepoint2 && codepoint2 <= 0xDFFF)) - { - // overwrite codepoint - codepoint = static_cast( - // high surrogate occupies the most significant 22 bits - (static_cast(codepoint1) << 10u) - // low surrogate occupies the least significant 15 bits - + static_cast(codepoint2) - // there is still the 0xD800, 0xDC00 and 0x10000 noise - // in the result so we have to subtract with: - // (0xD800 << 10) + DC00 - 0x10000 = 0x35FDC00 - - 0x35FDC00u); - } - else - { - error_message = "invalid string: surrogate U+D800..U+DBFF must be followed by U+DC00..U+DFFF"; - return token_type::parse_error; - } - } - else - { - error_message = "invalid string: surrogate U+D800..U+DBFF must be followed by U+DC00..U+DFFF"; - return token_type::parse_error; - } - } - else - { - if (JSON_HEDLEY_UNLIKELY(0xDC00 <= codepoint1 && codepoint1 <= 0xDFFF)) - { - error_message = "invalid string: surrogate U+DC00..U+DFFF must follow U+D800..U+DBFF"; - return token_type::parse_error; - } - } - - // result of the above calculation yields a proper codepoint - JSON_ASSERT(0x00 <= codepoint && codepoint <= 0x10FFFF); - - // translate codepoint into bytes - if (codepoint < 0x80) - { - // 1-byte characters: 0xxxxxxx (ASCII) - add(static_cast(codepoint)); - } - else if (codepoint <= 0x7FF) - { - // 2-byte characters: 110xxxxx 10xxxxxx - add(static_cast(0xC0u | (static_cast(codepoint) >> 6u))); - add(static_cast(0x80u | (static_cast(codepoint) & 0x3Fu))); - } - else if (codepoint <= 0xFFFF) - { - // 3-byte characters: 1110xxxx 10xxxxxx 10xxxxxx - add(static_cast(0xE0u | (static_cast(codepoint) >> 12u))); - add(static_cast(0x80u | ((static_cast(codepoint) >> 6u) & 0x3Fu))); - add(static_cast(0x80u | (static_cast(codepoint) & 0x3Fu))); - } - else - { - // 4-byte characters: 11110xxx 10xxxxxx 10xxxxxx 10xxxxxx - add(static_cast(0xF0u | (static_cast(codepoint) >> 18u))); - add(static_cast(0x80u | ((static_cast(codepoint) >> 12u) & 0x3Fu))); - add(static_cast(0x80u | ((static_cast(codepoint) >> 6u) & 0x3Fu))); - add(static_cast(0x80u | (static_cast(codepoint) & 0x3Fu))); - } - - break; - } - - // other characters after escape - default: - error_message = "invalid string: forbidden character after backslash"; - return token_type::parse_error; - } - - break; - } - - // invalid control characters - case 0x00: - { - error_message = "invalid string: control character U+0000 (NUL) must be escaped to \\u0000"; - return token_type::parse_error; - } - - case 0x01: - { - error_message = "invalid string: control character U+0001 (SOH) must be escaped to \\u0001"; - return token_type::parse_error; - } - - case 0x02: - { - error_message = "invalid string: control character U+0002 (STX) must be escaped to \\u0002"; - return token_type::parse_error; - } - - case 0x03: - { - error_message = "invalid string: control character U+0003 (ETX) must be escaped to \\u0003"; - return token_type::parse_error; - } - - case 0x04: - { - error_message = "invalid string: control character U+0004 (EOT) must be escaped to \\u0004"; - return token_type::parse_error; - } - - case 0x05: - { - error_message = "invalid string: control character U+0005 (ENQ) must be escaped to \\u0005"; - return token_type::parse_error; - } - - case 0x06: - { - error_message = "invalid string: control character U+0006 (ACK) must be escaped to \\u0006"; - return token_type::parse_error; - } - - case 0x07: - { - error_message = "invalid string: control character U+0007 (BEL) must be escaped to \\u0007"; - return token_type::parse_error; - } - - case 0x08: - { - error_message = "invalid string: control character U+0008 (BS) must be escaped to \\u0008 or \\b"; - return token_type::parse_error; - } - - case 0x09: - { - error_message = "invalid string: control character U+0009 (HT) must be escaped to \\u0009 or \\t"; - return token_type::parse_error; - } - - case 0x0A: - { - error_message = "invalid string: control character U+000A (LF) must be escaped to \\u000A or \\n"; - return token_type::parse_error; - } - - case 0x0B: - { - error_message = "invalid string: control character U+000B (VT) must be escaped to \\u000B"; - return token_type::parse_error; - } - - case 0x0C: - { - error_message = "invalid string: control character U+000C (FF) must be escaped to \\u000C or \\f"; - return token_type::parse_error; - } - - case 0x0D: - { - error_message = "invalid string: control character U+000D (CR) must be escaped to \\u000D or \\r"; - return token_type::parse_error; - } - - case 0x0E: - { - error_message = "invalid string: control character U+000E (SO) must be escaped to \\u000E"; - return token_type::parse_error; - } - - case 0x0F: - { - error_message = "invalid string: control character U+000F (SI) must be escaped to \\u000F"; - return token_type::parse_error; - } - - case 0x10: - { - error_message = "invalid string: control character U+0010 (DLE) must be escaped to \\u0010"; - return token_type::parse_error; - } - - case 0x11: - { - error_message = "invalid string: control character U+0011 (DC1) must be escaped to \\u0011"; - return token_type::parse_error; - } - - case 0x12: - { - error_message = "invalid string: control character U+0012 (DC2) must be escaped to \\u0012"; - return token_type::parse_error; - } - - case 0x13: - { - error_message = "invalid string: control character U+0013 (DC3) must be escaped to \\u0013"; - return token_type::parse_error; - } - - case 0x14: - { - error_message = "invalid string: control character U+0014 (DC4) must be escaped to \\u0014"; - return token_type::parse_error; - } - - case 0x15: - { - error_message = "invalid string: control character U+0015 (NAK) must be escaped to \\u0015"; - return token_type::parse_error; - } - - case 0x16: - { - error_message = "invalid string: control character U+0016 (SYN) must be escaped to \\u0016"; - return token_type::parse_error; - } - - case 0x17: - { - error_message = "invalid string: control character U+0017 (ETB) must be escaped to \\u0017"; - return token_type::parse_error; - } - - case 0x18: - { - error_message = "invalid string: control character U+0018 (CAN) must be escaped to \\u0018"; - return token_type::parse_error; - } - - case 0x19: - { - error_message = "invalid string: control character U+0019 (EM) must be escaped to \\u0019"; - return token_type::parse_error; - } - - case 0x1A: - { - error_message = "invalid string: control character U+001A (SUB) must be escaped to \\u001A"; - return token_type::parse_error; - } - - case 0x1B: - { - error_message = "invalid string: control character U+001B (ESC) must be escaped to \\u001B"; - return token_type::parse_error; - } - - case 0x1C: - { - error_message = "invalid string: control character U+001C (FS) must be escaped to \\u001C"; - return token_type::parse_error; - } - - case 0x1D: - { - error_message = "invalid string: control character U+001D (GS) must be escaped to \\u001D"; - return token_type::parse_error; - } - - case 0x1E: - { - error_message = "invalid string: control character U+001E (RS) must be escaped to \\u001E"; - return token_type::parse_error; - } - - case 0x1F: - { - error_message = "invalid string: control character U+001F (US) must be escaped to \\u001F"; - return token_type::parse_error; - } - - // U+0020..U+007F (except U+0022 (quote) and U+005C (backspace)) - case 0x20: - case 0x21: - case 0x23: - case 0x24: - case 0x25: - case 0x26: - case 0x27: - case 0x28: - case 0x29: - case 0x2A: - case 0x2B: - case 0x2C: - case 0x2D: - case 0x2E: - case 0x2F: - case 0x30: - case 0x31: - case 0x32: - case 0x33: - case 0x34: - case 0x35: - case 0x36: - case 0x37: - case 0x38: - case 0x39: - case 0x3A: - case 0x3B: - case 0x3C: - case 0x3D: - case 0x3E: - case 0x3F: - case 0x40: - case 0x41: - case 0x42: - case 0x43: - case 0x44: - case 0x45: - case 0x46: - case 0x47: - case 0x48: - case 0x49: - case 0x4A: - case 0x4B: - case 0x4C: - case 0x4D: - case 0x4E: - case 0x4F: - case 0x50: - case 0x51: - case 0x52: - case 0x53: - case 0x54: - case 0x55: - case 0x56: - case 0x57: - case 0x58: - case 0x59: - case 0x5A: - case 0x5B: - case 0x5D: - case 0x5E: - case 0x5F: - case 0x60: - case 0x61: - case 0x62: - case 0x63: - case 0x64: - case 0x65: - case 0x66: - case 0x67: - case 0x68: - case 0x69: - case 0x6A: - case 0x6B: - case 0x6C: - case 0x6D: - case 0x6E: - case 0x6F: - case 0x70: - case 0x71: - case 0x72: - case 0x73: - case 0x74: - case 0x75: - case 0x76: - case 0x77: - case 0x78: - case 0x79: - case 0x7A: - case 0x7B: - case 0x7C: - case 0x7D: - case 0x7E: - case 0x7F: - { - add(current); - break; - } - - // U+0080..U+07FF: bytes C2..DF 80..BF - case 0xC2: - case 0xC3: - case 0xC4: - case 0xC5: - case 0xC6: - case 0xC7: - case 0xC8: - case 0xC9: - case 0xCA: - case 0xCB: - case 0xCC: - case 0xCD: - case 0xCE: - case 0xCF: - case 0xD0: - case 0xD1: - case 0xD2: - case 0xD3: - case 0xD4: - case 0xD5: - case 0xD6: - case 0xD7: - case 0xD8: - case 0xD9: - case 0xDA: - case 0xDB: - case 0xDC: - case 0xDD: - case 0xDE: - case 0xDF: - { - if (JSON_HEDLEY_UNLIKELY(!next_byte_in_range({0x80, 0xBF}))) - { - return token_type::parse_error; - } - break; - } - - // U+0800..U+0FFF: bytes E0 A0..BF 80..BF - case 0xE0: - { - if (JSON_HEDLEY_UNLIKELY(!(next_byte_in_range({0xA0, 0xBF, 0x80, 0xBF})))) - { - return token_type::parse_error; - } - break; - } - - // U+1000..U+CFFF: bytes E1..EC 80..BF 80..BF - // U+E000..U+FFFF: bytes EE..EF 80..BF 80..BF - case 0xE1: - case 0xE2: - case 0xE3: - case 0xE4: - case 0xE5: - case 0xE6: - case 0xE7: - case 0xE8: - case 0xE9: - case 0xEA: - case 0xEB: - case 0xEC: - case 0xEE: - case 0xEF: - { - if (JSON_HEDLEY_UNLIKELY(!(next_byte_in_range({0x80, 0xBF, 0x80, 0xBF})))) - { - return token_type::parse_error; - } - break; - } - - // U+D000..U+D7FF: bytes ED 80..9F 80..BF - case 0xED: - { - if (JSON_HEDLEY_UNLIKELY(!(next_byte_in_range({0x80, 0x9F, 0x80, 0xBF})))) - { - return token_type::parse_error; - } - break; - } - - // U+10000..U+3FFFF F0 90..BF 80..BF 80..BF - case 0xF0: - { - if (JSON_HEDLEY_UNLIKELY(!(next_byte_in_range({0x90, 0xBF, 0x80, 0xBF, 0x80, 0xBF})))) - { - return token_type::parse_error; - } - break; - } - - // U+40000..U+FFFFF F1..F3 80..BF 80..BF 80..BF - case 0xF1: - case 0xF2: - case 0xF3: - { - if (JSON_HEDLEY_UNLIKELY(!(next_byte_in_range({0x80, 0xBF, 0x80, 0xBF, 0x80, 0xBF})))) - { - return token_type::parse_error; - } - break; - } - - // U+100000..U+10FFFF F4 80..8F 80..BF 80..BF - case 0xF4: - { - if (JSON_HEDLEY_UNLIKELY(!(next_byte_in_range({0x80, 0x8F, 0x80, 0xBF, 0x80, 0xBF})))) - { - return token_type::parse_error; - } - break; - } - - // remaining bytes (80..C1 and F5..FF) are ill-formed - default: - { - error_message = "invalid string: ill-formed UTF-8 byte"; - return token_type::parse_error; - } - } - } - } - - /*! - * @brief scan a comment - * @return whether comment could be scanned successfully - */ - bool scan_comment() - { - switch (get()) - { - // single-line comments skip input until a newline or EOF is read - case '/': - { - while (true) - { - switch (get()) - { - case '\n': - case '\r': - case std::char_traits::eof(): - case '\0': - return true; - - default: - break; - } - } - } - - // multi-line comments skip input until */ is read - case '*': - { - while (true) - { - switch (get()) - { - case std::char_traits::eof(): - case '\0': - { - error_message = "invalid comment; missing closing '*/'"; - return false; - } - - case '*': - { - switch (get()) - { - case '/': - return true; - - default: - { - unget(); - continue; - } - } - } - - default: - continue; - } - } - } - - // unexpected character after reading '/' - default: - { - error_message = "invalid comment; expecting '/' or '*' after '/'"; - return false; - } - } - } - - JSON_HEDLEY_NON_NULL(2) - static void strtof(float& f, const char* str, char** endptr) noexcept - { - f = std::strtof(str, endptr); - } - - JSON_HEDLEY_NON_NULL(2) - static void strtof(double& f, const char* str, char** endptr) noexcept - { - f = std::strtod(str, endptr); - } - - JSON_HEDLEY_NON_NULL(2) - static void strtof(long double& f, const char* str, char** endptr) noexcept - { - f = std::strtold(str, endptr); - } - - /*! - @brief scan a number literal - - This function scans a string according to Sect. 6 of RFC 7159. - - The function is realized with a deterministic finite state machine derived - from the grammar described in RFC 7159. Starting in state "init", the - input is read and used to determined the next state. Only state "done" - accepts the number. State "error" is a trap state to model errors. In the - table below, "anything" means any character but the ones listed before. - - state | 0 | 1-9 | e E | + | - | . | anything - ---------|----------|----------|----------|---------|---------|----------|----------- - init | zero | any1 | [error] | [error] | minus | [error] | [error] - minus | zero | any1 | [error] | [error] | [error] | [error] | [error] - zero | done | done | exponent | done | done | decimal1 | done - any1 | any1 | any1 | exponent | done | done | decimal1 | done - decimal1 | decimal2 | decimal2 | [error] | [error] | [error] | [error] | [error] - decimal2 | decimal2 | decimal2 | exponent | done | done | done | done - exponent | any2 | any2 | [error] | sign | sign | [error] | [error] - sign | any2 | any2 | [error] | [error] | [error] | [error] | [error] - any2 | any2 | any2 | done | done | done | done | done - - The state machine is realized with one label per state (prefixed with - "scan_number_") and `goto` statements between them. The state machine - contains cycles, but any cycle can be left when EOF is read. Therefore, - the function is guaranteed to terminate. - - During scanning, the read bytes are stored in token_buffer. This string is - then converted to a signed integer, an unsigned integer, or a - floating-point number. - - @return token_type::value_unsigned, token_type::value_integer, or - token_type::value_float if number could be successfully scanned, - token_type::parse_error otherwise - - @note The scanner is independent of the current locale. Internally, the - locale's decimal point is used instead of `.` to work with the - locale-dependent converters. - */ - token_type scan_number() // lgtm [cpp/use-of-goto] - { - // reset token_buffer to store the number's bytes - reset(); - - // the type of the parsed number; initially set to unsigned; will be - // changed if minus sign, decimal point or exponent is read - token_type number_type = token_type::value_unsigned; - - // state (init): we just found out we need to scan a number - switch (current) - { - case '-': - { - add(current); - goto scan_number_minus; - } - - case '0': - { - add(current); - goto scan_number_zero; - } - - case '1': - case '2': - case '3': - case '4': - case '5': - case '6': - case '7': - case '8': - case '9': - { - add(current); - goto scan_number_any1; - } - - // all other characters are rejected outside scan_number() - default: // LCOV_EXCL_LINE - JSON_ASSERT(false); // LCOV_EXCL_LINE - } - -scan_number_minus: - // state: we just parsed a leading minus sign - number_type = token_type::value_integer; - switch (get()) - { - case '0': - { - add(current); - goto scan_number_zero; - } - - case '1': - case '2': - case '3': - case '4': - case '5': - case '6': - case '7': - case '8': - case '9': - { - add(current); - goto scan_number_any1; - } - - default: - { - error_message = "invalid number; expected digit after '-'"; - return token_type::parse_error; - } - } - -scan_number_zero: - // state: we just parse a zero (maybe with a leading minus sign) - switch (get()) - { - case '.': - { - add(decimal_point_char); - goto scan_number_decimal1; - } - - case 'e': - case 'E': - { - add(current); - goto scan_number_exponent; - } - - default: - goto scan_number_done; - } - -scan_number_any1: - // state: we just parsed a number 0-9 (maybe with a leading minus sign) - switch (get()) - { - case '0': - case '1': - case '2': - case '3': - case '4': - case '5': - case '6': - case '7': - case '8': - case '9': - { - add(current); - goto scan_number_any1; - } - - case '.': - { - add(decimal_point_char); - goto scan_number_decimal1; - } - - case 'e': - case 'E': - { - add(current); - goto scan_number_exponent; - } - - default: - goto scan_number_done; - } - -scan_number_decimal1: - // state: we just parsed a decimal point - number_type = token_type::value_float; - switch (get()) - { - case '0': - case '1': - case '2': - case '3': - case '4': - case '5': - case '6': - case '7': - case '8': - case '9': - { - add(current); - goto scan_number_decimal2; - } - - default: - { - error_message = "invalid number; expected digit after '.'"; - return token_type::parse_error; - } - } - -scan_number_decimal2: - // we just parsed at least one number after a decimal point - switch (get()) - { - case '0': - case '1': - case '2': - case '3': - case '4': - case '5': - case '6': - case '7': - case '8': - case '9': - { - add(current); - goto scan_number_decimal2; - } - - case 'e': - case 'E': - { - add(current); - goto scan_number_exponent; - } - - default: - goto scan_number_done; - } - -scan_number_exponent: - // we just parsed an exponent - number_type = token_type::value_float; - switch (get()) - { - case '+': - case '-': - { - add(current); - goto scan_number_sign; - } - - case '0': - case '1': - case '2': - case '3': - case '4': - case '5': - case '6': - case '7': - case '8': - case '9': - { - add(current); - goto scan_number_any2; - } - - default: - { - error_message = - "invalid number; expected '+', '-', or digit after exponent"; - return token_type::parse_error; - } - } - -scan_number_sign: - // we just parsed an exponent sign - switch (get()) - { - case '0': - case '1': - case '2': - case '3': - case '4': - case '5': - case '6': - case '7': - case '8': - case '9': - { - add(current); - goto scan_number_any2; - } - - default: - { - error_message = "invalid number; expected digit after exponent sign"; - return token_type::parse_error; - } - } - -scan_number_any2: - // we just parsed a number after the exponent or exponent sign - switch (get()) - { - case '0': - case '1': - case '2': - case '3': - case '4': - case '5': - case '6': - case '7': - case '8': - case '9': - { - add(current); - goto scan_number_any2; - } - - default: - goto scan_number_done; - } - -scan_number_done: - // unget the character after the number (we only read it to know that - // we are done scanning a number) - unget(); - - char* endptr = nullptr; - errno = 0; - - // try to parse integers first and fall back to floats - if (number_type == token_type::value_unsigned) - { - const auto x = std::strtoull(token_buffer.data(), &endptr, 10); - - // we checked the number format before - JSON_ASSERT(endptr == token_buffer.data() + token_buffer.size()); - - if (errno == 0) - { - value_unsigned = static_cast(x); - if (value_unsigned == x) - { - return token_type::value_unsigned; - } - } - } - else if (number_type == token_type::value_integer) - { - const auto x = std::strtoll(token_buffer.data(), &endptr, 10); - - // we checked the number format before - JSON_ASSERT(endptr == token_buffer.data() + token_buffer.size()); - - if (errno == 0) - { - value_integer = static_cast(x); - if (value_integer == x) - { - return token_type::value_integer; - } - } - } - - // this code is reached if we parse a floating-point number or if an - // integer conversion above failed - strtof(value_float, token_buffer.data(), &endptr); - - // we checked the number format before - JSON_ASSERT(endptr == token_buffer.data() + token_buffer.size()); - - return token_type::value_float; - } - - /*! - @param[in] literal_text the literal text to expect - @param[in] length the length of the passed literal text - @param[in] return_type the token type to return on success - */ - JSON_HEDLEY_NON_NULL(2) - token_type scan_literal(const char_type* literal_text, const std::size_t length, - token_type return_type) - { - JSON_ASSERT(std::char_traits::to_char_type(current) == literal_text[0]); - for (std::size_t i = 1; i < length; ++i) - { - if (JSON_HEDLEY_UNLIKELY(std::char_traits::to_char_type(get()) != literal_text[i])) - { - error_message = "invalid literal"; - return token_type::parse_error; - } - } - return return_type; - } - - ///////////////////// - // input management - ///////////////////// - - /// reset token_buffer; current character is beginning of token - void reset() noexcept - { - token_buffer.clear(); - token_string.clear(); - token_string.push_back(std::char_traits::to_char_type(current)); - } - - /* - @brief get next character from the input - - This function provides the interface to the used input adapter. It does - not throw in case the input reached EOF, but returns a - `std::char_traits::eof()` in that case. Stores the scanned characters - for use in error messages. - - @return character read from the input - */ - char_int_type get() - { - ++position.chars_read_total; - ++position.chars_read_current_line; - - if (next_unget) - { - // just reset the next_unget variable and work with current - next_unget = false; - } - else - { - current = ia.get_character(); - } - - if (JSON_HEDLEY_LIKELY(current != std::char_traits::eof())) - { - token_string.push_back(std::char_traits::to_char_type(current)); - } - - if (current == '\n') - { - ++position.lines_read; - position.chars_read_current_line = 0; - } - - return current; - } - - /*! - @brief unget current character (read it again on next get) - - We implement unget by setting variable next_unget to true. The input is not - changed - we just simulate ungetting by modifying chars_read_total, - chars_read_current_line, and token_string. The next call to get() will - behave as if the unget character is read again. - */ - void unget() - { - next_unget = true; - - --position.chars_read_total; - - // in case we "unget" a newline, we have to also decrement the lines_read - if (position.chars_read_current_line == 0) - { - if (position.lines_read > 0) - { - --position.lines_read; - } - } - else - { - --position.chars_read_current_line; - } - - if (JSON_HEDLEY_LIKELY(current != std::char_traits::eof())) - { - JSON_ASSERT(!token_string.empty()); - token_string.pop_back(); - } - } - - /// add a character to token_buffer - void add(char_int_type c) - { - token_buffer.push_back(static_cast(c)); - } - - public: - ///////////////////// - // value getters - ///////////////////// - - /// return integer value - constexpr number_integer_t get_number_integer() const noexcept - { - return value_integer; - } - - /// return unsigned integer value - constexpr number_unsigned_t get_number_unsigned() const noexcept - { - return value_unsigned; - } - - /// return floating-point value - constexpr number_float_t get_number_float() const noexcept - { - return value_float; - } - - /// return current string value (implicitly resets the token; useful only once) - string_t& get_string() - { - return token_buffer; - } - - ///////////////////// - // diagnostics - ///////////////////// - - /// return position of last read token - constexpr position_t get_position() const noexcept - { - return position; - } - - /// return the last read token (for errors only). Will never contain EOF - /// (an arbitrary value that is not a valid char value, often -1), because - /// 255 may legitimately occur. May contain NUL, which should be escaped. - std::string get_token_string() const - { - // escape control characters - std::string result; - for (const auto c : token_string) - { - if (static_cast(c) <= '\x1F') - { - // escape control characters - std::array cs{{}}; - (std::snprintf)(cs.data(), cs.size(), "", static_cast(c)); - result += cs.data(); - } - else - { - // add character as is - result.push_back(static_cast(c)); - } - } - - return result; - } - - /// return syntax error message - JSON_HEDLEY_RETURNS_NON_NULL - constexpr const char* get_error_message() const noexcept - { - return error_message; - } - - ///////////////////// - // actual scanner - ///////////////////// - - /*! - @brief skip the UTF-8 byte order mark - @return true iff there is no BOM or the correct BOM has been skipped - */ - bool skip_bom() - { - if (get() == 0xEF) - { - // check if we completely parse the BOM - return get() == 0xBB && get() == 0xBF; - } - - // the first character is not the beginning of the BOM; unget it to - // process is later - unget(); - return true; - } - - void skip_whitespace() - { - do - { - get(); - } - while (current == ' ' || current == '\t' || current == '\n' || current == '\r'); - } - - token_type scan() - { - // initially, skip the BOM - if (position.chars_read_total == 0 && !skip_bom()) - { - error_message = "invalid BOM; must be 0xEF 0xBB 0xBF if given"; - return token_type::parse_error; - } - - // read next character and ignore whitespace - skip_whitespace(); - - // ignore comments - while (ignore_comments && current == '/') - { - if (!scan_comment()) - { - return token_type::parse_error; - } - - // skip following whitespace - skip_whitespace(); - } - - switch (current) - { - // structural characters - case '[': - return token_type::begin_array; - case ']': - return token_type::end_array; - case '{': - return token_type::begin_object; - case '}': - return token_type::end_object; - case ':': - return token_type::name_separator; - case ',': - return token_type::value_separator; - - // literals - case 't': - { - std::array true_literal = {{'t', 'r', 'u', 'e'}}; - return scan_literal(true_literal.data(), true_literal.size(), token_type::literal_true); - } - case 'f': - { - std::array false_literal = {{'f', 'a', 'l', 's', 'e'}}; - return scan_literal(false_literal.data(), false_literal.size(), token_type::literal_false); - } - case 'n': - { - std::array null_literal = {{'n', 'u', 'l', 'l'}}; - return scan_literal(null_literal.data(), null_literal.size(), token_type::literal_null); - } - - // string - case '\"': - return scan_string(); - - // number - case '-': - case '0': - case '1': - case '2': - case '3': - case '4': - case '5': - case '6': - case '7': - case '8': - case '9': - return scan_number(); - - // end of input (the null byte is needed when parsing from - // string literals) - case '\0': - case std::char_traits::eof(): - return token_type::end_of_input; - - // error - default: - error_message = "invalid literal"; - return token_type::parse_error; - } - } - - private: - /// input adapter - InputAdapterType ia; - - /// whether comments should be ignored (true) or signaled as errors (false) - const bool ignore_comments = false; - - /// the current character - char_int_type current = std::char_traits::eof(); - - /// whether the next get() call should just return current - bool next_unget = false; - - /// the start position of the current token - position_t position {}; - - /// raw input token string (for error messages) - std::vector token_string {}; - - /// buffer for variable-length tokens (numbers, strings) - string_t token_buffer {}; - - /// a description of occurred lexer errors - const char* error_message = ""; - - // number values - number_integer_t value_integer = 0; - number_unsigned_t value_unsigned = 0; - number_float_t value_float = 0; - - /// the decimal point - const char_int_type decimal_point_char = '.'; -}; -} // namespace detail -} // namespace nlohmann - -// #include - -// #include - - -#include // size_t -#include // declval -#include // string - -// #include - -// #include - - -namespace nlohmann -{ -namespace detail -{ -template -using null_function_t = decltype(std::declval().null()); - -template -using boolean_function_t = - decltype(std::declval().boolean(std::declval())); - -template -using number_integer_function_t = - decltype(std::declval().number_integer(std::declval())); - -template -using number_unsigned_function_t = - decltype(std::declval().number_unsigned(std::declval())); - -template -using number_float_function_t = decltype(std::declval().number_float( - std::declval(), std::declval())); - -template -using string_function_t = - decltype(std::declval().string(std::declval())); - -template -using binary_function_t = - decltype(std::declval().binary(std::declval())); - -template -using start_object_function_t = - decltype(std::declval().start_object(std::declval())); - -template -using key_function_t = - decltype(std::declval().key(std::declval())); - -template -using end_object_function_t = decltype(std::declval().end_object()); - -template -using start_array_function_t = - decltype(std::declval().start_array(std::declval())); - -template -using end_array_function_t = decltype(std::declval().end_array()); - -template -using parse_error_function_t = decltype(std::declval().parse_error( - std::declval(), std::declval(), - std::declval())); - -template -struct is_sax -{ - private: - static_assert(is_basic_json::value, - "BasicJsonType must be of type basic_json<...>"); - - using number_integer_t = typename BasicJsonType::number_integer_t; - using number_unsigned_t = typename BasicJsonType::number_unsigned_t; - using number_float_t = typename BasicJsonType::number_float_t; - using string_t = typename BasicJsonType::string_t; - using binary_t = typename BasicJsonType::binary_t; - using exception_t = typename BasicJsonType::exception; - - public: - static constexpr bool value = - is_detected_exact::value && - is_detected_exact::value && - is_detected_exact::value && - is_detected_exact::value && - is_detected_exact::value && - is_detected_exact::value && - is_detected_exact::value && - is_detected_exact::value && - is_detected_exact::value && - is_detected_exact::value && - is_detected_exact::value && - is_detected_exact::value && - is_detected_exact::value; -}; - -template -struct is_sax_static_asserts -{ - private: - static_assert(is_basic_json::value, - "BasicJsonType must be of type basic_json<...>"); - - using number_integer_t = typename BasicJsonType::number_integer_t; - using number_unsigned_t = typename BasicJsonType::number_unsigned_t; - using number_float_t = typename BasicJsonType::number_float_t; - using string_t = typename BasicJsonType::string_t; - using binary_t = typename BasicJsonType::binary_t; - using exception_t = typename BasicJsonType::exception; - - public: - static_assert(is_detected_exact::value, - "Missing/invalid function: bool null()"); - static_assert(is_detected_exact::value, - "Missing/invalid function: bool boolean(bool)"); - static_assert(is_detected_exact::value, - "Missing/invalid function: bool boolean(bool)"); - static_assert( - is_detected_exact::value, - "Missing/invalid function: bool number_integer(number_integer_t)"); - static_assert( - is_detected_exact::value, - "Missing/invalid function: bool number_unsigned(number_unsigned_t)"); - static_assert(is_detected_exact::value, - "Missing/invalid function: bool number_float(number_float_t, const string_t&)"); - static_assert( - is_detected_exact::value, - "Missing/invalid function: bool string(string_t&)"); - static_assert( - is_detected_exact::value, - "Missing/invalid function: bool binary(binary_t&)"); - static_assert(is_detected_exact::value, - "Missing/invalid function: bool start_object(std::size_t)"); - static_assert(is_detected_exact::value, - "Missing/invalid function: bool key(string_t&)"); - static_assert(is_detected_exact::value, - "Missing/invalid function: bool end_object()"); - static_assert(is_detected_exact::value, - "Missing/invalid function: bool start_array(std::size_t)"); - static_assert(is_detected_exact::value, - "Missing/invalid function: bool end_array()"); - static_assert( - is_detected_exact::value, - "Missing/invalid function: bool parse_error(std::size_t, const " - "std::string&, const exception&)"); -}; -} // namespace detail -} // namespace nlohmann - -// #include - - -namespace nlohmann -{ -namespace detail -{ - -/// how to treat CBOR tags -enum class cbor_tag_handler_t -{ - error, ///< throw a parse_error exception in case of a tag - ignore ///< ignore tags -}; - -/*! -@brief determine system byte order - -@return true if and only if system's byte order is little endian - -@note from https://stackoverflow.com/a/1001328/266378 -*/ -static inline bool little_endianess(int num = 1) noexcept -{ - return *reinterpret_cast(&num) == 1; -} - - -/////////////////// -// binary reader // -/////////////////// - -/*! -@brief deserialization of CBOR, MessagePack, and UBJSON values -*/ -template> -class binary_reader -{ - using number_integer_t = typename BasicJsonType::number_integer_t; - using number_unsigned_t = typename BasicJsonType::number_unsigned_t; - using number_float_t = typename BasicJsonType::number_float_t; - using string_t = typename BasicJsonType::string_t; - using binary_t = typename BasicJsonType::binary_t; - using json_sax_t = SAX; - using char_type = typename InputAdapterType::char_type; - using char_int_type = typename std::char_traits::int_type; - - public: - /*! - @brief create a binary reader - - @param[in] adapter input adapter to read from - */ - explicit binary_reader(InputAdapterType&& adapter) : ia(std::move(adapter)) - { - (void)detail::is_sax_static_asserts {}; - } - - // make class move-only - binary_reader(const binary_reader&) = delete; - binary_reader(binary_reader&&) = default; - binary_reader& operator=(const binary_reader&) = delete; - binary_reader& operator=(binary_reader&&) = default; - ~binary_reader() = default; - - /*! - @param[in] format the binary format to parse - @param[in] sax_ a SAX event processor - @param[in] strict whether to expect the input to be consumed completed - @param[in] tag_handler how to treat CBOR tags - - @return - */ - JSON_HEDLEY_NON_NULL(3) - bool sax_parse(const input_format_t format, - json_sax_t* sax_, - const bool strict = true, - const cbor_tag_handler_t tag_handler = cbor_tag_handler_t::error) - { - sax = sax_; - bool result = false; - - switch (format) - { - case input_format_t::bson: - result = parse_bson_internal(); - break; - - case input_format_t::cbor: - result = parse_cbor_internal(true, tag_handler); - break; - - case input_format_t::msgpack: - result = parse_msgpack_internal(); - break; - - case input_format_t::ubjson: - result = parse_ubjson_internal(); - break; - - default: // LCOV_EXCL_LINE - JSON_ASSERT(false); // LCOV_EXCL_LINE - } - - // strict mode: next byte must be EOF - if (result && strict) - { - if (format == input_format_t::ubjson) - { - get_ignore_noop(); - } - else - { - get(); - } - - if (JSON_HEDLEY_UNLIKELY(current != std::char_traits::eof())) - { - return sax->parse_error(chars_read, get_token_string(), - parse_error::create(110, chars_read, exception_message(format, "expected end of input; last byte: 0x" + get_token_string(), "value"))); - } - } - - return result; - } - - private: - ////////// - // BSON // - ////////// - - /*! - @brief Reads in a BSON-object and passes it to the SAX-parser. - @return whether a valid BSON-value was passed to the SAX parser - */ - bool parse_bson_internal() - { - std::int32_t document_size{}; - get_number(input_format_t::bson, document_size); - - if (JSON_HEDLEY_UNLIKELY(!sax->start_object(std::size_t(-1)))) - { - return false; - } - - if (JSON_HEDLEY_UNLIKELY(!parse_bson_element_list(/*is_array*/false))) - { - return false; - } - - return sax->end_object(); - } - - /*! - @brief Parses a C-style string from the BSON input. - @param[in, out] result A reference to the string variable where the read - string is to be stored. - @return `true` if the \x00-byte indicating the end of the string was - encountered before the EOF; false` indicates an unexpected EOF. - */ - bool get_bson_cstr(string_t& result) - { - auto out = std::back_inserter(result); - while (true) - { - get(); - if (JSON_HEDLEY_UNLIKELY(!unexpect_eof(input_format_t::bson, "cstring"))) - { - return false; - } - if (current == 0x00) - { - return true; - } - *out++ = static_cast(current); - } - } - - /*! - @brief Parses a zero-terminated string of length @a len from the BSON - input. - @param[in] len The length (including the zero-byte at the end) of the - string to be read. - @param[in, out] result A reference to the string variable where the read - string is to be stored. - @tparam NumberType The type of the length @a len - @pre len >= 1 - @return `true` if the string was successfully parsed - */ - template - bool get_bson_string(const NumberType len, string_t& result) - { - if (JSON_HEDLEY_UNLIKELY(len < 1)) - { - auto last_token = get_token_string(); - return sax->parse_error(chars_read, last_token, parse_error::create(112, chars_read, exception_message(input_format_t::bson, "string length must be at least 1, is " + std::to_string(len), "string"))); - } - - return get_string(input_format_t::bson, len - static_cast(1), result) && get() != std::char_traits::eof(); - } - - /*! - @brief Parses a byte array input of length @a len from the BSON input. - @param[in] len The length of the byte array to be read. - @param[in, out] result A reference to the binary variable where the read - array is to be stored. - @tparam NumberType The type of the length @a len - @pre len >= 0 - @return `true` if the byte array was successfully parsed - */ - template - bool get_bson_binary(const NumberType len, binary_t& result) - { - if (JSON_HEDLEY_UNLIKELY(len < 0)) - { - auto last_token = get_token_string(); - return sax->parse_error(chars_read, last_token, parse_error::create(112, chars_read, exception_message(input_format_t::bson, "byte array length cannot be negative, is " + std::to_string(len), "binary"))); - } - - // All BSON binary values have a subtype - std::uint8_t subtype{}; - get_number(input_format_t::bson, subtype); - result.set_subtype(subtype); - - return get_binary(input_format_t::bson, len, result); - } - - /*! - @brief Read a BSON document element of the given @a element_type. - @param[in] element_type The BSON element type, c.f. http://bsonspec.org/spec.html - @param[in] element_type_parse_position The position in the input stream, - where the `element_type` was read. - @warning Not all BSON element types are supported yet. An unsupported - @a element_type will give rise to a parse_error.114: - Unsupported BSON record type 0x... - @return whether a valid BSON-object/array was passed to the SAX parser - */ - bool parse_bson_element_internal(const char_int_type element_type, - const std::size_t element_type_parse_position) - { - switch (element_type) - { - case 0x01: // double - { - double number{}; - return get_number(input_format_t::bson, number) && sax->number_float(static_cast(number), ""); - } - - case 0x02: // string - { - std::int32_t len{}; - string_t value; - return get_number(input_format_t::bson, len) && get_bson_string(len, value) && sax->string(value); - } - - case 0x03: // object - { - return parse_bson_internal(); - } - - case 0x04: // array - { - return parse_bson_array(); - } - - case 0x05: // binary - { - std::int32_t len{}; - binary_t value; - return get_number(input_format_t::bson, len) && get_bson_binary(len, value) && sax->binary(value); - } - - case 0x08: // boolean - { - return sax->boolean(get() != 0); - } - - case 0x0A: // null - { - return sax->null(); - } - - case 0x10: // int32 - { - std::int32_t value{}; - return get_number(input_format_t::bson, value) && sax->number_integer(value); - } - - case 0x12: // int64 - { - std::int64_t value{}; - return get_number(input_format_t::bson, value) && sax->number_integer(value); - } - - default: // anything else not supported (yet) - { - std::array cr{{}}; - (std::snprintf)(cr.data(), cr.size(), "%.2hhX", static_cast(element_type)); - return sax->parse_error(element_type_parse_position, std::string(cr.data()), parse_error::create(114, element_type_parse_position, "Unsupported BSON record type 0x" + std::string(cr.data()))); - } - } - } - - /*! - @brief Read a BSON element list (as specified in the BSON-spec) - - The same binary layout is used for objects and arrays, hence it must be - indicated with the argument @a is_array which one is expected - (true --> array, false --> object). - - @param[in] is_array Determines if the element list being read is to be - treated as an object (@a is_array == false), or as an - array (@a is_array == true). - @return whether a valid BSON-object/array was passed to the SAX parser - */ - bool parse_bson_element_list(const bool is_array) - { - string_t key; - - while (auto element_type = get()) - { - if (JSON_HEDLEY_UNLIKELY(!unexpect_eof(input_format_t::bson, "element list"))) - { - return false; - } - - const std::size_t element_type_parse_position = chars_read; - if (JSON_HEDLEY_UNLIKELY(!get_bson_cstr(key))) - { - return false; - } - - if (!is_array && !sax->key(key)) - { - return false; - } - - if (JSON_HEDLEY_UNLIKELY(!parse_bson_element_internal(element_type, element_type_parse_position))) - { - return false; - } - - // get_bson_cstr only appends - key.clear(); - } - - return true; - } - - /*! - @brief Reads an array from the BSON input and passes it to the SAX-parser. - @return whether a valid BSON-array was passed to the SAX parser - */ - bool parse_bson_array() - { - std::int32_t document_size{}; - get_number(input_format_t::bson, document_size); - - if (JSON_HEDLEY_UNLIKELY(!sax->start_array(std::size_t(-1)))) - { - return false; - } - - if (JSON_HEDLEY_UNLIKELY(!parse_bson_element_list(/*is_array*/true))) - { - return false; - } - - return sax->end_array(); - } - - ////////// - // CBOR // - ////////// - - /*! - @param[in] get_char whether a new character should be retrieved from the - input (true) or whether the last read character should - be considered instead (false) - @param[in] tag_handler how CBOR tags should be treated - - @return whether a valid CBOR value was passed to the SAX parser - */ - bool parse_cbor_internal(const bool get_char, - const cbor_tag_handler_t tag_handler) - { - switch (get_char ? get() : current) - { - // EOF - case std::char_traits::eof(): - return unexpect_eof(input_format_t::cbor, "value"); - - // Integer 0x00..0x17 (0..23) - case 0x00: - case 0x01: - case 0x02: - case 0x03: - case 0x04: - case 0x05: - case 0x06: - case 0x07: - case 0x08: - case 0x09: - case 0x0A: - case 0x0B: - case 0x0C: - case 0x0D: - case 0x0E: - case 0x0F: - case 0x10: - case 0x11: - case 0x12: - case 0x13: - case 0x14: - case 0x15: - case 0x16: - case 0x17: - return sax->number_unsigned(static_cast(current)); - - case 0x18: // Unsigned integer (one-byte uint8_t follows) - { - std::uint8_t number{}; - return get_number(input_format_t::cbor, number) && sax->number_unsigned(number); - } - - case 0x19: // Unsigned integer (two-byte uint16_t follows) - { - std::uint16_t number{}; - return get_number(input_format_t::cbor, number) && sax->number_unsigned(number); - } - - case 0x1A: // Unsigned integer (four-byte uint32_t follows) - { - std::uint32_t number{}; - return get_number(input_format_t::cbor, number) && sax->number_unsigned(number); - } - - case 0x1B: // Unsigned integer (eight-byte uint64_t follows) - { - std::uint64_t number{}; - return get_number(input_format_t::cbor, number) && sax->number_unsigned(number); - } - - // Negative integer -1-0x00..-1-0x17 (-1..-24) - case 0x20: - case 0x21: - case 0x22: - case 0x23: - case 0x24: - case 0x25: - case 0x26: - case 0x27: - case 0x28: - case 0x29: - case 0x2A: - case 0x2B: - case 0x2C: - case 0x2D: - case 0x2E: - case 0x2F: - case 0x30: - case 0x31: - case 0x32: - case 0x33: - case 0x34: - case 0x35: - case 0x36: - case 0x37: - return sax->number_integer(static_cast(0x20 - 1 - current)); - - case 0x38: // Negative integer (one-byte uint8_t follows) - { - std::uint8_t number{}; - return get_number(input_format_t::cbor, number) && sax->number_integer(static_cast(-1) - number); - } - - case 0x39: // Negative integer -1-n (two-byte uint16_t follows) - { - std::uint16_t number{}; - return get_number(input_format_t::cbor, number) && sax->number_integer(static_cast(-1) - number); - } - - case 0x3A: // Negative integer -1-n (four-byte uint32_t follows) - { - std::uint32_t number{}; - return get_number(input_format_t::cbor, number) && sax->number_integer(static_cast(-1) - number); - } - - case 0x3B: // Negative integer -1-n (eight-byte uint64_t follows) - { - std::uint64_t number{}; - return get_number(input_format_t::cbor, number) && sax->number_integer(static_cast(-1) - - static_cast(number)); - } - - // Binary data (0x00..0x17 bytes follow) - case 0x40: - case 0x41: - case 0x42: - case 0x43: - case 0x44: - case 0x45: - case 0x46: - case 0x47: - case 0x48: - case 0x49: - case 0x4A: - case 0x4B: - case 0x4C: - case 0x4D: - case 0x4E: - case 0x4F: - case 0x50: - case 0x51: - case 0x52: - case 0x53: - case 0x54: - case 0x55: - case 0x56: - case 0x57: - case 0x58: // Binary data (one-byte uint8_t for n follows) - case 0x59: // Binary data (two-byte uint16_t for n follow) - case 0x5A: // Binary data (four-byte uint32_t for n follow) - case 0x5B: // Binary data (eight-byte uint64_t for n follow) - case 0x5F: // Binary data (indefinite length) - { - binary_t b; - return get_cbor_binary(b) && sax->binary(b); - } - - // UTF-8 string (0x00..0x17 bytes follow) - case 0x60: - case 0x61: - case 0x62: - case 0x63: - case 0x64: - case 0x65: - case 0x66: - case 0x67: - case 0x68: - case 0x69: - case 0x6A: - case 0x6B: - case 0x6C: - case 0x6D: - case 0x6E: - case 0x6F: - case 0x70: - case 0x71: - case 0x72: - case 0x73: - case 0x74: - case 0x75: - case 0x76: - case 0x77: - case 0x78: // UTF-8 string (one-byte uint8_t for n follows) - case 0x79: // UTF-8 string (two-byte uint16_t for n follow) - case 0x7A: // UTF-8 string (four-byte uint32_t for n follow) - case 0x7B: // UTF-8 string (eight-byte uint64_t for n follow) - case 0x7F: // UTF-8 string (indefinite length) - { - string_t s; - return get_cbor_string(s) && sax->string(s); - } - - // array (0x00..0x17 data items follow) - case 0x80: - case 0x81: - case 0x82: - case 0x83: - case 0x84: - case 0x85: - case 0x86: - case 0x87: - case 0x88: - case 0x89: - case 0x8A: - case 0x8B: - case 0x8C: - case 0x8D: - case 0x8E: - case 0x8F: - case 0x90: - case 0x91: - case 0x92: - case 0x93: - case 0x94: - case 0x95: - case 0x96: - case 0x97: - return get_cbor_array(static_cast(static_cast(current) & 0x1Fu), tag_handler); - - case 0x98: // array (one-byte uint8_t for n follows) - { - std::uint8_t len{}; - return get_number(input_format_t::cbor, len) && get_cbor_array(static_cast(len), tag_handler); - } - - case 0x99: // array (two-byte uint16_t for n follow) - { - std::uint16_t len{}; - return get_number(input_format_t::cbor, len) && get_cbor_array(static_cast(len), tag_handler); - } - - case 0x9A: // array (four-byte uint32_t for n follow) - { - std::uint32_t len{}; - return get_number(input_format_t::cbor, len) && get_cbor_array(static_cast(len), tag_handler); - } - - case 0x9B: // array (eight-byte uint64_t for n follow) - { - std::uint64_t len{}; - return get_number(input_format_t::cbor, len) && get_cbor_array(static_cast(len), tag_handler); - } - - case 0x9F: // array (indefinite length) - return get_cbor_array(std::size_t(-1), tag_handler); - - // map (0x00..0x17 pairs of data items follow) - case 0xA0: - case 0xA1: - case 0xA2: - case 0xA3: - case 0xA4: - case 0xA5: - case 0xA6: - case 0xA7: - case 0xA8: - case 0xA9: - case 0xAA: - case 0xAB: - case 0xAC: - case 0xAD: - case 0xAE: - case 0xAF: - case 0xB0: - case 0xB1: - case 0xB2: - case 0xB3: - case 0xB4: - case 0xB5: - case 0xB6: - case 0xB7: - return get_cbor_object(static_cast(static_cast(current) & 0x1Fu), tag_handler); - - case 0xB8: // map (one-byte uint8_t for n follows) - { - std::uint8_t len{}; - return get_number(input_format_t::cbor, len) && get_cbor_object(static_cast(len), tag_handler); - } - - case 0xB9: // map (two-byte uint16_t for n follow) - { - std::uint16_t len{}; - return get_number(input_format_t::cbor, len) && get_cbor_object(static_cast(len), tag_handler); - } - - case 0xBA: // map (four-byte uint32_t for n follow) - { - std::uint32_t len{}; - return get_number(input_format_t::cbor, len) && get_cbor_object(static_cast(len), tag_handler); - } - - case 0xBB: // map (eight-byte uint64_t for n follow) - { - std::uint64_t len{}; - return get_number(input_format_t::cbor, len) && get_cbor_object(static_cast(len), tag_handler); - } - - case 0xBF: // map (indefinite length) - return get_cbor_object(std::size_t(-1), tag_handler); - - case 0xC6: // tagged item - case 0xC7: - case 0xC8: - case 0xC9: - case 0xCA: - case 0xCB: - case 0xCC: - case 0xCD: - case 0xCE: - case 0xCF: - case 0xD0: - case 0xD1: - case 0xD2: - case 0xD3: - case 0xD4: - case 0xD8: // tagged item (1 bytes follow) - case 0xD9: // tagged item (2 bytes follow) - case 0xDA: // tagged item (4 bytes follow) - case 0xDB: // tagged item (8 bytes follow) - { - switch (tag_handler) - { - case cbor_tag_handler_t::error: - { - auto last_token = get_token_string(); - return sax->parse_error(chars_read, last_token, parse_error::create(112, chars_read, exception_message(input_format_t::cbor, "invalid byte: 0x" + last_token, "value"))); - } - - case cbor_tag_handler_t::ignore: - { - switch (current) - { - case 0xD8: - { - std::uint8_t len{}; - get_number(input_format_t::cbor, len); - break; - } - case 0xD9: - { - std::uint16_t len{}; - get_number(input_format_t::cbor, len); - break; - } - case 0xDA: - { - std::uint32_t len{}; - get_number(input_format_t::cbor, len); - break; - } - case 0xDB: - { - std::uint64_t len{}; - get_number(input_format_t::cbor, len); - break; - } - default: - break; - } - return parse_cbor_internal(true, tag_handler); - } - - default: // LCOV_EXCL_LINE - JSON_ASSERT(false); // LCOV_EXCL_LINE - } - } - - case 0xF4: // false - return sax->boolean(false); - - case 0xF5: // true - return sax->boolean(true); - - case 0xF6: // null - return sax->null(); - - case 0xF9: // Half-Precision Float (two-byte IEEE 754) - { - const auto byte1_raw = get(); - if (JSON_HEDLEY_UNLIKELY(!unexpect_eof(input_format_t::cbor, "number"))) - { - return false; - } - const auto byte2_raw = get(); - if (JSON_HEDLEY_UNLIKELY(!unexpect_eof(input_format_t::cbor, "number"))) - { - return false; - } - - const auto byte1 = static_cast(byte1_raw); - const auto byte2 = static_cast(byte2_raw); - - // code from RFC 7049, Appendix D, Figure 3: - // As half-precision floating-point numbers were only added - // to IEEE 754 in 2008, today's programming platforms often - // still only have limited support for them. It is very - // easy to include at least decoding support for them even - // without such support. An example of a small decoder for - // half-precision floating-point numbers in the C language - // is shown in Fig. 3. - const auto half = static_cast((byte1 << 8u) + byte2); - const double val = [&half] - { - const int exp = (half >> 10u) & 0x1Fu; - const unsigned int mant = half & 0x3FFu; - JSON_ASSERT(0 <= exp&& exp <= 32); - JSON_ASSERT(mant <= 1024); - switch (exp) - { - case 0: - return std::ldexp(mant, -24); - case 31: - return (mant == 0) - ? std::numeric_limits::infinity() - : std::numeric_limits::quiet_NaN(); - default: - return std::ldexp(mant + 1024, exp - 25); - } - }(); - return sax->number_float((half & 0x8000u) != 0 - ? static_cast(-val) - : static_cast(val), ""); - } - - case 0xFA: // Single-Precision Float (four-byte IEEE 754) - { - float number{}; - return get_number(input_format_t::cbor, number) && sax->number_float(static_cast(number), ""); - } - - case 0xFB: // Double-Precision Float (eight-byte IEEE 754) - { - double number{}; - return get_number(input_format_t::cbor, number) && sax->number_float(static_cast(number), ""); - } - - default: // anything else (0xFF is handled inside the other types) - { - auto last_token = get_token_string(); - return sax->parse_error(chars_read, last_token, parse_error::create(112, chars_read, exception_message(input_format_t::cbor, "invalid byte: 0x" + last_token, "value"))); - } - } - } - - /*! - @brief reads a CBOR string - - This function first reads starting bytes to determine the expected - string length and then copies this number of bytes into a string. - Additionally, CBOR's strings with indefinite lengths are supported. - - @param[out] result created string - - @return whether string creation completed - */ - bool get_cbor_string(string_t& result) - { - if (JSON_HEDLEY_UNLIKELY(!unexpect_eof(input_format_t::cbor, "string"))) - { - return false; - } - - switch (current) - { - // UTF-8 string (0x00..0x17 bytes follow) - case 0x60: - case 0x61: - case 0x62: - case 0x63: - case 0x64: - case 0x65: - case 0x66: - case 0x67: - case 0x68: - case 0x69: - case 0x6A: - case 0x6B: - case 0x6C: - case 0x6D: - case 0x6E: - case 0x6F: - case 0x70: - case 0x71: - case 0x72: - case 0x73: - case 0x74: - case 0x75: - case 0x76: - case 0x77: - { - return get_string(input_format_t::cbor, static_cast(current) & 0x1Fu, result); - } - - case 0x78: // UTF-8 string (one-byte uint8_t for n follows) - { - std::uint8_t len{}; - return get_number(input_format_t::cbor, len) && get_string(input_format_t::cbor, len, result); - } - - case 0x79: // UTF-8 string (two-byte uint16_t for n follow) - { - std::uint16_t len{}; - return get_number(input_format_t::cbor, len) && get_string(input_format_t::cbor, len, result); - } - - case 0x7A: // UTF-8 string (four-byte uint32_t for n follow) - { - std::uint32_t len{}; - return get_number(input_format_t::cbor, len) && get_string(input_format_t::cbor, len, result); - } - - case 0x7B: // UTF-8 string (eight-byte uint64_t for n follow) - { - std::uint64_t len{}; - return get_number(input_format_t::cbor, len) && get_string(input_format_t::cbor, len, result); - } - - case 0x7F: // UTF-8 string (indefinite length) - { - while (get() != 0xFF) - { - string_t chunk; - if (!get_cbor_string(chunk)) - { - return false; - } - result.append(chunk); - } - return true; - } - - default: - { - auto last_token = get_token_string(); - return sax->parse_error(chars_read, last_token, parse_error::create(113, chars_read, exception_message(input_format_t::cbor, "expected length specification (0x60-0x7B) or indefinite string type (0x7F); last byte: 0x" + last_token, "string"))); - } - } - } - - /*! - @brief reads a CBOR byte array - - This function first reads starting bytes to determine the expected - byte array length and then copies this number of bytes into the byte array. - Additionally, CBOR's byte arrays with indefinite lengths are supported. - - @param[out] result created byte array - - @return whether byte array creation completed - */ - bool get_cbor_binary(binary_t& result) - { - if (JSON_HEDLEY_UNLIKELY(!unexpect_eof(input_format_t::cbor, "binary"))) - { - return false; - } - - switch (current) - { - // Binary data (0x00..0x17 bytes follow) - case 0x40: - case 0x41: - case 0x42: - case 0x43: - case 0x44: - case 0x45: - case 0x46: - case 0x47: - case 0x48: - case 0x49: - case 0x4A: - case 0x4B: - case 0x4C: - case 0x4D: - case 0x4E: - case 0x4F: - case 0x50: - case 0x51: - case 0x52: - case 0x53: - case 0x54: - case 0x55: - case 0x56: - case 0x57: - { - return get_binary(input_format_t::cbor, static_cast(current) & 0x1Fu, result); - } - - case 0x58: // Binary data (one-byte uint8_t for n follows) - { - std::uint8_t len{}; - return get_number(input_format_t::cbor, len) && - get_binary(input_format_t::cbor, len, result); - } - - case 0x59: // Binary data (two-byte uint16_t for n follow) - { - std::uint16_t len{}; - return get_number(input_format_t::cbor, len) && - get_binary(input_format_t::cbor, len, result); - } - - case 0x5A: // Binary data (four-byte uint32_t for n follow) - { - std::uint32_t len{}; - return get_number(input_format_t::cbor, len) && - get_binary(input_format_t::cbor, len, result); - } - - case 0x5B: // Binary data (eight-byte uint64_t for n follow) - { - std::uint64_t len{}; - return get_number(input_format_t::cbor, len) && - get_binary(input_format_t::cbor, len, result); - } - - case 0x5F: // Binary data (indefinite length) - { - while (get() != 0xFF) - { - binary_t chunk; - if (!get_cbor_binary(chunk)) - { - return false; - } - result.insert(result.end(), chunk.begin(), chunk.end()); - } - return true; - } - - default: - { - auto last_token = get_token_string(); - return sax->parse_error(chars_read, last_token, parse_error::create(113, chars_read, exception_message(input_format_t::cbor, "expected length specification (0x40-0x5B) or indefinite binary array type (0x5F); last byte: 0x" + last_token, "binary"))); - } - } - } - - /*! - @param[in] len the length of the array or std::size_t(-1) for an - array of indefinite size - @param[in] tag_handler how CBOR tags should be treated - @return whether array creation completed - */ - bool get_cbor_array(const std::size_t len, - const cbor_tag_handler_t tag_handler) - { - if (JSON_HEDLEY_UNLIKELY(!sax->start_array(len))) - { - return false; - } - - if (len != std::size_t(-1)) - { - for (std::size_t i = 0; i < len; ++i) - { - if (JSON_HEDLEY_UNLIKELY(!parse_cbor_internal(true, tag_handler))) - { - return false; - } - } - } - else - { - while (get() != 0xFF) - { - if (JSON_HEDLEY_UNLIKELY(!parse_cbor_internal(false, tag_handler))) - { - return false; - } - } - } - - return sax->end_array(); - } - - /*! - @param[in] len the length of the object or std::size_t(-1) for an - object of indefinite size - @param[in] tag_handler how CBOR tags should be treated - @return whether object creation completed - */ - bool get_cbor_object(const std::size_t len, - const cbor_tag_handler_t tag_handler) - { - if (JSON_HEDLEY_UNLIKELY(!sax->start_object(len))) - { - return false; - } - - string_t key; - if (len != std::size_t(-1)) - { - for (std::size_t i = 0; i < len; ++i) - { - get(); - if (JSON_HEDLEY_UNLIKELY(!get_cbor_string(key) || !sax->key(key))) - { - return false; - } - - if (JSON_HEDLEY_UNLIKELY(!parse_cbor_internal(true, tag_handler))) - { - return false; - } - key.clear(); - } - } - else - { - while (get() != 0xFF) - { - if (JSON_HEDLEY_UNLIKELY(!get_cbor_string(key) || !sax->key(key))) - { - return false; - } - - if (JSON_HEDLEY_UNLIKELY(!parse_cbor_internal(true, tag_handler))) - { - return false; - } - key.clear(); - } - } - - return sax->end_object(); - } - - ///////////// - // MsgPack // - ///////////// - - /*! - @return whether a valid MessagePack value was passed to the SAX parser - */ - bool parse_msgpack_internal() - { - switch (get()) - { - // EOF - case std::char_traits::eof(): - return unexpect_eof(input_format_t::msgpack, "value"); - - // positive fixint - case 0x00: - case 0x01: - case 0x02: - case 0x03: - case 0x04: - case 0x05: - case 0x06: - case 0x07: - case 0x08: - case 0x09: - case 0x0A: - case 0x0B: - case 0x0C: - case 0x0D: - case 0x0E: - case 0x0F: - case 0x10: - case 0x11: - case 0x12: - case 0x13: - case 0x14: - case 0x15: - case 0x16: - case 0x17: - case 0x18: - case 0x19: - case 0x1A: - case 0x1B: - case 0x1C: - case 0x1D: - case 0x1E: - case 0x1F: - case 0x20: - case 0x21: - case 0x22: - case 0x23: - case 0x24: - case 0x25: - case 0x26: - case 0x27: - case 0x28: - case 0x29: - case 0x2A: - case 0x2B: - case 0x2C: - case 0x2D: - case 0x2E: - case 0x2F: - case 0x30: - case 0x31: - case 0x32: - case 0x33: - case 0x34: - case 0x35: - case 0x36: - case 0x37: - case 0x38: - case 0x39: - case 0x3A: - case 0x3B: - case 0x3C: - case 0x3D: - case 0x3E: - case 0x3F: - case 0x40: - case 0x41: - case 0x42: - case 0x43: - case 0x44: - case 0x45: - case 0x46: - case 0x47: - case 0x48: - case 0x49: - case 0x4A: - case 0x4B: - case 0x4C: - case 0x4D: - case 0x4E: - case 0x4F: - case 0x50: - case 0x51: - case 0x52: - case 0x53: - case 0x54: - case 0x55: - case 0x56: - case 0x57: - case 0x58: - case 0x59: - case 0x5A: - case 0x5B: - case 0x5C: - case 0x5D: - case 0x5E: - case 0x5F: - case 0x60: - case 0x61: - case 0x62: - case 0x63: - case 0x64: - case 0x65: - case 0x66: - case 0x67: - case 0x68: - case 0x69: - case 0x6A: - case 0x6B: - case 0x6C: - case 0x6D: - case 0x6E: - case 0x6F: - case 0x70: - case 0x71: - case 0x72: - case 0x73: - case 0x74: - case 0x75: - case 0x76: - case 0x77: - case 0x78: - case 0x79: - case 0x7A: - case 0x7B: - case 0x7C: - case 0x7D: - case 0x7E: - case 0x7F: - return sax->number_unsigned(static_cast(current)); - - // fixmap - case 0x80: - case 0x81: - case 0x82: - case 0x83: - case 0x84: - case 0x85: - case 0x86: - case 0x87: - case 0x88: - case 0x89: - case 0x8A: - case 0x8B: - case 0x8C: - case 0x8D: - case 0x8E: - case 0x8F: - return get_msgpack_object(static_cast(static_cast(current) & 0x0Fu)); - - // fixarray - case 0x90: - case 0x91: - case 0x92: - case 0x93: - case 0x94: - case 0x95: - case 0x96: - case 0x97: - case 0x98: - case 0x99: - case 0x9A: - case 0x9B: - case 0x9C: - case 0x9D: - case 0x9E: - case 0x9F: - return get_msgpack_array(static_cast(static_cast(current) & 0x0Fu)); - - // fixstr - case 0xA0: - case 0xA1: - case 0xA2: - case 0xA3: - case 0xA4: - case 0xA5: - case 0xA6: - case 0xA7: - case 0xA8: - case 0xA9: - case 0xAA: - case 0xAB: - case 0xAC: - case 0xAD: - case 0xAE: - case 0xAF: - case 0xB0: - case 0xB1: - case 0xB2: - case 0xB3: - case 0xB4: - case 0xB5: - case 0xB6: - case 0xB7: - case 0xB8: - case 0xB9: - case 0xBA: - case 0xBB: - case 0xBC: - case 0xBD: - case 0xBE: - case 0xBF: - case 0xD9: // str 8 - case 0xDA: // str 16 - case 0xDB: // str 32 - { - string_t s; - return get_msgpack_string(s) && sax->string(s); - } - - case 0xC0: // nil - return sax->null(); - - case 0xC2: // false - return sax->boolean(false); - - case 0xC3: // true - return sax->boolean(true); - - case 0xC4: // bin 8 - case 0xC5: // bin 16 - case 0xC6: // bin 32 - case 0xC7: // ext 8 - case 0xC8: // ext 16 - case 0xC9: // ext 32 - case 0xD4: // fixext 1 - case 0xD5: // fixext 2 - case 0xD6: // fixext 4 - case 0xD7: // fixext 8 - case 0xD8: // fixext 16 - { - binary_t b; - return get_msgpack_binary(b) && sax->binary(b); - } - - case 0xCA: // float 32 - { - float number{}; - return get_number(input_format_t::msgpack, number) && sax->number_float(static_cast(number), ""); - } - - case 0xCB: // float 64 - { - double number{}; - return get_number(input_format_t::msgpack, number) && sax->number_float(static_cast(number), ""); - } - - case 0xCC: // uint 8 - { - std::uint8_t number{}; - return get_number(input_format_t::msgpack, number) && sax->number_unsigned(number); - } - - case 0xCD: // uint 16 - { - std::uint16_t number{}; - return get_number(input_format_t::msgpack, number) && sax->number_unsigned(number); - } - - case 0xCE: // uint 32 - { - std::uint32_t number{}; - return get_number(input_format_t::msgpack, number) && sax->number_unsigned(number); - } - - case 0xCF: // uint 64 - { - std::uint64_t number{}; - return get_number(input_format_t::msgpack, number) && sax->number_unsigned(number); - } - - case 0xD0: // int 8 - { - std::int8_t number{}; - return get_number(input_format_t::msgpack, number) && sax->number_integer(number); - } - - case 0xD1: // int 16 - { - std::int16_t number{}; - return get_number(input_format_t::msgpack, number) && sax->number_integer(number); - } - - case 0xD2: // int 32 - { - std::int32_t number{}; - return get_number(input_format_t::msgpack, number) && sax->number_integer(number); - } - - case 0xD3: // int 64 - { - std::int64_t number{}; - return get_number(input_format_t::msgpack, number) && sax->number_integer(number); - } - - case 0xDC: // array 16 - { - std::uint16_t len{}; - return get_number(input_format_t::msgpack, len) && get_msgpack_array(static_cast(len)); - } - - case 0xDD: // array 32 - { - std::uint32_t len{}; - return get_number(input_format_t::msgpack, len) && get_msgpack_array(static_cast(len)); - } - - case 0xDE: // map 16 - { - std::uint16_t len{}; - return get_number(input_format_t::msgpack, len) && get_msgpack_object(static_cast(len)); - } - - case 0xDF: // map 32 - { - std::uint32_t len{}; - return get_number(input_format_t::msgpack, len) && get_msgpack_object(static_cast(len)); - } - - // negative fixint - case 0xE0: - case 0xE1: - case 0xE2: - case 0xE3: - case 0xE4: - case 0xE5: - case 0xE6: - case 0xE7: - case 0xE8: - case 0xE9: - case 0xEA: - case 0xEB: - case 0xEC: - case 0xED: - case 0xEE: - case 0xEF: - case 0xF0: - case 0xF1: - case 0xF2: - case 0xF3: - case 0xF4: - case 0xF5: - case 0xF6: - case 0xF7: - case 0xF8: - case 0xF9: - case 0xFA: - case 0xFB: - case 0xFC: - case 0xFD: - case 0xFE: - case 0xFF: - return sax->number_integer(static_cast(current)); - - default: // anything else - { - auto last_token = get_token_string(); - return sax->parse_error(chars_read, last_token, parse_error::create(112, chars_read, exception_message(input_format_t::msgpack, "invalid byte: 0x" + last_token, "value"))); - } - } - } - - /*! - @brief reads a MessagePack string - - This function first reads starting bytes to determine the expected - string length and then copies this number of bytes into a string. - - @param[out] result created string - - @return whether string creation completed - */ - bool get_msgpack_string(string_t& result) - { - if (JSON_HEDLEY_UNLIKELY(!unexpect_eof(input_format_t::msgpack, "string"))) - { - return false; - } - - switch (current) - { - // fixstr - case 0xA0: - case 0xA1: - case 0xA2: - case 0xA3: - case 0xA4: - case 0xA5: - case 0xA6: - case 0xA7: - case 0xA8: - case 0xA9: - case 0xAA: - case 0xAB: - case 0xAC: - case 0xAD: - case 0xAE: - case 0xAF: - case 0xB0: - case 0xB1: - case 0xB2: - case 0xB3: - case 0xB4: - case 0xB5: - case 0xB6: - case 0xB7: - case 0xB8: - case 0xB9: - case 0xBA: - case 0xBB: - case 0xBC: - case 0xBD: - case 0xBE: - case 0xBF: - { - return get_string(input_format_t::msgpack, static_cast(current) & 0x1Fu, result); - } - - case 0xD9: // str 8 - { - std::uint8_t len{}; - return get_number(input_format_t::msgpack, len) && get_string(input_format_t::msgpack, len, result); - } - - case 0xDA: // str 16 - { - std::uint16_t len{}; - return get_number(input_format_t::msgpack, len) && get_string(input_format_t::msgpack, len, result); - } - - case 0xDB: // str 32 - { - std::uint32_t len{}; - return get_number(input_format_t::msgpack, len) && get_string(input_format_t::msgpack, len, result); - } - - default: - { - auto last_token = get_token_string(); - return sax->parse_error(chars_read, last_token, parse_error::create(113, chars_read, exception_message(input_format_t::msgpack, "expected length specification (0xA0-0xBF, 0xD9-0xDB); last byte: 0x" + last_token, "string"))); - } - } - } - - /*! - @brief reads a MessagePack byte array - - This function first reads starting bytes to determine the expected - byte array length and then copies this number of bytes into a byte array. - - @param[out] result created byte array - - @return whether byte array creation completed - */ - bool get_msgpack_binary(binary_t& result) - { - // helper function to set the subtype - auto assign_and_return_true = [&result](std::int8_t subtype) - { - result.set_subtype(static_cast(subtype)); - return true; - }; - - switch (current) - { - case 0xC4: // bin 8 - { - std::uint8_t len{}; - return get_number(input_format_t::msgpack, len) && - get_binary(input_format_t::msgpack, len, result); - } - - case 0xC5: // bin 16 - { - std::uint16_t len{}; - return get_number(input_format_t::msgpack, len) && - get_binary(input_format_t::msgpack, len, result); - } - - case 0xC6: // bin 32 - { - std::uint32_t len{}; - return get_number(input_format_t::msgpack, len) && - get_binary(input_format_t::msgpack, len, result); - } - - case 0xC7: // ext 8 - { - std::uint8_t len{}; - std::int8_t subtype{}; - return get_number(input_format_t::msgpack, len) && - get_number(input_format_t::msgpack, subtype) && - get_binary(input_format_t::msgpack, len, result) && - assign_and_return_true(subtype); - } - - case 0xC8: // ext 16 - { - std::uint16_t len{}; - std::int8_t subtype{}; - return get_number(input_format_t::msgpack, len) && - get_number(input_format_t::msgpack, subtype) && - get_binary(input_format_t::msgpack, len, result) && - assign_and_return_true(subtype); - } - - case 0xC9: // ext 32 - { - std::uint32_t len{}; - std::int8_t subtype{}; - return get_number(input_format_t::msgpack, len) && - get_number(input_format_t::msgpack, subtype) && - get_binary(input_format_t::msgpack, len, result) && - assign_and_return_true(subtype); - } - - case 0xD4: // fixext 1 - { - std::int8_t subtype{}; - return get_number(input_format_t::msgpack, subtype) && - get_binary(input_format_t::msgpack, 1, result) && - assign_and_return_true(subtype); - } - - case 0xD5: // fixext 2 - { - std::int8_t subtype{}; - return get_number(input_format_t::msgpack, subtype) && - get_binary(input_format_t::msgpack, 2, result) && - assign_and_return_true(subtype); - } - - case 0xD6: // fixext 4 - { - std::int8_t subtype{}; - return get_number(input_format_t::msgpack, subtype) && - get_binary(input_format_t::msgpack, 4, result) && - assign_and_return_true(subtype); - } - - case 0xD7: // fixext 8 - { - std::int8_t subtype{}; - return get_number(input_format_t::msgpack, subtype) && - get_binary(input_format_t::msgpack, 8, result) && - assign_and_return_true(subtype); - } - - case 0xD8: // fixext 16 - { - std::int8_t subtype{}; - return get_number(input_format_t::msgpack, subtype) && - get_binary(input_format_t::msgpack, 16, result) && - assign_and_return_true(subtype); - } - - default: // LCOV_EXCL_LINE - return false; // LCOV_EXCL_LINE - } - } - - /*! - @param[in] len the length of the array - @return whether array creation completed - */ - bool get_msgpack_array(const std::size_t len) - { - if (JSON_HEDLEY_UNLIKELY(!sax->start_array(len))) - { - return false; - } - - for (std::size_t i = 0; i < len; ++i) - { - if (JSON_HEDLEY_UNLIKELY(!parse_msgpack_internal())) - { - return false; - } - } - - return sax->end_array(); - } - - /*! - @param[in] len the length of the object - @return whether object creation completed - */ - bool get_msgpack_object(const std::size_t len) - { - if (JSON_HEDLEY_UNLIKELY(!sax->start_object(len))) - { - return false; - } - - string_t key; - for (std::size_t i = 0; i < len; ++i) - { - get(); - if (JSON_HEDLEY_UNLIKELY(!get_msgpack_string(key) || !sax->key(key))) - { - return false; - } - - if (JSON_HEDLEY_UNLIKELY(!parse_msgpack_internal())) - { - return false; - } - key.clear(); - } - - return sax->end_object(); - } - - //////////// - // UBJSON // - //////////// - - /*! - @param[in] get_char whether a new character should be retrieved from the - input (true, default) or whether the last read - character should be considered instead - - @return whether a valid UBJSON value was passed to the SAX parser - */ - bool parse_ubjson_internal(const bool get_char = true) - { - return get_ubjson_value(get_char ? get_ignore_noop() : current); - } - - /*! - @brief reads a UBJSON string - - This function is either called after reading the 'S' byte explicitly - indicating a string, or in case of an object key where the 'S' byte can be - left out. - - @param[out] result created string - @param[in] get_char whether a new character should be retrieved from the - input (true, default) or whether the last read - character should be considered instead - - @return whether string creation completed - */ - bool get_ubjson_string(string_t& result, const bool get_char = true) - { - if (get_char) - { - get(); // TODO(niels): may we ignore N here? - } - - if (JSON_HEDLEY_UNLIKELY(!unexpect_eof(input_format_t::ubjson, "value"))) - { - return false; - } - - switch (current) - { - case 'U': - { - std::uint8_t len{}; - return get_number(input_format_t::ubjson, len) && get_string(input_format_t::ubjson, len, result); - } - - case 'i': - { - std::int8_t len{}; - return get_number(input_format_t::ubjson, len) && get_string(input_format_t::ubjson, len, result); - } - - case 'I': - { - std::int16_t len{}; - return get_number(input_format_t::ubjson, len) && get_string(input_format_t::ubjson, len, result); - } - - case 'l': - { - std::int32_t len{}; - return get_number(input_format_t::ubjson, len) && get_string(input_format_t::ubjson, len, result); - } - - case 'L': - { - std::int64_t len{}; - return get_number(input_format_t::ubjson, len) && get_string(input_format_t::ubjson, len, result); - } - - default: - auto last_token = get_token_string(); - return sax->parse_error(chars_read, last_token, parse_error::create(113, chars_read, exception_message(input_format_t::ubjson, "expected length type specification (U, i, I, l, L); last byte: 0x" + last_token, "string"))); - } - } - - /*! - @param[out] result determined size - @return whether size determination completed - */ - bool get_ubjson_size_value(std::size_t& result) - { - switch (get_ignore_noop()) - { - case 'U': - { - std::uint8_t number{}; - if (JSON_HEDLEY_UNLIKELY(!get_number(input_format_t::ubjson, number))) - { - return false; - } - result = static_cast(number); - return true; - } - - case 'i': - { - std::int8_t number{}; - if (JSON_HEDLEY_UNLIKELY(!get_number(input_format_t::ubjson, number))) - { - return false; - } - result = static_cast(number); - return true; - } - - case 'I': - { - std::int16_t number{}; - if (JSON_HEDLEY_UNLIKELY(!get_number(input_format_t::ubjson, number))) - { - return false; - } - result = static_cast(number); - return true; - } - - case 'l': - { - std::int32_t number{}; - if (JSON_HEDLEY_UNLIKELY(!get_number(input_format_t::ubjson, number))) - { - return false; - } - result = static_cast(number); - return true; - } - - case 'L': - { - std::int64_t number{}; - if (JSON_HEDLEY_UNLIKELY(!get_number(input_format_t::ubjson, number))) - { - return false; - } - result = static_cast(number); - return true; - } - - default: - { - auto last_token = get_token_string(); - return sax->parse_error(chars_read, last_token, parse_error::create(113, chars_read, exception_message(input_format_t::ubjson, "expected length type specification (U, i, I, l, L) after '#'; last byte: 0x" + last_token, "size"))); - } - } - } - - /*! - @brief determine the type and size for a container - - In the optimized UBJSON format, a type and a size can be provided to allow - for a more compact representation. - - @param[out] result pair of the size and the type - - @return whether pair creation completed - */ - bool get_ubjson_size_type(std::pair& result) - { - result.first = string_t::npos; // size - result.second = 0; // type - - get_ignore_noop(); - - if (current == '$') - { - result.second = get(); // must not ignore 'N', because 'N' maybe the type - if (JSON_HEDLEY_UNLIKELY(!unexpect_eof(input_format_t::ubjson, "type"))) - { - return false; - } - - get_ignore_noop(); - if (JSON_HEDLEY_UNLIKELY(current != '#')) - { - if (JSON_HEDLEY_UNLIKELY(!unexpect_eof(input_format_t::ubjson, "value"))) - { - return false; - } - auto last_token = get_token_string(); - return sax->parse_error(chars_read, last_token, parse_error::create(112, chars_read, exception_message(input_format_t::ubjson, "expected '#' after type information; last byte: 0x" + last_token, "size"))); - } - - return get_ubjson_size_value(result.first); - } - - if (current == '#') - { - return get_ubjson_size_value(result.first); - } - - return true; - } - - /*! - @param prefix the previously read or set type prefix - @return whether value creation completed - */ - bool get_ubjson_value(const char_int_type prefix) - { - switch (prefix) - { - case std::char_traits::eof(): // EOF - return unexpect_eof(input_format_t::ubjson, "value"); - - case 'T': // true - return sax->boolean(true); - case 'F': // false - return sax->boolean(false); - - case 'Z': // null - return sax->null(); - - case 'U': - { - std::uint8_t number{}; - return get_number(input_format_t::ubjson, number) && sax->number_unsigned(number); - } - - case 'i': - { - std::int8_t number{}; - return get_number(input_format_t::ubjson, number) && sax->number_integer(number); - } - - case 'I': - { - std::int16_t number{}; - return get_number(input_format_t::ubjson, number) && sax->number_integer(number); - } - - case 'l': - { - std::int32_t number{}; - return get_number(input_format_t::ubjson, number) && sax->number_integer(number); - } - - case 'L': - { - std::int64_t number{}; - return get_number(input_format_t::ubjson, number) && sax->number_integer(number); - } - - case 'd': - { - float number{}; - return get_number(input_format_t::ubjson, number) && sax->number_float(static_cast(number), ""); - } - - case 'D': - { - double number{}; - return get_number(input_format_t::ubjson, number) && sax->number_float(static_cast(number), ""); - } - - case 'H': - { - return get_ubjson_high_precision_number(); - } - - case 'C': // char - { - get(); - if (JSON_HEDLEY_UNLIKELY(!unexpect_eof(input_format_t::ubjson, "char"))) - { - return false; - } - if (JSON_HEDLEY_UNLIKELY(current > 127)) - { - auto last_token = get_token_string(); - return sax->parse_error(chars_read, last_token, parse_error::create(113, chars_read, exception_message(input_format_t::ubjson, "byte after 'C' must be in range 0x00..0x7F; last byte: 0x" + last_token, "char"))); - } - string_t s(1, static_cast(current)); - return sax->string(s); - } - - case 'S': // string - { - string_t s; - return get_ubjson_string(s) && sax->string(s); - } - - case '[': // array - return get_ubjson_array(); - - case '{': // object - return get_ubjson_object(); - - default: // anything else - { - auto last_token = get_token_string(); - return sax->parse_error(chars_read, last_token, parse_error::create(112, chars_read, exception_message(input_format_t::ubjson, "invalid byte: 0x" + last_token, "value"))); - } - } - } - - /*! - @return whether array creation completed - */ - bool get_ubjson_array() - { - std::pair size_and_type; - if (JSON_HEDLEY_UNLIKELY(!get_ubjson_size_type(size_and_type))) - { - return false; - } - - if (size_and_type.first != string_t::npos) - { - if (JSON_HEDLEY_UNLIKELY(!sax->start_array(size_and_type.first))) - { - return false; - } - - if (size_and_type.second != 0) - { - if (size_and_type.second != 'N') - { - for (std::size_t i = 0; i < size_and_type.first; ++i) - { - if (JSON_HEDLEY_UNLIKELY(!get_ubjson_value(size_and_type.second))) - { - return false; - } - } - } - } - else - { - for (std::size_t i = 0; i < size_and_type.first; ++i) - { - if (JSON_HEDLEY_UNLIKELY(!parse_ubjson_internal())) - { - return false; - } - } - } - } - else - { - if (JSON_HEDLEY_UNLIKELY(!sax->start_array(std::size_t(-1)))) - { - return false; - } - - while (current != ']') - { - if (JSON_HEDLEY_UNLIKELY(!parse_ubjson_internal(false))) - { - return false; - } - get_ignore_noop(); - } - } - - return sax->end_array(); - } - - /*! - @return whether object creation completed - */ - bool get_ubjson_object() - { - std::pair size_and_type; - if (JSON_HEDLEY_UNLIKELY(!get_ubjson_size_type(size_and_type))) - { - return false; - } - - string_t key; - if (size_and_type.first != string_t::npos) - { - if (JSON_HEDLEY_UNLIKELY(!sax->start_object(size_and_type.first))) - { - return false; - } - - if (size_and_type.second != 0) - { - for (std::size_t i = 0; i < size_and_type.first; ++i) - { - if (JSON_HEDLEY_UNLIKELY(!get_ubjson_string(key) || !sax->key(key))) - { - return false; - } - if (JSON_HEDLEY_UNLIKELY(!get_ubjson_value(size_and_type.second))) - { - return false; - } - key.clear(); - } - } - else - { - for (std::size_t i = 0; i < size_and_type.first; ++i) - { - if (JSON_HEDLEY_UNLIKELY(!get_ubjson_string(key) || !sax->key(key))) - { - return false; - } - if (JSON_HEDLEY_UNLIKELY(!parse_ubjson_internal())) - { - return false; - } - key.clear(); - } - } - } - else - { - if (JSON_HEDLEY_UNLIKELY(!sax->start_object(std::size_t(-1)))) - { - return false; - } - - while (current != '}') - { - if (JSON_HEDLEY_UNLIKELY(!get_ubjson_string(key, false) || !sax->key(key))) - { - return false; - } - if (JSON_HEDLEY_UNLIKELY(!parse_ubjson_internal())) - { - return false; - } - get_ignore_noop(); - key.clear(); - } - } - - return sax->end_object(); - } - - // Note, no reader for UBJSON binary types is implemented because they do - // not exist - - bool get_ubjson_high_precision_number() - { - // get size of following number string - std::size_t size{}; - auto res = get_ubjson_size_value(size); - if (JSON_HEDLEY_UNLIKELY(!res)) - { - return res; - } - - // get number string - std::vector number_vector; - for (std::size_t i = 0; i < size; ++i) - { - get(); - if (JSON_HEDLEY_UNLIKELY(!unexpect_eof(input_format_t::ubjson, "number"))) - { - return false; - } - number_vector.push_back(static_cast(current)); - } - - // parse number string - auto number_ia = detail::input_adapter(std::forward(number_vector)); - auto number_lexer = detail::lexer(std::move(number_ia), false); - const auto result_number = number_lexer.scan(); - const auto number_string = number_lexer.get_token_string(); - const auto result_remainder = number_lexer.scan(); - - using token_type = typename detail::lexer_base::token_type; - - if (JSON_HEDLEY_UNLIKELY(result_remainder != token_type::end_of_input)) - { - return sax->parse_error(chars_read, number_string, parse_error::create(115, chars_read, exception_message(input_format_t::ubjson, "invalid number text: " + number_lexer.get_token_string(), "high-precision number"))); - } - - switch (result_number) - { - case token_type::value_integer: - return sax->number_integer(number_lexer.get_number_integer()); - case token_type::value_unsigned: - return sax->number_unsigned(number_lexer.get_number_unsigned()); - case token_type::value_float: - return sax->number_float(number_lexer.get_number_float(), std::move(number_string)); - default: - return sax->parse_error(chars_read, number_string, parse_error::create(115, chars_read, exception_message(input_format_t::ubjson, "invalid number text: " + number_lexer.get_token_string(), "high-precision number"))); - } - } - - /////////////////////// - // Utility functions // - /////////////////////// - - /*! - @brief get next character from the input - - This function provides the interface to the used input adapter. It does - not throw in case the input reached EOF, but returns a -'ve valued - `std::char_traits::eof()` in that case. - - @return character read from the input - */ - char_int_type get() - { - ++chars_read; - return current = ia.get_character(); - } - - /*! - @return character read from the input after ignoring all 'N' entries - */ - char_int_type get_ignore_noop() - { - do - { - get(); - } - while (current == 'N'); - - return current; - } - - /* - @brief read a number from the input - - @tparam NumberType the type of the number - @param[in] format the current format (for diagnostics) - @param[out] result number of type @a NumberType - - @return whether conversion completed - - @note This function needs to respect the system's endianess, because - bytes in CBOR, MessagePack, and UBJSON are stored in network order - (big endian) and therefore need reordering on little endian systems. - */ - template - bool get_number(const input_format_t format, NumberType& result) - { - // step 1: read input into array with system's byte order - std::array vec; - for (std::size_t i = 0; i < sizeof(NumberType); ++i) - { - get(); - if (JSON_HEDLEY_UNLIKELY(!unexpect_eof(format, "number"))) - { - return false; - } - - // reverse byte order prior to conversion if necessary - if (is_little_endian != InputIsLittleEndian) - { - vec[sizeof(NumberType) - i - 1] = static_cast(current); - } - else - { - vec[i] = static_cast(current); // LCOV_EXCL_LINE - } - } - - // step 2: convert array into number of type T and return - std::memcpy(&result, vec.data(), sizeof(NumberType)); - return true; - } - - /*! - @brief create a string by reading characters from the input - - @tparam NumberType the type of the number - @param[in] format the current format (for diagnostics) - @param[in] len number of characters to read - @param[out] result string created by reading @a len bytes - - @return whether string creation completed - - @note We can not reserve @a len bytes for the result, because @a len - may be too large. Usually, @ref unexpect_eof() detects the end of - the input before we run out of string memory. - */ - template - bool get_string(const input_format_t format, - const NumberType len, - string_t& result) - { - bool success = true; - for (NumberType i = 0; i < len; i++) - { - get(); - if (JSON_HEDLEY_UNLIKELY(!unexpect_eof(format, "string"))) - { - success = false; - break; - } - result.push_back(static_cast(current)); - }; - return success; - } - - /*! - @brief create a byte array by reading bytes from the input - - @tparam NumberType the type of the number - @param[in] format the current format (for diagnostics) - @param[in] len number of bytes to read - @param[out] result byte array created by reading @a len bytes - - @return whether byte array creation completed - - @note We can not reserve @a len bytes for the result, because @a len - may be too large. Usually, @ref unexpect_eof() detects the end of - the input before we run out of memory. - */ - template - bool get_binary(const input_format_t format, - const NumberType len, - binary_t& result) - { - bool success = true; - for (NumberType i = 0; i < len; i++) - { - get(); - if (JSON_HEDLEY_UNLIKELY(!unexpect_eof(format, "binary"))) - { - success = false; - break; - } - result.push_back(static_cast(current)); - } - return success; - } - - /*! - @param[in] format the current format (for diagnostics) - @param[in] context further context information (for diagnostics) - @return whether the last read character is not EOF - */ - JSON_HEDLEY_NON_NULL(3) - bool unexpect_eof(const input_format_t format, const char* context) const - { - if (JSON_HEDLEY_UNLIKELY(current == std::char_traits::eof())) - { - return sax->parse_error(chars_read, "", - parse_error::create(110, chars_read, exception_message(format, "unexpected end of input", context))); - } - return true; - } - - /*! - @return a string representation of the last read byte - */ - std::string get_token_string() const - { - std::array cr{{}}; - (std::snprintf)(cr.data(), cr.size(), "%.2hhX", static_cast(current)); - return std::string{cr.data()}; - } - - /*! - @param[in] format the current format - @param[in] detail a detailed error message - @param[in] context further context information - @return a message string to use in the parse_error exceptions - */ - std::string exception_message(const input_format_t format, - const std::string& detail, - const std::string& context) const - { - std::string error_msg = "syntax error while parsing "; - - switch (format) - { - case input_format_t::cbor: - error_msg += "CBOR"; - break; - - case input_format_t::msgpack: - error_msg += "MessagePack"; - break; - - case input_format_t::ubjson: - error_msg += "UBJSON"; - break; - - case input_format_t::bson: - error_msg += "BSON"; - break; - - default: // LCOV_EXCL_LINE - JSON_ASSERT(false); // LCOV_EXCL_LINE - } - - return error_msg + " " + context + ": " + detail; - } - - private: - /// input adapter - InputAdapterType ia; - - /// the current character - char_int_type current = std::char_traits::eof(); - - /// the number of characters read - std::size_t chars_read = 0; - - /// whether we can assume little endianess - const bool is_little_endian = little_endianess(); - - /// the SAX parser - json_sax_t* sax = nullptr; -}; -} // namespace detail -} // namespace nlohmann - -// #include - -// #include - -// #include - - -#include // isfinite -#include // uint8_t -#include // function -#include // string -#include // move -#include // vector - -// #include - -// #include - -// #include - -// #include - -// #include - -// #include - -// #include - - -namespace nlohmann -{ -namespace detail -{ -//////////// -// parser // -//////////// - -enum class parse_event_t : uint8_t -{ - /// the parser read `{` and started to process a JSON object - object_start, - /// the parser read `}` and finished processing a JSON object - object_end, - /// the parser read `[` and started to process a JSON array - array_start, - /// the parser read `]` and finished processing a JSON array - array_end, - /// the parser read a key of a value in an object - key, - /// the parser finished reading a JSON value - value -}; - -template -using parser_callback_t = - std::function; - -/*! -@brief syntax analysis - -This class implements a recursive descent parser. -*/ -template -class parser -{ - using number_integer_t = typename BasicJsonType::number_integer_t; - using number_unsigned_t = typename BasicJsonType::number_unsigned_t; - using number_float_t = typename BasicJsonType::number_float_t; - using string_t = typename BasicJsonType::string_t; - using lexer_t = lexer; - using token_type = typename lexer_t::token_type; - - public: - /// a parser reading from an input adapter - explicit parser(InputAdapterType&& adapter, - const parser_callback_t cb = nullptr, - const bool allow_exceptions_ = true, - const bool skip_comments = false) - : callback(cb) - , m_lexer(std::move(adapter), skip_comments) - , allow_exceptions(allow_exceptions_) - { - // read first token - get_token(); - } - - /*! - @brief public parser interface - - @param[in] strict whether to expect the last token to be EOF - @param[in,out] result parsed JSON value - - @throw parse_error.101 in case of an unexpected token - @throw parse_error.102 if to_unicode fails or surrogate error - @throw parse_error.103 if to_unicode fails - */ - void parse(const bool strict, BasicJsonType& result) - { - if (callback) - { - json_sax_dom_callback_parser sdp(result, callback, allow_exceptions); - sax_parse_internal(&sdp); - result.assert_invariant(); - - // in strict mode, input must be completely read - if (strict && (get_token() != token_type::end_of_input)) - { - sdp.parse_error(m_lexer.get_position(), - m_lexer.get_token_string(), - parse_error::create(101, m_lexer.get_position(), - exception_message(token_type::end_of_input, "value"))); - } - - // in case of an error, return discarded value - if (sdp.is_errored()) - { - result = value_t::discarded; - return; - } - - // set top-level value to null if it was discarded by the callback - // function - if (result.is_discarded()) - { - result = nullptr; - } - } - else - { - json_sax_dom_parser sdp(result, allow_exceptions); - sax_parse_internal(&sdp); - result.assert_invariant(); - - // in strict mode, input must be completely read - if (strict && (get_token() != token_type::end_of_input)) - { - sdp.parse_error(m_lexer.get_position(), - m_lexer.get_token_string(), - parse_error::create(101, m_lexer.get_position(), - exception_message(token_type::end_of_input, "value"))); - } - - // in case of an error, return discarded value - if (sdp.is_errored()) - { - result = value_t::discarded; - return; - } - } - } - - /*! - @brief public accept interface - - @param[in] strict whether to expect the last token to be EOF - @return whether the input is a proper JSON text - */ - bool accept(const bool strict = true) - { - json_sax_acceptor sax_acceptor; - return sax_parse(&sax_acceptor, strict); - } - - template - JSON_HEDLEY_NON_NULL(2) - bool sax_parse(SAX* sax, const bool strict = true) - { - (void)detail::is_sax_static_asserts {}; - const bool result = sax_parse_internal(sax); - - // strict mode: next byte must be EOF - if (result && strict && (get_token() != token_type::end_of_input)) - { - return sax->parse_error(m_lexer.get_position(), - m_lexer.get_token_string(), - parse_error::create(101, m_lexer.get_position(), - exception_message(token_type::end_of_input, "value"))); - } - - return result; - } - - private: - template - JSON_HEDLEY_NON_NULL(2) - bool sax_parse_internal(SAX* sax) - { - // stack to remember the hierarchy of structured values we are parsing - // true = array; false = object - std::vector states; - // value to avoid a goto (see comment where set to true) - bool skip_to_state_evaluation = false; - - while (true) - { - if (!skip_to_state_evaluation) - { - // invariant: get_token() was called before each iteration - switch (last_token) - { - case token_type::begin_object: - { - if (JSON_HEDLEY_UNLIKELY(!sax->start_object(std::size_t(-1)))) - { - return false; - } - - // closing } -> we are done - if (get_token() == token_type::end_object) - { - if (JSON_HEDLEY_UNLIKELY(!sax->end_object())) - { - return false; - } - break; - } - - // parse key - if (JSON_HEDLEY_UNLIKELY(last_token != token_type::value_string)) - { - return sax->parse_error(m_lexer.get_position(), - m_lexer.get_token_string(), - parse_error::create(101, m_lexer.get_position(), - exception_message(token_type::value_string, "object key"))); - } - if (JSON_HEDLEY_UNLIKELY(!sax->key(m_lexer.get_string()))) - { - return false; - } - - // parse separator (:) - if (JSON_HEDLEY_UNLIKELY(get_token() != token_type::name_separator)) - { - return sax->parse_error(m_lexer.get_position(), - m_lexer.get_token_string(), - parse_error::create(101, m_lexer.get_position(), - exception_message(token_type::name_separator, "object separator"))); - } - - // remember we are now inside an object - states.push_back(false); - - // parse values - get_token(); - continue; - } - - case token_type::begin_array: - { - if (JSON_HEDLEY_UNLIKELY(!sax->start_array(std::size_t(-1)))) - { - return false; - } - - // closing ] -> we are done - if (get_token() == token_type::end_array) - { - if (JSON_HEDLEY_UNLIKELY(!sax->end_array())) - { - return false; - } - break; - } - - // remember we are now inside an array - states.push_back(true); - - // parse values (no need to call get_token) - continue; - } - - case token_type::value_float: - { - const auto res = m_lexer.get_number_float(); - - if (JSON_HEDLEY_UNLIKELY(!std::isfinite(res))) - { - return sax->parse_error(m_lexer.get_position(), - m_lexer.get_token_string(), - out_of_range::create(406, "number overflow parsing '" + m_lexer.get_token_string() + "'")); - } - - if (JSON_HEDLEY_UNLIKELY(!sax->number_float(res, m_lexer.get_string()))) - { - return false; - } - - break; - } - - case token_type::literal_false: - { - if (JSON_HEDLEY_UNLIKELY(!sax->boolean(false))) - { - return false; - } - break; - } - - case token_type::literal_null: - { - if (JSON_HEDLEY_UNLIKELY(!sax->null())) - { - return false; - } - break; - } - - case token_type::literal_true: - { - if (JSON_HEDLEY_UNLIKELY(!sax->boolean(true))) - { - return false; - } - break; - } - - case token_type::value_integer: - { - if (JSON_HEDLEY_UNLIKELY(!sax->number_integer(m_lexer.get_number_integer()))) - { - return false; - } - break; - } - - case token_type::value_string: - { - if (JSON_HEDLEY_UNLIKELY(!sax->string(m_lexer.get_string()))) - { - return false; - } - break; - } - - case token_type::value_unsigned: - { - if (JSON_HEDLEY_UNLIKELY(!sax->number_unsigned(m_lexer.get_number_unsigned()))) - { - return false; - } - break; - } - - case token_type::parse_error: - { - // using "uninitialized" to avoid "expected" message - return sax->parse_error(m_lexer.get_position(), - m_lexer.get_token_string(), - parse_error::create(101, m_lexer.get_position(), - exception_message(token_type::uninitialized, "value"))); - } - - default: // the last token was unexpected - { - return sax->parse_error(m_lexer.get_position(), - m_lexer.get_token_string(), - parse_error::create(101, m_lexer.get_position(), - exception_message(token_type::literal_or_value, "value"))); - } - } - } - else - { - skip_to_state_evaluation = false; - } - - // we reached this line after we successfully parsed a value - if (states.empty()) - { - // empty stack: we reached the end of the hierarchy: done - return true; - } - - if (states.back()) // array - { - // comma -> next value - if (get_token() == token_type::value_separator) - { - // parse a new value - get_token(); - continue; - } - - // closing ] - if (JSON_HEDLEY_LIKELY(last_token == token_type::end_array)) - { - if (JSON_HEDLEY_UNLIKELY(!sax->end_array())) - { - return false; - } - - // We are done with this array. Before we can parse a - // new value, we need to evaluate the new state first. - // By setting skip_to_state_evaluation to false, we - // are effectively jumping to the beginning of this if. - JSON_ASSERT(!states.empty()); - states.pop_back(); - skip_to_state_evaluation = true; - continue; - } - - return sax->parse_error(m_lexer.get_position(), - m_lexer.get_token_string(), - parse_error::create(101, m_lexer.get_position(), - exception_message(token_type::end_array, "array"))); - } - else // object - { - // comma -> next value - if (get_token() == token_type::value_separator) - { - // parse key - if (JSON_HEDLEY_UNLIKELY(get_token() != token_type::value_string)) - { - return sax->parse_error(m_lexer.get_position(), - m_lexer.get_token_string(), - parse_error::create(101, m_lexer.get_position(), - exception_message(token_type::value_string, "object key"))); - } - - if (JSON_HEDLEY_UNLIKELY(!sax->key(m_lexer.get_string()))) - { - return false; - } - - // parse separator (:) - if (JSON_HEDLEY_UNLIKELY(get_token() != token_type::name_separator)) - { - return sax->parse_error(m_lexer.get_position(), - m_lexer.get_token_string(), - parse_error::create(101, m_lexer.get_position(), - exception_message(token_type::name_separator, "object separator"))); - } - - // parse values - get_token(); - continue; - } - - // closing } - if (JSON_HEDLEY_LIKELY(last_token == token_type::end_object)) - { - if (JSON_HEDLEY_UNLIKELY(!sax->end_object())) - { - return false; - } - - // We are done with this object. Before we can parse a - // new value, we need to evaluate the new state first. - // By setting skip_to_state_evaluation to false, we - // are effectively jumping to the beginning of this if. - JSON_ASSERT(!states.empty()); - states.pop_back(); - skip_to_state_evaluation = true; - continue; - } - - return sax->parse_error(m_lexer.get_position(), - m_lexer.get_token_string(), - parse_error::create(101, m_lexer.get_position(), - exception_message(token_type::end_object, "object"))); - } - } - } - - /// get next token from lexer - token_type get_token() - { - return last_token = m_lexer.scan(); - } - - std::string exception_message(const token_type expected, const std::string& context) - { - std::string error_msg = "syntax error "; - - if (!context.empty()) - { - error_msg += "while parsing " + context + " "; - } - - error_msg += "- "; - - if (last_token == token_type::parse_error) - { - error_msg += std::string(m_lexer.get_error_message()) + "; last read: '" + - m_lexer.get_token_string() + "'"; - } - else - { - error_msg += "unexpected " + std::string(lexer_t::token_type_name(last_token)); - } - - if (expected != token_type::uninitialized) - { - error_msg += "; expected " + std::string(lexer_t::token_type_name(expected)); - } - - return error_msg; - } - - private: - /// callback function - const parser_callback_t callback = nullptr; - /// the type of the last read token - token_type last_token = token_type::uninitialized; - /// the lexer - lexer_t m_lexer; - /// whether to throw exceptions in case of errors - const bool allow_exceptions = true; -}; -} // namespace detail -} // namespace nlohmann - -// #include - - -// #include - - -#include // ptrdiff_t -#include // numeric_limits - -namespace nlohmann -{ -namespace detail -{ -/* -@brief an iterator for primitive JSON types - -This class models an iterator for primitive JSON types (boolean, number, -string). It's only purpose is to allow the iterator/const_iterator classes -to "iterate" over primitive values. Internally, the iterator is modeled by -a `difference_type` variable. Value begin_value (`0`) models the begin, -end_value (`1`) models past the end. -*/ -class primitive_iterator_t -{ - private: - using difference_type = std::ptrdiff_t; - static constexpr difference_type begin_value = 0; - static constexpr difference_type end_value = begin_value + 1; - - /// iterator as signed integer type - difference_type m_it = (std::numeric_limits::min)(); - - public: - constexpr difference_type get_value() const noexcept - { - return m_it; - } - - /// set iterator to a defined beginning - void set_begin() noexcept - { - m_it = begin_value; - } - - /// set iterator to a defined past the end - void set_end() noexcept - { - m_it = end_value; - } - - /// return whether the iterator can be dereferenced - constexpr bool is_begin() const noexcept - { - return m_it == begin_value; - } - - /// return whether the iterator is at end - constexpr bool is_end() const noexcept - { - return m_it == end_value; - } - - friend constexpr bool operator==(primitive_iterator_t lhs, primitive_iterator_t rhs) noexcept - { - return lhs.m_it == rhs.m_it; - } - - friend constexpr bool operator<(primitive_iterator_t lhs, primitive_iterator_t rhs) noexcept - { - return lhs.m_it < rhs.m_it; - } - - primitive_iterator_t operator+(difference_type n) noexcept - { - auto result = *this; - result += n; - return result; - } - - friend constexpr difference_type operator-(primitive_iterator_t lhs, primitive_iterator_t rhs) noexcept - { - return lhs.m_it - rhs.m_it; - } - - primitive_iterator_t& operator++() noexcept - { - ++m_it; - return *this; - } - - primitive_iterator_t const operator++(int) noexcept - { - auto result = *this; - ++m_it; - return result; - } - - primitive_iterator_t& operator--() noexcept - { - --m_it; - return *this; - } - - primitive_iterator_t const operator--(int) noexcept - { - auto result = *this; - --m_it; - return result; - } - - primitive_iterator_t& operator+=(difference_type n) noexcept - { - m_it += n; - return *this; - } - - primitive_iterator_t& operator-=(difference_type n) noexcept - { - m_it -= n; - return *this; - } -}; -} // namespace detail -} // namespace nlohmann - - -namespace nlohmann -{ -namespace detail -{ -/*! -@brief an iterator value - -@note This structure could easily be a union, but MSVC currently does not allow -unions members with complex constructors, see https://github.com/nlohmann/json/pull/105. -*/ -template struct internal_iterator -{ - /// iterator for JSON objects - typename BasicJsonType::object_t::iterator object_iterator {}; - /// iterator for JSON arrays - typename BasicJsonType::array_t::iterator array_iterator {}; - /// generic iterator for all other types - primitive_iterator_t primitive_iterator {}; -}; -} // namespace detail -} // namespace nlohmann - -// #include - - -#include // iterator, random_access_iterator_tag, bidirectional_iterator_tag, advance, next -#include // conditional, is_const, remove_const - -// #include - -// #include - -// #include - -// #include - -// #include - -// #include - -// #include - - -namespace nlohmann -{ -namespace detail -{ -// forward declare, to be able to friend it later on -template class iteration_proxy; -template class iteration_proxy_value; - -/*! -@brief a template for a bidirectional iterator for the @ref basic_json class -This class implements a both iterators (iterator and const_iterator) for the -@ref basic_json class. -@note An iterator is called *initialized* when a pointer to a JSON value has - been set (e.g., by a constructor or a copy assignment). If the iterator is - default-constructed, it is *uninitialized* and most methods are undefined. - **The library uses assertions to detect calls on uninitialized iterators.** -@requirement The class satisfies the following concept requirements: -- -[BidirectionalIterator](https://en.cppreference.com/w/cpp/named_req/BidirectionalIterator): - The iterator that can be moved can be moved in both directions (i.e. - incremented and decremented). -@since version 1.0.0, simplified in version 2.0.9, change to bidirectional - iterators in version 3.0.0 (see https://github.com/nlohmann/json/issues/593) -*/ -template -class iter_impl -{ - /// allow basic_json to access private members - friend iter_impl::value, typename std::remove_const::type, const BasicJsonType>::type>; - friend BasicJsonType; - friend iteration_proxy; - friend iteration_proxy_value; - - using object_t = typename BasicJsonType::object_t; - using array_t = typename BasicJsonType::array_t; - // make sure BasicJsonType is basic_json or const basic_json - static_assert(is_basic_json::type>::value, - "iter_impl only accepts (const) basic_json"); - - public: - - /// The std::iterator class template (used as a base class to provide typedefs) is deprecated in C++17. - /// The C++ Standard has never required user-defined iterators to derive from std::iterator. - /// A user-defined iterator should provide publicly accessible typedefs named - /// iterator_category, value_type, difference_type, pointer, and reference. - /// Note that value_type is required to be non-const, even for constant iterators. - using iterator_category = std::bidirectional_iterator_tag; - - /// the type of the values when the iterator is dereferenced - using value_type = typename BasicJsonType::value_type; - /// a type to represent differences between iterators - using difference_type = typename BasicJsonType::difference_type; - /// defines a pointer to the type iterated over (value_type) - using pointer = typename std::conditional::value, - typename BasicJsonType::const_pointer, - typename BasicJsonType::pointer>::type; - /// defines a reference to the type iterated over (value_type) - using reference = - typename std::conditional::value, - typename BasicJsonType::const_reference, - typename BasicJsonType::reference>::type; - - /// default constructor - iter_impl() = default; - - /*! - @brief constructor for a given JSON instance - @param[in] object pointer to a JSON object for this iterator - @pre object != nullptr - @post The iterator is initialized; i.e. `m_object != nullptr`. - */ - explicit iter_impl(pointer object) noexcept : m_object(object) - { - JSON_ASSERT(m_object != nullptr); - - switch (m_object->m_type) - { - case value_t::object: - { - m_it.object_iterator = typename object_t::iterator(); - break; - } - - case value_t::array: - { - m_it.array_iterator = typename array_t::iterator(); - break; - } - - default: - { - m_it.primitive_iterator = primitive_iterator_t(); - break; - } - } - } - - /*! - @note The conventional copy constructor and copy assignment are implicitly - defined. Combined with the following converting constructor and - assignment, they support: (1) copy from iterator to iterator, (2) - copy from const iterator to const iterator, and (3) conversion from - iterator to const iterator. However conversion from const iterator - to iterator is not defined. - */ - - /*! - @brief const copy constructor - @param[in] other const iterator to copy from - @note This copy constructor had to be defined explicitly to circumvent a bug - occurring on msvc v19.0 compiler (VS 2015) debug build. For more - information refer to: https://github.com/nlohmann/json/issues/1608 - */ - iter_impl(const iter_impl& other) noexcept - : m_object(other.m_object), m_it(other.m_it) - {} - - /*! - @brief converting assignment - @param[in] other const iterator to copy from - @return const/non-const iterator - @note It is not checked whether @a other is initialized. - */ - iter_impl& operator=(const iter_impl& other) noexcept - { - m_object = other.m_object; - m_it = other.m_it; - return *this; - } - - /*! - @brief converting constructor - @param[in] other non-const iterator to copy from - @note It is not checked whether @a other is initialized. - */ - iter_impl(const iter_impl::type>& other) noexcept - : m_object(other.m_object), m_it(other.m_it) - {} - - /*! - @brief converting assignment - @param[in] other non-const iterator to copy from - @return const/non-const iterator - @note It is not checked whether @a other is initialized. - */ - iter_impl& operator=(const iter_impl::type>& other) noexcept - { - m_object = other.m_object; - m_it = other.m_it; - return *this; - } - - private: - /*! - @brief set the iterator to the first value - @pre The iterator is initialized; i.e. `m_object != nullptr`. - */ - void set_begin() noexcept - { - JSON_ASSERT(m_object != nullptr); - - switch (m_object->m_type) - { - case value_t::object: - { - m_it.object_iterator = m_object->m_value.object->begin(); - break; - } - - case value_t::array: - { - m_it.array_iterator = m_object->m_value.array->begin(); - break; - } - - case value_t::null: - { - // set to end so begin()==end() is true: null is empty - m_it.primitive_iterator.set_end(); - break; - } - - default: - { - m_it.primitive_iterator.set_begin(); - break; - } - } - } - - /*! - @brief set the iterator past the last value - @pre The iterator is initialized; i.e. `m_object != nullptr`. - */ - void set_end() noexcept - { - JSON_ASSERT(m_object != nullptr); - - switch (m_object->m_type) - { - case value_t::object: - { - m_it.object_iterator = m_object->m_value.object->end(); - break; - } - - case value_t::array: - { - m_it.array_iterator = m_object->m_value.array->end(); - break; - } - - default: - { - m_it.primitive_iterator.set_end(); - break; - } - } - } - - public: - /*! - @brief return a reference to the value pointed to by the iterator - @pre The iterator is initialized; i.e. `m_object != nullptr`. - */ - reference operator*() const - { - JSON_ASSERT(m_object != nullptr); - - switch (m_object->m_type) - { - case value_t::object: - { - JSON_ASSERT(m_it.object_iterator != m_object->m_value.object->end()); - return m_it.object_iterator->second; - } - - case value_t::array: - { - JSON_ASSERT(m_it.array_iterator != m_object->m_value.array->end()); - return *m_it.array_iterator; - } - - case value_t::null: - JSON_THROW(invalid_iterator::create(214, "cannot get value")); - - default: - { - if (JSON_HEDLEY_LIKELY(m_it.primitive_iterator.is_begin())) - { - return *m_object; - } - - JSON_THROW(invalid_iterator::create(214, "cannot get value")); - } - } - } - - /*! - @brief dereference the iterator - @pre The iterator is initialized; i.e. `m_object != nullptr`. - */ - pointer operator->() const - { - JSON_ASSERT(m_object != nullptr); - - switch (m_object->m_type) - { - case value_t::object: - { - JSON_ASSERT(m_it.object_iterator != m_object->m_value.object->end()); - return &(m_it.object_iterator->second); - } - - case value_t::array: - { - JSON_ASSERT(m_it.array_iterator != m_object->m_value.array->end()); - return &*m_it.array_iterator; - } - - default: - { - if (JSON_HEDLEY_LIKELY(m_it.primitive_iterator.is_begin())) - { - return m_object; - } - - JSON_THROW(invalid_iterator::create(214, "cannot get value")); - } - } - } - - /*! - @brief post-increment (it++) - @pre The iterator is initialized; i.e. `m_object != nullptr`. - */ - iter_impl const operator++(int) - { - auto result = *this; - ++(*this); - return result; - } - - /*! - @brief pre-increment (++it) - @pre The iterator is initialized; i.e. `m_object != nullptr`. - */ - iter_impl& operator++() - { - JSON_ASSERT(m_object != nullptr); - - switch (m_object->m_type) - { - case value_t::object: - { - std::advance(m_it.object_iterator, 1); - break; - } - - case value_t::array: - { - std::advance(m_it.array_iterator, 1); - break; - } - - default: - { - ++m_it.primitive_iterator; - break; - } - } - - return *this; - } - - /*! - @brief post-decrement (it--) - @pre The iterator is initialized; i.e. `m_object != nullptr`. - */ - iter_impl const operator--(int) - { - auto result = *this; - --(*this); - return result; - } - - /*! - @brief pre-decrement (--it) - @pre The iterator is initialized; i.e. `m_object != nullptr`. - */ - iter_impl& operator--() - { - JSON_ASSERT(m_object != nullptr); - - switch (m_object->m_type) - { - case value_t::object: - { - std::advance(m_it.object_iterator, -1); - break; - } - - case value_t::array: - { - std::advance(m_it.array_iterator, -1); - break; - } - - default: - { - --m_it.primitive_iterator; - break; - } - } - - return *this; - } - - /*! - @brief comparison: equal - @pre The iterator is initialized; i.e. `m_object != nullptr`. - */ - bool operator==(const iter_impl& other) const - { - // if objects are not the same, the comparison is undefined - if (JSON_HEDLEY_UNLIKELY(m_object != other.m_object)) - { - JSON_THROW(invalid_iterator::create(212, "cannot compare iterators of different containers")); - } - - JSON_ASSERT(m_object != nullptr); - - switch (m_object->m_type) - { - case value_t::object: - return (m_it.object_iterator == other.m_it.object_iterator); - - case value_t::array: - return (m_it.array_iterator == other.m_it.array_iterator); - - default: - return (m_it.primitive_iterator == other.m_it.primitive_iterator); - } - } - - /*! - @brief comparison: not equal - @pre The iterator is initialized; i.e. `m_object != nullptr`. - */ - bool operator!=(const iter_impl& other) const - { - return !operator==(other); - } - - /*! - @brief comparison: smaller - @pre The iterator is initialized; i.e. `m_object != nullptr`. - */ - bool operator<(const iter_impl& other) const - { - // if objects are not the same, the comparison is undefined - if (JSON_HEDLEY_UNLIKELY(m_object != other.m_object)) - { - JSON_THROW(invalid_iterator::create(212, "cannot compare iterators of different containers")); - } - - JSON_ASSERT(m_object != nullptr); - - switch (m_object->m_type) - { - case value_t::object: - JSON_THROW(invalid_iterator::create(213, "cannot compare order of object iterators")); - - case value_t::array: - return (m_it.array_iterator < other.m_it.array_iterator); - - default: - return (m_it.primitive_iterator < other.m_it.primitive_iterator); - } - } - - /*! - @brief comparison: less than or equal - @pre The iterator is initialized; i.e. `m_object != nullptr`. - */ - bool operator<=(const iter_impl& other) const - { - return !other.operator < (*this); - } - - /*! - @brief comparison: greater than - @pre The iterator is initialized; i.e. `m_object != nullptr`. - */ - bool operator>(const iter_impl& other) const - { - return !operator<=(other); - } - - /*! - @brief comparison: greater than or equal - @pre The iterator is initialized; i.e. `m_object != nullptr`. - */ - bool operator>=(const iter_impl& other) const - { - return !operator<(other); - } - - /*! - @brief add to iterator - @pre The iterator is initialized; i.e. `m_object != nullptr`. - */ - iter_impl& operator+=(difference_type i) - { - JSON_ASSERT(m_object != nullptr); - - switch (m_object->m_type) - { - case value_t::object: - JSON_THROW(invalid_iterator::create(209, "cannot use offsets with object iterators")); - - case value_t::array: - { - std::advance(m_it.array_iterator, i); - break; - } - - default: - { - m_it.primitive_iterator += i; - break; - } - } - - return *this; - } - - /*! - @brief subtract from iterator - @pre The iterator is initialized; i.e. `m_object != nullptr`. - */ - iter_impl& operator-=(difference_type i) - { - return operator+=(-i); - } - - /*! - @brief add to iterator - @pre The iterator is initialized; i.e. `m_object != nullptr`. - */ - iter_impl operator+(difference_type i) const - { - auto result = *this; - result += i; - return result; - } - - /*! - @brief addition of distance and iterator - @pre The iterator is initialized; i.e. `m_object != nullptr`. - */ - friend iter_impl operator+(difference_type i, const iter_impl& it) - { - auto result = it; - result += i; - return result; - } - - /*! - @brief subtract from iterator - @pre The iterator is initialized; i.e. `m_object != nullptr`. - */ - iter_impl operator-(difference_type i) const - { - auto result = *this; - result -= i; - return result; - } - - /*! - @brief return difference - @pre The iterator is initialized; i.e. `m_object != nullptr`. - */ - difference_type operator-(const iter_impl& other) const - { - JSON_ASSERT(m_object != nullptr); - - switch (m_object->m_type) - { - case value_t::object: - JSON_THROW(invalid_iterator::create(209, "cannot use offsets with object iterators")); - - case value_t::array: - return m_it.array_iterator - other.m_it.array_iterator; - - default: - return m_it.primitive_iterator - other.m_it.primitive_iterator; - } - } - - /*! - @brief access to successor - @pre The iterator is initialized; i.e. `m_object != nullptr`. - */ - reference operator[](difference_type n) const - { - JSON_ASSERT(m_object != nullptr); - - switch (m_object->m_type) - { - case value_t::object: - JSON_THROW(invalid_iterator::create(208, "cannot use operator[] for object iterators")); - - case value_t::array: - return *std::next(m_it.array_iterator, n); - - case value_t::null: - JSON_THROW(invalid_iterator::create(214, "cannot get value")); - - default: - { - if (JSON_HEDLEY_LIKELY(m_it.primitive_iterator.get_value() == -n)) - { - return *m_object; - } - - JSON_THROW(invalid_iterator::create(214, "cannot get value")); - } - } - } - - /*! - @brief return the key of an object iterator - @pre The iterator is initialized; i.e. `m_object != nullptr`. - */ - const typename object_t::key_type& key() const - { - JSON_ASSERT(m_object != nullptr); - - if (JSON_HEDLEY_LIKELY(m_object->is_object())) - { - return m_it.object_iterator->first; - } - - JSON_THROW(invalid_iterator::create(207, "cannot use key() for non-object iterators")); - } - - /*! - @brief return the value of an iterator - @pre The iterator is initialized; i.e. `m_object != nullptr`. - */ - reference value() const - { - return operator*(); - } - - private: - /// associated JSON instance - pointer m_object = nullptr; - /// the actual iterator of the associated instance - internal_iterator::type> m_it {}; -}; -} // namespace detail -} // namespace nlohmann - -// #include - -// #include - - -#include // ptrdiff_t -#include // reverse_iterator -#include // declval - -namespace nlohmann -{ -namespace detail -{ -////////////////////// -// reverse_iterator // -////////////////////// - -/*! -@brief a template for a reverse iterator class - -@tparam Base the base iterator type to reverse. Valid types are @ref -iterator (to create @ref reverse_iterator) and @ref const_iterator (to -create @ref const_reverse_iterator). - -@requirement The class satisfies the following concept requirements: -- -[BidirectionalIterator](https://en.cppreference.com/w/cpp/named_req/BidirectionalIterator): - The iterator that can be moved can be moved in both directions (i.e. - incremented and decremented). -- [OutputIterator](https://en.cppreference.com/w/cpp/named_req/OutputIterator): - It is possible to write to the pointed-to element (only if @a Base is - @ref iterator). - -@since version 1.0.0 -*/ -template -class json_reverse_iterator : public std::reverse_iterator -{ - public: - using difference_type = std::ptrdiff_t; - /// shortcut to the reverse iterator adapter - using base_iterator = std::reverse_iterator; - /// the reference type for the pointed-to element - using reference = typename Base::reference; - - /// create reverse iterator from iterator - explicit json_reverse_iterator(const typename base_iterator::iterator_type& it) noexcept - : base_iterator(it) {} - - /// create reverse iterator from base class - explicit json_reverse_iterator(const base_iterator& it) noexcept : base_iterator(it) {} - - /// post-increment (it++) - json_reverse_iterator const operator++(int) - { - return static_cast(base_iterator::operator++(1)); - } - - /// pre-increment (++it) - json_reverse_iterator& operator++() - { - return static_cast(base_iterator::operator++()); - } - - /// post-decrement (it--) - json_reverse_iterator const operator--(int) - { - return static_cast(base_iterator::operator--(1)); - } - - /// pre-decrement (--it) - json_reverse_iterator& operator--() - { - return static_cast(base_iterator::operator--()); - } - - /// add to iterator - json_reverse_iterator& operator+=(difference_type i) - { - return static_cast(base_iterator::operator+=(i)); - } - - /// add to iterator - json_reverse_iterator operator+(difference_type i) const - { - return static_cast(base_iterator::operator+(i)); - } - - /// subtract from iterator - json_reverse_iterator operator-(difference_type i) const - { - return static_cast(base_iterator::operator-(i)); - } - - /// return difference - difference_type operator-(const json_reverse_iterator& other) const - { - return base_iterator(*this) - base_iterator(other); - } - - /// access to successor - reference operator[](difference_type n) const - { - return *(this->operator+(n)); - } - - /// return the key of an object iterator - auto key() const -> decltype(std::declval().key()) - { - auto it = --this->base(); - return it.key(); - } - - /// return the value of an iterator - reference value() const - { - auto it = --this->base(); - return it.operator * (); - } -}; -} // namespace detail -} // namespace nlohmann - -// #include - -// #include - - -#include // all_of -#include // isdigit -#include // max -#include // accumulate -#include // string -#include // move -#include // vector - -// #include - -// #include - -// #include - - -namespace nlohmann -{ -template -class json_pointer -{ - // allow basic_json to access private members - NLOHMANN_BASIC_JSON_TPL_DECLARATION - friend class basic_json; - - public: - /*! - @brief create JSON pointer - - Create a JSON pointer according to the syntax described in - [Section 3 of RFC6901](https://tools.ietf.org/html/rfc6901#section-3). - - @param[in] s string representing the JSON pointer; if omitted, the empty - string is assumed which references the whole JSON value - - @throw parse_error.107 if the given JSON pointer @a s is nonempty and does - not begin with a slash (`/`); see example below - - @throw parse_error.108 if a tilde (`~`) in the given JSON pointer @a s is - not followed by `0` (representing `~`) or `1` (representing `/`); see - example below - - @liveexample{The example shows the construction several valid JSON pointers - as well as the exceptional behavior.,json_pointer} - - @since version 2.0.0 - */ - explicit json_pointer(const std::string& s = "") - : reference_tokens(split(s)) - {} - - /*! - @brief return a string representation of the JSON pointer - - @invariant For each JSON pointer `ptr`, it holds: - @code {.cpp} - ptr == json_pointer(ptr.to_string()); - @endcode - - @return a string representation of the JSON pointer - - @liveexample{The example shows the result of `to_string`.,json_pointer__to_string} - - @since version 2.0.0 - */ - std::string to_string() const - { - return std::accumulate(reference_tokens.begin(), reference_tokens.end(), - std::string{}, - [](const std::string & a, const std::string & b) - { - return a + "/" + escape(b); - }); - } - - /// @copydoc to_string() - operator std::string() const - { - return to_string(); - } - - /*! - @brief append another JSON pointer at the end of this JSON pointer - - @param[in] ptr JSON pointer to append - @return JSON pointer with @a ptr appended - - @liveexample{The example shows the usage of `operator/=`.,json_pointer__operator_add} - - @complexity Linear in the length of @a ptr. - - @sa @ref operator/=(std::string) to append a reference token - @sa @ref operator/=(std::size_t) to append an array index - @sa @ref operator/(const json_pointer&, const json_pointer&) for a binary operator - - @since version 3.6.0 - */ - json_pointer& operator/=(const json_pointer& ptr) - { - reference_tokens.insert(reference_tokens.end(), - ptr.reference_tokens.begin(), - ptr.reference_tokens.end()); - return *this; - } - - /*! - @brief append an unescaped reference token at the end of this JSON pointer - - @param[in] token reference token to append - @return JSON pointer with @a token appended without escaping @a token - - @liveexample{The example shows the usage of `operator/=`.,json_pointer__operator_add} - - @complexity Amortized constant. - - @sa @ref operator/=(const json_pointer&) to append a JSON pointer - @sa @ref operator/=(std::size_t) to append an array index - @sa @ref operator/(const json_pointer&, std::size_t) for a binary operator - - @since version 3.6.0 - */ - json_pointer& operator/=(std::string token) - { - push_back(std::move(token)); - return *this; - } - - /*! - @brief append an array index at the end of this JSON pointer - - @param[in] array_idx array index to append - @return JSON pointer with @a array_idx appended - - @liveexample{The example shows the usage of `operator/=`.,json_pointer__operator_add} - - @complexity Amortized constant. - - @sa @ref operator/=(const json_pointer&) to append a JSON pointer - @sa @ref operator/=(std::string) to append a reference token - @sa @ref operator/(const json_pointer&, std::string) for a binary operator - - @since version 3.6.0 - */ - json_pointer& operator/=(std::size_t array_idx) - { - return *this /= std::to_string(array_idx); - } - - /*! - @brief create a new JSON pointer by appending the right JSON pointer at the end of the left JSON pointer - - @param[in] lhs JSON pointer - @param[in] rhs JSON pointer - @return a new JSON pointer with @a rhs appended to @a lhs - - @liveexample{The example shows the usage of `operator/`.,json_pointer__operator_add_binary} - - @complexity Linear in the length of @a lhs and @a rhs. - - @sa @ref operator/=(const json_pointer&) to append a JSON pointer - - @since version 3.6.0 - */ - friend json_pointer operator/(const json_pointer& lhs, - const json_pointer& rhs) - { - return json_pointer(lhs) /= rhs; - } - - /*! - @brief create a new JSON pointer by appending the unescaped token at the end of the JSON pointer - - @param[in] ptr JSON pointer - @param[in] token reference token - @return a new JSON pointer with unescaped @a token appended to @a ptr - - @liveexample{The example shows the usage of `operator/`.,json_pointer__operator_add_binary} - - @complexity Linear in the length of @a ptr. - - @sa @ref operator/=(std::string) to append a reference token - - @since version 3.6.0 - */ - friend json_pointer operator/(const json_pointer& ptr, std::string token) - { - return json_pointer(ptr) /= std::move(token); - } - - /*! - @brief create a new JSON pointer by appending the array-index-token at the end of the JSON pointer - - @param[in] ptr JSON pointer - @param[in] array_idx array index - @return a new JSON pointer with @a array_idx appended to @a ptr - - @liveexample{The example shows the usage of `operator/`.,json_pointer__operator_add_binary} - - @complexity Linear in the length of @a ptr. - - @sa @ref operator/=(std::size_t) to append an array index - - @since version 3.6.0 - */ - friend json_pointer operator/(const json_pointer& ptr, std::size_t array_idx) - { - return json_pointer(ptr) /= array_idx; - } - - /*! - @brief returns the parent of this JSON pointer - - @return parent of this JSON pointer; in case this JSON pointer is the root, - the root itself is returned - - @complexity Linear in the length of the JSON pointer. - - @liveexample{The example shows the result of `parent_pointer` for different - JSON Pointers.,json_pointer__parent_pointer} - - @since version 3.6.0 - */ - json_pointer parent_pointer() const - { - if (empty()) - { - return *this; - } - - json_pointer res = *this; - res.pop_back(); - return res; - } - - /*! - @brief remove last reference token - - @pre not `empty()` - - @liveexample{The example shows the usage of `pop_back`.,json_pointer__pop_back} - - @complexity Constant. - - @throw out_of_range.405 if JSON pointer has no parent - - @since version 3.6.0 - */ - void pop_back() - { - if (JSON_HEDLEY_UNLIKELY(empty())) - { - JSON_THROW(detail::out_of_range::create(405, "JSON pointer has no parent")); - } - - reference_tokens.pop_back(); - } - - /*! - @brief return last reference token - - @pre not `empty()` - @return last reference token - - @liveexample{The example shows the usage of `back`.,json_pointer__back} - - @complexity Constant. - - @throw out_of_range.405 if JSON pointer has no parent - - @since version 3.6.0 - */ - const std::string& back() const - { - if (JSON_HEDLEY_UNLIKELY(empty())) - { - JSON_THROW(detail::out_of_range::create(405, "JSON pointer has no parent")); - } - - return reference_tokens.back(); - } - - /*! - @brief append an unescaped token at the end of the reference pointer - - @param[in] token token to add - - @complexity Amortized constant. - - @liveexample{The example shows the result of `push_back` for different - JSON Pointers.,json_pointer__push_back} - - @since version 3.6.0 - */ - void push_back(const std::string& token) - { - reference_tokens.push_back(token); - } - - /// @copydoc push_back(const std::string&) - void push_back(std::string&& token) - { - reference_tokens.push_back(std::move(token)); - } - - /*! - @brief return whether pointer points to the root document - - @return true iff the JSON pointer points to the root document - - @complexity Constant. - - @exceptionsafety No-throw guarantee: this function never throws exceptions. - - @liveexample{The example shows the result of `empty` for different JSON - Pointers.,json_pointer__empty} - - @since version 3.6.0 - */ - bool empty() const noexcept - { - return reference_tokens.empty(); - } - - private: - /*! - @param[in] s reference token to be converted into an array index - - @return integer representation of @a s - - @throw parse_error.106 if an array index begins with '0' - @throw parse_error.109 if an array index begins not with a digit - @throw out_of_range.404 if string @a s could not be converted to an integer - @throw out_of_range.410 if an array index exceeds size_type - */ - static typename BasicJsonType::size_type array_index(const std::string& s) - { - using size_type = typename BasicJsonType::size_type; - - // error condition (cf. RFC 6901, Sect. 4) - if (JSON_HEDLEY_UNLIKELY(s.size() > 1 && s[0] == '0')) - { - JSON_THROW(detail::parse_error::create(106, 0, - "array index '" + s + - "' must not begin with '0'")); - } - - // error condition (cf. RFC 6901, Sect. 4) - if (JSON_HEDLEY_UNLIKELY(s.size() > 1 && !(s[0] >= '1' && s[0] <= '9'))) - { - JSON_THROW(detail::parse_error::create(109, 0, "array index '" + s + "' is not a number")); - } - - std::size_t processed_chars = 0; - unsigned long long res = 0; - JSON_TRY - { - res = std::stoull(s, &processed_chars); - } - JSON_CATCH(std::out_of_range&) - { - JSON_THROW(detail::out_of_range::create(404, "unresolved reference token '" + s + "'")); - } - - // check if the string was completely read - if (JSON_HEDLEY_UNLIKELY(processed_chars != s.size())) - { - JSON_THROW(detail::out_of_range::create(404, "unresolved reference token '" + s + "'")); - } - - // only triggered on special platforms (like 32bit), see also - // https://github.com/nlohmann/json/pull/2203 - if (res >= static_cast((std::numeric_limits::max)())) - { - JSON_THROW(detail::out_of_range::create(410, "array index " + s + " exceeds size_type")); // LCOV_EXCL_LINE - } - - return static_cast(res); - } - - json_pointer top() const - { - if (JSON_HEDLEY_UNLIKELY(empty())) - { - JSON_THROW(detail::out_of_range::create(405, "JSON pointer has no parent")); - } - - json_pointer result = *this; - result.reference_tokens = {reference_tokens[0]}; - return result; - } - - /*! - @brief create and return a reference to the pointed to value - - @complexity Linear in the number of reference tokens. - - @throw parse_error.109 if array index is not a number - @throw type_error.313 if value cannot be unflattened - */ - BasicJsonType& get_and_create(BasicJsonType& j) const - { - auto result = &j; - - // in case no reference tokens exist, return a reference to the JSON value - // j which will be overwritten by a primitive value - for (const auto& reference_token : reference_tokens) - { - switch (result->type()) - { - case detail::value_t::null: - { - if (reference_token == "0") - { - // start a new array if reference token is 0 - result = &result->operator[](0); - } - else - { - // start a new object otherwise - result = &result->operator[](reference_token); - } - break; - } - - case detail::value_t::object: - { - // create an entry in the object - result = &result->operator[](reference_token); - break; - } - - case detail::value_t::array: - { - // create an entry in the array - result = &result->operator[](array_index(reference_token)); - break; - } - - /* - The following code is only reached if there exists a reference - token _and_ the current value is primitive. In this case, we have - an error situation, because primitive values may only occur as - single value; that is, with an empty list of reference tokens. - */ - default: - JSON_THROW(detail::type_error::create(313, "invalid value to unflatten")); - } - } - - return *result; - } - - /*! - @brief return a reference to the pointed to value - - @note This version does not throw if a value is not present, but tries to - create nested values instead. For instance, calling this function - with pointer `"/this/that"` on a null value is equivalent to calling - `operator[]("this").operator[]("that")` on that value, effectively - changing the null value to an object. - - @param[in] ptr a JSON value - - @return reference to the JSON value pointed to by the JSON pointer - - @complexity Linear in the length of the JSON pointer. - - @throw parse_error.106 if an array index begins with '0' - @throw parse_error.109 if an array index was not a number - @throw out_of_range.404 if the JSON pointer can not be resolved - */ - BasicJsonType& get_unchecked(BasicJsonType* ptr) const - { - for (const auto& reference_token : reference_tokens) - { - // convert null values to arrays or objects before continuing - if (ptr->is_null()) - { - // check if reference token is a number - const bool nums = - std::all_of(reference_token.begin(), reference_token.end(), - [](const unsigned char x) - { - return std::isdigit(x); - }); - - // change value to array for numbers or "-" or to object otherwise - *ptr = (nums || reference_token == "-") - ? detail::value_t::array - : detail::value_t::object; - } - - switch (ptr->type()) - { - case detail::value_t::object: - { - // use unchecked object access - ptr = &ptr->operator[](reference_token); - break; - } - - case detail::value_t::array: - { - if (reference_token == "-") - { - // explicitly treat "-" as index beyond the end - ptr = &ptr->operator[](ptr->m_value.array->size()); - } - else - { - // convert array index to number; unchecked access - ptr = &ptr->operator[](array_index(reference_token)); - } - break; - } - - default: - JSON_THROW(detail::out_of_range::create(404, "unresolved reference token '" + reference_token + "'")); - } - } - - return *ptr; - } - - /*! - @throw parse_error.106 if an array index begins with '0' - @throw parse_error.109 if an array index was not a number - @throw out_of_range.402 if the array index '-' is used - @throw out_of_range.404 if the JSON pointer can not be resolved - */ - BasicJsonType& get_checked(BasicJsonType* ptr) const - { - for (const auto& reference_token : reference_tokens) - { - switch (ptr->type()) - { - case detail::value_t::object: - { - // note: at performs range check - ptr = &ptr->at(reference_token); - break; - } - - case detail::value_t::array: - { - if (JSON_HEDLEY_UNLIKELY(reference_token == "-")) - { - // "-" always fails the range check - JSON_THROW(detail::out_of_range::create(402, - "array index '-' (" + std::to_string(ptr->m_value.array->size()) + - ") is out of range")); - } - - // note: at performs range check - ptr = &ptr->at(array_index(reference_token)); - break; - } - - default: - JSON_THROW(detail::out_of_range::create(404, "unresolved reference token '" + reference_token + "'")); - } - } - - return *ptr; - } - - /*! - @brief return a const reference to the pointed to value - - @param[in] ptr a JSON value - - @return const reference to the JSON value pointed to by the JSON - pointer - - @throw parse_error.106 if an array index begins with '0' - @throw parse_error.109 if an array index was not a number - @throw out_of_range.402 if the array index '-' is used - @throw out_of_range.404 if the JSON pointer can not be resolved - */ - const BasicJsonType& get_unchecked(const BasicJsonType* ptr) const - { - for (const auto& reference_token : reference_tokens) - { - switch (ptr->type()) - { - case detail::value_t::object: - { - // use unchecked object access - ptr = &ptr->operator[](reference_token); - break; - } - - case detail::value_t::array: - { - if (JSON_HEDLEY_UNLIKELY(reference_token == "-")) - { - // "-" cannot be used for const access - JSON_THROW(detail::out_of_range::create(402, - "array index '-' (" + std::to_string(ptr->m_value.array->size()) + - ") is out of range")); - } - - // use unchecked array access - ptr = &ptr->operator[](array_index(reference_token)); - break; - } - - default: - JSON_THROW(detail::out_of_range::create(404, "unresolved reference token '" + reference_token + "'")); - } - } - - return *ptr; - } - - /*! - @throw parse_error.106 if an array index begins with '0' - @throw parse_error.109 if an array index was not a number - @throw out_of_range.402 if the array index '-' is used - @throw out_of_range.404 if the JSON pointer can not be resolved - */ - const BasicJsonType& get_checked(const BasicJsonType* ptr) const - { - for (const auto& reference_token : reference_tokens) - { - switch (ptr->type()) - { - case detail::value_t::object: - { - // note: at performs range check - ptr = &ptr->at(reference_token); - break; - } - - case detail::value_t::array: - { - if (JSON_HEDLEY_UNLIKELY(reference_token == "-")) - { - // "-" always fails the range check - JSON_THROW(detail::out_of_range::create(402, - "array index '-' (" + std::to_string(ptr->m_value.array->size()) + - ") is out of range")); - } - - // note: at performs range check - ptr = &ptr->at(array_index(reference_token)); - break; - } - - default: - JSON_THROW(detail::out_of_range::create(404, "unresolved reference token '" + reference_token + "'")); - } - } - - return *ptr; - } - - /*! - @throw parse_error.106 if an array index begins with '0' - @throw parse_error.109 if an array index was not a number - */ - bool contains(const BasicJsonType* ptr) const - { - for (const auto& reference_token : reference_tokens) - { - switch (ptr->type()) - { - case detail::value_t::object: - { - if (!ptr->contains(reference_token)) - { - // we did not find the key in the object - return false; - } - - ptr = &ptr->operator[](reference_token); - break; - } - - case detail::value_t::array: - { - if (JSON_HEDLEY_UNLIKELY(reference_token == "-")) - { - // "-" always fails the range check - return false; - } - if (JSON_HEDLEY_UNLIKELY(reference_token.size() == 1 && !("0" <= reference_token && reference_token <= "9"))) - { - // invalid char - return false; - } - if (JSON_HEDLEY_UNLIKELY(reference_token.size() > 1)) - { - if (JSON_HEDLEY_UNLIKELY(!('1' <= reference_token[0] && reference_token[0] <= '9'))) - { - // first char should be between '1' and '9' - return false; - } - for (std::size_t i = 1; i < reference_token.size(); i++) - { - if (JSON_HEDLEY_UNLIKELY(!('0' <= reference_token[i] && reference_token[i] <= '9'))) - { - // other char should be between '0' and '9' - return false; - } - } - } - - const auto idx = array_index(reference_token); - if (idx >= ptr->size()) - { - // index out of range - return false; - } - - ptr = &ptr->operator[](idx); - break; - } - - default: - { - // we do not expect primitive values if there is still a - // reference token to process - return false; - } - } - } - - // no reference token left means we found a primitive value - return true; - } - - /*! - @brief split the string input to reference tokens - - @note This function is only called by the json_pointer constructor. - All exceptions below are documented there. - - @throw parse_error.107 if the pointer is not empty or begins with '/' - @throw parse_error.108 if character '~' is not followed by '0' or '1' - */ - static std::vector split(const std::string& reference_string) - { - std::vector result; - - // special case: empty reference string -> no reference tokens - if (reference_string.empty()) - { - return result; - } - - // check if nonempty reference string begins with slash - if (JSON_HEDLEY_UNLIKELY(reference_string[0] != '/')) - { - JSON_THROW(detail::parse_error::create(107, 1, - "JSON pointer must be empty or begin with '/' - was: '" + - reference_string + "'")); - } - - // extract the reference tokens: - // - slash: position of the last read slash (or end of string) - // - start: position after the previous slash - for ( - // search for the first slash after the first character - std::size_t slash = reference_string.find_first_of('/', 1), - // set the beginning of the first reference token - start = 1; - // we can stop if start == 0 (if slash == std::string::npos) - start != 0; - // set the beginning of the next reference token - // (will eventually be 0 if slash == std::string::npos) - start = (slash == std::string::npos) ? 0 : slash + 1, - // find next slash - slash = reference_string.find_first_of('/', start)) - { - // use the text between the beginning of the reference token - // (start) and the last slash (slash). - auto reference_token = reference_string.substr(start, slash - start); - - // check reference tokens are properly escaped - for (std::size_t pos = reference_token.find_first_of('~'); - pos != std::string::npos; - pos = reference_token.find_first_of('~', pos + 1)) - { - JSON_ASSERT(reference_token[pos] == '~'); - - // ~ must be followed by 0 or 1 - if (JSON_HEDLEY_UNLIKELY(pos == reference_token.size() - 1 || - (reference_token[pos + 1] != '0' && - reference_token[pos + 1] != '1'))) - { - JSON_THROW(detail::parse_error::create(108, 0, "escape character '~' must be followed with '0' or '1'")); - } - } - - // finally, store the reference token - unescape(reference_token); - result.push_back(reference_token); - } - - return result; - } - - /*! - @brief replace all occurrences of a substring by another string - - @param[in,out] s the string to manipulate; changed so that all - occurrences of @a f are replaced with @a t - @param[in] f the substring to replace with @a t - @param[in] t the string to replace @a f - - @pre The search string @a f must not be empty. **This precondition is - enforced with an assertion.** - - @since version 2.0.0 - */ - static void replace_substring(std::string& s, const std::string& f, - const std::string& t) - { - JSON_ASSERT(!f.empty()); - for (auto pos = s.find(f); // find first occurrence of f - pos != std::string::npos; // make sure f was found - s.replace(pos, f.size(), t), // replace with t, and - pos = s.find(f, pos + t.size())) // find next occurrence of f - {} - } - - /// escape "~" to "~0" and "/" to "~1" - static std::string escape(std::string s) - { - replace_substring(s, "~", "~0"); - replace_substring(s, "/", "~1"); - return s; - } - - /// unescape "~1" to tilde and "~0" to slash (order is important!) - static void unescape(std::string& s) - { - replace_substring(s, "~1", "/"); - replace_substring(s, "~0", "~"); - } - - /*! - @param[in] reference_string the reference string to the current value - @param[in] value the value to consider - @param[in,out] result the result object to insert values to - - @note Empty objects or arrays are flattened to `null`. - */ - static void flatten(const std::string& reference_string, - const BasicJsonType& value, - BasicJsonType& result) - { - switch (value.type()) - { - case detail::value_t::array: - { - if (value.m_value.array->empty()) - { - // flatten empty array as null - result[reference_string] = nullptr; - } - else - { - // iterate array and use index as reference string - for (std::size_t i = 0; i < value.m_value.array->size(); ++i) - { - flatten(reference_string + "/" + std::to_string(i), - value.m_value.array->operator[](i), result); - } - } - break; - } - - case detail::value_t::object: - { - if (value.m_value.object->empty()) - { - // flatten empty object as null - result[reference_string] = nullptr; - } - else - { - // iterate object and use keys as reference string - for (const auto& element : *value.m_value.object) - { - flatten(reference_string + "/" + escape(element.first), element.second, result); - } - } - break; - } - - default: - { - // add primitive value with its reference string - result[reference_string] = value; - break; - } - } - } - - /*! - @param[in] value flattened JSON - - @return unflattened JSON - - @throw parse_error.109 if array index is not a number - @throw type_error.314 if value is not an object - @throw type_error.315 if object values are not primitive - @throw type_error.313 if value cannot be unflattened - */ - static BasicJsonType - unflatten(const BasicJsonType& value) - { - if (JSON_HEDLEY_UNLIKELY(!value.is_object())) - { - JSON_THROW(detail::type_error::create(314, "only objects can be unflattened")); - } - - BasicJsonType result; - - // iterate the JSON object values - for (const auto& element : *value.m_value.object) - { - if (JSON_HEDLEY_UNLIKELY(!element.second.is_primitive())) - { - JSON_THROW(detail::type_error::create(315, "values in object must be primitive")); - } - - // assign value to reference pointed to by JSON pointer; Note that if - // the JSON pointer is "" (i.e., points to the whole value), function - // get_and_create returns a reference to result itself. An assignment - // will then create a primitive value. - json_pointer(element.first).get_and_create(result) = element.second; - } - - return result; - } - - /*! - @brief compares two JSON pointers for equality - - @param[in] lhs JSON pointer to compare - @param[in] rhs JSON pointer to compare - @return whether @a lhs is equal to @a rhs - - @complexity Linear in the length of the JSON pointer - - @exceptionsafety No-throw guarantee: this function never throws exceptions. - */ - friend bool operator==(json_pointer const& lhs, - json_pointer const& rhs) noexcept - { - return lhs.reference_tokens == rhs.reference_tokens; - } - - /*! - @brief compares two JSON pointers for inequality - - @param[in] lhs JSON pointer to compare - @param[in] rhs JSON pointer to compare - @return whether @a lhs is not equal @a rhs - - @complexity Linear in the length of the JSON pointer - - @exceptionsafety No-throw guarantee: this function never throws exceptions. - */ - friend bool operator!=(json_pointer const& lhs, - json_pointer const& rhs) noexcept - { - return !(lhs == rhs); - } - - /// the reference tokens - std::vector reference_tokens; -}; -} // namespace nlohmann - -// #include - - -#include -#include - -// #include - - -namespace nlohmann -{ -namespace detail -{ -template -class json_ref -{ - public: - using value_type = BasicJsonType; - - json_ref(value_type&& value) - : owned_value(std::move(value)) - , value_ref(&owned_value) - , is_rvalue(true) - {} - - json_ref(const value_type& value) - : value_ref(const_cast(&value)) - , is_rvalue(false) - {} - - json_ref(std::initializer_list init) - : owned_value(init) - , value_ref(&owned_value) - , is_rvalue(true) - {} - - template < - class... Args, - enable_if_t::value, int> = 0 > - json_ref(Args && ... args) - : owned_value(std::forward(args)...) - , value_ref(&owned_value) - , is_rvalue(true) - {} - - // class should be movable only - json_ref(json_ref&&) = default; - json_ref(const json_ref&) = delete; - json_ref& operator=(const json_ref&) = delete; - json_ref& operator=(json_ref&&) = delete; - ~json_ref() = default; - - value_type moved_or_copied() const - { - if (is_rvalue) - { - return std::move(*value_ref); - } - return *value_ref; - } - - value_type const& operator*() const - { - return *static_cast(value_ref); - } - - value_type const* operator->() const - { - return static_cast(value_ref); - } - - private: - mutable value_type owned_value = nullptr; - value_type* value_ref = nullptr; - const bool is_rvalue = true; -}; -} // namespace detail -} // namespace nlohmann - -// #include - -// #include - -// #include - -// #include - - -#include // reverse -#include // array -#include // uint8_t, uint16_t, uint32_t, uint64_t -#include // memcpy -#include // numeric_limits -#include // string -#include // isnan, isinf - -// #include - -// #include - -// #include - - -#include // copy -#include // size_t -#include // streamsize -#include // back_inserter -#include // shared_ptr, make_shared -#include // basic_ostream -#include // basic_string -#include // vector -// #include - - -namespace nlohmann -{ -namespace detail -{ -/// abstract output adapter interface -template struct output_adapter_protocol -{ - virtual void write_character(CharType c) = 0; - virtual void write_characters(const CharType* s, std::size_t length) = 0; - virtual ~output_adapter_protocol() = default; -}; - -/// a type to simplify interfaces -template -using output_adapter_t = std::shared_ptr>; - -/// output adapter for byte vectors -template -class output_vector_adapter : public output_adapter_protocol -{ - public: - explicit output_vector_adapter(std::vector& vec) noexcept - : v(vec) - {} - - void write_character(CharType c) override - { - v.push_back(c); - } - - JSON_HEDLEY_NON_NULL(2) - void write_characters(const CharType* s, std::size_t length) override - { - std::copy(s, s + length, std::back_inserter(v)); - } - - private: - std::vector& v; -}; - -/// output adapter for output streams -template -class output_stream_adapter : public output_adapter_protocol -{ - public: - explicit output_stream_adapter(std::basic_ostream& s) noexcept - : stream(s) - {} - - void write_character(CharType c) override - { - stream.put(c); - } - - JSON_HEDLEY_NON_NULL(2) - void write_characters(const CharType* s, std::size_t length) override - { - stream.write(s, static_cast(length)); - } - - private: - std::basic_ostream& stream; -}; - -/// output adapter for basic_string -template> -class output_string_adapter : public output_adapter_protocol -{ - public: - explicit output_string_adapter(StringType& s) noexcept - : str(s) - {} - - void write_character(CharType c) override - { - str.push_back(c); - } - - JSON_HEDLEY_NON_NULL(2) - void write_characters(const CharType* s, std::size_t length) override - { - str.append(s, length); - } - - private: - StringType& str; -}; - -template> -class output_adapter -{ - public: - output_adapter(std::vector& vec) - : oa(std::make_shared>(vec)) {} - - output_adapter(std::basic_ostream& s) - : oa(std::make_shared>(s)) {} - - output_adapter(StringType& s) - : oa(std::make_shared>(s)) {} - - operator output_adapter_t() - { - return oa; - } - - private: - output_adapter_t oa = nullptr; -}; -} // namespace detail -} // namespace nlohmann - - -namespace nlohmann -{ -namespace detail -{ -/////////////////// -// binary writer // -/////////////////// - -/*! -@brief serialization to CBOR and MessagePack values -*/ -template -class binary_writer -{ - using string_t = typename BasicJsonType::string_t; - using binary_t = typename BasicJsonType::binary_t; - using number_float_t = typename BasicJsonType::number_float_t; - - public: - /*! - @brief create a binary writer - - @param[in] adapter output adapter to write to - */ - explicit binary_writer(output_adapter_t adapter) : oa(adapter) - { - JSON_ASSERT(oa); - } - - /*! - @param[in] j JSON value to serialize - @pre j.type() == value_t::object - */ - void write_bson(const BasicJsonType& j) - { - switch (j.type()) - { - case value_t::object: - { - write_bson_object(*j.m_value.object); - break; - } - - default: - { - JSON_THROW(type_error::create(317, "to serialize to BSON, top-level type must be object, but is " + std::string(j.type_name()))); - } - } - } - - /*! - @param[in] j JSON value to serialize - */ - void write_cbor(const BasicJsonType& j) - { - switch (j.type()) - { - case value_t::null: - { - oa->write_character(to_char_type(0xF6)); - break; - } - - case value_t::boolean: - { - oa->write_character(j.m_value.boolean - ? to_char_type(0xF5) - : to_char_type(0xF4)); - break; - } - - case value_t::number_integer: - { - if (j.m_value.number_integer >= 0) - { - // CBOR does not differentiate between positive signed - // integers and unsigned integers. Therefore, we used the - // code from the value_t::number_unsigned case here. - if (j.m_value.number_integer <= 0x17) - { - write_number(static_cast(j.m_value.number_integer)); - } - else if (j.m_value.number_integer <= (std::numeric_limits::max)()) - { - oa->write_character(to_char_type(0x18)); - write_number(static_cast(j.m_value.number_integer)); - } - else if (j.m_value.number_integer <= (std::numeric_limits::max)()) - { - oa->write_character(to_char_type(0x19)); - write_number(static_cast(j.m_value.number_integer)); - } - else if (j.m_value.number_integer <= (std::numeric_limits::max)()) - { - oa->write_character(to_char_type(0x1A)); - write_number(static_cast(j.m_value.number_integer)); - } - else - { - oa->write_character(to_char_type(0x1B)); - write_number(static_cast(j.m_value.number_integer)); - } - } - else - { - // The conversions below encode the sign in the first - // byte, and the value is converted to a positive number. - const auto positive_number = -1 - j.m_value.number_integer; - if (j.m_value.number_integer >= -24) - { - write_number(static_cast(0x20 + positive_number)); - } - else if (positive_number <= (std::numeric_limits::max)()) - { - oa->write_character(to_char_type(0x38)); - write_number(static_cast(positive_number)); - } - else if (positive_number <= (std::numeric_limits::max)()) - { - oa->write_character(to_char_type(0x39)); - write_number(static_cast(positive_number)); - } - else if (positive_number <= (std::numeric_limits::max)()) - { - oa->write_character(to_char_type(0x3A)); - write_number(static_cast(positive_number)); - } - else - { - oa->write_character(to_char_type(0x3B)); - write_number(static_cast(positive_number)); - } - } - break; - } - - case value_t::number_unsigned: - { - if (j.m_value.number_unsigned <= 0x17) - { - write_number(static_cast(j.m_value.number_unsigned)); - } - else if (j.m_value.number_unsigned <= (std::numeric_limits::max)()) - { - oa->write_character(to_char_type(0x18)); - write_number(static_cast(j.m_value.number_unsigned)); - } - else if (j.m_value.number_unsigned <= (std::numeric_limits::max)()) - { - oa->write_character(to_char_type(0x19)); - write_number(static_cast(j.m_value.number_unsigned)); - } - else if (j.m_value.number_unsigned <= (std::numeric_limits::max)()) - { - oa->write_character(to_char_type(0x1A)); - write_number(static_cast(j.m_value.number_unsigned)); - } - else - { - oa->write_character(to_char_type(0x1B)); - write_number(static_cast(j.m_value.number_unsigned)); - } - break; - } - - case value_t::number_float: - { - if (std::isnan(j.m_value.number_float)) - { - // NaN is 0xf97e00 in CBOR - oa->write_character(to_char_type(0xF9)); - oa->write_character(to_char_type(0x7E)); - oa->write_character(to_char_type(0x00)); - } - else if (std::isinf(j.m_value.number_float)) - { - // Infinity is 0xf97c00, -Infinity is 0xf9fc00 - oa->write_character(to_char_type(0xf9)); - oa->write_character(j.m_value.number_float > 0 ? to_char_type(0x7C) : to_char_type(0xFC)); - oa->write_character(to_char_type(0x00)); - } - else - { - write_compact_float(j.m_value.number_float, detail::input_format_t::cbor); - } - break; - } - - case value_t::string: - { - // step 1: write control byte and the string length - const auto N = j.m_value.string->size(); - if (N <= 0x17) - { - write_number(static_cast(0x60 + N)); - } - else if (N <= (std::numeric_limits::max)()) - { - oa->write_character(to_char_type(0x78)); - write_number(static_cast(N)); - } - else if (N <= (std::numeric_limits::max)()) - { - oa->write_character(to_char_type(0x79)); - write_number(static_cast(N)); - } - else if (N <= (std::numeric_limits::max)()) - { - oa->write_character(to_char_type(0x7A)); - write_number(static_cast(N)); - } - // LCOV_EXCL_START - else if (N <= (std::numeric_limits::max)()) - { - oa->write_character(to_char_type(0x7B)); - write_number(static_cast(N)); - } - // LCOV_EXCL_STOP - - // step 2: write the string - oa->write_characters( - reinterpret_cast(j.m_value.string->c_str()), - j.m_value.string->size()); - break; - } - - case value_t::array: - { - // step 1: write control byte and the array size - const auto N = j.m_value.array->size(); - if (N <= 0x17) - { - write_number(static_cast(0x80 + N)); - } - else if (N <= (std::numeric_limits::max)()) - { - oa->write_character(to_char_type(0x98)); - write_number(static_cast(N)); - } - else if (N <= (std::numeric_limits::max)()) - { - oa->write_character(to_char_type(0x99)); - write_number(static_cast(N)); - } - else if (N <= (std::numeric_limits::max)()) - { - oa->write_character(to_char_type(0x9A)); - write_number(static_cast(N)); - } - // LCOV_EXCL_START - else if (N <= (std::numeric_limits::max)()) - { - oa->write_character(to_char_type(0x9B)); - write_number(static_cast(N)); - } - // LCOV_EXCL_STOP - - // step 2: write each element - for (const auto& el : *j.m_value.array) - { - write_cbor(el); - } - break; - } - - case value_t::binary: - { - if (j.m_value.binary->has_subtype()) - { - write_number(static_cast(0xd8)); - write_number(j.m_value.binary->subtype()); - } - - // step 1: write control byte and the binary array size - const auto N = j.m_value.binary->size(); - if (N <= 0x17) - { - write_number(static_cast(0x40 + N)); - } - else if (N <= (std::numeric_limits::max)()) - { - oa->write_character(to_char_type(0x58)); - write_number(static_cast(N)); - } - else if (N <= (std::numeric_limits::max)()) - { - oa->write_character(to_char_type(0x59)); - write_number(static_cast(N)); - } - else if (N <= (std::numeric_limits::max)()) - { - oa->write_character(to_char_type(0x5A)); - write_number(static_cast(N)); - } - // LCOV_EXCL_START - else if (N <= (std::numeric_limits::max)()) - { - oa->write_character(to_char_type(0x5B)); - write_number(static_cast(N)); - } - // LCOV_EXCL_STOP - - // step 2: write each element - oa->write_characters( - reinterpret_cast(j.m_value.binary->data()), - N); - - break; - } - - case value_t::object: - { - // step 1: write control byte and the object size - const auto N = j.m_value.object->size(); - if (N <= 0x17) - { - write_number(static_cast(0xA0 + N)); - } - else if (N <= (std::numeric_limits::max)()) - { - oa->write_character(to_char_type(0xB8)); - write_number(static_cast(N)); - } - else if (N <= (std::numeric_limits::max)()) - { - oa->write_character(to_char_type(0xB9)); - write_number(static_cast(N)); - } - else if (N <= (std::numeric_limits::max)()) - { - oa->write_character(to_char_type(0xBA)); - write_number(static_cast(N)); - } - // LCOV_EXCL_START - else if (N <= (std::numeric_limits::max)()) - { - oa->write_character(to_char_type(0xBB)); - write_number(static_cast(N)); - } - // LCOV_EXCL_STOP - - // step 2: write each element - for (const auto& el : *j.m_value.object) - { - write_cbor(el.first); - write_cbor(el.second); - } - break; - } - - default: - break; - } - } - - /*! - @param[in] j JSON value to serialize - */ - void write_msgpack(const BasicJsonType& j) - { - switch (j.type()) - { - case value_t::null: // nil - { - oa->write_character(to_char_type(0xC0)); - break; - } - - case value_t::boolean: // true and false - { - oa->write_character(j.m_value.boolean - ? to_char_type(0xC3) - : to_char_type(0xC2)); - break; - } - - case value_t::number_integer: - { - if (j.m_value.number_integer >= 0) - { - // MessagePack does not differentiate between positive - // signed integers and unsigned integers. Therefore, we used - // the code from the value_t::number_unsigned case here. - if (j.m_value.number_unsigned < 128) - { - // positive fixnum - write_number(static_cast(j.m_value.number_integer)); - } - else if (j.m_value.number_unsigned <= (std::numeric_limits::max)()) - { - // uint 8 - oa->write_character(to_char_type(0xCC)); - write_number(static_cast(j.m_value.number_integer)); - } - else if (j.m_value.number_unsigned <= (std::numeric_limits::max)()) - { - // uint 16 - oa->write_character(to_char_type(0xCD)); - write_number(static_cast(j.m_value.number_integer)); - } - else if (j.m_value.number_unsigned <= (std::numeric_limits::max)()) - { - // uint 32 - oa->write_character(to_char_type(0xCE)); - write_number(static_cast(j.m_value.number_integer)); - } - else if (j.m_value.number_unsigned <= (std::numeric_limits::max)()) - { - // uint 64 - oa->write_character(to_char_type(0xCF)); - write_number(static_cast(j.m_value.number_integer)); - } - } - else - { - if (j.m_value.number_integer >= -32) - { - // negative fixnum - write_number(static_cast(j.m_value.number_integer)); - } - else if (j.m_value.number_integer >= (std::numeric_limits::min)() && - j.m_value.number_integer <= (std::numeric_limits::max)()) - { - // int 8 - oa->write_character(to_char_type(0xD0)); - write_number(static_cast(j.m_value.number_integer)); - } - else if (j.m_value.number_integer >= (std::numeric_limits::min)() && - j.m_value.number_integer <= (std::numeric_limits::max)()) - { - // int 16 - oa->write_character(to_char_type(0xD1)); - write_number(static_cast(j.m_value.number_integer)); - } - else if (j.m_value.number_integer >= (std::numeric_limits::min)() && - j.m_value.number_integer <= (std::numeric_limits::max)()) - { - // int 32 - oa->write_character(to_char_type(0xD2)); - write_number(static_cast(j.m_value.number_integer)); - } - else if (j.m_value.number_integer >= (std::numeric_limits::min)() && - j.m_value.number_integer <= (std::numeric_limits::max)()) - { - // int 64 - oa->write_character(to_char_type(0xD3)); - write_number(static_cast(j.m_value.number_integer)); - } - } - break; - } - - case value_t::number_unsigned: - { - if (j.m_value.number_unsigned < 128) - { - // positive fixnum - write_number(static_cast(j.m_value.number_integer)); - } - else if (j.m_value.number_unsigned <= (std::numeric_limits::max)()) - { - // uint 8 - oa->write_character(to_char_type(0xCC)); - write_number(static_cast(j.m_value.number_integer)); - } - else if (j.m_value.number_unsigned <= (std::numeric_limits::max)()) - { - // uint 16 - oa->write_character(to_char_type(0xCD)); - write_number(static_cast(j.m_value.number_integer)); - } - else if (j.m_value.number_unsigned <= (std::numeric_limits::max)()) - { - // uint 32 - oa->write_character(to_char_type(0xCE)); - write_number(static_cast(j.m_value.number_integer)); - } - else if (j.m_value.number_unsigned <= (std::numeric_limits::max)()) - { - // uint 64 - oa->write_character(to_char_type(0xCF)); - write_number(static_cast(j.m_value.number_integer)); - } - break; - } - - case value_t::number_float: - { - write_compact_float(j.m_value.number_float, detail::input_format_t::msgpack); - break; - } - - case value_t::string: - { - // step 1: write control byte and the string length - const auto N = j.m_value.string->size(); - if (N <= 31) - { - // fixstr - write_number(static_cast(0xA0 | N)); - } - else if (N <= (std::numeric_limits::max)()) - { - // str 8 - oa->write_character(to_char_type(0xD9)); - write_number(static_cast(N)); - } - else if (N <= (std::numeric_limits::max)()) - { - // str 16 - oa->write_character(to_char_type(0xDA)); - write_number(static_cast(N)); - } - else if (N <= (std::numeric_limits::max)()) - { - // str 32 - oa->write_character(to_char_type(0xDB)); - write_number(static_cast(N)); - } - - // step 2: write the string - oa->write_characters( - reinterpret_cast(j.m_value.string->c_str()), - j.m_value.string->size()); - break; - } - - case value_t::array: - { - // step 1: write control byte and the array size - const auto N = j.m_value.array->size(); - if (N <= 15) - { - // fixarray - write_number(static_cast(0x90 | N)); - } - else if (N <= (std::numeric_limits::max)()) - { - // array 16 - oa->write_character(to_char_type(0xDC)); - write_number(static_cast(N)); - } - else if (N <= (std::numeric_limits::max)()) - { - // array 32 - oa->write_character(to_char_type(0xDD)); - write_number(static_cast(N)); - } - - // step 2: write each element - for (const auto& el : *j.m_value.array) - { - write_msgpack(el); - } - break; - } - - case value_t::binary: - { - // step 0: determine if the binary type has a set subtype to - // determine whether or not to use the ext or fixext types - const bool use_ext = j.m_value.binary->has_subtype(); - - // step 1: write control byte and the byte string length - const auto N = j.m_value.binary->size(); - if (N <= (std::numeric_limits::max)()) - { - std::uint8_t output_type{}; - bool fixed = true; - if (use_ext) - { - switch (N) - { - case 1: - output_type = 0xD4; // fixext 1 - break; - case 2: - output_type = 0xD5; // fixext 2 - break; - case 4: - output_type = 0xD6; // fixext 4 - break; - case 8: - output_type = 0xD7; // fixext 8 - break; - case 16: - output_type = 0xD8; // fixext 16 - break; - default: - output_type = 0xC7; // ext 8 - fixed = false; - break; - } - - } - else - { - output_type = 0xC4; // bin 8 - fixed = false; - } - - oa->write_character(to_char_type(output_type)); - if (!fixed) - { - write_number(static_cast(N)); - } - } - else if (N <= (std::numeric_limits::max)()) - { - std::uint8_t output_type = use_ext - ? 0xC8 // ext 16 - : 0xC5; // bin 16 - - oa->write_character(to_char_type(output_type)); - write_number(static_cast(N)); - } - else if (N <= (std::numeric_limits::max)()) - { - std::uint8_t output_type = use_ext - ? 0xC9 // ext 32 - : 0xC6; // bin 32 - - oa->write_character(to_char_type(output_type)); - write_number(static_cast(N)); - } - - // step 1.5: if this is an ext type, write the subtype - if (use_ext) - { - write_number(static_cast(j.m_value.binary->subtype())); - } - - // step 2: write the byte string - oa->write_characters( - reinterpret_cast(j.m_value.binary->data()), - N); - - break; - } - - case value_t::object: - { - // step 1: write control byte and the object size - const auto N = j.m_value.object->size(); - if (N <= 15) - { - // fixmap - write_number(static_cast(0x80 | (N & 0xF))); - } - else if (N <= (std::numeric_limits::max)()) - { - // map 16 - oa->write_character(to_char_type(0xDE)); - write_number(static_cast(N)); - } - else if (N <= (std::numeric_limits::max)()) - { - // map 32 - oa->write_character(to_char_type(0xDF)); - write_number(static_cast(N)); - } - - // step 2: write each element - for (const auto& el : *j.m_value.object) - { - write_msgpack(el.first); - write_msgpack(el.second); - } - break; - } - - default: - break; - } - } - - /*! - @param[in] j JSON value to serialize - @param[in] use_count whether to use '#' prefixes (optimized format) - @param[in] use_type whether to use '$' prefixes (optimized format) - @param[in] add_prefix whether prefixes need to be used for this value - */ - void write_ubjson(const BasicJsonType& j, const bool use_count, - const bool use_type, const bool add_prefix = true) - { - switch (j.type()) - { - case value_t::null: - { - if (add_prefix) - { - oa->write_character(to_char_type('Z')); - } - break; - } - - case value_t::boolean: - { - if (add_prefix) - { - oa->write_character(j.m_value.boolean - ? to_char_type('T') - : to_char_type('F')); - } - break; - } - - case value_t::number_integer: - { - write_number_with_ubjson_prefix(j.m_value.number_integer, add_prefix); - break; - } - - case value_t::number_unsigned: - { - write_number_with_ubjson_prefix(j.m_value.number_unsigned, add_prefix); - break; - } - - case value_t::number_float: - { - write_number_with_ubjson_prefix(j.m_value.number_float, add_prefix); - break; - } - - case value_t::string: - { - if (add_prefix) - { - oa->write_character(to_char_type('S')); - } - write_number_with_ubjson_prefix(j.m_value.string->size(), true); - oa->write_characters( - reinterpret_cast(j.m_value.string->c_str()), - j.m_value.string->size()); - break; - } - - case value_t::array: - { - if (add_prefix) - { - oa->write_character(to_char_type('[')); - } - - bool prefix_required = true; - if (use_type && !j.m_value.array->empty()) - { - JSON_ASSERT(use_count); - const CharType first_prefix = ubjson_prefix(j.front()); - const bool same_prefix = std::all_of(j.begin() + 1, j.end(), - [this, first_prefix](const BasicJsonType & v) - { - return ubjson_prefix(v) == first_prefix; - }); - - if (same_prefix) - { - prefix_required = false; - oa->write_character(to_char_type('$')); - oa->write_character(first_prefix); - } - } - - if (use_count) - { - oa->write_character(to_char_type('#')); - write_number_with_ubjson_prefix(j.m_value.array->size(), true); - } - - for (const auto& el : *j.m_value.array) - { - write_ubjson(el, use_count, use_type, prefix_required); - } - - if (!use_count) - { - oa->write_character(to_char_type(']')); - } - - break; - } - - case value_t::binary: - { - if (add_prefix) - { - oa->write_character(to_char_type('[')); - } - - if (use_type && !j.m_value.binary->empty()) - { - JSON_ASSERT(use_count); - oa->write_character(to_char_type('$')); - oa->write_character('U'); - } - - if (use_count) - { - oa->write_character(to_char_type('#')); - write_number_with_ubjson_prefix(j.m_value.binary->size(), true); - } - - if (use_type) - { - oa->write_characters( - reinterpret_cast(j.m_value.binary->data()), - j.m_value.binary->size()); - } - else - { - for (size_t i = 0; i < j.m_value.binary->size(); ++i) - { - oa->write_character(to_char_type('U')); - oa->write_character(j.m_value.binary->data()[i]); - } - } - - if (!use_count) - { - oa->write_character(to_char_type(']')); - } - - break; - } - - case value_t::object: - { - if (add_prefix) - { - oa->write_character(to_char_type('{')); - } - - bool prefix_required = true; - if (use_type && !j.m_value.object->empty()) - { - JSON_ASSERT(use_count); - const CharType first_prefix = ubjson_prefix(j.front()); - const bool same_prefix = std::all_of(j.begin(), j.end(), - [this, first_prefix](const BasicJsonType & v) - { - return ubjson_prefix(v) == first_prefix; - }); - - if (same_prefix) - { - prefix_required = false; - oa->write_character(to_char_type('$')); - oa->write_character(first_prefix); - } - } - - if (use_count) - { - oa->write_character(to_char_type('#')); - write_number_with_ubjson_prefix(j.m_value.object->size(), true); - } - - for (const auto& el : *j.m_value.object) - { - write_number_with_ubjson_prefix(el.first.size(), true); - oa->write_characters( - reinterpret_cast(el.first.c_str()), - el.first.size()); - write_ubjson(el.second, use_count, use_type, prefix_required); - } - - if (!use_count) - { - oa->write_character(to_char_type('}')); - } - - break; - } - - default: - break; - } - } - - private: - ////////// - // BSON // - ////////// - - /*! - @return The size of a BSON document entry header, including the id marker - and the entry name size (and its null-terminator). - */ - static std::size_t calc_bson_entry_header_size(const string_t& name) - { - const auto it = name.find(static_cast(0)); - if (JSON_HEDLEY_UNLIKELY(it != BasicJsonType::string_t::npos)) - { - JSON_THROW(out_of_range::create(409, - "BSON key cannot contain code point U+0000 (at byte " + std::to_string(it) + ")")); - } - - return /*id*/ 1ul + name.size() + /*zero-terminator*/1u; - } - - /*! - @brief Writes the given @a element_type and @a name to the output adapter - */ - void write_bson_entry_header(const string_t& name, - const std::uint8_t element_type) - { - oa->write_character(to_char_type(element_type)); // boolean - oa->write_characters( - reinterpret_cast(name.c_str()), - name.size() + 1u); - } - - /*! - @brief Writes a BSON element with key @a name and boolean value @a value - */ - void write_bson_boolean(const string_t& name, - const bool value) - { - write_bson_entry_header(name, 0x08); - oa->write_character(value ? to_char_type(0x01) : to_char_type(0x00)); - } - - /*! - @brief Writes a BSON element with key @a name and double value @a value - */ - void write_bson_double(const string_t& name, - const double value) - { - write_bson_entry_header(name, 0x01); - write_number(value); - } - - /*! - @return The size of the BSON-encoded string in @a value - */ - static std::size_t calc_bson_string_size(const string_t& value) - { - return sizeof(std::int32_t) + value.size() + 1ul; - } - - /*! - @brief Writes a BSON element with key @a name and string value @a value - */ - void write_bson_string(const string_t& name, - const string_t& value) - { - write_bson_entry_header(name, 0x02); - - write_number(static_cast(value.size() + 1ul)); - oa->write_characters( - reinterpret_cast(value.c_str()), - value.size() + 1); - } - - /*! - @brief Writes a BSON element with key @a name and null value - */ - void write_bson_null(const string_t& name) - { - write_bson_entry_header(name, 0x0A); - } - - /*! - @return The size of the BSON-encoded integer @a value - */ - static std::size_t calc_bson_integer_size(const std::int64_t value) - { - return (std::numeric_limits::min)() <= value && value <= (std::numeric_limits::max)() - ? sizeof(std::int32_t) - : sizeof(std::int64_t); - } - - /*! - @brief Writes a BSON element with key @a name and integer @a value - */ - void write_bson_integer(const string_t& name, - const std::int64_t value) - { - if ((std::numeric_limits::min)() <= value && value <= (std::numeric_limits::max)()) - { - write_bson_entry_header(name, 0x10); // int32 - write_number(static_cast(value)); - } - else - { - write_bson_entry_header(name, 0x12); // int64 - write_number(static_cast(value)); - } - } - - /*! - @return The size of the BSON-encoded unsigned integer in @a j - */ - static constexpr std::size_t calc_bson_unsigned_size(const std::uint64_t value) noexcept - { - return (value <= static_cast((std::numeric_limits::max)())) - ? sizeof(std::int32_t) - : sizeof(std::int64_t); - } - - /*! - @brief Writes a BSON element with key @a name and unsigned @a value - */ - void write_bson_unsigned(const string_t& name, - const std::uint64_t value) - { - if (value <= static_cast((std::numeric_limits::max)())) - { - write_bson_entry_header(name, 0x10 /* int32 */); - write_number(static_cast(value)); - } - else if (value <= static_cast((std::numeric_limits::max)())) - { - write_bson_entry_header(name, 0x12 /* int64 */); - write_number(static_cast(value)); - } - else - { - JSON_THROW(out_of_range::create(407, "integer number " + std::to_string(value) + " cannot be represented by BSON as it does not fit int64")); - } - } - - /*! - @brief Writes a BSON element with key @a name and object @a value - */ - void write_bson_object_entry(const string_t& name, - const typename BasicJsonType::object_t& value) - { - write_bson_entry_header(name, 0x03); // object - write_bson_object(value); - } - - /*! - @return The size of the BSON-encoded array @a value - */ - static std::size_t calc_bson_array_size(const typename BasicJsonType::array_t& value) - { - std::size_t array_index = 0ul; - - const std::size_t embedded_document_size = std::accumulate(std::begin(value), std::end(value), std::size_t(0), [&array_index](std::size_t result, const typename BasicJsonType::array_t::value_type & el) - { - return result + calc_bson_element_size(std::to_string(array_index++), el); - }); - - return sizeof(std::int32_t) + embedded_document_size + 1ul; - } - - /*! - @return The size of the BSON-encoded binary array @a value - */ - static std::size_t calc_bson_binary_size(const typename BasicJsonType::binary_t& value) - { - return sizeof(std::int32_t) + value.size() + 1ul; - } - - /*! - @brief Writes a BSON element with key @a name and array @a value - */ - void write_bson_array(const string_t& name, - const typename BasicJsonType::array_t& value) - { - write_bson_entry_header(name, 0x04); // array - write_number(static_cast(calc_bson_array_size(value))); - - std::size_t array_index = 0ul; - - for (const auto& el : value) - { - write_bson_element(std::to_string(array_index++), el); - } - - oa->write_character(to_char_type(0x00)); - } - - /*! - @brief Writes a BSON element with key @a name and binary value @a value - */ - void write_bson_binary(const string_t& name, - const binary_t& value) - { - write_bson_entry_header(name, 0x05); - - write_number(static_cast(value.size())); - write_number(value.has_subtype() ? value.subtype() : std::uint8_t(0x00)); - - oa->write_characters(reinterpret_cast(value.data()), value.size()); - } - - /*! - @brief Calculates the size necessary to serialize the JSON value @a j with its @a name - @return The calculated size for the BSON document entry for @a j with the given @a name. - */ - static std::size_t calc_bson_element_size(const string_t& name, - const BasicJsonType& j) - { - const auto header_size = calc_bson_entry_header_size(name); - switch (j.type()) - { - case value_t::object: - return header_size + calc_bson_object_size(*j.m_value.object); - - case value_t::array: - return header_size + calc_bson_array_size(*j.m_value.array); - - case value_t::binary: - return header_size + calc_bson_binary_size(*j.m_value.binary); - - case value_t::boolean: - return header_size + 1ul; - - case value_t::number_float: - return header_size + 8ul; - - case value_t::number_integer: - return header_size + calc_bson_integer_size(j.m_value.number_integer); - - case value_t::number_unsigned: - return header_size + calc_bson_unsigned_size(j.m_value.number_unsigned); - - case value_t::string: - return header_size + calc_bson_string_size(*j.m_value.string); - - case value_t::null: - return header_size + 0ul; - - // LCOV_EXCL_START - default: - JSON_ASSERT(false); - return 0ul; - // LCOV_EXCL_STOP - } - } - - /*! - @brief Serializes the JSON value @a j to BSON and associates it with the - key @a name. - @param name The name to associate with the JSON entity @a j within the - current BSON document - @return The size of the BSON entry - */ - void write_bson_element(const string_t& name, - const BasicJsonType& j) - { - switch (j.type()) - { - case value_t::object: - return write_bson_object_entry(name, *j.m_value.object); - - case value_t::array: - return write_bson_array(name, *j.m_value.array); - - case value_t::binary: - return write_bson_binary(name, *j.m_value.binary); - - case value_t::boolean: - return write_bson_boolean(name, j.m_value.boolean); - - case value_t::number_float: - return write_bson_double(name, j.m_value.number_float); - - case value_t::number_integer: - return write_bson_integer(name, j.m_value.number_integer); - - case value_t::number_unsigned: - return write_bson_unsigned(name, j.m_value.number_unsigned); - - case value_t::string: - return write_bson_string(name, *j.m_value.string); - - case value_t::null: - return write_bson_null(name); - - // LCOV_EXCL_START - default: - JSON_ASSERT(false); - return; - // LCOV_EXCL_STOP - } - } - - /*! - @brief Calculates the size of the BSON serialization of the given - JSON-object @a j. - @param[in] j JSON value to serialize - @pre j.type() == value_t::object - */ - static std::size_t calc_bson_object_size(const typename BasicJsonType::object_t& value) - { - std::size_t document_size = std::accumulate(value.begin(), value.end(), std::size_t(0), - [](size_t result, const typename BasicJsonType::object_t::value_type & el) - { - return result += calc_bson_element_size(el.first, el.second); - }); - - return sizeof(std::int32_t) + document_size + 1ul; - } - - /*! - @param[in] j JSON value to serialize - @pre j.type() == value_t::object - */ - void write_bson_object(const typename BasicJsonType::object_t& value) - { - write_number(static_cast(calc_bson_object_size(value))); - - for (const auto& el : value) - { - write_bson_element(el.first, el.second); - } - - oa->write_character(to_char_type(0x00)); - } - - ////////// - // CBOR // - ////////// - - static constexpr CharType get_cbor_float_prefix(float /*unused*/) - { - return to_char_type(0xFA); // Single-Precision Float - } - - static constexpr CharType get_cbor_float_prefix(double /*unused*/) - { - return to_char_type(0xFB); // Double-Precision Float - } - - ///////////// - // MsgPack // - ///////////// - - static constexpr CharType get_msgpack_float_prefix(float /*unused*/) - { - return to_char_type(0xCA); // float 32 - } - - static constexpr CharType get_msgpack_float_prefix(double /*unused*/) - { - return to_char_type(0xCB); // float 64 - } - - //////////// - // UBJSON // - //////////// - - // UBJSON: write number (floating point) - template::value, int>::type = 0> - void write_number_with_ubjson_prefix(const NumberType n, - const bool add_prefix) - { - if (add_prefix) - { - oa->write_character(get_ubjson_float_prefix(n)); - } - write_number(n); - } - - // UBJSON: write number (unsigned integer) - template::value, int>::type = 0> - void write_number_with_ubjson_prefix(const NumberType n, - const bool add_prefix) - { - if (n <= static_cast((std::numeric_limits::max)())) - { - if (add_prefix) - { - oa->write_character(to_char_type('i')); // int8 - } - write_number(static_cast(n)); - } - else if (n <= (std::numeric_limits::max)()) - { - if (add_prefix) - { - oa->write_character(to_char_type('U')); // uint8 - } - write_number(static_cast(n)); - } - else if (n <= static_cast((std::numeric_limits::max)())) - { - if (add_prefix) - { - oa->write_character(to_char_type('I')); // int16 - } - write_number(static_cast(n)); - } - else if (n <= static_cast((std::numeric_limits::max)())) - { - if (add_prefix) - { - oa->write_character(to_char_type('l')); // int32 - } - write_number(static_cast(n)); - } - else if (n <= static_cast((std::numeric_limits::max)())) - { - if (add_prefix) - { - oa->write_character(to_char_type('L')); // int64 - } - write_number(static_cast(n)); - } - else - { - if (add_prefix) - { - oa->write_character(to_char_type('H')); // high-precision number - } - - const auto number = BasicJsonType(n).dump(); - write_number_with_ubjson_prefix(number.size(), true); - for (std::size_t i = 0; i < number.size(); ++i) - { - oa->write_character(to_char_type(static_cast(number[i]))); - } - } - } - - // UBJSON: write number (signed integer) - template < typename NumberType, typename std::enable_if < - std::is_signed::value&& - !std::is_floating_point::value, int >::type = 0 > - void write_number_with_ubjson_prefix(const NumberType n, - const bool add_prefix) - { - if ((std::numeric_limits::min)() <= n && n <= (std::numeric_limits::max)()) - { - if (add_prefix) - { - oa->write_character(to_char_type('i')); // int8 - } - write_number(static_cast(n)); - } - else if (static_cast((std::numeric_limits::min)()) <= n && n <= static_cast((std::numeric_limits::max)())) - { - if (add_prefix) - { - oa->write_character(to_char_type('U')); // uint8 - } - write_number(static_cast(n)); - } - else if ((std::numeric_limits::min)() <= n && n <= (std::numeric_limits::max)()) - { - if (add_prefix) - { - oa->write_character(to_char_type('I')); // int16 - } - write_number(static_cast(n)); - } - else if ((std::numeric_limits::min)() <= n && n <= (std::numeric_limits::max)()) - { - if (add_prefix) - { - oa->write_character(to_char_type('l')); // int32 - } - write_number(static_cast(n)); - } - else if ((std::numeric_limits::min)() <= n && n <= (std::numeric_limits::max)()) - { - if (add_prefix) - { - oa->write_character(to_char_type('L')); // int64 - } - write_number(static_cast(n)); - } - // LCOV_EXCL_START - else - { - if (add_prefix) - { - oa->write_character(to_char_type('H')); // high-precision number - } - - const auto number = BasicJsonType(n).dump(); - write_number_with_ubjson_prefix(number.size(), true); - for (std::size_t i = 0; i < number.size(); ++i) - { - oa->write_character(to_char_type(static_cast(number[i]))); - } - } - // LCOV_EXCL_STOP - } - - /*! - @brief determine the type prefix of container values - */ - CharType ubjson_prefix(const BasicJsonType& j) const noexcept - { - switch (j.type()) - { - case value_t::null: - return 'Z'; - - case value_t::boolean: - return j.m_value.boolean ? 'T' : 'F'; - - case value_t::number_integer: - { - if ((std::numeric_limits::min)() <= j.m_value.number_integer && j.m_value.number_integer <= (std::numeric_limits::max)()) - { - return 'i'; - } - if ((std::numeric_limits::min)() <= j.m_value.number_integer && j.m_value.number_integer <= (std::numeric_limits::max)()) - { - return 'U'; - } - if ((std::numeric_limits::min)() <= j.m_value.number_integer && j.m_value.number_integer <= (std::numeric_limits::max)()) - { - return 'I'; - } - if ((std::numeric_limits::min)() <= j.m_value.number_integer && j.m_value.number_integer <= (std::numeric_limits::max)()) - { - return 'l'; - } - if ((std::numeric_limits::min)() <= j.m_value.number_integer && j.m_value.number_integer <= (std::numeric_limits::max)()) - { - return 'L'; - } - // anything else is treated as high-precision number - return 'H'; // LCOV_EXCL_LINE - } - - case value_t::number_unsigned: - { - if (j.m_value.number_unsigned <= static_cast((std::numeric_limits::max)())) - { - return 'i'; - } - if (j.m_value.number_unsigned <= static_cast((std::numeric_limits::max)())) - { - return 'U'; - } - if (j.m_value.number_unsigned <= static_cast((std::numeric_limits::max)())) - { - return 'I'; - } - if (j.m_value.number_unsigned <= static_cast((std::numeric_limits::max)())) - { - return 'l'; - } - if (j.m_value.number_unsigned <= static_cast((std::numeric_limits::max)())) - { - return 'L'; - } - // anything else is treated as high-precision number - return 'H'; // LCOV_EXCL_LINE - } - - case value_t::number_float: - return get_ubjson_float_prefix(j.m_value.number_float); - - case value_t::string: - return 'S'; - - case value_t::array: // fallthrough - case value_t::binary: - return '['; - - case value_t::object: - return '{'; - - default: // discarded values - return 'N'; - } - } - - static constexpr CharType get_ubjson_float_prefix(float /*unused*/) - { - return 'd'; // float 32 - } - - static constexpr CharType get_ubjson_float_prefix(double /*unused*/) - { - return 'D'; // float 64 - } - - /////////////////////// - // Utility functions // - /////////////////////// - - /* - @brief write a number to output input - @param[in] n number of type @a NumberType - @tparam NumberType the type of the number - @tparam OutputIsLittleEndian Set to true if output data is - required to be little endian - - @note This function needs to respect the system's endianess, because bytes - in CBOR, MessagePack, and UBJSON are stored in network order (big - endian) and therefore need reordering on little endian systems. - */ - template - void write_number(const NumberType n) - { - // step 1: write number to array of length NumberType - std::array vec; - std::memcpy(vec.data(), &n, sizeof(NumberType)); - - // step 2: write array to output (with possible reordering) - if (is_little_endian != OutputIsLittleEndian) - { - // reverse byte order prior to conversion if necessary - std::reverse(vec.begin(), vec.end()); - } - - oa->write_characters(vec.data(), sizeof(NumberType)); - } - - void write_compact_float(const number_float_t n, detail::input_format_t format) - { - if (static_cast(n) >= static_cast(std::numeric_limits::lowest()) && - static_cast(n) <= static_cast((std::numeric_limits::max)()) && - static_cast(static_cast(n)) == static_cast(n)) - { - oa->write_character(format == detail::input_format_t::cbor - ? get_cbor_float_prefix(static_cast(n)) - : get_msgpack_float_prefix(static_cast(n))); - write_number(static_cast(n)); - } - else - { - oa->write_character(format == detail::input_format_t::cbor - ? get_cbor_float_prefix(n) - : get_msgpack_float_prefix(n)); - write_number(n); - } - } - - public: - // The following to_char_type functions are implement the conversion - // between uint8_t and CharType. In case CharType is not unsigned, - // such a conversion is required to allow values greater than 128. - // See for a discussion. - template < typename C = CharType, - enable_if_t < std::is_signed::value && std::is_signed::value > * = nullptr > - static constexpr CharType to_char_type(std::uint8_t x) noexcept - { - return *reinterpret_cast(&x); - } - - template < typename C = CharType, - enable_if_t < std::is_signed::value && std::is_unsigned::value > * = nullptr > - static CharType to_char_type(std::uint8_t x) noexcept - { - static_assert(sizeof(std::uint8_t) == sizeof(CharType), "size of CharType must be equal to std::uint8_t"); - static_assert(std::is_trivial::value, "CharType must be trivial"); - CharType result; - std::memcpy(&result, &x, sizeof(x)); - return result; - } - - template::value>* = nullptr> - static constexpr CharType to_char_type(std::uint8_t x) noexcept - { - return x; - } - - template < typename InputCharType, typename C = CharType, - enable_if_t < - std::is_signed::value && - std::is_signed::value && - std::is_same::type>::value - > * = nullptr > - static constexpr CharType to_char_type(InputCharType x) noexcept - { - return x; - } - - private: - /// whether we can assume little endianess - const bool is_little_endian = little_endianess(); - - /// the output - output_adapter_t oa = nullptr; -}; -} // namespace detail -} // namespace nlohmann - -// #include - -// #include - - -#include // reverse, remove, fill, find, none_of -#include // array -#include // localeconv, lconv -#include // labs, isfinite, isnan, signbit -#include // size_t, ptrdiff_t -#include // uint8_t -#include // snprintf -#include // numeric_limits -#include // string, char_traits -#include // is_same -#include // move - -// #include - - -#include // array -#include // signbit, isfinite -#include // intN_t, uintN_t -#include // memcpy, memmove -#include // numeric_limits -#include // conditional - -// #include - - -namespace nlohmann -{ -namespace detail -{ - -/*! -@brief implements the Grisu2 algorithm for binary to decimal floating-point -conversion. - -This implementation is a slightly modified version of the reference -implementation which may be obtained from -http://florian.loitsch.com/publications (bench.tar.gz). - -The code is distributed under the MIT license, Copyright (c) 2009 Florian Loitsch. - -For a detailed description of the algorithm see: - -[1] Loitsch, "Printing Floating-Point Numbers Quickly and Accurately with - Integers", Proceedings of the ACM SIGPLAN 2010 Conference on Programming - Language Design and Implementation, PLDI 2010 -[2] Burger, Dybvig, "Printing Floating-Point Numbers Quickly and Accurately", - Proceedings of the ACM SIGPLAN 1996 Conference on Programming Language - Design and Implementation, PLDI 1996 -*/ -namespace dtoa_impl -{ - -template -Target reinterpret_bits(const Source source) -{ - static_assert(sizeof(Target) == sizeof(Source), "size mismatch"); - - Target target; - std::memcpy(&target, &source, sizeof(Source)); - return target; -} - -struct diyfp // f * 2^e -{ - static constexpr int kPrecision = 64; // = q - - std::uint64_t f = 0; - int e = 0; - - constexpr diyfp(std::uint64_t f_, int e_) noexcept : f(f_), e(e_) {} - - /*! - @brief returns x - y - @pre x.e == y.e and x.f >= y.f - */ - static diyfp sub(const diyfp& x, const diyfp& y) noexcept - { - JSON_ASSERT(x.e == y.e); - JSON_ASSERT(x.f >= y.f); - - return {x.f - y.f, x.e}; - } - - /*! - @brief returns x * y - @note The result is rounded. (Only the upper q bits are returned.) - */ - static diyfp mul(const diyfp& x, const diyfp& y) noexcept - { - static_assert(kPrecision == 64, "internal error"); - - // Computes: - // f = round((x.f * y.f) / 2^q) - // e = x.e + y.e + q - - // Emulate the 64-bit * 64-bit multiplication: - // - // p = u * v - // = (u_lo + 2^32 u_hi) (v_lo + 2^32 v_hi) - // = (u_lo v_lo ) + 2^32 ((u_lo v_hi ) + (u_hi v_lo )) + 2^64 (u_hi v_hi ) - // = (p0 ) + 2^32 ((p1 ) + (p2 )) + 2^64 (p3 ) - // = (p0_lo + 2^32 p0_hi) + 2^32 ((p1_lo + 2^32 p1_hi) + (p2_lo + 2^32 p2_hi)) + 2^64 (p3 ) - // = (p0_lo ) + 2^32 (p0_hi + p1_lo + p2_lo ) + 2^64 (p1_hi + p2_hi + p3) - // = (p0_lo ) + 2^32 (Q ) + 2^64 (H ) - // = (p0_lo ) + 2^32 (Q_lo + 2^32 Q_hi ) + 2^64 (H ) - // - // (Since Q might be larger than 2^32 - 1) - // - // = (p0_lo + 2^32 Q_lo) + 2^64 (Q_hi + H) - // - // (Q_hi + H does not overflow a 64-bit int) - // - // = p_lo + 2^64 p_hi - - const std::uint64_t u_lo = x.f & 0xFFFFFFFFu; - const std::uint64_t u_hi = x.f >> 32u; - const std::uint64_t v_lo = y.f & 0xFFFFFFFFu; - const std::uint64_t v_hi = y.f >> 32u; - - const std::uint64_t p0 = u_lo * v_lo; - const std::uint64_t p1 = u_lo * v_hi; - const std::uint64_t p2 = u_hi * v_lo; - const std::uint64_t p3 = u_hi * v_hi; - - const std::uint64_t p0_hi = p0 >> 32u; - const std::uint64_t p1_lo = p1 & 0xFFFFFFFFu; - const std::uint64_t p1_hi = p1 >> 32u; - const std::uint64_t p2_lo = p2 & 0xFFFFFFFFu; - const std::uint64_t p2_hi = p2 >> 32u; - - std::uint64_t Q = p0_hi + p1_lo + p2_lo; - - // The full product might now be computed as - // - // p_hi = p3 + p2_hi + p1_hi + (Q >> 32) - // p_lo = p0_lo + (Q << 32) - // - // But in this particular case here, the full p_lo is not required. - // Effectively we only need to add the highest bit in p_lo to p_hi (and - // Q_hi + 1 does not overflow). - - Q += std::uint64_t{1} << (64u - 32u - 1u); // round, ties up - - const std::uint64_t h = p3 + p2_hi + p1_hi + (Q >> 32u); - - return {h, x.e + y.e + 64}; - } - - /*! - @brief normalize x such that the significand is >= 2^(q-1) - @pre x.f != 0 - */ - static diyfp normalize(diyfp x) noexcept - { - JSON_ASSERT(x.f != 0); - - while ((x.f >> 63u) == 0) - { - x.f <<= 1u; - x.e--; - } - - return x; - } - - /*! - @brief normalize x such that the result has the exponent E - @pre e >= x.e and the upper e - x.e bits of x.f must be zero. - */ - static diyfp normalize_to(const diyfp& x, const int target_exponent) noexcept - { - const int delta = x.e - target_exponent; - - JSON_ASSERT(delta >= 0); - JSON_ASSERT(((x.f << delta) >> delta) == x.f); - - return {x.f << delta, target_exponent}; - } -}; - -struct boundaries -{ - diyfp w; - diyfp minus; - diyfp plus; -}; - -/*! -Compute the (normalized) diyfp representing the input number 'value' and its -boundaries. - -@pre value must be finite and positive -*/ -template -boundaries compute_boundaries(FloatType value) -{ - JSON_ASSERT(std::isfinite(value)); - JSON_ASSERT(value > 0); - - // Convert the IEEE representation into a diyfp. - // - // If v is denormal: - // value = 0.F * 2^(1 - bias) = ( F) * 2^(1 - bias - (p-1)) - // If v is normalized: - // value = 1.F * 2^(E - bias) = (2^(p-1) + F) * 2^(E - bias - (p-1)) - - static_assert(std::numeric_limits::is_iec559, - "internal error: dtoa_short requires an IEEE-754 floating-point implementation"); - - constexpr int kPrecision = std::numeric_limits::digits; // = p (includes the hidden bit) - constexpr int kBias = std::numeric_limits::max_exponent - 1 + (kPrecision - 1); - constexpr int kMinExp = 1 - kBias; - constexpr std::uint64_t kHiddenBit = std::uint64_t{1} << (kPrecision - 1); // = 2^(p-1) - - using bits_type = typename std::conditional::type; - - const std::uint64_t bits = reinterpret_bits(value); - const std::uint64_t E = bits >> (kPrecision - 1); - const std::uint64_t F = bits & (kHiddenBit - 1); - - const bool is_denormal = E == 0; - const diyfp v = is_denormal - ? diyfp(F, kMinExp) - : diyfp(F + kHiddenBit, static_cast(E) - kBias); - - // Compute the boundaries m- and m+ of the floating-point value - // v = f * 2^e. - // - // Determine v- and v+, the floating-point predecessor and successor if v, - // respectively. - // - // v- = v - 2^e if f != 2^(p-1) or e == e_min (A) - // = v - 2^(e-1) if f == 2^(p-1) and e > e_min (B) - // - // v+ = v + 2^e - // - // Let m- = (v- + v) / 2 and m+ = (v + v+) / 2. All real numbers _strictly_ - // between m- and m+ round to v, regardless of how the input rounding - // algorithm breaks ties. - // - // ---+-------------+-------------+-------------+-------------+--- (A) - // v- m- v m+ v+ - // - // -----------------+------+------+-------------+-------------+--- (B) - // v- m- v m+ v+ - - const bool lower_boundary_is_closer = F == 0 && E > 1; - const diyfp m_plus = diyfp(2 * v.f + 1, v.e - 1); - const diyfp m_minus = lower_boundary_is_closer - ? diyfp(4 * v.f - 1, v.e - 2) // (B) - : diyfp(2 * v.f - 1, v.e - 1); // (A) - - // Determine the normalized w+ = m+. - const diyfp w_plus = diyfp::normalize(m_plus); - - // Determine w- = m- such that e_(w-) = e_(w+). - const diyfp w_minus = diyfp::normalize_to(m_minus, w_plus.e); - - return {diyfp::normalize(v), w_minus, w_plus}; -} - -// Given normalized diyfp w, Grisu needs to find a (normalized) cached -// power-of-ten c, such that the exponent of the product c * w = f * 2^e lies -// within a certain range [alpha, gamma] (Definition 3.2 from [1]) -// -// alpha <= e = e_c + e_w + q <= gamma -// -// or -// -// f_c * f_w * 2^alpha <= f_c 2^(e_c) * f_w 2^(e_w) * 2^q -// <= f_c * f_w * 2^gamma -// -// Since c and w are normalized, i.e. 2^(q-1) <= f < 2^q, this implies -// -// 2^(q-1) * 2^(q-1) * 2^alpha <= c * w * 2^q < 2^q * 2^q * 2^gamma -// -// or -// -// 2^(q - 2 + alpha) <= c * w < 2^(q + gamma) -// -// The choice of (alpha,gamma) determines the size of the table and the form of -// the digit generation procedure. Using (alpha,gamma)=(-60,-32) works out well -// in practice: -// -// The idea is to cut the number c * w = f * 2^e into two parts, which can be -// processed independently: An integral part p1, and a fractional part p2: -// -// f * 2^e = ( (f div 2^-e) * 2^-e + (f mod 2^-e) ) * 2^e -// = (f div 2^-e) + (f mod 2^-e) * 2^e -// = p1 + p2 * 2^e -// -// The conversion of p1 into decimal form requires a series of divisions and -// modulos by (a power of) 10. These operations are faster for 32-bit than for -// 64-bit integers, so p1 should ideally fit into a 32-bit integer. This can be -// achieved by choosing -// -// -e >= 32 or e <= -32 := gamma -// -// In order to convert the fractional part -// -// p2 * 2^e = p2 / 2^-e = d[-1] / 10^1 + d[-2] / 10^2 + ... -// -// into decimal form, the fraction is repeatedly multiplied by 10 and the digits -// d[-i] are extracted in order: -// -// (10 * p2) div 2^-e = d[-1] -// (10 * p2) mod 2^-e = d[-2] / 10^1 + ... -// -// The multiplication by 10 must not overflow. It is sufficient to choose -// -// 10 * p2 < 16 * p2 = 2^4 * p2 <= 2^64. -// -// Since p2 = f mod 2^-e < 2^-e, -// -// -e <= 60 or e >= -60 := alpha - -constexpr int kAlpha = -60; -constexpr int kGamma = -32; - -struct cached_power // c = f * 2^e ~= 10^k -{ - std::uint64_t f; - int e; - int k; -}; - -/*! -For a normalized diyfp w = f * 2^e, this function returns a (normalized) cached -power-of-ten c = f_c * 2^e_c, such that the exponent of the product w * c -satisfies (Definition 3.2 from [1]) - - alpha <= e_c + e + q <= gamma. -*/ -inline cached_power get_cached_power_for_binary_exponent(int e) -{ - // Now - // - // alpha <= e_c + e + q <= gamma (1) - // ==> f_c * 2^alpha <= c * 2^e * 2^q - // - // and since the c's are normalized, 2^(q-1) <= f_c, - // - // ==> 2^(q - 1 + alpha) <= c * 2^(e + q) - // ==> 2^(alpha - e - 1) <= c - // - // If c were an exact power of ten, i.e. c = 10^k, one may determine k as - // - // k = ceil( log_10( 2^(alpha - e - 1) ) ) - // = ceil( (alpha - e - 1) * log_10(2) ) - // - // From the paper: - // "In theory the result of the procedure could be wrong since c is rounded, - // and the computation itself is approximated [...]. In practice, however, - // this simple function is sufficient." - // - // For IEEE double precision floating-point numbers converted into - // normalized diyfp's w = f * 2^e, with q = 64, - // - // e >= -1022 (min IEEE exponent) - // -52 (p - 1) - // -52 (p - 1, possibly normalize denormal IEEE numbers) - // -11 (normalize the diyfp) - // = -1137 - // - // and - // - // e <= +1023 (max IEEE exponent) - // -52 (p - 1) - // -11 (normalize the diyfp) - // = 960 - // - // This binary exponent range [-1137,960] results in a decimal exponent - // range [-307,324]. One does not need to store a cached power for each - // k in this range. For each such k it suffices to find a cached power - // such that the exponent of the product lies in [alpha,gamma]. - // This implies that the difference of the decimal exponents of adjacent - // table entries must be less than or equal to - // - // floor( (gamma - alpha) * log_10(2) ) = 8. - // - // (A smaller distance gamma-alpha would require a larger table.) - - // NB: - // Actually this function returns c, such that -60 <= e_c + e + 64 <= -34. - - constexpr int kCachedPowersMinDecExp = -300; - constexpr int kCachedPowersDecStep = 8; - - static constexpr std::array kCachedPowers = - { - { - { 0xAB70FE17C79AC6CA, -1060, -300 }, - { 0xFF77B1FCBEBCDC4F, -1034, -292 }, - { 0xBE5691EF416BD60C, -1007, -284 }, - { 0x8DD01FAD907FFC3C, -980, -276 }, - { 0xD3515C2831559A83, -954, -268 }, - { 0x9D71AC8FADA6C9B5, -927, -260 }, - { 0xEA9C227723EE8BCB, -901, -252 }, - { 0xAECC49914078536D, -874, -244 }, - { 0x823C12795DB6CE57, -847, -236 }, - { 0xC21094364DFB5637, -821, -228 }, - { 0x9096EA6F3848984F, -794, -220 }, - { 0xD77485CB25823AC7, -768, -212 }, - { 0xA086CFCD97BF97F4, -741, -204 }, - { 0xEF340A98172AACE5, -715, -196 }, - { 0xB23867FB2A35B28E, -688, -188 }, - { 0x84C8D4DFD2C63F3B, -661, -180 }, - { 0xC5DD44271AD3CDBA, -635, -172 }, - { 0x936B9FCEBB25C996, -608, -164 }, - { 0xDBAC6C247D62A584, -582, -156 }, - { 0xA3AB66580D5FDAF6, -555, -148 }, - { 0xF3E2F893DEC3F126, -529, -140 }, - { 0xB5B5ADA8AAFF80B8, -502, -132 }, - { 0x87625F056C7C4A8B, -475, -124 }, - { 0xC9BCFF6034C13053, -449, -116 }, - { 0x964E858C91BA2655, -422, -108 }, - { 0xDFF9772470297EBD, -396, -100 }, - { 0xA6DFBD9FB8E5B88F, -369, -92 }, - { 0xF8A95FCF88747D94, -343, -84 }, - { 0xB94470938FA89BCF, -316, -76 }, - { 0x8A08F0F8BF0F156B, -289, -68 }, - { 0xCDB02555653131B6, -263, -60 }, - { 0x993FE2C6D07B7FAC, -236, -52 }, - { 0xE45C10C42A2B3B06, -210, -44 }, - { 0xAA242499697392D3, -183, -36 }, - { 0xFD87B5F28300CA0E, -157, -28 }, - { 0xBCE5086492111AEB, -130, -20 }, - { 0x8CBCCC096F5088CC, -103, -12 }, - { 0xD1B71758E219652C, -77, -4 }, - { 0x9C40000000000000, -50, 4 }, - { 0xE8D4A51000000000, -24, 12 }, - { 0xAD78EBC5AC620000, 3, 20 }, - { 0x813F3978F8940984, 30, 28 }, - { 0xC097CE7BC90715B3, 56, 36 }, - { 0x8F7E32CE7BEA5C70, 83, 44 }, - { 0xD5D238A4ABE98068, 109, 52 }, - { 0x9F4F2726179A2245, 136, 60 }, - { 0xED63A231D4C4FB27, 162, 68 }, - { 0xB0DE65388CC8ADA8, 189, 76 }, - { 0x83C7088E1AAB65DB, 216, 84 }, - { 0xC45D1DF942711D9A, 242, 92 }, - { 0x924D692CA61BE758, 269, 100 }, - { 0xDA01EE641A708DEA, 295, 108 }, - { 0xA26DA3999AEF774A, 322, 116 }, - { 0xF209787BB47D6B85, 348, 124 }, - { 0xB454E4A179DD1877, 375, 132 }, - { 0x865B86925B9BC5C2, 402, 140 }, - { 0xC83553C5C8965D3D, 428, 148 }, - { 0x952AB45CFA97A0B3, 455, 156 }, - { 0xDE469FBD99A05FE3, 481, 164 }, - { 0xA59BC234DB398C25, 508, 172 }, - { 0xF6C69A72A3989F5C, 534, 180 }, - { 0xB7DCBF5354E9BECE, 561, 188 }, - { 0x88FCF317F22241E2, 588, 196 }, - { 0xCC20CE9BD35C78A5, 614, 204 }, - { 0x98165AF37B2153DF, 641, 212 }, - { 0xE2A0B5DC971F303A, 667, 220 }, - { 0xA8D9D1535CE3B396, 694, 228 }, - { 0xFB9B7CD9A4A7443C, 720, 236 }, - { 0xBB764C4CA7A44410, 747, 244 }, - { 0x8BAB8EEFB6409C1A, 774, 252 }, - { 0xD01FEF10A657842C, 800, 260 }, - { 0x9B10A4E5E9913129, 827, 268 }, - { 0xE7109BFBA19C0C9D, 853, 276 }, - { 0xAC2820D9623BF429, 880, 284 }, - { 0x80444B5E7AA7CF85, 907, 292 }, - { 0xBF21E44003ACDD2D, 933, 300 }, - { 0x8E679C2F5E44FF8F, 960, 308 }, - { 0xD433179D9C8CB841, 986, 316 }, - { 0x9E19DB92B4E31BA9, 1013, 324 }, - } - }; - - // This computation gives exactly the same results for k as - // k = ceil((kAlpha - e - 1) * 0.30102999566398114) - // for |e| <= 1500, but doesn't require floating-point operations. - // NB: log_10(2) ~= 78913 / 2^18 - JSON_ASSERT(e >= -1500); - JSON_ASSERT(e <= 1500); - const int f = kAlpha - e - 1; - const int k = (f * 78913) / (1 << 18) + static_cast(f > 0); - - const int index = (-kCachedPowersMinDecExp + k + (kCachedPowersDecStep - 1)) / kCachedPowersDecStep; - JSON_ASSERT(index >= 0); - JSON_ASSERT(static_cast(index) < kCachedPowers.size()); - - const cached_power cached = kCachedPowers[static_cast(index)]; - JSON_ASSERT(kAlpha <= cached.e + e + 64); - JSON_ASSERT(kGamma >= cached.e + e + 64); - - return cached; -} - -/*! -For n != 0, returns k, such that pow10 := 10^(k-1) <= n < 10^k. -For n == 0, returns 1 and sets pow10 := 1. -*/ -inline int find_largest_pow10(const std::uint32_t n, std::uint32_t& pow10) -{ - // LCOV_EXCL_START - if (n >= 1000000000) - { - pow10 = 1000000000; - return 10; - } - // LCOV_EXCL_STOP - else if (n >= 100000000) - { - pow10 = 100000000; - return 9; - } - else if (n >= 10000000) - { - pow10 = 10000000; - return 8; - } - else if (n >= 1000000) - { - pow10 = 1000000; - return 7; - } - else if (n >= 100000) - { - pow10 = 100000; - return 6; - } - else if (n >= 10000) - { - pow10 = 10000; - return 5; - } - else if (n >= 1000) - { - pow10 = 1000; - return 4; - } - else if (n >= 100) - { - pow10 = 100; - return 3; - } - else if (n >= 10) - { - pow10 = 10; - return 2; - } - else - { - pow10 = 1; - return 1; - } -} - -inline void grisu2_round(char* buf, int len, std::uint64_t dist, std::uint64_t delta, - std::uint64_t rest, std::uint64_t ten_k) -{ - JSON_ASSERT(len >= 1); - JSON_ASSERT(dist <= delta); - JSON_ASSERT(rest <= delta); - JSON_ASSERT(ten_k > 0); - - // <--------------------------- delta ----> - // <---- dist ---------> - // --------------[------------------+-------------------]-------------- - // M- w M+ - // - // ten_k - // <------> - // <---- rest ----> - // --------------[------------------+----+--------------]-------------- - // w V - // = buf * 10^k - // - // ten_k represents a unit-in-the-last-place in the decimal representation - // stored in buf. - // Decrement buf by ten_k while this takes buf closer to w. - - // The tests are written in this order to avoid overflow in unsigned - // integer arithmetic. - - while (rest < dist - && delta - rest >= ten_k - && (rest + ten_k < dist || dist - rest > rest + ten_k - dist)) - { - JSON_ASSERT(buf[len - 1] != '0'); - buf[len - 1]--; - rest += ten_k; - } -} - -/*! -Generates V = buffer * 10^decimal_exponent, such that M- <= V <= M+. -M- and M+ must be normalized and share the same exponent -60 <= e <= -32. -*/ -inline void grisu2_digit_gen(char* buffer, int& length, int& decimal_exponent, - diyfp M_minus, diyfp w, diyfp M_plus) -{ - static_assert(kAlpha >= -60, "internal error"); - static_assert(kGamma <= -32, "internal error"); - - // Generates the digits (and the exponent) of a decimal floating-point - // number V = buffer * 10^decimal_exponent in the range [M-, M+]. The diyfp's - // w, M- and M+ share the same exponent e, which satisfies alpha <= e <= gamma. - // - // <--------------------------- delta ----> - // <---- dist ---------> - // --------------[------------------+-------------------]-------------- - // M- w M+ - // - // Grisu2 generates the digits of M+ from left to right and stops as soon as - // V is in [M-,M+]. - - JSON_ASSERT(M_plus.e >= kAlpha); - JSON_ASSERT(M_plus.e <= kGamma); - - std::uint64_t delta = diyfp::sub(M_plus, M_minus).f; // (significand of (M+ - M-), implicit exponent is e) - std::uint64_t dist = diyfp::sub(M_plus, w ).f; // (significand of (M+ - w ), implicit exponent is e) - - // Split M+ = f * 2^e into two parts p1 and p2 (note: e < 0): - // - // M+ = f * 2^e - // = ((f div 2^-e) * 2^-e + (f mod 2^-e)) * 2^e - // = ((p1 ) * 2^-e + (p2 )) * 2^e - // = p1 + p2 * 2^e - - const diyfp one(std::uint64_t{1} << -M_plus.e, M_plus.e); - - auto p1 = static_cast(M_plus.f >> -one.e); // p1 = f div 2^-e (Since -e >= 32, p1 fits into a 32-bit int.) - std::uint64_t p2 = M_plus.f & (one.f - 1); // p2 = f mod 2^-e - - // 1) - // - // Generate the digits of the integral part p1 = d[n-1]...d[1]d[0] - - JSON_ASSERT(p1 > 0); - - std::uint32_t pow10; - const int k = find_largest_pow10(p1, pow10); - - // 10^(k-1) <= p1 < 10^k, pow10 = 10^(k-1) - // - // p1 = (p1 div 10^(k-1)) * 10^(k-1) + (p1 mod 10^(k-1)) - // = (d[k-1] ) * 10^(k-1) + (p1 mod 10^(k-1)) - // - // M+ = p1 + p2 * 2^e - // = d[k-1] * 10^(k-1) + (p1 mod 10^(k-1)) + p2 * 2^e - // = d[k-1] * 10^(k-1) + ((p1 mod 10^(k-1)) * 2^-e + p2) * 2^e - // = d[k-1] * 10^(k-1) + ( rest) * 2^e - // - // Now generate the digits d[n] of p1 from left to right (n = k-1,...,0) - // - // p1 = d[k-1]...d[n] * 10^n + d[n-1]...d[0] - // - // but stop as soon as - // - // rest * 2^e = (d[n-1]...d[0] * 2^-e + p2) * 2^e <= delta * 2^e - - int n = k; - while (n > 0) - { - // Invariants: - // M+ = buffer * 10^n + (p1 + p2 * 2^e) (buffer = 0 for n = k) - // pow10 = 10^(n-1) <= p1 < 10^n - // - const std::uint32_t d = p1 / pow10; // d = p1 div 10^(n-1) - const std::uint32_t r = p1 % pow10; // r = p1 mod 10^(n-1) - // - // M+ = buffer * 10^n + (d * 10^(n-1) + r) + p2 * 2^e - // = (buffer * 10 + d) * 10^(n-1) + (r + p2 * 2^e) - // - JSON_ASSERT(d <= 9); - buffer[length++] = static_cast('0' + d); // buffer := buffer * 10 + d - // - // M+ = buffer * 10^(n-1) + (r + p2 * 2^e) - // - p1 = r; - n--; - // - // M+ = buffer * 10^n + (p1 + p2 * 2^e) - // pow10 = 10^n - // - - // Now check if enough digits have been generated. - // Compute - // - // p1 + p2 * 2^e = (p1 * 2^-e + p2) * 2^e = rest * 2^e - // - // Note: - // Since rest and delta share the same exponent e, it suffices to - // compare the significands. - const std::uint64_t rest = (std::uint64_t{p1} << -one.e) + p2; - if (rest <= delta) - { - // V = buffer * 10^n, with M- <= V <= M+. - - decimal_exponent += n; - - // We may now just stop. But instead look if the buffer could be - // decremented to bring V closer to w. - // - // pow10 = 10^n is now 1 ulp in the decimal representation V. - // The rounding procedure works with diyfp's with an implicit - // exponent of e. - // - // 10^n = (10^n * 2^-e) * 2^e = ulp * 2^e - // - const std::uint64_t ten_n = std::uint64_t{pow10} << -one.e; - grisu2_round(buffer, length, dist, delta, rest, ten_n); - - return; - } - - pow10 /= 10; - // - // pow10 = 10^(n-1) <= p1 < 10^n - // Invariants restored. - } - - // 2) - // - // The digits of the integral part have been generated: - // - // M+ = d[k-1]...d[1]d[0] + p2 * 2^e - // = buffer + p2 * 2^e - // - // Now generate the digits of the fractional part p2 * 2^e. - // - // Note: - // No decimal point is generated: the exponent is adjusted instead. - // - // p2 actually represents the fraction - // - // p2 * 2^e - // = p2 / 2^-e - // = d[-1] / 10^1 + d[-2] / 10^2 + ... - // - // Now generate the digits d[-m] of p1 from left to right (m = 1,2,...) - // - // p2 * 2^e = d[-1]d[-2]...d[-m] * 10^-m - // + 10^-m * (d[-m-1] / 10^1 + d[-m-2] / 10^2 + ...) - // - // using - // - // 10^m * p2 = ((10^m * p2) div 2^-e) * 2^-e + ((10^m * p2) mod 2^-e) - // = ( d) * 2^-e + ( r) - // - // or - // 10^m * p2 * 2^e = d + r * 2^e - // - // i.e. - // - // M+ = buffer + p2 * 2^e - // = buffer + 10^-m * (d + r * 2^e) - // = (buffer * 10^m + d) * 10^-m + 10^-m * r * 2^e - // - // and stop as soon as 10^-m * r * 2^e <= delta * 2^e - - JSON_ASSERT(p2 > delta); - - int m = 0; - for (;;) - { - // Invariant: - // M+ = buffer * 10^-m + 10^-m * (d[-m-1] / 10 + d[-m-2] / 10^2 + ...) * 2^e - // = buffer * 10^-m + 10^-m * (p2 ) * 2^e - // = buffer * 10^-m + 10^-m * (1/10 * (10 * p2) ) * 2^e - // = buffer * 10^-m + 10^-m * (1/10 * ((10*p2 div 2^-e) * 2^-e + (10*p2 mod 2^-e)) * 2^e - // - JSON_ASSERT(p2 <= (std::numeric_limits::max)() / 10); - p2 *= 10; - const std::uint64_t d = p2 >> -one.e; // d = (10 * p2) div 2^-e - const std::uint64_t r = p2 & (one.f - 1); // r = (10 * p2) mod 2^-e - // - // M+ = buffer * 10^-m + 10^-m * (1/10 * (d * 2^-e + r) * 2^e - // = buffer * 10^-m + 10^-m * (1/10 * (d + r * 2^e)) - // = (buffer * 10 + d) * 10^(-m-1) + 10^(-m-1) * r * 2^e - // - JSON_ASSERT(d <= 9); - buffer[length++] = static_cast('0' + d); // buffer := buffer * 10 + d - // - // M+ = buffer * 10^(-m-1) + 10^(-m-1) * r * 2^e - // - p2 = r; - m++; - // - // M+ = buffer * 10^-m + 10^-m * p2 * 2^e - // Invariant restored. - - // Check if enough digits have been generated. - // - // 10^-m * p2 * 2^e <= delta * 2^e - // p2 * 2^e <= 10^m * delta * 2^e - // p2 <= 10^m * delta - delta *= 10; - dist *= 10; - if (p2 <= delta) - { - break; - } - } - - // V = buffer * 10^-m, with M- <= V <= M+. - - decimal_exponent -= m; - - // 1 ulp in the decimal representation is now 10^-m. - // Since delta and dist are now scaled by 10^m, we need to do the - // same with ulp in order to keep the units in sync. - // - // 10^m * 10^-m = 1 = 2^-e * 2^e = ten_m * 2^e - // - const std::uint64_t ten_m = one.f; - grisu2_round(buffer, length, dist, delta, p2, ten_m); - - // By construction this algorithm generates the shortest possible decimal - // number (Loitsch, Theorem 6.2) which rounds back to w. - // For an input number of precision p, at least - // - // N = 1 + ceil(p * log_10(2)) - // - // decimal digits are sufficient to identify all binary floating-point - // numbers (Matula, "In-and-Out conversions"). - // This implies that the algorithm does not produce more than N decimal - // digits. - // - // N = 17 for p = 53 (IEEE double precision) - // N = 9 for p = 24 (IEEE single precision) -} - -/*! -v = buf * 10^decimal_exponent -len is the length of the buffer (number of decimal digits) -The buffer must be large enough, i.e. >= max_digits10. -*/ -JSON_HEDLEY_NON_NULL(1) -inline void grisu2(char* buf, int& len, int& decimal_exponent, - diyfp m_minus, diyfp v, diyfp m_plus) -{ - JSON_ASSERT(m_plus.e == m_minus.e); - JSON_ASSERT(m_plus.e == v.e); - - // --------(-----------------------+-----------------------)-------- (A) - // m- v m+ - // - // --------------------(-----------+-----------------------)-------- (B) - // m- v m+ - // - // First scale v (and m- and m+) such that the exponent is in the range - // [alpha, gamma]. - - const cached_power cached = get_cached_power_for_binary_exponent(m_plus.e); - - const diyfp c_minus_k(cached.f, cached.e); // = c ~= 10^-k - - // The exponent of the products is = v.e + c_minus_k.e + q and is in the range [alpha,gamma] - const diyfp w = diyfp::mul(v, c_minus_k); - const diyfp w_minus = diyfp::mul(m_minus, c_minus_k); - const diyfp w_plus = diyfp::mul(m_plus, c_minus_k); - - // ----(---+---)---------------(---+---)---------------(---+---)---- - // w- w w+ - // = c*m- = c*v = c*m+ - // - // diyfp::mul rounds its result and c_minus_k is approximated too. w, w- and - // w+ are now off by a small amount. - // In fact: - // - // w - v * 10^k < 1 ulp - // - // To account for this inaccuracy, add resp. subtract 1 ulp. - // - // --------+---[---------------(---+---)---------------]---+-------- - // w- M- w M+ w+ - // - // Now any number in [M-, M+] (bounds included) will round to w when input, - // regardless of how the input rounding algorithm breaks ties. - // - // And digit_gen generates the shortest possible such number in [M-, M+]. - // Note that this does not mean that Grisu2 always generates the shortest - // possible number in the interval (m-, m+). - const diyfp M_minus(w_minus.f + 1, w_minus.e); - const diyfp M_plus (w_plus.f - 1, w_plus.e ); - - decimal_exponent = -cached.k; // = -(-k) = k - - grisu2_digit_gen(buf, len, decimal_exponent, M_minus, w, M_plus); -} - -/*! -v = buf * 10^decimal_exponent -len is the length of the buffer (number of decimal digits) -The buffer must be large enough, i.e. >= max_digits10. -*/ -template -JSON_HEDLEY_NON_NULL(1) -void grisu2(char* buf, int& len, int& decimal_exponent, FloatType value) -{ - static_assert(diyfp::kPrecision >= std::numeric_limits::digits + 3, - "internal error: not enough precision"); - - JSON_ASSERT(std::isfinite(value)); - JSON_ASSERT(value > 0); - - // If the neighbors (and boundaries) of 'value' are always computed for double-precision - // numbers, all float's can be recovered using strtod (and strtof). However, the resulting - // decimal representations are not exactly "short". - // - // The documentation for 'std::to_chars' (https://en.cppreference.com/w/cpp/utility/to_chars) - // says "value is converted to a string as if by std::sprintf in the default ("C") locale" - // and since sprintf promotes float's to double's, I think this is exactly what 'std::to_chars' - // does. - // On the other hand, the documentation for 'std::to_chars' requires that "parsing the - // representation using the corresponding std::from_chars function recovers value exactly". That - // indicates that single precision floating-point numbers should be recovered using - // 'std::strtof'. - // - // NB: If the neighbors are computed for single-precision numbers, there is a single float - // (7.0385307e-26f) which can't be recovered using strtod. The resulting double precision - // value is off by 1 ulp. -#if 0 - const boundaries w = compute_boundaries(static_cast(value)); -#else - const boundaries w = compute_boundaries(value); -#endif - - grisu2(buf, len, decimal_exponent, w.minus, w.w, w.plus); -} - -/*! -@brief appends a decimal representation of e to buf -@return a pointer to the element following the exponent. -@pre -1000 < e < 1000 -*/ -JSON_HEDLEY_NON_NULL(1) -JSON_HEDLEY_RETURNS_NON_NULL -inline char* append_exponent(char* buf, int e) -{ - JSON_ASSERT(e > -1000); - JSON_ASSERT(e < 1000); - - if (e < 0) - { - e = -e; - *buf++ = '-'; - } - else - { - *buf++ = '+'; - } - - auto k = static_cast(e); - if (k < 10) - { - // Always print at least two digits in the exponent. - // This is for compatibility with printf("%g"). - *buf++ = '0'; - *buf++ = static_cast('0' + k); - } - else if (k < 100) - { - *buf++ = static_cast('0' + k / 10); - k %= 10; - *buf++ = static_cast('0' + k); - } - else - { - *buf++ = static_cast('0' + k / 100); - k %= 100; - *buf++ = static_cast('0' + k / 10); - k %= 10; - *buf++ = static_cast('0' + k); - } - - return buf; -} - -/*! -@brief prettify v = buf * 10^decimal_exponent - -If v is in the range [10^min_exp, 10^max_exp) it will be printed in fixed-point -notation. Otherwise it will be printed in exponential notation. - -@pre min_exp < 0 -@pre max_exp > 0 -*/ -JSON_HEDLEY_NON_NULL(1) -JSON_HEDLEY_RETURNS_NON_NULL -inline char* format_buffer(char* buf, int len, int decimal_exponent, - int min_exp, int max_exp) -{ - JSON_ASSERT(min_exp < 0); - JSON_ASSERT(max_exp > 0); - - const int k = len; - const int n = len + decimal_exponent; - - // v = buf * 10^(n-k) - // k is the length of the buffer (number of decimal digits) - // n is the position of the decimal point relative to the start of the buffer. - - if (k <= n && n <= max_exp) - { - // digits[000] - // len <= max_exp + 2 - - std::memset(buf + k, '0', static_cast(n) - static_cast(k)); - // Make it look like a floating-point number (#362, #378) - buf[n + 0] = '.'; - buf[n + 1] = '0'; - return buf + (static_cast(n) + 2); - } - - if (0 < n && n <= max_exp) - { - // dig.its - // len <= max_digits10 + 1 - - JSON_ASSERT(k > n); - - std::memmove(buf + (static_cast(n) + 1), buf + n, static_cast(k) - static_cast(n)); - buf[n] = '.'; - return buf + (static_cast(k) + 1U); - } - - if (min_exp < n && n <= 0) - { - // 0.[000]digits - // len <= 2 + (-min_exp - 1) + max_digits10 - - std::memmove(buf + (2 + static_cast(-n)), buf, static_cast(k)); - buf[0] = '0'; - buf[1] = '.'; - std::memset(buf + 2, '0', static_cast(-n)); - return buf + (2U + static_cast(-n) + static_cast(k)); - } - - if (k == 1) - { - // dE+123 - // len <= 1 + 5 - - buf += 1; - } - else - { - // d.igitsE+123 - // len <= max_digits10 + 1 + 5 - - std::memmove(buf + 2, buf + 1, static_cast(k) - 1); - buf[1] = '.'; - buf += 1 + static_cast(k); - } - - *buf++ = 'e'; - return append_exponent(buf, n - 1); -} - -} // namespace dtoa_impl - -/*! -@brief generates a decimal representation of the floating-point number value in [first, last). - -The format of the resulting decimal representation is similar to printf's %g -format. Returns an iterator pointing past-the-end of the decimal representation. - -@note The input number must be finite, i.e. NaN's and Inf's are not supported. -@note The buffer must be large enough. -@note The result is NOT null-terminated. -*/ -template -JSON_HEDLEY_NON_NULL(1, 2) -JSON_HEDLEY_RETURNS_NON_NULL -char* to_chars(char* first, const char* last, FloatType value) -{ - static_cast(last); // maybe unused - fix warning - JSON_ASSERT(std::isfinite(value)); - - // Use signbit(value) instead of (value < 0) since signbit works for -0. - if (std::signbit(value)) - { - value = -value; - *first++ = '-'; - } - - if (value == 0) // +-0 - { - *first++ = '0'; - // Make it look like a floating-point number (#362, #378) - *first++ = '.'; - *first++ = '0'; - return first; - } - - JSON_ASSERT(last - first >= std::numeric_limits::max_digits10); - - // Compute v = buffer * 10^decimal_exponent. - // The decimal digits are stored in the buffer, which needs to be interpreted - // as an unsigned decimal integer. - // len is the length of the buffer, i.e. the number of decimal digits. - int len = 0; - int decimal_exponent = 0; - dtoa_impl::grisu2(first, len, decimal_exponent, value); - - JSON_ASSERT(len <= std::numeric_limits::max_digits10); - - // Format the buffer like printf("%.*g", prec, value) - constexpr int kMinExp = -4; - // Use digits10 here to increase compatibility with version 2. - constexpr int kMaxExp = std::numeric_limits::digits10; - - JSON_ASSERT(last - first >= kMaxExp + 2); - JSON_ASSERT(last - first >= 2 + (-kMinExp - 1) + std::numeric_limits::max_digits10); - JSON_ASSERT(last - first >= std::numeric_limits::max_digits10 + 6); - - return dtoa_impl::format_buffer(first, len, decimal_exponent, kMinExp, kMaxExp); -} - -} // namespace detail -} // namespace nlohmann - -// #include - -// #include - -// #include - -// #include - -// #include - -// #include - - -namespace nlohmann -{ -namespace detail -{ -/////////////////// -// serialization // -/////////////////// - -/// how to treat decoding errors -enum class error_handler_t -{ - strict, ///< throw a type_error exception in case of invalid UTF-8 - replace, ///< replace invalid UTF-8 sequences with U+FFFD - ignore ///< ignore invalid UTF-8 sequences -}; - -template -class serializer -{ - using string_t = typename BasicJsonType::string_t; - using number_float_t = typename BasicJsonType::number_float_t; - using number_integer_t = typename BasicJsonType::number_integer_t; - using number_unsigned_t = typename BasicJsonType::number_unsigned_t; - using binary_char_t = typename BasicJsonType::binary_t::value_type; - static constexpr std::uint8_t UTF8_ACCEPT = 0; - static constexpr std::uint8_t UTF8_REJECT = 1; - - public: - /*! - @param[in] s output stream to serialize to - @param[in] ichar indentation character to use - @param[in] error_handler_ how to react on decoding errors - */ - serializer(output_adapter_t s, const char ichar, - error_handler_t error_handler_ = error_handler_t::strict) - : o(std::move(s)) - , loc(std::localeconv()) - , thousands_sep(loc->thousands_sep == nullptr ? '\0' : std::char_traits::to_char_type(* (loc->thousands_sep))) - , decimal_point(loc->decimal_point == nullptr ? '\0' : std::char_traits::to_char_type(* (loc->decimal_point))) - , indent_char(ichar) - , indent_string(512, indent_char) - , error_handler(error_handler_) - {} - - // delete because of pointer members - serializer(const serializer&) = delete; - serializer& operator=(const serializer&) = delete; - serializer(serializer&&) = delete; - serializer& operator=(serializer&&) = delete; - ~serializer() = default; - - /*! - @brief internal implementation of the serialization function - - This function is called by the public member function dump and organizes - the serialization internally. The indentation level is propagated as - additional parameter. In case of arrays and objects, the function is - called recursively. - - - strings and object keys are escaped using `escape_string()` - - integer numbers are converted implicitly via `operator<<` - - floating-point numbers are converted to a string using `"%g"` format - - binary values are serialized as objects containing the subtype and the - byte array - - @param[in] val value to serialize - @param[in] pretty_print whether the output shall be pretty-printed - @param[in] ensure_ascii If @a ensure_ascii is true, all non-ASCII characters - in the output are escaped with `\uXXXX` sequences, and the result consists - of ASCII characters only. - @param[in] indent_step the indent level - @param[in] current_indent the current indent level (only used internally) - */ - void dump(const BasicJsonType& val, - const bool pretty_print, - const bool ensure_ascii, - const unsigned int indent_step, - const unsigned int current_indent = 0) - { - switch (val.m_type) - { - case value_t::object: - { - if (val.m_value.object->empty()) - { - o->write_characters("{}", 2); - return; - } - - if (pretty_print) - { - o->write_characters("{\n", 2); - - // variable to hold indentation for recursive calls - const auto new_indent = current_indent + indent_step; - if (JSON_HEDLEY_UNLIKELY(indent_string.size() < new_indent)) - { - indent_string.resize(indent_string.size() * 2, ' '); - } - - // first n-1 elements - auto i = val.m_value.object->cbegin(); - for (std::size_t cnt = 0; cnt < val.m_value.object->size() - 1; ++cnt, ++i) - { - o->write_characters(indent_string.c_str(), new_indent); - o->write_character('\"'); - dump_escaped(i->first, ensure_ascii); - o->write_characters("\": ", 3); - dump(i->second, true, ensure_ascii, indent_step, new_indent); - o->write_characters(",\n", 2); - } - - // last element - JSON_ASSERT(i != val.m_value.object->cend()); - JSON_ASSERT(std::next(i) == val.m_value.object->cend()); - o->write_characters(indent_string.c_str(), new_indent); - o->write_character('\"'); - dump_escaped(i->first, ensure_ascii); - o->write_characters("\": ", 3); - dump(i->second, true, ensure_ascii, indent_step, new_indent); - - o->write_character('\n'); - o->write_characters(indent_string.c_str(), current_indent); - o->write_character('}'); - } - else - { - o->write_character('{'); - - // first n-1 elements - auto i = val.m_value.object->cbegin(); - for (std::size_t cnt = 0; cnt < val.m_value.object->size() - 1; ++cnt, ++i) - { - o->write_character('\"'); - dump_escaped(i->first, ensure_ascii); - o->write_characters("\":", 2); - dump(i->second, false, ensure_ascii, indent_step, current_indent); - o->write_character(','); - } - - // last element - JSON_ASSERT(i != val.m_value.object->cend()); - JSON_ASSERT(std::next(i) == val.m_value.object->cend()); - o->write_character('\"'); - dump_escaped(i->first, ensure_ascii); - o->write_characters("\":", 2); - dump(i->second, false, ensure_ascii, indent_step, current_indent); - - o->write_character('}'); - } - - return; - } - - case value_t::array: - { - if (val.m_value.array->empty()) - { - o->write_characters("[]", 2); - return; - } - - if (pretty_print) - { - o->write_characters("[\n", 2); - - // variable to hold indentation for recursive calls - const auto new_indent = current_indent + indent_step; - if (JSON_HEDLEY_UNLIKELY(indent_string.size() < new_indent)) - { - indent_string.resize(indent_string.size() * 2, ' '); - } - - // first n-1 elements - for (auto i = val.m_value.array->cbegin(); - i != val.m_value.array->cend() - 1; ++i) - { - o->write_characters(indent_string.c_str(), new_indent); - dump(*i, true, ensure_ascii, indent_step, new_indent); - o->write_characters(",\n", 2); - } - - // last element - JSON_ASSERT(!val.m_value.array->empty()); - o->write_characters(indent_string.c_str(), new_indent); - dump(val.m_value.array->back(), true, ensure_ascii, indent_step, new_indent); - - o->write_character('\n'); - o->write_characters(indent_string.c_str(), current_indent); - o->write_character(']'); - } - else - { - o->write_character('['); - - // first n-1 elements - for (auto i = val.m_value.array->cbegin(); - i != val.m_value.array->cend() - 1; ++i) - { - dump(*i, false, ensure_ascii, indent_step, current_indent); - o->write_character(','); - } - - // last element - JSON_ASSERT(!val.m_value.array->empty()); - dump(val.m_value.array->back(), false, ensure_ascii, indent_step, current_indent); - - o->write_character(']'); - } - - return; - } - - case value_t::string: - { - o->write_character('\"'); - dump_escaped(*val.m_value.string, ensure_ascii); - o->write_character('\"'); - return; - } - - case value_t::binary: - { - if (pretty_print) - { - o->write_characters("{\n", 2); - - // variable to hold indentation for recursive calls - const auto new_indent = current_indent + indent_step; - if (JSON_HEDLEY_UNLIKELY(indent_string.size() < new_indent)) - { - indent_string.resize(indent_string.size() * 2, ' '); - } - - o->write_characters(indent_string.c_str(), new_indent); - - o->write_characters("\"bytes\": [", 10); - - if (!val.m_value.binary->empty()) - { - for (auto i = val.m_value.binary->cbegin(); - i != val.m_value.binary->cend() - 1; ++i) - { - dump_integer(*i); - o->write_characters(", ", 2); - } - dump_integer(val.m_value.binary->back()); - } - - o->write_characters("],\n", 3); - o->write_characters(indent_string.c_str(), new_indent); - - o->write_characters("\"subtype\": ", 11); - if (val.m_value.binary->has_subtype()) - { - dump_integer(val.m_value.binary->subtype()); - } - else - { - o->write_characters("null", 4); - } - o->write_character('\n'); - o->write_characters(indent_string.c_str(), current_indent); - o->write_character('}'); - } - else - { - o->write_characters("{\"bytes\":[", 10); - - if (!val.m_value.binary->empty()) - { - for (auto i = val.m_value.binary->cbegin(); - i != val.m_value.binary->cend() - 1; ++i) - { - dump_integer(*i); - o->write_character(','); - } - dump_integer(val.m_value.binary->back()); - } - - o->write_characters("],\"subtype\":", 12); - if (val.m_value.binary->has_subtype()) - { - dump_integer(val.m_value.binary->subtype()); - o->write_character('}'); - } - else - { - o->write_characters("null}", 5); - } - } - return; - } - - case value_t::boolean: - { - if (val.m_value.boolean) - { - o->write_characters("true", 4); - } - else - { - o->write_characters("false", 5); - } - return; - } - - case value_t::number_integer: - { - dump_integer(val.m_value.number_integer); - return; - } - - case value_t::number_unsigned: - { - dump_integer(val.m_value.number_unsigned); - return; - } - - case value_t::number_float: - { - dump_float(val.m_value.number_float); - return; - } - - case value_t::discarded: - { - o->write_characters("", 11); - return; - } - - case value_t::null: - { - o->write_characters("null", 4); - return; - } - - default: // LCOV_EXCL_LINE - JSON_ASSERT(false); // LCOV_EXCL_LINE - } - } - - private: - /*! - @brief dump escaped string - - Escape a string by replacing certain special characters by a sequence of an - escape character (backslash) and another character and other control - characters by a sequence of "\u" followed by a four-digit hex - representation. The escaped string is written to output stream @a o. - - @param[in] s the string to escape - @param[in] ensure_ascii whether to escape non-ASCII characters with - \uXXXX sequences - - @complexity Linear in the length of string @a s. - */ - void dump_escaped(const string_t& s, const bool ensure_ascii) - { - std::uint32_t codepoint; - std::uint8_t state = UTF8_ACCEPT; - std::size_t bytes = 0; // number of bytes written to string_buffer - - // number of bytes written at the point of the last valid byte - std::size_t bytes_after_last_accept = 0; - std::size_t undumped_chars = 0; - - for (std::size_t i = 0; i < s.size(); ++i) - { - const auto byte = static_cast(s[i]); - - switch (decode(state, codepoint, byte)) - { - case UTF8_ACCEPT: // decode found a new code point - { - switch (codepoint) - { - case 0x08: // backspace - { - string_buffer[bytes++] = '\\'; - string_buffer[bytes++] = 'b'; - break; - } - - case 0x09: // horizontal tab - { - string_buffer[bytes++] = '\\'; - string_buffer[bytes++] = 't'; - break; - } - - case 0x0A: // newline - { - string_buffer[bytes++] = '\\'; - string_buffer[bytes++] = 'n'; - break; - } - - case 0x0C: // formfeed - { - string_buffer[bytes++] = '\\'; - string_buffer[bytes++] = 'f'; - break; - } - - case 0x0D: // carriage return - { - string_buffer[bytes++] = '\\'; - string_buffer[bytes++] = 'r'; - break; - } - - case 0x22: // quotation mark - { - string_buffer[bytes++] = '\\'; - string_buffer[bytes++] = '\"'; - break; - } - - case 0x5C: // reverse solidus - { - string_buffer[bytes++] = '\\'; - string_buffer[bytes++] = '\\'; - break; - } - - default: - { - // escape control characters (0x00..0x1F) or, if - // ensure_ascii parameter is used, non-ASCII characters - if ((codepoint <= 0x1F) || (ensure_ascii && (codepoint >= 0x7F))) - { - if (codepoint <= 0xFFFF) - { - (std::snprintf)(string_buffer.data() + bytes, 7, "\\u%04x", - static_cast(codepoint)); - bytes += 6; - } - else - { - (std::snprintf)(string_buffer.data() + bytes, 13, "\\u%04x\\u%04x", - static_cast(0xD7C0u + (codepoint >> 10u)), - static_cast(0xDC00u + (codepoint & 0x3FFu))); - bytes += 12; - } - } - else - { - // copy byte to buffer (all previous bytes - // been copied have in default case above) - string_buffer[bytes++] = s[i]; - } - break; - } - } - - // write buffer and reset index; there must be 13 bytes - // left, as this is the maximal number of bytes to be - // written ("\uxxxx\uxxxx\0") for one code point - if (string_buffer.size() - bytes < 13) - { - o->write_characters(string_buffer.data(), bytes); - bytes = 0; - } - - // remember the byte position of this accept - bytes_after_last_accept = bytes; - undumped_chars = 0; - break; - } - - case UTF8_REJECT: // decode found invalid UTF-8 byte - { - switch (error_handler) - { - case error_handler_t::strict: - { - std::string sn(3, '\0'); - (std::snprintf)(&sn[0], sn.size(), "%.2X", byte); - JSON_THROW(type_error::create(316, "invalid UTF-8 byte at index " + std::to_string(i) + ": 0x" + sn)); - } - - case error_handler_t::ignore: - case error_handler_t::replace: - { - // in case we saw this character the first time, we - // would like to read it again, because the byte - // may be OK for itself, but just not OK for the - // previous sequence - if (undumped_chars > 0) - { - --i; - } - - // reset length buffer to the last accepted index; - // thus removing/ignoring the invalid characters - bytes = bytes_after_last_accept; - - if (error_handler == error_handler_t::replace) - { - // add a replacement character - if (ensure_ascii) - { - string_buffer[bytes++] = '\\'; - string_buffer[bytes++] = 'u'; - string_buffer[bytes++] = 'f'; - string_buffer[bytes++] = 'f'; - string_buffer[bytes++] = 'f'; - string_buffer[bytes++] = 'd'; - } - else - { - string_buffer[bytes++] = detail::binary_writer::to_char_type('\xEF'); - string_buffer[bytes++] = detail::binary_writer::to_char_type('\xBF'); - string_buffer[bytes++] = detail::binary_writer::to_char_type('\xBD'); - } - - // write buffer and reset index; there must be 13 bytes - // left, as this is the maximal number of bytes to be - // written ("\uxxxx\uxxxx\0") for one code point - if (string_buffer.size() - bytes < 13) - { - o->write_characters(string_buffer.data(), bytes); - bytes = 0; - } - - bytes_after_last_accept = bytes; - } - - undumped_chars = 0; - - // continue processing the string - state = UTF8_ACCEPT; - break; - } - - default: // LCOV_EXCL_LINE - JSON_ASSERT(false); // LCOV_EXCL_LINE - } - break; - } - - default: // decode found yet incomplete multi-byte code point - { - if (!ensure_ascii) - { - // code point will not be escaped - copy byte to buffer - string_buffer[bytes++] = s[i]; - } - ++undumped_chars; - break; - } - } - } - - // we finished processing the string - if (JSON_HEDLEY_LIKELY(state == UTF8_ACCEPT)) - { - // write buffer - if (bytes > 0) - { - o->write_characters(string_buffer.data(), bytes); - } - } - else - { - // we finish reading, but do not accept: string was incomplete - switch (error_handler) - { - case error_handler_t::strict: - { - std::string sn(3, '\0'); - (std::snprintf)(&sn[0], sn.size(), "%.2X", static_cast(s.back())); - JSON_THROW(type_error::create(316, "incomplete UTF-8 string; last byte: 0x" + sn)); - } - - case error_handler_t::ignore: - { - // write all accepted bytes - o->write_characters(string_buffer.data(), bytes_after_last_accept); - break; - } - - case error_handler_t::replace: - { - // write all accepted bytes - o->write_characters(string_buffer.data(), bytes_after_last_accept); - // add a replacement character - if (ensure_ascii) - { - o->write_characters("\\ufffd", 6); - } - else - { - o->write_characters("\xEF\xBF\xBD", 3); - } - break; - } - - default: // LCOV_EXCL_LINE - JSON_ASSERT(false); // LCOV_EXCL_LINE - } - } - } - - /*! - @brief count digits - - Count the number of decimal (base 10) digits for an input unsigned integer. - - @param[in] x unsigned integer number to count its digits - @return number of decimal digits - */ - inline unsigned int count_digits(number_unsigned_t x) noexcept - { - unsigned int n_digits = 1; - for (;;) - { - if (x < 10) - { - return n_digits; - } - if (x < 100) - { - return n_digits + 1; - } - if (x < 1000) - { - return n_digits + 2; - } - if (x < 10000) - { - return n_digits + 3; - } - x = x / 10000u; - n_digits += 4; - } - } - - /*! - @brief dump an integer - - Dump a given integer to output stream @a o. Works internally with - @a number_buffer. - - @param[in] x integer number (signed or unsigned) to dump - @tparam NumberType either @a number_integer_t or @a number_unsigned_t - */ - template < typename NumberType, detail::enable_if_t < - std::is_same::value || - std::is_same::value || - std::is_same::value, - int > = 0 > - void dump_integer(NumberType x) - { - static constexpr std::array, 100> digits_to_99 - { - { - {{'0', '0'}}, {{'0', '1'}}, {{'0', '2'}}, {{'0', '3'}}, {{'0', '4'}}, {{'0', '5'}}, {{'0', '6'}}, {{'0', '7'}}, {{'0', '8'}}, {{'0', '9'}}, - {{'1', '0'}}, {{'1', '1'}}, {{'1', '2'}}, {{'1', '3'}}, {{'1', '4'}}, {{'1', '5'}}, {{'1', '6'}}, {{'1', '7'}}, {{'1', '8'}}, {{'1', '9'}}, - {{'2', '0'}}, {{'2', '1'}}, {{'2', '2'}}, {{'2', '3'}}, {{'2', '4'}}, {{'2', '5'}}, {{'2', '6'}}, {{'2', '7'}}, {{'2', '8'}}, {{'2', '9'}}, - {{'3', '0'}}, {{'3', '1'}}, {{'3', '2'}}, {{'3', '3'}}, {{'3', '4'}}, {{'3', '5'}}, {{'3', '6'}}, {{'3', '7'}}, {{'3', '8'}}, {{'3', '9'}}, - {{'4', '0'}}, {{'4', '1'}}, {{'4', '2'}}, {{'4', '3'}}, {{'4', '4'}}, {{'4', '5'}}, {{'4', '6'}}, {{'4', '7'}}, {{'4', '8'}}, {{'4', '9'}}, - {{'5', '0'}}, {{'5', '1'}}, {{'5', '2'}}, {{'5', '3'}}, {{'5', '4'}}, {{'5', '5'}}, {{'5', '6'}}, {{'5', '7'}}, {{'5', '8'}}, {{'5', '9'}}, - {{'6', '0'}}, {{'6', '1'}}, {{'6', '2'}}, {{'6', '3'}}, {{'6', '4'}}, {{'6', '5'}}, {{'6', '6'}}, {{'6', '7'}}, {{'6', '8'}}, {{'6', '9'}}, - {{'7', '0'}}, {{'7', '1'}}, {{'7', '2'}}, {{'7', '3'}}, {{'7', '4'}}, {{'7', '5'}}, {{'7', '6'}}, {{'7', '7'}}, {{'7', '8'}}, {{'7', '9'}}, - {{'8', '0'}}, {{'8', '1'}}, {{'8', '2'}}, {{'8', '3'}}, {{'8', '4'}}, {{'8', '5'}}, {{'8', '6'}}, {{'8', '7'}}, {{'8', '8'}}, {{'8', '9'}}, - {{'9', '0'}}, {{'9', '1'}}, {{'9', '2'}}, {{'9', '3'}}, {{'9', '4'}}, {{'9', '5'}}, {{'9', '6'}}, {{'9', '7'}}, {{'9', '8'}}, {{'9', '9'}}, - } - }; - - // special case for "0" - if (x == 0) - { - o->write_character('0'); - return; - } - - // use a pointer to fill the buffer - auto buffer_ptr = number_buffer.begin(); - - const bool is_negative = std::is_same::value && !(x >= 0); // see issue #755 - number_unsigned_t abs_value; - - unsigned int n_chars; - - if (is_negative) - { - *buffer_ptr = '-'; - abs_value = remove_sign(static_cast(x)); - - // account one more byte for the minus sign - n_chars = 1 + count_digits(abs_value); - } - else - { - abs_value = static_cast(x); - n_chars = count_digits(abs_value); - } - - // spare 1 byte for '\0' - JSON_ASSERT(n_chars < number_buffer.size() - 1); - - // jump to the end to generate the string from backward - // so we later avoid reversing the result - buffer_ptr += n_chars; - - // Fast int2ascii implementation inspired by "Fastware" talk by Andrei Alexandrescu - // See: https://www.youtube.com/watch?v=o4-CwDo2zpg - while (abs_value >= 100) - { - const auto digits_index = static_cast((abs_value % 100)); - abs_value /= 100; - *(--buffer_ptr) = digits_to_99[digits_index][1]; - *(--buffer_ptr) = digits_to_99[digits_index][0]; - } - - if (abs_value >= 10) - { - const auto digits_index = static_cast(abs_value); - *(--buffer_ptr) = digits_to_99[digits_index][1]; - *(--buffer_ptr) = digits_to_99[digits_index][0]; - } - else - { - *(--buffer_ptr) = static_cast('0' + abs_value); - } - - o->write_characters(number_buffer.data(), n_chars); - } - - /*! - @brief dump a floating-point number - - Dump a given floating-point number to output stream @a o. Works internally - with @a number_buffer. - - @param[in] x floating-point number to dump - */ - void dump_float(number_float_t x) - { - // NaN / inf - if (!std::isfinite(x)) - { - o->write_characters("null", 4); - return; - } - - // If number_float_t is an IEEE-754 single or double precision number, - // use the Grisu2 algorithm to produce short numbers which are - // guaranteed to round-trip, using strtof and strtod, resp. - // - // NB: The test below works if == . - static constexpr bool is_ieee_single_or_double - = (std::numeric_limits::is_iec559 && std::numeric_limits::digits == 24 && std::numeric_limits::max_exponent == 128) || - (std::numeric_limits::is_iec559 && std::numeric_limits::digits == 53 && std::numeric_limits::max_exponent == 1024); - - dump_float(x, std::integral_constant()); - } - - void dump_float(number_float_t x, std::true_type /*is_ieee_single_or_double*/) - { - char* begin = number_buffer.data(); - char* end = ::nlohmann::detail::to_chars(begin, begin + number_buffer.size(), x); - - o->write_characters(begin, static_cast(end - begin)); - } - - void dump_float(number_float_t x, std::false_type /*is_ieee_single_or_double*/) - { - // get number of digits for a float -> text -> float round-trip - static constexpr auto d = std::numeric_limits::max_digits10; - - // the actual conversion - std::ptrdiff_t len = (std::snprintf)(number_buffer.data(), number_buffer.size(), "%.*g", d, x); - - // negative value indicates an error - JSON_ASSERT(len > 0); - // check if buffer was large enough - JSON_ASSERT(static_cast(len) < number_buffer.size()); - - // erase thousands separator - if (thousands_sep != '\0') - { - const auto end = std::remove(number_buffer.begin(), - number_buffer.begin() + len, thousands_sep); - std::fill(end, number_buffer.end(), '\0'); - JSON_ASSERT((end - number_buffer.begin()) <= len); - len = (end - number_buffer.begin()); - } - - // convert decimal point to '.' - if (decimal_point != '\0' && decimal_point != '.') - { - const auto dec_pos = std::find(number_buffer.begin(), number_buffer.end(), decimal_point); - if (dec_pos != number_buffer.end()) - { - *dec_pos = '.'; - } - } - - o->write_characters(number_buffer.data(), static_cast(len)); - - // determine if need to append ".0" - const bool value_is_int_like = - std::none_of(number_buffer.begin(), number_buffer.begin() + len + 1, - [](char c) - { - return c == '.' || c == 'e'; - }); - - if (value_is_int_like) - { - o->write_characters(".0", 2); - } - } - - /*! - @brief check whether a string is UTF-8 encoded - - The function checks each byte of a string whether it is UTF-8 encoded. The - result of the check is stored in the @a state parameter. The function must - be called initially with state 0 (accept). State 1 means the string must - be rejected, because the current byte is not allowed. If the string is - completely processed, but the state is non-zero, the string ended - prematurely; that is, the last byte indicated more bytes should have - followed. - - @param[in,out] state the state of the decoding - @param[in,out] codep codepoint (valid only if resulting state is UTF8_ACCEPT) - @param[in] byte next byte to decode - @return new state - - @note The function has been edited: a std::array is used. - - @copyright Copyright (c) 2008-2009 Bjoern Hoehrmann - @sa http://bjoern.hoehrmann.de/utf-8/decoder/dfa/ - */ - static std::uint8_t decode(std::uint8_t& state, std::uint32_t& codep, const std::uint8_t byte) noexcept - { - static const std::array utf8d = - { - { - 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, // 00..1F - 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, // 20..3F - 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, // 40..5F - 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, // 60..7F - 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, // 80..9F - 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, // A0..BF - 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, // C0..DF - 0xA, 0x3, 0x3, 0x3, 0x3, 0x3, 0x3, 0x3, 0x3, 0x3, 0x3, 0x3, 0x3, 0x4, 0x3, 0x3, // E0..EF - 0xB, 0x6, 0x6, 0x6, 0x5, 0x8, 0x8, 0x8, 0x8, 0x8, 0x8, 0x8, 0x8, 0x8, 0x8, 0x8, // F0..FF - 0x0, 0x1, 0x2, 0x3, 0x5, 0x8, 0x7, 0x1, 0x1, 0x1, 0x4, 0x6, 0x1, 0x1, 0x1, 0x1, // s0..s0 - 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 0, 1, 0, 1, 1, 1, 1, 1, 1, // s1..s2 - 1, 2, 1, 1, 1, 1, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, // s3..s4 - 1, 2, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 3, 1, 1, 1, 1, 1, 1, // s5..s6 - 1, 3, 1, 1, 1, 1, 1, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 // s7..s8 - } - }; - - const std::uint8_t type = utf8d[byte]; - - codep = (state != UTF8_ACCEPT) - ? (byte & 0x3fu) | (codep << 6u) - : (0xFFu >> type) & (byte); - - std::size_t index = 256u + static_cast(state) * 16u + static_cast(type); - JSON_ASSERT(index < 400); - state = utf8d[index]; - return state; - } - - /* - * Overload to make the compiler happy while it is instantiating - * dump_integer for number_unsigned_t. - * Must never be called. - */ - number_unsigned_t remove_sign(number_unsigned_t x) - { - JSON_ASSERT(false); // LCOV_EXCL_LINE - return x; // LCOV_EXCL_LINE - } - - /* - * Helper function for dump_integer - * - * This function takes a negative signed integer and returns its absolute - * value as unsigned integer. The plus/minus shuffling is necessary as we can - * not directly remove the sign of an arbitrary signed integer as the - * absolute values of INT_MIN and INT_MAX are usually not the same. See - * #1708 for details. - */ - inline number_unsigned_t remove_sign(number_integer_t x) noexcept - { - JSON_ASSERT(x < 0 && x < (std::numeric_limits::max)()); - return static_cast(-(x + 1)) + 1; - } - - private: - /// the output of the serializer - output_adapter_t o = nullptr; - - /// a (hopefully) large enough character buffer - std::array number_buffer{{}}; - - /// the locale - const std::lconv* loc = nullptr; - /// the locale's thousand separator character - const char thousands_sep = '\0'; - /// the locale's decimal point character - const char decimal_point = '\0'; - - /// string buffer - std::array string_buffer{{}}; - - /// the indentation character - const char indent_char; - /// the indentation string - string_t indent_string; - - /// error_handler how to react on decoding errors - const error_handler_t error_handler; -}; -} // namespace detail -} // namespace nlohmann - -// #include - -// #include - -// #include - - -#include // less -#include // allocator -#include // pair -#include // vector - -namespace nlohmann -{ - -/// ordered_map: a minimal map-like container that preserves insertion order -/// for use within nlohmann::basic_json -template , - class Allocator = std::allocator>> - struct ordered_map : std::vector, Allocator> -{ - using key_type = Key; - using mapped_type = T; - using Container = std::vector, Allocator>; - using typename Container::iterator; - using typename Container::const_iterator; - using typename Container::size_type; - using typename Container::value_type; - - // Explicit constructors instead of `using Container::Container` - // otherwise older compilers choke on it (GCC <= 5.5, xcode <= 9.4) - ordered_map(const Allocator& alloc = Allocator()) : Container{alloc} {} - template - ordered_map(It first, It last, const Allocator& alloc = Allocator()) - : Container{first, last, alloc} {} - ordered_map(std::initializer_list init, const Allocator& alloc = Allocator() ) - : Container{init, alloc} {} - - std::pair emplace(const key_type& key, T&& t) - { - for (auto it = this->begin(); it != this->end(); ++it) - { - if (it->first == key) - { - return {it, false}; - } - } - Container::emplace_back(key, t); - return {--this->end(), true}; - } - - T& operator[](const Key& key) - { - return emplace(key, T{}).first->second; - } - - const T& operator[](const Key& key) const - { - return at(key); - } - - T& at(const Key& key) - { - for (auto it = this->begin(); it != this->end(); ++it) - { - if (it->first == key) - { - return it->second; - } - } - - throw std::out_of_range("key not found"); - } - - const T& at(const Key& key) const - { - for (auto it = this->begin(); it != this->end(); ++it) - { - if (it->first == key) - { - return it->second; - } - } - - throw std::out_of_range("key not found"); - } - - size_type erase(const Key& key) - { - for (auto it = this->begin(); it != this->end(); ++it) - { - if (it->first == key) - { - // Since we cannot move const Keys, re-construct them in place - for (auto next = it; ++next != this->end(); ++it) - { - it->~value_type(); // Destroy but keep allocation - new (&*it) value_type{std::move(*next)}; - } - Container::pop_back(); - return 1; - } - } - return 0; - } - - iterator erase(iterator pos) - { - auto it = pos; - - // Since we cannot move const Keys, re-construct them in place - for (auto next = it; ++next != this->end(); ++it) - { - it->~value_type(); // Destroy but keep allocation - new (&*it) value_type{std::move(*next)}; - } - Container::pop_back(); - return pos; - } - - size_type count(const Key& key) const - { - for (auto it = this->begin(); it != this->end(); ++it) - { - if (it->first == key) - { - return 1; - } - } - return 0; - } - - iterator find(const Key& key) - { - for (auto it = this->begin(); it != this->end(); ++it) - { - if (it->first == key) - { - return it; - } - } - return Container::end(); - } - - const_iterator find(const Key& key) const - { - for (auto it = this->begin(); it != this->end(); ++it) - { - if (it->first == key) - { - return it; - } - } - return Container::end(); - } - - std::pair insert( value_type&& value ) - { - return emplace(value.first, std::move(value.second)); - } - - std::pair insert( const value_type& value ) - { - for (auto it = this->begin(); it != this->end(); ++it) - { - if (it->first == value.first) - { - return {it, false}; - } - } - Container::push_back(value); - return {--this->end(), true}; - } -}; - -} // namespace nlohmann - - -/*! -@brief namespace for Niels Lohmann -@see https://github.com/nlohmann -@since version 1.0.0 -*/ -namespace nlohmann -{ - -/*! -@brief a class to store JSON values - -@tparam ObjectType type for JSON objects (`std::map` by default; will be used -in @ref object_t) -@tparam ArrayType type for JSON arrays (`std::vector` by default; will be used -in @ref array_t) -@tparam StringType type for JSON strings and object keys (`std::string` by -default; will be used in @ref string_t) -@tparam BooleanType type for JSON booleans (`bool` by default; will be used -in @ref boolean_t) -@tparam NumberIntegerType type for JSON integer numbers (`int64_t` by -default; will be used in @ref number_integer_t) -@tparam NumberUnsignedType type for JSON unsigned integer numbers (@c -`uint64_t` by default; will be used in @ref number_unsigned_t) -@tparam NumberFloatType type for JSON floating-point numbers (`double` by -default; will be used in @ref number_float_t) -@tparam BinaryType type for packed binary data for compatibility with binary -serialization formats (`std::vector` by default; will be used in -@ref binary_t) -@tparam AllocatorType type of the allocator to use (`std::allocator` by -default) -@tparam JSONSerializer the serializer to resolve internal calls to `to_json()` -and `from_json()` (@ref adl_serializer by default) - -@requirement The class satisfies the following concept requirements: -- Basic - - [DefaultConstructible](https://en.cppreference.com/w/cpp/named_req/DefaultConstructible): - JSON values can be default constructed. The result will be a JSON null - value. - - [MoveConstructible](https://en.cppreference.com/w/cpp/named_req/MoveConstructible): - A JSON value can be constructed from an rvalue argument. - - [CopyConstructible](https://en.cppreference.com/w/cpp/named_req/CopyConstructible): - A JSON value can be copy-constructed from an lvalue expression. - - [MoveAssignable](https://en.cppreference.com/w/cpp/named_req/MoveAssignable): - A JSON value van be assigned from an rvalue argument. - - [CopyAssignable](https://en.cppreference.com/w/cpp/named_req/CopyAssignable): - A JSON value can be copy-assigned from an lvalue expression. - - [Destructible](https://en.cppreference.com/w/cpp/named_req/Destructible): - JSON values can be destructed. -- Layout - - [StandardLayoutType](https://en.cppreference.com/w/cpp/named_req/StandardLayoutType): - JSON values have - [standard layout](https://en.cppreference.com/w/cpp/language/data_members#Standard_layout): - All non-static data members are private and standard layout types, the - class has no virtual functions or (virtual) base classes. -- Library-wide - - [EqualityComparable](https://en.cppreference.com/w/cpp/named_req/EqualityComparable): - JSON values can be compared with `==`, see @ref - operator==(const_reference,const_reference). - - [LessThanComparable](https://en.cppreference.com/w/cpp/named_req/LessThanComparable): - JSON values can be compared with `<`, see @ref - operator<(const_reference,const_reference). - - [Swappable](https://en.cppreference.com/w/cpp/named_req/Swappable): - Any JSON lvalue or rvalue of can be swapped with any lvalue or rvalue of - other compatible types, using unqualified function call @ref swap(). - - [NullablePointer](https://en.cppreference.com/w/cpp/named_req/NullablePointer): - JSON values can be compared against `std::nullptr_t` objects which are used - to model the `null` value. -- Container - - [Container](https://en.cppreference.com/w/cpp/named_req/Container): - JSON values can be used like STL containers and provide iterator access. - - [ReversibleContainer](https://en.cppreference.com/w/cpp/named_req/ReversibleContainer); - JSON values can be used like STL containers and provide reverse iterator - access. - -@invariant The member variables @a m_value and @a m_type have the following -relationship: -- If `m_type == value_t::object`, then `m_value.object != nullptr`. -- If `m_type == value_t::array`, then `m_value.array != nullptr`. -- If `m_type == value_t::string`, then `m_value.string != nullptr`. -The invariants are checked by member function assert_invariant(). - -@internal -@note ObjectType trick from https://stackoverflow.com/a/9860911 -@endinternal - -@see [RFC 7159: The JavaScript Object Notation (JSON) Data Interchange -Format](http://rfc7159.net/rfc7159) - -@since version 1.0.0 - -@nosubgrouping -*/ -NLOHMANN_BASIC_JSON_TPL_DECLARATION -class basic_json -{ - private: - template friend struct detail::external_constructor; - friend ::nlohmann::json_pointer; - - template - friend class ::nlohmann::detail::parser; - friend ::nlohmann::detail::serializer; - template - friend class ::nlohmann::detail::iter_impl; - template - friend class ::nlohmann::detail::binary_writer; - template - friend class ::nlohmann::detail::binary_reader; - template - friend class ::nlohmann::detail::json_sax_dom_parser; - template - friend class ::nlohmann::detail::json_sax_dom_callback_parser; - - /// workaround type for MSVC - using basic_json_t = NLOHMANN_BASIC_JSON_TPL; - - // convenience aliases for types residing in namespace detail; - using lexer = ::nlohmann::detail::lexer_base; - - template - static ::nlohmann::detail::parser parser( - InputAdapterType adapter, - detail::parser_callback_tcb = nullptr, - const bool allow_exceptions = true, - const bool ignore_comments = false - ) - { - return ::nlohmann::detail::parser(std::move(adapter), - std::move(cb), allow_exceptions, ignore_comments); - } - - using primitive_iterator_t = ::nlohmann::detail::primitive_iterator_t; - template - using internal_iterator = ::nlohmann::detail::internal_iterator; - template - using iter_impl = ::nlohmann::detail::iter_impl; - template - using iteration_proxy = ::nlohmann::detail::iteration_proxy; - template using json_reverse_iterator = ::nlohmann::detail::json_reverse_iterator; - - template - using output_adapter_t = ::nlohmann::detail::output_adapter_t; - - template - using binary_reader = ::nlohmann::detail::binary_reader; - template using binary_writer = ::nlohmann::detail::binary_writer; - - using serializer = ::nlohmann::detail::serializer; - - public: - using value_t = detail::value_t; - /// JSON Pointer, see @ref nlohmann::json_pointer - using json_pointer = ::nlohmann::json_pointer; - template - using json_serializer = JSONSerializer; - /// how to treat decoding errors - using error_handler_t = detail::error_handler_t; - /// how to treat CBOR tags - using cbor_tag_handler_t = detail::cbor_tag_handler_t; - /// helper type for initializer lists of basic_json values - using initializer_list_t = std::initializer_list>; - - using input_format_t = detail::input_format_t; - /// SAX interface type, see @ref nlohmann::json_sax - using json_sax_t = json_sax; - - //////////////// - // exceptions // - //////////////// - - /// @name exceptions - /// Classes to implement user-defined exceptions. - /// @{ - - /// @copydoc detail::exception - using exception = detail::exception; - /// @copydoc detail::parse_error - using parse_error = detail::parse_error; - /// @copydoc detail::invalid_iterator - using invalid_iterator = detail::invalid_iterator; - /// @copydoc detail::type_error - using type_error = detail::type_error; - /// @copydoc detail::out_of_range - using out_of_range = detail::out_of_range; - /// @copydoc detail::other_error - using other_error = detail::other_error; - - /// @} - - - ///////////////////// - // container types // - ///////////////////// - - /// @name container types - /// The canonic container types to use @ref basic_json like any other STL - /// container. - /// @{ - - /// the type of elements in a basic_json container - using value_type = basic_json; - - /// the type of an element reference - using reference = value_type&; - /// the type of an element const reference - using const_reference = const value_type&; - - /// a type to represent differences between iterators - using difference_type = std::ptrdiff_t; - /// a type to represent container sizes - using size_type = std::size_t; - - /// the allocator type - using allocator_type = AllocatorType; - - /// the type of an element pointer - using pointer = typename std::allocator_traits::pointer; - /// the type of an element const pointer - using const_pointer = typename std::allocator_traits::const_pointer; - - /// an iterator for a basic_json container - using iterator = iter_impl; - /// a const iterator for a basic_json container - using const_iterator = iter_impl; - /// a reverse iterator for a basic_json container - using reverse_iterator = json_reverse_iterator; - /// a const reverse iterator for a basic_json container - using const_reverse_iterator = json_reverse_iterator; - - /// @} - - - /*! - @brief returns the allocator associated with the container - */ - static allocator_type get_allocator() - { - return allocator_type(); - } - - /*! - @brief returns version information on the library - - This function returns a JSON object with information about the library, - including the version number and information on the platform and compiler. - - @return JSON object holding version information - key | description - ----------- | --------------- - `compiler` | Information on the used compiler. It is an object with the following keys: `c++` (the used C++ standard), `family` (the compiler family; possible values are `clang`, `icc`, `gcc`, `ilecpp`, `msvc`, `pgcpp`, `sunpro`, and `unknown`), and `version` (the compiler version). - `copyright` | The copyright line for the library as string. - `name` | The name of the library as string. - `platform` | The used platform as string. Possible values are `win32`, `linux`, `apple`, `unix`, and `unknown`. - `url` | The URL of the project as string. - `version` | The version of the library. It is an object with the following keys: `major`, `minor`, and `patch` as defined by [Semantic Versioning](http://semver.org), and `string` (the version string). - - @liveexample{The following code shows an example output of the `meta()` - function.,meta} - - @exceptionsafety Strong guarantee: if an exception is thrown, there are no - changes to any JSON value. - - @complexity Constant. - - @since 2.1.0 - */ - JSON_HEDLEY_WARN_UNUSED_RESULT - static basic_json meta() - { - basic_json result; - - result["copyright"] = "(C) 2013-2020 Niels Lohmann"; - result["name"] = "JSON for Modern C++"; - result["url"] = "https://github.com/nlohmann/json"; - result["version"]["string"] = - std::to_string(NLOHMANN_JSON_VERSION_MAJOR) + "." + - std::to_string(NLOHMANN_JSON_VERSION_MINOR) + "." + - std::to_string(NLOHMANN_JSON_VERSION_PATCH); - result["version"]["major"] = NLOHMANN_JSON_VERSION_MAJOR; - result["version"]["minor"] = NLOHMANN_JSON_VERSION_MINOR; - result["version"]["patch"] = NLOHMANN_JSON_VERSION_PATCH; - -#ifdef _WIN32 - result["platform"] = "win32"; -#elif defined __linux__ - result["platform"] = "linux"; -#elif defined __APPLE__ - result["platform"] = "apple"; -#elif defined __unix__ - result["platform"] = "unix"; -#else - result["platform"] = "unknown"; -#endif - -#if defined(__ICC) || defined(__INTEL_COMPILER) - result["compiler"] = {{"family", "icc"}, {"version", __INTEL_COMPILER}}; -#elif defined(__clang__) - result["compiler"] = {{"family", "clang"}, {"version", __clang_version__}}; -#elif defined(__GNUC__) || defined(__GNUG__) - result["compiler"] = {{"family", "gcc"}, {"version", std::to_string(__GNUC__) + "." + std::to_string(__GNUC_MINOR__) + "." + std::to_string(__GNUC_PATCHLEVEL__)}}; -#elif defined(__HP_cc) || defined(__HP_aCC) - result["compiler"] = "hp" -#elif defined(__IBMCPP__) - result["compiler"] = {{"family", "ilecpp"}, {"version", __IBMCPP__}}; -#elif defined(_MSC_VER) - result["compiler"] = {{"family", "msvc"}, {"version", _MSC_VER}}; -#elif defined(__PGI) - result["compiler"] = {{"family", "pgcpp"}, {"version", __PGI}}; -#elif defined(__SUNPRO_CC) - result["compiler"] = {{"family", "sunpro"}, {"version", __SUNPRO_CC}}; -#else - result["compiler"] = {{"family", "unknown"}, {"version", "unknown"}}; -#endif - -#ifdef __cplusplus - result["compiler"]["c++"] = std::to_string(__cplusplus); -#else - result["compiler"]["c++"] = "unknown"; -#endif - return result; - } - - - /////////////////////////// - // JSON value data types // - /////////////////////////// - - /// @name JSON value data types - /// The data types to store a JSON value. These types are derived from - /// the template arguments passed to class @ref basic_json. - /// @{ - -#if defined(JSON_HAS_CPP_14) - // Use transparent comparator if possible, combined with perfect forwarding - // on find() and count() calls prevents unnecessary string construction. - using object_comparator_t = std::less<>; -#else - using object_comparator_t = std::less; -#endif - - /*! - @brief a type for an object - - [RFC 7159](http://rfc7159.net/rfc7159) describes JSON objects as follows: - > An object is an unordered collection of zero or more name/value pairs, - > where a name is a string and a value is a string, number, boolean, null, - > object, or array. - - To store objects in C++, a type is defined by the template parameters - described below. - - @tparam ObjectType the container to store objects (e.g., `std::map` or - `std::unordered_map`) - @tparam StringType the type of the keys or names (e.g., `std::string`). - The comparison function `std::less` is used to order elements - inside the container. - @tparam AllocatorType the allocator to use for objects (e.g., - `std::allocator`) - - #### Default type - - With the default values for @a ObjectType (`std::map`), @a StringType - (`std::string`), and @a AllocatorType (`std::allocator`), the default - value for @a object_t is: - - @code {.cpp} - std::map< - std::string, // key_type - basic_json, // value_type - std::less, // key_compare - std::allocator> // allocator_type - > - @endcode - - #### Behavior - - The choice of @a object_t influences the behavior of the JSON class. With - the default type, objects have the following behavior: - - - When all names are unique, objects will be interoperable in the sense - that all software implementations receiving that object will agree on - the name-value mappings. - - When the names within an object are not unique, it is unspecified which - one of the values for a given key will be chosen. For instance, - `{"key": 2, "key": 1}` could be equal to either `{"key": 1}` or - `{"key": 2}`. - - Internally, name/value pairs are stored in lexicographical order of the - names. Objects will also be serialized (see @ref dump) in this order. - For instance, `{"b": 1, "a": 2}` and `{"a": 2, "b": 1}` will be stored - and serialized as `{"a": 2, "b": 1}`. - - When comparing objects, the order of the name/value pairs is irrelevant. - This makes objects interoperable in the sense that they will not be - affected by these differences. For instance, `{"b": 1, "a": 2}` and - `{"a": 2, "b": 1}` will be treated as equal. - - #### Limits - - [RFC 7159](http://rfc7159.net/rfc7159) specifies: - > An implementation may set limits on the maximum depth of nesting. - - In this class, the object's limit of nesting is not explicitly constrained. - However, a maximum depth of nesting may be introduced by the compiler or - runtime environment. A theoretical limit can be queried by calling the - @ref max_size function of a JSON object. - - #### Storage - - Objects are stored as pointers in a @ref basic_json type. That is, for any - access to object values, a pointer of type `object_t*` must be - dereferenced. - - @sa @ref array_t -- type for an array value - - @since version 1.0.0 - - @note The order name/value pairs are added to the object is *not* - preserved by the library. Therefore, iterating an object may return - name/value pairs in a different order than they were originally stored. In - fact, keys will be traversed in alphabetical order as `std::map` with - `std::less` is used by default. Please note this behavior conforms to [RFC - 7159](http://rfc7159.net/rfc7159), because any order implements the - specified "unordered" nature of JSON objects. - */ - using object_t = ObjectType>>; - - /*! - @brief a type for an array - - [RFC 7159](http://rfc7159.net/rfc7159) describes JSON arrays as follows: - > An array is an ordered sequence of zero or more values. - - To store objects in C++, a type is defined by the template parameters - explained below. - - @tparam ArrayType container type to store arrays (e.g., `std::vector` or - `std::list`) - @tparam AllocatorType allocator to use for arrays (e.g., `std::allocator`) - - #### Default type - - With the default values for @a ArrayType (`std::vector`) and @a - AllocatorType (`std::allocator`), the default value for @a array_t is: - - @code {.cpp} - std::vector< - basic_json, // value_type - std::allocator // allocator_type - > - @endcode - - #### Limits - - [RFC 7159](http://rfc7159.net/rfc7159) specifies: - > An implementation may set limits on the maximum depth of nesting. - - In this class, the array's limit of nesting is not explicitly constrained. - However, a maximum depth of nesting may be introduced by the compiler or - runtime environment. A theoretical limit can be queried by calling the - @ref max_size function of a JSON array. - - #### Storage - - Arrays are stored as pointers in a @ref basic_json type. That is, for any - access to array values, a pointer of type `array_t*` must be dereferenced. - - @sa @ref object_t -- type for an object value - - @since version 1.0.0 - */ - using array_t = ArrayType>; - - /*! - @brief a type for a string - - [RFC 7159](http://rfc7159.net/rfc7159) describes JSON strings as follows: - > A string is a sequence of zero or more Unicode characters. - - To store objects in C++, a type is defined by the template parameter - described below. Unicode values are split by the JSON class into - byte-sized characters during deserialization. - - @tparam StringType the container to store strings (e.g., `std::string`). - Note this container is used for keys/names in objects, see @ref object_t. - - #### Default type - - With the default values for @a StringType (`std::string`), the default - value for @a string_t is: - - @code {.cpp} - std::string - @endcode - - #### Encoding - - Strings are stored in UTF-8 encoding. Therefore, functions like - `std::string::size()` or `std::string::length()` return the number of - bytes in the string rather than the number of characters or glyphs. - - #### String comparison - - [RFC 7159](http://rfc7159.net/rfc7159) states: - > Software implementations are typically required to test names of object - > members for equality. Implementations that transform the textual - > representation into sequences of Unicode code units and then perform the - > comparison numerically, code unit by code unit, are interoperable in the - > sense that implementations will agree in all cases on equality or - > inequality of two strings. For example, implementations that compare - > strings with escaped characters unconverted may incorrectly find that - > `"a\\b"` and `"a\u005Cb"` are not equal. - - This implementation is interoperable as it does compare strings code unit - by code unit. - - #### Storage - - String values are stored as pointers in a @ref basic_json type. That is, - for any access to string values, a pointer of type `string_t*` must be - dereferenced. - - @since version 1.0.0 - */ - using string_t = StringType; - - /*! - @brief a type for a boolean - - [RFC 7159](http://rfc7159.net/rfc7159) implicitly describes a boolean as a - type which differentiates the two literals `true` and `false`. - - To store objects in C++, a type is defined by the template parameter @a - BooleanType which chooses the type to use. - - #### Default type - - With the default values for @a BooleanType (`bool`), the default value for - @a boolean_t is: - - @code {.cpp} - bool - @endcode - - #### Storage - - Boolean values are stored directly inside a @ref basic_json type. - - @since version 1.0.0 - */ - using boolean_t = BooleanType; - - /*! - @brief a type for a number (integer) - - [RFC 7159](http://rfc7159.net/rfc7159) describes numbers as follows: - > The representation of numbers is similar to that used in most - > programming languages. A number is represented in base 10 using decimal - > digits. It contains an integer component that may be prefixed with an - > optional minus sign, which may be followed by a fraction part and/or an - > exponent part. Leading zeros are not allowed. (...) Numeric values that - > cannot be represented in the grammar below (such as Infinity and NaN) - > are not permitted. - - This description includes both integer and floating-point numbers. - However, C++ allows more precise storage if it is known whether the number - is a signed integer, an unsigned integer or a floating-point number. - Therefore, three different types, @ref number_integer_t, @ref - number_unsigned_t and @ref number_float_t are used. - - To store integer numbers in C++, a type is defined by the template - parameter @a NumberIntegerType which chooses the type to use. - - #### Default type - - With the default values for @a NumberIntegerType (`int64_t`), the default - value for @a number_integer_t is: - - @code {.cpp} - int64_t - @endcode - - #### Default behavior - - - The restrictions about leading zeros is not enforced in C++. Instead, - leading zeros in integer literals lead to an interpretation as octal - number. Internally, the value will be stored as decimal number. For - instance, the C++ integer literal `010` will be serialized to `8`. - During deserialization, leading zeros yield an error. - - Not-a-number (NaN) values will be serialized to `null`. - - #### Limits - - [RFC 7159](http://rfc7159.net/rfc7159) specifies: - > An implementation may set limits on the range and precision of numbers. - - When the default type is used, the maximal integer number that can be - stored is `9223372036854775807` (INT64_MAX) and the minimal integer number - that can be stored is `-9223372036854775808` (INT64_MIN). Integer numbers - that are out of range will yield over/underflow when used in a - constructor. During deserialization, too large or small integer numbers - will be automatically be stored as @ref number_unsigned_t or @ref - number_float_t. - - [RFC 7159](http://rfc7159.net/rfc7159) further states: - > Note that when such software is used, numbers that are integers and are - > in the range \f$[-2^{53}+1, 2^{53}-1]\f$ are interoperable in the sense - > that implementations will agree exactly on their numeric values. - - As this range is a subrange of the exactly supported range [INT64_MIN, - INT64_MAX], this class's integer type is interoperable. - - #### Storage - - Integer number values are stored directly inside a @ref basic_json type. - - @sa @ref number_float_t -- type for number values (floating-point) - - @sa @ref number_unsigned_t -- type for number values (unsigned integer) - - @since version 1.0.0 - */ - using number_integer_t = NumberIntegerType; - - /*! - @brief a type for a number (unsigned) - - [RFC 7159](http://rfc7159.net/rfc7159) describes numbers as follows: - > The representation of numbers is similar to that used in most - > programming languages. A number is represented in base 10 using decimal - > digits. It contains an integer component that may be prefixed with an - > optional minus sign, which may be followed by a fraction part and/or an - > exponent part. Leading zeros are not allowed. (...) Numeric values that - > cannot be represented in the grammar below (such as Infinity and NaN) - > are not permitted. - - This description includes both integer and floating-point numbers. - However, C++ allows more precise storage if it is known whether the number - is a signed integer, an unsigned integer or a floating-point number. - Therefore, three different types, @ref number_integer_t, @ref - number_unsigned_t and @ref number_float_t are used. - - To store unsigned integer numbers in C++, a type is defined by the - template parameter @a NumberUnsignedType which chooses the type to use. - - #### Default type - - With the default values for @a NumberUnsignedType (`uint64_t`), the - default value for @a number_unsigned_t is: - - @code {.cpp} - uint64_t - @endcode - - #### Default behavior - - - The restrictions about leading zeros is not enforced in C++. Instead, - leading zeros in integer literals lead to an interpretation as octal - number. Internally, the value will be stored as decimal number. For - instance, the C++ integer literal `010` will be serialized to `8`. - During deserialization, leading zeros yield an error. - - Not-a-number (NaN) values will be serialized to `null`. - - #### Limits - - [RFC 7159](http://rfc7159.net/rfc7159) specifies: - > An implementation may set limits on the range and precision of numbers. - - When the default type is used, the maximal integer number that can be - stored is `18446744073709551615` (UINT64_MAX) and the minimal integer - number that can be stored is `0`. Integer numbers that are out of range - will yield over/underflow when used in a constructor. During - deserialization, too large or small integer numbers will be automatically - be stored as @ref number_integer_t or @ref number_float_t. - - [RFC 7159](http://rfc7159.net/rfc7159) further states: - > Note that when such software is used, numbers that are integers and are - > in the range \f$[-2^{53}+1, 2^{53}-1]\f$ are interoperable in the sense - > that implementations will agree exactly on their numeric values. - - As this range is a subrange (when considered in conjunction with the - number_integer_t type) of the exactly supported range [0, UINT64_MAX], - this class's integer type is interoperable. - - #### Storage - - Integer number values are stored directly inside a @ref basic_json type. - - @sa @ref number_float_t -- type for number values (floating-point) - @sa @ref number_integer_t -- type for number values (integer) - - @since version 2.0.0 - */ - using number_unsigned_t = NumberUnsignedType; - - /*! - @brief a type for a number (floating-point) - - [RFC 7159](http://rfc7159.net/rfc7159) describes numbers as follows: - > The representation of numbers is similar to that used in most - > programming languages. A number is represented in base 10 using decimal - > digits. It contains an integer component that may be prefixed with an - > optional minus sign, which may be followed by a fraction part and/or an - > exponent part. Leading zeros are not allowed. (...) Numeric values that - > cannot be represented in the grammar below (such as Infinity and NaN) - > are not permitted. - - This description includes both integer and floating-point numbers. - However, C++ allows more precise storage if it is known whether the number - is a signed integer, an unsigned integer or a floating-point number. - Therefore, three different types, @ref number_integer_t, @ref - number_unsigned_t and @ref number_float_t are used. - - To store floating-point numbers in C++, a type is defined by the template - parameter @a NumberFloatType which chooses the type to use. - - #### Default type - - With the default values for @a NumberFloatType (`double`), the default - value for @a number_float_t is: - - @code {.cpp} - double - @endcode - - #### Default behavior - - - The restrictions about leading zeros is not enforced in C++. Instead, - leading zeros in floating-point literals will be ignored. Internally, - the value will be stored as decimal number. For instance, the C++ - floating-point literal `01.2` will be serialized to `1.2`. During - deserialization, leading zeros yield an error. - - Not-a-number (NaN) values will be serialized to `null`. - - #### Limits - - [RFC 7159](http://rfc7159.net/rfc7159) states: - > This specification allows implementations to set limits on the range and - > precision of numbers accepted. Since software that implements IEEE - > 754-2008 binary64 (double precision) numbers is generally available and - > widely used, good interoperability can be achieved by implementations - > that expect no more precision or range than these provide, in the sense - > that implementations will approximate JSON numbers within the expected - > precision. - - This implementation does exactly follow this approach, as it uses double - precision floating-point numbers. Note values smaller than - `-1.79769313486232e+308` and values greater than `1.79769313486232e+308` - will be stored as NaN internally and be serialized to `null`. - - #### Storage - - Floating-point number values are stored directly inside a @ref basic_json - type. - - @sa @ref number_integer_t -- type for number values (integer) - - @sa @ref number_unsigned_t -- type for number values (unsigned integer) - - @since version 1.0.0 - */ - using number_float_t = NumberFloatType; - - /*! - @brief a type for a packed binary type - - This type is a type designed to carry binary data that appears in various - serialized formats, such as CBOR's Major Type 2, MessagePack's bin, and - BSON's generic binary subtype. This type is NOT a part of standard JSON and - exists solely for compatibility with these binary types. As such, it is - simply defined as an ordered sequence of zero or more byte values. - - Additionally, as an implementation detail, the subtype of the binary data is - carried around as a `std::uint8_t`, which is compatible with both of the - binary data formats that use binary subtyping, (though the specific - numbering is incompatible with each other, and it is up to the user to - translate between them). - - [CBOR's RFC 7049](https://tools.ietf.org/html/rfc7049) describes this type - as: - > Major type 2: a byte string. The string's length in bytes is represented - > following the rules for positive integers (major type 0). - - [MessagePack's documentation on the bin type - family](https://github.com/msgpack/msgpack/blob/master/spec.md#bin-format-family) - describes this type as: - > Bin format family stores an byte array in 2, 3, or 5 bytes of extra bytes - > in addition to the size of the byte array. - - [BSON's specifications](http://bsonspec.org/spec.html) describe several - binary types; however, this type is intended to represent the generic binary - type which has the description: - > Generic binary subtype - This is the most commonly used binary subtype and - > should be the 'default' for drivers and tools. - - None of these impose any limitations on the internal representation other - than the basic unit of storage be some type of array whose parts are - decomposable into bytes. - - The default representation of this binary format is a - `std::vector`, which is a very common way to represent a byte - array in modern C++. - - #### Default type - - The default values for @a BinaryType is `std::vector` - - #### Storage - - Binary Arrays are stored as pointers in a @ref basic_json type. That is, - for any access to array values, a pointer of the type `binary_t*` must be - dereferenced. - - #### Notes on subtypes - - - CBOR - - Binary values are represented as byte strings. No subtypes are - supported and will be ignored when CBOR is written. - - MessagePack - - If a subtype is given and the binary array contains exactly 1, 2, 4, 8, - or 16 elements, the fixext family (fixext1, fixext2, fixext4, fixext8) - is used. For other sizes, the ext family (ext8, ext16, ext32) is used. - The subtype is then added as singed 8-bit integer. - - If no subtype is given, the bin family (bin8, bin16, bin32) is used. - - BSON - - If a subtype is given, it is used and added as unsigned 8-bit integer. - - If no subtype is given, the generic binary subtype 0x00 is used. - - @sa @ref binary -- create a binary array - - @since version 3.8.0 - */ - using binary_t = nlohmann::byte_container_with_subtype; - /// @} - - private: - - /// helper for exception-safe object creation - template - JSON_HEDLEY_RETURNS_NON_NULL - static T* create(Args&& ... args) - { - AllocatorType alloc; - using AllocatorTraits = std::allocator_traits>; - - auto deleter = [&](T * object) - { - AllocatorTraits::deallocate(alloc, object, 1); - }; - std::unique_ptr object(AllocatorTraits::allocate(alloc, 1), deleter); - AllocatorTraits::construct(alloc, object.get(), std::forward(args)...); - JSON_ASSERT(object != nullptr); - return object.release(); - } - - //////////////////////// - // JSON value storage // - //////////////////////// - - /*! - @brief a JSON value - - The actual storage for a JSON value of the @ref basic_json class. This - union combines the different storage types for the JSON value types - defined in @ref value_t. - - JSON type | value_t type | used type - --------- | --------------- | ------------------------ - object | object | pointer to @ref object_t - array | array | pointer to @ref array_t - string | string | pointer to @ref string_t - boolean | boolean | @ref boolean_t - number | number_integer | @ref number_integer_t - number | number_unsigned | @ref number_unsigned_t - number | number_float | @ref number_float_t - binary | binary | pointer to @ref binary_t - null | null | *no value is stored* - - @note Variable-length types (objects, arrays, and strings) are stored as - pointers. The size of the union should not exceed 64 bits if the default - value types are used. - - @since version 1.0.0 - */ - union json_value - { - /// object (stored with pointer to save storage) - object_t* object; - /// array (stored with pointer to save storage) - array_t* array; - /// string (stored with pointer to save storage) - string_t* string; - /// binary (stored with pointer to save storage) - binary_t* binary; - /// boolean - boolean_t boolean; - /// number (integer) - number_integer_t number_integer; - /// number (unsigned integer) - number_unsigned_t number_unsigned; - /// number (floating-point) - number_float_t number_float; - - /// default constructor (for null values) - json_value() = default; - /// constructor for booleans - json_value(boolean_t v) noexcept : boolean(v) {} - /// constructor for numbers (integer) - json_value(number_integer_t v) noexcept : number_integer(v) {} - /// constructor for numbers (unsigned) - json_value(number_unsigned_t v) noexcept : number_unsigned(v) {} - /// constructor for numbers (floating-point) - json_value(number_float_t v) noexcept : number_float(v) {} - /// constructor for empty values of a given type - json_value(value_t t) - { - switch (t) - { - case value_t::object: - { - object = create(); - break; - } - - case value_t::array: - { - array = create(); - break; - } - - case value_t::string: - { - string = create(""); - break; - } - - case value_t::binary: - { - binary = create(); - break; - } - - case value_t::boolean: - { - boolean = boolean_t(false); - break; - } - - case value_t::number_integer: - { - number_integer = number_integer_t(0); - break; - } - - case value_t::number_unsigned: - { - number_unsigned = number_unsigned_t(0); - break; - } - - case value_t::number_float: - { - number_float = number_float_t(0.0); - break; - } - - case value_t::null: - { - object = nullptr; // silence warning, see #821 - break; - } - - default: - { - object = nullptr; // silence warning, see #821 - if (JSON_HEDLEY_UNLIKELY(t == value_t::null)) - { - JSON_THROW(other_error::create(500, "961c151d2e87f2686a955a9be24d316f1362bf21 3.9.1")); // LCOV_EXCL_LINE - } - break; - } - } - } - - /// constructor for strings - json_value(const string_t& value) - { - string = create(value); - } - - /// constructor for rvalue strings - json_value(string_t&& value) - { - string = create(std::move(value)); - } - - /// constructor for objects - json_value(const object_t& value) - { - object = create(value); - } - - /// constructor for rvalue objects - json_value(object_t&& value) - { - object = create(std::move(value)); - } - - /// constructor for arrays - json_value(const array_t& value) - { - array = create(value); - } - - /// constructor for rvalue arrays - json_value(array_t&& value) - { - array = create(std::move(value)); - } - - /// constructor for binary arrays - json_value(const typename binary_t::container_type& value) - { - binary = create(value); - } - - /// constructor for rvalue binary arrays - json_value(typename binary_t::container_type&& value) - { - binary = create(std::move(value)); - } - - /// constructor for binary arrays (internal type) - json_value(const binary_t& value) - { - binary = create(value); - } - - /// constructor for rvalue binary arrays (internal type) - json_value(binary_t&& value) - { - binary = create(std::move(value)); - } - - void destroy(value_t t) noexcept - { - // flatten the current json_value to a heap-allocated stack - std::vector stack; - - // move the top-level items to stack - if (t == value_t::array) - { - stack.reserve(array->size()); - std::move(array->begin(), array->end(), std::back_inserter(stack)); - } - else if (t == value_t::object) - { - stack.reserve(object->size()); - for (auto&& it : *object) - { - stack.push_back(std::move(it.second)); - } - } - - while (!stack.empty()) - { - // move the last item to local variable to be processed - basic_json current_item(std::move(stack.back())); - stack.pop_back(); - - // if current_item is array/object, move - // its children to the stack to be processed later - if (current_item.is_array()) - { - std::move(current_item.m_value.array->begin(), current_item.m_value.array->end(), - std::back_inserter(stack)); - - current_item.m_value.array->clear(); - } - else if (current_item.is_object()) - { - for (auto&& it : *current_item.m_value.object) - { - stack.push_back(std::move(it.second)); - } - - current_item.m_value.object->clear(); - } - - // it's now safe that current_item get destructed - // since it doesn't have any children - } - - switch (t) - { - case value_t::object: - { - AllocatorType alloc; - std::allocator_traits::destroy(alloc, object); - std::allocator_traits::deallocate(alloc, object, 1); - break; - } - - case value_t::array: - { - AllocatorType alloc; - std::allocator_traits::destroy(alloc, array); - std::allocator_traits::deallocate(alloc, array, 1); - break; - } - - case value_t::string: - { - AllocatorType alloc; - std::allocator_traits::destroy(alloc, string); - std::allocator_traits::deallocate(alloc, string, 1); - break; - } - - case value_t::binary: - { - AllocatorType alloc; - std::allocator_traits::destroy(alloc, binary); - std::allocator_traits::deallocate(alloc, binary, 1); - break; - } - - default: - { - break; - } - } - } - }; - - /*! - @brief checks the class invariants - - This function asserts the class invariants. It needs to be called at the - end of every constructor to make sure that created objects respect the - invariant. Furthermore, it has to be called each time the type of a JSON - value is changed, because the invariant expresses a relationship between - @a m_type and @a m_value. - */ - void assert_invariant() const noexcept - { - JSON_ASSERT(m_type != value_t::object || m_value.object != nullptr); - JSON_ASSERT(m_type != value_t::array || m_value.array != nullptr); - JSON_ASSERT(m_type != value_t::string || m_value.string != nullptr); - JSON_ASSERT(m_type != value_t::binary || m_value.binary != nullptr); - } - - public: - ////////////////////////// - // JSON parser callback // - ////////////////////////// - - /*! - @brief parser event types - - The parser callback distinguishes the following events: - - `object_start`: the parser read `{` and started to process a JSON object - - `key`: the parser read a key of a value in an object - - `object_end`: the parser read `}` and finished processing a JSON object - - `array_start`: the parser read `[` and started to process a JSON array - - `array_end`: the parser read `]` and finished processing a JSON array - - `value`: the parser finished reading a JSON value - - @image html callback_events.png "Example when certain parse events are triggered" - - @sa @ref parser_callback_t for more information and examples - */ - using parse_event_t = detail::parse_event_t; - - /*! - @brief per-element parser callback type - - With a parser callback function, the result of parsing a JSON text can be - influenced. When passed to @ref parse, it is called on certain events - (passed as @ref parse_event_t via parameter @a event) with a set recursion - depth @a depth and context JSON value @a parsed. The return value of the - callback function is a boolean indicating whether the element that emitted - the callback shall be kept or not. - - We distinguish six scenarios (determined by the event type) in which the - callback function can be called. The following table describes the values - of the parameters @a depth, @a event, and @a parsed. - - parameter @a event | description | parameter @a depth | parameter @a parsed - ------------------ | ----------- | ------------------ | ------------------- - parse_event_t::object_start | the parser read `{` and started to process a JSON object | depth of the parent of the JSON object | a JSON value with type discarded - parse_event_t::key | the parser read a key of a value in an object | depth of the currently parsed JSON object | a JSON string containing the key - parse_event_t::object_end | the parser read `}` and finished processing a JSON object | depth of the parent of the JSON object | the parsed JSON object - parse_event_t::array_start | the parser read `[` and started to process a JSON array | depth of the parent of the JSON array | a JSON value with type discarded - parse_event_t::array_end | the parser read `]` and finished processing a JSON array | depth of the parent of the JSON array | the parsed JSON array - parse_event_t::value | the parser finished reading a JSON value | depth of the value | the parsed JSON value - - @image html callback_events.png "Example when certain parse events are triggered" - - Discarding a value (i.e., returning `false`) has different effects - depending on the context in which function was called: - - - Discarded values in structured types are skipped. That is, the parser - will behave as if the discarded value was never read. - - In case a value outside a structured type is skipped, it is replaced - with `null`. This case happens if the top-level element is skipped. - - @param[in] depth the depth of the recursion during parsing - - @param[in] event an event of type parse_event_t indicating the context in - the callback function has been called - - @param[in,out] parsed the current intermediate parse result; note that - writing to this value has no effect for parse_event_t::key events - - @return Whether the JSON value which called the function during parsing - should be kept (`true`) or not (`false`). In the latter case, it is either - skipped completely or replaced by an empty discarded object. - - @sa @ref parse for examples - - @since version 1.0.0 - */ - using parser_callback_t = detail::parser_callback_t; - - ////////////////// - // constructors // - ////////////////// - - /// @name constructors and destructors - /// Constructors of class @ref basic_json, copy/move constructor, copy - /// assignment, static functions creating objects, and the destructor. - /// @{ - - /*! - @brief create an empty value with a given type - - Create an empty JSON value with a given type. The value will be default - initialized with an empty value which depends on the type: - - Value type | initial value - ----------- | ------------- - null | `null` - boolean | `false` - string | `""` - number | `0` - object | `{}` - array | `[]` - binary | empty array - - @param[in] v the type of the value to create - - @complexity Constant. - - @exceptionsafety Strong guarantee: if an exception is thrown, there are no - changes to any JSON value. - - @liveexample{The following code shows the constructor for different @ref - value_t values,basic_json__value_t} - - @sa @ref clear() -- restores the postcondition of this constructor - - @since version 1.0.0 - */ - basic_json(const value_t v) - : m_type(v), m_value(v) - { - assert_invariant(); - } - - /*! - @brief create a null object - - Create a `null` JSON value. It either takes a null pointer as parameter - (explicitly creating `null`) or no parameter (implicitly creating `null`). - The passed null pointer itself is not read -- it is only used to choose - the right constructor. - - @complexity Constant. - - @exceptionsafety No-throw guarantee: this constructor never throws - exceptions. - - @liveexample{The following code shows the constructor with and without a - null pointer parameter.,basic_json__nullptr_t} - - @since version 1.0.0 - */ - basic_json(std::nullptr_t = nullptr) noexcept - : basic_json(value_t::null) - { - assert_invariant(); - } - - /*! - @brief create a JSON value - - This is a "catch all" constructor for all compatible JSON types; that is, - types for which a `to_json()` method exists. The constructor forwards the - parameter @a val to that method (to `json_serializer::to_json` method - with `U = uncvref_t`, to be exact). - - Template type @a CompatibleType includes, but is not limited to, the - following types: - - **arrays**: @ref array_t and all kinds of compatible containers such as - `std::vector`, `std::deque`, `std::list`, `std::forward_list`, - `std::array`, `std::valarray`, `std::set`, `std::unordered_set`, - `std::multiset`, and `std::unordered_multiset` with a `value_type` from - which a @ref basic_json value can be constructed. - - **objects**: @ref object_t and all kinds of compatible associative - containers such as `std::map`, `std::unordered_map`, `std::multimap`, - and `std::unordered_multimap` with a `key_type` compatible to - @ref string_t and a `value_type` from which a @ref basic_json value can - be constructed. - - **strings**: @ref string_t, string literals, and all compatible string - containers can be used. - - **numbers**: @ref number_integer_t, @ref number_unsigned_t, - @ref number_float_t, and all convertible number types such as `int`, - `size_t`, `int64_t`, `float` or `double` can be used. - - **boolean**: @ref boolean_t / `bool` can be used. - - **binary**: @ref binary_t / `std::vector` may be used, - unfortunately because string literals cannot be distinguished from binary - character arrays by the C++ type system, all types compatible with `const - char*` will be directed to the string constructor instead. This is both - for backwards compatibility, and due to the fact that a binary type is not - a standard JSON type. - - See the examples below. - - @tparam CompatibleType a type such that: - - @a CompatibleType is not derived from `std::istream`, - - @a CompatibleType is not @ref basic_json (to avoid hijacking copy/move - constructors), - - @a CompatibleType is not a different @ref basic_json type (i.e. with different template arguments) - - @a CompatibleType is not a @ref basic_json nested type (e.g., - @ref json_pointer, @ref iterator, etc ...) - - @ref @ref json_serializer has a - `to_json(basic_json_t&, CompatibleType&&)` method - - @tparam U = `uncvref_t` - - @param[in] val the value to be forwarded to the respective constructor - - @complexity Usually linear in the size of the passed @a val, also - depending on the implementation of the called `to_json()` - method. - - @exceptionsafety Depends on the called constructor. For types directly - supported by the library (i.e., all types for which no `to_json()` function - was provided), strong guarantee holds: if an exception is thrown, there are - no changes to any JSON value. - - @liveexample{The following code shows the constructor with several - compatible types.,basic_json__CompatibleType} - - @since version 2.1.0 - */ - template < typename CompatibleType, - typename U = detail::uncvref_t, - detail::enable_if_t < - !detail::is_basic_json::value && detail::is_compatible_type::value, int > = 0 > - basic_json(CompatibleType && val) noexcept(noexcept( - JSONSerializer::to_json(std::declval(), - std::forward(val)))) - { - JSONSerializer::to_json(*this, std::forward(val)); - assert_invariant(); - } - - /*! - @brief create a JSON value from an existing one - - This is a constructor for existing @ref basic_json types. - It does not hijack copy/move constructors, since the parameter has different - template arguments than the current ones. - - The constructor tries to convert the internal @ref m_value of the parameter. - - @tparam BasicJsonType a type such that: - - @a BasicJsonType is a @ref basic_json type. - - @a BasicJsonType has different template arguments than @ref basic_json_t. - - @param[in] val the @ref basic_json value to be converted. - - @complexity Usually linear in the size of the passed @a val, also - depending on the implementation of the called `to_json()` - method. - - @exceptionsafety Depends on the called constructor. For types directly - supported by the library (i.e., all types for which no `to_json()` function - was provided), strong guarantee holds: if an exception is thrown, there are - no changes to any JSON value. - - @since version 3.2.0 - */ - template < typename BasicJsonType, - detail::enable_if_t < - detail::is_basic_json::value&& !std::is_same::value, int > = 0 > - basic_json(const BasicJsonType& val) - { - using other_boolean_t = typename BasicJsonType::boolean_t; - using other_number_float_t = typename BasicJsonType::number_float_t; - using other_number_integer_t = typename BasicJsonType::number_integer_t; - using other_number_unsigned_t = typename BasicJsonType::number_unsigned_t; - using other_string_t = typename BasicJsonType::string_t; - using other_object_t = typename BasicJsonType::object_t; - using other_array_t = typename BasicJsonType::array_t; - using other_binary_t = typename BasicJsonType::binary_t; - - switch (val.type()) - { - case value_t::boolean: - JSONSerializer::to_json(*this, val.template get()); - break; - case value_t::number_float: - JSONSerializer::to_json(*this, val.template get()); - break; - case value_t::number_integer: - JSONSerializer::to_json(*this, val.template get()); - break; - case value_t::number_unsigned: - JSONSerializer::to_json(*this, val.template get()); - break; - case value_t::string: - JSONSerializer::to_json(*this, val.template get_ref()); - break; - case value_t::object: - JSONSerializer::to_json(*this, val.template get_ref()); - break; - case value_t::array: - JSONSerializer::to_json(*this, val.template get_ref()); - break; - case value_t::binary: - JSONSerializer::to_json(*this, val.template get_ref()); - break; - case value_t::null: - *this = nullptr; - break; - case value_t::discarded: - m_type = value_t::discarded; - break; - default: // LCOV_EXCL_LINE - JSON_ASSERT(false); // LCOV_EXCL_LINE - } - assert_invariant(); - } - - /*! - @brief create a container (array or object) from an initializer list - - Creates a JSON value of type array or object from the passed initializer - list @a init. In case @a type_deduction is `true` (default), the type of - the JSON value to be created is deducted from the initializer list @a init - according to the following rules: - - 1. If the list is empty, an empty JSON object value `{}` is created. - 2. If the list consists of pairs whose first element is a string, a JSON - object value is created where the first elements of the pairs are - treated as keys and the second elements are as values. - 3. In all other cases, an array is created. - - The rules aim to create the best fit between a C++ initializer list and - JSON values. The rationale is as follows: - - 1. The empty initializer list is written as `{}` which is exactly an empty - JSON object. - 2. C++ has no way of describing mapped types other than to list a list of - pairs. As JSON requires that keys must be of type string, rule 2 is the - weakest constraint one can pose on initializer lists to interpret them - as an object. - 3. In all other cases, the initializer list could not be interpreted as - JSON object type, so interpreting it as JSON array type is safe. - - With the rules described above, the following JSON values cannot be - expressed by an initializer list: - - - the empty array (`[]`): use @ref array(initializer_list_t) - with an empty initializer list in this case - - arrays whose elements satisfy rule 2: use @ref - array(initializer_list_t) with the same initializer list - in this case - - @note When used without parentheses around an empty initializer list, @ref - basic_json() is called instead of this function, yielding the JSON null - value. - - @param[in] init initializer list with JSON values - - @param[in] type_deduction internal parameter; when set to `true`, the type - of the JSON value is deducted from the initializer list @a init; when set - to `false`, the type provided via @a manual_type is forced. This mode is - used by the functions @ref array(initializer_list_t) and - @ref object(initializer_list_t). - - @param[in] manual_type internal parameter; when @a type_deduction is set - to `false`, the created JSON value will use the provided type (only @ref - value_t::array and @ref value_t::object are valid); when @a type_deduction - is set to `true`, this parameter has no effect - - @throw type_error.301 if @a type_deduction is `false`, @a manual_type is - `value_t::object`, but @a init contains an element which is not a pair - whose first element is a string. In this case, the constructor could not - create an object. If @a type_deduction would have be `true`, an array - would have been created. See @ref object(initializer_list_t) - for an example. - - @complexity Linear in the size of the initializer list @a init. - - @exceptionsafety Strong guarantee: if an exception is thrown, there are no - changes to any JSON value. - - @liveexample{The example below shows how JSON values are created from - initializer lists.,basic_json__list_init_t} - - @sa @ref array(initializer_list_t) -- create a JSON array - value from an initializer list - @sa @ref object(initializer_list_t) -- create a JSON object - value from an initializer list - - @since version 1.0.0 - */ - basic_json(initializer_list_t init, - bool type_deduction = true, - value_t manual_type = value_t::array) - { - // check if each element is an array with two elements whose first - // element is a string - bool is_an_object = std::all_of(init.begin(), init.end(), - [](const detail::json_ref& element_ref) - { - return element_ref->is_array() && element_ref->size() == 2 && (*element_ref)[0].is_string(); - }); - - // adjust type if type deduction is not wanted - if (!type_deduction) - { - // if array is wanted, do not create an object though possible - if (manual_type == value_t::array) - { - is_an_object = false; - } - - // if object is wanted but impossible, throw an exception - if (JSON_HEDLEY_UNLIKELY(manual_type == value_t::object && !is_an_object)) - { - JSON_THROW(type_error::create(301, "cannot create object from initializer list")); - } - } - - if (is_an_object) - { - // the initializer list is a list of pairs -> create object - m_type = value_t::object; - m_value = value_t::object; - - std::for_each(init.begin(), init.end(), [this](const detail::json_ref& element_ref) - { - auto element = element_ref.moved_or_copied(); - m_value.object->emplace( - std::move(*((*element.m_value.array)[0].m_value.string)), - std::move((*element.m_value.array)[1])); - }); - } - else - { - // the initializer list describes an array -> create array - m_type = value_t::array; - m_value.array = create(init.begin(), init.end()); - } - - assert_invariant(); - } - - /*! - @brief explicitly create a binary array (without subtype) - - Creates a JSON binary array value from a given binary container. Binary - values are part of various binary formats, such as CBOR, MessagePack, and - BSON. This constructor is used to create a value for serialization to those - formats. - - @note Note, this function exists because of the difficulty in correctly - specifying the correct template overload in the standard value ctor, as both - JSON arrays and JSON binary arrays are backed with some form of a - `std::vector`. Because JSON binary arrays are a non-standard extension it - was decided that it would be best to prevent automatic initialization of a - binary array type, for backwards compatibility and so it does not happen on - accident. - - @param[in] init container containing bytes to use as binary type - - @return JSON binary array value - - @complexity Linear in the size of @a init. - - @exceptionsafety Strong guarantee: if an exception is thrown, there are no - changes to any JSON value. - - @since version 3.8.0 - */ - JSON_HEDLEY_WARN_UNUSED_RESULT - static basic_json binary(const typename binary_t::container_type& init) - { - auto res = basic_json(); - res.m_type = value_t::binary; - res.m_value = init; - return res; - } - - /*! - @brief explicitly create a binary array (with subtype) - - Creates a JSON binary array value from a given binary container. Binary - values are part of various binary formats, such as CBOR, MessagePack, and - BSON. This constructor is used to create a value for serialization to those - formats. - - @note Note, this function exists because of the difficulty in correctly - specifying the correct template overload in the standard value ctor, as both - JSON arrays and JSON binary arrays are backed with some form of a - `std::vector`. Because JSON binary arrays are a non-standard extension it - was decided that it would be best to prevent automatic initialization of a - binary array type, for backwards compatibility and so it does not happen on - accident. - - @param[in] init container containing bytes to use as binary type - @param[in] subtype subtype to use in MessagePack and BSON - - @return JSON binary array value - - @complexity Linear in the size of @a init. - - @exceptionsafety Strong guarantee: if an exception is thrown, there are no - changes to any JSON value. - - @since version 3.8.0 - */ - JSON_HEDLEY_WARN_UNUSED_RESULT - static basic_json binary(const typename binary_t::container_type& init, std::uint8_t subtype) - { - auto res = basic_json(); - res.m_type = value_t::binary; - res.m_value = binary_t(init, subtype); - return res; - } - - /// @copydoc binary(const typename binary_t::container_type&) - JSON_HEDLEY_WARN_UNUSED_RESULT - static basic_json binary(typename binary_t::container_type&& init) - { - auto res = basic_json(); - res.m_type = value_t::binary; - res.m_value = std::move(init); - return res; - } - - /// @copydoc binary(const typename binary_t::container_type&, std::uint8_t) - JSON_HEDLEY_WARN_UNUSED_RESULT - static basic_json binary(typename binary_t::container_type&& init, std::uint8_t subtype) - { - auto res = basic_json(); - res.m_type = value_t::binary; - res.m_value = binary_t(std::move(init), subtype); - return res; - } - - /*! - @brief explicitly create an array from an initializer list - - Creates a JSON array value from a given initializer list. That is, given a - list of values `a, b, c`, creates the JSON value `[a, b, c]`. If the - initializer list is empty, the empty array `[]` is created. - - @note This function is only needed to express two edge cases that cannot - be realized with the initializer list constructor (@ref - basic_json(initializer_list_t, bool, value_t)). These cases - are: - 1. creating an array whose elements are all pairs whose first element is a - string -- in this case, the initializer list constructor would create an - object, taking the first elements as keys - 2. creating an empty array -- passing the empty initializer list to the - initializer list constructor yields an empty object - - @param[in] init initializer list with JSON values to create an array from - (optional) - - @return JSON array value - - @complexity Linear in the size of @a init. - - @exceptionsafety Strong guarantee: if an exception is thrown, there are no - changes to any JSON value. - - @liveexample{The following code shows an example for the `array` - function.,array} - - @sa @ref basic_json(initializer_list_t, bool, value_t) -- - create a JSON value from an initializer list - @sa @ref object(initializer_list_t) -- create a JSON object - value from an initializer list - - @since version 1.0.0 - */ - JSON_HEDLEY_WARN_UNUSED_RESULT - static basic_json array(initializer_list_t init = {}) - { - return basic_json(init, false, value_t::array); - } - - /*! - @brief explicitly create an object from an initializer list - - Creates a JSON object value from a given initializer list. The initializer - lists elements must be pairs, and their first elements must be strings. If - the initializer list is empty, the empty object `{}` is created. - - @note This function is only added for symmetry reasons. In contrast to the - related function @ref array(initializer_list_t), there are - no cases which can only be expressed by this function. That is, any - initializer list @a init can also be passed to the initializer list - constructor @ref basic_json(initializer_list_t, bool, value_t). - - @param[in] init initializer list to create an object from (optional) - - @return JSON object value - - @throw type_error.301 if @a init is not a list of pairs whose first - elements are strings. In this case, no object can be created. When such a - value is passed to @ref basic_json(initializer_list_t, bool, value_t), - an array would have been created from the passed initializer list @a init. - See example below. - - @complexity Linear in the size of @a init. - - @exceptionsafety Strong guarantee: if an exception is thrown, there are no - changes to any JSON value. - - @liveexample{The following code shows an example for the `object` - function.,object} - - @sa @ref basic_json(initializer_list_t, bool, value_t) -- - create a JSON value from an initializer list - @sa @ref array(initializer_list_t) -- create a JSON array - value from an initializer list - - @since version 1.0.0 - */ - JSON_HEDLEY_WARN_UNUSED_RESULT - static basic_json object(initializer_list_t init = {}) - { - return basic_json(init, false, value_t::object); - } - - /*! - @brief construct an array with count copies of given value - - Constructs a JSON array value by creating @a cnt copies of a passed value. - In case @a cnt is `0`, an empty array is created. - - @param[in] cnt the number of JSON copies of @a val to create - @param[in] val the JSON value to copy - - @post `std::distance(begin(),end()) == cnt` holds. - - @complexity Linear in @a cnt. - - @exceptionsafety Strong guarantee: if an exception is thrown, there are no - changes to any JSON value. - - @liveexample{The following code shows examples for the @ref - basic_json(size_type\, const basic_json&) - constructor.,basic_json__size_type_basic_json} - - @since version 1.0.0 - */ - basic_json(size_type cnt, const basic_json& val) - : m_type(value_t::array) - { - m_value.array = create(cnt, val); - assert_invariant(); - } - - /*! - @brief construct a JSON container given an iterator range - - Constructs the JSON value with the contents of the range `[first, last)`. - The semantics depends on the different types a JSON value can have: - - In case of a null type, invalid_iterator.206 is thrown. - - In case of other primitive types (number, boolean, or string), @a first - must be `begin()` and @a last must be `end()`. In this case, the value is - copied. Otherwise, invalid_iterator.204 is thrown. - - In case of structured types (array, object), the constructor behaves as - similar versions for `std::vector` or `std::map`; that is, a JSON array - or object is constructed from the values in the range. - - @tparam InputIT an input iterator type (@ref iterator or @ref - const_iterator) - - @param[in] first begin of the range to copy from (included) - @param[in] last end of the range to copy from (excluded) - - @pre Iterators @a first and @a last must be initialized. **This - precondition is enforced with an assertion (see warning).** If - assertions are switched off, a violation of this precondition yields - undefined behavior. - - @pre Range `[first, last)` is valid. Usually, this precondition cannot be - checked efficiently. Only certain edge cases are detected; see the - description of the exceptions below. A violation of this precondition - yields undefined behavior. - - @warning A precondition is enforced with a runtime assertion that will - result in calling `std::abort` if this precondition is not met. - Assertions can be disabled by defining `NDEBUG` at compile time. - See https://en.cppreference.com/w/cpp/error/assert for more - information. - - @throw invalid_iterator.201 if iterators @a first and @a last are not - compatible (i.e., do not belong to the same JSON value). In this case, - the range `[first, last)` is undefined. - @throw invalid_iterator.204 if iterators @a first and @a last belong to a - primitive type (number, boolean, or string), but @a first does not point - to the first element any more. In this case, the range `[first, last)` is - undefined. See example code below. - @throw invalid_iterator.206 if iterators @a first and @a last belong to a - null value. In this case, the range `[first, last)` is undefined. - - @complexity Linear in distance between @a first and @a last. - - @exceptionsafety Strong guarantee: if an exception is thrown, there are no - changes to any JSON value. - - @liveexample{The example below shows several ways to create JSON values by - specifying a subrange with iterators.,basic_json__InputIt_InputIt} - - @since version 1.0.0 - */ - template < class InputIT, typename std::enable_if < - std::is_same::value || - std::is_same::value, int >::type = 0 > - basic_json(InputIT first, InputIT last) - { - JSON_ASSERT(first.m_object != nullptr); - JSON_ASSERT(last.m_object != nullptr); - - // make sure iterator fits the current value - if (JSON_HEDLEY_UNLIKELY(first.m_object != last.m_object)) - { - JSON_THROW(invalid_iterator::create(201, "iterators are not compatible")); - } - - // copy type from first iterator - m_type = first.m_object->m_type; - - // check if iterator range is complete for primitive values - switch (m_type) - { - case value_t::boolean: - case value_t::number_float: - case value_t::number_integer: - case value_t::number_unsigned: - case value_t::string: - { - if (JSON_HEDLEY_UNLIKELY(!first.m_it.primitive_iterator.is_begin() - || !last.m_it.primitive_iterator.is_end())) - { - JSON_THROW(invalid_iterator::create(204, "iterators out of range")); - } - break; - } - - default: - break; - } - - switch (m_type) - { - case value_t::number_integer: - { - m_value.number_integer = first.m_object->m_value.number_integer; - break; - } - - case value_t::number_unsigned: - { - m_value.number_unsigned = first.m_object->m_value.number_unsigned; - break; - } - - case value_t::number_float: - { - m_value.number_float = first.m_object->m_value.number_float; - break; - } - - case value_t::boolean: - { - m_value.boolean = first.m_object->m_value.boolean; - break; - } - - case value_t::string: - { - m_value = *first.m_object->m_value.string; - break; - } - - case value_t::object: - { - m_value.object = create(first.m_it.object_iterator, - last.m_it.object_iterator); - break; - } - - case value_t::array: - { - m_value.array = create(first.m_it.array_iterator, - last.m_it.array_iterator); - break; - } - - case value_t::binary: - { - m_value = *first.m_object->m_value.binary; - break; - } - - default: - JSON_THROW(invalid_iterator::create(206, "cannot construct with iterators from " + - std::string(first.m_object->type_name()))); - } - - assert_invariant(); - } - - - /////////////////////////////////////// - // other constructors and destructor // - /////////////////////////////////////// - - template, - std::is_same>::value, int> = 0 > - basic_json(const JsonRef& ref) : basic_json(ref.moved_or_copied()) {} - - /*! - @brief copy constructor - - Creates a copy of a given JSON value. - - @param[in] other the JSON value to copy - - @post `*this == other` - - @complexity Linear in the size of @a other. - - @exceptionsafety Strong guarantee: if an exception is thrown, there are no - changes to any JSON value. - - @requirement This function helps `basic_json` satisfying the - [Container](https://en.cppreference.com/w/cpp/named_req/Container) - requirements: - - The complexity is linear. - - As postcondition, it holds: `other == basic_json(other)`. - - @liveexample{The following code shows an example for the copy - constructor.,basic_json__basic_json} - - @since version 1.0.0 - */ - basic_json(const basic_json& other) - : m_type(other.m_type) - { - // check of passed value is valid - other.assert_invariant(); - - switch (m_type) - { - case value_t::object: - { - m_value = *other.m_value.object; - break; - } - - case value_t::array: - { - m_value = *other.m_value.array; - break; - } - - case value_t::string: - { - m_value = *other.m_value.string; - break; - } - - case value_t::boolean: - { - m_value = other.m_value.boolean; - break; - } - - case value_t::number_integer: - { - m_value = other.m_value.number_integer; - break; - } - - case value_t::number_unsigned: - { - m_value = other.m_value.number_unsigned; - break; - } - - case value_t::number_float: - { - m_value = other.m_value.number_float; - break; - } - - case value_t::binary: - { - m_value = *other.m_value.binary; - break; - } - - default: - break; - } - - assert_invariant(); - } - - /*! - @brief move constructor - - Move constructor. Constructs a JSON value with the contents of the given - value @a other using move semantics. It "steals" the resources from @a - other and leaves it as JSON null value. - - @param[in,out] other value to move to this object - - @post `*this` has the same value as @a other before the call. - @post @a other is a JSON null value. - - @complexity Constant. - - @exceptionsafety No-throw guarantee: this constructor never throws - exceptions. - - @requirement This function helps `basic_json` satisfying the - [MoveConstructible](https://en.cppreference.com/w/cpp/named_req/MoveConstructible) - requirements. - - @liveexample{The code below shows the move constructor explicitly called - via std::move.,basic_json__moveconstructor} - - @since version 1.0.0 - */ - basic_json(basic_json&& other) noexcept - : m_type(std::move(other.m_type)), - m_value(std::move(other.m_value)) - { - // check that passed value is valid - other.assert_invariant(); - - // invalidate payload - other.m_type = value_t::null; - other.m_value = {}; - - assert_invariant(); - } - - /*! - @brief copy assignment - - Copy assignment operator. Copies a JSON value via the "copy and swap" - strategy: It is expressed in terms of the copy constructor, destructor, - and the `swap()` member function. - - @param[in] other value to copy from - - @complexity Linear. - - @requirement This function helps `basic_json` satisfying the - [Container](https://en.cppreference.com/w/cpp/named_req/Container) - requirements: - - The complexity is linear. - - @liveexample{The code below shows and example for the copy assignment. It - creates a copy of value `a` which is then swapped with `b`. Finally\, the - copy of `a` (which is the null value after the swap) is - destroyed.,basic_json__copyassignment} - - @since version 1.0.0 - */ - basic_json& operator=(basic_json other) noexcept ( - std::is_nothrow_move_constructible::value&& - std::is_nothrow_move_assignable::value&& - std::is_nothrow_move_constructible::value&& - std::is_nothrow_move_assignable::value - ) - { - // check that passed value is valid - other.assert_invariant(); - - using std::swap; - swap(m_type, other.m_type); - swap(m_value, other.m_value); - - assert_invariant(); - return *this; - } - - /*! - @brief destructor - - Destroys the JSON value and frees all allocated memory. - - @complexity Linear. - - @requirement This function helps `basic_json` satisfying the - [Container](https://en.cppreference.com/w/cpp/named_req/Container) - requirements: - - The complexity is linear. - - All stored elements are destroyed and all memory is freed. - - @since version 1.0.0 - */ - ~basic_json() noexcept - { - assert_invariant(); - m_value.destroy(m_type); - } - - /// @} - - public: - /////////////////////// - // object inspection // - /////////////////////// - - /// @name object inspection - /// Functions to inspect the type of a JSON value. - /// @{ - - /*! - @brief serialization - - Serialization function for JSON values. The function tries to mimic - Python's `json.dumps()` function, and currently supports its @a indent - and @a ensure_ascii parameters. - - @param[in] indent If indent is nonnegative, then array elements and object - members will be pretty-printed with that indent level. An indent level of - `0` will only insert newlines. `-1` (the default) selects the most compact - representation. - @param[in] indent_char The character to use for indentation if @a indent is - greater than `0`. The default is ` ` (space). - @param[in] ensure_ascii If @a ensure_ascii is true, all non-ASCII characters - in the output are escaped with `\uXXXX` sequences, and the result consists - of ASCII characters only. - @param[in] error_handler how to react on decoding errors; there are three - possible values: `strict` (throws and exception in case a decoding error - occurs; default), `replace` (replace invalid UTF-8 sequences with U+FFFD), - and `ignore` (ignore invalid UTF-8 sequences during serialization; all - bytes are copied to the output unchanged). - - @return string containing the serialization of the JSON value - - @throw type_error.316 if a string stored inside the JSON value is not - UTF-8 encoded and @a error_handler is set to strict - - @note Binary values are serialized as object containing two keys: - - "bytes": an array of bytes as integers - - "subtype": the subtype as integer or "null" if the binary has no subtype - - @complexity Linear. - - @exceptionsafety Strong guarantee: if an exception is thrown, there are no - changes in the JSON value. - - @liveexample{The following example shows the effect of different @a indent\, - @a indent_char\, and @a ensure_ascii parameters to the result of the - serialization.,dump} - - @see https://docs.python.org/2/library/json.html#json.dump - - @since version 1.0.0; indentation character @a indent_char, option - @a ensure_ascii and exceptions added in version 3.0.0; error - handlers added in version 3.4.0; serialization of binary values added - in version 3.8.0. - */ - string_t dump(const int indent = -1, - const char indent_char = ' ', - const bool ensure_ascii = false, - const error_handler_t error_handler = error_handler_t::strict) const - { - string_t result; - serializer s(detail::output_adapter(result), indent_char, error_handler); - - if (indent >= 0) - { - s.dump(*this, true, ensure_ascii, static_cast(indent)); - } - else - { - s.dump(*this, false, ensure_ascii, 0); - } - - return result; - } - - /*! - @brief return the type of the JSON value (explicit) - - Return the type of the JSON value as a value from the @ref value_t - enumeration. - - @return the type of the JSON value - Value type | return value - ------------------------- | ------------------------- - null | value_t::null - boolean | value_t::boolean - string | value_t::string - number (integer) | value_t::number_integer - number (unsigned integer) | value_t::number_unsigned - number (floating-point) | value_t::number_float - object | value_t::object - array | value_t::array - binary | value_t::binary - discarded | value_t::discarded - - @complexity Constant. - - @exceptionsafety No-throw guarantee: this member function never throws - exceptions. - - @liveexample{The following code exemplifies `type()` for all JSON - types.,type} - - @sa @ref operator value_t() -- return the type of the JSON value (implicit) - @sa @ref type_name() -- return the type as string - - @since version 1.0.0 - */ - constexpr value_t type() const noexcept - { - return m_type; - } - - /*! - @brief return whether type is primitive - - This function returns true if and only if the JSON type is primitive - (string, number, boolean, or null). - - @return `true` if type is primitive (string, number, boolean, or null), - `false` otherwise. - - @complexity Constant. - - @exceptionsafety No-throw guarantee: this member function never throws - exceptions. - - @liveexample{The following code exemplifies `is_primitive()` for all JSON - types.,is_primitive} - - @sa @ref is_structured() -- returns whether JSON value is structured - @sa @ref is_null() -- returns whether JSON value is `null` - @sa @ref is_string() -- returns whether JSON value is a string - @sa @ref is_boolean() -- returns whether JSON value is a boolean - @sa @ref is_number() -- returns whether JSON value is a number - @sa @ref is_binary() -- returns whether JSON value is a binary array - - @since version 1.0.0 - */ - constexpr bool is_primitive() const noexcept - { - return is_null() || is_string() || is_boolean() || is_number() || is_binary(); - } - - /*! - @brief return whether type is structured - - This function returns true if and only if the JSON type is structured - (array or object). - - @return `true` if type is structured (array or object), `false` otherwise. - - @complexity Constant. - - @exceptionsafety No-throw guarantee: this member function never throws - exceptions. - - @liveexample{The following code exemplifies `is_structured()` for all JSON - types.,is_structured} - - @sa @ref is_primitive() -- returns whether value is primitive - @sa @ref is_array() -- returns whether value is an array - @sa @ref is_object() -- returns whether value is an object - - @since version 1.0.0 - */ - constexpr bool is_structured() const noexcept - { - return is_array() || is_object(); - } - - /*! - @brief return whether value is null - - This function returns true if and only if the JSON value is null. - - @return `true` if type is null, `false` otherwise. - - @complexity Constant. - - @exceptionsafety No-throw guarantee: this member function never throws - exceptions. - - @liveexample{The following code exemplifies `is_null()` for all JSON - types.,is_null} - - @since version 1.0.0 - */ - constexpr bool is_null() const noexcept - { - return m_type == value_t::null; - } - - /*! - @brief return whether value is a boolean - - This function returns true if and only if the JSON value is a boolean. - - @return `true` if type is boolean, `false` otherwise. - - @complexity Constant. - - @exceptionsafety No-throw guarantee: this member function never throws - exceptions. - - @liveexample{The following code exemplifies `is_boolean()` for all JSON - types.,is_boolean} - - @since version 1.0.0 - */ - constexpr bool is_boolean() const noexcept - { - return m_type == value_t::boolean; - } - - /*! - @brief return whether value is a number - - This function returns true if and only if the JSON value is a number. This - includes both integer (signed and unsigned) and floating-point values. - - @return `true` if type is number (regardless whether integer, unsigned - integer or floating-type), `false` otherwise. - - @complexity Constant. - - @exceptionsafety No-throw guarantee: this member function never throws - exceptions. - - @liveexample{The following code exemplifies `is_number()` for all JSON - types.,is_number} - - @sa @ref is_number_integer() -- check if value is an integer or unsigned - integer number - @sa @ref is_number_unsigned() -- check if value is an unsigned integer - number - @sa @ref is_number_float() -- check if value is a floating-point number - - @since version 1.0.0 - */ - constexpr bool is_number() const noexcept - { - return is_number_integer() || is_number_float(); - } - - /*! - @brief return whether value is an integer number - - This function returns true if and only if the JSON value is a signed or - unsigned integer number. This excludes floating-point values. - - @return `true` if type is an integer or unsigned integer number, `false` - otherwise. - - @complexity Constant. - - @exceptionsafety No-throw guarantee: this member function never throws - exceptions. - - @liveexample{The following code exemplifies `is_number_integer()` for all - JSON types.,is_number_integer} - - @sa @ref is_number() -- check if value is a number - @sa @ref is_number_unsigned() -- check if value is an unsigned integer - number - @sa @ref is_number_float() -- check if value is a floating-point number - - @since version 1.0.0 - */ - constexpr bool is_number_integer() const noexcept - { - return m_type == value_t::number_integer || m_type == value_t::number_unsigned; - } - - /*! - @brief return whether value is an unsigned integer number - - This function returns true if and only if the JSON value is an unsigned - integer number. This excludes floating-point and signed integer values. - - @return `true` if type is an unsigned integer number, `false` otherwise. - - @complexity Constant. - - @exceptionsafety No-throw guarantee: this member function never throws - exceptions. - - @liveexample{The following code exemplifies `is_number_unsigned()` for all - JSON types.,is_number_unsigned} - - @sa @ref is_number() -- check if value is a number - @sa @ref is_number_integer() -- check if value is an integer or unsigned - integer number - @sa @ref is_number_float() -- check if value is a floating-point number - - @since version 2.0.0 - */ - constexpr bool is_number_unsigned() const noexcept - { - return m_type == value_t::number_unsigned; - } - - /*! - @brief return whether value is a floating-point number - - This function returns true if and only if the JSON value is a - floating-point number. This excludes signed and unsigned integer values. - - @return `true` if type is a floating-point number, `false` otherwise. - - @complexity Constant. - - @exceptionsafety No-throw guarantee: this member function never throws - exceptions. - - @liveexample{The following code exemplifies `is_number_float()` for all - JSON types.,is_number_float} - - @sa @ref is_number() -- check if value is number - @sa @ref is_number_integer() -- check if value is an integer number - @sa @ref is_number_unsigned() -- check if value is an unsigned integer - number - - @since version 1.0.0 - */ - constexpr bool is_number_float() const noexcept - { - return m_type == value_t::number_float; - } - - /*! - @brief return whether value is an object - - This function returns true if and only if the JSON value is an object. - - @return `true` if type is object, `false` otherwise. - - @complexity Constant. - - @exceptionsafety No-throw guarantee: this member function never throws - exceptions. - - @liveexample{The following code exemplifies `is_object()` for all JSON - types.,is_object} - - @since version 1.0.0 - */ - constexpr bool is_object() const noexcept - { - return m_type == value_t::object; - } - - /*! - @brief return whether value is an array - - This function returns true if and only if the JSON value is an array. - - @return `true` if type is array, `false` otherwise. - - @complexity Constant. - - @exceptionsafety No-throw guarantee: this member function never throws - exceptions. - - @liveexample{The following code exemplifies `is_array()` for all JSON - types.,is_array} - - @since version 1.0.0 - */ - constexpr bool is_array() const noexcept - { - return m_type == value_t::array; - } - - /*! - @brief return whether value is a string - - This function returns true if and only if the JSON value is a string. - - @return `true` if type is string, `false` otherwise. - - @complexity Constant. - - @exceptionsafety No-throw guarantee: this member function never throws - exceptions. - - @liveexample{The following code exemplifies `is_string()` for all JSON - types.,is_string} - - @since version 1.0.0 - */ - constexpr bool is_string() const noexcept - { - return m_type == value_t::string; - } - - /*! - @brief return whether value is a binary array - - This function returns true if and only if the JSON value is a binary array. - - @return `true` if type is binary array, `false` otherwise. - - @complexity Constant. - - @exceptionsafety No-throw guarantee: this member function never throws - exceptions. - - @liveexample{The following code exemplifies `is_binary()` for all JSON - types.,is_binary} - - @since version 3.8.0 - */ - constexpr bool is_binary() const noexcept - { - return m_type == value_t::binary; - } - - /*! - @brief return whether value is discarded - - This function returns true if and only if the JSON value was discarded - during parsing with a callback function (see @ref parser_callback_t). - - @note This function will always be `false` for JSON values after parsing. - That is, discarded values can only occur during parsing, but will be - removed when inside a structured value or replaced by null in other cases. - - @return `true` if type is discarded, `false` otherwise. - - @complexity Constant. - - @exceptionsafety No-throw guarantee: this member function never throws - exceptions. - - @liveexample{The following code exemplifies `is_discarded()` for all JSON - types.,is_discarded} - - @since version 1.0.0 - */ - constexpr bool is_discarded() const noexcept - { - return m_type == value_t::discarded; - } - - /*! - @brief return the type of the JSON value (implicit) - - Implicitly return the type of the JSON value as a value from the @ref - value_t enumeration. - - @return the type of the JSON value - - @complexity Constant. - - @exceptionsafety No-throw guarantee: this member function never throws - exceptions. - - @liveexample{The following code exemplifies the @ref value_t operator for - all JSON types.,operator__value_t} - - @sa @ref type() -- return the type of the JSON value (explicit) - @sa @ref type_name() -- return the type as string - - @since version 1.0.0 - */ - constexpr operator value_t() const noexcept - { - return m_type; - } - - /// @} - - private: - ////////////////// - // value access // - ////////////////// - - /// get a boolean (explicit) - boolean_t get_impl(boolean_t* /*unused*/) const - { - if (JSON_HEDLEY_LIKELY(is_boolean())) - { - return m_value.boolean; - } - - JSON_THROW(type_error::create(302, "type must be boolean, but is " + std::string(type_name()))); - } - - /// get a pointer to the value (object) - object_t* get_impl_ptr(object_t* /*unused*/) noexcept - { - return is_object() ? m_value.object : nullptr; - } - - /// get a pointer to the value (object) - constexpr const object_t* get_impl_ptr(const object_t* /*unused*/) const noexcept - { - return is_object() ? m_value.object : nullptr; - } - - /// get a pointer to the value (array) - array_t* get_impl_ptr(array_t* /*unused*/) noexcept - { - return is_array() ? m_value.array : nullptr; - } - - /// get a pointer to the value (array) - constexpr const array_t* get_impl_ptr(const array_t* /*unused*/) const noexcept - { - return is_array() ? m_value.array : nullptr; - } - - /// get a pointer to the value (string) - string_t* get_impl_ptr(string_t* /*unused*/) noexcept - { - return is_string() ? m_value.string : nullptr; - } - - /// get a pointer to the value (string) - constexpr const string_t* get_impl_ptr(const string_t* /*unused*/) const noexcept - { - return is_string() ? m_value.string : nullptr; - } - - /// get a pointer to the value (boolean) - boolean_t* get_impl_ptr(boolean_t* /*unused*/) noexcept - { - return is_boolean() ? &m_value.boolean : nullptr; - } - - /// get a pointer to the value (boolean) - constexpr const boolean_t* get_impl_ptr(const boolean_t* /*unused*/) const noexcept - { - return is_boolean() ? &m_value.boolean : nullptr; - } - - /// get a pointer to the value (integer number) - number_integer_t* get_impl_ptr(number_integer_t* /*unused*/) noexcept - { - return is_number_integer() ? &m_value.number_integer : nullptr; - } - - /// get a pointer to the value (integer number) - constexpr const number_integer_t* get_impl_ptr(const number_integer_t* /*unused*/) const noexcept - { - return is_number_integer() ? &m_value.number_integer : nullptr; - } - - /// get a pointer to the value (unsigned number) - number_unsigned_t* get_impl_ptr(number_unsigned_t* /*unused*/) noexcept - { - return is_number_unsigned() ? &m_value.number_unsigned : nullptr; - } - - /// get a pointer to the value (unsigned number) - constexpr const number_unsigned_t* get_impl_ptr(const number_unsigned_t* /*unused*/) const noexcept - { - return is_number_unsigned() ? &m_value.number_unsigned : nullptr; - } - - /// get a pointer to the value (floating-point number) - number_float_t* get_impl_ptr(number_float_t* /*unused*/) noexcept - { - return is_number_float() ? &m_value.number_float : nullptr; - } - - /// get a pointer to the value (floating-point number) - constexpr const number_float_t* get_impl_ptr(const number_float_t* /*unused*/) const noexcept - { - return is_number_float() ? &m_value.number_float : nullptr; - } - - /// get a pointer to the value (binary) - binary_t* get_impl_ptr(binary_t* /*unused*/) noexcept - { - return is_binary() ? m_value.binary : nullptr; - } - - /// get a pointer to the value (binary) - constexpr const binary_t* get_impl_ptr(const binary_t* /*unused*/) const noexcept - { - return is_binary() ? m_value.binary : nullptr; - } - - /*! - @brief helper function to implement get_ref() - - This function helps to implement get_ref() without code duplication for - const and non-const overloads - - @tparam ThisType will be deduced as `basic_json` or `const basic_json` - - @throw type_error.303 if ReferenceType does not match underlying value - type of the current JSON - */ - template - static ReferenceType get_ref_impl(ThisType& obj) - { - // delegate the call to get_ptr<>() - auto ptr = obj.template get_ptr::type>(); - - if (JSON_HEDLEY_LIKELY(ptr != nullptr)) - { - return *ptr; - } - - JSON_THROW(type_error::create(303, "incompatible ReferenceType for get_ref, actual type is " + std::string(obj.type_name()))); - } - - public: - /// @name value access - /// Direct access to the stored value of a JSON value. - /// @{ - - /*! - @brief get special-case overload - - This overloads avoids a lot of template boilerplate, it can be seen as the - identity method - - @tparam BasicJsonType == @ref basic_json - - @return a copy of *this - - @complexity Constant. - - @since version 2.1.0 - */ - template::type, basic_json_t>::value, - int> = 0> - basic_json get() const - { - return *this; - } - - /*! - @brief get special-case overload - - This overloads converts the current @ref basic_json in a different - @ref basic_json type - - @tparam BasicJsonType == @ref basic_json - - @return a copy of *this, converted into @tparam BasicJsonType - - @complexity Depending on the implementation of the called `from_json()` - method. - - @since version 3.2.0 - */ - template < typename BasicJsonType, detail::enable_if_t < - !std::is_same::value&& - detail::is_basic_json::value, int > = 0 > - BasicJsonType get() const - { - return *this; - } - - /*! - @brief get a value (explicit) - - Explicit type conversion between the JSON value and a compatible value - which is [CopyConstructible](https://en.cppreference.com/w/cpp/named_req/CopyConstructible) - and [DefaultConstructible](https://en.cppreference.com/w/cpp/named_req/DefaultConstructible). - The value is converted by calling the @ref json_serializer - `from_json()` method. - - The function is equivalent to executing - @code {.cpp} - ValueType ret; - JSONSerializer::from_json(*this, ret); - return ret; - @endcode - - This overloads is chosen if: - - @a ValueType is not @ref basic_json, - - @ref json_serializer has a `from_json()` method of the form - `void from_json(const basic_json&, ValueType&)`, and - - @ref json_serializer does not have a `from_json()` method of - the form `ValueType from_json(const basic_json&)` - - @tparam ValueTypeCV the provided value type - @tparam ValueType the returned value type - - @return copy of the JSON value, converted to @a ValueType - - @throw what @ref json_serializer `from_json()` method throws - - @liveexample{The example below shows several conversions from JSON values - to other types. There a few things to note: (1) Floating-point numbers can - be converted to integers\, (2) A JSON array can be converted to a standard - `std::vector`\, (3) A JSON object can be converted to C++ - associative containers such as `std::unordered_map`.,get__ValueType_const} - - @since version 2.1.0 - */ - template < typename ValueTypeCV, typename ValueType = detail::uncvref_t, - detail::enable_if_t < - !detail::is_basic_json::value && - detail::has_from_json::value && - !detail::has_non_default_from_json::value, - int > = 0 > - ValueType get() const noexcept(noexcept( - JSONSerializer::from_json(std::declval(), std::declval()))) - { - // we cannot static_assert on ValueTypeCV being non-const, because - // there is support for get(), which is why we - // still need the uncvref - static_assert(!std::is_reference::value, - "get() cannot be used with reference types, you might want to use get_ref()"); - static_assert(std::is_default_constructible::value, - "types must be DefaultConstructible when used with get()"); - - ValueType ret; - JSONSerializer::from_json(*this, ret); - return ret; - } - - /*! - @brief get a value (explicit); special case - - Explicit type conversion between the JSON value and a compatible value - which is **not** [CopyConstructible](https://en.cppreference.com/w/cpp/named_req/CopyConstructible) - and **not** [DefaultConstructible](https://en.cppreference.com/w/cpp/named_req/DefaultConstructible). - The value is converted by calling the @ref json_serializer - `from_json()` method. - - The function is equivalent to executing - @code {.cpp} - return JSONSerializer::from_json(*this); - @endcode - - This overloads is chosen if: - - @a ValueType is not @ref basic_json and - - @ref json_serializer has a `from_json()` method of the form - `ValueType from_json(const basic_json&)` - - @note If @ref json_serializer has both overloads of - `from_json()`, this one is chosen. - - @tparam ValueTypeCV the provided value type - @tparam ValueType the returned value type - - @return copy of the JSON value, converted to @a ValueType - - @throw what @ref json_serializer `from_json()` method throws - - @since version 2.1.0 - */ - template < typename ValueTypeCV, typename ValueType = detail::uncvref_t, - detail::enable_if_t < !std::is_same::value && - detail::has_non_default_from_json::value, - int > = 0 > - ValueType get() const noexcept(noexcept( - JSONSerializer::from_json(std::declval()))) - { - static_assert(!std::is_reference::value, - "get() cannot be used with reference types, you might want to use get_ref()"); - return JSONSerializer::from_json(*this); - } - - /*! - @brief get a value (explicit) - - Explicit type conversion between the JSON value and a compatible value. - The value is filled into the input parameter by calling the @ref json_serializer - `from_json()` method. - - The function is equivalent to executing - @code {.cpp} - ValueType v; - JSONSerializer::from_json(*this, v); - @endcode - - This overloads is chosen if: - - @a ValueType is not @ref basic_json, - - @ref json_serializer has a `from_json()` method of the form - `void from_json(const basic_json&, ValueType&)`, and - - @tparam ValueType the input parameter type. - - @return the input parameter, allowing chaining calls. - - @throw what @ref json_serializer `from_json()` method throws - - @liveexample{The example below shows several conversions from JSON values - to other types. There a few things to note: (1) Floating-point numbers can - be converted to integers\, (2) A JSON array can be converted to a standard - `std::vector`\, (3) A JSON object can be converted to C++ - associative containers such as `std::unordered_map`.,get_to} - - @since version 3.3.0 - */ - template < typename ValueType, - detail::enable_if_t < - !detail::is_basic_json::value&& - detail::has_from_json::value, - int > = 0 > - ValueType & get_to(ValueType& v) const noexcept(noexcept( - JSONSerializer::from_json(std::declval(), v))) - { - JSONSerializer::from_json(*this, v); - return v; - } - - // specialization to allow to call get_to with a basic_json value - // see https://github.com/nlohmann/json/issues/2175 - template::value, - int> = 0> - ValueType & get_to(ValueType& v) const - { - v = *this; - return v; - } - - template < - typename T, std::size_t N, - typename Array = T (&)[N], - detail::enable_if_t < - detail::has_from_json::value, int > = 0 > - Array get_to(T (&v)[N]) const - noexcept(noexcept(JSONSerializer::from_json( - std::declval(), v))) - { - JSONSerializer::from_json(*this, v); - return v; - } - - - /*! - @brief get a pointer value (implicit) - - Implicit pointer access to the internally stored JSON value. No copies are - made. - - @warning Writing data to the pointee of the result yields an undefined - state. - - @tparam PointerType pointer type; must be a pointer to @ref array_t, @ref - object_t, @ref string_t, @ref boolean_t, @ref number_integer_t, - @ref number_unsigned_t, or @ref number_float_t. Enforced by a static - assertion. - - @return pointer to the internally stored JSON value if the requested - pointer type @a PointerType fits to the JSON value; `nullptr` otherwise - - @complexity Constant. - - @liveexample{The example below shows how pointers to internal values of a - JSON value can be requested. Note that no type conversions are made and a - `nullptr` is returned if the value and the requested pointer type does not - match.,get_ptr} - - @since version 1.0.0 - */ - template::value, int>::type = 0> - auto get_ptr() noexcept -> decltype(std::declval().get_impl_ptr(std::declval())) - { - // delegate the call to get_impl_ptr<>() - return get_impl_ptr(static_cast(nullptr)); - } - - /*! - @brief get a pointer value (implicit) - @copydoc get_ptr() - */ - template < typename PointerType, typename std::enable_if < - std::is_pointer::value&& - std::is_const::type>::value, int >::type = 0 > - constexpr auto get_ptr() const noexcept -> decltype(std::declval().get_impl_ptr(std::declval())) - { - // delegate the call to get_impl_ptr<>() const - return get_impl_ptr(static_cast(nullptr)); - } - - /*! - @brief get a pointer value (explicit) - - Explicit pointer access to the internally stored JSON value. No copies are - made. - - @warning The pointer becomes invalid if the underlying JSON object - changes. - - @tparam PointerType pointer type; must be a pointer to @ref array_t, @ref - object_t, @ref string_t, @ref boolean_t, @ref number_integer_t, - @ref number_unsigned_t, or @ref number_float_t. - - @return pointer to the internally stored JSON value if the requested - pointer type @a PointerType fits to the JSON value; `nullptr` otherwise - - @complexity Constant. - - @liveexample{The example below shows how pointers to internal values of a - JSON value can be requested. Note that no type conversions are made and a - `nullptr` is returned if the value and the requested pointer type does not - match.,get__PointerType} - - @sa @ref get_ptr() for explicit pointer-member access - - @since version 1.0.0 - */ - template::value, int>::type = 0> - auto get() noexcept -> decltype(std::declval().template get_ptr()) - { - // delegate the call to get_ptr - return get_ptr(); - } - - /*! - @brief get a pointer value (explicit) - @copydoc get() - */ - template::value, int>::type = 0> - constexpr auto get() const noexcept -> decltype(std::declval().template get_ptr()) - { - // delegate the call to get_ptr - return get_ptr(); - } - - /*! - @brief get a reference value (implicit) - - Implicit reference access to the internally stored JSON value. No copies - are made. - - @warning Writing data to the referee of the result yields an undefined - state. - - @tparam ReferenceType reference type; must be a reference to @ref array_t, - @ref object_t, @ref string_t, @ref boolean_t, @ref number_integer_t, or - @ref number_float_t. Enforced by static assertion. - - @return reference to the internally stored JSON value if the requested - reference type @a ReferenceType fits to the JSON value; throws - type_error.303 otherwise - - @throw type_error.303 in case passed type @a ReferenceType is incompatible - with the stored JSON value; see example below - - @complexity Constant. - - @liveexample{The example shows several calls to `get_ref()`.,get_ref} - - @since version 1.1.0 - */ - template::value, int>::type = 0> - ReferenceType get_ref() - { - // delegate call to get_ref_impl - return get_ref_impl(*this); - } - - /*! - @brief get a reference value (implicit) - @copydoc get_ref() - */ - template < typename ReferenceType, typename std::enable_if < - std::is_reference::value&& - std::is_const::type>::value, int >::type = 0 > - ReferenceType get_ref() const - { - // delegate call to get_ref_impl - return get_ref_impl(*this); - } - - /*! - @brief get a value (implicit) - - Implicit type conversion between the JSON value and a compatible value. - The call is realized by calling @ref get() const. - - @tparam ValueType non-pointer type compatible to the JSON value, for - instance `int` for JSON integer numbers, `bool` for JSON booleans, or - `std::vector` types for JSON arrays. The character type of @ref string_t - as well as an initializer list of this type is excluded to avoid - ambiguities as these types implicitly convert to `std::string`. - - @return copy of the JSON value, converted to type @a ValueType - - @throw type_error.302 in case passed type @a ValueType is incompatible - to the JSON value type (e.g., the JSON value is of type boolean, but a - string is requested); see example below - - @complexity Linear in the size of the JSON value. - - @liveexample{The example below shows several conversions from JSON values - to other types. There a few things to note: (1) Floating-point numbers can - be converted to integers\, (2) A JSON array can be converted to a standard - `std::vector`\, (3) A JSON object can be converted to C++ - associative containers such as `std::unordered_map`.,operator__ValueType} - - @since version 1.0.0 - */ - template < typename ValueType, typename std::enable_if < - !std::is_pointer::value&& - !std::is_same>::value&& - !std::is_same::value&& - !detail::is_basic_json::value - && !std::is_same>::value -#if defined(JSON_HAS_CPP_17) && (defined(__GNUC__) || (defined(_MSC_VER) && _MSC_VER >= 1910 && _MSC_VER <= 1914)) - && !std::is_same::value -#endif - && detail::is_detected::value - , int >::type = 0 > - JSON_EXPLICIT operator ValueType() const - { - // delegate the call to get<>() const - return get(); - } - - /*! - @return reference to the binary value - - @throw type_error.302 if the value is not binary - - @sa @ref is_binary() to check if the value is binary - - @since version 3.8.0 - */ - binary_t& get_binary() - { - if (!is_binary()) - { - JSON_THROW(type_error::create(302, "type must be binary, but is " + std::string(type_name()))); - } - - return *get_ptr(); - } - - /// @copydoc get_binary() - const binary_t& get_binary() const - { - if (!is_binary()) - { - JSON_THROW(type_error::create(302, "type must be binary, but is " + std::string(type_name()))); - } - - return *get_ptr(); - } - - /// @} - - - //////////////////// - // element access // - //////////////////// - - /// @name element access - /// Access to the JSON value. - /// @{ - - /*! - @brief access specified array element with bounds checking - - Returns a reference to the element at specified location @a idx, with - bounds checking. - - @param[in] idx index of the element to access - - @return reference to the element at index @a idx - - @throw type_error.304 if the JSON value is not an array; in this case, - calling `at` with an index makes no sense. See example below. - @throw out_of_range.401 if the index @a idx is out of range of the array; - that is, `idx >= size()`. See example below. - - @exceptionsafety Strong guarantee: if an exception is thrown, there are no - changes in the JSON value. - - @complexity Constant. - - @since version 1.0.0 - - @liveexample{The example below shows how array elements can be read and - written using `at()`. It also demonstrates the different exceptions that - can be thrown.,at__size_type} - */ - reference at(size_type idx) - { - // at only works for arrays - if (JSON_HEDLEY_LIKELY(is_array())) - { - JSON_TRY - { - return m_value.array->at(idx); - } - JSON_CATCH (std::out_of_range&) - { - // create better exception explanation - JSON_THROW(out_of_range::create(401, "array index " + std::to_string(idx) + " is out of range")); - } - } - else - { - JSON_THROW(type_error::create(304, "cannot use at() with " + std::string(type_name()))); - } - } - - /*! - @brief access specified array element with bounds checking - - Returns a const reference to the element at specified location @a idx, - with bounds checking. - - @param[in] idx index of the element to access - - @return const reference to the element at index @a idx - - @throw type_error.304 if the JSON value is not an array; in this case, - calling `at` with an index makes no sense. See example below. - @throw out_of_range.401 if the index @a idx is out of range of the array; - that is, `idx >= size()`. See example below. - - @exceptionsafety Strong guarantee: if an exception is thrown, there are no - changes in the JSON value. - - @complexity Constant. - - @since version 1.0.0 - - @liveexample{The example below shows how array elements can be read using - `at()`. It also demonstrates the different exceptions that can be thrown., - at__size_type_const} - */ - const_reference at(size_type idx) const - { - // at only works for arrays - if (JSON_HEDLEY_LIKELY(is_array())) - { - JSON_TRY - { - return m_value.array->at(idx); - } - JSON_CATCH (std::out_of_range&) - { - // create better exception explanation - JSON_THROW(out_of_range::create(401, "array index " + std::to_string(idx) + " is out of range")); - } - } - else - { - JSON_THROW(type_error::create(304, "cannot use at() with " + std::string(type_name()))); - } - } - - /*! - @brief access specified object element with bounds checking - - Returns a reference to the element at with specified key @a key, with - bounds checking. - - @param[in] key key of the element to access - - @return reference to the element at key @a key - - @throw type_error.304 if the JSON value is not an object; in this case, - calling `at` with a key makes no sense. See example below. - @throw out_of_range.403 if the key @a key is is not stored in the object; - that is, `find(key) == end()`. See example below. - - @exceptionsafety Strong guarantee: if an exception is thrown, there are no - changes in the JSON value. - - @complexity Logarithmic in the size of the container. - - @sa @ref operator[](const typename object_t::key_type&) for unchecked - access by reference - @sa @ref value() for access by value with a default value - - @since version 1.0.0 - - @liveexample{The example below shows how object elements can be read and - written using `at()`. It also demonstrates the different exceptions that - can be thrown.,at__object_t_key_type} - */ - reference at(const typename object_t::key_type& key) - { - // at only works for objects - if (JSON_HEDLEY_LIKELY(is_object())) - { - JSON_TRY - { - return m_value.object->at(key); - } - JSON_CATCH (std::out_of_range&) - { - // create better exception explanation - JSON_THROW(out_of_range::create(403, "key '" + key + "' not found")); - } - } - else - { - JSON_THROW(type_error::create(304, "cannot use at() with " + std::string(type_name()))); - } - } - - /*! - @brief access specified object element with bounds checking - - Returns a const reference to the element at with specified key @a key, - with bounds checking. - - @param[in] key key of the element to access - - @return const reference to the element at key @a key - - @throw type_error.304 if the JSON value is not an object; in this case, - calling `at` with a key makes no sense. See example below. - @throw out_of_range.403 if the key @a key is is not stored in the object; - that is, `find(key) == end()`. See example below. - - @exceptionsafety Strong guarantee: if an exception is thrown, there are no - changes in the JSON value. - - @complexity Logarithmic in the size of the container. - - @sa @ref operator[](const typename object_t::key_type&) for unchecked - access by reference - @sa @ref value() for access by value with a default value - - @since version 1.0.0 - - @liveexample{The example below shows how object elements can be read using - `at()`. It also demonstrates the different exceptions that can be thrown., - at__object_t_key_type_const} - */ - const_reference at(const typename object_t::key_type& key) const - { - // at only works for objects - if (JSON_HEDLEY_LIKELY(is_object())) - { - JSON_TRY - { - return m_value.object->at(key); - } - JSON_CATCH (std::out_of_range&) - { - // create better exception explanation - JSON_THROW(out_of_range::create(403, "key '" + key + "' not found")); - } - } - else - { - JSON_THROW(type_error::create(304, "cannot use at() with " + std::string(type_name()))); - } - } - - /*! - @brief access specified array element - - Returns a reference to the element at specified location @a idx. - - @note If @a idx is beyond the range of the array (i.e., `idx >= size()`), - then the array is silently filled up with `null` values to make `idx` a - valid reference to the last stored element. - - @param[in] idx index of the element to access - - @return reference to the element at index @a idx - - @throw type_error.305 if the JSON value is not an array or null; in that - cases, using the [] operator with an index makes no sense. - - @complexity Constant if @a idx is in the range of the array. Otherwise - linear in `idx - size()`. - - @liveexample{The example below shows how array elements can be read and - written using `[]` operator. Note the addition of `null` - values.,operatorarray__size_type} - - @since version 1.0.0 - */ - reference operator[](size_type idx) - { - // implicitly convert null value to an empty array - if (is_null()) - { - m_type = value_t::array; - m_value.array = create(); - assert_invariant(); - } - - // operator[] only works for arrays - if (JSON_HEDLEY_LIKELY(is_array())) - { - // fill up array with null values if given idx is outside range - if (idx >= m_value.array->size()) - { - m_value.array->insert(m_value.array->end(), - idx - m_value.array->size() + 1, - basic_json()); - } - - return m_value.array->operator[](idx); - } - - JSON_THROW(type_error::create(305, "cannot use operator[] with a numeric argument with " + std::string(type_name()))); - } - - /*! - @brief access specified array element - - Returns a const reference to the element at specified location @a idx. - - @param[in] idx index of the element to access - - @return const reference to the element at index @a idx - - @throw type_error.305 if the JSON value is not an array; in that case, - using the [] operator with an index makes no sense. - - @complexity Constant. - - @liveexample{The example below shows how array elements can be read using - the `[]` operator.,operatorarray__size_type_const} - - @since version 1.0.0 - */ - const_reference operator[](size_type idx) const - { - // const operator[] only works for arrays - if (JSON_HEDLEY_LIKELY(is_array())) - { - return m_value.array->operator[](idx); - } - - JSON_THROW(type_error::create(305, "cannot use operator[] with a numeric argument with " + std::string(type_name()))); - } - - /*! - @brief access specified object element - - Returns a reference to the element at with specified key @a key. - - @note If @a key is not found in the object, then it is silently added to - the object and filled with a `null` value to make `key` a valid reference. - In case the value was `null` before, it is converted to an object. - - @param[in] key key of the element to access - - @return reference to the element at key @a key - - @throw type_error.305 if the JSON value is not an object or null; in that - cases, using the [] operator with a key makes no sense. - - @complexity Logarithmic in the size of the container. - - @liveexample{The example below shows how object elements can be read and - written using the `[]` operator.,operatorarray__key_type} - - @sa @ref at(const typename object_t::key_type&) for access by reference - with range checking - @sa @ref value() for access by value with a default value - - @since version 1.0.0 - */ - reference operator[](const typename object_t::key_type& key) - { - // implicitly convert null value to an empty object - if (is_null()) - { - m_type = value_t::object; - m_value.object = create(); - assert_invariant(); - } - - // operator[] only works for objects - if (JSON_HEDLEY_LIKELY(is_object())) - { - return m_value.object->operator[](key); - } - - JSON_THROW(type_error::create(305, "cannot use operator[] with a string argument with " + std::string(type_name()))); - } - - /*! - @brief read-only access specified object element - - Returns a const reference to the element at with specified key @a key. No - bounds checking is performed. - - @warning If the element with key @a key does not exist, the behavior is - undefined. - - @param[in] key key of the element to access - - @return const reference to the element at key @a key - - @pre The element with key @a key must exist. **This precondition is - enforced with an assertion.** - - @throw type_error.305 if the JSON value is not an object; in that case, - using the [] operator with a key makes no sense. - - @complexity Logarithmic in the size of the container. - - @liveexample{The example below shows how object elements can be read using - the `[]` operator.,operatorarray__key_type_const} - - @sa @ref at(const typename object_t::key_type&) for access by reference - with range checking - @sa @ref value() for access by value with a default value - - @since version 1.0.0 - */ - const_reference operator[](const typename object_t::key_type& key) const - { - // const operator[] only works for objects - if (JSON_HEDLEY_LIKELY(is_object())) - { - JSON_ASSERT(m_value.object->find(key) != m_value.object->end()); - return m_value.object->find(key)->second; - } - - JSON_THROW(type_error::create(305, "cannot use operator[] with a string argument with " + std::string(type_name()))); - } - - /*! - @brief access specified object element - - Returns a reference to the element at with specified key @a key. - - @note If @a key is not found in the object, then it is silently added to - the object and filled with a `null` value to make `key` a valid reference. - In case the value was `null` before, it is converted to an object. - - @param[in] key key of the element to access - - @return reference to the element at key @a key - - @throw type_error.305 if the JSON value is not an object or null; in that - cases, using the [] operator with a key makes no sense. - - @complexity Logarithmic in the size of the container. - - @liveexample{The example below shows how object elements can be read and - written using the `[]` operator.,operatorarray__key_type} - - @sa @ref at(const typename object_t::key_type&) for access by reference - with range checking - @sa @ref value() for access by value with a default value - - @since version 1.1.0 - */ - template - JSON_HEDLEY_NON_NULL(2) - reference operator[](T* key) - { - // implicitly convert null to object - if (is_null()) - { - m_type = value_t::object; - m_value = value_t::object; - assert_invariant(); - } - - // at only works for objects - if (JSON_HEDLEY_LIKELY(is_object())) - { - return m_value.object->operator[](key); - } - - JSON_THROW(type_error::create(305, "cannot use operator[] with a string argument with " + std::string(type_name()))); - } - - /*! - @brief read-only access specified object element - - Returns a const reference to the element at with specified key @a key. No - bounds checking is performed. - - @warning If the element with key @a key does not exist, the behavior is - undefined. - - @param[in] key key of the element to access - - @return const reference to the element at key @a key - - @pre The element with key @a key must exist. **This precondition is - enforced with an assertion.** - - @throw type_error.305 if the JSON value is not an object; in that case, - using the [] operator with a key makes no sense. - - @complexity Logarithmic in the size of the container. - - @liveexample{The example below shows how object elements can be read using - the `[]` operator.,operatorarray__key_type_const} - - @sa @ref at(const typename object_t::key_type&) for access by reference - with range checking - @sa @ref value() for access by value with a default value - - @since version 1.1.0 - */ - template - JSON_HEDLEY_NON_NULL(2) - const_reference operator[](T* key) const - { - // at only works for objects - if (JSON_HEDLEY_LIKELY(is_object())) - { - JSON_ASSERT(m_value.object->find(key) != m_value.object->end()); - return m_value.object->find(key)->second; - } - - JSON_THROW(type_error::create(305, "cannot use operator[] with a string argument with " + std::string(type_name()))); - } - - /*! - @brief access specified object element with default value - - Returns either a copy of an object's element at the specified key @a key - or a given default value if no element with key @a key exists. - - The function is basically equivalent to executing - @code {.cpp} - try { - return at(key); - } catch(out_of_range) { - return default_value; - } - @endcode - - @note Unlike @ref at(const typename object_t::key_type&), this function - does not throw if the given key @a key was not found. - - @note Unlike @ref operator[](const typename object_t::key_type& key), this - function does not implicitly add an element to the position defined by @a - key. This function is furthermore also applicable to const objects. - - @param[in] key key of the element to access - @param[in] default_value the value to return if @a key is not found - - @tparam ValueType type compatible to JSON values, for instance `int` for - JSON integer numbers, `bool` for JSON booleans, or `std::vector` types for - JSON arrays. Note the type of the expected value at @a key and the default - value @a default_value must be compatible. - - @return copy of the element at key @a key or @a default_value if @a key - is not found - - @throw type_error.302 if @a default_value does not match the type of the - value at @a key - @throw type_error.306 if the JSON value is not an object; in that case, - using `value()` with a key makes no sense. - - @complexity Logarithmic in the size of the container. - - @liveexample{The example below shows how object elements can be queried - with a default value.,basic_json__value} - - @sa @ref at(const typename object_t::key_type&) for access by reference - with range checking - @sa @ref operator[](const typename object_t::key_type&) for unchecked - access by reference - - @since version 1.0.0 - */ - // using std::is_convertible in a std::enable_if will fail when using explicit conversions - template < class ValueType, typename std::enable_if < - detail::is_getable::value - && !std::is_same::value, int >::type = 0 > - ValueType value(const typename object_t::key_type& key, const ValueType& default_value) const - { - // at only works for objects - if (JSON_HEDLEY_LIKELY(is_object())) - { - // if key is found, return value and given default value otherwise - const auto it = find(key); - if (it != end()) - { - return it->template get(); - } - - return default_value; - } - - JSON_THROW(type_error::create(306, "cannot use value() with " + std::string(type_name()))); - } - - /*! - @brief overload for a default value of type const char* - @copydoc basic_json::value(const typename object_t::key_type&, const ValueType&) const - */ - string_t value(const typename object_t::key_type& key, const char* default_value) const - { - return value(key, string_t(default_value)); - } - - /*! - @brief access specified object element via JSON Pointer with default value - - Returns either a copy of an object's element at the specified key @a key - or a given default value if no element with key @a key exists. - - The function is basically equivalent to executing - @code {.cpp} - try { - return at(ptr); - } catch(out_of_range) { - return default_value; - } - @endcode - - @note Unlike @ref at(const json_pointer&), this function does not throw - if the given key @a key was not found. - - @param[in] ptr a JSON pointer to the element to access - @param[in] default_value the value to return if @a ptr found no value - - @tparam ValueType type compatible to JSON values, for instance `int` for - JSON integer numbers, `bool` for JSON booleans, or `std::vector` types for - JSON arrays. Note the type of the expected value at @a key and the default - value @a default_value must be compatible. - - @return copy of the element at key @a key or @a default_value if @a key - is not found - - @throw type_error.302 if @a default_value does not match the type of the - value at @a ptr - @throw type_error.306 if the JSON value is not an object; in that case, - using `value()` with a key makes no sense. - - @complexity Logarithmic in the size of the container. - - @liveexample{The example below shows how object elements can be queried - with a default value.,basic_json__value_ptr} - - @sa @ref operator[](const json_pointer&) for unchecked access by reference - - @since version 2.0.2 - */ - template::value, int>::type = 0> - ValueType value(const json_pointer& ptr, const ValueType& default_value) const - { - // at only works for objects - if (JSON_HEDLEY_LIKELY(is_object())) - { - // if pointer resolves a value, return it or use default value - JSON_TRY - { - return ptr.get_checked(this).template get(); - } - JSON_INTERNAL_CATCH (out_of_range&) - { - return default_value; - } - } - - JSON_THROW(type_error::create(306, "cannot use value() with " + std::string(type_name()))); - } - - /*! - @brief overload for a default value of type const char* - @copydoc basic_json::value(const json_pointer&, ValueType) const - */ - JSON_HEDLEY_NON_NULL(3) - string_t value(const json_pointer& ptr, const char* default_value) const - { - return value(ptr, string_t(default_value)); - } - - /*! - @brief access the first element - - Returns a reference to the first element in the container. For a JSON - container `c`, the expression `c.front()` is equivalent to `*c.begin()`. - - @return In case of a structured type (array or object), a reference to the - first element is returned. In case of number, string, boolean, or binary - values, a reference to the value is returned. - - @complexity Constant. - - @pre The JSON value must not be `null` (would throw `std::out_of_range`) - or an empty array or object (undefined behavior, **guarded by - assertions**). - @post The JSON value remains unchanged. - - @throw invalid_iterator.214 when called on `null` value - - @liveexample{The following code shows an example for `front()`.,front} - - @sa @ref back() -- access the last element - - @since version 1.0.0 - */ - reference front() - { - return *begin(); - } - - /*! - @copydoc basic_json::front() - */ - const_reference front() const - { - return *cbegin(); - } - - /*! - @brief access the last element - - Returns a reference to the last element in the container. For a JSON - container `c`, the expression `c.back()` is equivalent to - @code {.cpp} - auto tmp = c.end(); - --tmp; - return *tmp; - @endcode - - @return In case of a structured type (array or object), a reference to the - last element is returned. In case of number, string, boolean, or binary - values, a reference to the value is returned. - - @complexity Constant. - - @pre The JSON value must not be `null` (would throw `std::out_of_range`) - or an empty array or object (undefined behavior, **guarded by - assertions**). - @post The JSON value remains unchanged. - - @throw invalid_iterator.214 when called on a `null` value. See example - below. - - @liveexample{The following code shows an example for `back()`.,back} - - @sa @ref front() -- access the first element - - @since version 1.0.0 - */ - reference back() - { - auto tmp = end(); - --tmp; - return *tmp; - } - - /*! - @copydoc basic_json::back() - */ - const_reference back() const - { - auto tmp = cend(); - --tmp; - return *tmp; - } - - /*! - @brief remove element given an iterator - - Removes the element specified by iterator @a pos. The iterator @a pos must - be valid and dereferenceable. Thus the `end()` iterator (which is valid, - but is not dereferenceable) cannot be used as a value for @a pos. - - If called on a primitive type other than `null`, the resulting JSON value - will be `null`. - - @param[in] pos iterator to the element to remove - @return Iterator following the last removed element. If the iterator @a - pos refers to the last element, the `end()` iterator is returned. - - @tparam IteratorType an @ref iterator or @ref const_iterator - - @post Invalidates iterators and references at or after the point of the - erase, including the `end()` iterator. - - @throw type_error.307 if called on a `null` value; example: `"cannot use - erase() with null"` - @throw invalid_iterator.202 if called on an iterator which does not belong - to the current JSON value; example: `"iterator does not fit current - value"` - @throw invalid_iterator.205 if called on a primitive type with invalid - iterator (i.e., any iterator which is not `begin()`); example: `"iterator - out of range"` - - @complexity The complexity depends on the type: - - objects: amortized constant - - arrays: linear in distance between @a pos and the end of the container - - strings and binary: linear in the length of the member - - other types: constant - - @liveexample{The example shows the result of `erase()` for different JSON - types.,erase__IteratorType} - - @sa @ref erase(IteratorType, IteratorType) -- removes the elements in - the given range - @sa @ref erase(const typename object_t::key_type&) -- removes the element - from an object at the given key - @sa @ref erase(const size_type) -- removes the element from an array at - the given index - - @since version 1.0.0 - */ - template < class IteratorType, typename std::enable_if < - std::is_same::value || - std::is_same::value, int >::type - = 0 > - IteratorType erase(IteratorType pos) - { - // make sure iterator fits the current value - if (JSON_HEDLEY_UNLIKELY(this != pos.m_object)) - { - JSON_THROW(invalid_iterator::create(202, "iterator does not fit current value")); - } - - IteratorType result = end(); - - switch (m_type) - { - case value_t::boolean: - case value_t::number_float: - case value_t::number_integer: - case value_t::number_unsigned: - case value_t::string: - case value_t::binary: - { - if (JSON_HEDLEY_UNLIKELY(!pos.m_it.primitive_iterator.is_begin())) - { - JSON_THROW(invalid_iterator::create(205, "iterator out of range")); - } - - if (is_string()) - { - AllocatorType alloc; - std::allocator_traits::destroy(alloc, m_value.string); - std::allocator_traits::deallocate(alloc, m_value.string, 1); - m_value.string = nullptr; - } - else if (is_binary()) - { - AllocatorType alloc; - std::allocator_traits::destroy(alloc, m_value.binary); - std::allocator_traits::deallocate(alloc, m_value.binary, 1); - m_value.binary = nullptr; - } - - m_type = value_t::null; - assert_invariant(); - break; - } - - case value_t::object: - { - result.m_it.object_iterator = m_value.object->erase(pos.m_it.object_iterator); - break; - } - - case value_t::array: - { - result.m_it.array_iterator = m_value.array->erase(pos.m_it.array_iterator); - break; - } - - default: - JSON_THROW(type_error::create(307, "cannot use erase() with " + std::string(type_name()))); - } - - return result; - } - - /*! - @brief remove elements given an iterator range - - Removes the element specified by the range `[first; last)`. The iterator - @a first does not need to be dereferenceable if `first == last`: erasing - an empty range is a no-op. - - If called on a primitive type other than `null`, the resulting JSON value - will be `null`. - - @param[in] first iterator to the beginning of the range to remove - @param[in] last iterator past the end of the range to remove - @return Iterator following the last removed element. If the iterator @a - second refers to the last element, the `end()` iterator is returned. - - @tparam IteratorType an @ref iterator or @ref const_iterator - - @post Invalidates iterators and references at or after the point of the - erase, including the `end()` iterator. - - @throw type_error.307 if called on a `null` value; example: `"cannot use - erase() with null"` - @throw invalid_iterator.203 if called on iterators which does not belong - to the current JSON value; example: `"iterators do not fit current value"` - @throw invalid_iterator.204 if called on a primitive type with invalid - iterators (i.e., if `first != begin()` and `last != end()`); example: - `"iterators out of range"` - - @complexity The complexity depends on the type: - - objects: `log(size()) + std::distance(first, last)` - - arrays: linear in the distance between @a first and @a last, plus linear - in the distance between @a last and end of the container - - strings and binary: linear in the length of the member - - other types: constant - - @liveexample{The example shows the result of `erase()` for different JSON - types.,erase__IteratorType_IteratorType} - - @sa @ref erase(IteratorType) -- removes the element at a given position - @sa @ref erase(const typename object_t::key_type&) -- removes the element - from an object at the given key - @sa @ref erase(const size_type) -- removes the element from an array at - the given index - - @since version 1.0.0 - */ - template < class IteratorType, typename std::enable_if < - std::is_same::value || - std::is_same::value, int >::type - = 0 > - IteratorType erase(IteratorType first, IteratorType last) - { - // make sure iterator fits the current value - if (JSON_HEDLEY_UNLIKELY(this != first.m_object || this != last.m_object)) - { - JSON_THROW(invalid_iterator::create(203, "iterators do not fit current value")); - } - - IteratorType result = end(); - - switch (m_type) - { - case value_t::boolean: - case value_t::number_float: - case value_t::number_integer: - case value_t::number_unsigned: - case value_t::string: - case value_t::binary: - { - if (JSON_HEDLEY_LIKELY(!first.m_it.primitive_iterator.is_begin() - || !last.m_it.primitive_iterator.is_end())) - { - JSON_THROW(invalid_iterator::create(204, "iterators out of range")); - } - - if (is_string()) - { - AllocatorType alloc; - std::allocator_traits::destroy(alloc, m_value.string); - std::allocator_traits::deallocate(alloc, m_value.string, 1); - m_value.string = nullptr; - } - else if (is_binary()) - { - AllocatorType alloc; - std::allocator_traits::destroy(alloc, m_value.binary); - std::allocator_traits::deallocate(alloc, m_value.binary, 1); - m_value.binary = nullptr; - } - - m_type = value_t::null; - assert_invariant(); - break; - } - - case value_t::object: - { - result.m_it.object_iterator = m_value.object->erase(first.m_it.object_iterator, - last.m_it.object_iterator); - break; - } - - case value_t::array: - { - result.m_it.array_iterator = m_value.array->erase(first.m_it.array_iterator, - last.m_it.array_iterator); - break; - } - - default: - JSON_THROW(type_error::create(307, "cannot use erase() with " + std::string(type_name()))); - } - - return result; - } - - /*! - @brief remove element from a JSON object given a key - - Removes elements from a JSON object with the key value @a key. - - @param[in] key value of the elements to remove - - @return Number of elements removed. If @a ObjectType is the default - `std::map` type, the return value will always be `0` (@a key was not - found) or `1` (@a key was found). - - @post References and iterators to the erased elements are invalidated. - Other references and iterators are not affected. - - @throw type_error.307 when called on a type other than JSON object; - example: `"cannot use erase() with null"` - - @complexity `log(size()) + count(key)` - - @liveexample{The example shows the effect of `erase()`.,erase__key_type} - - @sa @ref erase(IteratorType) -- removes the element at a given position - @sa @ref erase(IteratorType, IteratorType) -- removes the elements in - the given range - @sa @ref erase(const size_type) -- removes the element from an array at - the given index - - @since version 1.0.0 - */ - size_type erase(const typename object_t::key_type& key) - { - // this erase only works for objects - if (JSON_HEDLEY_LIKELY(is_object())) - { - return m_value.object->erase(key); - } - - JSON_THROW(type_error::create(307, "cannot use erase() with " + std::string(type_name()))); - } - - /*! - @brief remove element from a JSON array given an index - - Removes element from a JSON array at the index @a idx. - - @param[in] idx index of the element to remove - - @throw type_error.307 when called on a type other than JSON object; - example: `"cannot use erase() with null"` - @throw out_of_range.401 when `idx >= size()`; example: `"array index 17 - is out of range"` - - @complexity Linear in distance between @a idx and the end of the container. - - @liveexample{The example shows the effect of `erase()`.,erase__size_type} - - @sa @ref erase(IteratorType) -- removes the element at a given position - @sa @ref erase(IteratorType, IteratorType) -- removes the elements in - the given range - @sa @ref erase(const typename object_t::key_type&) -- removes the element - from an object at the given key - - @since version 1.0.0 - */ - void erase(const size_type idx) - { - // this erase only works for arrays - if (JSON_HEDLEY_LIKELY(is_array())) - { - if (JSON_HEDLEY_UNLIKELY(idx >= size())) - { - JSON_THROW(out_of_range::create(401, "array index " + std::to_string(idx) + " is out of range")); - } - - m_value.array->erase(m_value.array->begin() + static_cast(idx)); - } - else - { - JSON_THROW(type_error::create(307, "cannot use erase() with " + std::string(type_name()))); - } - } - - /// @} - - - //////////// - // lookup // - //////////// - - /// @name lookup - /// @{ - - /*! - @brief find an element in a JSON object - - Finds an element in a JSON object with key equivalent to @a key. If the - element is not found or the JSON value is not an object, end() is - returned. - - @note This method always returns @ref end() when executed on a JSON type - that is not an object. - - @param[in] key key value of the element to search for. - - @return Iterator to an element with key equivalent to @a key. If no such - element is found or the JSON value is not an object, past-the-end (see - @ref end()) iterator is returned. - - @complexity Logarithmic in the size of the JSON object. - - @liveexample{The example shows how `find()` is used.,find__key_type} - - @sa @ref contains(KeyT&&) const -- checks whether a key exists - - @since version 1.0.0 - */ - template - iterator find(KeyT&& key) - { - auto result = end(); - - if (is_object()) - { - result.m_it.object_iterator = m_value.object->find(std::forward(key)); - } - - return result; - } - - /*! - @brief find an element in a JSON object - @copydoc find(KeyT&&) - */ - template - const_iterator find(KeyT&& key) const - { - auto result = cend(); - - if (is_object()) - { - result.m_it.object_iterator = m_value.object->find(std::forward(key)); - } - - return result; - } - - /*! - @brief returns the number of occurrences of a key in a JSON object - - Returns the number of elements with key @a key. If ObjectType is the - default `std::map` type, the return value will always be `0` (@a key was - not found) or `1` (@a key was found). - - @note This method always returns `0` when executed on a JSON type that is - not an object. - - @param[in] key key value of the element to count - - @return Number of elements with key @a key. If the JSON value is not an - object, the return value will be `0`. - - @complexity Logarithmic in the size of the JSON object. - - @liveexample{The example shows how `count()` is used.,count} - - @since version 1.0.0 - */ - template - size_type count(KeyT&& key) const - { - // return 0 for all nonobject types - return is_object() ? m_value.object->count(std::forward(key)) : 0; - } - - /*! - @brief check the existence of an element in a JSON object - - Check whether an element exists in a JSON object with key equivalent to - @a key. If the element is not found or the JSON value is not an object, - false is returned. - - @note This method always returns false when executed on a JSON type - that is not an object. - - @param[in] key key value to check its existence. - - @return true if an element with specified @a key exists. If no such - element with such key is found or the JSON value is not an object, - false is returned. - - @complexity Logarithmic in the size of the JSON object. - - @liveexample{The following code shows an example for `contains()`.,contains} - - @sa @ref find(KeyT&&) -- returns an iterator to an object element - @sa @ref contains(const json_pointer&) const -- checks the existence for a JSON pointer - - @since version 3.6.0 - */ - template < typename KeyT, typename std::enable_if < - !std::is_same::type, json_pointer>::value, int >::type = 0 > - bool contains(KeyT && key) const - { - return is_object() && m_value.object->find(std::forward(key)) != m_value.object->end(); - } - - /*! - @brief check the existence of an element in a JSON object given a JSON pointer - - Check whether the given JSON pointer @a ptr can be resolved in the current - JSON value. - - @note This method can be executed on any JSON value type. - - @param[in] ptr JSON pointer to check its existence. - - @return true if the JSON pointer can be resolved to a stored value, false - otherwise. - - @post If `j.contains(ptr)` returns true, it is safe to call `j[ptr]`. - - @throw parse_error.106 if an array index begins with '0' - @throw parse_error.109 if an array index was not a number - - @complexity Logarithmic in the size of the JSON object. - - @liveexample{The following code shows an example for `contains()`.,contains_json_pointer} - - @sa @ref contains(KeyT &&) const -- checks the existence of a key - - @since version 3.7.0 - */ - bool contains(const json_pointer& ptr) const - { - return ptr.contains(this); - } - - /// @} - - - /////////////// - // iterators // - /////////////// - - /// @name iterators - /// @{ - - /*! - @brief returns an iterator to the first element - - Returns an iterator to the first element. - - @image html range-begin-end.svg "Illustration from cppreference.com" - - @return iterator to the first element - - @complexity Constant. - - @requirement This function helps `basic_json` satisfying the - [Container](https://en.cppreference.com/w/cpp/named_req/Container) - requirements: - - The complexity is constant. - - @liveexample{The following code shows an example for `begin()`.,begin} - - @sa @ref cbegin() -- returns a const iterator to the beginning - @sa @ref end() -- returns an iterator to the end - @sa @ref cend() -- returns a const iterator to the end - - @since version 1.0.0 - */ - iterator begin() noexcept - { - iterator result(this); - result.set_begin(); - return result; - } - - /*! - @copydoc basic_json::cbegin() - */ - const_iterator begin() const noexcept - { - return cbegin(); - } - - /*! - @brief returns a const iterator to the first element - - Returns a const iterator to the first element. - - @image html range-begin-end.svg "Illustration from cppreference.com" - - @return const iterator to the first element - - @complexity Constant. - - @requirement This function helps `basic_json` satisfying the - [Container](https://en.cppreference.com/w/cpp/named_req/Container) - requirements: - - The complexity is constant. - - Has the semantics of `const_cast(*this).begin()`. - - @liveexample{The following code shows an example for `cbegin()`.,cbegin} - - @sa @ref begin() -- returns an iterator to the beginning - @sa @ref end() -- returns an iterator to the end - @sa @ref cend() -- returns a const iterator to the end - - @since version 1.0.0 - */ - const_iterator cbegin() const noexcept - { - const_iterator result(this); - result.set_begin(); - return result; - } - - /*! - @brief returns an iterator to one past the last element - - Returns an iterator to one past the last element. - - @image html range-begin-end.svg "Illustration from cppreference.com" - - @return iterator one past the last element - - @complexity Constant. - - @requirement This function helps `basic_json` satisfying the - [Container](https://en.cppreference.com/w/cpp/named_req/Container) - requirements: - - The complexity is constant. - - @liveexample{The following code shows an example for `end()`.,end} - - @sa @ref cend() -- returns a const iterator to the end - @sa @ref begin() -- returns an iterator to the beginning - @sa @ref cbegin() -- returns a const iterator to the beginning - - @since version 1.0.0 - */ - iterator end() noexcept - { - iterator result(this); - result.set_end(); - return result; - } - - /*! - @copydoc basic_json::cend() - */ - const_iterator end() const noexcept - { - return cend(); - } - - /*! - @brief returns a const iterator to one past the last element - - Returns a const iterator to one past the last element. - - @image html range-begin-end.svg "Illustration from cppreference.com" - - @return const iterator one past the last element - - @complexity Constant. - - @requirement This function helps `basic_json` satisfying the - [Container](https://en.cppreference.com/w/cpp/named_req/Container) - requirements: - - The complexity is constant. - - Has the semantics of `const_cast(*this).end()`. - - @liveexample{The following code shows an example for `cend()`.,cend} - - @sa @ref end() -- returns an iterator to the end - @sa @ref begin() -- returns an iterator to the beginning - @sa @ref cbegin() -- returns a const iterator to the beginning - - @since version 1.0.0 - */ - const_iterator cend() const noexcept - { - const_iterator result(this); - result.set_end(); - return result; - } - - /*! - @brief returns an iterator to the reverse-beginning - - Returns an iterator to the reverse-beginning; that is, the last element. - - @image html range-rbegin-rend.svg "Illustration from cppreference.com" - - @complexity Constant. - - @requirement This function helps `basic_json` satisfying the - [ReversibleContainer](https://en.cppreference.com/w/cpp/named_req/ReversibleContainer) - requirements: - - The complexity is constant. - - Has the semantics of `reverse_iterator(end())`. - - @liveexample{The following code shows an example for `rbegin()`.,rbegin} - - @sa @ref crbegin() -- returns a const reverse iterator to the beginning - @sa @ref rend() -- returns a reverse iterator to the end - @sa @ref crend() -- returns a const reverse iterator to the end - - @since version 1.0.0 - */ - reverse_iterator rbegin() noexcept - { - return reverse_iterator(end()); - } - - /*! - @copydoc basic_json::crbegin() - */ - const_reverse_iterator rbegin() const noexcept - { - return crbegin(); - } - - /*! - @brief returns an iterator to the reverse-end - - Returns an iterator to the reverse-end; that is, one before the first - element. - - @image html range-rbegin-rend.svg "Illustration from cppreference.com" - - @complexity Constant. - - @requirement This function helps `basic_json` satisfying the - [ReversibleContainer](https://en.cppreference.com/w/cpp/named_req/ReversibleContainer) - requirements: - - The complexity is constant. - - Has the semantics of `reverse_iterator(begin())`. - - @liveexample{The following code shows an example for `rend()`.,rend} - - @sa @ref crend() -- returns a const reverse iterator to the end - @sa @ref rbegin() -- returns a reverse iterator to the beginning - @sa @ref crbegin() -- returns a const reverse iterator to the beginning - - @since version 1.0.0 - */ - reverse_iterator rend() noexcept - { - return reverse_iterator(begin()); - } - - /*! - @copydoc basic_json::crend() - */ - const_reverse_iterator rend() const noexcept - { - return crend(); - } - - /*! - @brief returns a const reverse iterator to the last element - - Returns a const iterator to the reverse-beginning; that is, the last - element. - - @image html range-rbegin-rend.svg "Illustration from cppreference.com" - - @complexity Constant. - - @requirement This function helps `basic_json` satisfying the - [ReversibleContainer](https://en.cppreference.com/w/cpp/named_req/ReversibleContainer) - requirements: - - The complexity is constant. - - Has the semantics of `const_cast(*this).rbegin()`. - - @liveexample{The following code shows an example for `crbegin()`.,crbegin} - - @sa @ref rbegin() -- returns a reverse iterator to the beginning - @sa @ref rend() -- returns a reverse iterator to the end - @sa @ref crend() -- returns a const reverse iterator to the end - - @since version 1.0.0 - */ - const_reverse_iterator crbegin() const noexcept - { - return const_reverse_iterator(cend()); - } - - /*! - @brief returns a const reverse iterator to one before the first - - Returns a const reverse iterator to the reverse-end; that is, one before - the first element. - - @image html range-rbegin-rend.svg "Illustration from cppreference.com" - - @complexity Constant. - - @requirement This function helps `basic_json` satisfying the - [ReversibleContainer](https://en.cppreference.com/w/cpp/named_req/ReversibleContainer) - requirements: - - The complexity is constant. - - Has the semantics of `const_cast(*this).rend()`. - - @liveexample{The following code shows an example for `crend()`.,crend} - - @sa @ref rend() -- returns a reverse iterator to the end - @sa @ref rbegin() -- returns a reverse iterator to the beginning - @sa @ref crbegin() -- returns a const reverse iterator to the beginning - - @since version 1.0.0 - */ - const_reverse_iterator crend() const noexcept - { - return const_reverse_iterator(cbegin()); - } - - public: - /*! - @brief wrapper to access iterator member functions in range-based for - - This function allows to access @ref iterator::key() and @ref - iterator::value() during range-based for loops. In these loops, a - reference to the JSON values is returned, so there is no access to the - underlying iterator. - - For loop without iterator_wrapper: - - @code{cpp} - for (auto it = j_object.begin(); it != j_object.end(); ++it) - { - std::cout << "key: " << it.key() << ", value:" << it.value() << '\n'; - } - @endcode - - Range-based for loop without iterator proxy: - - @code{cpp} - for (auto it : j_object) - { - // "it" is of type json::reference and has no key() member - std::cout << "value: " << it << '\n'; - } - @endcode - - Range-based for loop with iterator proxy: - - @code{cpp} - for (auto it : json::iterator_wrapper(j_object)) - { - std::cout << "key: " << it.key() << ", value:" << it.value() << '\n'; - } - @endcode - - @note When iterating over an array, `key()` will return the index of the - element as string (see example). - - @param[in] ref reference to a JSON value - @return iteration proxy object wrapping @a ref with an interface to use in - range-based for loops - - @liveexample{The following code shows how the wrapper is used,iterator_wrapper} - - @exceptionsafety Strong guarantee: if an exception is thrown, there are no - changes in the JSON value. - - @complexity Constant. - - @note The name of this function is not yet final and may change in the - future. - - @deprecated This stream operator is deprecated and will be removed in - future 4.0.0 of the library. Please use @ref items() instead; - that is, replace `json::iterator_wrapper(j)` with `j.items()`. - */ - JSON_HEDLEY_DEPRECATED_FOR(3.1.0, items()) - static iteration_proxy iterator_wrapper(reference ref) noexcept - { - return ref.items(); - } - - /*! - @copydoc iterator_wrapper(reference) - */ - JSON_HEDLEY_DEPRECATED_FOR(3.1.0, items()) - static iteration_proxy iterator_wrapper(const_reference ref) noexcept - { - return ref.items(); - } - - /*! - @brief helper to access iterator member functions in range-based for - - This function allows to access @ref iterator::key() and @ref - iterator::value() during range-based for loops. In these loops, a - reference to the JSON values is returned, so there is no access to the - underlying iterator. - - For loop without `items()` function: - - @code{cpp} - for (auto it = j_object.begin(); it != j_object.end(); ++it) - { - std::cout << "key: " << it.key() << ", value:" << it.value() << '\n'; - } - @endcode - - Range-based for loop without `items()` function: - - @code{cpp} - for (auto it : j_object) - { - // "it" is of type json::reference and has no key() member - std::cout << "value: " << it << '\n'; - } - @endcode - - Range-based for loop with `items()` function: - - @code{cpp} - for (auto& el : j_object.items()) - { - std::cout << "key: " << el.key() << ", value:" << el.value() << '\n'; - } - @endcode - - The `items()` function also allows to use - [structured bindings](https://en.cppreference.com/w/cpp/language/structured_binding) - (C++17): - - @code{cpp} - for (auto& [key, val] : j_object.items()) - { - std::cout << "key: " << key << ", value:" << val << '\n'; - } - @endcode - - @note When iterating over an array, `key()` will return the index of the - element as string (see example). For primitive types (e.g., numbers), - `key()` returns an empty string. - - @warning Using `items()` on temporary objects is dangerous. Make sure the - object's lifetime exeeds the iteration. See - for more - information. - - @return iteration proxy object wrapping @a ref with an interface to use in - range-based for loops - - @liveexample{The following code shows how the function is used.,items} - - @exceptionsafety Strong guarantee: if an exception is thrown, there are no - changes in the JSON value. - - @complexity Constant. - - @since version 3.1.0, structured bindings support since 3.5.0. - */ - iteration_proxy items() noexcept - { - return iteration_proxy(*this); - } - - /*! - @copydoc items() - */ - iteration_proxy items() const noexcept - { - return iteration_proxy(*this); - } - - /// @} - - - ////////////// - // capacity // - ////////////// - - /// @name capacity - /// @{ - - /*! - @brief checks whether the container is empty. - - Checks if a JSON value has no elements (i.e. whether its @ref size is `0`). - - @return The return value depends on the different types and is - defined as follows: - Value type | return value - ----------- | ------------- - null | `true` - boolean | `false` - string | `false` - number | `false` - binary | `false` - object | result of function `object_t::empty()` - array | result of function `array_t::empty()` - - @liveexample{The following code uses `empty()` to check if a JSON - object contains any elements.,empty} - - @complexity Constant, as long as @ref array_t and @ref object_t satisfy - the Container concept; that is, their `empty()` functions have constant - complexity. - - @iterators No changes. - - @exceptionsafety No-throw guarantee: this function never throws exceptions. - - @note This function does not return whether a string stored as JSON value - is empty - it returns whether the JSON container itself is empty which is - false in the case of a string. - - @requirement This function helps `basic_json` satisfying the - [Container](https://en.cppreference.com/w/cpp/named_req/Container) - requirements: - - The complexity is constant. - - Has the semantics of `begin() == end()`. - - @sa @ref size() -- returns the number of elements - - @since version 1.0.0 - */ - bool empty() const noexcept - { - switch (m_type) - { - case value_t::null: - { - // null values are empty - return true; - } - - case value_t::array: - { - // delegate call to array_t::empty() - return m_value.array->empty(); - } - - case value_t::object: - { - // delegate call to object_t::empty() - return m_value.object->empty(); - } - - default: - { - // all other types are nonempty - return false; - } - } - } - - /*! - @brief returns the number of elements - - Returns the number of elements in a JSON value. - - @return The return value depends on the different types and is - defined as follows: - Value type | return value - ----------- | ------------- - null | `0` - boolean | `1` - string | `1` - number | `1` - binary | `1` - object | result of function object_t::size() - array | result of function array_t::size() - - @liveexample{The following code calls `size()` on the different value - types.,size} - - @complexity Constant, as long as @ref array_t and @ref object_t satisfy - the Container concept; that is, their size() functions have constant - complexity. - - @iterators No changes. - - @exceptionsafety No-throw guarantee: this function never throws exceptions. - - @note This function does not return the length of a string stored as JSON - value - it returns the number of elements in the JSON value which is 1 in - the case of a string. - - @requirement This function helps `basic_json` satisfying the - [Container](https://en.cppreference.com/w/cpp/named_req/Container) - requirements: - - The complexity is constant. - - Has the semantics of `std::distance(begin(), end())`. - - @sa @ref empty() -- checks whether the container is empty - @sa @ref max_size() -- returns the maximal number of elements - - @since version 1.0.0 - */ - size_type size() const noexcept - { - switch (m_type) - { - case value_t::null: - { - // null values are empty - return 0; - } - - case value_t::array: - { - // delegate call to array_t::size() - return m_value.array->size(); - } - - case value_t::object: - { - // delegate call to object_t::size() - return m_value.object->size(); - } - - default: - { - // all other types have size 1 - return 1; - } - } - } - - /*! - @brief returns the maximum possible number of elements - - Returns the maximum number of elements a JSON value is able to hold due to - system or library implementation limitations, i.e. `std::distance(begin(), - end())` for the JSON value. - - @return The return value depends on the different types and is - defined as follows: - Value type | return value - ----------- | ------------- - null | `0` (same as `size()`) - boolean | `1` (same as `size()`) - string | `1` (same as `size()`) - number | `1` (same as `size()`) - binary | `1` (same as `size()`) - object | result of function `object_t::max_size()` - array | result of function `array_t::max_size()` - - @liveexample{The following code calls `max_size()` on the different value - types. Note the output is implementation specific.,max_size} - - @complexity Constant, as long as @ref array_t and @ref object_t satisfy - the Container concept; that is, their `max_size()` functions have constant - complexity. - - @iterators No changes. - - @exceptionsafety No-throw guarantee: this function never throws exceptions. - - @requirement This function helps `basic_json` satisfying the - [Container](https://en.cppreference.com/w/cpp/named_req/Container) - requirements: - - The complexity is constant. - - Has the semantics of returning `b.size()` where `b` is the largest - possible JSON value. - - @sa @ref size() -- returns the number of elements - - @since version 1.0.0 - */ - size_type max_size() const noexcept - { - switch (m_type) - { - case value_t::array: - { - // delegate call to array_t::max_size() - return m_value.array->max_size(); - } - - case value_t::object: - { - // delegate call to object_t::max_size() - return m_value.object->max_size(); - } - - default: - { - // all other types have max_size() == size() - return size(); - } - } - } - - /// @} - - - /////////////// - // modifiers // - /////////////// - - /// @name modifiers - /// @{ - - /*! - @brief clears the contents - - Clears the content of a JSON value and resets it to the default value as - if @ref basic_json(value_t) would have been called with the current value - type from @ref type(): - - Value type | initial value - ----------- | ------------- - null | `null` - boolean | `false` - string | `""` - number | `0` - binary | An empty byte vector - object | `{}` - array | `[]` - - @post Has the same effect as calling - @code {.cpp} - *this = basic_json(type()); - @endcode - - @liveexample{The example below shows the effect of `clear()` to different - JSON types.,clear} - - @complexity Linear in the size of the JSON value. - - @iterators All iterators, pointers and references related to this container - are invalidated. - - @exceptionsafety No-throw guarantee: this function never throws exceptions. - - @sa @ref basic_json(value_t) -- constructor that creates an object with the - same value than calling `clear()` - - @since version 1.0.0 - */ - void clear() noexcept - { - switch (m_type) - { - case value_t::number_integer: - { - m_value.number_integer = 0; - break; - } - - case value_t::number_unsigned: - { - m_value.number_unsigned = 0; - break; - } - - case value_t::number_float: - { - m_value.number_float = 0.0; - break; - } - - case value_t::boolean: - { - m_value.boolean = false; - break; - } - - case value_t::string: - { - m_value.string->clear(); - break; - } - - case value_t::binary: - { - m_value.binary->clear(); - break; - } - - case value_t::array: - { - m_value.array->clear(); - break; - } - - case value_t::object: - { - m_value.object->clear(); - break; - } - - default: - break; - } - } - - /*! - @brief add an object to an array - - Appends the given element @a val to the end of the JSON value. If the - function is called on a JSON null value, an empty array is created before - appending @a val. - - @param[in] val the value to add to the JSON array - - @throw type_error.308 when called on a type other than JSON array or - null; example: `"cannot use push_back() with number"` - - @complexity Amortized constant. - - @liveexample{The example shows how `push_back()` and `+=` can be used to - add elements to a JSON array. Note how the `null` value was silently - converted to a JSON array.,push_back} - - @since version 1.0.0 - */ - void push_back(basic_json&& val) - { - // push_back only works for null objects or arrays - if (JSON_HEDLEY_UNLIKELY(!(is_null() || is_array()))) - { - JSON_THROW(type_error::create(308, "cannot use push_back() with " + std::string(type_name()))); - } - - // transform null object into an array - if (is_null()) - { - m_type = value_t::array; - m_value = value_t::array; - assert_invariant(); - } - - // add element to array (move semantics) - m_value.array->push_back(std::move(val)); - // if val is moved from, basic_json move constructor marks it null so we do not call the destructor - } - - /*! - @brief add an object to an array - @copydoc push_back(basic_json&&) - */ - reference operator+=(basic_json&& val) - { - push_back(std::move(val)); - return *this; - } - - /*! - @brief add an object to an array - @copydoc push_back(basic_json&&) - */ - void push_back(const basic_json& val) - { - // push_back only works for null objects or arrays - if (JSON_HEDLEY_UNLIKELY(!(is_null() || is_array()))) - { - JSON_THROW(type_error::create(308, "cannot use push_back() with " + std::string(type_name()))); - } - - // transform null object into an array - if (is_null()) - { - m_type = value_t::array; - m_value = value_t::array; - assert_invariant(); - } - - // add element to array - m_value.array->push_back(val); - } - - /*! - @brief add an object to an array - @copydoc push_back(basic_json&&) - */ - reference operator+=(const basic_json& val) - { - push_back(val); - return *this; - } - - /*! - @brief add an object to an object - - Inserts the given element @a val to the JSON object. If the function is - called on a JSON null value, an empty object is created before inserting - @a val. - - @param[in] val the value to add to the JSON object - - @throw type_error.308 when called on a type other than JSON object or - null; example: `"cannot use push_back() with number"` - - @complexity Logarithmic in the size of the container, O(log(`size()`)). - - @liveexample{The example shows how `push_back()` and `+=` can be used to - add elements to a JSON object. Note how the `null` value was silently - converted to a JSON object.,push_back__object_t__value} - - @since version 1.0.0 - */ - void push_back(const typename object_t::value_type& val) - { - // push_back only works for null objects or objects - if (JSON_HEDLEY_UNLIKELY(!(is_null() || is_object()))) - { - JSON_THROW(type_error::create(308, "cannot use push_back() with " + std::string(type_name()))); - } - - // transform null object into an object - if (is_null()) - { - m_type = value_t::object; - m_value = value_t::object; - assert_invariant(); - } - - // add element to array - m_value.object->insert(val); - } - - /*! - @brief add an object to an object - @copydoc push_back(const typename object_t::value_type&) - */ - reference operator+=(const typename object_t::value_type& val) - { - push_back(val); - return *this; - } - - /*! - @brief add an object to an object - - This function allows to use `push_back` with an initializer list. In case - - 1. the current value is an object, - 2. the initializer list @a init contains only two elements, and - 3. the first element of @a init is a string, - - @a init is converted into an object element and added using - @ref push_back(const typename object_t::value_type&). Otherwise, @a init - is converted to a JSON value and added using @ref push_back(basic_json&&). - - @param[in] init an initializer list - - @complexity Linear in the size of the initializer list @a init. - - @note This function is required to resolve an ambiguous overload error, - because pairs like `{"key", "value"}` can be both interpreted as - `object_t::value_type` or `std::initializer_list`, see - https://github.com/nlohmann/json/issues/235 for more information. - - @liveexample{The example shows how initializer lists are treated as - objects when possible.,push_back__initializer_list} - */ - void push_back(initializer_list_t init) - { - if (is_object() && init.size() == 2 && (*init.begin())->is_string()) - { - basic_json&& key = init.begin()->moved_or_copied(); - push_back(typename object_t::value_type( - std::move(key.get_ref()), (init.begin() + 1)->moved_or_copied())); - } - else - { - push_back(basic_json(init)); - } - } - - /*! - @brief add an object to an object - @copydoc push_back(initializer_list_t) - */ - reference operator+=(initializer_list_t init) - { - push_back(init); - return *this; - } - - /*! - @brief add an object to an array - - Creates a JSON value from the passed parameters @a args to the end of the - JSON value. If the function is called on a JSON null value, an empty array - is created before appending the value created from @a args. - - @param[in] args arguments to forward to a constructor of @ref basic_json - @tparam Args compatible types to create a @ref basic_json object - - @return reference to the inserted element - - @throw type_error.311 when called on a type other than JSON array or - null; example: `"cannot use emplace_back() with number"` - - @complexity Amortized constant. - - @liveexample{The example shows how `push_back()` can be used to add - elements to a JSON array. Note how the `null` value was silently converted - to a JSON array.,emplace_back} - - @since version 2.0.8, returns reference since 3.7.0 - */ - template - reference emplace_back(Args&& ... args) - { - // emplace_back only works for null objects or arrays - if (JSON_HEDLEY_UNLIKELY(!(is_null() || is_array()))) - { - JSON_THROW(type_error::create(311, "cannot use emplace_back() with " + std::string(type_name()))); - } - - // transform null object into an array - if (is_null()) - { - m_type = value_t::array; - m_value = value_t::array; - assert_invariant(); - } - - // add element to array (perfect forwarding) -#ifdef JSON_HAS_CPP_17 - return m_value.array->emplace_back(std::forward(args)...); -#else - m_value.array->emplace_back(std::forward(args)...); - return m_value.array->back(); -#endif - } - - /*! - @brief add an object to an object if key does not exist - - Inserts a new element into a JSON object constructed in-place with the - given @a args if there is no element with the key in the container. If the - function is called on a JSON null value, an empty object is created before - appending the value created from @a args. - - @param[in] args arguments to forward to a constructor of @ref basic_json - @tparam Args compatible types to create a @ref basic_json object - - @return a pair consisting of an iterator to the inserted element, or the - already-existing element if no insertion happened, and a bool - denoting whether the insertion took place. - - @throw type_error.311 when called on a type other than JSON object or - null; example: `"cannot use emplace() with number"` - - @complexity Logarithmic in the size of the container, O(log(`size()`)). - - @liveexample{The example shows how `emplace()` can be used to add elements - to a JSON object. Note how the `null` value was silently converted to a - JSON object. Further note how no value is added if there was already one - value stored with the same key.,emplace} - - @since version 2.0.8 - */ - template - std::pair emplace(Args&& ... args) - { - // emplace only works for null objects or arrays - if (JSON_HEDLEY_UNLIKELY(!(is_null() || is_object()))) - { - JSON_THROW(type_error::create(311, "cannot use emplace() with " + std::string(type_name()))); - } - - // transform null object into an object - if (is_null()) - { - m_type = value_t::object; - m_value = value_t::object; - assert_invariant(); - } - - // add element to array (perfect forwarding) - auto res = m_value.object->emplace(std::forward(args)...); - // create result iterator and set iterator to the result of emplace - auto it = begin(); - it.m_it.object_iterator = res.first; - - // return pair of iterator and boolean - return {it, res.second}; - } - - /// Helper for insertion of an iterator - /// @note: This uses std::distance to support GCC 4.8, - /// see https://github.com/nlohmann/json/pull/1257 - template - iterator insert_iterator(const_iterator pos, Args&& ... args) - { - iterator result(this); - JSON_ASSERT(m_value.array != nullptr); - - auto insert_pos = std::distance(m_value.array->begin(), pos.m_it.array_iterator); - m_value.array->insert(pos.m_it.array_iterator, std::forward(args)...); - result.m_it.array_iterator = m_value.array->begin() + insert_pos; - - // This could have been written as: - // result.m_it.array_iterator = m_value.array->insert(pos.m_it.array_iterator, cnt, val); - // but the return value of insert is missing in GCC 4.8, so it is written this way instead. - - return result; - } - - /*! - @brief inserts element - - Inserts element @a val before iterator @a pos. - - @param[in] pos iterator before which the content will be inserted; may be - the end() iterator - @param[in] val element to insert - @return iterator pointing to the inserted @a val. - - @throw type_error.309 if called on JSON values other than arrays; - example: `"cannot use insert() with string"` - @throw invalid_iterator.202 if @a pos is not an iterator of *this; - example: `"iterator does not fit current value"` - - @complexity Constant plus linear in the distance between @a pos and end of - the container. - - @liveexample{The example shows how `insert()` is used.,insert} - - @since version 1.0.0 - */ - iterator insert(const_iterator pos, const basic_json& val) - { - // insert only works for arrays - if (JSON_HEDLEY_LIKELY(is_array())) - { - // check if iterator pos fits to this JSON value - if (JSON_HEDLEY_UNLIKELY(pos.m_object != this)) - { - JSON_THROW(invalid_iterator::create(202, "iterator does not fit current value")); - } - - // insert to array and return iterator - return insert_iterator(pos, val); - } - - JSON_THROW(type_error::create(309, "cannot use insert() with " + std::string(type_name()))); - } - - /*! - @brief inserts element - @copydoc insert(const_iterator, const basic_json&) - */ - iterator insert(const_iterator pos, basic_json&& val) - { - return insert(pos, val); - } - - /*! - @brief inserts elements - - Inserts @a cnt copies of @a val before iterator @a pos. - - @param[in] pos iterator before which the content will be inserted; may be - the end() iterator - @param[in] cnt number of copies of @a val to insert - @param[in] val element to insert - @return iterator pointing to the first element inserted, or @a pos if - `cnt==0` - - @throw type_error.309 if called on JSON values other than arrays; example: - `"cannot use insert() with string"` - @throw invalid_iterator.202 if @a pos is not an iterator of *this; - example: `"iterator does not fit current value"` - - @complexity Linear in @a cnt plus linear in the distance between @a pos - and end of the container. - - @liveexample{The example shows how `insert()` is used.,insert__count} - - @since version 1.0.0 - */ - iterator insert(const_iterator pos, size_type cnt, const basic_json& val) - { - // insert only works for arrays - if (JSON_HEDLEY_LIKELY(is_array())) - { - // check if iterator pos fits to this JSON value - if (JSON_HEDLEY_UNLIKELY(pos.m_object != this)) - { - JSON_THROW(invalid_iterator::create(202, "iterator does not fit current value")); - } - - // insert to array and return iterator - return insert_iterator(pos, cnt, val); - } - - JSON_THROW(type_error::create(309, "cannot use insert() with " + std::string(type_name()))); - } - - /*! - @brief inserts elements - - Inserts elements from range `[first, last)` before iterator @a pos. - - @param[in] pos iterator before which the content will be inserted; may be - the end() iterator - @param[in] first begin of the range of elements to insert - @param[in] last end of the range of elements to insert - - @throw type_error.309 if called on JSON values other than arrays; example: - `"cannot use insert() with string"` - @throw invalid_iterator.202 if @a pos is not an iterator of *this; - example: `"iterator does not fit current value"` - @throw invalid_iterator.210 if @a first and @a last do not belong to the - same JSON value; example: `"iterators do not fit"` - @throw invalid_iterator.211 if @a first or @a last are iterators into - container for which insert is called; example: `"passed iterators may not - belong to container"` - - @return iterator pointing to the first element inserted, or @a pos if - `first==last` - - @complexity Linear in `std::distance(first, last)` plus linear in the - distance between @a pos and end of the container. - - @liveexample{The example shows how `insert()` is used.,insert__range} - - @since version 1.0.0 - */ - iterator insert(const_iterator pos, const_iterator first, const_iterator last) - { - // insert only works for arrays - if (JSON_HEDLEY_UNLIKELY(!is_array())) - { - JSON_THROW(type_error::create(309, "cannot use insert() with " + std::string(type_name()))); - } - - // check if iterator pos fits to this JSON value - if (JSON_HEDLEY_UNLIKELY(pos.m_object != this)) - { - JSON_THROW(invalid_iterator::create(202, "iterator does not fit current value")); - } - - // check if range iterators belong to the same JSON object - if (JSON_HEDLEY_UNLIKELY(first.m_object != last.m_object)) - { - JSON_THROW(invalid_iterator::create(210, "iterators do not fit")); - } - - if (JSON_HEDLEY_UNLIKELY(first.m_object == this)) - { - JSON_THROW(invalid_iterator::create(211, "passed iterators may not belong to container")); - } - - // insert to array and return iterator - return insert_iterator(pos, first.m_it.array_iterator, last.m_it.array_iterator); - } - - /*! - @brief inserts elements - - Inserts elements from initializer list @a ilist before iterator @a pos. - - @param[in] pos iterator before which the content will be inserted; may be - the end() iterator - @param[in] ilist initializer list to insert the values from - - @throw type_error.309 if called on JSON values other than arrays; example: - `"cannot use insert() with string"` - @throw invalid_iterator.202 if @a pos is not an iterator of *this; - example: `"iterator does not fit current value"` - - @return iterator pointing to the first element inserted, or @a pos if - `ilist` is empty - - @complexity Linear in `ilist.size()` plus linear in the distance between - @a pos and end of the container. - - @liveexample{The example shows how `insert()` is used.,insert__ilist} - - @since version 1.0.0 - */ - iterator insert(const_iterator pos, initializer_list_t ilist) - { - // insert only works for arrays - if (JSON_HEDLEY_UNLIKELY(!is_array())) - { - JSON_THROW(type_error::create(309, "cannot use insert() with " + std::string(type_name()))); - } - - // check if iterator pos fits to this JSON value - if (JSON_HEDLEY_UNLIKELY(pos.m_object != this)) - { - JSON_THROW(invalid_iterator::create(202, "iterator does not fit current value")); - } - - // insert to array and return iterator - return insert_iterator(pos, ilist.begin(), ilist.end()); - } - - /*! - @brief inserts elements - - Inserts elements from range `[first, last)`. - - @param[in] first begin of the range of elements to insert - @param[in] last end of the range of elements to insert - - @throw type_error.309 if called on JSON values other than objects; example: - `"cannot use insert() with string"` - @throw invalid_iterator.202 if iterator @a first or @a last does does not - point to an object; example: `"iterators first and last must point to - objects"` - @throw invalid_iterator.210 if @a first and @a last do not belong to the - same JSON value; example: `"iterators do not fit"` - - @complexity Logarithmic: `O(N*log(size() + N))`, where `N` is the number - of elements to insert. - - @liveexample{The example shows how `insert()` is used.,insert__range_object} - - @since version 3.0.0 - */ - void insert(const_iterator first, const_iterator last) - { - // insert only works for objects - if (JSON_HEDLEY_UNLIKELY(!is_object())) - { - JSON_THROW(type_error::create(309, "cannot use insert() with " + std::string(type_name()))); - } - - // check if range iterators belong to the same JSON object - if (JSON_HEDLEY_UNLIKELY(first.m_object != last.m_object)) - { - JSON_THROW(invalid_iterator::create(210, "iterators do not fit")); - } - - // passed iterators must belong to objects - if (JSON_HEDLEY_UNLIKELY(!first.m_object->is_object())) - { - JSON_THROW(invalid_iterator::create(202, "iterators first and last must point to objects")); - } - - m_value.object->insert(first.m_it.object_iterator, last.m_it.object_iterator); - } - - /*! - @brief updates a JSON object from another object, overwriting existing keys - - Inserts all values from JSON object @a j and overwrites existing keys. - - @param[in] j JSON object to read values from - - @throw type_error.312 if called on JSON values other than objects; example: - `"cannot use update() with string"` - - @complexity O(N*log(size() + N)), where N is the number of elements to - insert. - - @liveexample{The example shows how `update()` is used.,update} - - @sa https://docs.python.org/3.6/library/stdtypes.html#dict.update - - @since version 3.0.0 - */ - void update(const_reference j) - { - // implicitly convert null value to an empty object - if (is_null()) - { - m_type = value_t::object; - m_value.object = create(); - assert_invariant(); - } - - if (JSON_HEDLEY_UNLIKELY(!is_object())) - { - JSON_THROW(type_error::create(312, "cannot use update() with " + std::string(type_name()))); - } - if (JSON_HEDLEY_UNLIKELY(!j.is_object())) - { - JSON_THROW(type_error::create(312, "cannot use update() with " + std::string(j.type_name()))); - } - - for (auto it = j.cbegin(); it != j.cend(); ++it) - { - m_value.object->operator[](it.key()) = it.value(); - } - } - - /*! - @brief updates a JSON object from another object, overwriting existing keys - - Inserts all values from from range `[first, last)` and overwrites existing - keys. - - @param[in] first begin of the range of elements to insert - @param[in] last end of the range of elements to insert - - @throw type_error.312 if called on JSON values other than objects; example: - `"cannot use update() with string"` - @throw invalid_iterator.202 if iterator @a first or @a last does does not - point to an object; example: `"iterators first and last must point to - objects"` - @throw invalid_iterator.210 if @a first and @a last do not belong to the - same JSON value; example: `"iterators do not fit"` - - @complexity O(N*log(size() + N)), where N is the number of elements to - insert. - - @liveexample{The example shows how `update()` is used__range.,update} - - @sa https://docs.python.org/3.6/library/stdtypes.html#dict.update - - @since version 3.0.0 - */ - void update(const_iterator first, const_iterator last) - { - // implicitly convert null value to an empty object - if (is_null()) - { - m_type = value_t::object; - m_value.object = create(); - assert_invariant(); - } - - if (JSON_HEDLEY_UNLIKELY(!is_object())) - { - JSON_THROW(type_error::create(312, "cannot use update() with " + std::string(type_name()))); - } - - // check if range iterators belong to the same JSON object - if (JSON_HEDLEY_UNLIKELY(first.m_object != last.m_object)) - { - JSON_THROW(invalid_iterator::create(210, "iterators do not fit")); - } - - // passed iterators must belong to objects - if (JSON_HEDLEY_UNLIKELY(!first.m_object->is_object() - || !last.m_object->is_object())) - { - JSON_THROW(invalid_iterator::create(202, "iterators first and last must point to objects")); - } - - for (auto it = first; it != last; ++it) - { - m_value.object->operator[](it.key()) = it.value(); - } - } - - /*! - @brief exchanges the values - - Exchanges the contents of the JSON value with those of @a other. Does not - invoke any move, copy, or swap operations on individual elements. All - iterators and references remain valid. The past-the-end iterator is - invalidated. - - @param[in,out] other JSON value to exchange the contents with - - @complexity Constant. - - @liveexample{The example below shows how JSON values can be swapped with - `swap()`.,swap__reference} - - @since version 1.0.0 - */ - void swap(reference other) noexcept ( - std::is_nothrow_move_constructible::value&& - std::is_nothrow_move_assignable::value&& - std::is_nothrow_move_constructible::value&& - std::is_nothrow_move_assignable::value - ) - { - std::swap(m_type, other.m_type); - std::swap(m_value, other.m_value); - assert_invariant(); - } - - /*! - @brief exchanges the values - - Exchanges the contents of the JSON value from @a left with those of @a right. Does not - invoke any move, copy, or swap operations on individual elements. All - iterators and references remain valid. The past-the-end iterator is - invalidated. implemented as a friend function callable via ADL. - - @param[in,out] left JSON value to exchange the contents with - @param[in,out] right JSON value to exchange the contents with - - @complexity Constant. - - @liveexample{The example below shows how JSON values can be swapped with - `swap()`.,swap__reference} - - @since version 1.0.0 - */ - friend void swap(reference left, reference right) noexcept ( - std::is_nothrow_move_constructible::value&& - std::is_nothrow_move_assignable::value&& - std::is_nothrow_move_constructible::value&& - std::is_nothrow_move_assignable::value - ) - { - left.swap(right); - } - - /*! - @brief exchanges the values - - Exchanges the contents of a JSON array with those of @a other. Does not - invoke any move, copy, or swap operations on individual elements. All - iterators and references remain valid. The past-the-end iterator is - invalidated. - - @param[in,out] other array to exchange the contents with - - @throw type_error.310 when JSON value is not an array; example: `"cannot - use swap() with string"` - - @complexity Constant. - - @liveexample{The example below shows how arrays can be swapped with - `swap()`.,swap__array_t} - - @since version 1.0.0 - */ - void swap(array_t& other) - { - // swap only works for arrays - if (JSON_HEDLEY_LIKELY(is_array())) - { - std::swap(*(m_value.array), other); - } - else - { - JSON_THROW(type_error::create(310, "cannot use swap() with " + std::string(type_name()))); - } - } - - /*! - @brief exchanges the values - - Exchanges the contents of a JSON object with those of @a other. Does not - invoke any move, copy, or swap operations on individual elements. All - iterators and references remain valid. The past-the-end iterator is - invalidated. - - @param[in,out] other object to exchange the contents with - - @throw type_error.310 when JSON value is not an object; example: - `"cannot use swap() with string"` - - @complexity Constant. - - @liveexample{The example below shows how objects can be swapped with - `swap()`.,swap__object_t} - - @since version 1.0.0 - */ - void swap(object_t& other) - { - // swap only works for objects - if (JSON_HEDLEY_LIKELY(is_object())) - { - std::swap(*(m_value.object), other); - } - else - { - JSON_THROW(type_error::create(310, "cannot use swap() with " + std::string(type_name()))); - } - } - - /*! - @brief exchanges the values - - Exchanges the contents of a JSON string with those of @a other. Does not - invoke any move, copy, or swap operations on individual elements. All - iterators and references remain valid. The past-the-end iterator is - invalidated. - - @param[in,out] other string to exchange the contents with - - @throw type_error.310 when JSON value is not a string; example: `"cannot - use swap() with boolean"` - - @complexity Constant. - - @liveexample{The example below shows how strings can be swapped with - `swap()`.,swap__string_t} - - @since version 1.0.0 - */ - void swap(string_t& other) - { - // swap only works for strings - if (JSON_HEDLEY_LIKELY(is_string())) - { - std::swap(*(m_value.string), other); - } - else - { - JSON_THROW(type_error::create(310, "cannot use swap() with " + std::string(type_name()))); - } - } - - /*! - @brief exchanges the values - - Exchanges the contents of a JSON string with those of @a other. Does not - invoke any move, copy, or swap operations on individual elements. All - iterators and references remain valid. The past-the-end iterator is - invalidated. - - @param[in,out] other binary to exchange the contents with - - @throw type_error.310 when JSON value is not a string; example: `"cannot - use swap() with boolean"` - - @complexity Constant. - - @liveexample{The example below shows how strings can be swapped with - `swap()`.,swap__binary_t} - - @since version 3.8.0 - */ - void swap(binary_t& other) - { - // swap only works for strings - if (JSON_HEDLEY_LIKELY(is_binary())) - { - std::swap(*(m_value.binary), other); - } - else - { - JSON_THROW(type_error::create(310, "cannot use swap() with " + std::string(type_name()))); - } - } - - /// @copydoc swap(binary_t) - void swap(typename binary_t::container_type& other) - { - // swap only works for strings - if (JSON_HEDLEY_LIKELY(is_binary())) - { - std::swap(*(m_value.binary), other); - } - else - { - JSON_THROW(type_error::create(310, "cannot use swap() with " + std::string(type_name()))); - } - } - - /// @} - - public: - ////////////////////////////////////////// - // lexicographical comparison operators // - ////////////////////////////////////////// - - /// @name lexicographical comparison operators - /// @{ - - /*! - @brief comparison: equal - - Compares two JSON values for equality according to the following rules: - - Two JSON values are equal if (1) they are from the same type and (2) - their stored values are the same according to their respective - `operator==`. - - Integer and floating-point numbers are automatically converted before - comparison. Note that two NaN values are always treated as unequal. - - Two JSON null values are equal. - - @note Floating-point inside JSON values numbers are compared with - `json::number_float_t::operator==` which is `double::operator==` by - default. To compare floating-point while respecting an epsilon, an alternative - [comparison function](https://github.com/mariokonrad/marnav/blob/master/include/marnav/math/floatingpoint.hpp#L34-#L39) - could be used, for instance - @code {.cpp} - template::value, T>::type> - inline bool is_same(T a, T b, T epsilon = std::numeric_limits::epsilon()) noexcept - { - return std::abs(a - b) <= epsilon; - } - @endcode - Or you can self-defined operator equal function like this: - @code {.cpp} - bool my_equal(const_reference lhs, const_reference rhs) { - const auto lhs_type lhs.type(); - const auto rhs_type rhs.type(); - if (lhs_type == rhs_type) { - switch(lhs_type) - // self_defined case - case value_t::number_float: - return std::abs(lhs - rhs) <= std::numeric_limits::epsilon(); - // other cases remain the same with the original - ... - } - ... - } - @endcode - - @note NaN values never compare equal to themselves or to other NaN values. - - @param[in] lhs first JSON value to consider - @param[in] rhs second JSON value to consider - @return whether the values @a lhs and @a rhs are equal - - @exceptionsafety No-throw guarantee: this function never throws exceptions. - - @complexity Linear. - - @liveexample{The example demonstrates comparing several JSON - types.,operator__equal} - - @since version 1.0.0 - */ - friend bool operator==(const_reference lhs, const_reference rhs) noexcept - { - const auto lhs_type = lhs.type(); - const auto rhs_type = rhs.type(); - - if (lhs_type == rhs_type) - { - switch (lhs_type) - { - case value_t::array: - return *lhs.m_value.array == *rhs.m_value.array; - - case value_t::object: - return *lhs.m_value.object == *rhs.m_value.object; - - case value_t::null: - return true; - - case value_t::string: - return *lhs.m_value.string == *rhs.m_value.string; - - case value_t::boolean: - return lhs.m_value.boolean == rhs.m_value.boolean; - - case value_t::number_integer: - return lhs.m_value.number_integer == rhs.m_value.number_integer; - - case value_t::number_unsigned: - return lhs.m_value.number_unsigned == rhs.m_value.number_unsigned; - - case value_t::number_float: - return lhs.m_value.number_float == rhs.m_value.number_float; - - case value_t::binary: - return *lhs.m_value.binary == *rhs.m_value.binary; - - default: - return false; - } - } - else if (lhs_type == value_t::number_integer && rhs_type == value_t::number_float) - { - return static_cast(lhs.m_value.number_integer) == rhs.m_value.number_float; - } - else if (lhs_type == value_t::number_float && rhs_type == value_t::number_integer) - { - return lhs.m_value.number_float == static_cast(rhs.m_value.number_integer); - } - else if (lhs_type == value_t::number_unsigned && rhs_type == value_t::number_float) - { - return static_cast(lhs.m_value.number_unsigned) == rhs.m_value.number_float; - } - else if (lhs_type == value_t::number_float && rhs_type == value_t::number_unsigned) - { - return lhs.m_value.number_float == static_cast(rhs.m_value.number_unsigned); - } - else if (lhs_type == value_t::number_unsigned && rhs_type == value_t::number_integer) - { - return static_cast(lhs.m_value.number_unsigned) == rhs.m_value.number_integer; - } - else if (lhs_type == value_t::number_integer && rhs_type == value_t::number_unsigned) - { - return lhs.m_value.number_integer == static_cast(rhs.m_value.number_unsigned); - } - - return false; - } - - /*! - @brief comparison: equal - @copydoc operator==(const_reference, const_reference) - */ - template::value, int>::type = 0> - friend bool operator==(const_reference lhs, const ScalarType rhs) noexcept - { - return lhs == basic_json(rhs); - } - - /*! - @brief comparison: equal - @copydoc operator==(const_reference, const_reference) - */ - template::value, int>::type = 0> - friend bool operator==(const ScalarType lhs, const_reference rhs) noexcept - { - return basic_json(lhs) == rhs; - } - - /*! - @brief comparison: not equal - - Compares two JSON values for inequality by calculating `not (lhs == rhs)`. - - @param[in] lhs first JSON value to consider - @param[in] rhs second JSON value to consider - @return whether the values @a lhs and @a rhs are not equal - - @complexity Linear. - - @exceptionsafety No-throw guarantee: this function never throws exceptions. - - @liveexample{The example demonstrates comparing several JSON - types.,operator__notequal} - - @since version 1.0.0 - */ - friend bool operator!=(const_reference lhs, const_reference rhs) noexcept - { - return !(lhs == rhs); - } - - /*! - @brief comparison: not equal - @copydoc operator!=(const_reference, const_reference) - */ - template::value, int>::type = 0> - friend bool operator!=(const_reference lhs, const ScalarType rhs) noexcept - { - return lhs != basic_json(rhs); - } - - /*! - @brief comparison: not equal - @copydoc operator!=(const_reference, const_reference) - */ - template::value, int>::type = 0> - friend bool operator!=(const ScalarType lhs, const_reference rhs) noexcept - { - return basic_json(lhs) != rhs; - } - - /*! - @brief comparison: less than - - Compares whether one JSON value @a lhs is less than another JSON value @a - rhs according to the following rules: - - If @a lhs and @a rhs have the same type, the values are compared using - the default `<` operator. - - Integer and floating-point numbers are automatically converted before - comparison - - In case @a lhs and @a rhs have different types, the values are ignored - and the order of the types is considered, see - @ref operator<(const value_t, const value_t). - - @param[in] lhs first JSON value to consider - @param[in] rhs second JSON value to consider - @return whether @a lhs is less than @a rhs - - @complexity Linear. - - @exceptionsafety No-throw guarantee: this function never throws exceptions. - - @liveexample{The example demonstrates comparing several JSON - types.,operator__less} - - @since version 1.0.0 - */ - friend bool operator<(const_reference lhs, const_reference rhs) noexcept - { - const auto lhs_type = lhs.type(); - const auto rhs_type = rhs.type(); - - if (lhs_type == rhs_type) - { - switch (lhs_type) - { - case value_t::array: - // note parentheses are necessary, see - // https://github.com/nlohmann/json/issues/1530 - return (*lhs.m_value.array) < (*rhs.m_value.array); - - case value_t::object: - return (*lhs.m_value.object) < (*rhs.m_value.object); - - case value_t::null: - return false; - - case value_t::string: - return (*lhs.m_value.string) < (*rhs.m_value.string); - - case value_t::boolean: - return (lhs.m_value.boolean) < (rhs.m_value.boolean); - - case value_t::number_integer: - return (lhs.m_value.number_integer) < (rhs.m_value.number_integer); - - case value_t::number_unsigned: - return (lhs.m_value.number_unsigned) < (rhs.m_value.number_unsigned); - - case value_t::number_float: - return (lhs.m_value.number_float) < (rhs.m_value.number_float); - - case value_t::binary: - return (*lhs.m_value.binary) < (*rhs.m_value.binary); - - default: - return false; - } - } - else if (lhs_type == value_t::number_integer && rhs_type == value_t::number_float) - { - return static_cast(lhs.m_value.number_integer) < rhs.m_value.number_float; - } - else if (lhs_type == value_t::number_float && rhs_type == value_t::number_integer) - { - return lhs.m_value.number_float < static_cast(rhs.m_value.number_integer); - } - else if (lhs_type == value_t::number_unsigned && rhs_type == value_t::number_float) - { - return static_cast(lhs.m_value.number_unsigned) < rhs.m_value.number_float; - } - else if (lhs_type == value_t::number_float && rhs_type == value_t::number_unsigned) - { - return lhs.m_value.number_float < static_cast(rhs.m_value.number_unsigned); - } - else if (lhs_type == value_t::number_integer && rhs_type == value_t::number_unsigned) - { - return lhs.m_value.number_integer < static_cast(rhs.m_value.number_unsigned); - } - else if (lhs_type == value_t::number_unsigned && rhs_type == value_t::number_integer) - { - return static_cast(lhs.m_value.number_unsigned) < rhs.m_value.number_integer; - } - - // We only reach this line if we cannot compare values. In that case, - // we compare types. Note we have to call the operator explicitly, - // because MSVC has problems otherwise. - return operator<(lhs_type, rhs_type); - } - - /*! - @brief comparison: less than - @copydoc operator<(const_reference, const_reference) - */ - template::value, int>::type = 0> - friend bool operator<(const_reference lhs, const ScalarType rhs) noexcept - { - return lhs < basic_json(rhs); - } - - /*! - @brief comparison: less than - @copydoc operator<(const_reference, const_reference) - */ - template::value, int>::type = 0> - friend bool operator<(const ScalarType lhs, const_reference rhs) noexcept - { - return basic_json(lhs) < rhs; - } - - /*! - @brief comparison: less than or equal - - Compares whether one JSON value @a lhs is less than or equal to another - JSON value by calculating `not (rhs < lhs)`. - - @param[in] lhs first JSON value to consider - @param[in] rhs second JSON value to consider - @return whether @a lhs is less than or equal to @a rhs - - @complexity Linear. - - @exceptionsafety No-throw guarantee: this function never throws exceptions. - - @liveexample{The example demonstrates comparing several JSON - types.,operator__greater} - - @since version 1.0.0 - */ - friend bool operator<=(const_reference lhs, const_reference rhs) noexcept - { - return !(rhs < lhs); - } - - /*! - @brief comparison: less than or equal - @copydoc operator<=(const_reference, const_reference) - */ - template::value, int>::type = 0> - friend bool operator<=(const_reference lhs, const ScalarType rhs) noexcept - { - return lhs <= basic_json(rhs); - } - - /*! - @brief comparison: less than or equal - @copydoc operator<=(const_reference, const_reference) - */ - template::value, int>::type = 0> - friend bool operator<=(const ScalarType lhs, const_reference rhs) noexcept - { - return basic_json(lhs) <= rhs; - } - - /*! - @brief comparison: greater than - - Compares whether one JSON value @a lhs is greater than another - JSON value by calculating `not (lhs <= rhs)`. - - @param[in] lhs first JSON value to consider - @param[in] rhs second JSON value to consider - @return whether @a lhs is greater than to @a rhs - - @complexity Linear. - - @exceptionsafety No-throw guarantee: this function never throws exceptions. - - @liveexample{The example demonstrates comparing several JSON - types.,operator__lessequal} - - @since version 1.0.0 - */ - friend bool operator>(const_reference lhs, const_reference rhs) noexcept - { - return !(lhs <= rhs); - } - - /*! - @brief comparison: greater than - @copydoc operator>(const_reference, const_reference) - */ - template::value, int>::type = 0> - friend bool operator>(const_reference lhs, const ScalarType rhs) noexcept - { - return lhs > basic_json(rhs); - } - - /*! - @brief comparison: greater than - @copydoc operator>(const_reference, const_reference) - */ - template::value, int>::type = 0> - friend bool operator>(const ScalarType lhs, const_reference rhs) noexcept - { - return basic_json(lhs) > rhs; - } - - /*! - @brief comparison: greater than or equal - - Compares whether one JSON value @a lhs is greater than or equal to another - JSON value by calculating `not (lhs < rhs)`. - - @param[in] lhs first JSON value to consider - @param[in] rhs second JSON value to consider - @return whether @a lhs is greater than or equal to @a rhs - - @complexity Linear. - - @exceptionsafety No-throw guarantee: this function never throws exceptions. - - @liveexample{The example demonstrates comparing several JSON - types.,operator__greaterequal} - - @since version 1.0.0 - */ - friend bool operator>=(const_reference lhs, const_reference rhs) noexcept - { - return !(lhs < rhs); - } - - /*! - @brief comparison: greater than or equal - @copydoc operator>=(const_reference, const_reference) - */ - template::value, int>::type = 0> - friend bool operator>=(const_reference lhs, const ScalarType rhs) noexcept - { - return lhs >= basic_json(rhs); - } - - /*! - @brief comparison: greater than or equal - @copydoc operator>=(const_reference, const_reference) - */ - template::value, int>::type = 0> - friend bool operator>=(const ScalarType lhs, const_reference rhs) noexcept - { - return basic_json(lhs) >= rhs; - } - - /// @} - - /////////////////// - // serialization // - /////////////////// - - /// @name serialization - /// @{ - - /*! - @brief serialize to stream - - Serialize the given JSON value @a j to the output stream @a o. The JSON - value will be serialized using the @ref dump member function. - - - The indentation of the output can be controlled with the member variable - `width` of the output stream @a o. For instance, using the manipulator - `std::setw(4)` on @a o sets the indentation level to `4` and the - serialization result is the same as calling `dump(4)`. - - - The indentation character can be controlled with the member variable - `fill` of the output stream @a o. For instance, the manipulator - `std::setfill('\\t')` sets indentation to use a tab character rather than - the default space character. - - @param[in,out] o stream to serialize to - @param[in] j JSON value to serialize - - @return the stream @a o - - @throw type_error.316 if a string stored inside the JSON value is not - UTF-8 encoded - - @complexity Linear. - - @liveexample{The example below shows the serialization with different - parameters to `width` to adjust the indentation level.,operator_serialize} - - @since version 1.0.0; indentation character added in version 3.0.0 - */ - friend std::ostream& operator<<(std::ostream& o, const basic_json& j) - { - // read width member and use it as indentation parameter if nonzero - const bool pretty_print = o.width() > 0; - const auto indentation = pretty_print ? o.width() : 0; - - // reset width to 0 for subsequent calls to this stream - o.width(0); - - // do the actual serialization - serializer s(detail::output_adapter(o), o.fill()); - s.dump(j, pretty_print, false, static_cast(indentation)); - return o; - } - - /*! - @brief serialize to stream - @deprecated This stream operator is deprecated and will be removed in - future 4.0.0 of the library. Please use - @ref operator<<(std::ostream&, const basic_json&) - instead; that is, replace calls like `j >> o;` with `o << j;`. - @since version 1.0.0; deprecated since version 3.0.0 - */ - JSON_HEDLEY_DEPRECATED_FOR(3.0.0, operator<<(std::ostream&, const basic_json&)) - friend std::ostream& operator>>(const basic_json& j, std::ostream& o) - { - return o << j; - } - - /// @} - - - ///////////////////// - // deserialization // - ///////////////////// - - /// @name deserialization - /// @{ - - /*! - @brief deserialize from a compatible input - - @tparam InputType A compatible input, for instance - - an std::istream object - - a FILE pointer - - a C-style array of characters - - a pointer to a null-terminated string of single byte characters - - an object obj for which begin(obj) and end(obj) produces a valid pair of - iterators. - - @param[in] i input to read from - @param[in] cb a parser callback function of type @ref parser_callback_t - which is used to control the deserialization by filtering unwanted values - (optional) - @param[in] allow_exceptions whether to throw exceptions in case of a - parse error (optional, true by default) - @param[in] ignore_comments whether comments should be ignored and treated - like whitespace (true) or yield a parse error (true); (optional, false by - default) - - @return deserialized JSON value; in case of a parse error and - @a allow_exceptions set to `false`, the return value will be - value_t::discarded. - - @throw parse_error.101 if a parse error occurs; example: `""unexpected end - of input; expected string literal""` - @throw parse_error.102 if to_unicode fails or surrogate error - @throw parse_error.103 if to_unicode fails - - @complexity Linear in the length of the input. The parser is a predictive - LL(1) parser. The complexity can be higher if the parser callback function - @a cb or reading from the input @a i has a super-linear complexity. - - @note A UTF-8 byte order mark is silently ignored. - - @liveexample{The example below demonstrates the `parse()` function reading - from an array.,parse__array__parser_callback_t} - - @liveexample{The example below demonstrates the `parse()` function with - and without callback function.,parse__string__parser_callback_t} - - @liveexample{The example below demonstrates the `parse()` function with - and without callback function.,parse__istream__parser_callback_t} - - @liveexample{The example below demonstrates the `parse()` function reading - from a contiguous container.,parse__contiguouscontainer__parser_callback_t} - - @since version 2.0.3 (contiguous containers); version 3.9.0 allowed to - ignore comments. - */ - template - JSON_HEDLEY_WARN_UNUSED_RESULT - static basic_json parse(InputType&& i, - const parser_callback_t cb = nullptr, - const bool allow_exceptions = true, - const bool ignore_comments = false) - { - basic_json result; - parser(detail::input_adapter(std::forward(i)), cb, allow_exceptions, ignore_comments).parse(true, result); - return result; - } - - /*! - @brief deserialize from a pair of character iterators - - The value_type of the iterator must be a integral type with size of 1, 2 or - 4 bytes, which will be interpreted respectively as UTF-8, UTF-16 and UTF-32. - - @param[in] first iterator to start of character range - @param[in] last iterator to end of character range - @param[in] cb a parser callback function of type @ref parser_callback_t - which is used to control the deserialization by filtering unwanted values - (optional) - @param[in] allow_exceptions whether to throw exceptions in case of a - parse error (optional, true by default) - @param[in] ignore_comments whether comments should be ignored and treated - like whitespace (true) or yield a parse error (true); (optional, false by - default) - - @return deserialized JSON value; in case of a parse error and - @a allow_exceptions set to `false`, the return value will be - value_t::discarded. - - @throw parse_error.101 if a parse error occurs; example: `""unexpected end - of input; expected string literal""` - @throw parse_error.102 if to_unicode fails or surrogate error - @throw parse_error.103 if to_unicode fails - */ - template - JSON_HEDLEY_WARN_UNUSED_RESULT - static basic_json parse(IteratorType first, - IteratorType last, - const parser_callback_t cb = nullptr, - const bool allow_exceptions = true, - const bool ignore_comments = false) - { - basic_json result; - parser(detail::input_adapter(std::move(first), std::move(last)), cb, allow_exceptions, ignore_comments).parse(true, result); - return result; - } - - JSON_HEDLEY_WARN_UNUSED_RESULT - JSON_HEDLEY_DEPRECATED_FOR(3.8.0, parse(ptr, ptr + len)) - static basic_json parse(detail::span_input_adapter&& i, - const parser_callback_t cb = nullptr, - const bool allow_exceptions = true, - const bool ignore_comments = false) - { - basic_json result; - parser(i.get(), cb, allow_exceptions, ignore_comments).parse(true, result); - return result; - } - - /*! - @brief check if the input is valid JSON - - Unlike the @ref parse(InputType&&, const parser_callback_t,const bool) - function, this function neither throws an exception in case of invalid JSON - input (i.e., a parse error) nor creates diagnostic information. - - @tparam InputType A compatible input, for instance - - an std::istream object - - a FILE pointer - - a C-style array of characters - - a pointer to a null-terminated string of single byte characters - - an object obj for which begin(obj) and end(obj) produces a valid pair of - iterators. - - @param[in] i input to read from - @param[in] ignore_comments whether comments should be ignored and treated - like whitespace (true) or yield a parse error (true); (optional, false by - default) - - @return Whether the input read from @a i is valid JSON. - - @complexity Linear in the length of the input. The parser is a predictive - LL(1) parser. - - @note A UTF-8 byte order mark is silently ignored. - - @liveexample{The example below demonstrates the `accept()` function reading - from a string.,accept__string} - */ - template - static bool accept(InputType&& i, - const bool ignore_comments = false) - { - return parser(detail::input_adapter(std::forward(i)), nullptr, false, ignore_comments).accept(true); - } - - template - static bool accept(IteratorType first, IteratorType last, - const bool ignore_comments = false) - { - return parser(detail::input_adapter(std::move(first), std::move(last)), nullptr, false, ignore_comments).accept(true); - } - - JSON_HEDLEY_WARN_UNUSED_RESULT - JSON_HEDLEY_DEPRECATED_FOR(3.8.0, accept(ptr, ptr + len)) - static bool accept(detail::span_input_adapter&& i, - const bool ignore_comments = false) - { - return parser(i.get(), nullptr, false, ignore_comments).accept(true); - } - - /*! - @brief generate SAX events - - The SAX event lister must follow the interface of @ref json_sax. - - This function reads from a compatible input. Examples are: - - an std::istream object - - a FILE pointer - - a C-style array of characters - - a pointer to a null-terminated string of single byte characters - - an object obj for which begin(obj) and end(obj) produces a valid pair of - iterators. - - @param[in] i input to read from - @param[in,out] sax SAX event listener - @param[in] format the format to parse (JSON, CBOR, MessagePack, or UBJSON) - @param[in] strict whether the input has to be consumed completely - @param[in] ignore_comments whether comments should be ignored and treated - like whitespace (true) or yield a parse error (true); (optional, false by - default); only applies to the JSON file format. - - @return return value of the last processed SAX event - - @throw parse_error.101 if a parse error occurs; example: `""unexpected end - of input; expected string literal""` - @throw parse_error.102 if to_unicode fails or surrogate error - @throw parse_error.103 if to_unicode fails - - @complexity Linear in the length of the input. The parser is a predictive - LL(1) parser. The complexity can be higher if the SAX consumer @a sax has - a super-linear complexity. - - @note A UTF-8 byte order mark is silently ignored. - - @liveexample{The example below demonstrates the `sax_parse()` function - reading from string and processing the events with a user-defined SAX - event consumer.,sax_parse} - - @since version 3.2.0 - */ - template - JSON_HEDLEY_NON_NULL(2) - static bool sax_parse(InputType&& i, SAX* sax, - input_format_t format = input_format_t::json, - const bool strict = true, - const bool ignore_comments = false) - { - auto ia = detail::input_adapter(std::forward(i)); - return format == input_format_t::json - ? parser(std::move(ia), nullptr, true, ignore_comments).sax_parse(sax, strict) - : detail::binary_reader(std::move(ia)).sax_parse(format, sax, strict); - } - - template - JSON_HEDLEY_NON_NULL(3) - static bool sax_parse(IteratorType first, IteratorType last, SAX* sax, - input_format_t format = input_format_t::json, - const bool strict = true, - const bool ignore_comments = false) - { - auto ia = detail::input_adapter(std::move(first), std::move(last)); - return format == input_format_t::json - ? parser(std::move(ia), nullptr, true, ignore_comments).sax_parse(sax, strict) - : detail::binary_reader(std::move(ia)).sax_parse(format, sax, strict); - } - - template - JSON_HEDLEY_DEPRECATED_FOR(3.8.0, sax_parse(ptr, ptr + len, ...)) - JSON_HEDLEY_NON_NULL(2) - static bool sax_parse(detail::span_input_adapter&& i, SAX* sax, - input_format_t format = input_format_t::json, - const bool strict = true, - const bool ignore_comments = false) - { - auto ia = i.get(); - return format == input_format_t::json - ? parser(std::move(ia), nullptr, true, ignore_comments).sax_parse(sax, strict) - : detail::binary_reader(std::move(ia)).sax_parse(format, sax, strict); - } - - /*! - @brief deserialize from stream - @deprecated This stream operator is deprecated and will be removed in - version 4.0.0 of the library. Please use - @ref operator>>(std::istream&, basic_json&) - instead; that is, replace calls like `j << i;` with `i >> j;`. - @since version 1.0.0; deprecated since version 3.0.0 - */ - JSON_HEDLEY_DEPRECATED_FOR(3.0.0, operator>>(std::istream&, basic_json&)) - friend std::istream& operator<<(basic_json& j, std::istream& i) - { - return operator>>(i, j); - } - - /*! - @brief deserialize from stream - - Deserializes an input stream to a JSON value. - - @param[in,out] i input stream to read a serialized JSON value from - @param[in,out] j JSON value to write the deserialized input to - - @throw parse_error.101 in case of an unexpected token - @throw parse_error.102 if to_unicode fails or surrogate error - @throw parse_error.103 if to_unicode fails - - @complexity Linear in the length of the input. The parser is a predictive - LL(1) parser. - - @note A UTF-8 byte order mark is silently ignored. - - @liveexample{The example below shows how a JSON value is constructed by - reading a serialization from a stream.,operator_deserialize} - - @sa parse(std::istream&, const parser_callback_t) for a variant with a - parser callback function to filter values while parsing - - @since version 1.0.0 - */ - friend std::istream& operator>>(std::istream& i, basic_json& j) - { - parser(detail::input_adapter(i)).parse(false, j); - return i; - } - - /// @} - - /////////////////////////// - // convenience functions // - /////////////////////////// - - /*! - @brief return the type as string - - Returns the type name as string to be used in error messages - usually to - indicate that a function was called on a wrong JSON type. - - @return a string representation of a the @a m_type member: - Value type | return value - ----------- | ------------- - null | `"null"` - boolean | `"boolean"` - string | `"string"` - number | `"number"` (for all number types) - object | `"object"` - array | `"array"` - binary | `"binary"` - discarded | `"discarded"` - - @exceptionsafety No-throw guarantee: this function never throws exceptions. - - @complexity Constant. - - @liveexample{The following code exemplifies `type_name()` for all JSON - types.,type_name} - - @sa @ref type() -- return the type of the JSON value - @sa @ref operator value_t() -- return the type of the JSON value (implicit) - - @since version 1.0.0, public since 2.1.0, `const char*` and `noexcept` - since 3.0.0 - */ - JSON_HEDLEY_RETURNS_NON_NULL - const char* type_name() const noexcept - { - { - switch (m_type) - { - case value_t::null: - return "null"; - case value_t::object: - return "object"; - case value_t::array: - return "array"; - case value_t::string: - return "string"; - case value_t::boolean: - return "boolean"; - case value_t::binary: - return "binary"; - case value_t::discarded: - return "discarded"; - default: - return "number"; - } - } - } - - - private: - ////////////////////// - // member variables // - ////////////////////// - - /// the type of the current element - value_t m_type = value_t::null; - - /// the value of the current element - json_value m_value = {}; - - ////////////////////////////////////////// - // binary serialization/deserialization // - ////////////////////////////////////////// - - /// @name binary serialization/deserialization support - /// @{ - - public: - /*! - @brief create a CBOR serialization of a given JSON value - - Serializes a given JSON value @a j to a byte vector using the CBOR (Concise - Binary Object Representation) serialization format. CBOR is a binary - serialization format which aims to be more compact than JSON itself, yet - more efficient to parse. - - The library uses the following mapping from JSON values types to - CBOR types according to the CBOR specification (RFC 7049): - - JSON value type | value/range | CBOR type | first byte - --------------- | ------------------------------------------ | ---------------------------------- | --------------- - null | `null` | Null | 0xF6 - boolean | `true` | True | 0xF5 - boolean | `false` | False | 0xF4 - number_integer | -9223372036854775808..-2147483649 | Negative integer (8 bytes follow) | 0x3B - number_integer | -2147483648..-32769 | Negative integer (4 bytes follow) | 0x3A - number_integer | -32768..-129 | Negative integer (2 bytes follow) | 0x39 - number_integer | -128..-25 | Negative integer (1 byte follow) | 0x38 - number_integer | -24..-1 | Negative integer | 0x20..0x37 - number_integer | 0..23 | Integer | 0x00..0x17 - number_integer | 24..255 | Unsigned integer (1 byte follow) | 0x18 - number_integer | 256..65535 | Unsigned integer (2 bytes follow) | 0x19 - number_integer | 65536..4294967295 | Unsigned integer (4 bytes follow) | 0x1A - number_integer | 4294967296..18446744073709551615 | Unsigned integer (8 bytes follow) | 0x1B - number_unsigned | 0..23 | Integer | 0x00..0x17 - number_unsigned | 24..255 | Unsigned integer (1 byte follow) | 0x18 - number_unsigned | 256..65535 | Unsigned integer (2 bytes follow) | 0x19 - number_unsigned | 65536..4294967295 | Unsigned integer (4 bytes follow) | 0x1A - number_unsigned | 4294967296..18446744073709551615 | Unsigned integer (8 bytes follow) | 0x1B - number_float | *any value representable by a float* | Single-Precision Float | 0xFA - number_float | *any value NOT representable by a float* | Double-Precision Float | 0xFB - string | *length*: 0..23 | UTF-8 string | 0x60..0x77 - string | *length*: 23..255 | UTF-8 string (1 byte follow) | 0x78 - string | *length*: 256..65535 | UTF-8 string (2 bytes follow) | 0x79 - string | *length*: 65536..4294967295 | UTF-8 string (4 bytes follow) | 0x7A - string | *length*: 4294967296..18446744073709551615 | UTF-8 string (8 bytes follow) | 0x7B - array | *size*: 0..23 | array | 0x80..0x97 - array | *size*: 23..255 | array (1 byte follow) | 0x98 - array | *size*: 256..65535 | array (2 bytes follow) | 0x99 - array | *size*: 65536..4294967295 | array (4 bytes follow) | 0x9A - array | *size*: 4294967296..18446744073709551615 | array (8 bytes follow) | 0x9B - object | *size*: 0..23 | map | 0xA0..0xB7 - object | *size*: 23..255 | map (1 byte follow) | 0xB8 - object | *size*: 256..65535 | map (2 bytes follow) | 0xB9 - object | *size*: 65536..4294967295 | map (4 bytes follow) | 0xBA - object | *size*: 4294967296..18446744073709551615 | map (8 bytes follow) | 0xBB - binary | *size*: 0..23 | byte string | 0x40..0x57 - binary | *size*: 23..255 | byte string (1 byte follow) | 0x58 - binary | *size*: 256..65535 | byte string (2 bytes follow) | 0x59 - binary | *size*: 65536..4294967295 | byte string (4 bytes follow) | 0x5A - binary | *size*: 4294967296..18446744073709551615 | byte string (8 bytes follow) | 0x5B - - @note The mapping is **complete** in the sense that any JSON value type - can be converted to a CBOR value. - - @note If NaN or Infinity are stored inside a JSON number, they are - serialized properly. This behavior differs from the @ref dump() - function which serializes NaN or Infinity to `null`. - - @note The following CBOR types are not used in the conversion: - - UTF-8 strings terminated by "break" (0x7F) - - arrays terminated by "break" (0x9F) - - maps terminated by "break" (0xBF) - - byte strings terminated by "break" (0x5F) - - date/time (0xC0..0xC1) - - bignum (0xC2..0xC3) - - decimal fraction (0xC4) - - bigfloat (0xC5) - - expected conversions (0xD5..0xD7) - - simple values (0xE0..0xF3, 0xF8) - - undefined (0xF7) - - half-precision floats (0xF9) - - break (0xFF) - - @param[in] j JSON value to serialize - @return CBOR serialization as byte vector - - @complexity Linear in the size of the JSON value @a j. - - @liveexample{The example shows the serialization of a JSON value to a byte - vector in CBOR format.,to_cbor} - - @sa http://cbor.io - @sa @ref from_cbor(detail::input_adapter&&, const bool, const bool, const cbor_tag_handler_t) for the - analogous deserialization - @sa @ref to_msgpack(const basic_json&) for the related MessagePack format - @sa @ref to_ubjson(const basic_json&, const bool, const bool) for the - related UBJSON format - - @since version 2.0.9; compact representation of floating-point numbers - since version 3.8.0 - */ - static std::vector to_cbor(const basic_json& j) - { - std::vector result; - to_cbor(j, result); - return result; - } - - static void to_cbor(const basic_json& j, detail::output_adapter o) - { - binary_writer(o).write_cbor(j); - } - - static void to_cbor(const basic_json& j, detail::output_adapter o) - { - binary_writer(o).write_cbor(j); - } - - /*! - @brief create a MessagePack serialization of a given JSON value - - Serializes a given JSON value @a j to a byte vector using the MessagePack - serialization format. MessagePack is a binary serialization format which - aims to be more compact than JSON itself, yet more efficient to parse. - - The library uses the following mapping from JSON values types to - MessagePack types according to the MessagePack specification: - - JSON value type | value/range | MessagePack type | first byte - --------------- | --------------------------------- | ---------------- | ---------- - null | `null` | nil | 0xC0 - boolean | `true` | true | 0xC3 - boolean | `false` | false | 0xC2 - number_integer | -9223372036854775808..-2147483649 | int64 | 0xD3 - number_integer | -2147483648..-32769 | int32 | 0xD2 - number_integer | -32768..-129 | int16 | 0xD1 - number_integer | -128..-33 | int8 | 0xD0 - number_integer | -32..-1 | negative fixint | 0xE0..0xFF - number_integer | 0..127 | positive fixint | 0x00..0x7F - number_integer | 128..255 | uint 8 | 0xCC - number_integer | 256..65535 | uint 16 | 0xCD - number_integer | 65536..4294967295 | uint 32 | 0xCE - number_integer | 4294967296..18446744073709551615 | uint 64 | 0xCF - number_unsigned | 0..127 | positive fixint | 0x00..0x7F - number_unsigned | 128..255 | uint 8 | 0xCC - number_unsigned | 256..65535 | uint 16 | 0xCD - number_unsigned | 65536..4294967295 | uint 32 | 0xCE - number_unsigned | 4294967296..18446744073709551615 | uint 64 | 0xCF - number_float | *any value representable by a float* | float 32 | 0xCA - number_float | *any value NOT representable by a float* | float 64 | 0xCB - string | *length*: 0..31 | fixstr | 0xA0..0xBF - string | *length*: 32..255 | str 8 | 0xD9 - string | *length*: 256..65535 | str 16 | 0xDA - string | *length*: 65536..4294967295 | str 32 | 0xDB - array | *size*: 0..15 | fixarray | 0x90..0x9F - array | *size*: 16..65535 | array 16 | 0xDC - array | *size*: 65536..4294967295 | array 32 | 0xDD - object | *size*: 0..15 | fix map | 0x80..0x8F - object | *size*: 16..65535 | map 16 | 0xDE - object | *size*: 65536..4294967295 | map 32 | 0xDF - binary | *size*: 0..255 | bin 8 | 0xC4 - binary | *size*: 256..65535 | bin 16 | 0xC5 - binary | *size*: 65536..4294967295 | bin 32 | 0xC6 - - @note The mapping is **complete** in the sense that any JSON value type - can be converted to a MessagePack value. - - @note The following values can **not** be converted to a MessagePack value: - - strings with more than 4294967295 bytes - - byte strings with more than 4294967295 bytes - - arrays with more than 4294967295 elements - - objects with more than 4294967295 elements - - @note Any MessagePack output created @ref to_msgpack can be successfully - parsed by @ref from_msgpack. - - @note If NaN or Infinity are stored inside a JSON number, they are - serialized properly. This behavior differs from the @ref dump() - function which serializes NaN or Infinity to `null`. - - @param[in] j JSON value to serialize - @return MessagePack serialization as byte vector - - @complexity Linear in the size of the JSON value @a j. - - @liveexample{The example shows the serialization of a JSON value to a byte - vector in MessagePack format.,to_msgpack} - - @sa http://msgpack.org - @sa @ref from_msgpack for the analogous deserialization - @sa @ref to_cbor(const basic_json& for the related CBOR format - @sa @ref to_ubjson(const basic_json&, const bool, const bool) for the - related UBJSON format - - @since version 2.0.9 - */ - static std::vector to_msgpack(const basic_json& j) - { - std::vector result; - to_msgpack(j, result); - return result; - } - - static void to_msgpack(const basic_json& j, detail::output_adapter o) - { - binary_writer(o).write_msgpack(j); - } - - static void to_msgpack(const basic_json& j, detail::output_adapter o) - { - binary_writer(o).write_msgpack(j); - } - - /*! - @brief create a UBJSON serialization of a given JSON value - - Serializes a given JSON value @a j to a byte vector using the UBJSON - (Universal Binary JSON) serialization format. UBJSON aims to be more compact - than JSON itself, yet more efficient to parse. - - The library uses the following mapping from JSON values types to - UBJSON types according to the UBJSON specification: - - JSON value type | value/range | UBJSON type | marker - --------------- | --------------------------------- | ----------- | ------ - null | `null` | null | `Z` - boolean | `true` | true | `T` - boolean | `false` | false | `F` - number_integer | -9223372036854775808..-2147483649 | int64 | `L` - number_integer | -2147483648..-32769 | int32 | `l` - number_integer | -32768..-129 | int16 | `I` - number_integer | -128..127 | int8 | `i` - number_integer | 128..255 | uint8 | `U` - number_integer | 256..32767 | int16 | `I` - number_integer | 32768..2147483647 | int32 | `l` - number_integer | 2147483648..9223372036854775807 | int64 | `L` - number_unsigned | 0..127 | int8 | `i` - number_unsigned | 128..255 | uint8 | `U` - number_unsigned | 256..32767 | int16 | `I` - number_unsigned | 32768..2147483647 | int32 | `l` - number_unsigned | 2147483648..9223372036854775807 | int64 | `L` - number_unsigned | 2147483649..18446744073709551615 | high-precision | `H` - number_float | *any value* | float64 | `D` - string | *with shortest length indicator* | string | `S` - array | *see notes on optimized format* | array | `[` - object | *see notes on optimized format* | map | `{` - - @note The mapping is **complete** in the sense that any JSON value type - can be converted to a UBJSON value. - - @note The following values can **not** be converted to a UBJSON value: - - strings with more than 9223372036854775807 bytes (theoretical) - - @note The following markers are not used in the conversion: - - `Z`: no-op values are not created. - - `C`: single-byte strings are serialized with `S` markers. - - @note Any UBJSON output created @ref to_ubjson can be successfully parsed - by @ref from_ubjson. - - @note If NaN or Infinity are stored inside a JSON number, they are - serialized properly. This behavior differs from the @ref dump() - function which serializes NaN or Infinity to `null`. - - @note The optimized formats for containers are supported: Parameter - @a use_size adds size information to the beginning of a container and - removes the closing marker. Parameter @a use_type further checks - whether all elements of a container have the same type and adds the - type marker to the beginning of the container. The @a use_type - parameter must only be used together with @a use_size = true. Note - that @a use_size = true alone may result in larger representations - - the benefit of this parameter is that the receiving side is - immediately informed on the number of elements of the container. - - @note If the JSON data contains the binary type, the value stored is a list - of integers, as suggested by the UBJSON documentation. In particular, - this means that serialization and the deserialization of a JSON - containing binary values into UBJSON and back will result in a - different JSON object. - - @param[in] j JSON value to serialize - @param[in] use_size whether to add size annotations to container types - @param[in] use_type whether to add type annotations to container types - (must be combined with @a use_size = true) - @return UBJSON serialization as byte vector - - @complexity Linear in the size of the JSON value @a j. - - @liveexample{The example shows the serialization of a JSON value to a byte - vector in UBJSON format.,to_ubjson} - - @sa http://ubjson.org - @sa @ref from_ubjson(detail::input_adapter&&, const bool, const bool) for the - analogous deserialization - @sa @ref to_cbor(const basic_json& for the related CBOR format - @sa @ref to_msgpack(const basic_json&) for the related MessagePack format - - @since version 3.1.0 - */ - static std::vector to_ubjson(const basic_json& j, - const bool use_size = false, - const bool use_type = false) - { - std::vector result; - to_ubjson(j, result, use_size, use_type); - return result; - } - - static void to_ubjson(const basic_json& j, detail::output_adapter o, - const bool use_size = false, const bool use_type = false) - { - binary_writer(o).write_ubjson(j, use_size, use_type); - } - - static void to_ubjson(const basic_json& j, detail::output_adapter o, - const bool use_size = false, const bool use_type = false) - { - binary_writer(o).write_ubjson(j, use_size, use_type); - } - - - /*! - @brief Serializes the given JSON object `j` to BSON and returns a vector - containing the corresponding BSON-representation. - - BSON (Binary JSON) is a binary format in which zero or more ordered key/value pairs are - stored as a single entity (a so-called document). - - The library uses the following mapping from JSON values types to BSON types: - - JSON value type | value/range | BSON type | marker - --------------- | --------------------------------- | ----------- | ------ - null | `null` | null | 0x0A - boolean | `true`, `false` | boolean | 0x08 - number_integer | -9223372036854775808..-2147483649 | int64 | 0x12 - number_integer | -2147483648..2147483647 | int32 | 0x10 - number_integer | 2147483648..9223372036854775807 | int64 | 0x12 - number_unsigned | 0..2147483647 | int32 | 0x10 - number_unsigned | 2147483648..9223372036854775807 | int64 | 0x12 - number_unsigned | 9223372036854775808..18446744073709551615| -- | -- - number_float | *any value* | double | 0x01 - string | *any value* | string | 0x02 - array | *any value* | document | 0x04 - object | *any value* | document | 0x03 - binary | *any value* | binary | 0x05 - - @warning The mapping is **incomplete**, since only JSON-objects (and things - contained therein) can be serialized to BSON. - Also, integers larger than 9223372036854775807 cannot be serialized to BSON, - and the keys may not contain U+0000, since they are serialized a - zero-terminated c-strings. - - @throw out_of_range.407 if `j.is_number_unsigned() && j.get() > 9223372036854775807` - @throw out_of_range.409 if a key in `j` contains a NULL (U+0000) - @throw type_error.317 if `!j.is_object()` - - @pre The input `j` is required to be an object: `j.is_object() == true`. - - @note Any BSON output created via @ref to_bson can be successfully parsed - by @ref from_bson. - - @param[in] j JSON value to serialize - @return BSON serialization as byte vector - - @complexity Linear in the size of the JSON value @a j. - - @liveexample{The example shows the serialization of a JSON value to a byte - vector in BSON format.,to_bson} - - @sa http://bsonspec.org/spec.html - @sa @ref from_bson(detail::input_adapter&&, const bool strict) for the - analogous deserialization - @sa @ref to_ubjson(const basic_json&, const bool, const bool) for the - related UBJSON format - @sa @ref to_cbor(const basic_json&) for the related CBOR format - @sa @ref to_msgpack(const basic_json&) for the related MessagePack format - */ - static std::vector to_bson(const basic_json& j) - { - std::vector result; - to_bson(j, result); - return result; - } - - /*! - @brief Serializes the given JSON object `j` to BSON and forwards the - corresponding BSON-representation to the given output_adapter `o`. - @param j The JSON object to convert to BSON. - @param o The output adapter that receives the binary BSON representation. - @pre The input `j` shall be an object: `j.is_object() == true` - @sa @ref to_bson(const basic_json&) - */ - static void to_bson(const basic_json& j, detail::output_adapter o) - { - binary_writer(o).write_bson(j); - } - - /*! - @copydoc to_bson(const basic_json&, detail::output_adapter) - */ - static void to_bson(const basic_json& j, detail::output_adapter o) - { - binary_writer(o).write_bson(j); - } - - - /*! - @brief create a JSON value from an input in CBOR format - - Deserializes a given input @a i to a JSON value using the CBOR (Concise - Binary Object Representation) serialization format. - - The library maps CBOR types to JSON value types as follows: - - CBOR type | JSON value type | first byte - ---------------------- | --------------- | ---------- - Integer | number_unsigned | 0x00..0x17 - Unsigned integer | number_unsigned | 0x18 - Unsigned integer | number_unsigned | 0x19 - Unsigned integer | number_unsigned | 0x1A - Unsigned integer | number_unsigned | 0x1B - Negative integer | number_integer | 0x20..0x37 - Negative integer | number_integer | 0x38 - Negative integer | number_integer | 0x39 - Negative integer | number_integer | 0x3A - Negative integer | number_integer | 0x3B - Byte string | binary | 0x40..0x57 - Byte string | binary | 0x58 - Byte string | binary | 0x59 - Byte string | binary | 0x5A - Byte string | binary | 0x5B - UTF-8 string | string | 0x60..0x77 - UTF-8 string | string | 0x78 - UTF-8 string | string | 0x79 - UTF-8 string | string | 0x7A - UTF-8 string | string | 0x7B - UTF-8 string | string | 0x7F - array | array | 0x80..0x97 - array | array | 0x98 - array | array | 0x99 - array | array | 0x9A - array | array | 0x9B - array | array | 0x9F - map | object | 0xA0..0xB7 - map | object | 0xB8 - map | object | 0xB9 - map | object | 0xBA - map | object | 0xBB - map | object | 0xBF - False | `false` | 0xF4 - True | `true` | 0xF5 - Null | `null` | 0xF6 - Half-Precision Float | number_float | 0xF9 - Single-Precision Float | number_float | 0xFA - Double-Precision Float | number_float | 0xFB - - @warning The mapping is **incomplete** in the sense that not all CBOR - types can be converted to a JSON value. The following CBOR types - are not supported and will yield parse errors (parse_error.112): - - date/time (0xC0..0xC1) - - bignum (0xC2..0xC3) - - decimal fraction (0xC4) - - bigfloat (0xC5) - - expected conversions (0xD5..0xD7) - - simple values (0xE0..0xF3, 0xF8) - - undefined (0xF7) - - @warning CBOR allows map keys of any type, whereas JSON only allows - strings as keys in object values. Therefore, CBOR maps with keys - other than UTF-8 strings are rejected (parse_error.113). - - @note Any CBOR output created @ref to_cbor can be successfully parsed by - @ref from_cbor. - - @param[in] i an input in CBOR format convertible to an input adapter - @param[in] strict whether to expect the input to be consumed until EOF - (true by default) - @param[in] allow_exceptions whether to throw exceptions in case of a - parse error (optional, true by default) - @param[in] tag_handler how to treat CBOR tags (optional, error by default) - - @return deserialized JSON value; in case of a parse error and - @a allow_exceptions set to `false`, the return value will be - value_t::discarded. - - @throw parse_error.110 if the given input ends prematurely or the end of - file was not reached when @a strict was set to true - @throw parse_error.112 if unsupported features from CBOR were - used in the given input @a v or if the input is not valid CBOR - @throw parse_error.113 if a string was expected as map key, but not found - - @complexity Linear in the size of the input @a i. - - @liveexample{The example shows the deserialization of a byte vector in CBOR - format to a JSON value.,from_cbor} - - @sa http://cbor.io - @sa @ref to_cbor(const basic_json&) for the analogous serialization - @sa @ref from_msgpack(detail::input_adapter&&, const bool, const bool) for the - related MessagePack format - @sa @ref from_ubjson(detail::input_adapter&&, const bool, const bool) for the - related UBJSON format - - @since version 2.0.9; parameter @a start_index since 2.1.1; changed to - consume input adapters, removed start_index parameter, and added - @a strict parameter since 3.0.0; added @a allow_exceptions parameter - since 3.2.0; added @a tag_handler parameter since 3.9.0. - */ - template - JSON_HEDLEY_WARN_UNUSED_RESULT - static basic_json from_cbor(InputType&& i, - const bool strict = true, - const bool allow_exceptions = true, - const cbor_tag_handler_t tag_handler = cbor_tag_handler_t::error) - { - basic_json result; - detail::json_sax_dom_parser sdp(result, allow_exceptions); - auto ia = detail::input_adapter(std::forward(i)); - const bool res = binary_reader(std::move(ia)).sax_parse(input_format_t::cbor, &sdp, strict, tag_handler); - return res ? result : basic_json(value_t::discarded); - } - - /*! - @copydoc from_cbor(detail::input_adapter&&, const bool, const bool, const cbor_tag_handler_t) - */ - template - JSON_HEDLEY_WARN_UNUSED_RESULT - static basic_json from_cbor(IteratorType first, IteratorType last, - const bool strict = true, - const bool allow_exceptions = true, - const cbor_tag_handler_t tag_handler = cbor_tag_handler_t::error) - { - basic_json result; - detail::json_sax_dom_parser sdp(result, allow_exceptions); - auto ia = detail::input_adapter(std::move(first), std::move(last)); - const bool res = binary_reader(std::move(ia)).sax_parse(input_format_t::cbor, &sdp, strict, tag_handler); - return res ? result : basic_json(value_t::discarded); - } - - template - JSON_HEDLEY_WARN_UNUSED_RESULT - JSON_HEDLEY_DEPRECATED_FOR(3.8.0, from_cbor(ptr, ptr + len)) - static basic_json from_cbor(const T* ptr, std::size_t len, - const bool strict = true, - const bool allow_exceptions = true, - const cbor_tag_handler_t tag_handler = cbor_tag_handler_t::error) - { - return from_cbor(ptr, ptr + len, strict, allow_exceptions, tag_handler); - } - - - JSON_HEDLEY_WARN_UNUSED_RESULT - JSON_HEDLEY_DEPRECATED_FOR(3.8.0, from_cbor(ptr, ptr + len)) - static basic_json from_cbor(detail::span_input_adapter&& i, - const bool strict = true, - const bool allow_exceptions = true, - const cbor_tag_handler_t tag_handler = cbor_tag_handler_t::error) - { - basic_json result; - detail::json_sax_dom_parser sdp(result, allow_exceptions); - auto ia = i.get(); - const bool res = binary_reader(std::move(ia)).sax_parse(input_format_t::cbor, &sdp, strict, tag_handler); - return res ? result : basic_json(value_t::discarded); - } - - /*! - @brief create a JSON value from an input in MessagePack format - - Deserializes a given input @a i to a JSON value using the MessagePack - serialization format. - - The library maps MessagePack types to JSON value types as follows: - - MessagePack type | JSON value type | first byte - ---------------- | --------------- | ---------- - positive fixint | number_unsigned | 0x00..0x7F - fixmap | object | 0x80..0x8F - fixarray | array | 0x90..0x9F - fixstr | string | 0xA0..0xBF - nil | `null` | 0xC0 - false | `false` | 0xC2 - true | `true` | 0xC3 - float 32 | number_float | 0xCA - float 64 | number_float | 0xCB - uint 8 | number_unsigned | 0xCC - uint 16 | number_unsigned | 0xCD - uint 32 | number_unsigned | 0xCE - uint 64 | number_unsigned | 0xCF - int 8 | number_integer | 0xD0 - int 16 | number_integer | 0xD1 - int 32 | number_integer | 0xD2 - int 64 | number_integer | 0xD3 - str 8 | string | 0xD9 - str 16 | string | 0xDA - str 32 | string | 0xDB - array 16 | array | 0xDC - array 32 | array | 0xDD - map 16 | object | 0xDE - map 32 | object | 0xDF - bin 8 | binary | 0xC4 - bin 16 | binary | 0xC5 - bin 32 | binary | 0xC6 - ext 8 | binary | 0xC7 - ext 16 | binary | 0xC8 - ext 32 | binary | 0xC9 - fixext 1 | binary | 0xD4 - fixext 2 | binary | 0xD5 - fixext 4 | binary | 0xD6 - fixext 8 | binary | 0xD7 - fixext 16 | binary | 0xD8 - negative fixint | number_integer | 0xE0-0xFF - - @note Any MessagePack output created @ref to_msgpack can be successfully - parsed by @ref from_msgpack. - - @param[in] i an input in MessagePack format convertible to an input - adapter - @param[in] strict whether to expect the input to be consumed until EOF - (true by default) - @param[in] allow_exceptions whether to throw exceptions in case of a - parse error (optional, true by default) - - @return deserialized JSON value; in case of a parse error and - @a allow_exceptions set to `false`, the return value will be - value_t::discarded. - - @throw parse_error.110 if the given input ends prematurely or the end of - file was not reached when @a strict was set to true - @throw parse_error.112 if unsupported features from MessagePack were - used in the given input @a i or if the input is not valid MessagePack - @throw parse_error.113 if a string was expected as map key, but not found - - @complexity Linear in the size of the input @a i. - - @liveexample{The example shows the deserialization of a byte vector in - MessagePack format to a JSON value.,from_msgpack} - - @sa http://msgpack.org - @sa @ref to_msgpack(const basic_json&) for the analogous serialization - @sa @ref from_cbor(detail::input_adapter&&, const bool, const bool, const cbor_tag_handler_t) for the - related CBOR format - @sa @ref from_ubjson(detail::input_adapter&&, const bool, const bool) for - the related UBJSON format - @sa @ref from_bson(detail::input_adapter&&, const bool, const bool) for - the related BSON format - - @since version 2.0.9; parameter @a start_index since 2.1.1; changed to - consume input adapters, removed start_index parameter, and added - @a strict parameter since 3.0.0; added @a allow_exceptions parameter - since 3.2.0 - */ - template - JSON_HEDLEY_WARN_UNUSED_RESULT - static basic_json from_msgpack(InputType&& i, - const bool strict = true, - const bool allow_exceptions = true) - { - basic_json result; - detail::json_sax_dom_parser sdp(result, allow_exceptions); - auto ia = detail::input_adapter(std::forward(i)); - const bool res = binary_reader(std::move(ia)).sax_parse(input_format_t::msgpack, &sdp, strict); - return res ? result : basic_json(value_t::discarded); - } - - /*! - @copydoc from_msgpack(detail::input_adapter&&, const bool, const bool) - */ - template - JSON_HEDLEY_WARN_UNUSED_RESULT - static basic_json from_msgpack(IteratorType first, IteratorType last, - const bool strict = true, - const bool allow_exceptions = true) - { - basic_json result; - detail::json_sax_dom_parser sdp(result, allow_exceptions); - auto ia = detail::input_adapter(std::move(first), std::move(last)); - const bool res = binary_reader(std::move(ia)).sax_parse(input_format_t::msgpack, &sdp, strict); - return res ? result : basic_json(value_t::discarded); - } - - - template - JSON_HEDLEY_WARN_UNUSED_RESULT - JSON_HEDLEY_DEPRECATED_FOR(3.8.0, from_msgpack(ptr, ptr + len)) - static basic_json from_msgpack(const T* ptr, std::size_t len, - const bool strict = true, - const bool allow_exceptions = true) - { - return from_msgpack(ptr, ptr + len, strict, allow_exceptions); - } - - JSON_HEDLEY_WARN_UNUSED_RESULT - JSON_HEDLEY_DEPRECATED_FOR(3.8.0, from_msgpack(ptr, ptr + len)) - static basic_json from_msgpack(detail::span_input_adapter&& i, - const bool strict = true, - const bool allow_exceptions = true) - { - basic_json result; - detail::json_sax_dom_parser sdp(result, allow_exceptions); - auto ia = i.get(); - const bool res = binary_reader(std::move(ia)).sax_parse(input_format_t::msgpack, &sdp, strict); - return res ? result : basic_json(value_t::discarded); - } - - - /*! - @brief create a JSON value from an input in UBJSON format - - Deserializes a given input @a i to a JSON value using the UBJSON (Universal - Binary JSON) serialization format. - - The library maps UBJSON types to JSON value types as follows: - - UBJSON type | JSON value type | marker - ----------- | --------------------------------------- | ------ - no-op | *no value, next value is read* | `N` - null | `null` | `Z` - false | `false` | `F` - true | `true` | `T` - float32 | number_float | `d` - float64 | number_float | `D` - uint8 | number_unsigned | `U` - int8 | number_integer | `i` - int16 | number_integer | `I` - int32 | number_integer | `l` - int64 | number_integer | `L` - high-precision number | number_integer, number_unsigned, or number_float - depends on number string | 'H' - string | string | `S` - char | string | `C` - array | array (optimized values are supported) | `[` - object | object (optimized values are supported) | `{` - - @note The mapping is **complete** in the sense that any UBJSON value can - be converted to a JSON value. - - @param[in] i an input in UBJSON format convertible to an input adapter - @param[in] strict whether to expect the input to be consumed until EOF - (true by default) - @param[in] allow_exceptions whether to throw exceptions in case of a - parse error (optional, true by default) - - @return deserialized JSON value; in case of a parse error and - @a allow_exceptions set to `false`, the return value will be - value_t::discarded. - - @throw parse_error.110 if the given input ends prematurely or the end of - file was not reached when @a strict was set to true - @throw parse_error.112 if a parse error occurs - @throw parse_error.113 if a string could not be parsed successfully - - @complexity Linear in the size of the input @a i. - - @liveexample{The example shows the deserialization of a byte vector in - UBJSON format to a JSON value.,from_ubjson} - - @sa http://ubjson.org - @sa @ref to_ubjson(const basic_json&, const bool, const bool) for the - analogous serialization - @sa @ref from_cbor(detail::input_adapter&&, const bool, const bool, const cbor_tag_handler_t) for the - related CBOR format - @sa @ref from_msgpack(detail::input_adapter&&, const bool, const bool) for - the related MessagePack format - @sa @ref from_bson(detail::input_adapter&&, const bool, const bool) for - the related BSON format - - @since version 3.1.0; added @a allow_exceptions parameter since 3.2.0 - */ - template - JSON_HEDLEY_WARN_UNUSED_RESULT - static basic_json from_ubjson(InputType&& i, - const bool strict = true, - const bool allow_exceptions = true) - { - basic_json result; - detail::json_sax_dom_parser sdp(result, allow_exceptions); - auto ia = detail::input_adapter(std::forward(i)); - const bool res = binary_reader(std::move(ia)).sax_parse(input_format_t::ubjson, &sdp, strict); - return res ? result : basic_json(value_t::discarded); - } - - /*! - @copydoc from_ubjson(detail::input_adapter&&, const bool, const bool) - */ - template - JSON_HEDLEY_WARN_UNUSED_RESULT - static basic_json from_ubjson(IteratorType first, IteratorType last, - const bool strict = true, - const bool allow_exceptions = true) - { - basic_json result; - detail::json_sax_dom_parser sdp(result, allow_exceptions); - auto ia = detail::input_adapter(std::move(first), std::move(last)); - const bool res = binary_reader(std::move(ia)).sax_parse(input_format_t::ubjson, &sdp, strict); - return res ? result : basic_json(value_t::discarded); - } - - template - JSON_HEDLEY_WARN_UNUSED_RESULT - JSON_HEDLEY_DEPRECATED_FOR(3.8.0, from_ubjson(ptr, ptr + len)) - static basic_json from_ubjson(const T* ptr, std::size_t len, - const bool strict = true, - const bool allow_exceptions = true) - { - return from_ubjson(ptr, ptr + len, strict, allow_exceptions); - } - - JSON_HEDLEY_WARN_UNUSED_RESULT - JSON_HEDLEY_DEPRECATED_FOR(3.8.0, from_ubjson(ptr, ptr + len)) - static basic_json from_ubjson(detail::span_input_adapter&& i, - const bool strict = true, - const bool allow_exceptions = true) - { - basic_json result; - detail::json_sax_dom_parser sdp(result, allow_exceptions); - auto ia = i.get(); - const bool res = binary_reader(std::move(ia)).sax_parse(input_format_t::ubjson, &sdp, strict); - return res ? result : basic_json(value_t::discarded); - } - - - /*! - @brief Create a JSON value from an input in BSON format - - Deserializes a given input @a i to a JSON value using the BSON (Binary JSON) - serialization format. - - The library maps BSON record types to JSON value types as follows: - - BSON type | BSON marker byte | JSON value type - --------------- | ---------------- | --------------------------- - double | 0x01 | number_float - string | 0x02 | string - document | 0x03 | object - array | 0x04 | array - binary | 0x05 | still unsupported - undefined | 0x06 | still unsupported - ObjectId | 0x07 | still unsupported - boolean | 0x08 | boolean - UTC Date-Time | 0x09 | still unsupported - null | 0x0A | null - Regular Expr. | 0x0B | still unsupported - DB Pointer | 0x0C | still unsupported - JavaScript Code | 0x0D | still unsupported - Symbol | 0x0E | still unsupported - JavaScript Code | 0x0F | still unsupported - int32 | 0x10 | number_integer - Timestamp | 0x11 | still unsupported - 128-bit decimal float | 0x13 | still unsupported - Max Key | 0x7F | still unsupported - Min Key | 0xFF | still unsupported - - @warning The mapping is **incomplete**. The unsupported mappings - are indicated in the table above. - - @param[in] i an input in BSON format convertible to an input adapter - @param[in] strict whether to expect the input to be consumed until EOF - (true by default) - @param[in] allow_exceptions whether to throw exceptions in case of a - parse error (optional, true by default) - - @return deserialized JSON value; in case of a parse error and - @a allow_exceptions set to `false`, the return value will be - value_t::discarded. - - @throw parse_error.114 if an unsupported BSON record type is encountered - - @complexity Linear in the size of the input @a i. - - @liveexample{The example shows the deserialization of a byte vector in - BSON format to a JSON value.,from_bson} - - @sa http://bsonspec.org/spec.html - @sa @ref to_bson(const basic_json&) for the analogous serialization - @sa @ref from_cbor(detail::input_adapter&&, const bool, const bool, const cbor_tag_handler_t) for the - related CBOR format - @sa @ref from_msgpack(detail::input_adapter&&, const bool, const bool) for - the related MessagePack format - @sa @ref from_ubjson(detail::input_adapter&&, const bool, const bool) for the - related UBJSON format - */ - template - JSON_HEDLEY_WARN_UNUSED_RESULT - static basic_json from_bson(InputType&& i, - const bool strict = true, - const bool allow_exceptions = true) - { - basic_json result; - detail::json_sax_dom_parser sdp(result, allow_exceptions); - auto ia = detail::input_adapter(std::forward(i)); - const bool res = binary_reader(std::move(ia)).sax_parse(input_format_t::bson, &sdp, strict); - return res ? result : basic_json(value_t::discarded); - } - - /*! - @copydoc from_bson(detail::input_adapter&&, const bool, const bool) - */ - template - JSON_HEDLEY_WARN_UNUSED_RESULT - static basic_json from_bson(IteratorType first, IteratorType last, - const bool strict = true, - const bool allow_exceptions = true) - { - basic_json result; - detail::json_sax_dom_parser sdp(result, allow_exceptions); - auto ia = detail::input_adapter(std::move(first), std::move(last)); - const bool res = binary_reader(std::move(ia)).sax_parse(input_format_t::bson, &sdp, strict); - return res ? result : basic_json(value_t::discarded); - } - - template - JSON_HEDLEY_WARN_UNUSED_RESULT - JSON_HEDLEY_DEPRECATED_FOR(3.8.0, from_bson(ptr, ptr + len)) - static basic_json from_bson(const T* ptr, std::size_t len, - const bool strict = true, - const bool allow_exceptions = true) - { - return from_bson(ptr, ptr + len, strict, allow_exceptions); - } - - JSON_HEDLEY_WARN_UNUSED_RESULT - JSON_HEDLEY_DEPRECATED_FOR(3.8.0, from_bson(ptr, ptr + len)) - static basic_json from_bson(detail::span_input_adapter&& i, - const bool strict = true, - const bool allow_exceptions = true) - { - basic_json result; - detail::json_sax_dom_parser sdp(result, allow_exceptions); - auto ia = i.get(); - const bool res = binary_reader(std::move(ia)).sax_parse(input_format_t::bson, &sdp, strict); - return res ? result : basic_json(value_t::discarded); - } - /// @} - - ////////////////////////// - // JSON Pointer support // - ////////////////////////// - - /// @name JSON Pointer functions - /// @{ - - /*! - @brief access specified element via JSON Pointer - - Uses a JSON pointer to retrieve a reference to the respective JSON value. - No bound checking is performed. Similar to @ref operator[](const typename - object_t::key_type&), `null` values are created in arrays and objects if - necessary. - - In particular: - - If the JSON pointer points to an object key that does not exist, it - is created an filled with a `null` value before a reference to it - is returned. - - If the JSON pointer points to an array index that does not exist, it - is created an filled with a `null` value before a reference to it - is returned. All indices between the current maximum and the given - index are also filled with `null`. - - The special value `-` is treated as a synonym for the index past the - end. - - @param[in] ptr a JSON pointer - - @return reference to the element pointed to by @a ptr - - @complexity Constant. - - @throw parse_error.106 if an array index begins with '0' - @throw parse_error.109 if an array index was not a number - @throw out_of_range.404 if the JSON pointer can not be resolved - - @liveexample{The behavior is shown in the example.,operatorjson_pointer} - - @since version 2.0.0 - */ - reference operator[](const json_pointer& ptr) - { - return ptr.get_unchecked(this); - } - - /*! - @brief access specified element via JSON Pointer - - Uses a JSON pointer to retrieve a reference to the respective JSON value. - No bound checking is performed. The function does not change the JSON - value; no `null` values are created. In particular, the special value - `-` yields an exception. - - @param[in] ptr JSON pointer to the desired element - - @return const reference to the element pointed to by @a ptr - - @complexity Constant. - - @throw parse_error.106 if an array index begins with '0' - @throw parse_error.109 if an array index was not a number - @throw out_of_range.402 if the array index '-' is used - @throw out_of_range.404 if the JSON pointer can not be resolved - - @liveexample{The behavior is shown in the example.,operatorjson_pointer_const} - - @since version 2.0.0 - */ - const_reference operator[](const json_pointer& ptr) const - { - return ptr.get_unchecked(this); - } - - /*! - @brief access specified element via JSON Pointer - - Returns a reference to the element at with specified JSON pointer @a ptr, - with bounds checking. - - @param[in] ptr JSON pointer to the desired element - - @return reference to the element pointed to by @a ptr - - @throw parse_error.106 if an array index in the passed JSON pointer @a ptr - begins with '0'. See example below. - - @throw parse_error.109 if an array index in the passed JSON pointer @a ptr - is not a number. See example below. - - @throw out_of_range.401 if an array index in the passed JSON pointer @a ptr - is out of range. See example below. - - @throw out_of_range.402 if the array index '-' is used in the passed JSON - pointer @a ptr. As `at` provides checked access (and no elements are - implicitly inserted), the index '-' is always invalid. See example below. - - @throw out_of_range.403 if the JSON pointer describes a key of an object - which cannot be found. See example below. - - @throw out_of_range.404 if the JSON pointer @a ptr can not be resolved. - See example below. - - @exceptionsafety Strong guarantee: if an exception is thrown, there are no - changes in the JSON value. - - @complexity Constant. - - @since version 2.0.0 - - @liveexample{The behavior is shown in the example.,at_json_pointer} - */ - reference at(const json_pointer& ptr) - { - return ptr.get_checked(this); - } - - /*! - @brief access specified element via JSON Pointer - - Returns a const reference to the element at with specified JSON pointer @a - ptr, with bounds checking. - - @param[in] ptr JSON pointer to the desired element - - @return reference to the element pointed to by @a ptr - - @throw parse_error.106 if an array index in the passed JSON pointer @a ptr - begins with '0'. See example below. - - @throw parse_error.109 if an array index in the passed JSON pointer @a ptr - is not a number. See example below. - - @throw out_of_range.401 if an array index in the passed JSON pointer @a ptr - is out of range. See example below. - - @throw out_of_range.402 if the array index '-' is used in the passed JSON - pointer @a ptr. As `at` provides checked access (and no elements are - implicitly inserted), the index '-' is always invalid. See example below. - - @throw out_of_range.403 if the JSON pointer describes a key of an object - which cannot be found. See example below. - - @throw out_of_range.404 if the JSON pointer @a ptr can not be resolved. - See example below. - - @exceptionsafety Strong guarantee: if an exception is thrown, there are no - changes in the JSON value. - - @complexity Constant. - - @since version 2.0.0 - - @liveexample{The behavior is shown in the example.,at_json_pointer_const} - */ - const_reference at(const json_pointer& ptr) const - { - return ptr.get_checked(this); - } - - /*! - @brief return flattened JSON value - - The function creates a JSON object whose keys are JSON pointers (see [RFC - 6901](https://tools.ietf.org/html/rfc6901)) and whose values are all - primitive. The original JSON value can be restored using the @ref - unflatten() function. - - @return an object that maps JSON pointers to primitive values - - @note Empty objects and arrays are flattened to `null` and will not be - reconstructed correctly by the @ref unflatten() function. - - @complexity Linear in the size the JSON value. - - @liveexample{The following code shows how a JSON object is flattened to an - object whose keys consist of JSON pointers.,flatten} - - @sa @ref unflatten() for the reverse function - - @since version 2.0.0 - */ - basic_json flatten() const - { - basic_json result(value_t::object); - json_pointer::flatten("", *this, result); - return result; - } - - /*! - @brief unflatten a previously flattened JSON value - - The function restores the arbitrary nesting of a JSON value that has been - flattened before using the @ref flatten() function. The JSON value must - meet certain constraints: - 1. The value must be an object. - 2. The keys must be JSON pointers (see - [RFC 6901](https://tools.ietf.org/html/rfc6901)) - 3. The mapped values must be primitive JSON types. - - @return the original JSON from a flattened version - - @note Empty objects and arrays are flattened by @ref flatten() to `null` - values and can not unflattened to their original type. Apart from - this example, for a JSON value `j`, the following is always true: - `j == j.flatten().unflatten()`. - - @complexity Linear in the size the JSON value. - - @throw type_error.314 if value is not an object - @throw type_error.315 if object values are not primitive - - @liveexample{The following code shows how a flattened JSON object is - unflattened into the original nested JSON object.,unflatten} - - @sa @ref flatten() for the reverse function - - @since version 2.0.0 - */ - basic_json unflatten() const - { - return json_pointer::unflatten(*this); - } - - /// @} - - ////////////////////////// - // JSON Patch functions // - ////////////////////////// - - /// @name JSON Patch functions - /// @{ - - /*! - @brief applies a JSON patch - - [JSON Patch](http://jsonpatch.com) defines a JSON document structure for - expressing a sequence of operations to apply to a JSON) document. With - this function, a JSON Patch is applied to the current JSON value by - executing all operations from the patch. - - @param[in] json_patch JSON patch document - @return patched document - - @note The application of a patch is atomic: Either all operations succeed - and the patched document is returned or an exception is thrown. In - any case, the original value is not changed: the patch is applied - to a copy of the value. - - @throw parse_error.104 if the JSON patch does not consist of an array of - objects - - @throw parse_error.105 if the JSON patch is malformed (e.g., mandatory - attributes are missing); example: `"operation add must have member path"` - - @throw out_of_range.401 if an array index is out of range. - - @throw out_of_range.403 if a JSON pointer inside the patch could not be - resolved successfully in the current JSON value; example: `"key baz not - found"` - - @throw out_of_range.405 if JSON pointer has no parent ("add", "remove", - "move") - - @throw other_error.501 if "test" operation was unsuccessful - - @complexity Linear in the size of the JSON value and the length of the - JSON patch. As usually only a fraction of the JSON value is affected by - the patch, the complexity can usually be neglected. - - @liveexample{The following code shows how a JSON patch is applied to a - value.,patch} - - @sa @ref diff -- create a JSON patch by comparing two JSON values - - @sa [RFC 6902 (JSON Patch)](https://tools.ietf.org/html/rfc6902) - @sa [RFC 6901 (JSON Pointer)](https://tools.ietf.org/html/rfc6901) - - @since version 2.0.0 - */ - basic_json patch(const basic_json& json_patch) const - { - // make a working copy to apply the patch to - basic_json result = *this; - - // the valid JSON Patch operations - enum class patch_operations {add, remove, replace, move, copy, test, invalid}; - - const auto get_op = [](const std::string & op) - { - if (op == "add") - { - return patch_operations::add; - } - if (op == "remove") - { - return patch_operations::remove; - } - if (op == "replace") - { - return patch_operations::replace; - } - if (op == "move") - { - return patch_operations::move; - } - if (op == "copy") - { - return patch_operations::copy; - } - if (op == "test") - { - return patch_operations::test; - } - - return patch_operations::invalid; - }; - - // wrapper for "add" operation; add value at ptr - const auto operation_add = [&result](json_pointer & ptr, basic_json val) - { - // adding to the root of the target document means replacing it - if (ptr.empty()) - { - result = val; - return; - } - - // make sure the top element of the pointer exists - json_pointer top_pointer = ptr.top(); - if (top_pointer != ptr) - { - result.at(top_pointer); - } - - // get reference to parent of JSON pointer ptr - const auto last_path = ptr.back(); - ptr.pop_back(); - basic_json& parent = result[ptr]; - - switch (parent.m_type) - { - case value_t::null: - case value_t::object: - { - // use operator[] to add value - parent[last_path] = val; - break; - } - - case value_t::array: - { - if (last_path == "-") - { - // special case: append to back - parent.push_back(val); - } - else - { - const auto idx = json_pointer::array_index(last_path); - if (JSON_HEDLEY_UNLIKELY(idx > parent.size())) - { - // avoid undefined behavior - JSON_THROW(out_of_range::create(401, "array index " + std::to_string(idx) + " is out of range")); - } - - // default case: insert add offset - parent.insert(parent.begin() + static_cast(idx), val); - } - break; - } - - // if there exists a parent it cannot be primitive - default: // LCOV_EXCL_LINE - JSON_ASSERT(false); // LCOV_EXCL_LINE - } - }; - - // wrapper for "remove" operation; remove value at ptr - const auto operation_remove = [&result](json_pointer & ptr) - { - // get reference to parent of JSON pointer ptr - const auto last_path = ptr.back(); - ptr.pop_back(); - basic_json& parent = result.at(ptr); - - // remove child - if (parent.is_object()) - { - // perform range check - auto it = parent.find(last_path); - if (JSON_HEDLEY_LIKELY(it != parent.end())) - { - parent.erase(it); - } - else - { - JSON_THROW(out_of_range::create(403, "key '" + last_path + "' not found")); - } - } - else if (parent.is_array()) - { - // note erase performs range check - parent.erase(json_pointer::array_index(last_path)); - } - }; - - // type check: top level value must be an array - if (JSON_HEDLEY_UNLIKELY(!json_patch.is_array())) - { - JSON_THROW(parse_error::create(104, 0, "JSON patch must be an array of objects")); - } - - // iterate and apply the operations - for (const auto& val : json_patch) - { - // wrapper to get a value for an operation - const auto get_value = [&val](const std::string & op, - const std::string & member, - bool string_type) -> basic_json & - { - // find value - auto it = val.m_value.object->find(member); - - // context-sensitive error message - const auto error_msg = (op == "op") ? "operation" : "operation '" + op + "'"; - - // check if desired value is present - if (JSON_HEDLEY_UNLIKELY(it == val.m_value.object->end())) - { - JSON_THROW(parse_error::create(105, 0, error_msg + " must have member '" + member + "'")); - } - - // check if result is of type string - if (JSON_HEDLEY_UNLIKELY(string_type && !it->second.is_string())) - { - JSON_THROW(parse_error::create(105, 0, error_msg + " must have string member '" + member + "'")); - } - - // no error: return value - return it->second; - }; - - // type check: every element of the array must be an object - if (JSON_HEDLEY_UNLIKELY(!val.is_object())) - { - JSON_THROW(parse_error::create(104, 0, "JSON patch must be an array of objects")); - } - - // collect mandatory members - const auto op = get_value("op", "op", true).template get(); - const auto path = get_value(op, "path", true).template get(); - json_pointer ptr(path); - - switch (get_op(op)) - { - case patch_operations::add: - { - operation_add(ptr, get_value("add", "value", false)); - break; - } - - case patch_operations::remove: - { - operation_remove(ptr); - break; - } - - case patch_operations::replace: - { - // the "path" location must exist - use at() - result.at(ptr) = get_value("replace", "value", false); - break; - } - - case patch_operations::move: - { - const auto from_path = get_value("move", "from", true).template get(); - json_pointer from_ptr(from_path); - - // the "from" location must exist - use at() - basic_json v = result.at(from_ptr); - - // The move operation is functionally identical to a - // "remove" operation on the "from" location, followed - // immediately by an "add" operation at the target - // location with the value that was just removed. - operation_remove(from_ptr); - operation_add(ptr, v); - break; - } - - case patch_operations::copy: - { - const auto from_path = get_value("copy", "from", true).template get(); - const json_pointer from_ptr(from_path); - - // the "from" location must exist - use at() - basic_json v = result.at(from_ptr); - - // The copy is functionally identical to an "add" - // operation at the target location using the value - // specified in the "from" member. - operation_add(ptr, v); - break; - } - - case patch_operations::test: - { - bool success = false; - JSON_TRY - { - // check if "value" matches the one at "path" - // the "path" location must exist - use at() - success = (result.at(ptr) == get_value("test", "value", false)); - } - JSON_INTERNAL_CATCH (out_of_range&) - { - // ignore out of range errors: success remains false - } - - // throw an exception if test fails - if (JSON_HEDLEY_UNLIKELY(!success)) - { - JSON_THROW(other_error::create(501, "unsuccessful: " + val.dump())); - } - - break; - } - - default: - { - // op must be "add", "remove", "replace", "move", "copy", or - // "test" - JSON_THROW(parse_error::create(105, 0, "operation value '" + op + "' is invalid")); - } - } - } - - return result; - } - - /*! - @brief creates a diff as a JSON patch - - Creates a [JSON Patch](http://jsonpatch.com) so that value @a source can - be changed into the value @a target by calling @ref patch function. - - @invariant For two JSON values @a source and @a target, the following code - yields always `true`: - @code {.cpp} - source.patch(diff(source, target)) == target; - @endcode - - @note Currently, only `remove`, `add`, and `replace` operations are - generated. - - @param[in] source JSON value to compare from - @param[in] target JSON value to compare against - @param[in] path helper value to create JSON pointers - - @return a JSON patch to convert the @a source to @a target - - @complexity Linear in the lengths of @a source and @a target. - - @liveexample{The following code shows how a JSON patch is created as a - diff for two JSON values.,diff} - - @sa @ref patch -- apply a JSON patch - @sa @ref merge_patch -- apply a JSON Merge Patch - - @sa [RFC 6902 (JSON Patch)](https://tools.ietf.org/html/rfc6902) - - @since version 2.0.0 - */ - JSON_HEDLEY_WARN_UNUSED_RESULT - static basic_json diff(const basic_json& source, const basic_json& target, - const std::string& path = "") - { - // the patch - basic_json result(value_t::array); - - // if the values are the same, return empty patch - if (source == target) - { - return result; - } - - if (source.type() != target.type()) - { - // different types: replace value - result.push_back( - { - {"op", "replace"}, {"path", path}, {"value", target} - }); - return result; - } - - switch (source.type()) - { - case value_t::array: - { - // first pass: traverse common elements - std::size_t i = 0; - while (i < source.size() && i < target.size()) - { - // recursive call to compare array values at index i - auto temp_diff = diff(source[i], target[i], path + "/" + std::to_string(i)); - result.insert(result.end(), temp_diff.begin(), temp_diff.end()); - ++i; - } - - // i now reached the end of at least one array - // in a second pass, traverse the remaining elements - - // remove my remaining elements - const auto end_index = static_cast(result.size()); - while (i < source.size()) - { - // add operations in reverse order to avoid invalid - // indices - result.insert(result.begin() + end_index, object( - { - {"op", "remove"}, - {"path", path + "/" + std::to_string(i)} - })); - ++i; - } - - // add other remaining elements - while (i < target.size()) - { - result.push_back( - { - {"op", "add"}, - {"path", path + "/-"}, - {"value", target[i]} - }); - ++i; - } - - break; - } - - case value_t::object: - { - // first pass: traverse this object's elements - for (auto it = source.cbegin(); it != source.cend(); ++it) - { - // escape the key name to be used in a JSON patch - const auto key = json_pointer::escape(it.key()); - - if (target.find(it.key()) != target.end()) - { - // recursive call to compare object values at key it - auto temp_diff = diff(it.value(), target[it.key()], path + "/" + key); - result.insert(result.end(), temp_diff.begin(), temp_diff.end()); - } - else - { - // found a key that is not in o -> remove it - result.push_back(object( - { - {"op", "remove"}, {"path", path + "/" + key} - })); - } - } - - // second pass: traverse other object's elements - for (auto it = target.cbegin(); it != target.cend(); ++it) - { - if (source.find(it.key()) == source.end()) - { - // found a key that is not in this -> add it - const auto key = json_pointer::escape(it.key()); - result.push_back( - { - {"op", "add"}, {"path", path + "/" + key}, - {"value", it.value()} - }); - } - } - - break; - } - - default: - { - // both primitive type: replace value - result.push_back( - { - {"op", "replace"}, {"path", path}, {"value", target} - }); - break; - } - } - - return result; - } - - /// @} - - //////////////////////////////// - // JSON Merge Patch functions // - //////////////////////////////// - - /// @name JSON Merge Patch functions - /// @{ - - /*! - @brief applies a JSON Merge Patch - - The merge patch format is primarily intended for use with the HTTP PATCH - method as a means of describing a set of modifications to a target - resource's content. This function applies a merge patch to the current - JSON value. - - The function implements the following algorithm from Section 2 of - [RFC 7396 (JSON Merge Patch)](https://tools.ietf.org/html/rfc7396): - - ``` - define MergePatch(Target, Patch): - if Patch is an Object: - if Target is not an Object: - Target = {} // Ignore the contents and set it to an empty Object - for each Name/Value pair in Patch: - if Value is null: - if Name exists in Target: - remove the Name/Value pair from Target - else: - Target[Name] = MergePatch(Target[Name], Value) - return Target - else: - return Patch - ``` - - Thereby, `Target` is the current object; that is, the patch is applied to - the current value. - - @param[in] apply_patch the patch to apply - - @complexity Linear in the lengths of @a patch. - - @liveexample{The following code shows how a JSON Merge Patch is applied to - a JSON document.,merge_patch} - - @sa @ref patch -- apply a JSON patch - @sa [RFC 7396 (JSON Merge Patch)](https://tools.ietf.org/html/rfc7396) - - @since version 3.0.0 - */ - void merge_patch(const basic_json& apply_patch) - { - if (apply_patch.is_object()) - { - if (!is_object()) - { - *this = object(); - } - for (auto it = apply_patch.begin(); it != apply_patch.end(); ++it) - { - if (it.value().is_null()) - { - erase(it.key()); - } - else - { - operator[](it.key()).merge_patch(it.value()); - } - } - } - else - { - *this = apply_patch; - } - } - - /// @} -}; - -/*! -@brief user-defined to_string function for JSON values - -This function implements a user-defined to_string for JSON objects. - -@param[in] j a JSON object -@return a std::string object -*/ - -NLOHMANN_BASIC_JSON_TPL_DECLARATION -std::string to_string(const NLOHMANN_BASIC_JSON_TPL& j) -{ - return j.dump(); -} -} // namespace nlohmann - -/////////////////////// -// nonmember support // -/////////////////////// - -// specialization of std::swap, and std::hash -namespace std -{ - -/// hash value for JSON objects -template<> -struct hash -{ - /*! - @brief return a hash value for a JSON object - - @since version 1.0.0 - */ - std::size_t operator()(const nlohmann::json& j) const - { - return nlohmann::detail::hash(j); - } -}; - -/// specialization for std::less -/// @note: do not remove the space after '<', -/// see https://github.com/nlohmann/json/pull/679 -template<> -struct less<::nlohmann::detail::value_t> -{ - /*! - @brief compare two value_t enum values - @since version 3.0.0 - */ - bool operator()(nlohmann::detail::value_t lhs, - nlohmann::detail::value_t rhs) const noexcept - { - return nlohmann::detail::operator<(lhs, rhs); - } -}; - -// C++20 prohibit function specialization in the std namespace. -#ifndef JSON_HAS_CPP_20 - -/*! -@brief exchanges the values of two JSON objects - -@since version 1.0.0 -*/ -template<> -inline void swap(nlohmann::json& j1, nlohmann::json& j2) noexcept( - is_nothrow_move_constructible::value&& - is_nothrow_move_assignable::value - ) -{ - j1.swap(j2); -} - -#endif - -} // namespace std - -/*! -@brief user-defined string literal for JSON values - -This operator implements a user-defined string literal for JSON objects. It -can be used by adding `"_json"` to a string literal and returns a JSON object -if no parse error occurred. - -@param[in] s a string representation of a JSON object -@param[in] n the length of string @a s -@return a JSON object - -@since version 1.0.0 -*/ -JSON_HEDLEY_NON_NULL(1) -inline nlohmann::json operator "" _json(const char* s, std::size_t n) -{ - return nlohmann::json::parse(s, s + n); -} - -/*! -@brief user-defined string literal for JSON pointer - -This operator implements a user-defined string literal for JSON Pointers. It -can be used by adding `"_json_pointer"` to a string literal and returns a JSON pointer -object if no parse error occurred. - -@param[in] s a string representation of a JSON Pointer -@param[in] n the length of string @a s -@return a JSON pointer object - -@since version 2.0.0 -*/ -JSON_HEDLEY_NON_NULL(1) -inline nlohmann::json::json_pointer operator "" _json_pointer(const char* s, std::size_t n) -{ - return nlohmann::json::json_pointer(std::string(s, n)); -} - -// #include - - -// restore GCC/clang diagnostic settings -#if defined(__clang__) || defined(__GNUC__) || defined(__GNUG__) - #pragma GCC diagnostic pop -#endif -#if defined(__clang__) - #pragma GCC diagnostic pop -#endif - -// clean up -#undef JSON_ASSERT -#undef JSON_INTERNAL_CATCH -#undef JSON_CATCH -#undef JSON_THROW -#undef JSON_TRY -#undef JSON_HAS_CPP_14 -#undef JSON_HAS_CPP_17 -#undef NLOHMANN_BASIC_JSON_TPL_DECLARATION -#undef NLOHMANN_BASIC_JSON_TPL -#undef JSON_EXPLICIT - -// #include -#undef JSON_HEDLEY_ALWAYS_INLINE -#undef JSON_HEDLEY_ARM_VERSION -#undef JSON_HEDLEY_ARM_VERSION_CHECK -#undef JSON_HEDLEY_ARRAY_PARAM -#undef JSON_HEDLEY_ASSUME -#undef JSON_HEDLEY_BEGIN_C_DECLS -#undef JSON_HEDLEY_CLANG_HAS_ATTRIBUTE -#undef JSON_HEDLEY_CLANG_HAS_BUILTIN -#undef JSON_HEDLEY_CLANG_HAS_CPP_ATTRIBUTE -#undef JSON_HEDLEY_CLANG_HAS_DECLSPEC_DECLSPEC_ATTRIBUTE -#undef JSON_HEDLEY_CLANG_HAS_EXTENSION -#undef JSON_HEDLEY_CLANG_HAS_FEATURE -#undef JSON_HEDLEY_CLANG_HAS_WARNING -#undef JSON_HEDLEY_COMPCERT_VERSION -#undef JSON_HEDLEY_COMPCERT_VERSION_CHECK -#undef JSON_HEDLEY_CONCAT -#undef JSON_HEDLEY_CONCAT3 -#undef JSON_HEDLEY_CONCAT3_EX -#undef JSON_HEDLEY_CONCAT_EX -#undef JSON_HEDLEY_CONST -#undef JSON_HEDLEY_CONSTEXPR -#undef JSON_HEDLEY_CONST_CAST -#undef JSON_HEDLEY_CPP_CAST -#undef JSON_HEDLEY_CRAY_VERSION -#undef JSON_HEDLEY_CRAY_VERSION_CHECK -#undef JSON_HEDLEY_C_DECL -#undef JSON_HEDLEY_DEPRECATED -#undef JSON_HEDLEY_DEPRECATED_FOR -#undef JSON_HEDLEY_DIAGNOSTIC_DISABLE_CAST_QUAL -#undef JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_ -#undef JSON_HEDLEY_DIAGNOSTIC_DISABLE_DEPRECATED -#undef JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_CPP_ATTRIBUTES -#undef JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_PRAGMAS -#undef JSON_HEDLEY_DIAGNOSTIC_POP -#undef JSON_HEDLEY_DIAGNOSTIC_PUSH -#undef JSON_HEDLEY_DMC_VERSION -#undef JSON_HEDLEY_DMC_VERSION_CHECK -#undef JSON_HEDLEY_EMPTY_BASES -#undef JSON_HEDLEY_EMSCRIPTEN_VERSION -#undef JSON_HEDLEY_EMSCRIPTEN_VERSION_CHECK -#undef JSON_HEDLEY_END_C_DECLS -#undef JSON_HEDLEY_FLAGS -#undef JSON_HEDLEY_FLAGS_CAST -#undef JSON_HEDLEY_GCC_HAS_ATTRIBUTE -#undef JSON_HEDLEY_GCC_HAS_BUILTIN -#undef JSON_HEDLEY_GCC_HAS_CPP_ATTRIBUTE -#undef JSON_HEDLEY_GCC_HAS_DECLSPEC_ATTRIBUTE -#undef JSON_HEDLEY_GCC_HAS_EXTENSION -#undef JSON_HEDLEY_GCC_HAS_FEATURE -#undef JSON_HEDLEY_GCC_HAS_WARNING -#undef JSON_HEDLEY_GCC_NOT_CLANG_VERSION_CHECK -#undef JSON_HEDLEY_GCC_VERSION -#undef JSON_HEDLEY_GCC_VERSION_CHECK -#undef JSON_HEDLEY_GNUC_HAS_ATTRIBUTE -#undef JSON_HEDLEY_GNUC_HAS_BUILTIN -#undef JSON_HEDLEY_GNUC_HAS_CPP_ATTRIBUTE -#undef JSON_HEDLEY_GNUC_HAS_DECLSPEC_ATTRIBUTE -#undef JSON_HEDLEY_GNUC_HAS_EXTENSION -#undef JSON_HEDLEY_GNUC_HAS_FEATURE -#undef JSON_HEDLEY_GNUC_HAS_WARNING -#undef JSON_HEDLEY_GNUC_VERSION -#undef JSON_HEDLEY_GNUC_VERSION_CHECK -#undef JSON_HEDLEY_HAS_ATTRIBUTE -#undef JSON_HEDLEY_HAS_BUILTIN -#undef JSON_HEDLEY_HAS_CPP_ATTRIBUTE -#undef JSON_HEDLEY_HAS_CPP_ATTRIBUTE_NS -#undef JSON_HEDLEY_HAS_DECLSPEC_ATTRIBUTE -#undef JSON_HEDLEY_HAS_EXTENSION -#undef JSON_HEDLEY_HAS_FEATURE -#undef JSON_HEDLEY_HAS_WARNING -#undef JSON_HEDLEY_IAR_VERSION -#undef JSON_HEDLEY_IAR_VERSION_CHECK -#undef JSON_HEDLEY_IBM_VERSION -#undef JSON_HEDLEY_IBM_VERSION_CHECK -#undef JSON_HEDLEY_IMPORT -#undef JSON_HEDLEY_INLINE -#undef JSON_HEDLEY_INTEL_VERSION -#undef JSON_HEDLEY_INTEL_VERSION_CHECK -#undef JSON_HEDLEY_IS_CONSTANT -#undef JSON_HEDLEY_IS_CONSTEXPR_ -#undef JSON_HEDLEY_LIKELY -#undef JSON_HEDLEY_MALLOC -#undef JSON_HEDLEY_MESSAGE -#undef JSON_HEDLEY_MSVC_VERSION -#undef JSON_HEDLEY_MSVC_VERSION_CHECK -#undef JSON_HEDLEY_NEVER_INLINE -#undef JSON_HEDLEY_NON_NULL -#undef JSON_HEDLEY_NO_ESCAPE -#undef JSON_HEDLEY_NO_RETURN -#undef JSON_HEDLEY_NO_THROW -#undef JSON_HEDLEY_NULL -#undef JSON_HEDLEY_PELLES_VERSION -#undef JSON_HEDLEY_PELLES_VERSION_CHECK -#undef JSON_HEDLEY_PGI_VERSION -#undef JSON_HEDLEY_PGI_VERSION_CHECK -#undef JSON_HEDLEY_PREDICT -#undef JSON_HEDLEY_PRINTF_FORMAT -#undef JSON_HEDLEY_PRIVATE -#undef JSON_HEDLEY_PUBLIC -#undef JSON_HEDLEY_PURE -#undef JSON_HEDLEY_REINTERPRET_CAST -#undef JSON_HEDLEY_REQUIRE -#undef JSON_HEDLEY_REQUIRE_CONSTEXPR -#undef JSON_HEDLEY_REQUIRE_MSG -#undef JSON_HEDLEY_RESTRICT -#undef JSON_HEDLEY_RETURNS_NON_NULL -#undef JSON_HEDLEY_SENTINEL -#undef JSON_HEDLEY_STATIC_ASSERT -#undef JSON_HEDLEY_STATIC_CAST -#undef JSON_HEDLEY_STRINGIFY -#undef JSON_HEDLEY_STRINGIFY_EX -#undef JSON_HEDLEY_SUNPRO_VERSION -#undef JSON_HEDLEY_SUNPRO_VERSION_CHECK -#undef JSON_HEDLEY_TINYC_VERSION -#undef JSON_HEDLEY_TINYC_VERSION_CHECK -#undef JSON_HEDLEY_TI_ARMCL_VERSION -#undef JSON_HEDLEY_TI_ARMCL_VERSION_CHECK -#undef JSON_HEDLEY_TI_CL2000_VERSION -#undef JSON_HEDLEY_TI_CL2000_VERSION_CHECK -#undef JSON_HEDLEY_TI_CL430_VERSION -#undef JSON_HEDLEY_TI_CL430_VERSION_CHECK -#undef JSON_HEDLEY_TI_CL6X_VERSION -#undef JSON_HEDLEY_TI_CL6X_VERSION_CHECK -#undef JSON_HEDLEY_TI_CL7X_VERSION -#undef JSON_HEDLEY_TI_CL7X_VERSION_CHECK -#undef JSON_HEDLEY_TI_CLPRU_VERSION -#undef JSON_HEDLEY_TI_CLPRU_VERSION_CHECK -#undef JSON_HEDLEY_TI_VERSION -#undef JSON_HEDLEY_TI_VERSION_CHECK -#undef JSON_HEDLEY_UNAVAILABLE -#undef JSON_HEDLEY_UNLIKELY -#undef JSON_HEDLEY_UNPREDICTABLE -#undef JSON_HEDLEY_UNREACHABLE -#undef JSON_HEDLEY_UNREACHABLE_RETURN -#undef JSON_HEDLEY_VERSION -#undef JSON_HEDLEY_VERSION_DECODE_MAJOR -#undef JSON_HEDLEY_VERSION_DECODE_MINOR -#undef JSON_HEDLEY_VERSION_DECODE_REVISION -#undef JSON_HEDLEY_VERSION_ENCODE -#undef JSON_HEDLEY_WARNING -#undef JSON_HEDLEY_WARN_UNUSED_RESULT -#undef JSON_HEDLEY_WARN_UNUSED_RESULT_MSG -#undef JSON_HEDLEY_FALL_THROUGH - - - -#endif // INCLUDE_NLOHMANN_JSON_HPP_ diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/README.md b/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/README.md deleted file mode 100644 index 27967a6..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/README.md +++ /dev/null @@ -1,2 +0,0 @@ -Contains a subset (LICENSE and headers) of the Sparsepp library (https://github.com/greg7mdp/sparsepp), commit e40d7a0. - diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/LICENSE b/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/LICENSE deleted file mode 100644 index 865d273..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/LICENSE +++ /dev/null @@ -1,36 +0,0 @@ -// ---------------------------------------------------------------------- -// Copyright (c) 2016, Gregory Popovitch - greg7mdp@gmail.com -// All rights reserved. -// -// This work is derived from Google's sparsehash library -// -// Copyright (c) 2005, Google Inc. -// All rights reserved. -// -// Redistribution and use in source and binary forms, with or without -// modification, are permitted provided that the following conditions are -// met: -// -// * Redistributions of source code must retain the above copyright -// notice, this list of conditions and the following disclaimer. -// * Redistributions in binary form must reproduce the above -// copyright notice, this list of conditions and the following disclaimer -// in the documentation and/or other materials provided with the -// distribution. -// * Neither the name of Google Inc. nor the names of its -// contributors may be used to endorse or promote products derived from -// this software without specific prior written permission. -// -// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS -// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT -// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR -// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT -// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, -// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT -// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, -// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY -// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE -// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -// ---------------------------------------------------------------------- - diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp.h b/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp.h deleted file mode 100644 index 26aa200..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp.h +++ /dev/null @@ -1,4361 +0,0 @@ -#if !defined(sparsepp_h_guard_) -#define sparsepp_h_guard_ - - -// ---------------------------------------------------------------------- -// Copyright (c) 2016, Gregory Popovitch - greg7mdp@gmail.com -// All rights reserved. -// -// This work is derived from Google's sparsehash library -// -// Copyright (c) 2005, Google Inc. -// All rights reserved. -// -// Redistribution and use in source and binary forms, with or without -// modification, are permitted provided that the following conditions are -// met: -// -// * Redistributions of source code must retain the above copyright -// notice, this list of conditions and the following disclaimer. -// * Redistributions in binary form must reproduce the above -// copyright notice, this list of conditions and the following disclaimer -// in the documentation and/or other materials provided with the -// distribution. -// * Neither the name of Google Inc. nor the names of its -// contributors may be used to endorse or promote products derived from -// this software without specific prior written permission. -// -// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS -// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT -// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR -// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT -// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, -// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT -// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, -// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY -// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE -// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -// ---------------------------------------------------------------------- - - -// some macros for portability -// --------------------------- -// includes -// -------- -#include -#include -#include -#include // for numeric_limits -#include // For swap(), eg -#include // for iterator tags -#include // for equal_to<>, select1st<>, std::unary_function, etc -#include // for alloc, uninitialized_copy, uninitialized_fill -#include // for malloc/realloc/free -#include // for ptrdiff_t -#include // for placement new -#include // For length_error -#include // for pair<> -#include -#include -#include - -#include "spp_stdint.h" // includes spp_config.h -#include "spp_traits.h" -#include "spp_utils.h" - -#ifdef SPP_INCLUDE_SPP_ALLOC - #include "spp_dlalloc.h" -#endif - -#if !defined(SPP_NO_CXX11_HDR_INITIALIZER_LIST) - #include -#endif - -#if (SPP_GROUP_SIZE == 32) - #define SPP_SHIFT_ 5 - #define SPP_MASK_ 0x1F - typedef uint32_t group_bm_type; -#elif (SPP_GROUP_SIZE == 64) - #define SPP_SHIFT_ 6 - #define SPP_MASK_ 0x3F - typedef uint64_t group_bm_type; -#else - #error "SPP_GROUP_SIZE must be either 32 or 64" -#endif - -namespace spp_ { - -// ---------------------------------------------------------------------- -// U T I L F U N C T I O N S -// ---------------------------------------------------------------------- -template -inline void throw_exception(const E& exception) -{ -#if !defined(SPP_NO_EXCEPTIONS) - throw exception; -#else - assert(0); - abort(); -#endif -} - -// ---------------------------------------------------------------------- -// M U T A B L E P A I R H A C K -// turn std::pair into mutable std::pair -// ---------------------------------------------------------------------- -template -struct cvt -{ - typedef T type; -}; - -template -struct cvt > -{ - typedef std::pair type; -}; - -template -struct cvt > -{ - typedef const std::pair type; -}; - -// ---------------------------------------------------------------------- -// M O V E I T E R A T O R -// ---------------------------------------------------------------------- -#ifdef SPP_NO_CXX11_RVALUE_REFERENCES - #define MK_MOVE_IT(p) (p) -#else - #define MK_MOVE_IT(p) std::make_move_iterator(p) -#endif - - -// ---------------------------------------------------------------------- -// I N T E R N A L S T U F F -// ---------------------------------------------------------------------- -#ifdef SPP_NO_CXX11_STATIC_ASSERT - template struct SppCompileAssert { }; - #define SPP_COMPILE_ASSERT(expr, msg) \ - SPP_ATTRIBUTE_UNUSED typedef SppCompileAssert<(bool(expr))> spp_bogus_[bool(expr) ? 1 : -1] -#else - #define SPP_COMPILE_ASSERT static_assert -#endif - -namespace sparsehash_internal -{ - -// Adaptor methods for reading/writing data from an INPUT or OUPTUT -// variable passed to serialize() or unserialize(). For now we -// have implemented INPUT/OUTPUT for FILE*, istream*/ostream* (note -// they are pointers, unlike typical use), or else a pointer to -// something that supports a Read()/Write() method. -// -// For technical reasons, we implement read_data/write_data in two -// stages. The actual work is done in *_data_internal, which takes -// the stream argument twice: once as a template type, and once with -// normal type information. (We only use the second version.) We do -// this because of how C++ picks what function overload to use. If we -// implemented this the naive way: -// bool read_data(istream* is, const void* data, size_t length); -// template read_data(T* fp, const void* data, size_t length); -// C++ would prefer the second version for every stream type except -// istream. However, we want C++ to prefer the first version for -// streams that are *subclasses* of istream, such as istringstream. -// This is not possible given the way template types are resolved. So -// we split the stream argument in two, one of which is templated and -// one of which is not. The specialized functions (like the istream -// version above) ignore the template arg and use the second, 'type' -// arg, getting subclass matching as normal. The 'catch-all' -// functions (the second version above) use the template arg to deduce -// the type, and use a second, void* arg to achieve the desired -// 'catch-all' semantics. - - // ----- low-level I/O for FILE* ---- - - template - inline bool read_data_internal(Ignored* /*unused*/, FILE* fp, - void* data, size_t length) - { - return fread(data, length, 1, fp) == 1; - } - - template - inline bool write_data_internal(Ignored* /*unused*/, FILE* fp, - const void* data, size_t length) - { - return fwrite(data, length, 1, fp) == 1; - } - - // ----- low-level I/O for iostream ---- - - // We want the caller to be responsible for #including , not - // us, because iostream is a big header! According to the standard, - // it's only legal to delay the instantiation the way we want to if - // the istream/ostream is a template type. So we jump through hoops. - template - inline bool read_data_internal_for_istream(ISTREAM* fp, - void* data, size_t length) - { - return fp->read(reinterpret_cast(data), - static_cast(length)).good(); - } - template - inline bool read_data_internal(Ignored* /*unused*/, std::istream* fp, - void* data, size_t length) - { - return read_data_internal_for_istream(fp, data, length); - } - - template - inline bool write_data_internal_for_ostream(OSTREAM* fp, - const void* data, size_t length) - { - return fp->write(reinterpret_cast(data), - static_cast(length)).good(); - } - template - inline bool write_data_internal(Ignored* /*unused*/, std::ostream* fp, - const void* data, size_t length) - { - return write_data_internal_for_ostream(fp, data, length); - } - - // ----- low-level I/O for custom streams ---- - - // The INPUT type needs to support a Read() method that takes a - // buffer and a length and returns the number of bytes read. - template - inline bool read_data_internal(INPUT* fp, void* /*unused*/, - void* data, size_t length) - { - return static_cast(fp->Read(data, length)) == length; - } - - // The OUTPUT type needs to support a Write() operation that takes - // a buffer and a length and returns the number of bytes written. - template - inline bool write_data_internal(OUTPUT* fp, void* /*unused*/, - const void* data, size_t length) - { - return static_cast(fp->Write(data, length)) == length; - } - - // ----- low-level I/O: the public API ---- - - template - inline bool read_data(INPUT* fp, void* data, size_t length) - { - return read_data_internal(fp, fp, data, length); - } - - template - inline bool write_data(OUTPUT* fp, const void* data, size_t length) - { - return write_data_internal(fp, fp, data, length); - } - - // Uses read_data() and write_data() to read/write an integer. - // length is the number of bytes to read/write (which may differ - // from sizeof(IntType), allowing us to save on a 32-bit system - // and load on a 64-bit system). Excess bytes are taken to be 0. - // INPUT and OUTPUT must match legal inputs to read/write_data (above). - // -------------------------------------------------------------------- - template - bool read_bigendian_number(INPUT* fp, IntType* value, size_t length) - { - *value = 0; - unsigned char byte; - // We require IntType to be unsigned or else the shifting gets all screwy. - SPP_COMPILE_ASSERT(static_cast(-1) > static_cast(0), "serializing_int_requires_an_unsigned_type"); - for (size_t i = 0; i < length; ++i) - { - if (!read_data(fp, &byte, sizeof(byte))) - return false; - *value |= static_cast(byte) << ((length - 1 - i) * 8); - } - return true; - } - - template - bool write_bigendian_number(OUTPUT* fp, IntType value, size_t length) - { - unsigned char byte; - // We require IntType to be unsigned or else the shifting gets all screwy. - SPP_COMPILE_ASSERT(static_cast(-1) > static_cast(0), "serializing_int_requires_an_unsigned_type"); - for (size_t i = 0; i < length; ++i) - { - byte = (sizeof(value) <= length-1 - i) - ? static_cast(0) : static_cast((value >> ((length-1 - i) * 8)) & 255); - if (!write_data(fp, &byte, sizeof(byte))) return false; - } - return true; - } - - // If your keys and values are simple enough, you can pass this - // serializer to serialize()/unserialize(). "Simple enough" means - // value_type is a POD type that contains no pointers. Note, - // however, we don't try to normalize endianness. - // This is the type used for NopointerSerializer. - // --------------------------------------------------------------- - template struct pod_serializer - { - template - bool operator()(INPUT* fp, value_type* value) const - { - return read_data(fp, value, sizeof(*value)); - } - - template - bool operator()(OUTPUT* fp, const value_type& value) const - { - return write_data(fp, &value, sizeof(value)); - } - }; - - - // Settings contains parameters for growing and shrinking the table. - // It also packages zero-size functor (ie. hasher). - // - // It does some munging of the hash value for the cases where - // the original hash function is not be very good. - // --------------------------------------------------------------- - template - class sh_hashtable_settings : public HashFunc - { - private: -#ifndef SPP_MIX_HASH - template struct Mixer - { - inline T operator()(T h) const { return h; } - }; -#else - template struct Mixer - { - inline T operator()(T h) const; - }; - - template struct Mixer - { - inline T operator()(T h) const - { - // from Thomas Wang - https://gist.github.com/badboy/6267743 - // --------------------------------------------------------- - h = (h ^ 61) ^ (h >> 16); - h = h + (h << 3); - h = h ^ (h >> 4); - h = h * 0x27d4eb2d; - h = h ^ (h >> 15); - return h; - } - }; - - template struct Mixer - { - inline T operator()(T h) const - { - // from Thomas Wang - https://gist.github.com/badboy/6267743 - // --------------------------------------------------------- - h = (~h) + (h << 21); // h = (h << 21) - h - 1; - h = h ^ (h >> 24); - h = (h + (h << 3)) + (h << 8); // h * 265 - h = h ^ (h >> 14); - h = (h + (h << 2)) + (h << 4); // h * 21 - h = h ^ (h >> 28); - h = h + (h << 31); - return h; - } - }; -#endif - - public: - typedef Key key_type; - typedef HashFunc hasher; - typedef SizeType size_type; - - public: - sh_hashtable_settings(const hasher& hf, - const float ht_occupancy_flt, - const float ht_empty_flt) - : hasher(hf), - enlarge_threshold_(0), - shrink_threshold_(0), - consider_shrink_(false), - num_ht_copies_(0) - { - set_enlarge_factor(ht_occupancy_flt); - set_shrink_factor(ht_empty_flt); - } - - size_t hash(const key_type& v) const - { - size_t h = hasher::operator()(v); - Mixer mixer; - - return mixer(h); - } - - float enlarge_factor() const { return enlarge_factor_; } - void set_enlarge_factor(float f) { enlarge_factor_ = f; } - float shrink_factor() const { return shrink_factor_; } - void set_shrink_factor(float f) { shrink_factor_ = f; } - - size_type enlarge_threshold() const { return enlarge_threshold_; } - void set_enlarge_threshold(size_type t) { enlarge_threshold_ = t; } - size_type shrink_threshold() const { return shrink_threshold_; } - void set_shrink_threshold(size_type t) { shrink_threshold_ = t; } - - size_type enlarge_size(size_type x) const { return static_cast(x * enlarge_factor_); } - size_type shrink_size(size_type x) const { return static_cast(x * shrink_factor_); } - - bool consider_shrink() const { return consider_shrink_; } - void set_consider_shrink(bool t) { consider_shrink_ = t; } - - unsigned int num_ht_copies() const { return num_ht_copies_; } - void inc_num_ht_copies() { ++num_ht_copies_; } - - // Reset the enlarge and shrink thresholds - void reset_thresholds(size_type num_buckets) - { - set_enlarge_threshold(enlarge_size(num_buckets)); - set_shrink_threshold(shrink_size(num_buckets)); - // whatever caused us to reset already considered - set_consider_shrink(false); - } - - // Caller is resposible for calling reset_threshold right after - // set_resizing_parameters. - // ------------------------------------------------------------ - void set_resizing_parameters(float shrink, float grow) - { - assert(shrink >= 0); - assert(grow <= 1); - if (shrink > grow/2.0f) - shrink = grow / 2.0f; // otherwise we thrash hashtable size - set_shrink_factor(shrink); - set_enlarge_factor(grow); - } - - // This is the smallest size a hashtable can be without being too crowded - // If you like, you can give a min #buckets as well as a min #elts - // ---------------------------------------------------------------------- - size_type min_buckets(size_type num_elts, size_type min_buckets_wanted) - { - float enlarge = enlarge_factor(); - size_type sz = HT_MIN_BUCKETS; // min buckets allowed - while (sz < min_buckets_wanted || - num_elts >= static_cast(sz * enlarge)) - { - // This just prevents overflowing size_type, since sz can exceed - // max_size() here. - // ------------------------------------------------------------- - if (static_cast(sz * 2) < sz) - throw_exception(std::length_error("resize overflow")); // protect against overflow - sz *= 2; - } - return sz; - } - - private: - size_type enlarge_threshold_; // table.size() * enlarge_factor - size_type shrink_threshold_; // table.size() * shrink_factor - float enlarge_factor_; // how full before resize - float shrink_factor_; // how empty before resize - bool consider_shrink_; // if we should try to shrink before next insert - - unsigned int num_ht_copies_; // num_ht_copies is a counter incremented every Copy/Move - }; - -} // namespace sparsehash_internal - -#undef SPP_COMPILE_ASSERT - -// ---------------------------------------------------------------------- -// S P A R S E T A B L E -// ---------------------------------------------------------------------- -// -// A sparsetable is a random container that implements a sparse array, -// that is, an array that uses very little memory to store unassigned -// indices (in this case, between 1-2 bits per unassigned index). For -// instance, if you allocate an array of size 5 and assign a[2] = , then a[2] will take up a lot of memory but a[0], a[1], -// a[3], and a[4] will not. Array elements that have a value are -// called "assigned". Array elements that have no value yet, or have -// had their value cleared using erase() or clear(), are called -// "unassigned". -// -// Unassigned values seem to have the default value of T (see below). -// Nevertheless, there is a difference between an unassigned index and -// one explicitly assigned the value of T(). The latter is considered -// assigned. -// -// Access to an array element is constant time, as is insertion and -// deletion. Insertion and deletion may be fairly slow, however: -// because of this container's memory economy, each insert and delete -// causes a memory reallocation. -// -// NOTE: You should not test(), get(), or set() any index that is -// greater than sparsetable.size(). If you need to do that, call -// resize() first. -// -// --- Template parameters -// PARAMETER DESCRIPTION DEFAULT -// T The value of the array: the type of -- -// object that is stored in the array. -// -// Alloc: Allocator to use to allocate memory. -// -// --- Model of -// Random Access Container -// -// --- Type requirements -// T must be Copy Constructible. It need not be Assignable. -// -// --- Public base classes -// None. -// -// --- Members -// -// [*] All iterators are const in a sparsetable (though nonempty_iterators -// may not be). Use get() and set() to assign values, not iterators. -// -// [+] iterators are random-access iterators. nonempty_iterators are -// bidirectional iterators. - -// [*] If you shrink a sparsetable using resize(), assigned elements -// past the end of the table are removed using erase(). If you grow -// a sparsetable, new unassigned indices are created. -// -// [+] Note that operator[] returns a const reference. You must use -// set() to change the value of a table element. -// -// [!] Unassignment also calls the destructor. -// -// Iterators are invalidated whenever an item is inserted or -// deleted (ie set() or erase() is used) or when the size of -// the table changes (ie resize() or clear() is used). - - - -// --------------------------------------------------------------------------- -// Our iterator as simple as iterators can be: basically it's just -// the index into our table. Dereference, the only complicated -// thing, we punt to the table class. This just goes to show how -// much machinery STL requires to do even the most trivial tasks. -// -// A NOTE ON ASSIGNING: -// A sparse table does not actually allocate memory for entries -// that are not filled. Because of this, it becomes complicated -// to have a non-const iterator: we don't know, if the iterator points -// to a not-filled bucket, whether you plan to fill it with something -// or whether you plan to read its value (in which case you'll get -// the default bucket value). Therefore, while we can define const -// operations in a pretty 'normal' way, for non-const operations, we -// define something that returns a helper object with operator= and -// operator& that allocate a bucket lazily. We use this for table[] -// and also for regular table iterators. - -// --------------------------------------------------------------------------- -// --------------------------------------------------------------------------- -// Our iterator as simple as iterators can be: basically it's just -// the index into our table. Dereference, the only complicated -// thing, we punt to the table class. This just goes to show how -// much machinery STL requires to do even the most trivial tasks. -// -// By templatizing over tabletype, we have one iterator type which -// we can use for both sparsetables and sparsebins. In fact it -// works on any class that allows size() and operator[] (eg vector), -// as long as it does the standard STL typedefs too (eg value_type). - -// --------------------------------------------------------------------------- -// --------------------------------------------------------------------------- -template -class table_iterator -{ -public: - typedef table_iterator iterator; - - typedef std::random_access_iterator_tag iterator_category; - typedef typename tabletype::value_type value_type; - typedef typename tabletype::difference_type difference_type; - typedef typename tabletype::size_type size_type; - - explicit table_iterator(tabletype *tbl = 0, size_type p = 0) : - table(tbl), pos(p) - { } - - // Helper function to assert things are ok; eg pos is still in range - void check() const - { - assert(table); - assert(pos <= table->size()); - } - - // Arithmetic: we just do arithmetic on pos. We don't even need to - // do bounds checking, since STL doesn't consider that its job. :-) - iterator& operator+=(size_type t) { pos += t; check(); return *this; } - iterator& operator-=(size_type t) { pos -= t; check(); return *this; } - iterator& operator++() { ++pos; check(); return *this; } - iterator& operator--() { --pos; check(); return *this; } - iterator operator++(int) - { - iterator tmp(*this); // for x++ - ++pos; check(); return tmp; - } - - iterator operator--(int) - { - iterator tmp(*this); // for x-- - --pos; check(); return tmp; - } - - iterator operator+(difference_type i) const - { - iterator tmp(*this); - tmp += i; return tmp; - } - - iterator operator-(difference_type i) const - { - iterator tmp(*this); - tmp -= i; return tmp; - } - - difference_type operator-(iterator it) const - { - // for "x = it2 - it" - assert(table == it.table); - return pos - it.pos; - } - - // Comparisons. - bool operator==(const iterator& it) const - { - return table == it.table && pos == it.pos; - } - - bool operator<(const iterator& it) const - { - assert(table == it.table); // life is bad bad bad otherwise - return pos < it.pos; - } - - bool operator!=(const iterator& it) const { return !(*this == it); } - bool operator<=(const iterator& it) const { return !(it < *this); } - bool operator>(const iterator& it) const { return it < *this; } - bool operator>=(const iterator& it) const { return !(*this < it); } - - // Here's the info we actually need to be an iterator - tabletype *table; // so we can dereference and bounds-check - size_type pos; // index into the table -}; - -// --------------------------------------------------------------------------- -// --------------------------------------------------------------------------- -template -class const_table_iterator -{ -public: - typedef table_iterator iterator; - typedef const_table_iterator const_iterator; - - typedef std::random_access_iterator_tag iterator_category; - typedef typename tabletype::value_type value_type; - typedef typename tabletype::difference_type difference_type; - typedef typename tabletype::size_type size_type; - typedef typename tabletype::const_reference reference; // we're const-only - typedef typename tabletype::const_pointer pointer; - - // The "real" constructor - const_table_iterator(const tabletype *tbl, size_type p) - : table(tbl), pos(p) { } - - // The default constructor, used when I define vars of type table::iterator - const_table_iterator() : table(NULL), pos(0) { } - - // The copy constructor, for when I say table::iterator foo = tbl.begin() - // Also converts normal iterators to const iterators // not explicit on purpose - const_table_iterator(const iterator &from) - : table(from.table), pos(from.pos) { } - - // The default destructor is fine; we don't define one - // The default operator= is fine; we don't define one - - // The main thing our iterator does is dereference. If the table entry - // we point to is empty, we return the default value type. - reference operator*() const { return (*table)[pos]; } - pointer operator->() const { return &(operator*()); } - - // Helper function to assert things are ok; eg pos is still in range - void check() const - { - assert(table); - assert(pos <= table->size()); - } - - // Arithmetic: we just do arithmetic on pos. We don't even need to - // do bounds checking, since STL doesn't consider that its job. :-) - const_iterator& operator+=(size_type t) { pos += t; check(); return *this; } - const_iterator& operator-=(size_type t) { pos -= t; check(); return *this; } - const_iterator& operator++() { ++pos; check(); return *this; } - const_iterator& operator--() { --pos; check(); return *this; } - const_iterator operator++(int) - { - const_iterator tmp(*this); // for x++ - ++pos; check(); - return tmp; - } - const_iterator operator--(int) - { - const_iterator tmp(*this); // for x-- - --pos; check(); - return tmp; - } - const_iterator operator+(difference_type i) const - { - const_iterator tmp(*this); - tmp += i; - return tmp; - } - const_iterator operator-(difference_type i) const - { - const_iterator tmp(*this); - tmp -= i; - return tmp; - } - difference_type operator-(const_iterator it) const - { - // for "x = it2 - it" - assert(table == it.table); - return pos - it.pos; - } - reference operator[](difference_type n) const - { - return *(*this + n); // simple though not totally efficient - } - - // Comparisons. - bool operator==(const const_iterator& it) const - { - return table == it.table && pos == it.pos; - } - - bool operator<(const const_iterator& it) const - { - assert(table == it.table); // life is bad bad bad otherwise - return pos < it.pos; - } - bool operator!=(const const_iterator& it) const { return !(*this == it); } - bool operator<=(const const_iterator& it) const { return !(it < *this); } - bool operator>(const const_iterator& it) const { return it < *this; } - bool operator>=(const const_iterator& it) const { return !(*this < it); } - - // Here's the info we actually need to be an iterator - const tabletype *table; // so we can dereference and bounds-check - size_type pos; // index into the table -}; - -// --------------------------------------------------------------------------- -// This is a 2-D iterator. You specify a begin and end over a list -// of *containers*. We iterate over each container by iterating over -// it. It's actually simple: -// VECTOR.begin() VECTOR[0].begin() --------> VECTOR[0].end() ---, -// | ________________________________________________/ -// | \_> VECTOR[1].begin() --------> VECTOR[1].end() -, -// | ___________________________________________________/ -// v \_> ...... -// VECTOR.end() -// -// It's impossible to do random access on one of these things in constant -// time, so it's just a bidirectional iterator. -// -// Unfortunately, because we need to use this for a non-empty iterator, -// we use ne_begin() and ne_end() instead of begin() and end() -// (though only going across, not down). -// --------------------------------------------------------------------------- - -// --------------------------------------------------------------------------- -// --------------------------------------------------------------------------- -template -class Two_d_iterator -{ -public: - typedef Two_d_iterator iterator; - typedef iter_type iterator_category; - typedef T value_type; - typedef std::ptrdiff_t difference_type; - typedef T* pointer; - typedef T& reference; - - explicit Two_d_iterator(row_it curr) : row_current(curr), col_current(0) - { - if (row_current && !row_current->is_marked()) - { - col_current = row_current->ne_begin(); - advance_past_end(); // in case cur->begin() == cur->end() - } - } - - explicit Two_d_iterator(row_it curr, col_it col) : row_current(curr), col_current(col) - { - assert(col); - } - - // The default constructor - Two_d_iterator() : row_current(0), col_current(0) { } - - // Need this explicitly so we can convert normal iterators <=> const iterators - // not explicit on purpose - // --------------------------------------------------------------------------- - template - Two_d_iterator(const Two_d_iterator& it) : - row_current (*(row_it *)&it.row_current), - col_current (*(col_it *)&it.col_current) - { } - - // The default destructor is fine; we don't define one - // The default operator= is fine; we don't define one - - value_type& operator*() const { return *(col_current); } - value_type* operator->() const { return &(operator*()); } - - // Arithmetic: we just do arithmetic on pos. We don't even need to - // do bounds checking, since STL doesn't consider that its job. :-) - // NOTE: this is not amortized constant time! What do we do about it? - // ------------------------------------------------------------------ - void advance_past_end() - { - // used when col_current points to end() - while (col_current == row_current->ne_end()) - { - // end of current row - // ------------------ - ++row_current; // go to beginning of next - if (!row_current->is_marked()) // col is irrelevant at end - col_current = row_current->ne_begin(); - else - break; // don't go past row_end - } - } - - friend size_t operator-(iterator l, iterator f) - { - if (f.row_current->is_marked()) - return 0; - - size_t diff(0); - while (f != l) - { - ++diff; - ++f; - } - return diff; - } - - iterator& operator++() - { - // assert(!row_current->is_marked()); // how to ++ from there? - ++col_current; - advance_past_end(); // in case col_current is at end() - return *this; - } - - iterator& operator--() - { - while (row_current->is_marked() || - col_current == row_current->ne_begin()) - { - --row_current; - col_current = row_current->ne_end(); // this is 1 too far - } - --col_current; - return *this; - } - iterator operator++(int) { iterator tmp(*this); ++*this; return tmp; } - iterator operator--(int) { iterator tmp(*this); --*this; return tmp; } - - - // Comparisons. - bool operator==(const iterator& it) const - { - return (row_current == it.row_current && - (!row_current || row_current->is_marked() || col_current == it.col_current)); - } - - bool operator!=(const iterator& it) const { return !(*this == it); } - - // Here's the info we actually need to be an iterator - // These need to be public so we convert from iterator to const_iterator - // --------------------------------------------------------------------- - row_it row_current; - col_it col_current; -}; - - -// --------------------------------------------------------------------------- -// --------------------------------------------------------------------------- -template -class Two_d_destructive_iterator : public Two_d_iterator -{ -public: - typedef Two_d_destructive_iterator iterator; - - Two_d_destructive_iterator(Alloc &alloc, row_it curr) : - _alloc(alloc) - { - this->row_current = curr; - this->col_current = 0; - if (this->row_current && !this->row_current->is_marked()) - { - this->col_current = this->row_current->ne_begin(); - advance_past_end(); // in case cur->begin() == cur->end() - } - } - - // Arithmetic: we just do arithmetic on pos. We don't even need to - // do bounds checking, since STL doesn't consider that its job. :-) - // NOTE: this is not amortized constant time! What do we do about it? - // ------------------------------------------------------------------ - void advance_past_end() - { - // used when col_current points to end() - while (this->col_current == this->row_current->ne_end()) - { - this->row_current->clear(_alloc, true); // This is what differs from non-destructive iterators above - - // end of current row - // ------------------ - ++this->row_current; // go to beginning of next - if (!this->row_current->is_marked()) // col is irrelevant at end - this->col_current = this->row_current->ne_begin(); - else - break; // don't go past row_end - } - } - - iterator& operator++() - { - // assert(!this->row_current->is_marked()); // how to ++ from there? - ++this->col_current; - advance_past_end(); // in case col_current is at end() - return *this; - } - -private: - Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); - - Alloc &_alloc; -}; - - -// --------------------------------------------------------------------------- -// --------------------------------------------------------------------------- -#if defined(SPP_POPCNT_CHECK) -static inline bool spp_popcount_check() -{ - int cpuInfo[4] = { -1 }; - spp_cpuid(cpuInfo, 1); - if (cpuInfo[2] & (1 << 23)) - return true; // means SPP_POPCNT supported - return false; -} -#endif - -#if defined(SPP_POPCNT_CHECK) && defined(SPP_POPCNT) - -static inline uint32_t spp_popcount(uint32_t i) -{ - static const bool s_ok = spp_popcount_check(); - return s_ok ? SPP_POPCNT(i) : s_spp_popcount_default(i); -} - -#else - -static inline uint32_t spp_popcount(uint32_t i) -{ -#if defined(SPP_POPCNT) - return static_cast(SPP_POPCNT(i)); -#else - return s_spp_popcount_default(i); -#endif -} - -#endif - -#if defined(SPP_POPCNT_CHECK) && defined(SPP_POPCNT64) - -static inline uint32_t spp_popcount(uint64_t i) -{ - static const bool s_ok = spp_popcount_check(); - return s_ok ? (uint32_t)SPP_POPCNT64(i) : s_spp_popcount_default(i); -} - -#else - -static inline uint32_t spp_popcount(uint64_t i) -{ -#if defined(SPP_POPCNT64) - return static_cast(SPP_POPCNT64(i)); -#elif 1 - return s_spp_popcount_default(i); -#endif -} - -#endif - -// --------------------------------------------------------------------------- -// SPARSE-TABLE -// ------------ -// The idea is that a table with (logically) t buckets is divided -// into t/M *groups* of M buckets each. (M is a constant, typically -// 32) Each group is stored sparsely. -// Thus, inserting into the table causes some array to grow, which is -// slow but still constant time. Lookup involves doing a -// logical-position-to-sparse-position lookup, which is also slow but -// constant time. The larger M is, the slower these operations are -// but the less overhead (slightly). -// -// To store the sparse array, we store a bitmap B, where B[i] = 1 iff -// bucket i is non-empty. Then to look up bucket i we really look up -// array[# of 1s before i in B]. This is constant time for fixed M. -// -// Terminology: the position of an item in the overall table (from -// 1 .. t) is called its "location." The logical position in a group -// (from 1 .. M) is called its "position." The actual location in -// the array (from 1 .. # of non-empty buckets in the group) is -// called its "offset." -// --------------------------------------------------------------------------- - -template -class sparsegroup -{ -public: - // Basic types - typedef T value_type; - typedef Alloc allocator_type; - typedef value_type& reference; - typedef const value_type& const_reference; - typedef value_type* pointer; - typedef const value_type* const_pointer; - - typedef uint8_t size_type; // max # of buckets - - // These are our special iterators, that go over non-empty buckets in a - // group. These aren't const-only because you can change non-empty bcks. - // --------------------------------------------------------------------- - typedef pointer ne_iterator; - typedef const_pointer const_ne_iterator; - typedef std::reverse_iterator reverse_ne_iterator; - typedef std::reverse_iterator const_reverse_ne_iterator; - - // We'll have versions for our special non-empty iterator too - // ---------------------------------------------------------- - ne_iterator ne_begin() { return reinterpret_cast(_group); } - const_ne_iterator ne_begin() const { return reinterpret_cast(_group); } - const_ne_iterator ne_cbegin() const { return reinterpret_cast(_group); } - ne_iterator ne_end() { return reinterpret_cast(_group + _num_items()); } - const_ne_iterator ne_end() const { return reinterpret_cast(_group + _num_items()); } - const_ne_iterator ne_cend() const { return reinterpret_cast(_group + _num_items()); } - reverse_ne_iterator ne_rbegin() { return reverse_ne_iterator(ne_end()); } - const_reverse_ne_iterator ne_rbegin() const { return const_reverse_ne_iterator(ne_cend()); } - const_reverse_ne_iterator ne_crbegin() const { return const_reverse_ne_iterator(ne_cend()); } - reverse_ne_iterator ne_rend() { return reverse_ne_iterator(ne_begin()); } - const_reverse_ne_iterator ne_rend() const { return const_reverse_ne_iterator(ne_cbegin()); } - const_reverse_ne_iterator ne_crend() const { return const_reverse_ne_iterator(ne_cbegin()); } - -private: - // T can be std::pair, but sometime we need to cast to a mutable type - // ------------------------------------------------------------------------------ - typedef typename spp_::cvt::type mutable_value_type; - typedef mutable_value_type & mutable_reference; - typedef mutable_value_type * mutable_pointer; - typedef const mutable_value_type * const_mutable_pointer; - - bool _bmtest(size_type i) const { return !!(_bitmap & (static_cast(1) << i)); } - void _bmset(size_type i) { _bitmap |= static_cast(1) << i; } - void _bmclear(size_type i) { _bitmap &= ~(static_cast(1) << i); } - - bool _bme_test(size_type i) const { return !!(_bm_erased & (static_cast(1) << i)); } - void _bme_set(size_type i) { _bm_erased |= static_cast(1) << i; } - void _bme_clear(size_type i) { _bm_erased &= ~(static_cast(1) << i); } - - bool _bmtest_strict(size_type i) const - { return !!((_bitmap | _bm_erased) & (static_cast(1) << i)); } - - - static uint32_t _sizing(uint32_t n) - { -#if !defined(SPP_ALLOC_SZ) || (SPP_ALLOC_SZ == 0) - // aggressive allocation first, then decreasing as sparsegroups fill up - // -------------------------------------------------------------------- - struct alloc_batch_size - { - // 32 bit bitmap - // ........ .... .... .. .. .. .. . . . . . . . . - // 8 12 16 18 20 22 24 25 26 ... 32 - // ------------------------------------------------------ - SPP_CXX14_CONSTEXPR alloc_batch_size() - : data() - { - uint8_t group_sz = SPP_GROUP_SIZE / 4; - uint8_t group_start_alloc = SPP_GROUP_SIZE / 8; //4; - uint8_t alloc_sz = group_start_alloc; - for (int i=0; i<4; ++i) - { - for (int j=0; j 2) - group_start_alloc /= 2; - alloc_sz += group_start_alloc; - } - } - uint8_t data[SPP_GROUP_SIZE]; - }; - - static alloc_batch_size s_alloc_batch_sz; - return n ? static_cast(s_alloc_batch_sz.data[n-1]) : 0; // more aggressive alloc at the beginning - -#elif (SPP_ALLOC_SZ == 1) - // use as little memory as possible - slowest insert/delete in table - // ----------------------------------------------------------------- - return n; -#else - // decent compromise when SPP_ALLOC_SZ == 2 - // ---------------------------------------- - static size_type sz_minus_1 = SPP_ALLOC_SZ - 1; - return (n + sz_minus_1) & ~sz_minus_1; -#endif - } - - pointer _allocate_group(allocator_type &alloc, uint32_t n /* , bool tight = false */) - { - // ignore tight since we don't store num_alloc - // num_alloc = (uint8_t)(tight ? n : _sizing(n)); - - uint32_t num_alloc = (uint8_t)_sizing(n); - _set_num_alloc(num_alloc); - pointer retval = alloc.allocate(static_cast(num_alloc)); - if (retval == NULL) - { - // the allocator is supposed to throw an exception if the allocation fails. - throw_exception(std::bad_alloc()); - } - return retval; - } - - void _free_group(allocator_type &alloc, uint32_t num_alloc) - { - if (_group) - { - uint32_t num_buckets = _num_items(); - if (num_buckets) - { - mutable_pointer end_it = (mutable_pointer)(_group + num_buckets); - for (mutable_pointer p = (mutable_pointer)_group; p != end_it; ++p) - p->~mutable_value_type(); - } - alloc.deallocate(_group, (typename allocator_type::size_type)num_alloc); - _group = NULL; - } - } - - // private because should not be called - no allocator! - sparsegroup &operator=(const sparsegroup& x); - - static size_type _pos_to_offset(group_bm_type bm, size_type pos) - { - //return (size_type)((uint32_t)~((int32_t(-1) + pos) >> 31) & spp_popcount(bm << (SPP_GROUP_SIZE - pos))); - //return (size_type)(pos ? spp_popcount(bm << (SPP_GROUP_SIZE - pos)) : 0); - return static_cast(spp_popcount(bm & ((static_cast(1) << pos) - 1))); - } - -public: - - // get_iter() in sparsetable needs it - size_type pos_to_offset(size_type pos) const - { - return _pos_to_offset(_bitmap, pos); - } - -#ifdef _MSC_VER -#pragma warning(push) -#pragma warning(disable : 4146) -#endif - - // Returns the (logical) position in the bm[] array, i, such that - // bm[i] is the offset-th set bit in the array. It is the inverse - // of pos_to_offset. get_pos() uses this function to find the index - // of an ne_iterator in the table. Bit-twiddling from - // http://hackersdelight.org/basics.pdf - // ----------------------------------------------------------------- - static size_type offset_to_pos(group_bm_type bm, size_type offset) - { - for (; offset > 0; offset--) - bm &= (bm-1); // remove right-most set bit - - // Clear all bits to the left of the rightmost bit (the &), - // and then clear the rightmost bit but set all bits to the - // right of it (the -1). - // -------------------------------------------------------- - bm = (bm & -bm) - 1; - return static_cast(spp_popcount(bm)); - } - -#ifdef _MSC_VER -#pragma warning(pop) -#endif - - size_type offset_to_pos(size_type offset) const - { - return offset_to_pos(_bitmap, offset); - } - -public: - // Constructors -- default and copy -- and destructor - explicit sparsegroup() : - _group(0), _bitmap(0), _bm_erased(0) - { - _set_num_items(0); - _set_num_alloc(0); - } - - sparsegroup(const sparsegroup& x) : - _group(0), _bitmap(x._bitmap), _bm_erased(x._bm_erased) - { - _set_num_items(0); - _set_num_alloc(0); - assert(_group == 0); - } - - sparsegroup(const sparsegroup& x, allocator_type& a) : - _group(0), _bitmap(x._bitmap), _bm_erased(x._bm_erased) - { - _set_num_items(0); - _set_num_alloc(0); - - uint32_t num_items = x._num_items(); - if (num_items) - { - _group = _allocate_group(a, num_items /* , true */); - _set_num_items(num_items); - std::uninitialized_copy(x._group, x._group + num_items, _group); - } - } - - ~sparsegroup() { assert(_group == 0); } - - void destruct(allocator_type& a) { _free_group(a, _num_alloc()); } - - // Many STL algorithms use swap instead of copy constructors - void swap(sparsegroup& x) - { - using std::swap; - - swap(_group, x._group); - swap(_bitmap, x._bitmap); - swap(_bm_erased, x._bm_erased); -#ifdef SPP_STORE_NUM_ITEMS - swap(_num_buckets, x._num_buckets); - swap(_num_allocated, x._num_allocated); -#endif - } - - // It's always nice to be able to clear a table without deallocating it - void clear(allocator_type &alloc, bool erased) - { - _free_group(alloc, _num_alloc()); - _bitmap = 0; - if (erased) - _bm_erased = 0; - _set_num_items(0); - _set_num_alloc(0); - } - - // Functions that tell you about size. Alas, these aren't so useful - // because our table is always fixed size. - size_type size() const { return static_cast(SPP_GROUP_SIZE); } - size_type max_size() const { return static_cast(SPP_GROUP_SIZE); } - - bool empty() const { return false; } - - // We also may want to know how many *used* buckets there are - size_type num_nonempty() const { return (size_type)_num_items(); } - - // TODO(csilvers): make protected + friend - // This is used by sparse_hashtable to get an element from the table - // when we know it exists. - reference unsafe_get(size_type i) const - { - // assert(_bmtest(i)); - return (reference)_group[pos_to_offset(i)]; - } - - typedef std::pair SetResult; - -private: - //typedef spp_::integral_constant::value> check_relocatable; - typedef spp_::true_type realloc_ok_type; - typedef spp_::false_type realloc_not_ok_type; - - //typedef spp_::zero_type libc_reloc_type; - //typedef spp_::one_type spp_reloc_type; - //typedef spp_::two_type spp_not_reloc_type; - //typedef spp_::three_type generic_alloc_type; - -#if 1 - typedef typename if_<((spp_::is_same >::value || - spp_::is_same >::value) && - spp_::is_relocatable::value), realloc_ok_type, realloc_not_ok_type>::type - check_alloc_type; -#else - typedef typename if_ >::value, - typename if_::value, spp_reloc_type, spp_not_reloc_type>::type, - typename if_<(spp_::is_same >::value && - spp_::is_relocatable::value), libc_reloc_type, generic_alloc_type>::type >::type - check_alloc_type; -#endif - - - //typedef if_ >::value, - // libc_alloc_type, - // if_ >::value, - // spp_alloc_type, user_alloc_type> > check_alloc_type; - - //typedef spp_::integral_constant::value && - // (spp_::is_same >::value || - // spp_::is_same >::value)) > - // realloc_and_memmove_ok; - - // ------------------------- memory at *p is uninitialized => need to construct - void _init_val(mutable_value_type *p, reference val) - { -#if !defined(SPP_NO_CXX11_RVALUE_REFERENCES) - ::new (p) value_type(std::move((mutable_reference)val)); -#else - ::new (p) value_type((mutable_reference)val); -#endif - } - - // ------------------------- memory at *p is uninitialized => need to construct - void _init_val(mutable_value_type *p, const_reference val) - { - ::new (p) value_type(val); - } - - // ------------------------------------------------ memory at *p is initialized - void _set_val(value_type *p, reference val) - { -#if !defined(SPP_NO_CXX11_RVALUE_REFERENCES) - *(mutable_pointer)p = std::move((mutable_reference)val); -#else - using std::swap; - swap(*(mutable_pointer)p, *(mutable_pointer)&val); -#endif - } - - // ------------------------------------------------ memory at *p is initialized - void _set_val(value_type *p, const_reference val) - { - *(mutable_pointer)p = *(const_mutable_pointer)&val; - } - - // Create space at _group[offset], assuming value_type is relocatable, and the - // allocator_type is the spp allocator. - // return true if the slot was constructed (i.e. contains a valid value_type - // --------------------------------------------------------------------------------- - template - void _set_aux(allocator_type &alloc, size_type offset, Val &val, realloc_ok_type) - { - //static int x=0; if (++x < 10) printf("x\n"); // check we are getting here - - uint32_t num_items = _num_items(); - uint32_t num_alloc = _sizing(num_items); - - if (num_items == num_alloc) - { - num_alloc = _sizing(num_items + 1); - _group = alloc.reallocate(_group, num_alloc); - _set_num_alloc(num_alloc); - } - - for (uint32_t i = num_items; i > offset; --i) - memcpy(static_cast(_group + i), _group + i-1, sizeof(*_group)); - - _init_val((mutable_pointer)(_group + offset), val); - } - - // Create space at _group[offset], assuming value_type is *not* relocatable, and the - // allocator_type is the spp allocator. - // return true if the slot was constructed (i.e. contains a valid value_type - // --------------------------------------------------------------------------------- - template - void _set_aux(allocator_type &alloc, size_type offset, Val &val, realloc_not_ok_type) - { - uint32_t num_items = _num_items(); - uint32_t num_alloc = _sizing(num_items); - - //assert(num_alloc == (uint32_t)_num_allocated); - if (num_items < num_alloc) - { - // create new object at end and rotate it to position - _init_val((mutable_pointer)&_group[num_items], val); - std::rotate((mutable_pointer)(_group + offset), - (mutable_pointer)(_group + num_items), - (mutable_pointer)(_group + num_items + 1)); - return; - } - - // This is valid because 0 <= offset <= num_items - pointer p = _allocate_group(alloc, _sizing(num_items + 1)); - if (offset) - std::uninitialized_copy(MK_MOVE_IT((mutable_pointer)_group), - MK_MOVE_IT((mutable_pointer)(_group + offset)), - (mutable_pointer)p); - if (num_items > offset) - std::uninitialized_copy(MK_MOVE_IT((mutable_pointer)(_group + offset)), - MK_MOVE_IT((mutable_pointer)(_group + num_items)), - (mutable_pointer)(p + offset + 1)); - _init_val((mutable_pointer)(p + offset), val); - _free_group(alloc, num_alloc); - _group = p; - } - - // ---------------------------------------------------------------------------------- - template - void _set(allocator_type &alloc, size_type i, size_type offset, Val &val) - { - if (!_bmtest(i)) - { - _set_aux(alloc, offset, val, check_alloc_type()); - _incr_num_items(); - _bmset(i); - } - else - _set_val(&_group[offset], val); - } - -public: - - // This returns the pointer to the inserted item - // --------------------------------------------- - template - pointer set(allocator_type &alloc, size_type i, Val &val) - { - _bme_clear(i); // in case this was an "erased" location - - size_type offset = pos_to_offset(i); - _set(alloc, i, offset, val); // may change _group pointer - return (pointer)(_group + offset); - } - - // We let you see if a bucket is non-empty without retrieving it - // ------------------------------------------------------------- - bool test(size_type i) const - { - return _bmtest(i); - } - - // also tests for erased values - // ---------------------------- - bool test_strict(size_type i) const - { - return _bmtest_strict(i); - } - -private: - // Shrink the array, assuming value_type is relocatable, and the - // allocator_type is the libc allocator (supporting reallocate). - // ------------------------------------------------------------- - void _group_erase_aux(allocator_type &alloc, size_type offset, realloc_ok_type) - { - // static int x=0; if (++x < 10) printf("Y\n"); // check we are getting here - uint32_t num_items = _num_items(); - uint32_t num_alloc = _sizing(num_items); - - if (num_items == 1) - { - assert(offset == 0); - _free_group(alloc, num_alloc); - _set_num_alloc(0); - return; - } - - _group[offset].~value_type(); - - for (size_type i = offset; i < num_items - 1; ++i) - memcpy(static_cast(_group + i), _group + i + 1, sizeof(*_group)); - - if (_sizing(num_items - 1) != num_alloc) - { - num_alloc = _sizing(num_items - 1); - assert(num_alloc); // because we have at least 1 item left - _set_num_alloc(num_alloc); - _group = alloc.reallocate(_group, num_alloc); - } - } - - // Shrink the array, without any special assumptions about value_type and - // allocator_type. - // -------------------------------------------------------------------------- - void _group_erase_aux(allocator_type &alloc, size_type offset, realloc_not_ok_type) - { - uint32_t num_items = _num_items(); - uint32_t num_alloc = _sizing(num_items); - - if (_sizing(num_items - 1) != num_alloc) - { - pointer p = 0; - if (num_items > 1) - { - p = _allocate_group(alloc, num_items - 1); - if (offset) - std::uninitialized_copy(MK_MOVE_IT((mutable_pointer)(_group)), - MK_MOVE_IT((mutable_pointer)(_group + offset)), - (mutable_pointer)(p)); - if (static_cast(offset + 1) < num_items) - std::uninitialized_copy(MK_MOVE_IT((mutable_pointer)(_group + offset + 1)), - MK_MOVE_IT((mutable_pointer)(_group + num_items)), - (mutable_pointer)(p + offset)); - } - else - { - assert(offset == 0); - _set_num_alloc(0); - } - _free_group(alloc, num_alloc); - _group = p; - } - else - { - std::rotate((mutable_pointer)(_group + offset), - (mutable_pointer)(_group + offset + 1), - (mutable_pointer)(_group + num_items)); - ((mutable_pointer)(_group + num_items - 1))->~mutable_value_type(); - } - } - - void _group_erase(allocator_type &alloc, size_type offset) - { - _group_erase_aux(alloc, offset, check_alloc_type()); - } - -public: - template - bool erase_ne(allocator_type &alloc, twod_iter &it) - { - assert(_group && it.col_current != ne_end()); - size_type offset = (size_type)(it.col_current - ne_begin()); - size_type pos = offset_to_pos(offset); - - if (_num_items() <= 1) - { - clear(alloc, false); - it.col_current = 0; - } - else - { - _group_erase(alloc, offset); - _decr_num_items(); - _bmclear(pos); - - // in case _group_erase reallocated the buffer - it.col_current = reinterpret_cast(_group) + offset; - } - _bme_set(pos); // remember that this position has been erased - it.advance_past_end(); - return true; - } - - - // This takes the specified elements out of the group. This is - // "undefining", rather than "clearing". - // TODO(austern): Make this exception safe: handle exceptions from - // value_type's copy constructor. - // --------------------------------------------------------------- - void erase(allocator_type &alloc, size_type i) - { - if (_bmtest(i)) - { - // trivial to erase empty bucket - if (_num_items() == 1) - clear(alloc, false); - else - { - _group_erase(alloc, pos_to_offset(i)); - _decr_num_items(); - _bmclear(i); - } - _bme_set(i); // remember that this position has been erased - } - } - - // I/O - // We support reading and writing groups to disk. We don't store - // the actual array contents (which we don't know how to store), - // just the bitmap and size. Meant to be used with table I/O. - // -------------------------------------------------------------- - template bool write_metadata(OUTPUT *fp) const - { - // warning: we write 4 or 8 bytes for the bitmap, instead of 6 in the - // original google sparsehash - // ------------------------------------------------------------------ - if (!sparsehash_internal::write_data(fp, &_bitmap, sizeof(_bitmap))) - return false; - - return true; - } - - // Reading destroys the old group contents! Returns true if all was ok. - template bool read_metadata(allocator_type &alloc, INPUT *fp) - { - clear(alloc, true); - - if (!sparsehash_internal::read_data(fp, &_bitmap, sizeof(_bitmap))) - return false; - - // We'll allocate the space, but we won't fill it: it will be - // left as uninitialized raw memory. - uint32_t num_items = spp_popcount(_bitmap); // yes, _num_buckets not set - _set_num_items(num_items); - _group = num_items ? _allocate_group(alloc, num_items/* , true */) : 0; - return true; - } - - // Again, only meaningful if value_type is a POD. - template bool read_nopointer_data(INPUT *fp) - { - for (ne_iterator it = ne_begin(); it != ne_end(); ++it) - if (!sparsehash_internal::read_data(fp, &(*it), sizeof(*it))) - return false; - return true; - } - - // If your keys and values are simple enough, we can write them - // to disk for you. "simple enough" means POD and no pointers. - // However, we don't try to normalize endianness. - // ------------------------------------------------------------ - template bool write_nopointer_data(OUTPUT *fp) const - { - for (const_ne_iterator it = ne_begin(); it != ne_end(); ++it) - if (!sparsehash_internal::write_data(fp, &(*it), sizeof(*it))) - return false; - return true; - } - - - // Comparisons. We only need to define == and < -- we get - // != > <= >= via relops.h (which we happily included above). - // Note the comparisons are pretty arbitrary: we compare - // values of the first index that isn't equal (using default - // value for empty buckets). - // --------------------------------------------------------- - bool operator==(const sparsegroup& x) const - { - return (_bitmap == x._bitmap && - _bm_erased == x._bm_erased && - std::equal(_group, _group + _num_items(), x._group)); - } - - bool operator<(const sparsegroup& x) const - { - // also from - return std::lexicographical_compare(_group, _group + _num_items(), - x._group, x._group + x._num_items()); - } - - bool operator!=(const sparsegroup& x) const { return !(*this == x); } - bool operator<=(const sparsegroup& x) const { return !(x < *this); } - bool operator> (const sparsegroup& x) const { return x < *this; } - bool operator>=(const sparsegroup& x) const { return !(*this < x); } - - void mark() { _group = (value_type *)static_cast(-1); } - bool is_marked() const { return _group == (value_type *)static_cast(-1); } - -private: - // --------------------------------------------------------------------------- - template - class alloc_impl : public A - { - public: - typedef typename A::pointer pointer; - typedef typename A::size_type size_type; - - // Convert a normal allocator to one that has realloc_or_die() - explicit alloc_impl(const A& a) : A(a) { } - - // realloc_or_die should only be used when using the default - // allocator (spp::spp_allocator). - pointer realloc_or_die(pointer /*ptr*/, size_type /*n*/) - { - throw_exception(std::runtime_error("realloc_or_die is only supported for spp::spp_allocator\n")); - return NULL; - } - }; - - // A template specialization of alloc_impl for - // spp::libc_allocator that can handle realloc_or_die. - // ----------------------------------------------------------- - template - class alloc_impl > : public spp_::libc_allocator - { - public: - typedef typename spp_::libc_allocator::pointer pointer; - typedef typename spp_::libc_allocator::size_type size_type; - - explicit alloc_impl(const spp_::libc_allocator& a) - : spp_::libc_allocator(a) - { } - - pointer realloc_or_die(pointer ptr, size_type n) - { - pointer retval = this->reallocate(ptr, n); - if (retval == NULL) - { - // the allocator is supposed to throw an exception if the allocation fails. - throw_exception(std::bad_alloc()); - } - return retval; - } - }; - - // A template specialization of alloc_impl for - // spp::spp_allocator that can handle realloc_or_die. - // ----------------------------------------------------------- - template - class alloc_impl > : public spp_::spp_allocator - { - public: - typedef typename spp_::spp_allocator::pointer pointer; - typedef typename spp_::spp_allocator::size_type size_type; - - explicit alloc_impl(const spp_::spp_allocator& a) - : spp_::spp_allocator(a) - { } - - pointer realloc_or_die(pointer ptr, size_type n) - { - pointer retval = this->reallocate(ptr, n); - if (retval == NULL) - { - // the allocator is supposed to throw an exception if the allocation fails. - throw_exception(std::bad_alloc()); - } - return retval; - } - }; - - -#ifdef SPP_STORE_NUM_ITEMS - uint32_t _num_items() const { return (uint32_t)_num_buckets; } - void _set_num_items(uint32_t val) { _num_buckets = static_cast(val); } - void _incr_num_items() { ++_num_buckets; } - void _decr_num_items() { --_num_buckets; } - uint32_t _num_alloc() const { return (uint32_t)_num_allocated; } - void _set_num_alloc(uint32_t val) { _num_allocated = static_cast(val); } -#else - uint32_t _num_items() const { return spp_popcount(_bitmap); } - void _set_num_items(uint32_t ) { } - void _incr_num_items() { } - void _decr_num_items() { } - uint32_t _num_alloc() const { return _sizing(_num_items()); } - void _set_num_alloc(uint32_t val) { } -#endif - - // The actual data - // --------------- - value_type * _group; // (small) array of T's - group_bm_type _bitmap; - group_bm_type _bm_erased; // ones where items have been erased - -#ifdef SPP_STORE_NUM_ITEMS - size_type _num_buckets; - size_type _num_allocated; -#endif -}; - -// --------------------------------------------------------------------------- -// --------------------------------------------------------------------------- -template -class sparsetable -{ -public: - typedef T value_type; - typedef Alloc allocator_type; - typedef sparsegroup group_type; - -private: - typedef typename Alloc::template rebind::other group_alloc_type; - typedef typename group_alloc_type::size_type group_size_type; - -public: - // Basic types - // ----------- - typedef typename allocator_type::size_type size_type; - typedef typename allocator_type::difference_type difference_type; - typedef value_type& reference; - typedef const value_type& const_reference; - typedef value_type* pointer; - typedef const value_type* const_pointer; - - typedef group_type& GroupsReference; - typedef const group_type& GroupsConstReference; - - typedef typename group_type::ne_iterator ColIterator; - typedef typename group_type::const_ne_iterator ColConstIterator; - - typedef table_iterator > iterator; // defined with index - typedef const_table_iterator > const_iterator; // defined with index - typedef std::reverse_iterator const_reverse_iterator; - typedef std::reverse_iterator reverse_iterator; - - // These are our special iterators, that go over non-empty buckets in a - // table. These aren't const only because you can change non-empty bcks. - // ---------------------------------------------------------------------- - typedef Two_d_iterator ne_iterator; - - typedef Two_d_iterator const_ne_iterator; - - // Another special iterator: it frees memory as it iterates (used to resize). - // Obviously, you can only iterate over it once, which is why it's an input iterator - // --------------------------------------------------------------------------------- - typedef Two_d_destructive_iterator destructive_iterator; - - typedef std::reverse_iterator reverse_ne_iterator; - typedef std::reverse_iterator const_reverse_ne_iterator; - - - // Iterator functions - // ------------------ - iterator begin() { return iterator(this, 0); } - const_iterator begin() const { return const_iterator(this, 0); } - const_iterator cbegin() const { return const_iterator(this, 0); } - iterator end() { return iterator(this, size()); } - const_iterator end() const { return const_iterator(this, size()); } - const_iterator cend() const { return const_iterator(this, size()); } - reverse_iterator rbegin() { return reverse_iterator(end()); } - const_reverse_iterator rbegin() const { return const_reverse_iterator(cend()); } - const_reverse_iterator crbegin() const { return const_reverse_iterator(cend()); } - reverse_iterator rend() { return reverse_iterator(begin()); } - const_reverse_iterator rend() const { return const_reverse_iterator(cbegin()); } - const_reverse_iterator crend() const { return const_reverse_iterator(cbegin()); } - - // Versions for our special non-empty iterator - // ------------------------------------------ - ne_iterator ne_begin() { return ne_iterator (_first_group); } - const_ne_iterator ne_begin() const { return const_ne_iterator(_first_group); } - const_ne_iterator ne_cbegin() const { return const_ne_iterator(_first_group); } - ne_iterator ne_end() { return ne_iterator (_last_group); } - const_ne_iterator ne_end() const { return const_ne_iterator(_last_group); } - const_ne_iterator ne_cend() const { return const_ne_iterator(_last_group); } - - reverse_ne_iterator ne_rbegin() { return reverse_ne_iterator(ne_end()); } - const_reverse_ne_iterator ne_rbegin() const { return const_reverse_ne_iterator(ne_end()); } - const_reverse_ne_iterator ne_crbegin() const { return const_reverse_ne_iterator(ne_end()); } - reverse_ne_iterator ne_rend() { return reverse_ne_iterator(ne_begin()); } - const_reverse_ne_iterator ne_rend() const { return const_reverse_ne_iterator(ne_begin()); } - const_reverse_ne_iterator ne_crend() const { return const_reverse_ne_iterator(ne_begin()); } - - destructive_iterator destructive_begin() - { - return destructive_iterator(_alloc, _first_group); - } - - destructive_iterator destructive_end() - { - return destructive_iterator(_alloc, _last_group); - } - - // How to deal with the proper group - static group_size_type num_groups(size_type num) - { - // how many to hold num buckets - return num == 0 ? (group_size_type)0 : - (group_size_type)(((num-1) / SPP_GROUP_SIZE) + 1); - } - - typename group_type::size_type pos_in_group(size_type i) const - { - return static_cast(i & SPP_MASK_); - } - - size_type group_num(size_type i) const - { - return (size_type)(i >> SPP_SHIFT_); - } - - GroupsReference which_group(size_type i) - { - return _first_group[group_num(i)]; - } - - GroupsConstReference which_group(size_type i) const - { - return _first_group[group_num(i)]; - } - - void _alloc_group_array(group_size_type sz, group_type *&first, group_type *&last) - { - if (sz) - { - first = _group_alloc.allocate((size_type)(sz + 1)); // + 1 for end marker - first[sz].mark(); // for the ne_iterator - last = first + sz; - } - } - - void _free_group_array(group_type *&first, group_type *&last) - { - if (first) - { - _group_alloc.deallocate(first, (group_size_type)(last - first + 1)); // + 1 for end marker - first = last = 0; - } - } - - void _allocate_groups(size_type sz) - { - if (sz) - { - _alloc_group_array(sz, _first_group, _last_group); - std::uninitialized_fill(_first_group, _last_group, group_type()); - } - } - - void _free_groups() - { - if (_first_group) - { - for (group_type *g = _first_group; g != _last_group; ++g) - g->destruct(_alloc); - _free_group_array(_first_group, _last_group); - } - } - - void _cleanup() - { - _free_groups(); // sets _first_group = _last_group = 0 - _table_size = 0; - _num_buckets = 0; - } - - void _init() - { - _first_group = 0; - _last_group = 0; - _table_size = 0; - _num_buckets = 0; - } - - void _copy(const sparsetable &o) - { - _table_size = o._table_size; - _num_buckets = o._num_buckets; - _alloc = o._alloc; // todo - copy or move allocator according to... - _group_alloc = o._group_alloc; // http://en.cppreference.com/w/cpp/container/unordered_map/unordered_map - - group_size_type sz = (group_size_type)(o._last_group - o._first_group); - if (sz) - { - _alloc_group_array(sz, _first_group, _last_group); - for (group_size_type i=0; iswap(o); - } - - sparsetable(sparsetable&& o, const allocator_type &alloc) - { - _init(); - this->swap(o); - _alloc = alloc; // [gp todo] is this correct? - } - - sparsetable& operator=(sparsetable&& o) - { - _cleanup(); - this->swap(o); - return *this; - } -#endif - - // Many STL algorithms use swap instead of copy constructors - void swap(sparsetable& o) - { - using std::swap; - - swap(_first_group, o._first_group); - swap(_last_group, o._last_group); - swap(_table_size, o._table_size); - swap(_num_buckets, o._num_buckets); - if (_alloc != o._alloc) - swap(_alloc, o._alloc); - if (_group_alloc != o._group_alloc) - swap(_group_alloc, o._group_alloc); - } - - // It's always nice to be able to clear a table without deallocating it - void clear() - { - _free_groups(); - _num_buckets = 0; - _table_size = 0; - } - - inline allocator_type get_allocator() const - { - return _alloc; - } - - - // Functions that tell you about size. - // NOTE: empty() is non-intuitive! It does not tell you the number - // of not-empty buckets (use num_nonempty() for that). Instead - // it says whether you've allocated any buckets or not. - // ---------------------------------------------------------------- - size_type size() const { return _table_size; } - size_type max_size() const { return _alloc.max_size(); } - bool empty() const { return _table_size == 0; } - size_type num_nonempty() const { return _num_buckets; } - - // OK, we'll let you resize one of these puppies - void resize(size_type new_size) - { - group_size_type sz = num_groups(new_size); - group_size_type old_sz = (group_size_type)(_last_group - _first_group); - - if (sz != old_sz) - { - // resize group array - // ------------------ - group_type *first = 0, *last = 0; - if (sz) - { - _alloc_group_array(sz, first, last); - if (old_sz) - memcpy(static_cast(first), _first_group, sizeof(*first) * (std::min)(sz, old_sz)); - } - - if (sz < old_sz) - { - for (group_type *g = _first_group + sz; g != _last_group; ++g) - g->destruct(_alloc); - } - else - std::uninitialized_fill(first + old_sz, last, group_type()); - - _free_group_array(_first_group, _last_group); - _first_group = first; - _last_group = last; - } -#if 0 - // used only in test program - // todo: fix if sparsetable to be used directly - // -------------------------------------------- - if (new_size < _table_size) - { - // lower num_buckets, clear last group - if (pos_in_group(new_size) > 0) // need to clear inside last group - groups.back().erase(_alloc, groups.back().begin() + pos_in_group(new_size), - groups.back().end()); - _num_buckets = 0; // refigure # of used buckets - for (const group_type *group = _first_group; group != _last_group; ++group) - _num_buckets += group->num_nonempty(); - } -#endif - _table_size = new_size; - } - - // We let you see if a bucket is non-empty without retrieving it - // ------------------------------------------------------------- - bool test(size_type i) const - { - // assert(i < _table_size); - return which_group(i).test(pos_in_group(i)); - } - - // also tests for erased values - // ---------------------------- - bool test_strict(size_type i) const - { - // assert(i < _table_size); - return which_group(i).test_strict(pos_in_group(i)); - } - - friend struct GrpPos; - - struct GrpPos - { - typedef typename sparsetable::ne_iterator ne_iter; - GrpPos(const sparsetable &table, size_type i) : - grp(table.which_group(i)), pos(table.pos_in_group(i)) {} - - bool test_strict() const { return grp.test_strict(pos); } - bool test() const { return grp.test(pos); } - typename sparsetable::reference unsafe_get() const { return grp.unsafe_get(pos); } - ne_iter get_iter(typename sparsetable::reference ref) - { - return ne_iter((group_type *)&grp, &ref); - } - - void erase(sparsetable &table) // item *must* be present - { - assert(table._num_buckets); - ((group_type &)grp).erase(table._alloc, pos); - --table._num_buckets; - } - - private: - GrpPos* operator=(const GrpPos&); - - const group_type &grp; - typename group_type::size_type pos; - }; - - bool test(iterator pos) const - { - return which_group(pos.pos).test(pos_in_group(pos.pos)); - } - - bool test(const_iterator pos) const - { - return which_group(pos.pos).test(pos_in_group(pos.pos)); - } - - // TODO(csilvers): make protected + friend - // This is used by sparse_hashtable to get an element from the table - // when we know it exists (because the caller has called test(i)). - // ----------------------------------------------------------------- - reference unsafe_get(size_type i) const - { - assert(i < _table_size); - // assert(test(i)); - return which_group(i).unsafe_get(pos_in_group(i)); - } - - // Needed for hashtables, gets as a ne_iterator. Crashes for empty bcks - const_ne_iterator get_iter(size_type i) const - { - //assert(test(i)); // how can a ne_iterator point to an empty bucket? - - size_type grp_idx = group_num(i); - - return const_ne_iterator(_first_group + grp_idx, - (_first_group[grp_idx].ne_begin() + - _first_group[grp_idx].pos_to_offset(pos_in_group(i)))); - } - - const_ne_iterator get_iter(size_type i, ColIterator col_it) const - { - return const_ne_iterator(_first_group + group_num(i), col_it); - } - - // For nonempty we can return a non-const version - ne_iterator get_iter(size_type i) - { - //assert(test(i)); // how can a nonempty_iterator point to an empty bucket? - - size_type grp_idx = group_num(i); - - return ne_iterator(_first_group + grp_idx, - (_first_group[grp_idx].ne_begin() + - _first_group[grp_idx].pos_to_offset(pos_in_group(i)))); - } - - ne_iterator get_iter(size_type i, ColIterator col_it) - { - return ne_iterator(_first_group + group_num(i), col_it); - } - - // And the reverse transformation. - size_type get_pos(const const_ne_iterator& it) const - { - difference_type current_row = it.row_current - _first_group; - difference_type current_col = (it.col_current - _first_group[current_row].ne_begin()); - return ((current_row * SPP_GROUP_SIZE) + - _first_group[current_row].offset_to_pos(current_col)); - } - - // Val can be reference or const_reference - // --------------------------------------- - template - reference set(size_type i, Val &val) - { - assert(i < _table_size); - group_type &group = which_group(i); - typename group_type::size_type old_numbuckets = group.num_nonempty(); - pointer p(group.set(_alloc, pos_in_group(i), val)); - _num_buckets += group.num_nonempty() - old_numbuckets; - return *p; - } - - // used in _move_from (where we can move the old value instead of copying it - void move(size_type i, reference val) - { - assert(i < _table_size); - which_group(i).set(_alloc, pos_in_group(i), val); - ++_num_buckets; - } - - // This takes the specified elements out of the table. - // -------------------------------------------------- - void erase(size_type i) - { - assert(i < _table_size); - - GroupsReference grp(which_group(i)); - typename group_type::size_type old_numbuckets = grp.num_nonempty(); - grp.erase(_alloc, pos_in_group(i)); - _num_buckets += grp.num_nonempty() - old_numbuckets; - } - - void erase(iterator pos) - { - erase(pos.pos); - } - - void erase(iterator start_it, iterator end_it) - { - // This could be more efficient, but then we'd need to figure - // out if we spanned groups or not. Doesn't seem worth it. - for (; start_it != end_it; ++start_it) - erase(start_it); - } - - const_ne_iterator erase(const_ne_iterator it) - { - ne_iterator res(it); - if (res.row_current->erase_ne(_alloc, res)) - _num_buckets--; - return res; - } - - const_ne_iterator erase(const_ne_iterator f, const_ne_iterator l) - { - size_t diff = l - f; - while (diff--) - f = erase(f); - return f; - } - - // We support reading and writing tables to disk. We don't store - // the actual array contents (which we don't know how to store), - // just the groups and sizes. Returns true if all went ok. - -private: - // Every time the disk format changes, this should probably change too - typedef unsigned long MagicNumberType; - static const MagicNumberType MAGIC_NUMBER = 0x24687531; - - // Old versions of this code write all data in 32 bits. We need to - // support these files as well as having support for 64-bit systems. - // So we use the following encoding scheme: for values < 2^32-1, we - // store in 4 bytes in big-endian order. For values > 2^32, we - // store 0xFFFFFFF followed by 8 bytes in big-endian order. This - // causes us to mis-read old-version code that stores exactly - // 0xFFFFFFF, but I don't think that is likely to have happened for - // these particular values. - template - static bool write_32_or_64(OUTPUT* fp, IntType value) - { - if (value < 0xFFFFFFFFULL) // fits in 4 bytes - { - if (!sparsehash_internal::write_bigendian_number(fp, value, 4)) - return false; - } - else - { - if (!sparsehash_internal::write_bigendian_number(fp, 0xFFFFFFFFUL, 4)) - return false; - if (!sparsehash_internal::write_bigendian_number(fp, value, 8)) - return false; - } - return true; - } - - template - static bool read_32_or_64(INPUT* fp, IntType *value) - { - // reads into value - MagicNumberType first4 = 0; // a convenient 32-bit unsigned type - if (!sparsehash_internal::read_bigendian_number(fp, &first4, 4)) - return false; - - if (first4 < 0xFFFFFFFFULL) - { - *value = first4; - } - else - { - if (!sparsehash_internal::read_bigendian_number(fp, value, 8)) - return false; - } - return true; - } - -public: - // read/write_metadata() and read_write/nopointer_data() are DEPRECATED. - // Use serialize() and unserialize(), below, for new code. - - template - bool write_metadata(OUTPUT *fp) const - { - if (!write_32_or_64(fp, MAGIC_NUMBER)) return false; - if (!write_32_or_64(fp, _table_size)) return false; - if (!write_32_or_64(fp, _num_buckets)) return false; - - for (const group_type *group = _first_group; group != _last_group; ++group) - if (group->write_metadata(fp) == false) - return false; - return true; - } - - // Reading destroys the old table contents! Returns true if read ok. - template - bool read_metadata(INPUT *fp) - { - size_type magic_read = 0; - if (!read_32_or_64(fp, &magic_read)) return false; - if (magic_read != MAGIC_NUMBER) - { - clear(); // just to be consistent - return false; - } - - if (!read_32_or_64(fp, &_table_size)) return false; - if (!read_32_or_64(fp, &_num_buckets)) return false; - - resize(_table_size); // so the vector's sized ok - for (group_type *group = _first_group; group != _last_group; ++group) - if (group->read_metadata(_alloc, fp) == false) - return false; - return true; - } - - // This code is identical to that for SparseGroup - // If your keys and values are simple enough, we can write them - // to disk for you. "simple enough" means no pointers. - // However, we don't try to normalize endianness - bool write_nopointer_data(FILE *fp) const - { - for (const_ne_iterator it = ne_begin(); it != ne_end(); ++it) - if (!fwrite(&*it, sizeof(*it), 1, fp)) - return false; - return true; - } - - // When reading, we have to override the potential const-ness of *it - bool read_nopointer_data(FILE *fp) - { - for (ne_iterator it = ne_begin(); it != ne_end(); ++it) - if (!fread(reinterpret_cast(&(*it)), sizeof(*it), 1, fp)) - return false; - return true; - } - - // INPUT and OUTPUT must be either a FILE, *or* a C++ stream - // (istream, ostream, etc) *or* a class providing - // Read(void*, size_t) and Write(const void*, size_t) - // (respectively), which writes a buffer into a stream - // (which the INPUT/OUTPUT instance presumably owns). - - typedef sparsehash_internal::pod_serializer NopointerSerializer; - - // ValueSerializer: a functor. operator()(OUTPUT*, const value_type&) - template - bool serialize(ValueSerializer serializer, OUTPUT *fp) - { - if (!write_metadata(fp)) - return false; - for (const_ne_iterator it = ne_begin(); it != ne_end(); ++it) - if (!serializer(fp, *it)) - return false; - return true; - } - - // ValueSerializer: a functor. operator()(INPUT*, value_type*) - template - bool unserialize(ValueSerializer serializer, INPUT *fp) - { - clear(); - if (!read_metadata(fp)) - return false; - for (ne_iterator it = ne_begin(); it != ne_end(); ++it) - if (!serializer(fp, &*it)) - return false; - return true; - } - - // Comparisons. Note the comparisons are pretty arbitrary: we - // compare values of the first index that isn't equal (using default - // value for empty buckets). - bool operator==(const sparsetable& x) const - { - return (_table_size == x._table_size && - _num_buckets == x._num_buckets && - _first_group == x._first_group); - } - - bool operator<(const sparsetable& x) const - { - return std::lexicographical_compare(begin(), end(), x.begin(), x.end()); - } - bool operator!=(const sparsetable& x) const { return !(*this == x); } - bool operator<=(const sparsetable& x) const { return !(x < *this); } - bool operator>(const sparsetable& x) const { return x < *this; } - bool operator>=(const sparsetable& x) const { return !(*this < x); } - - -private: - // The actual data - // --------------- - group_type * _first_group; - group_type * _last_group; - size_type _table_size; // how many buckets they want - size_type _num_buckets; // number of non-empty buckets - group_alloc_type _group_alloc; - allocator_type _alloc; -}; - -// ---------------------------------------------------------------------- -// S P A R S E _ H A S H T A B L E -// ---------------------------------------------------------------------- -// Hashtable class, used to implement the hashed associative containers -// hash_set and hash_map. -// -// Value: what is stored in the table (each bucket is a Value). -// Key: something in a 1-to-1 correspondence to a Value, that can be used -// to search for a Value in the table (find() takes a Key). -// HashFcn: Takes a Key and returns an integer, the more unique the better. -// ExtractKey: given a Value, returns the unique Key associated with it. -// Must inherit from unary_function, or at least have a -// result_type enum indicating the return type of operator(). -// EqualKey: Given two Keys, says whether they are the same (that is, -// if they are both associated with the same Value). -// Alloc: STL allocator to use to allocate memory. -// -// ---------------------------------------------------------------------- - -// The probing method -// ------------------ -// Linear probing -// #define JUMP_(key, num_probes) ( 1 ) -// Quadratic probing -#define JUMP_(key, num_probes) ( num_probes ) - - -// ------------------------------------------------------------------- -// ------------------------------------------------------------------- -template -class sparse_hashtable -{ -public: - typedef Key key_type; - typedef Value value_type; - typedef HashFcn hasher; // user provided or spp_hash - typedef EqualKey key_equal; - typedef Alloc allocator_type; - - typedef typename allocator_type::size_type size_type; - typedef typename allocator_type::difference_type difference_type; - typedef value_type& reference; - typedef const value_type& const_reference; - typedef value_type* pointer; - typedef const value_type* const_pointer; - - // Table is the main storage class. - typedef sparsetable Table; - typedef typename Table::ne_iterator ne_it; - typedef typename Table::const_ne_iterator cne_it; - typedef typename Table::destructive_iterator dest_it; - typedef typename Table::ColIterator ColIterator; - - typedef ne_it iterator; - typedef cne_it const_iterator; - typedef dest_it destructive_iterator; - - // These come from tr1. For us they're the same as regular iterators. - // ------------------------------------------------------------------- - typedef iterator local_iterator; - typedef const_iterator const_local_iterator; - - // How full we let the table get before we resize - // ---------------------------------------------- - static const int HT_OCCUPANCY_PCT; // = 80 (out of 100); - - // How empty we let the table get before we resize lower, by default. - // (0.0 means never resize lower.) - // It should be less than OCCUPANCY_PCT / 2 or we thrash resizing - // ------------------------------------------------------------------ - static const int HT_EMPTY_PCT; // = 0.4 * HT_OCCUPANCY_PCT; - - // Minimum size we're willing to let hashtables be. - // Must be a power of two, and at least 4. - // Note, however, that for a given hashtable, the initial size is a - // function of the first constructor arg, and may be >HT_MIN_BUCKETS. - // ------------------------------------------------------------------ - static const size_type HT_MIN_BUCKETS = 4; - - // By default, if you don't specify a hashtable size at - // construction-time, we use this size. Must be a power of two, and - // at least HT_MIN_BUCKETS. - // ----------------------------------------------------------------- - static const size_type HT_DEFAULT_STARTING_BUCKETS = 32; - - // iterators - // --------- - iterator begin() { return _mk_iterator(table.ne_begin()); } - iterator end() { return _mk_iterator(table.ne_end()); } - const_iterator begin() const { return _mk_const_iterator(table.ne_cbegin()); } - const_iterator end() const { return _mk_const_iterator(table.ne_cend()); } - const_iterator cbegin() const { return _mk_const_iterator(table.ne_cbegin()); } - const_iterator cend() const { return _mk_const_iterator(table.ne_cend()); } - - // These come from tr1 unordered_map. They iterate over 'bucket' n. - // For sparsehashtable, we could consider each 'group' to be a bucket, - // I guess, but I don't really see the point. We'll just consider - // bucket n to be the n-th element of the sparsetable, if it's occupied, - // or some empty element, otherwise. - // --------------------------------------------------------------------- - local_iterator begin(size_type i) - { - return _mk_iterator(table.test(i) ? table.get_iter(i) : table.ne_end()); - } - - local_iterator end(size_type i) - { - local_iterator it = begin(i); - if (table.test(i)) - ++it; - return _mk_iterator(it); - } - - const_local_iterator begin(size_type i) const - { - return _mk_const_iterator(table.test(i) ? table.get_iter(i) : table.ne_cend()); - } - - const_local_iterator end(size_type i) const - { - const_local_iterator it = begin(i); - if (table.test(i)) - ++it; - return _mk_const_iterator(it); - } - - const_local_iterator cbegin(size_type i) const { return begin(i); } - const_local_iterator cend(size_type i) const { return end(i); } - - // This is used when resizing - // -------------------------- - destructive_iterator destructive_begin() { return _mk_destructive_iterator(table.destructive_begin()); } - destructive_iterator destructive_end() { return _mk_destructive_iterator(table.destructive_end()); } - - - // accessor functions for the things we templatize on, basically - // ------------------------------------------------------------- - hasher hash_funct() const { return settings; } - key_equal key_eq() const { return key_info; } - allocator_type get_allocator() const { return table.get_allocator(); } - - // Accessor function for statistics gathering. - unsigned int num_table_copies() const { return settings.num_ht_copies(); } - -private: - // This is used as a tag for the copy constructor, saying to destroy its - // arg We have two ways of destructively copying: with potentially growing - // the hashtable as we copy, and without. To make sure the outside world - // can't do a destructive copy, we make the typename private. - // ----------------------------------------------------------------------- - enum MoveDontCopyT {MoveDontCopy, MoveDontGrow}; - - // creating iterators from sparsetable::ne_iterators - // ------------------------------------------------- - iterator _mk_iterator(ne_it it) const { return it; } - const_iterator _mk_const_iterator(cne_it it) const { return it; } - destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; } - -public: - size_type size() const { return table.num_nonempty(); } - size_type max_size() const { return table.max_size(); } - bool empty() const { return size() == 0; } - size_type bucket_count() const { return table.size(); } - size_type max_bucket_count() const { return max_size(); } - // These are tr1 methods. Their idea of 'bucket' doesn't map well to - // what we do. We just say every bucket has 0 or 1 items in it. - size_type bucket_size(size_type i) const - { - return (size_type)(begin(i) == end(i) ? 0 : 1); - } - -private: - // Because of the above, size_type(-1) is never legal; use it for errors - // --------------------------------------------------------------------- - static const size_type ILLEGAL_BUCKET = size_type(-1); - - // Used after a string of deletes. Returns true if we actually shrunk. - // TODO(csilvers): take a delta so we can take into account inserts - // done after shrinking. Maybe make part of the Settings class? - // -------------------------------------------------------------------- - bool _maybe_shrink() - { - assert((bucket_count() & (bucket_count()-1)) == 0); // is a power of two - assert(bucket_count() >= HT_MIN_BUCKETS); - bool retval = false; - - // If you construct a hashtable with < HT_DEFAULT_STARTING_BUCKETS, - // we'll never shrink until you get relatively big, and we'll never - // shrink below HT_DEFAULT_STARTING_BUCKETS. Otherwise, something - // like "dense_hash_set x; x.insert(4); x.erase(4);" will - // shrink us down to HT_MIN_BUCKETS buckets, which is too small. - // --------------------------------------------------------------- - const size_type num_remain = table.num_nonempty(); - const size_type shrink_threshold = settings.shrink_threshold(); - if (shrink_threshold > 0 && num_remain < shrink_threshold && - bucket_count() > HT_DEFAULT_STARTING_BUCKETS) - { - const float shrink_factor = settings.shrink_factor(); - size_type sz = (size_type)(bucket_count() / 2); // find how much we should shrink - while (sz > HT_DEFAULT_STARTING_BUCKETS && - num_remain < static_cast(sz * shrink_factor)) - { - sz /= 2; // stay a power of 2 - } - sparse_hashtable tmp(MoveDontCopy, *this, sz); - swap(tmp); // now we are tmp - retval = true; - } - settings.set_consider_shrink(false); // because we just considered it - return retval; - } - - // We'll let you resize a hashtable -- though this makes us copy all! - // When you resize, you say, "make it big enough for this many more elements" - // Returns true if we actually resized, false if size was already ok. - // -------------------------------------------------------------------------- - bool _resize_delta(size_type delta) - { - bool did_resize = false; - if (settings.consider_shrink()) - { - // see if lots of deletes happened - if (_maybe_shrink()) - did_resize = true; - } - if (table.num_nonempty() >= - (std::numeric_limits::max)() - delta) - { - throw_exception(std::length_error("resize overflow")); - } - - size_type num_occupied = (size_type)(table.num_nonempty() + num_deleted); - - if (bucket_count() >= HT_MIN_BUCKETS && - (num_occupied + delta) <= settings.enlarge_threshold()) - return did_resize; // we're ok as we are - - // Sometimes, we need to resize just to get rid of all the - // "deleted" buckets that are clogging up the hashtable. So when - // deciding whether to resize, count the deleted buckets (which - // are currently taking up room). - // ------------------------------------------------------------- - const size_type needed_size = - settings.min_buckets((size_type)(num_occupied + delta), (size_type)0); - - if (needed_size <= bucket_count()) // we have enough buckets - return did_resize; - - size_type resize_to = settings.min_buckets((size_type)(num_occupied + delta), bucket_count()); - - if (resize_to < needed_size && // may double resize_to - resize_to < (std::numeric_limits::max)() / 2) - { - // This situation means that we have enough deleted elements, - // that once we purge them, we won't actually have needed to - // grow. But we may want to grow anyway: if we just purge one - // element, say, we'll have to grow anyway next time we - // insert. Might as well grow now, since we're already going - // through the trouble of copying (in order to purge the - // deleted elements). - const size_type target = - static_cast(settings.shrink_size((size_type)(resize_to*2))); - if (table.num_nonempty() + delta >= target) - { - // Good, we won't be below the shrink threshhold even if we double. - resize_to *= 2; - } - } - - sparse_hashtable tmp(MoveDontCopy, *this, resize_to); - swap(tmp); // now we are tmp - return true; - } - - // Used to actually do the rehashing when we grow/shrink a hashtable - // ----------------------------------------------------------------- - void _copy_from(const sparse_hashtable &ht, size_type min_buckets_wanted) - { - clear(); // clear table, set num_deleted to 0 - - // If we need to change the size of our table, do it now - const size_type resize_to = settings.min_buckets(ht.size(), min_buckets_wanted); - - if (resize_to > bucket_count()) - { - // we don't have enough buckets - table.resize(resize_to); // sets the number of buckets - settings.reset_thresholds(bucket_count()); - } - - // We use a normal iterator to get bcks from ht - // We could use insert() here, but since we know there are - // no duplicates, we can be more efficient - assert((bucket_count() & (bucket_count()-1)) == 0); // a power of two - for (const_iterator it = ht.begin(); it != ht.end(); ++it) - { - size_type num_probes = 0; // how many times we've probed - size_type bucknum; - const size_type bucket_count_minus_one = bucket_count() - 1; - for (bucknum = hash(get_key(*it)) & bucket_count_minus_one; - table.test(bucknum); // table.test() OK since no erase() - bucknum = (bucknum + JUMP_(key, num_probes)) & bucket_count_minus_one) - { - ++num_probes; - assert(num_probes < bucket_count() - && "Hashtable is full: an error in key_equal<> or hash<>"); - } - table.set(bucknum, *it); // copies the value to here - } - settings.inc_num_ht_copies(); - } - - // Implementation is like _copy_from, but it destroys the table of the - // "from" guy by freeing sparsetable memory as we iterate. This is - // useful in resizing, since we're throwing away the "from" guy anyway. - // -------------------------------------------------------------------- - void _move_from(MoveDontCopyT mover, sparse_hashtable &ht, - size_type min_buckets_wanted) - { - clear(); - - // If we need to change the size of our table, do it now - size_type resize_to; - if (mover == MoveDontGrow) - resize_to = ht.bucket_count(); // keep same size as old ht - else // MoveDontCopy - resize_to = settings.min_buckets(ht.size(), min_buckets_wanted); - if (resize_to > bucket_count()) - { - // we don't have enough buckets - table.resize(resize_to); // sets the number of buckets - settings.reset_thresholds(bucket_count()); - } - - // We use a normal iterator to get bcks from ht - // We could use insert() here, but since we know there are - // no duplicates, we can be more efficient - assert((bucket_count() & (bucket_count()-1)) == 0); // a power of two - const size_type bucket_count_minus_one = (const size_type)(bucket_count() - 1); - - // THIS IS THE MAJOR LINE THAT DIFFERS FROM COPY_FROM(): - for (destructive_iterator it = ht.destructive_begin(); - it != ht.destructive_end(); ++it) - { - size_type num_probes = 0; - size_type bucknum; - for (bucknum = hash(get_key(*it)) & bucket_count_minus_one; - table.test(bucknum); // table.test() OK since no erase() - bucknum = (size_type)((bucknum + JUMP_(key, num_probes)) & (bucket_count()-1))) - { - ++num_probes; - assert(num_probes < bucket_count() - && "Hashtable is full: an error in key_equal<> or hash<>"); - } - table.move(bucknum, *it); // moves the value to here - } - settings.inc_num_ht_copies(); - } - - - // Required by the spec for hashed associative container -public: - // Though the docs say this should be num_buckets, I think it's much - // more useful as num_elements. As a special feature, calling with - // req_elements==0 will cause us to shrink if we can, saving space. - // ----------------------------------------------------------------- - void resize(size_type req_elements) - { - // resize to this or larger - if (settings.consider_shrink() || req_elements == 0) - _maybe_shrink(); - if (req_elements > table.num_nonempty()) // we only grow - _resize_delta((size_type)(req_elements - table.num_nonempty())); - } - - // Get and change the value of shrink_factor and enlarge_factor. The - // description at the beginning of this file explains how to choose - // the values. Setting the shrink parameter to 0.0 ensures that the - // table never shrinks. - // ------------------------------------------------------------------ - void get_resizing_parameters(float* shrink, float* grow) const - { - *shrink = settings.shrink_factor(); - *grow = settings.enlarge_factor(); - } - - float get_shrink_factor() const { return settings.shrink_factor(); } - float get_enlarge_factor() const { return settings.enlarge_factor(); } - - void set_resizing_parameters(float shrink, float grow) - { - settings.set_resizing_parameters(shrink, grow); - settings.reset_thresholds(bucket_count()); - } - - void set_shrink_factor(float shrink) - { - set_resizing_parameters(shrink, get_enlarge_factor()); - } - - void set_enlarge_factor(float grow) - { - set_resizing_parameters(get_shrink_factor(), grow); - } - - // CONSTRUCTORS -- as required by the specs, we take a size, - // but also let you specify a hashfunction, key comparator, - // and key extractor. We also define a copy constructor and =. - // DESTRUCTOR -- the default is fine, surprisingly. - // ------------------------------------------------------------ - explicit sparse_hashtable(size_type expected_max_items_in_table = 0, - const HashFcn& hf = HashFcn(), - const EqualKey& eql = EqualKey(), - const ExtractKey& ext = ExtractKey(), - const SetKey& set = SetKey(), - const allocator_type& alloc = allocator_type()) - : settings(hf), - key_info(ext, set, eql), - num_deleted(0), - table((expected_max_items_in_table == 0 - ? HT_DEFAULT_STARTING_BUCKETS - : settings.min_buckets(expected_max_items_in_table, 0)), - alloc) - { - settings.reset_thresholds(bucket_count()); - } - - // As a convenience for resize(), we allow an optional second argument - // which lets you make this new hashtable a different size than ht. - // We also provide a mechanism of saying you want to "move" the ht argument - // into us instead of copying. - // ------------------------------------------------------------------------ - sparse_hashtable(const sparse_hashtable& ht, - size_type min_buckets_wanted = HT_DEFAULT_STARTING_BUCKETS) - : settings(ht.settings), - key_info(ht.key_info), - num_deleted(0), - table(0) - { - settings.reset_thresholds(bucket_count()); - _copy_from(ht, min_buckets_wanted); - } - -#if !defined(SPP_NO_CXX11_RVALUE_REFERENCES) - - sparse_hashtable(sparse_hashtable&& o, const allocator_type& alloc = allocator_type()) : - settings(o.settings), - key_info(o.key_info), - num_deleted(0), - table(HT_DEFAULT_STARTING_BUCKETS, alloc) - { - settings.reset_thresholds(bucket_count()); - this->swap(o); - } - - sparse_hashtable& operator=(sparse_hashtable&& o) - { - this->swap(o); - return *this; - } -#endif - - sparse_hashtable(MoveDontCopyT mover, - sparse_hashtable& ht, - size_type min_buckets_wanted = HT_DEFAULT_STARTING_BUCKETS) - : settings(ht.settings), - key_info(ht.key_info), - num_deleted(0), - table(min_buckets_wanted, ht.table.get_allocator()) - //table(min_buckets_wanted) - { - settings.reset_thresholds(bucket_count()); - _move_from(mover, ht, min_buckets_wanted); - } - - sparse_hashtable& operator=(const sparse_hashtable& ht) - { - if (&ht == this) - return *this; // don't copy onto ourselves - settings = ht.settings; - key_info = ht.key_info; - num_deleted = ht.num_deleted; - - // _copy_from() calls clear and sets num_deleted to 0 too - _copy_from(ht, HT_MIN_BUCKETS); - - // we purposefully don't copy the allocator, which may not be copyable - return *this; - } - - // Many STL algorithms use swap instead of copy constructors - void swap(sparse_hashtable& ht) - { - using std::swap; - - swap(settings, ht.settings); - swap(key_info, ht.key_info); - swap(num_deleted, ht.num_deleted); - table.swap(ht.table); - settings.reset_thresholds(bucket_count()); // also resets consider_shrink - ht.settings.reset_thresholds(ht.bucket_count()); - // we purposefully don't swap the allocator, which may not be swap-able - } - - // It's always nice to be able to clear a table without deallocating it - void clear() - { - if (!empty() || num_deleted != 0) - { - table.clear(); - table = Table(HT_DEFAULT_STARTING_BUCKETS, table.get_allocator()); - } - settings.reset_thresholds(bucket_count()); - num_deleted = 0; - } - - // LOOKUP ROUTINES -private: - - enum pos_type { pt_empty = 0, pt_erased, pt_full }; - // ------------------------------------------------------------------- - class Position - { - public: - - Position() : _t(pt_empty) {} - Position(pos_type t, size_type idx) : _t(t), _idx(idx) {} - - pos_type _t; - size_type _idx; - }; - - // Returns a pair: - // - 'first' is a code, 2 if key already present, 0 or 1 otherwise. - // - 'second' is a position, where the key should go - // Note: because of deletions where-to-insert is not trivial: it's the - // first deleted bucket we see, as long as we don't find the key later - // ------------------------------------------------------------------- - Position _find_position(const key_type &key) const - { - size_type num_probes = 0; // how many times we've probed - const size_type bucket_count_minus_one = (const size_type)(bucket_count() - 1); - size_type bucknum = hash(key) & bucket_count_minus_one; - Position pos; - - while (1) - { - // probe until something happens - // ----------------------------- - typename Table::GrpPos grp_pos(table, bucknum); - - if (!grp_pos.test_strict()) - { - // bucket is empty => key not present - return pos._t ? pos : Position(pt_empty, bucknum); - } - else if (grp_pos.test()) - { - reference ref(grp_pos.unsafe_get()); - - if (equals(key, get_key(ref))) - return Position(pt_full, bucknum); - } - else if (pos._t == pt_empty) - { - // first erased position - pos._t = pt_erased; - pos._idx = bucknum; - } - - ++num_probes; // we're doing another probe - bucknum = (size_type)((bucknum + JUMP_(key, num_probes)) & bucket_count_minus_one); - assert(num_probes < bucket_count() - && "Hashtable is full: an error in key_equal<> or hash<>"); - } - } - -public: - // I hate to duplicate find() like that, but it is - // significantly faster to not have the intermediate pair - // ------------------------------------------------------------------ - iterator find(const key_type& key) - { - size_type num_probes = 0; // how many times we've probed - const size_type bucket_count_minus_one = bucket_count() - 1; - size_type bucknum = hash(key) & bucket_count_minus_one; - - while (1) // probe until something happens - { - typename Table::GrpPos grp_pos(table, bucknum); - - if (!grp_pos.test_strict()) - return end(); // bucket is empty - if (grp_pos.test()) - { - reference ref(grp_pos.unsafe_get()); - - if (equals(key, get_key(ref))) - return grp_pos.get_iter(ref); - } - ++num_probes; // we're doing another probe - bucknum = (bucknum + JUMP_(key, num_probes)) & bucket_count_minus_one; - assert(num_probes < bucket_count() - && "Hashtable is full: an error in key_equal<> or hash<>"); - } - } - - // Wish I could avoid the duplicate find() const and non-const. - // ------------------------------------------------------------ - const_iterator find(const key_type& key) const - { - size_type num_probes = 0; // how many times we've probed - const size_type bucket_count_minus_one = bucket_count() - 1; - size_type bucknum = hash(key) & bucket_count_minus_one; - - while (1) // probe until something happens - { - typename Table::GrpPos grp_pos(table, bucknum); - - if (!grp_pos.test_strict()) - return end(); // bucket is empty - else if (grp_pos.test()) - { - reference ref(grp_pos.unsafe_get()); - - if (equals(key, get_key(ref))) - return _mk_const_iterator(table.get_iter(bucknum, &ref)); - } - ++num_probes; // we're doing another probe - bucknum = (bucknum + JUMP_(key, num_probes)) & bucket_count_minus_one; - assert(num_probes < bucket_count() - && "Hashtable is full: an error in key_equal<> or hash<>"); - } - } - - // This is a tr1 method: the bucket a given key is in, or what bucket - // it would be put in, if it were to be inserted. Shrug. - // ------------------------------------------------------------------ - size_type bucket(const key_type& key) const - { - Position pos = _find_position(key); - return pos._idx; - } - - // Counts how many elements have key key. For maps, it's either 0 or 1. - // --------------------------------------------------------------------- - size_type count(const key_type &key) const - { - Position pos = _find_position(key); - return (size_type)(pos._t == pt_full ? 1 : 0); - } - - // Likewise, equal_range doesn't really make sense for us. Oh well. - // ----------------------------------------------------------------- - std::pair equal_range(const key_type& key) - { - iterator pos = find(key); // either an iterator or end - if (pos == end()) - return std::pair(pos, pos); - else - { - const iterator startpos = pos++; - return std::pair(startpos, pos); - } - } - - std::pair equal_range(const key_type& key) const - { - const_iterator pos = find(key); // either an iterator or end - if (pos == end()) - return std::pair(pos, pos); - else - { - const const_iterator startpos = pos++; - return std::pair(startpos, pos); - } - } - - - // INSERTION ROUTINES -private: - // Private method used by insert_noresize and find_or_insert. - template - reference _insert_at(T& obj, size_type pos, bool erased) - { - if (size() >= max_size()) - { - throw_exception(std::length_error("insert overflow")); - } - if (erased) - { - assert(num_deleted); - --num_deleted; - } - return table.set(pos, obj); - } - - // If you know *this is big enough to hold obj, use this routine - template - std::pair _insert_noresize(T& obj) - { - Position pos = _find_position(get_key(obj)); - bool already_there = (pos._t == pt_full); - - if (!already_there) - { - reference ref(_insert_at(obj, pos._idx, pos._t == pt_erased)); - return std::pair(_mk_iterator(table.get_iter(pos._idx, &ref)), true); - } - return std::pair(_mk_iterator(table.get_iter(pos._idx)), false); - } - - // Specializations of insert(it, it) depending on the power of the iterator: - // (1) Iterator supports operator-, resize before inserting - template - void _insert(ForwardIterator f, ForwardIterator l, std::forward_iterator_tag /*unused*/) - { - int64_t dist = std::distance(f, l); - if (dist < 0 || static_cast(dist) >= (std::numeric_limits::max)()) - throw_exception(std::length_error("insert-range overflow")); - - _resize_delta(static_cast(dist)); - - for (; dist > 0; --dist, ++f) - _insert_noresize(*f); - } - - // (2) Arbitrary iterator, can't tell how much to resize - template - void _insert(InputIterator f, InputIterator l, std::input_iterator_tag /*unused*/) - { - for (; f != l; ++f) - _insert(*f); - } - -public: - -#if !defined(SPP_NO_CXX11_VARIADIC_TEMPLATES) - template - std::pair emplace(Args&&... args) - { - _resize_delta(1); - value_type obj(std::forward(args)...); - return _insert_noresize(obj); - } -#endif - - // This is the normal insert routine, used by the outside world - std::pair insert(const_reference obj) - { - _resize_delta(1); // adding an object, grow if need be - return _insert_noresize(obj); - } - -#if !defined(SPP_NO_CXX11_RVALUE_REFERENCES) - template< class P > - std::pair insert(P &&obj) - { - _resize_delta(1); // adding an object, grow if need be - value_type val(std::forward

(obj)); - return _insert_noresize(val); - } -#endif - - // When inserting a lot at a time, we specialize on the type of iterator - template - void insert(InputIterator f, InputIterator l) - { - // specializes on iterator type - _insert(f, l, - typename std::iterator_traits::iterator_category()); - } - - // DefaultValue is a functor that takes a key and returns a value_type - // representing the default value to be inserted if none is found. -#if !defined(SPP_NO_CXX11_VARIADIC_TEMPLATES) - template - value_type& find_or_insert(KT&& key) -#else - template - value_type& find_or_insert(const key_type& key) -#endif - { - size_type num_probes = 0; // how many times we've probed - const size_type bucket_count_minus_one = bucket_count() - 1; - size_type bucknum = hash(key) & bucket_count_minus_one; - DefaultValue default_value; - size_type erased_pos = 0; - bool erased = false; - - while (1) // probe until something happens - { - typename Table::GrpPos grp_pos(table, bucknum); - - if (!grp_pos.test_strict()) - { - // not found -#if !defined(SPP_NO_CXX11_VARIADIC_TEMPLATES) - auto&& def(default_value(std::forward(key))); -#else - value_type def(default_value(key)); -#endif - if (_resize_delta(1)) - { - // needed to rehash to make room - // Since we resized, we can't use pos, so recalculate where to insert. - return *(_insert_noresize(def).first); - } - else - { - // no need to rehash, insert right here - return _insert_at(def, erased ? erased_pos : bucknum, erased); - } - } - if (grp_pos.test()) - { - reference ref(grp_pos.unsafe_get()); - - if (equals(key, get_key(ref))) - return ref; - } - else if (!erased) - { - // first erased position - erased_pos = bucknum; - erased = true; - } - - ++num_probes; // we're doing another probe - bucknum = (bucknum + JUMP_(key, num_probes)) & bucket_count_minus_one; - assert(num_probes < bucket_count() - && "Hashtable is full: an error in key_equal<> or hash<>"); - } - } - - size_type erase(const key_type& key) - { - size_type num_probes = 0; // how many times we've probed - const size_type bucket_count_minus_one = bucket_count() - 1; - size_type bucknum = hash(key) & bucket_count_minus_one; - - while (1) // probe until something happens - { - typename Table::GrpPos grp_pos(table, bucknum); - - if (!grp_pos.test_strict()) - return 0; // bucket is empty, we deleted nothing - if (grp_pos.test()) - { - reference ref(grp_pos.unsafe_get()); - - if (equals(key, get_key(ref))) - { - grp_pos.erase(table); - ++num_deleted; - settings.set_consider_shrink(true); // will think about shrink after next insert - return 1; // because we deleted one thing - } - } - ++num_probes; // we're doing another probe - bucknum = (bucknum + JUMP_(key, num_probes)) & bucket_count_minus_one; - assert(num_probes < bucket_count() - && "Hashtable is full: an error in key_equal<> or hash<>"); - } - } - - const_iterator erase(const_iterator pos) - { - if (pos == cend()) - return cend(); // sanity check - - const_iterator nextpos = table.erase(pos); - ++num_deleted; - settings.set_consider_shrink(true); - return nextpos; - } - - const_iterator erase(const_iterator f, const_iterator l) - { - if (f == cend()) - return cend(); // sanity check - - size_type num_before = table.num_nonempty(); - const_iterator nextpos = table.erase(f, l); - num_deleted += num_before - table.num_nonempty(); - settings.set_consider_shrink(true); - return nextpos; - } - - // Deleted key routines - just to keep google test framework happy - // we don't actually use the deleted key - // --------------------------------------------------------------- - void set_deleted_key(const key_type&) - { - } - - void clear_deleted_key() - { - } - - bool operator==(const sparse_hashtable& ht) const - { - if (this == &ht) - return true; - - if (size() != ht.size()) - return false; - - for (const_iterator it = begin(); it != end(); ++it) - { - const_iterator it2 = ht.find(get_key(*it)); - if ((it2 == ht.end()) || (*it != *it2)) - return false; - } - - return true; - } - - bool operator!=(const sparse_hashtable& ht) const - { - return !(*this == ht); - } - - - // I/O - // We support reading and writing hashtables to disk. NOTE that - // this only stores the hashtable metadata, not the stuff you've - // actually put in the hashtable! Alas, since I don't know how to - // write a hasher or key_equal, you have to make sure everything - // but the table is the same. We compact before writing. - // - // The OUTPUT type needs to support a Write() operation. File and - // OutputBuffer are appropriate types to pass in. - // - // The INPUT type needs to support a Read() operation. File and - // InputBuffer are appropriate types to pass in. - // ------------------------------------------------------------- - template - bool write_metadata(OUTPUT *fp) - { - return table.write_metadata(fp); - } - - template - bool read_metadata(INPUT *fp) - { - num_deleted = 0; // since we got rid before writing - const bool result = table.read_metadata(fp); - settings.reset_thresholds(bucket_count()); - return result; - } - - // Only meaningful if value_type is a POD. - template - bool write_nopointer_data(OUTPUT *fp) - { - return table.write_nopointer_data(fp); - } - - // Only meaningful if value_type is a POD. - template - bool read_nopointer_data(INPUT *fp) - { - return table.read_nopointer_data(fp); - } - - // INPUT and OUTPUT must be either a FILE, *or* a C++ stream - // (istream, ostream, etc) *or* a class providing - // Read(void*, size_t) and Write(const void*, size_t) - // (respectively), which writes a buffer into a stream - // (which the INPUT/OUTPUT instance presumably owns). - - typedef sparsehash_internal::pod_serializer NopointerSerializer; - - // ValueSerializer: a functor. operator()(OUTPUT*, const value_type&) - template - bool serialize(ValueSerializer serializer, OUTPUT *fp) - { - return table.serialize(serializer, fp); - } - - // ValueSerializer: a functor. operator()(INPUT*, value_type*) - template - bool unserialize(ValueSerializer serializer, INPUT *fp) - { - num_deleted = 0; // since we got rid before writing - const bool result = table.unserialize(serializer, fp); - settings.reset_thresholds(bucket_count()); - return result; - } - -private: - - // Package templated functors with the other types to eliminate memory - // needed for storing these zero-size operators. Since ExtractKey and - // hasher's operator() might have the same function signature, they - // must be packaged in different classes. - // ------------------------------------------------------------------------- - struct Settings : - sparsehash_internal::sh_hashtable_settings - { - explicit Settings(const hasher& hf) - : sparsehash_internal::sh_hashtable_settings - (hf, HT_OCCUPANCY_PCT / 100.0f, HT_EMPTY_PCT / 100.0f) {} - }; - - // KeyInfo stores delete key and packages zero-size functors: - // ExtractKey and SetKey. - // --------------------------------------------------------- - class KeyInfo : public ExtractKey, public SetKey, public EqualKey - { - public: - KeyInfo(const ExtractKey& ek, const SetKey& sk, const EqualKey& eq) - : ExtractKey(ek), SetKey(sk), EqualKey(eq) - { - } - - // We want to return the exact same type as ExtractKey: Key or const Key& - typename ExtractKey::result_type get_key(const_reference v) const - { - return ExtractKey::operator()(v); - } - - bool equals(const key_type& a, const key_type& b) const - { - return EqualKey::operator()(a, b); - } - }; - - // Utility functions to access the templated operators - size_t hash(const key_type& v) const - { - return settings.hash(v); - } - - bool equals(const key_type& a, const key_type& b) const - { - return key_info.equals(a, b); - } - - typename ExtractKey::result_type get_key(const_reference v) const - { - return key_info.get_key(v); - } - -private: - // Actual data - // ----------- - Settings settings; - KeyInfo key_info; - size_type num_deleted; - Table table; // holds num_buckets and num_elements too -}; - -#undef JUMP_ - -// ----------------------------------------------------------------------------- -template -const typename sparse_hashtable::size_type -sparse_hashtable::ILLEGAL_BUCKET; - -// How full we let the table get before we resize. Knuth says .8 is -// good -- higher causes us to probe too much, though saves memory -// ----------------------------------------------------------------------------- -template -const int sparse_hashtable::HT_OCCUPANCY_PCT = 50; - -// How empty we let the table get before we resize lower. -// It should be less than OCCUPANCY_PCT / 2 or we thrash resizing -// ----------------------------------------------------------------------------- -template -const int sparse_hashtable::HT_EMPTY_PCT -= static_cast(0.4 * - sparse_hashtable::HT_OCCUPANCY_PCT); - - -// ---------------------------------------------------------------------- -// S P A R S E _ H A S H _ M A P -// ---------------------------------------------------------------------- -template , - class EqualKey = std::equal_to, - class Alloc = SPP_DEFAULT_ALLOCATOR > > -class sparse_hash_map -{ -public: - typedef typename std::pair value_type; - -private: - // Apparently select1st is not stl-standard, so we define our own - struct SelectKey - { - typedef const Key& result_type; - - inline const Key& operator()(const value_type& p) const - { - return p.first; - } - }; - - struct SetKey - { - inline void operator()(value_type* value, const Key& new_key) const - { - *const_cast(&value->first) = new_key; - } - }; - - // For operator[]. - struct DefaultValue - { -#if !defined(SPP_NO_CXX11_VARIADIC_TEMPLATES) - template - inline value_type operator()(KT&& key) const - { - return { std::forward(key), T() }; - } -#else - inline value_type operator()(const Key& key) const - { - return std::make_pair(key, T()); - } -#endif - }; - - // The actual data - typedef sparse_hashtable ht; - -public: - typedef typename ht::key_type key_type; - typedef T data_type; - typedef T mapped_type; - typedef typename ht::hasher hasher; - typedef typename ht::key_equal key_equal; - typedef Alloc allocator_type; - - typedef typename ht::size_type size_type; - typedef typename ht::difference_type difference_type; - typedef typename ht::pointer pointer; - typedef typename ht::const_pointer const_pointer; - typedef typename ht::reference reference; - typedef typename ht::const_reference const_reference; - - typedef typename ht::iterator iterator; - typedef typename ht::const_iterator const_iterator; - typedef typename ht::local_iterator local_iterator; - typedef typename ht::const_local_iterator const_local_iterator; - - // Iterator functions - iterator begin() { return rep.begin(); } - iterator end() { return rep.end(); } - const_iterator begin() const { return rep.cbegin(); } - const_iterator end() const { return rep.cend(); } - const_iterator cbegin() const { return rep.cbegin(); } - const_iterator cend() const { return rep.cend(); } - - // These come from tr1's unordered_map. For us, a bucket has 0 or 1 elements. - local_iterator begin(size_type i) { return rep.begin(i); } - local_iterator end(size_type i) { return rep.end(i); } - const_local_iterator begin(size_type i) const { return rep.begin(i); } - const_local_iterator end(size_type i) const { return rep.end(i); } - const_local_iterator cbegin(size_type i) const { return rep.cbegin(i); } - const_local_iterator cend(size_type i) const { return rep.cend(i); } - - // Accessor functions - // ------------------ - allocator_type get_allocator() const { return rep.get_allocator(); } - hasher hash_funct() const { return rep.hash_funct(); } - hasher hash_function() const { return hash_funct(); } - key_equal key_eq() const { return rep.key_eq(); } - - - // Constructors - // ------------ - explicit sparse_hash_map(size_type n = 0, - const hasher& hf = hasher(), - const key_equal& eql = key_equal(), - const allocator_type& alloc = allocator_type()) - : rep(n, hf, eql, SelectKey(), SetKey(), alloc) - { - } - - explicit sparse_hash_map(const allocator_type& alloc) : - rep(0, hasher(), key_equal(), SelectKey(), SetKey(), alloc) - { - } - - sparse_hash_map(size_type n, const allocator_type& alloc) : - rep(n, hasher(), key_equal(), SelectKey(), SetKey(), alloc) - { - } - - sparse_hash_map(size_type n, const hasher& hf, const allocator_type& alloc) : - rep(n, hf, key_equal(), SelectKey(), SetKey(), alloc) - { - } - - template - sparse_hash_map(InputIterator f, InputIterator l, - size_type n = 0, - const hasher& hf = hasher(), - const key_equal& eql = key_equal(), - const allocator_type& alloc = allocator_type()) - : rep(n, hf, eql, SelectKey(), SetKey(), alloc) - { - rep.insert(f, l); - } - - template - sparse_hash_map(InputIterator f, InputIterator l, - size_type n, const allocator_type& alloc) - : rep(n, hasher(), key_equal(), SelectKey(), SetKey(), alloc) - { - rep.insert(f, l); - } - - template - sparse_hash_map(InputIterator f, InputIterator l, - size_type n, const hasher& hf, const allocator_type& alloc) - : rep(n, hf, key_equal(), SelectKey(), SetKey(), alloc) - { - rep.insert(f, l); - } - - sparse_hash_map(const sparse_hash_map &o) : - rep(o.rep) - {} - - sparse_hash_map(const sparse_hash_map &o, - const allocator_type& alloc) : - rep(o.rep, alloc) - {} - -#if !defined(SPP_NO_CXX11_RVALUE_REFERENCES) - sparse_hash_map(sparse_hash_map &&o) : - rep(std::move(o.rep)) - {} - - sparse_hash_map(sparse_hash_map &&o, - const allocator_type& alloc) : - rep(std::move(o.rep), alloc) - {} - - sparse_hash_map& operator=(sparse_hash_map &&o) - { - rep = std::move(o.rep); - } -#endif - -#if !defined(SPP_NO_CXX11_HDR_INITIALIZER_LIST) - sparse_hash_map(std::initializer_list init, - size_type n = 0, - const hasher& hf = hasher(), - const key_equal& eql = key_equal(), - const allocator_type& alloc = allocator_type()) - : rep(n, hf, eql, SelectKey(), SetKey(), alloc) - { - rep.insert(init.begin(), init.end()); - } - - sparse_hash_map(std::initializer_list init, - size_type n, const allocator_type& alloc) : - rep(n, hasher(), key_equal(), SelectKey(), SetKey(), alloc) - { - rep.insert(init.begin(), init.end()); - } - - sparse_hash_map(std::initializer_list init, - size_type n, const hasher& hf, const allocator_type& alloc) : - rep(n, hf, key_equal(), SelectKey(), SetKey(), alloc) - { - rep.insert(init.begin(), init.end()); - } - - sparse_hash_map& operator=(std::initializer_list init) - { - rep.clear(); - rep.insert(init.begin(), init.end()); - return *this; - } - - void insert(std::initializer_list init) - { - rep.insert(init.begin(), init.end()); - } -#endif - - sparse_hash_map& operator=(const sparse_hash_map &o) - { - rep = o.rep; - return *this; - } - - void clear() { rep.clear(); } - void swap(sparse_hash_map& hs) { rep.swap(hs.rep); } - - // Functions concerning size - // ------------------------- - size_type size() const { return rep.size(); } - size_type max_size() const { return rep.max_size(); } - bool empty() const { return rep.empty(); } - size_type bucket_count() const { return rep.bucket_count(); } - size_type max_bucket_count() const { return rep.max_bucket_count(); } - - size_type bucket_size(size_type i) const { return rep.bucket_size(i); } - size_type bucket(const key_type& key) const { return rep.bucket(key); } - float load_factor() const { return size() * 1.0f / bucket_count(); } - - float max_load_factor() const { return rep.get_enlarge_factor(); } - void max_load_factor(float grow) { rep.set_enlarge_factor(grow); } - - float min_load_factor() const { return rep.get_shrink_factor(); } - void min_load_factor(float shrink){ rep.set_shrink_factor(shrink); } - - void set_resizing_parameters(float shrink, float grow) - { - rep.set_resizing_parameters(shrink, grow); - } - - void resize(size_type cnt) { rep.resize(cnt); } - void rehash(size_type cnt) { resize(cnt); } // c++11 name - void reserve(size_type cnt) { resize(cnt); } // c++11 - - // Lookup - // ------ - iterator find(const key_type& key) { return rep.find(key); } - const_iterator find(const key_type& key) const { return rep.find(key); } - bool contains(const key_type& key) const { return rep.find(key) != rep.end(); } - -#if !defined(SPP_NO_CXX11_VARIADIC_TEMPLATES) - template - mapped_type& operator[](KT&& key) - { - return rep.template find_or_insert(std::forward(key)).second; - } -#else - mapped_type& operator[](const key_type& key) - { - return rep.template find_or_insert(key).second; - } -#endif - - size_type count(const key_type& key) const { return rep.count(key); } - - std::pair - equal_range(const key_type& key) { return rep.equal_range(key); } - - std::pair - equal_range(const key_type& key) const { return rep.equal_range(key); } - - mapped_type& at(const key_type& key) - { - iterator it = rep.find(key); - if (it == rep.end()) - throw_exception(std::out_of_range("at: key not present")); - return it->second; - } - - const mapped_type& at(const key_type& key) const - { - const_iterator it = rep.find(key); - if (it == rep.cend()) - throw_exception(std::out_of_range("at: key not present")); - return it->second; - } - -#if !defined(SPP_NO_CXX11_VARIADIC_TEMPLATES) - template - std::pair emplace(Args&&... args) - { - return rep.emplace(std::forward(args)...); - } - - template - iterator emplace_hint(const_iterator , Args&&... args) - { - return rep.emplace(std::forward(args)...).first; - } -#endif - - // Insert - // ------ - std::pair - insert(const value_type& obj) { return rep.insert(obj); } - -#if !defined(SPP_NO_CXX11_RVALUE_REFERENCES) - template< class P > - std::pair insert(P&& obj) { return rep.insert(std::forward

(obj)); } -#endif - - template - void insert(InputIterator f, InputIterator l) { rep.insert(f, l); } - - void insert(const_iterator f, const_iterator l) { rep.insert(f, l); } - - iterator insert(iterator /*unused*/, const value_type& obj) { return insert(obj).first; } - iterator insert(const_iterator /*unused*/, const value_type& obj) { return insert(obj).first; } - - // Deleted key routines - just to keep google test framework happy - // we don't actually use the deleted key - // --------------------------------------------------------------- - void set_deleted_key(const key_type& key) { rep.set_deleted_key(key); } - void clear_deleted_key() { rep.clear_deleted_key(); } - key_type deleted_key() const { return rep.deleted_key(); } - - // Erase - // ----- - size_type erase(const key_type& key) { return rep.erase(key); } - iterator erase(iterator it) { return rep.erase(it); } - iterator erase(iterator f, iterator l) { return rep.erase(f, l); } - iterator erase(const_iterator it) { return rep.erase(it); } - iterator erase(const_iterator f, const_iterator l){ return rep.erase(f, l); } - - // Comparison - // ---------- - bool operator==(const sparse_hash_map& hs) const { return rep == hs.rep; } - bool operator!=(const sparse_hash_map& hs) const { return rep != hs.rep; } - - - // I/O -- this is an add-on for writing metainformation to disk - // - // For maximum flexibility, this does not assume a particular - // file type (though it will probably be a FILE *). We just pass - // the fp through to rep. - - // If your keys and values are simple enough, you can pass this - // serializer to serialize()/unserialize(). "Simple enough" means - // value_type is a POD type that contains no pointers. Note, - // however, we don't try to normalize endianness. - // --------------------------------------------------------------- - typedef typename ht::NopointerSerializer NopointerSerializer; - - // serializer: a class providing operator()(OUTPUT*, const value_type&) - // (writing value_type to OUTPUT). You can specify a - // NopointerSerializer object if appropriate (see above). - // fp: either a FILE*, OR an ostream*/subclass_of_ostream*, OR a - // pointer to a class providing size_t Write(const void*, size_t), - // which writes a buffer into a stream (which fp presumably - // owns) and returns the number of bytes successfully written. - // Note basic_ostream is not currently supported. - // --------------------------------------------------------------- - template - bool serialize(ValueSerializer serializer, OUTPUT* fp) - { - return rep.serialize(serializer, fp); - } - - // serializer: a functor providing operator()(INPUT*, value_type*) - // (reading from INPUT and into value_type). You can specify a - // NopointerSerializer object if appropriate (see above). - // fp: either a FILE*, OR an istream*/subclass_of_istream*, OR a - // pointer to a class providing size_t Read(void*, size_t), - // which reads into a buffer from a stream (which fp presumably - // owns) and returns the number of bytes successfully read. - // Note basic_istream is not currently supported. - // NOTE: Since value_type is std::pair, ValueSerializer - // may need to do a const cast in order to fill in the key. - // NOTE: if Key or T are not POD types, the serializer MUST use - // placement-new to initialize their values, rather than a normal - // equals-assignment or similar. (The value_type* passed into the - // serializer points to garbage memory.) - // --------------------------------------------------------------- - template - bool unserialize(ValueSerializer serializer, INPUT* fp) - { - return rep.unserialize(serializer, fp); - } - - // The four methods below are DEPRECATED. - // Use serialize() and unserialize() for new code. - // ----------------------------------------------- - template - bool write_metadata(OUTPUT *fp) { return rep.write_metadata(fp); } - - template - bool read_metadata(INPUT *fp) { return rep.read_metadata(fp); } - - template - bool write_nopointer_data(OUTPUT *fp) { return rep.write_nopointer_data(fp); } - - template - bool read_nopointer_data(INPUT *fp) { return rep.read_nopointer_data(fp); } - - -private: - // The actual data - // --------------- - ht rep; -}; - -// ---------------------------------------------------------------------- -// S P A R S E _ H A S H _ S E T -// ---------------------------------------------------------------------- - -template , - class EqualKey = std::equal_to, - class Alloc = SPP_DEFAULT_ALLOCATOR > -class sparse_hash_set -{ -private: - // Apparently identity is not stl-standard, so we define our own - struct Identity - { - typedef const Value& result_type; - inline const Value& operator()(const Value& v) const { return v; } - }; - - struct SetKey - { - inline void operator()(Value* value, const Value& new_key) const - { - *value = new_key; - } - }; - - typedef sparse_hashtable ht; - -public: - typedef typename ht::key_type key_type; - typedef typename ht::value_type value_type; - typedef typename ht::hasher hasher; - typedef typename ht::key_equal key_equal; - typedef Alloc allocator_type; - - typedef typename ht::size_type size_type; - typedef typename ht::difference_type difference_type; - typedef typename ht::const_pointer pointer; - typedef typename ht::const_pointer const_pointer; - typedef typename ht::const_reference reference; - typedef typename ht::const_reference const_reference; - - typedef typename ht::const_iterator iterator; - typedef typename ht::const_iterator const_iterator; - typedef typename ht::const_local_iterator local_iterator; - typedef typename ht::const_local_iterator const_local_iterator; - - - // Iterator functions -- recall all iterators are const - iterator begin() const { return rep.begin(); } - iterator end() const { return rep.end(); } - const_iterator cbegin() const { return rep.cbegin(); } - const_iterator cend() const { return rep.cend(); } - - // These come from tr1's unordered_set. For us, a bucket has 0 or 1 elements. - local_iterator begin(size_type i) const { return rep.begin(i); } - local_iterator end(size_type i) const { return rep.end(i); } - local_iterator cbegin(size_type i) const { return rep.cbegin(i); } - local_iterator cend(size_type i) const { return rep.cend(i); } - - - // Accessor functions - // ------------------ - allocator_type get_allocator() const { return rep.get_allocator(); } - hasher hash_funct() const { return rep.hash_funct(); } - hasher hash_function() const { return hash_funct(); } // tr1 name - key_equal key_eq() const { return rep.key_eq(); } - - - // Constructors - // ------------ - explicit sparse_hash_set(size_type n = 0, - const hasher& hf = hasher(), - const key_equal& eql = key_equal(), - const allocator_type& alloc = allocator_type()) : - rep(n, hf, eql, Identity(), SetKey(), alloc) - { - } - - explicit sparse_hash_set(const allocator_type& alloc) : - rep(0, hasher(), key_equal(), Identity(), SetKey(), alloc) - { - } - - sparse_hash_set(size_type n, const allocator_type& alloc) : - rep(n, hasher(), key_equal(), Identity(), SetKey(), alloc) - { - } - - sparse_hash_set(size_type n, const hasher& hf, - const allocator_type& alloc) : - rep(n, hf, key_equal(), Identity(), SetKey(), alloc) - { - } - - template - sparse_hash_set(InputIterator f, InputIterator l, - size_type n = 0, - const hasher& hf = hasher(), - const key_equal& eql = key_equal(), - const allocator_type& alloc = allocator_type()) - : rep(n, hf, eql, Identity(), SetKey(), alloc) - { - rep.insert(f, l); - } - - template - sparse_hash_set(InputIterator f, InputIterator l, - size_type n, const allocator_type& alloc) - : rep(n, hasher(), key_equal(), Identity(), SetKey(), alloc) - { - rep.insert(f, l); - } - - template - sparse_hash_set(InputIterator f, InputIterator l, - size_type n, const hasher& hf, const allocator_type& alloc) - : rep(n, hf, key_equal(), Identity(), SetKey(), alloc) - { - rep.insert(f, l); - } - - sparse_hash_set(const sparse_hash_set &o) : - rep(o.rep) - {} - - sparse_hash_set(const sparse_hash_set &o, - const allocator_type& alloc) : - rep(o.rep, alloc) - {} - -#if !defined(SPP_NO_CXX11_RVALUE_REFERENCES) - sparse_hash_set(sparse_hash_set &&o) : - rep(std::move(o.rep)) - {} - - sparse_hash_set(sparse_hash_set &&o, - const allocator_type& alloc) : - rep(std::move(o.rep), alloc) - {} -#endif - -#if !defined(SPP_NO_CXX11_HDR_INITIALIZER_LIST) - sparse_hash_set(std::initializer_list init, - size_type n = 0, - const hasher& hf = hasher(), - const key_equal& eql = key_equal(), - const allocator_type& alloc = allocator_type()) : - rep(n, hf, eql, Identity(), SetKey(), alloc) - { - rep.insert(init.begin(), init.end()); - } - - sparse_hash_set(std::initializer_list init, - size_type n, const allocator_type& alloc) : - rep(n, hasher(), key_equal(), Identity(), SetKey(), alloc) - { - rep.insert(init.begin(), init.end()); - } - - sparse_hash_set(std::initializer_list init, - size_type n, const hasher& hf, - const allocator_type& alloc) : - rep(n, hf, key_equal(), Identity(), SetKey(), alloc) - { - rep.insert(init.begin(), init.end()); - } - - sparse_hash_set& operator=(std::initializer_list init) - { - rep.clear(); - rep.insert(init.begin(), init.end()); - return *this; - } - - void insert(std::initializer_list init) - { - rep.insert(init.begin(), init.end()); - } - -#endif - - sparse_hash_set& operator=(const sparse_hash_set &o) - { - rep = o.rep; - return *this; - } - - void clear() { rep.clear(); } - void swap(sparse_hash_set& hs) { rep.swap(hs.rep); } - - - // Functions concerning size - // ------------------------- - size_type size() const { return rep.size(); } - size_type max_size() const { return rep.max_size(); } - bool empty() const { return rep.empty(); } - size_type bucket_count() const { return rep.bucket_count(); } - size_type max_bucket_count() const { return rep.max_bucket_count(); } - - size_type bucket_size(size_type i) const { return rep.bucket_size(i); } - size_type bucket(const key_type& key) const { return rep.bucket(key); } - - float load_factor() const { return size() * 1.0f / bucket_count(); } - - float max_load_factor() const { return rep.get_enlarge_factor(); } - void max_load_factor(float grow) { rep.set_enlarge_factor(grow); } - - float min_load_factor() const { return rep.get_shrink_factor(); } - void min_load_factor(float shrink){ rep.set_shrink_factor(shrink); } - - void set_resizing_parameters(float shrink, float grow) - { - rep.set_resizing_parameters(shrink, grow); - } - - void resize(size_type cnt) { rep.resize(cnt); } - void rehash(size_type cnt) { resize(cnt); } // c++11 name - void reserve(size_type cnt) { resize(cnt); } // c++11 - - // Lookup - // ------ - iterator find(const key_type& key) const { return rep.find(key); } - bool contains(const key_type& key) const { return rep.find(key) != rep.end(); } - - size_type count(const key_type& key) const { return rep.count(key); } - - std::pair - equal_range(const key_type& key) const { return rep.equal_range(key); } - -#if !defined(SPP_NO_CXX11_VARIADIC_TEMPLATES) - template - std::pair emplace(Args&&... args) - { - return rep.emplace(std::forward(args)...); - } - - template - iterator emplace_hint(const_iterator , Args&&... args) - { - return rep.emplace(std::forward(args)...).first; - } -#endif - - // Insert - // ------ - std::pair insert(const value_type& obj) - { - std::pair p = rep.insert(obj); - return std::pair(p.first, p.second); // const to non-const - } - -#if !defined(SPP_NO_CXX11_RVALUE_REFERENCES) - template - std::pair insert(P&& obj) { return rep.insert(std::forward

(obj)); } -#endif - - template - void insert(InputIterator f, InputIterator l) { rep.insert(f, l); } - - void insert(const_iterator f, const_iterator l) { rep.insert(f, l); } - - iterator insert(iterator /*unused*/, const value_type& obj) { return insert(obj).first; } - - // Deleted key - do nothing - just to keep google test framework happy - // ------------------------------------------------------------------- - void set_deleted_key(const key_type& key) { rep.set_deleted_key(key); } - void clear_deleted_key() { rep.clear_deleted_key(); } - key_type deleted_key() const { return rep.deleted_key(); } - - // Erase - // ----- - size_type erase(const key_type& key) { return rep.erase(key); } - iterator erase(iterator it) { return rep.erase(it); } - iterator erase(iterator f, iterator l) { return rep.erase(f, l); } - - // Comparison - // ---------- - bool operator==(const sparse_hash_set& hs) const { return rep == hs.rep; } - bool operator!=(const sparse_hash_set& hs) const { return rep != hs.rep; } - - - // I/O -- this is an add-on for writing metainformation to disk - // - // For maximum flexibility, this does not assume a particular - // file type (though it will probably be a FILE *). We just pass - // the fp through to rep. - - // If your keys and values are simple enough, you can pass this - // serializer to serialize()/unserialize(). "Simple enough" means - // value_type is a POD type that contains no pointers. Note, - // however, we don't try to normalize endianness. - // --------------------------------------------------------------- - typedef typename ht::NopointerSerializer NopointerSerializer; - - // serializer: a class providing operator()(OUTPUT*, const value_type&) - // (writing value_type to OUTPUT). You can specify a - // NopointerSerializer object if appropriate (see above). - // fp: either a FILE*, OR an ostream*/subclass_of_ostream*, OR a - // pointer to a class providing size_t Write(const void*, size_t), - // which writes a buffer into a stream (which fp presumably - // owns) and returns the number of bytes successfully written. - // Note basic_ostream is not currently supported. - // --------------------------------------------------------------- - template - bool serialize(ValueSerializer serializer, OUTPUT* fp) - { - return rep.serialize(serializer, fp); - } - - // serializer: a functor providing operator()(INPUT*, value_type*) - // (reading from INPUT and into value_type). You can specify a - // NopointerSerializer object if appropriate (see above). - // fp: either a FILE*, OR an istream*/subclass_of_istream*, OR a - // pointer to a class providing size_t Read(void*, size_t), - // which reads into a buffer from a stream (which fp presumably - // owns) and returns the number of bytes successfully read. - // Note basic_istream is not currently supported. - // NOTE: Since value_type is const Key, ValueSerializer - // may need to do a const cast in order to fill in the key. - // NOTE: if Key is not a POD type, the serializer MUST use - // placement-new to initialize its value, rather than a normal - // equals-assignment or similar. (The value_type* passed into - // the serializer points to garbage memory.) - // --------------------------------------------------------------- - template - bool unserialize(ValueSerializer serializer, INPUT* fp) - { - return rep.unserialize(serializer, fp); - } - - // The four methods below are DEPRECATED. - // Use serialize() and unserialize() for new code. - // ----------------------------------------------- - template - bool write_metadata(OUTPUT *fp) { return rep.write_metadata(fp); } - - template - bool read_metadata(INPUT *fp) { return rep.read_metadata(fp); } - - template - bool write_nopointer_data(OUTPUT *fp) { return rep.write_nopointer_data(fp); } - - template - bool read_nopointer_data(INPUT *fp) { return rep.read_nopointer_data(fp); } - -private: - // The actual data - // --------------- - ht rep; -}; - -} // spp_ namespace - - -// We need a global swap for all our classes as well -// ------------------------------------------------- - -template -inline void swap(spp_::sparsegroup &x, spp_::sparsegroup &y) -{ - x.swap(y); -} - -template -inline void swap(spp_::sparsetable &x, spp_::sparsetable &y) -{ - x.swap(y); -} - -template -inline void swap(spp_::sparse_hashtable &x, - spp_::sparse_hashtable &y) -{ - x.swap(y); -} - -template -inline void swap(spp_::sparse_hash_map& hm1, - spp_::sparse_hash_map& hm2) -{ - hm1.swap(hm2); -} - -template -inline void swap(spp_::sparse_hash_set& hs1, - spp_::sparse_hash_set& hs2) -{ - hs1.swap(hs2); -} - -#endif // sparsepp_h_guard_ diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp_config.h b/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp_config.h deleted file mode 100644 index 46eeee5..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp_config.h +++ /dev/null @@ -1,781 +0,0 @@ -#if !defined(spp_config_h_guard) -#define spp_config_h_guard - -// -------------------------------------------------- -// Sparsepp config macros -// some can be overriden on the command line -// -------------------------------------------------- -#ifndef SPP_NAMESPACE - #define SPP_NAMESPACE spp -#endif - -#ifndef spp_ - #define spp_ SPP_NAMESPACE -#endif - -#ifndef SPP_DEFAULT_ALLOCATOR - #if (defined(SPP_USE_SPP_ALLOC) && SPP_USE_SPP_ALLOC) && defined(_MSC_VER) - // ----------------------------------------------------------------------------- - // When building with the Microsoft compiler, we use a custom allocator because - // the default one fragments memory when reallocating. This is desirable only - // when creating large sparsepp hash maps. If you create lots of small hash_maps, - // define the following before including spp.h: - // #define SPP_DEFAULT_ALLOCATOR spp::libc_allocator - // ----------------------------------------------------------------------------- - #define SPP_DEFAULT_ALLOCATOR spp_::spp_allocator - #define SPP_INCLUDE_SPP_ALLOC - #else - #define SPP_DEFAULT_ALLOCATOR spp_::libc_allocator - #endif -#endif - -#ifndef SPP_GROUP_SIZE - // must be 32 or 64 - #define SPP_GROUP_SIZE 32 -#endif - -#ifndef SPP_ALLOC_SZ - // must be power of 2 (0 = agressive alloc, 1 = smallest memory usage, 2 = good compromise) - #define SPP_ALLOC_SZ 0 -#endif - -#ifndef SPP_STORE_NUM_ITEMS - // 1 uses a little bit more memory, but faster!! - #define SPP_STORE_NUM_ITEMS 1 -#endif - - -// --------------------------------------------------------------------------- -// Compiler detection code (SPP_ proprocessor macros) derived from Boost -// libraries. Therefore Boost software licence reproduced below. -// --------------------------------------------------------------------------- -// Boost Software License - Version 1.0 - August 17th, 2003 -// -// Permission is hereby granted, free of charge, to any person or organization -// obtaining a copy of the software and accompanying documentation covered by -// this license (the "Software") to use, reproduce, display, distribute, -// execute, and transmit the Software, and to prepare derivative works of the -// Software, and to permit third-parties to whom the Software is furnished to -// do so, all subject to the following: -// -// The copyright notices in the Software and this entire statement, including -// the above license grant, this restriction and the following disclaimer, -// must be included in all copies of the Software, in whole or in part, and -// all derivative works of the Software, unless such copies or derivative -// works are solely in the form of machine-executable object code generated by -// a source language processor. -// -// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -// FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT -// SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE -// FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE, -// ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER -// DEALINGS IN THE SOFTWARE. -// --------------------------------------------------------------------------- - -// Boost like configuration -// ------------------------ -#if defined __clang__ - - #if defined(i386) - #include - inline void spp_cpuid(int info[4], int InfoType) { - __cpuid_count(InfoType, 0, info[0], info[1], info[2], info[3]); - } - #endif - - #define SPP_POPCNT __builtin_popcount - #define SPP_POPCNT64 __builtin_popcountll - - #define SPP_HAS_CSTDINT - - #ifndef __has_extension - #define __has_extension __has_feature - #endif - - #if !__has_feature(cxx_exceptions) && !defined(SPP_NO_EXCEPTIONS) - #define SPP_NO_EXCEPTIONS - #endif - - #if !__has_feature(cxx_rtti) && !defined(SPP_NO_RTTI) - #define SPP_NO_RTTI - #endif - - #if !__has_feature(cxx_rtti) && !defined(SPP_NO_TYPEID) - #define SPP_NO_TYPEID - #endif - - #if defined(__int64) && !defined(__GNUC__) - #define SPP_HAS_MS_INT64 - #endif - - #define SPP_HAS_NRVO - - // Branch prediction hints - #if defined(__has_builtin) - #if __has_builtin(__builtin_expect) - #define SPP_LIKELY(x) __builtin_expect(x, 1) - #define SPP_UNLIKELY(x) __builtin_expect(x, 0) - #endif - #endif - - // Clang supports "long long" in all compilation modes. - #define SPP_HAS_LONG_LONG - - #if !__has_feature(cxx_constexpr) - #define SPP_NO_CXX11_CONSTEXPR - #endif - - #if !__has_feature(cxx_decltype) - #define SPP_NO_CXX11_DECLTYPE - #endif - - #if !__has_feature(cxx_decltype_incomplete_return_types) - #define SPP_NO_CXX11_DECLTYPE_N3276 - #endif - - #if !__has_feature(cxx_defaulted_functions) - #define SPP_NO_CXX11_DEFAULTED_FUNCTIONS - #endif - - #if !__has_feature(cxx_deleted_functions) - #define SPP_NO_CXX11_DELETED_FUNCTIONS - #endif - - #if !__has_feature(cxx_explicit_conversions) - #define SPP_NO_CXX11_EXPLICIT_CONVERSION_OPERATORS - #endif - - #if !__has_feature(cxx_default_function_template_args) - #define SPP_NO_CXX11_FUNCTION_TEMPLATE_DEFAULT_ARGS - #endif - - #if !__has_feature(cxx_generalized_initializers) - #define SPP_NO_CXX11_HDR_INITIALIZER_LIST - #endif - - #if !__has_feature(cxx_lambdas) - #define SPP_NO_CXX11_LAMBDAS - #endif - - #if !__has_feature(cxx_local_type_template_args) - #define SPP_NO_CXX11_LOCAL_CLASS_TEMPLATE_PARAMETERS - #endif - - #if !__has_feature(cxx_raw_string_literals) - #define SPP_NO_CXX11_RAW_LITERALS - #endif - - #if !__has_feature(cxx_reference_qualified_functions) - #define SPP_NO_CXX11_REF_QUALIFIERS - #endif - - #if !__has_feature(cxx_generalized_initializers) - #define SPP_NO_CXX11_UNIFIED_INITIALIZATION_SYNTAX - #endif - - #if !__has_feature(cxx_rvalue_references) - #define SPP_NO_CXX11_RVALUE_REFERENCES - #endif - - #if !__has_feature(cxx_static_assert) - #define SPP_NO_CXX11_STATIC_ASSERT - #endif - - #if !__has_feature(cxx_alias_templates) - #define SPP_NO_CXX11_TEMPLATE_ALIASES - #endif - - #if !__has_feature(cxx_variadic_templates) - #define SPP_NO_CXX11_VARIADIC_TEMPLATES - #endif - - #if !__has_feature(cxx_user_literals) - #define SPP_NO_CXX11_USER_DEFINED_LITERALS - #endif - - #if !__has_feature(cxx_alignas) - #define SPP_NO_CXX11_ALIGNAS - #endif - - #if !__has_feature(cxx_trailing_return) - #define SPP_NO_CXX11_TRAILING_RESULT_TYPES - #endif - - #if !__has_feature(cxx_inline_namespaces) - #define SPP_NO_CXX11_INLINE_NAMESPACES - #endif - - #if !__has_feature(cxx_override_control) - #define SPP_NO_CXX11_FINAL - #endif - - #if !(__has_feature(__cxx_binary_literals__) || __has_extension(__cxx_binary_literals__)) - #define SPP_NO_CXX14_BINARY_LITERALS - #endif - - #if !__has_feature(__cxx_decltype_auto__) - #define SPP_NO_CXX14_DECLTYPE_AUTO - #endif - - #if !__has_feature(__cxx_init_captures__) - #define SPP_NO_CXX14_INITIALIZED_LAMBDA_CAPTURES - #endif - - #if !__has_feature(__cxx_generic_lambdas__) - #define SPP_NO_CXX14_GENERIC_LAMBDAS - #endif - - - #if !__has_feature(__cxx_generic_lambdas__) || !__has_feature(__cxx_relaxed_constexpr__) - #define SPP_NO_CXX14_CONSTEXPR - #endif - - #if !__has_feature(__cxx_return_type_deduction__) - #define SPP_NO_CXX14_RETURN_TYPE_DEDUCTION - #endif - - #if !__has_feature(__cxx_variable_templates__) - #define SPP_NO_CXX14_VARIABLE_TEMPLATES - #endif - - #if __cplusplus < 201400 - #define SPP_NO_CXX14_DIGIT_SEPARATORS - #endif - - #if defined(__has_builtin) && __has_builtin(__builtin_unreachable) - #define SPP_UNREACHABLE_RETURN(x) __builtin_unreachable(); - #endif - - #define SPP_ATTRIBUTE_UNUSED __attribute__((__unused__)) - - #ifndef SPP_COMPILER - #define SPP_COMPILER "Clang version " __clang_version__ - #endif - - #define SPP_CLANG 1 - - -#elif defined __GNUC__ - - #define SPP_GCC_VERSION (__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__) - - // definition to expand macro then apply to pragma message - // #define VALUE_TO_STRING(x) #x - // #define VALUE(x) VALUE_TO_STRING(x) - // #define VAR_NAME_VALUE(var) #var "=" VALUE(var) - // #pragma message(VAR_NAME_VALUE(SPP_GCC_VERSION)) - - #if defined(i386) - #include - inline void spp_cpuid(int info[4], int InfoType) { - __cpuid_count(InfoType, 0, info[0], info[1], info[2], info[3]); - } - #endif - - // __POPCNT__ defined when the compiled with popcount support - // (-mpopcnt compiler option is given for example) - #ifdef __POPCNT__ - // slower unless compiled iwith -mpopcnt - #define SPP_POPCNT __builtin_popcount - #define SPP_POPCNT64 __builtin_popcountll - #endif - - #if defined(__GXX_EXPERIMENTAL_CXX0X__) || (__cplusplus >= 201103L) - #define SPP_GCC_CXX11 - #endif - - #if __GNUC__ == 3 - #if defined (__PATHSCALE__) - #define SPP_NO_TWO_PHASE_NAME_LOOKUP - #define SPP_NO_IS_ABSTRACT - #endif - - #if __GNUC_MINOR__ < 4 - #define SPP_NO_IS_ABSTRACT - #endif - - #define SPP_NO_CXX11_EXTERN_TEMPLATE - #endif - - #if __GNUC__ < 4 - // - // All problems to gcc-3.x and earlier here: - // - #define SPP_NO_TWO_PHASE_NAME_LOOKUP - #ifdef __OPEN64__ - #define SPP_NO_IS_ABSTRACT - #endif - #endif - - // GCC prior to 3.4 had #pragma once too but it didn't work well with filesystem links - #if SPP_GCC_VERSION >= 30400 - #define SPP_HAS_PRAGMA_ONCE - #endif - - #if SPP_GCC_VERSION < 40400 - // Previous versions of GCC did not completely implement value-initialization: - // GCC Bug 30111, "Value-initialization of POD base class doesn't initialize - // members", reported by Jonathan Wakely in 2006, - // http://gcc.gnu.org/bugzilla/show_bug.cgi?id=30111 (fixed for GCC 4.4) - // GCC Bug 33916, "Default constructor fails to initialize array members", - // reported by Michael Elizabeth Chastain in 2007, - // http://gcc.gnu.org/bugzilla/show_bug.cgi?id=33916 (fixed for GCC 4.2.4) - // See also: http://www.boost.org/libs/utility/value_init.htm #compiler_issues - #define SPP_NO_COMPLETE_VALUE_INITIALIZATION - #endif - - #if !defined(__EXCEPTIONS) && !defined(SPP_NO_EXCEPTIONS) - #define SPP_NO_EXCEPTIONS - #endif - - // - // Threading support: Turn this on unconditionally here (except for - // those platforms where we can know for sure). It will get turned off again - // later if no threading API is detected. - // - #if !defined(__MINGW32__) && !defined(linux) && !defined(__linux) && !defined(__linux__) - #define SPP_HAS_THREADS - #endif - - // - // gcc has "long long" - // Except on Darwin with standard compliance enabled (-pedantic) - // Apple gcc helpfully defines this macro we can query - // - #if !defined(__DARWIN_NO_LONG_LONG) - #define SPP_HAS_LONG_LONG - #endif - - // - // gcc implements the named return value optimization since version 3.1 - // - #define SPP_HAS_NRVO - - // Branch prediction hints - #define SPP_LIKELY(x) __builtin_expect(x, 1) - #define SPP_UNLIKELY(x) __builtin_expect(x, 0) - - // - // Dynamic shared object (DSO) and dynamic-link library (DLL) support - // - #if __GNUC__ >= 4 - #if (defined(_WIN32) || defined(__WIN32__) || defined(WIN32)) && !defined(__CYGWIN__) - // All Win32 development environments, including 64-bit Windows and MinGW, define - // _WIN32 or one of its variant spellings. Note that Cygwin is a POSIX environment, - // so does not define _WIN32 or its variants. - #define SPP_HAS_DECLSPEC - #define SPP_SYMBOL_EXPORT __attribute__((__dllexport__)) - #define SPP_SYMBOL_IMPORT __attribute__((__dllimport__)) - #else - #define SPP_SYMBOL_EXPORT __attribute__((__visibility__("default"))) - #define SPP_SYMBOL_IMPORT - #endif - - #define SPP_SYMBOL_VISIBLE __attribute__((__visibility__("default"))) - #else - // config/platform/win32.hpp will define SPP_SYMBOL_EXPORT, etc., unless already defined - #define SPP_SYMBOL_EXPORT - #endif - - // - // RTTI and typeinfo detection is possible post gcc-4.3: - // - #if SPP_GCC_VERSION > 40300 - #ifndef __GXX_RTTI - #ifndef SPP_NO_TYPEID - #define SPP_NO_TYPEID - #endif - #ifndef SPP_NO_RTTI - #define SPP_NO_RTTI - #endif - #endif - #endif - - // - // Recent GCC versions have __int128 when in 64-bit mode. - // - // We disable this if the compiler is really nvcc with C++03 as it - // doesn't actually support __int128 as of CUDA_VERSION=7500 - // even though it defines __SIZEOF_INT128__. - // See https://svn.boost.org/trac/boost/ticket/8048 - // https://svn.boost.org/trac/boost/ticket/11852 - // Only re-enable this for nvcc if you're absolutely sure - // of the circumstances under which it's supported: - // - #if defined(__CUDACC__) - #if defined(SPP_GCC_CXX11) - #define SPP_NVCC_CXX11 - #else - #define SPP_NVCC_CXX03 - #endif - #endif - - #if defined(__SIZEOF_INT128__) && !defined(SPP_NVCC_CXX03) - #define SPP_HAS_INT128 - #endif - // - // Recent GCC versions have a __float128 native type, we need to - // include a std lib header to detect this - not ideal, but we'll - // be including later anyway when we select the std lib. - // - // Nevertheless, as of CUDA 7.5, using __float128 with the host - // compiler in pre-C++11 mode is still not supported. - // See https://svn.boost.org/trac/boost/ticket/11852 - // - #ifdef __cplusplus - #include - #else - #include - #endif - - #if defined(_GLIBCXX_USE_FLOAT128) && !defined(__STRICT_ANSI__) && !defined(SPP_NVCC_CXX03) - #define SPP_HAS_FLOAT128 - #endif - - // C++0x features in 4.3.n and later - // - #if (SPP_GCC_VERSION >= 40300) && defined(SPP_GCC_CXX11) - // C++0x features are only enabled when -std=c++0x or -std=gnu++0x are - // passed on the command line, which in turn defines - // __GXX_EXPERIMENTAL_CXX0X__. - #define SPP_HAS_DECLTYPE - #define SPP_HAS_RVALUE_REFS - #define SPP_HAS_STATIC_ASSERT - #define SPP_HAS_VARIADIC_TMPL - #define SPP_HAS_CSTDINT - #else - #define SPP_NO_CXX11_DECLTYPE - #define SPP_NO_CXX11_FUNCTION_TEMPLATE_DEFAULT_ARGS - #define SPP_NO_CXX11_RVALUE_REFERENCES - #define SPP_NO_CXX11_STATIC_ASSERT - #endif - - // C++0x features in 4.4.n and later - // - #if (SPP_GCC_VERSION < 40400) || !defined(SPP_GCC_CXX11) - #define SPP_NO_CXX11_AUTO_DECLARATIONS - #define SPP_NO_CXX11_AUTO_MULTIDECLARATIONS - #define SPP_NO_CXX11_CHAR16_T - #define SPP_NO_CXX11_CHAR32_T - #define SPP_NO_CXX11_HDR_INITIALIZER_LIST - #define SPP_NO_CXX11_DEFAULTED_FUNCTIONS - #define SPP_NO_CXX11_DELETED_FUNCTIONS - #define SPP_NO_CXX11_TRAILING_RESULT_TYPES - #define SPP_NO_CXX11_INLINE_NAMESPACES - #define SPP_NO_CXX11_VARIADIC_TEMPLATES - #endif - - #if SPP_GCC_VERSION < 40500 - #define SPP_NO_SFINAE_EXPR - #endif - - // GCC 4.5 forbids declaration of defaulted functions in private or protected sections - #if __GNUC__ < 4 || (__GNUC__ == 4 && __GNUC_MINOR__ == 5) || !defined(SPP_GCC_CXX11) - #define SPP_NO_CXX11_NON_PUBLIC_DEFAULTED_FUNCTIONS - #endif - - // C++0x features in 4.5.0 and later - // - #if (SPP_GCC_VERSION < 40500) || !defined(SPP_GCC_CXX11) - #define SPP_NO_CXX11_EXPLICIT_CONVERSION_OPERATORS - #define SPP_NO_CXX11_LAMBDAS - #define SPP_NO_CXX11_LOCAL_CLASS_TEMPLATE_PARAMETERS - #define SPP_NO_CXX11_RAW_LITERALS - #endif - - // C++0x features in 4.6.n and later - // - #if (SPP_GCC_VERSION < 40600) || !defined(SPP_GCC_CXX11) - #define SPP_NO_CXX11_CONSTEXPR - #define SPP_NO_CXX11_UNIFIED_INITIALIZATION_SYNTAX - #endif - - // C++0x features in 4.7.n and later - // - #if (SPP_GCC_VERSION < 40700) || !defined(SPP_GCC_CXX11) - #define SPP_NO_CXX11_FINAL - #define SPP_NO_CXX11_TEMPLATE_ALIASES - #define SPP_NO_CXX11_USER_DEFINED_LITERALS - #define SPP_NO_CXX11_FIXED_LENGTH_VARIADIC_TEMPLATE_EXPANSION_PACKS - #endif - - // C++0x features in 4.8.n and later - // - #if (SPP_GCC_VERSION < 40800) || !defined(SPP_GCC_CXX11) - #define SPP_NO_CXX11_ALIGNAS - #endif - - // C++0x features in 4.8.1 and later - // - #if (SPP_GCC_VERSION < 40801) || !defined(SPP_GCC_CXX11) - #define SPP_NO_CXX11_DECLTYPE_N3276 - #define SPP_NO_CXX11_REF_QUALIFIERS - #define SPP_NO_CXX14_BINARY_LITERALS - #endif - - // C++14 features in 4.9.0 and later - // - #if (SPP_GCC_VERSION < 40900) || (__cplusplus < 201300) - #define SPP_NO_CXX14_RETURN_TYPE_DEDUCTION - #define SPP_NO_CXX14_GENERIC_LAMBDAS - #define SPP_NO_CXX14_DIGIT_SEPARATORS - #define SPP_NO_CXX14_DECLTYPE_AUTO - #if !((SPP_GCC_VERSION >= 40801) && (SPP_GCC_VERSION < 40900) && defined(SPP_GCC_CXX11)) - #define SPP_NO_CXX14_INITIALIZED_LAMBDA_CAPTURES - #endif - #endif - - - // C++ 14: - #if !defined(__cpp_constexpr) || (__cpp_constexpr < 201304) - #define SPP_NO_CXX14_CONSTEXPR - #endif - #if !defined(__cpp_variable_templates) || (__cpp_variable_templates < 201304) - #define SPP_NO_CXX14_VARIABLE_TEMPLATES - #endif - - // - // Unused attribute: - #if __GNUC__ >= 4 - #define SPP_ATTRIBUTE_UNUSED __attribute__((__unused__)) - #endif - // - // __builtin_unreachable: - #if SPP_GCC_VERSION >= 40800 - #define SPP_UNREACHABLE_RETURN(x) __builtin_unreachable(); - #endif - - #ifndef SPP_COMPILER - #define SPP_COMPILER "GNU C++ version " __VERSION__ - #endif - - // ConceptGCC compiler: - // http://www.generic-programming.org/software/ConceptGCC/ - #ifdef __GXX_CONCEPTS__ - #define SPP_HAS_CONCEPTS - #define SPP_COMPILER "ConceptGCC version " __VERSION__ - #endif - -#elif defined _MSC_VER - - #include // for __popcnt() - - #define SPP_POPCNT_CHECK // slower when defined, but we have to check! - #define spp_cpuid(info, x) __cpuid(info, x) - - #define SPP_POPCNT __popcnt - #if (SPP_GROUP_SIZE == 64 && INTPTR_MAX == INT64_MAX) - #define SPP_POPCNT64 __popcnt64 - #endif - - // Attempt to suppress VC6 warnings about the length of decorated names (obsolete): - #pragma warning( disable : 4503 ) // warning: decorated name length exceeded - - #define SPP_HAS_PRAGMA_ONCE - #define SPP_HAS_CSTDINT - - // - // versions check: - // we don't support Visual C++ prior to version 7.1: - #if _MSC_VER < 1310 - #error "Antique compiler not supported" - #endif - - #if _MSC_FULL_VER < 180020827 - #define SPP_NO_FENV_H - #endif - - #if _MSC_VER < 1400 - // although a conforming signature for swprint exists in VC7.1 - // it appears not to actually work: - #define SPP_NO_SWPRINTF - - // Our extern template tests also fail for this compiler: - #define SPP_NO_CXX11_EXTERN_TEMPLATE - - // Variadic macros do not exist for VC7.1 and lower - #define SPP_NO_CXX11_VARIADIC_MACROS - #endif - - #if _MSC_VER < 1500 // 140X == VC++ 8.0 - #undef SPP_HAS_CSTDINT - #define SPP_NO_MEMBER_TEMPLATE_FRIENDS - #endif - - #if _MSC_VER < 1600 // 150X == VC++ 9.0 - // A bug in VC9: - #define SPP_NO_ADL_BARRIER - #endif - - - // MSVC (including the latest checked version) has not yet completely - // implemented value-initialization, as is reported: - // "VC++ does not value-initialize members of derived classes without - // user-declared constructor", reported in 2009 by Sylvester Hesp: - // https: //connect.microsoft.com/VisualStudio/feedback/details/484295 - // "Presence of copy constructor breaks member class initialization", - // reported in 2009 by Alex Vakulenko: - // https: //connect.microsoft.com/VisualStudio/feedback/details/499606 - // "Value-initialization in new-expression", reported in 2005 by - // Pavel Kuznetsov (MetaCommunications Engineering): - // https: //connect.microsoft.com/VisualStudio/feedback/details/100744 - // See also: http: //www.boost.org/libs/utility/value_init.htm #compiler_issues - // (Niels Dekker, LKEB, May 2010) - #define SPP_NO_COMPLETE_VALUE_INITIALIZATION - - #ifndef _NATIVE_WCHAR_T_DEFINED - #define SPP_NO_INTRINSIC_WCHAR_T - #endif - - // - // check for exception handling support: - #if !defined(_CPPUNWIND) && !defined(SPP_NO_EXCEPTIONS) - #define SPP_NO_EXCEPTIONS - #endif - - // - // __int64 support: - // - #define SPP_HAS_MS_INT64 - #if defined(_MSC_EXTENSIONS) || (_MSC_VER >= 1400) - #define SPP_HAS_LONG_LONG - #else - #define SPP_NO_LONG_LONG - #endif - - #if (_MSC_VER >= 1400) && !defined(_DEBUG) - #define SPP_HAS_NRVO - #endif - - #if _MSC_VER >= 1500 // 150X == VC++ 9.0 - #define SPP_HAS_PRAGMA_DETECT_MISMATCH - #endif - - // - // disable Win32 API's if compiler extensions are - // turned off: - // - #if !defined(_MSC_EXTENSIONS) && !defined(SPP_DISABLE_WIN32) - #define SPP_DISABLE_WIN32 - #endif - - #if !defined(_CPPRTTI) && !defined(SPP_NO_RTTI) - #define SPP_NO_RTTI - #endif - - // - // TR1 features: - // - #if _MSC_VER >= 1700 - // #define SPP_HAS_TR1_HASH // don't know if this is true yet. - // #define SPP_HAS_TR1_TYPE_TRAITS // don't know if this is true yet. - #define SPP_HAS_TR1_UNORDERED_MAP - #define SPP_HAS_TR1_UNORDERED_SET - #endif - - // - // C++0x features - // - // See above for SPP_NO_LONG_LONG - - // C++ features supported by VC++ 10 (aka 2010) - // - #if _MSC_VER < 1600 - #define SPP_NO_CXX11_AUTO_DECLARATIONS - #define SPP_NO_CXX11_AUTO_MULTIDECLARATIONS - #define SPP_NO_CXX11_LAMBDAS - #define SPP_NO_CXX11_RVALUE_REFERENCES - #define SPP_NO_CXX11_STATIC_ASSERT - #define SPP_NO_CXX11_DECLTYPE - #endif // _MSC_VER < 1600 - - #if _MSC_VER >= 1600 - #define SPP_HAS_STDINT_H - #endif - - // C++11 features supported by VC++ 11 (aka 2012) - // - #if _MSC_VER < 1700 - #define SPP_NO_CXX11_FINAL - #endif // _MSC_VER < 1700 - - // C++11 features supported by VC++ 12 (aka 2013). - // - #if _MSC_FULL_VER < 180020827 - #define SPP_NO_CXX11_DEFAULTED_FUNCTIONS - #define SPP_NO_CXX11_DELETED_FUNCTIONS - #define SPP_NO_CXX11_EXPLICIT_CONVERSION_OPERATORS - #define SPP_NO_CXX11_FUNCTION_TEMPLATE_DEFAULT_ARGS - #define SPP_NO_CXX11_RAW_LITERALS - #define SPP_NO_CXX11_TEMPLATE_ALIASES - #define SPP_NO_CXX11_TRAILING_RESULT_TYPES - #define SPP_NO_CXX11_VARIADIC_TEMPLATES - #define SPP_NO_CXX11_UNIFIED_INITIALIZATION_SYNTAX - #define SPP_NO_CXX11_DECLTYPE_N3276 - #endif - - // C++11 features supported by VC++ 14 (aka 2014) CTP1 - #if (_MSC_FULL_VER < 190021730) - #define SPP_NO_CXX11_REF_QUALIFIERS - #define SPP_NO_CXX11_USER_DEFINED_LITERALS - #define SPP_NO_CXX11_ALIGNAS - #define SPP_NO_CXX11_INLINE_NAMESPACES - #define SPP_NO_CXX14_DECLTYPE_AUTO - #define SPP_NO_CXX14_INITIALIZED_LAMBDA_CAPTURES - #define SPP_NO_CXX14_RETURN_TYPE_DEDUCTION - #define SPP_NO_CXX11_HDR_INITIALIZER_LIST - #endif - - // C++11 features not supported by any versions - #define SPP_NO_CXX11_CHAR16_T - #define SPP_NO_CXX11_CHAR32_T - #define SPP_NO_CXX11_CONSTEXPR - #define SPP_NO_SFINAE_EXPR - #define SPP_NO_TWO_PHASE_NAME_LOOKUP - - // C++ 14: - #if !defined(__cpp_binary_literals) || (__cpp_binary_literals < 201304) - #define SPP_NO_CXX14_BINARY_LITERALS - #endif - - #if !defined(__cpp_constexpr) || (__cpp_constexpr < 201304) - #define SPP_NO_CXX14_CONSTEXPR - #endif - - #if (__cplusplus < 201304) // There's no SD6 check for this.... - #define SPP_NO_CXX14_DIGIT_SEPARATORS - #endif - - #if !defined(__cpp_generic_lambdas) || (__cpp_generic_lambdas < 201304) - #define SPP_NO_CXX14_GENERIC_LAMBDAS - #endif - - #if !defined(__cpp_variable_templates) || (__cpp_variable_templates < 201304) - #define SPP_NO_CXX14_VARIABLE_TEMPLATES - #endif - -#endif - -// from boost/config/suffix.hpp -// ---------------------------- -#ifndef SPP_ATTRIBUTE_UNUSED - #define SPP_ATTRIBUTE_UNUSED -#endif - -/* - Try to persuade compilers to inline. -*/ -#ifndef SPP_FORCEINLINE - #if defined(__GNUC__) - #define SPP_FORCEINLINE __inline __attribute__ ((always_inline)) - #elif defined(_MSC_VER) - #define SPP_FORCEINLINE __forceinline - #else - #define SPP_FORCEINLINE inline - #endif -#endif - - -#endif // spp_config_h_guard diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp_dlalloc.h b/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp_dlalloc.h deleted file mode 100644 index f88aab7..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp_dlalloc.h +++ /dev/null @@ -1,4044 +0,0 @@ -#ifndef spp_dlalloc__h_ -#define spp_dlalloc__h_ - -/* This is a C++ allocator created from Doug Lea's dlmalloc - (Version 2.8.6 Wed Aug 29 06:57:58 2012) - see: http://g.oswego.edu/dl/html/malloc.html -*/ - -#include "spp_utils.h" -#include "spp_smartptr.h" - - -#ifndef SPP_FORCEINLINE - #if defined(__GNUC__) - #define SPP_FORCEINLINE __inline __attribute__ ((always_inline)) - #elif defined(_MSC_VER) - #define SPP_FORCEINLINE __forceinline - #else - #define SPP_FORCEINLINE inline - #endif -#endif - - -#ifndef SPP_IMPL - #define SPP_IMPL SPP_FORCEINLINE -#endif - -#ifndef SPP_API - #define SPP_API static -#endif - - -namespace spp -{ - // ---------------------- allocator internal API ----------------------- - typedef void* mspace; - - /* - create_mspace creates and returns a new independent space with the - given initial capacity, or, if 0, the default granularity size. It - returns null if there is no system memory available to create the - space. If argument locked is non-zero, the space uses a separate - lock to control access. The capacity of the space will grow - dynamically as needed to service mspace_malloc requests. You can - control the sizes of incremental increases of this space by - compiling with a different SPP_DEFAULT_GRANULARITY or dynamically - setting with mallopt(M_GRANULARITY, value). - */ - SPP_API mspace create_mspace(size_t capacity, int locked); - SPP_API size_t destroy_mspace(mspace msp); - SPP_API void* mspace_malloc(mspace msp, size_t bytes); - SPP_API void mspace_free(mspace msp, void* mem); - SPP_API void* mspace_realloc(mspace msp, void* mem, size_t newsize); - -#if 0 - SPP_API mspace create_mspace_with_base(void* base, size_t capacity, int locked); - SPP_API int mspace_track_large_chunks(mspace msp, int enable); - SPP_API void* mspace_calloc(mspace msp, size_t n_elements, size_t elem_size); - SPP_API void* mspace_memalign(mspace msp, size_t alignment, size_t bytes); - SPP_API void** mspace_independent_calloc(mspace msp, size_t n_elements, - size_t elem_size, void* chunks[]); - SPP_API void** mspace_independent_comalloc(mspace msp, size_t n_elements, - size_t sizes[], void* chunks[]); - SPP_API size_t mspace_footprint(mspace msp); - SPP_API size_t mspace_max_footprint(mspace msp); - SPP_API size_t mspace_usable_size(const void* mem); - SPP_API int mspace_trim(mspace msp, size_t pad); - SPP_API int mspace_mallopt(int, int); -#endif - - // ----------------------------------------------------------- - // ----------------------------------------------------------- - struct MSpace : public spp_rc - { - MSpace() : - _sp(create_mspace(0, 0)) - {} - - ~MSpace() - { - destroy_mspace(_sp); - } - - mspace _sp; - }; - - // ----------------------------------------------------------- - // ----------------------------------------------------------- - template - class spp_allocator - { - public: - typedef T value_type; - typedef T* pointer; - typedef ptrdiff_t difference_type; - typedef const T* const_pointer; - typedef size_t size_type; - - MSpace *getSpace() const { return _space.get(); } - - spp_allocator() : _space(new MSpace) {} - - template - spp_allocator(const spp_allocator &o) : _space(o.getSpace()) {} - - template - spp_allocator& operator=(const spp_allocator &o) - { - if (&o != this) - _space = o.getSpace(); - return *this; - } - - void swap(spp_allocator &o) - { - std::swap(_space, o._space); - } - - pointer allocate(size_t n, const_pointer /* unused */ = 0) - { - pointer res = static_cast(mspace_malloc(_space->_sp, n * sizeof(T))); - if (!res) - throw std::bad_alloc(); - return res; - } - - void deallocate(pointer p, size_t /* unused */) - { - mspace_free(_space->_sp, p); - } - - pointer reallocate(pointer p, size_t new_size) - { - pointer res = static_cast(mspace_realloc(_space->_sp, p, new_size * sizeof(T))); - if (!res) - throw std::bad_alloc(); - return res; - } - - pointer reallocate(pointer p, size_type /* old_size */, size_t new_size) - { - return reallocate(p, new_size); - } - - size_type max_size() const - { - return static_cast(-1) / sizeof(value_type); - } - - void construct(pointer p, const value_type& val) - { - new (p) value_type(val); - } - - void destroy(pointer p) { p->~value_type(); } - - template - struct rebind - { - // rebind to libc_allocator because we want to use malloc_inspect_all in destructive_iterator - // to reduce peak memory usage (we don't want mixed with value_type when - // we traverse the allocated memory). - typedef spp::spp_allocator other; - }; - - mspace space() const { return _space->_sp; } - - // check if we can clear the whole allocator memory at once => works only if the allocator - // is not be shared. If can_clear() returns true, we expect that the next allocator call - // will be clear() - not allocate() or deallocate() - bool can_clear() - { - assert(!_space_to_clear); - _space_to_clear.reset(); - _space_to_clear.swap(_space); - if (_space_to_clear->count() == 1) - return true; - else - _space_to_clear.swap(_space); - return false; - } - - void clear() - { - assert(!_space && !!_space_to_clear); - _space_to_clear.reset(); - _space = new MSpace; - } - - private: - spp_sptr _space; - spp_sptr _space_to_clear; - }; -} - - -// allocators are "equal" whenever memory allocated with one can be deallocated with the other -template -inline bool operator==(const spp_::spp_allocator &a, const spp_::spp_allocator &b) -{ - return a.space() == b.space(); -} - -template -inline bool operator!=(const spp_::spp_allocator &a, const spp_::spp_allocator &b) -{ - return !(a == b); -} - -namespace std -{ - template - inline void swap(spp_::spp_allocator &a, spp_::spp_allocator &b) - { - a.swap(b); - } -} - -#if !defined(SPP_EXCLUDE_IMPLEMENTATION) - -#ifndef WIN32 - #ifdef _WIN32 - #define WIN32 1 - #endif - #ifdef _WIN32_WCE - #define SPP_LACKS_FCNTL_H - #define WIN32 1 - #endif -#endif - -#ifdef WIN32 - #define WIN32_LEAN_AND_MEAN - #include - #include - #define SPP_HAVE_MMAP 1 - #define SPP_LACKS_UNISTD_H - #define SPP_LACKS_SYS_PARAM_H - #define SPP_LACKS_SYS_MMAN_H - #define SPP_LACKS_STRING_H - #define SPP_LACKS_STRINGS_H - #define SPP_LACKS_SYS_TYPES_H - #define SPP_LACKS_ERRNO_H - #define SPP_LACKS_SCHED_H - #ifndef SPP_MALLOC_FAILURE_ACTION - #define SPP_MALLOC_FAILURE_ACTION - #endif - #ifndef SPP_MMAP_CLEARS - #ifdef _WIN32_WCE /* WINCE reportedly does not clear */ - #define SPP_MMAP_CLEARS 0 - #else - #define SPP_MMAP_CLEARS 1 - #endif - #endif -#endif - -#if defined(DARWIN) || defined(_DARWIN) - #define SPP_HAVE_MMAP 1 - /* OSX allocators provide 16 byte alignment */ - #ifndef SPP_MALLOC_ALIGNMENT - #define SPP_MALLOC_ALIGNMENT ((size_t)16U) - #endif -#endif - -#ifndef SPP_LACKS_SYS_TYPES_H - #include /* For size_t */ -#endif - -#ifndef SPP_MALLOC_ALIGNMENT - #define SPP_MALLOC_ALIGNMENT ((size_t)(2 * sizeof(void *))) -#endif - -/* ------------------- size_t and alignment properties -------------------- */ -static const size_t spp_max_size_t = ~(size_t)0; -static const size_t spp_size_t_bitsize = sizeof(size_t) << 3; -static const size_t spp_half_max_size_t = spp_max_size_t / 2U; -static const size_t spp_chunk_align_mask = SPP_MALLOC_ALIGNMENT - 1; - -#if defined(SPP_DEBUG) || !defined(NDEBUG) -static bool spp_is_aligned(void *p) { return ((size_t)p & spp_chunk_align_mask) == 0; } -#endif - -// the number of bytes to offset an address to align it -static size_t align_offset(void *p) -{ - return (((size_t)p & spp_chunk_align_mask) == 0) ? 0 : - ((SPP_MALLOC_ALIGNMENT - ((size_t)p & spp_chunk_align_mask)) & spp_chunk_align_mask); -} - - -#ifndef SPP_FOOTERS - #define SPP_FOOTERS 0 -#endif - -#ifndef SPP_ABORT - #define SPP_ABORT abort() -#endif - -#ifndef SPP_ABORT_ON_ASSERT_FAILURE - #define SPP_ABORT_ON_ASSERT_FAILURE 1 -#endif - -#ifndef SPP_PROCEED_ON_ERROR - #define SPP_PROCEED_ON_ERROR 0 -#endif - -#ifndef SPP_INSECURE - #define SPP_INSECURE 0 -#endif - -#ifndef SPP_MALLOC_INSPECT_ALL - #define SPP_MALLOC_INSPECT_ALL 0 -#endif - -#ifndef SPP_HAVE_MMAP - #define SPP_HAVE_MMAP 1 -#endif - -#ifndef SPP_MMAP_CLEARS - #define SPP_MMAP_CLEARS 1 -#endif - -#ifndef SPP_HAVE_MREMAP - #ifdef linux - #define SPP_HAVE_MREMAP 1 - #ifndef _GNU_SOURCE - #define _GNU_SOURCE /* Turns on mremap() definition */ - #endif - #else - #define SPP_HAVE_MREMAP 0 - #endif -#endif - -#ifndef SPP_MALLOC_FAILURE_ACTION - // ENOMEM = 12 - #define SPP_MALLOC_FAILURE_ACTION errno = 12 -#endif - - -#ifndef SPP_DEFAULT_GRANULARITY - #if defined(WIN32) - #define SPP_DEFAULT_GRANULARITY (0) /* 0 means to compute in init_mparams */ - #else - #define SPP_DEFAULT_GRANULARITY ((size_t)64U * (size_t)1024U) - #endif -#endif - -#ifndef SPP_DEFAULT_TRIM_THRESHOLD - #define SPP_DEFAULT_TRIM_THRESHOLD ((size_t)2U * (size_t)1024U * (size_t)1024U) -#endif - -#ifndef SPP_DEFAULT_MMAP_THRESHOLD - #if SPP_HAVE_MMAP - #define SPP_DEFAULT_MMAP_THRESHOLD ((size_t)256U * (size_t)1024U) - #else - #define SPP_DEFAULT_MMAP_THRESHOLD spp_max_size_t - #endif -#endif - -#ifndef SPP_MAX_RELEASE_CHECK_RATE - #if SPP_HAVE_MMAP - #define SPP_MAX_RELEASE_CHECK_RATE 4095 - #else - #define SPP_MAX_RELEASE_CHECK_RATE spp_max_size_t - #endif -#endif - -#ifndef SPP_USE_BUILTIN_FFS - #define SPP_USE_BUILTIN_FFS 0 -#endif - -#ifndef SPP_USE_DEV_RANDOM - #define SPP_USE_DEV_RANDOM 0 -#endif - -#ifndef SPP_NO_SEGMENT_TRAVERSAL - #define SPP_NO_SEGMENT_TRAVERSAL 0 -#endif - - - -/*------------------------------ internal #includes ---------------------- */ - -#ifdef _MSC_VER - #pragma warning( disable : 4146 ) /* no "unsigned" warnings */ -#endif -#ifndef SPP_LACKS_ERRNO_H - #include /* for SPP_MALLOC_FAILURE_ACTION */ -#endif - -#ifdef SPP_DEBUG - #if SPP_ABORT_ON_ASSERT_FAILURE - #undef assert - #define assert(x) if(!(x)) SPP_ABORT - #else - #include - #endif -#else - #ifndef assert - #define assert(x) - #endif - #define SPP_DEBUG 0 -#endif - -#if !defined(WIN32) && !defined(SPP_LACKS_TIME_H) - #include /* for magic initialization */ -#endif - -#ifndef SPP_LACKS_STDLIB_H - #include /* for abort() */ -#endif - -#ifndef SPP_LACKS_STRING_H - #include /* for memset etc */ -#endif - -#if SPP_USE_BUILTIN_FFS - #ifndef SPP_LACKS_STRINGS_H - #include /* for ffs */ - #endif -#endif - -#if SPP_HAVE_MMAP - #ifndef SPP_LACKS_SYS_MMAN_H - /* On some versions of linux, mremap decl in mman.h needs __USE_GNU set */ - #if (defined(linux) && !defined(__USE_GNU)) - #define __USE_GNU 1 - #include /* for mmap */ - #undef __USE_GNU - #else - #include /* for mmap */ - #endif - #endif - #ifndef SPP_LACKS_FCNTL_H - #include - #endif -#endif - -#ifndef SPP_LACKS_UNISTD_H - #include /* for sbrk, sysconf */ -#else - #if !defined(__FreeBSD__) && !defined(__OpenBSD__) && !defined(__NetBSD__) - extern void* sbrk(ptrdiff_t); - #endif -#endif - -#include - -namespace spp -{ - -/* Declarations for bit scanning on win32 */ -#if defined(_MSC_VER) && _MSC_VER>=1300 - #ifndef BitScanForward /* Try to avoid pulling in WinNT.h */ - extern "C" { - unsigned char _BitScanForward(unsigned long *index, unsigned long mask); - unsigned char _BitScanReverse(unsigned long *index, unsigned long mask); - } - - #define BitScanForward _BitScanForward - #define BitScanReverse _BitScanReverse - #pragma intrinsic(_BitScanForward) - #pragma intrinsic(_BitScanReverse) - #endif /* BitScanForward */ -#endif /* defined(_MSC_VER) && _MSC_VER>=1300 */ - -#ifndef WIN32 - #ifndef malloc_getpagesize - #ifdef _SC_PAGESIZE /* some SVR4 systems omit an underscore */ - #ifndef _SC_PAGE_SIZE - #define _SC_PAGE_SIZE _SC_PAGESIZE - #endif - #endif - #ifdef _SC_PAGE_SIZE - #define malloc_getpagesize sysconf(_SC_PAGE_SIZE) - #else - #if defined(BSD) || defined(DGUX) || defined(HAVE_GETPAGESIZE) - extern size_t getpagesize(); - #define malloc_getpagesize getpagesize() - #else - #ifdef WIN32 /* use supplied emulation of getpagesize */ - #define malloc_getpagesize getpagesize() - #else - #ifndef SPP_LACKS_SYS_PARAM_H - #include - #endif - #ifdef EXEC_PAGESIZE - #define malloc_getpagesize EXEC_PAGESIZE - #else - #ifdef NBPG - #ifndef CLSIZE - #define malloc_getpagesize NBPG - #else - #define malloc_getpagesize (NBPG * CLSIZE) - #endif - #else - #ifdef NBPC - #define malloc_getpagesize NBPC - #else - #ifdef PAGESIZE - #define malloc_getpagesize PAGESIZE - #else /* just guess */ - #define malloc_getpagesize ((size_t)4096U) - #endif - #endif - #endif - #endif - #endif - #endif - #endif - #endif -#endif - -/* -------------------------- MMAP preliminaries ------------------------- */ - -/* - If SPP_HAVE_MORECORE or SPP_HAVE_MMAP are false, we just define calls and - checks to fail so compiler optimizer can delete code rather than - using so many "#if"s. -*/ - - -/* MMAP must return mfail on failure */ -static void *mfail = (void*)spp_max_size_t; -static char *cmfail = (char*)mfail; - -#if SPP_HAVE_MMAP - -#ifndef WIN32 - #define SPP_MUNMAP_DEFAULT(a, s) munmap((a), (s)) - #define SPP_MMAP_PROT (PROT_READ | PROT_WRITE) - #if !defined(MAP_ANONYMOUS) && defined(MAP_ANON) - #define MAP_ANONYMOUS MAP_ANON - #endif - - #ifdef MAP_ANONYMOUS - #define SPP_MMAP_FLAGS (MAP_PRIVATE | MAP_ANONYMOUS) - #define SPP_MMAP_DEFAULT(s) mmap(0, (s), SPP_MMAP_PROT, SPP_MMAP_FLAGS, -1, 0) - #else /* MAP_ANONYMOUS */ - /* - Nearly all versions of mmap support MAP_ANONYMOUS, so the following - is unlikely to be needed, but is supplied just in case. - */ - #define SPP_MMAP_FLAGS (MAP_PRIVATE) - static int dev_zero_fd = -1; /* Cached file descriptor for /dev/zero. */ - void SPP_MMAP_DEFAULT(size_t s) - { - if (dev_zero_fd < 0) - dev_zero_fd = open("/dev/zero", O_RDWR); - mmap(0, s, SPP_MMAP_PROT, SPP_MMAP_FLAGS, dev_zero_fd, 0); - } - #endif /* MAP_ANONYMOUS */ - - #define SPP_DIRECT_MMAP_DEFAULT(s) SPP_MMAP_DEFAULT(s) - -#else /* WIN32 */ - - /* Win32 MMAP via VirtualAlloc */ - static SPP_FORCEINLINE void* win32mmap(size_t size) - { - void* ptr = VirtualAlloc(0, size, MEM_RESERVE | MEM_COMMIT, PAGE_READWRITE); - return (ptr != 0) ? ptr : mfail; - } - - /* For direct MMAP, use MEM_TOP_DOWN to minimize interference */ - static SPP_FORCEINLINE void* win32direct_mmap(size_t size) - { - void* ptr = VirtualAlloc(0, size, MEM_RESERVE | MEM_COMMIT | MEM_TOP_DOWN, - PAGE_READWRITE); - return (ptr != 0) ? ptr : mfail; - } - - /* This function supports releasing coalesed segments */ - static SPP_FORCEINLINE int win32munmap(void* ptr, size_t size) - { - MEMORY_BASIC_INFORMATION minfo; - char* cptr = (char*)ptr; - while (size) - { - if (VirtualQuery(cptr, &minfo, sizeof(minfo)) == 0) - return -1; - if (minfo.BaseAddress != cptr || minfo.AllocationBase != cptr || - minfo.State != MEM_COMMIT || minfo.RegionSize > size) - return -1; - if (VirtualFree(cptr, 0, MEM_RELEASE) == 0) - return -1; - cptr += minfo.RegionSize; - size -= minfo.RegionSize; - } - return 0; - } - - #define SPP_MMAP_DEFAULT(s) win32mmap(s) - #define SPP_MUNMAP_DEFAULT(a, s) win32munmap((a), (s)) - #define SPP_DIRECT_MMAP_DEFAULT(s) win32direct_mmap(s) -#endif /* WIN32 */ -#endif /* SPP_HAVE_MMAP */ - -#if SPP_HAVE_MREMAP - #ifndef WIN32 - #define SPP_MREMAP_DEFAULT(addr, osz, nsz, mv) mremap((addr), (osz), (nsz), (mv)) - #endif -#endif - -/** - * Define SPP_CALL_MMAP/SPP_CALL_MUNMAP/SPP_CALL_DIRECT_MMAP - */ -#if SPP_HAVE_MMAP - #define USE_MMAP_BIT 1 - - #ifdef SPP_MMAP - #define SPP_CALL_MMAP(s) SPP_MMAP(s) - #else - #define SPP_CALL_MMAP(s) SPP_MMAP_DEFAULT(s) - #endif - - #ifdef SPP_MUNMAP - #define SPP_CALL_MUNMAP(a, s) SPP_MUNMAP((a), (s)) - #else - #define SPP_CALL_MUNMAP(a, s) SPP_MUNMAP_DEFAULT((a), (s)) - #endif - - #ifdef SPP_DIRECT_MMAP - #define SPP_CALL_DIRECT_MMAP(s) SPP_DIRECT_MMAP(s) - #else - #define SPP_CALL_DIRECT_MMAP(s) SPP_DIRECT_MMAP_DEFAULT(s) - #endif - -#else /* SPP_HAVE_MMAP */ - #define USE_MMAP_BIT 0 - - #define SPP_MMAP(s) mfail - #define SPP_MUNMAP(a, s) (-1) - #define SPP_DIRECT_MMAP(s) mfail - #define SPP_CALL_DIRECT_MMAP(s) SPP_DIRECT_MMAP(s) - #define SPP_CALL_MMAP(s) SPP_MMAP(s) - #define SPP_CALL_MUNMAP(a, s) SPP_MUNMAP((a), (s)) -#endif - -/** - * Define SPP_CALL_MREMAP - */ -#if SPP_HAVE_MMAP && SPP_HAVE_MREMAP - #ifdef MREMAP - #define SPP_CALL_MREMAP(addr, osz, nsz, mv) MREMAP((addr), (osz), (nsz), (mv)) - #else - #define SPP_CALL_MREMAP(addr, osz, nsz, mv) SPP_MREMAP_DEFAULT((addr), (osz), (nsz), (mv)) - #endif -#else - #define SPP_CALL_MREMAP(addr, osz, nsz, mv) mfail -#endif - -/* mstate bit set if continguous morecore disabled or failed */ -static const unsigned USE_NONCONTIGUOUS_BIT = 4U; - -/* segment bit set in create_mspace_with_base */ -static const unsigned EXTERN_BIT = 8U; - - -/* --------------------------- flags ------------------------ */ - -static const unsigned PINUSE_BIT = 1; -static const unsigned CINUSE_BIT = 2; -static const unsigned FLAG4_BIT = 4; -static const unsigned INUSE_BITS = (PINUSE_BIT | CINUSE_BIT); -static const unsigned FLAG_BITS = (PINUSE_BIT | CINUSE_BIT | FLAG4_BIT); - -/* ------------------- Chunks sizes and alignments ----------------------- */ - -#if SPP_FOOTERS - static const unsigned CHUNK_OVERHEAD = 2 * sizeof(size_t); -#else - static const unsigned CHUNK_OVERHEAD = sizeof(size_t); -#endif - -/* MMapped chunks need a second word of overhead ... */ -static const unsigned SPP_MMAP_CHUNK_OVERHEAD = 2 * sizeof(size_t); - -/* ... and additional padding for fake next-chunk at foot */ -static const unsigned SPP_MMAP_FOOT_PAD = 4 * sizeof(size_t); - -// =============================================================================== -struct malloc_chunk_header -{ - void set_size_and_pinuse_of_free_chunk(size_t s) - { - _head = s | PINUSE_BIT; - set_foot(s); - } - - void set_foot(size_t s) - { - ((malloc_chunk_header *)((char*)this + s))->_prev_foot = s; - } - - // extraction of fields from head words - bool cinuse() const { return !!(_head & CINUSE_BIT); } - bool pinuse() const { return !!(_head & PINUSE_BIT); } - bool flag4inuse() const { return !!(_head & FLAG4_BIT); } - bool is_inuse() const { return (_head & INUSE_BITS) != PINUSE_BIT; } - bool is_mmapped() const { return (_head & INUSE_BITS) == 0; } - - size_t chunksize() const { return _head & ~(FLAG_BITS); } - - void clear_pinuse() { _head &= ~PINUSE_BIT; } - void set_flag4() { _head |= FLAG4_BIT; } - void clear_flag4() { _head &= ~FLAG4_BIT; } - - // Treat space at ptr +/- offset as a chunk - malloc_chunk_header * chunk_plus_offset(size_t s) - { - return (malloc_chunk_header *)((char*)this + s); - } - malloc_chunk_header * chunk_minus_offset(size_t s) - { - return (malloc_chunk_header *)((char*)this - s); - } - - // Ptr to next or previous physical malloc_chunk. - malloc_chunk_header * next_chunk() - { - return (malloc_chunk_header *)((char*)this + (_head & ~FLAG_BITS)); - } - malloc_chunk_header * prev_chunk() - { - return (malloc_chunk_header *)((char*)this - (_prev_foot)); - } - - // extract next chunk's pinuse bit - size_t next_pinuse() { return next_chunk()->_head & PINUSE_BIT; } - - size_t _prev_foot; // Size of previous chunk (if free). - size_t _head; // Size and inuse bits. -}; - -// =============================================================================== -struct malloc_chunk : public malloc_chunk_header -{ - // Set size, pinuse bit, foot, and clear next pinuse - void set_free_with_pinuse(size_t s, malloc_chunk* n) - { - n->clear_pinuse(); - set_size_and_pinuse_of_free_chunk(s); - } - - // Get the internal overhead associated with chunk p - size_t overhead_for() { return is_mmapped() ? SPP_MMAP_CHUNK_OVERHEAD : CHUNK_OVERHEAD; } - - // Return true if malloced space is not necessarily cleared - bool calloc_must_clear() - { -#if SPP_MMAP_CLEARS - return !is_mmapped(); -#else - return true; -#endif - } - - struct malloc_chunk* _fd; // double links -- used only if free. - struct malloc_chunk* _bk; -}; - -static const unsigned MCHUNK_SIZE = sizeof(malloc_chunk); - -/* The smallest size we can malloc is an aligned minimal chunk */ -static const unsigned MIN_CHUNK_SIZE = (MCHUNK_SIZE + spp_chunk_align_mask) & ~spp_chunk_align_mask; - -typedef malloc_chunk mchunk; -typedef malloc_chunk* mchunkptr; -typedef malloc_chunk_header *hchunkptr; -typedef malloc_chunk* sbinptr; // The type of bins of chunks -typedef unsigned int bindex_t; // Described below -typedef unsigned int binmap_t; // Described below -typedef unsigned int flag_t; // The type of various bit flag sets - -// conversion from malloc headers to user pointers, and back -static SPP_FORCEINLINE void *chunk2mem(const void *p) { return (void *)((char *)p + 2 * sizeof(size_t)); } -static SPP_FORCEINLINE mchunkptr mem2chunk(const void *mem) { return (mchunkptr)((char *)mem - 2 * sizeof(size_t)); } - -// chunk associated with aligned address A -static SPP_FORCEINLINE mchunkptr align_as_chunk(char *A) { return (mchunkptr)(A + align_offset(chunk2mem(A))); } - -// Bounds on request (not chunk) sizes. -static const unsigned MAX_REQUEST = (-MIN_CHUNK_SIZE) << 2; -static const unsigned MIN_REQUEST = MIN_CHUNK_SIZE - CHUNK_OVERHEAD - 1; - -// pad request bytes into a usable size -static SPP_FORCEINLINE size_t pad_request(size_t req) -{ - return (req + CHUNK_OVERHEAD + spp_chunk_align_mask) & ~spp_chunk_align_mask; -} - -// pad request, checking for minimum (but not maximum) -static SPP_FORCEINLINE size_t request2size(size_t req) -{ - return req < MIN_REQUEST ? MIN_CHUNK_SIZE : pad_request(req); -} - - -/* ------------------ Operations on head and foot fields ----------------- */ - -/* - The head field of a chunk is or'ed with PINUSE_BIT when previous - adjacent chunk in use, and or'ed with CINUSE_BIT if this chunk is in - use, unless mmapped, in which case both bits are cleared. - - FLAG4_BIT is not used by this malloc, but might be useful in extensions. -*/ - -// Head value for fenceposts -static const unsigned FENCEPOST_HEAD = INUSE_BITS | sizeof(size_t); - - -/* ---------------------- Overlaid data structures ----------------------- */ - -/* - When chunks are not in use, they are treated as nodes of either - lists or trees. - - "Small" chunks are stored in circular doubly-linked lists, and look - like this: - - chunk-> +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ - | Size of previous chunk | - +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ - `head:' | Size of chunk, in bytes |P| - mem-> +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ - | Forward pointer to next chunk in list | - +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ - | Back pointer to previous chunk in list | - +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ - | Unused space (may be 0 bytes long) . - . . - . | -nextchunk-> +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ - `foot:' | Size of chunk, in bytes | - +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ - - Larger chunks are kept in a form of bitwise digital trees (aka - tries) keyed on chunksizes. Because malloc_tree_chunks are only for - free chunks greater than 256 bytes, their size doesn't impose any - constraints on user chunk sizes. Each node looks like: - - chunk-> +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ - | Size of previous chunk | - +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ - `head:' | Size of chunk, in bytes |P| - mem-> +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ - | Forward pointer to next chunk of same size | - +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ - | Back pointer to previous chunk of same size | - +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ - | Pointer to left child (child[0]) | - +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ - | Pointer to right child (child[1]) | - +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ - | Pointer to parent | - +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ - | bin index of this chunk | - +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ - | Unused space . - . | -nextchunk-> +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ - `foot:' | Size of chunk, in bytes | - +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ - - Each tree holding treenodes is a tree of unique chunk sizes. Chunks - of the same size are arranged in a circularly-linked list, with only - the oldest chunk (the next to be used, in our FIFO ordering) - actually in the tree. (Tree members are distinguished by a non-null - parent pointer.) If a chunk with the same size an an existing node - is inserted, it is linked off the existing node using pointers that - work in the same way as fd/bk pointers of small chunks. - - Each tree contains a power of 2 sized range of chunk sizes (the - smallest is 0x100 <= x < 0x180), which is is divided in half at each - tree level, with the chunks in the smaller half of the range (0x100 - <= x < 0x140 for the top nose) in the left subtree and the larger - half (0x140 <= x < 0x180) in the right subtree. This is, of course, - done by inspecting individual bits. - - Using these rules, each node's left subtree contains all smaller - sizes than its right subtree. However, the node at the root of each - subtree has no particular ordering relationship to either. (The - dividing line between the subtree sizes is based on trie relation.) - If we remove the last chunk of a given size from the interior of the - tree, we need to replace it with a leaf node. The tree ordering - rules permit a node to be replaced by any leaf below it. - - The smallest chunk in a tree (a common operation in a best-fit - allocator) can be found by walking a path to the leftmost leaf in - the tree. Unlike a usual binary tree, where we follow left child - pointers until we reach a null, here we follow the right child - pointer any time the left one is null, until we reach a leaf with - both child pointers null. The smallest chunk in the tree will be - somewhere along that path. - - The worst case number of steps to add, find, or remove a node is - bounded by the number of bits differentiating chunks within - bins. Under current bin calculations, this ranges from 6 up to 21 - (for 32 bit sizes) or up to 53 (for 64 bit sizes). The typical case - is of course much better. -*/ - -// =============================================================================== -struct malloc_tree_chunk : public malloc_chunk_header -{ - malloc_tree_chunk *leftmost_child() - { - return _child[0] ? _child[0] : _child[1]; - } - - - malloc_tree_chunk* _fd; - malloc_tree_chunk* _bk; - - malloc_tree_chunk* _child[2]; - malloc_tree_chunk* _parent; - bindex_t _index; -}; - -typedef malloc_tree_chunk tchunk; -typedef malloc_tree_chunk* tchunkptr; -typedef malloc_tree_chunk* tbinptr; // The type of bins of trees - -/* ----------------------------- Segments -------------------------------- */ - -/* - Each malloc space may include non-contiguous segments, held in a - list headed by an embedded malloc_segment record representing the - top-most space. Segments also include flags holding properties of - the space. Large chunks that are directly allocated by mmap are not - included in this list. They are instead independently created and - destroyed without otherwise keeping track of them. - - Segment management mainly comes into play for spaces allocated by - MMAP. Any call to MMAP might or might not return memory that is - adjacent to an existing segment. MORECORE normally contiguously - extends the current space, so this space is almost always adjacent, - which is simpler and faster to deal with. (This is why MORECORE is - used preferentially to MMAP when both are available -- see - sys_alloc.) When allocating using MMAP, we don't use any of the - hinting mechanisms (inconsistently) supported in various - implementations of unix mmap, or distinguish reserving from - committing memory. Instead, we just ask for space, and exploit - contiguity when we get it. It is probably possible to do - better than this on some systems, but no general scheme seems - to be significantly better. - - Management entails a simpler variant of the consolidation scheme - used for chunks to reduce fragmentation -- new adjacent memory is - normally prepended or appended to an existing segment. However, - there are limitations compared to chunk consolidation that mostly - reflect the fact that segment processing is relatively infrequent - (occurring only when getting memory from system) and that we - don't expect to have huge numbers of segments: - - * Segments are not indexed, so traversal requires linear scans. (It - would be possible to index these, but is not worth the extra - overhead and complexity for most programs on most platforms.) - * New segments are only appended to old ones when holding top-most - memory; if they cannot be prepended to others, they are held in - different segments. - - Except for the top-most segment of an mstate, each segment record - is kept at the tail of its segment. Segments are added by pushing - segment records onto the list headed by &mstate.seg for the - containing mstate. - - Segment flags control allocation/merge/deallocation policies: - * If EXTERN_BIT set, then we did not allocate this segment, - and so should not try to deallocate or merge with others. - (This currently holds only for the initial segment passed - into create_mspace_with_base.) - * If USE_MMAP_BIT set, the segment may be merged with - other surrounding mmapped segments and trimmed/de-allocated - using munmap. - * If neither bit is set, then the segment was obtained using - MORECORE so can be merged with surrounding MORECORE'd segments - and deallocated/trimmed using MORECORE with negative arguments. -*/ - -// =============================================================================== -struct malloc_segment -{ - bool is_mmapped_segment() { return !!(_sflags & USE_MMAP_BIT); } - bool is_extern_segment() { return !!(_sflags & EXTERN_BIT); } - - char* _base; // base address - size_t _size; // allocated size - malloc_segment* _next; // ptr to next segment - flag_t _sflags; // mmap and extern flag -}; - -typedef malloc_segment msegment; -typedef malloc_segment* msegmentptr; - -/* ------------- Malloc_params ------------------- */ - -/* - malloc_params holds global properties, including those that can be - dynamically set using mallopt. There is a single instance, mparams, - initialized in init_mparams. Note that the non-zeroness of "magic" - also serves as an initialization flag. -*/ - -// =============================================================================== -struct malloc_params -{ - malloc_params() : _magic(0) {} - - void ensure_initialization() - { - if (!_magic) - _init(); - } - - SPP_IMPL int change(int param_number, int value); - - size_t page_align(size_t sz) - { - return (sz + (_page_size - 1)) & ~(_page_size - 1); - } - - size_t granularity_align(size_t sz) - { - return (sz + (_granularity - 1)) & ~(_granularity - 1); - } - - bool is_page_aligned(char *S) - { - return ((size_t)S & (_page_size - 1)) == 0; - } - - SPP_IMPL int _init(); - - size_t _magic; - size_t _page_size; - size_t _granularity; - size_t _mmap_threshold; - size_t _trim_threshold; - flag_t _default_mflags; -}; - -static malloc_params mparams; - -/* ---------------------------- malloc_state ----------------------------- */ - -/* - A malloc_state holds all of the bookkeeping for a space. - The main fields are: - - Top - The topmost chunk of the currently active segment. Its size is - cached in topsize. The actual size of topmost space is - topsize+TOP_FOOT_SIZE, which includes space reserved for adding - fenceposts and segment records if necessary when getting more - space from the system. The size at which to autotrim top is - cached from mparams in trim_check, except that it is disabled if - an autotrim fails. - - Designated victim (dv) - This is the preferred chunk for servicing small requests that - don't have exact fits. It is normally the chunk split off most - recently to service another small request. Its size is cached in - dvsize. The link fields of this chunk are not maintained since it - is not kept in a bin. - - SmallBins - An array of bin headers for free chunks. These bins hold chunks - with sizes less than MIN_LARGE_SIZE bytes. Each bin contains - chunks of all the same size, spaced 8 bytes apart. To simplify - use in double-linked lists, each bin header acts as a malloc_chunk - pointing to the real first node, if it exists (else pointing to - itself). This avoids special-casing for headers. But to avoid - waste, we allocate only the fd/bk pointers of bins, and then use - repositioning tricks to treat these as the fields of a chunk. - - TreeBins - Treebins are pointers to the roots of trees holding a range of - sizes. There are 2 equally spaced treebins for each power of two - from TREE_SHIFT to TREE_SHIFT+16. The last bin holds anything - larger. - - Bin maps - There is one bit map for small bins ("smallmap") and one for - treebins ("treemap). Each bin sets its bit when non-empty, and - clears the bit when empty. Bit operations are then used to avoid - bin-by-bin searching -- nearly all "search" is done without ever - looking at bins that won't be selected. The bit maps - conservatively use 32 bits per map word, even if on 64bit system. - For a good description of some of the bit-based techniques used - here, see Henry S. Warren Jr's book "Hacker's Delight" (and - supplement at http://hackersdelight.org/). Many of these are - intended to reduce the branchiness of paths through malloc etc, as - well as to reduce the number of memory locations read or written. - - Segments - A list of segments headed by an embedded malloc_segment record - representing the initial space. - - Address check support - The least_addr field is the least address ever obtained from - MORECORE or MMAP. Attempted frees and reallocs of any address less - than this are trapped (unless SPP_INSECURE is defined). - - Magic tag - A cross-check field that should always hold same value as mparams._magic. - - Max allowed footprint - The maximum allowed bytes to allocate from system (zero means no limit) - - Flags - Bits recording whether to use MMAP, locks, or contiguous MORECORE - - Statistics - Each space keeps track of current and maximum system memory - obtained via MORECORE or MMAP. - - Trim support - Fields holding the amount of unused topmost memory that should trigger - trimming, and a counter to force periodic scanning to release unused - non-topmost segments. - - Extension support - A void* pointer and a size_t field that can be used to help implement - extensions to this malloc. -*/ - - -// ================================================================================ -class malloc_state -{ -public: - /* ----------------------- _malloc, _free, etc... --- */ - SPP_FORCEINLINE void* _malloc(size_t bytes); - SPP_FORCEINLINE void _free(mchunkptr p); - - - /* ------------------------ Relays to internal calls to malloc/free from realloc, memalign etc */ - void *internal_malloc(size_t b) { return mspace_malloc(this, b); } - void internal_free(void *mem) { mspace_free(this, mem); } - - /* ------------------------ ----------------------- */ - - SPP_IMPL void init_top(mchunkptr p, size_t psize); - SPP_IMPL void init_bins(); - SPP_IMPL void init(char* tbase, size_t tsize); - - /* ------------------------ System alloc/dealloc -------------------------- */ - SPP_IMPL void* sys_alloc(size_t nb); - SPP_IMPL size_t release_unused_segments(); - SPP_IMPL int sys_trim(size_t pad); - SPP_IMPL void dispose_chunk(mchunkptr p, size_t psize); - - /* ----------------------- Internal support for realloc, memalign, etc --- */ - SPP_IMPL mchunkptr try_realloc_chunk(mchunkptr p, size_t nb, int can_move); - SPP_IMPL void* internal_memalign(size_t alignment, size_t bytes); - SPP_IMPL void** ialloc(size_t n_elements, size_t* sizes, int opts, void* chunks[]); - SPP_IMPL size_t internal_bulk_free(void* array[], size_t nelem); - SPP_IMPL void internal_inspect_all(void(*handler)(void *start, void *end, - size_t used_bytes, void* callback_arg), - void* arg); - - /* -------------------------- system alloc setup (Operations on mflags) ----- */ - bool use_lock() const { return false; } - void enable_lock() {} - void set_lock(int) {} - void disable_lock() {} - - bool use_mmap() const { return !!(_mflags & USE_MMAP_BIT); } - void enable_mmap() { _mflags |= USE_MMAP_BIT; } - -#if SPP_HAVE_MMAP - void disable_mmap() { _mflags &= ~USE_MMAP_BIT; } -#else - void disable_mmap() {} -#endif - - /* ----------------------- Runtime Check Support ------------------------- */ - - /* - For security, the main invariant is that malloc/free/etc never - writes to a static address other than malloc_state, unless static - malloc_state itself has been corrupted, which cannot occur via - malloc (because of these checks). In essence this means that we - believe all pointers, sizes, maps etc held in malloc_state, but - check all of those linked or offsetted from other embedded data - structures. These checks are interspersed with main code in a way - that tends to minimize their run-time cost. - - When SPP_FOOTERS is defined, in addition to range checking, we also - verify footer fields of inuse chunks, which can be used guarantee - that the mstate controlling malloc/free is intact. This is a - streamlined version of the approach described by William Robertson - et al in "Run-time Detection of Heap-based Overflows" LISA'03 - http://www.usenix.org/events/lisa03/tech/robertson.html The footer - of an inuse chunk holds the xor of its mstate and a random seed, - that is checked upon calls to free() and realloc(). This is - (probabalistically) unguessable from outside the program, but can be - computed by any code successfully malloc'ing any chunk, so does not - itself provide protection against code that has already broken - security through some other means. Unlike Robertson et al, we - always dynamically check addresses of all offset chunks (previous, - next, etc). This turns out to be cheaper than relying on hashes. - */ - - -#if !SPP_INSECURE - // Check if address a is at least as high as any from MORECORE or MMAP - bool ok_address(void *a) const { return (char *)a >= _least_addr; } - - // Check if address of next chunk n is higher than base chunk p - static bool ok_next(void *p, void *n) { return p < n; } - - // Check if p has inuse status - static bool ok_inuse(mchunkptr p) { return p->is_inuse(); } - - // Check if p has its pinuse bit on - static bool ok_pinuse(mchunkptr p) { return p->pinuse(); } - - // Check if (alleged) mstate m has expected magic field - bool ok_magic() const { return _magic == mparams._magic; } - - // In gcc, use __builtin_expect to minimize impact of checks - #if defined(__GNUC__) && __GNUC__ >= 3 - static bool rtcheck(bool e) { return __builtin_expect(e, 1); } - #else - static bool rtcheck(bool e) { return e; } - #endif -#else - static bool ok_address(void *) { return true; } - static bool ok_next(void *, void *) { return true; } - static bool ok_inuse(mchunkptr) { return true; } - static bool ok_pinuse(mchunkptr) { return true; } - static bool ok_magic() { return true; } - static bool rtcheck(bool) { return true; } -#endif - - bool is_initialized() const { return _top != 0; } - - bool use_noncontiguous() const { return !!(_mflags & USE_NONCONTIGUOUS_BIT); } - void disable_contiguous() { _mflags |= USE_NONCONTIGUOUS_BIT; } - - // Return segment holding given address - msegmentptr segment_holding(char* addr) const - { - msegmentptr sp = (msegmentptr)&_seg; - for (;;) - { - if (addr >= sp->_base && addr < sp->_base + sp->_size) - return sp; - if ((sp = sp->_next) == 0) - return 0; - } - } - - // Return true if segment contains a segment link - int has_segment_link(msegmentptr ss) const - { - msegmentptr sp = (msegmentptr)&_seg; - for (;;) - { - if ((char*)sp >= ss->_base && (char*)sp < ss->_base + ss->_size) - return 1; - if ((sp = sp->_next) == 0) - return 0; - } - } - - bool should_trim(size_t s) const { return s > _trim_check; } - - /* -------------------------- Debugging setup ---------------------------- */ - -#if ! SPP_DEBUG - void check_free_chunk(mchunkptr) {} - void check_inuse_chunk(mchunkptr) {} - void check_malloced_chunk(void*, size_t) {} - void check_mmapped_chunk(mchunkptr) {} - void check_malloc_state() {} - void check_top_chunk(mchunkptr) {} -#else /* SPP_DEBUG */ - void check_free_chunk(mchunkptr p) { do_check_free_chunk(p); } - void check_inuse_chunk(mchunkptr p) { do_check_inuse_chunk(p); } - void check_malloced_chunk(void* p, size_t s) { do_check_malloced_chunk(p, s); } - void check_mmapped_chunk(mchunkptr p) { do_check_mmapped_chunk(p); } - void check_malloc_state() { do_check_malloc_state(); } - void check_top_chunk(mchunkptr p) { do_check_top_chunk(p); } - - void do_check_any_chunk(mchunkptr p) const; - void do_check_top_chunk(mchunkptr p) const; - void do_check_mmapped_chunk(mchunkptr p) const; - void do_check_inuse_chunk(mchunkptr p) const; - void do_check_free_chunk(mchunkptr p) const; - void do_check_malloced_chunk(void* mem, size_t s) const; - void do_check_tree(tchunkptr t); - void do_check_treebin(bindex_t i); - void do_check_smallbin(bindex_t i); - void do_check_malloc_state(); - int bin_find(mchunkptr x); - size_t traverse_and_check(); -#endif - -private: - - /* ---------------------------- Indexing Bins ---------------------------- */ - - static bool is_small(size_t s) { return (s >> SMALLBIN_SHIFT) < NSMALLBINS; } - static bindex_t small_index(size_t s) { return (bindex_t)(s >> SMALLBIN_SHIFT); } - static size_t small_index2size(size_t i) { return i << SMALLBIN_SHIFT; } - static bindex_t MIN_SMALL_INDEX() { return small_index(MIN_CHUNK_SIZE); } - - // assign tree index for size S to variable I. Use x86 asm if possible -#if defined(__GNUC__) && (defined(__i386__) || defined(__x86_64__)) - SPP_FORCEINLINE static bindex_t compute_tree_index(size_t S) - { - unsigned int X = S >> TREEBIN_SHIFT; - if (X == 0) - return 0; - else if (X > 0xFFFF) - return NTREEBINS - 1; - - unsigned int K = (unsigned) sizeof(X) * __CHAR_BIT__ - 1 - (unsigned) __builtin_clz(X); - return (bindex_t)((K << 1) + ((S >> (K + (TREEBIN_SHIFT - 1)) & 1))); - } - -#elif defined (__INTEL_COMPILER) - SPP_FORCEINLINE static bindex_t compute_tree_index(size_t S) - { - size_t X = S >> TREEBIN_SHIFT; - if (X == 0) - return 0; - else if (X > 0xFFFF) - return NTREEBINS - 1; - - unsigned int K = _bit_scan_reverse(X); - return (bindex_t)((K << 1) + ((S >> (K + (TREEBIN_SHIFT - 1)) & 1))); - } - -#elif defined(_MSC_VER) && _MSC_VER>=1300 - SPP_FORCEINLINE static bindex_t compute_tree_index(size_t S) - { - size_t X = S >> TREEBIN_SHIFT; - if (X == 0) - return 0; - else if (X > 0xFFFF) - return NTREEBINS - 1; - - unsigned int K; - _BitScanReverse((DWORD *) &K, (DWORD) X); - return (bindex_t)((K << 1) + ((S >> (K + (TREEBIN_SHIFT - 1)) & 1))); - } - -#else // GNUC - SPP_FORCEINLINE static bindex_t compute_tree_index(size_t S) - { - size_t X = S >> TREEBIN_SHIFT; - if (X == 0) - return 0; - else if (X > 0xFFFF) - return NTREEBINS - 1; - - unsigned int Y = (unsigned int)X; - unsigned int N = ((Y - 0x100) >> 16) & 8; - unsigned int K = (((Y <<= N) - 0x1000) >> 16) & 4; - N += K; - N += K = (((Y <<= K) - 0x4000) >> 16) & 2; - K = 14 - N + ((Y <<= K) >> 15); - return (K << 1) + ((S >> (K + (TREEBIN_SHIFT - 1)) & 1)); - } -#endif - - // Shift placing maximum resolved bit in a treebin at i as sign bit - static bindex_t leftshift_for_tree_index(bindex_t i) - { - return (i == NTREEBINS - 1) ? 0 : - ((spp_size_t_bitsize - 1) - ((i >> 1) + TREEBIN_SHIFT - 2)); - } - - // The size of the smallest chunk held in bin with index i - static bindex_t minsize_for_tree_index(bindex_t i) - { - return ((size_t)1 << ((i >> 1) + TREEBIN_SHIFT)) | - (((size_t)(i & 1)) << ((i >> 1) + TREEBIN_SHIFT - 1)); - } - - - // ----------- isolate the least set bit of a bitmap - static binmap_t least_bit(binmap_t x) { return x & -x; } - - // ----------- mask with all bits to left of least bit of x on - static binmap_t left_bits(binmap_t x) { return (x << 1) | -(x << 1); } - - // index corresponding to given bit. Use x86 asm if possible -#if defined(__GNUC__) && (defined(__i386__) || defined(__x86_64__)) - static bindex_t compute_bit2idx(binmap_t X) - { - unsigned int J; - J = __builtin_ctz(X); - return (bindex_t)J; - } - -#elif defined (__INTEL_COMPILER) - static bindex_t compute_bit2idx(binmap_t X) - { - unsigned int J; - J = _bit_scan_forward(X); - return (bindex_t)J; - } - -#elif defined(_MSC_VER) && _MSC_VER>=1300 - static bindex_t compute_bit2idx(binmap_t X) - { - unsigned int J; - _BitScanForward((DWORD *) &J, X); - return (bindex_t)J; - } - -#elif SPP_USE_BUILTIN_FFS - static bindex_t compute_bit2idx(binmap_t X) { return ffs(X) - 1; } - -#else - static bindex_t compute_bit2idx(binmap_t X) - { - unsigned int Y = X - 1; - unsigned int K = Y >> (16 - 4) & 16; - unsigned int N = K; Y >>= K; - N += K = Y >> (8 - 3) & 8; Y >>= K; - N += K = Y >> (4 - 2) & 4; Y >>= K; - N += K = Y >> (2 - 1) & 2; Y >>= K; - N += K = Y >> (1 - 0) & 1; Y >>= K; - return (bindex_t)(N + Y); - } -#endif - - /* ------------------------ Set up inuse chunks with or without footers ---*/ -#if !SPP_FOOTERS - void mark_inuse_foot(malloc_chunk_header *, size_t) {} -#else - //Set foot of inuse chunk to be xor of mstate and seed - void mark_inuse_foot(malloc_chunk_header *p, size_t s) - { - (((mchunkptr)((char*)p + s))->prev_foot = (size_t)this ^ mparams._magic); - } -#endif - - void set_inuse(malloc_chunk_header *p, size_t s) - { - p->_head = (p->_head & PINUSE_BIT) | s | CINUSE_BIT; - ((mchunkptr)(((char*)p) + s))->_head |= PINUSE_BIT; - mark_inuse_foot(p, s); - } - - void set_inuse_and_pinuse(malloc_chunk_header *p, size_t s) - { - p->_head = s | PINUSE_BIT | CINUSE_BIT; - ((mchunkptr)(((char*)p) + s))->_head |= PINUSE_BIT; - mark_inuse_foot(p, s); - } - - void set_size_and_pinuse_of_inuse_chunk(malloc_chunk_header *p, size_t s) - { - p->_head = s | PINUSE_BIT | CINUSE_BIT; - mark_inuse_foot(p, s); - } - - /* ------------------------ Addressing by index. See about smallbin repositioning --- */ - sbinptr smallbin_at(bindex_t i) const { return (sbinptr)((char*)&_smallbins[i << 1]); } - tbinptr* treebin_at(bindex_t i) { return &_treebins[i]; } - - /* ----------------------- bit corresponding to given index ---------*/ - static binmap_t idx2bit(bindex_t i) { return ((binmap_t)1 << i); } - - // --------------- Mark/Clear bits with given index - void mark_smallmap(bindex_t i) { _smallmap |= idx2bit(i); } - void clear_smallmap(bindex_t i) { _smallmap &= ~idx2bit(i); } - binmap_t smallmap_is_marked(bindex_t i) const { return _smallmap & idx2bit(i); } - - void mark_treemap(bindex_t i) { _treemap |= idx2bit(i); } - void clear_treemap(bindex_t i) { _treemap &= ~idx2bit(i); } - binmap_t treemap_is_marked(bindex_t i) const { return _treemap & idx2bit(i); } - - /* ------------------------ ----------------------- */ - SPP_FORCEINLINE void insert_small_chunk(mchunkptr P, size_t S); - SPP_FORCEINLINE void unlink_small_chunk(mchunkptr P, size_t S); - SPP_FORCEINLINE void unlink_first_small_chunk(mchunkptr B, mchunkptr P, bindex_t I); - SPP_FORCEINLINE void replace_dv(mchunkptr P, size_t S); - - /* ------------------------- Operations on trees ------------------------- */ - SPP_FORCEINLINE void insert_large_chunk(tchunkptr X, size_t S); - SPP_FORCEINLINE void unlink_large_chunk(tchunkptr X); - - /* ------------------------ Relays to large vs small bin operations */ - SPP_FORCEINLINE void insert_chunk(mchunkptr P, size_t S); - SPP_FORCEINLINE void unlink_chunk(mchunkptr P, size_t S); - - /* ----------------------- Direct-mmapping chunks ----------------------- */ - SPP_IMPL void* mmap_alloc(size_t nb); - SPP_IMPL mchunkptr mmap_resize(mchunkptr oldp, size_t nb, int flags); - - SPP_IMPL void reset_on_error(); - SPP_IMPL void* prepend_alloc(char* newbase, char* oldbase, size_t nb); - SPP_IMPL void add_segment(char* tbase, size_t tsize, flag_t mmapped); - - /* ------------------------ malloc --------------------------- */ - SPP_IMPL void* tmalloc_large(size_t nb); - SPP_IMPL void* tmalloc_small(size_t nb); - - /* ------------------------Bin types, widths and sizes -------- */ - static const size_t NSMALLBINS = 32; - static const size_t NTREEBINS = 32; - static const size_t SMALLBIN_SHIFT = 3; - static const size_t SMALLBIN_WIDTH = 1 << SMALLBIN_SHIFT; - static const size_t TREEBIN_SHIFT = 8; - static const size_t MIN_LARGE_SIZE = 1 << TREEBIN_SHIFT; - static const size_t MAX_SMALL_SIZE = (MIN_LARGE_SIZE - 1); - static const size_t MAX_SMALL_REQUEST = (MAX_SMALL_SIZE - spp_chunk_align_mask - CHUNK_OVERHEAD); - - /* ------------------------ data members --------------------------- */ - binmap_t _smallmap; - binmap_t _treemap; - size_t _dvsize; - size_t _topsize; - char* _least_addr; - mchunkptr _dv; - mchunkptr _top; - size_t _trim_check; - size_t _release_checks; - size_t _magic; - mchunkptr _smallbins[(NSMALLBINS + 1) * 2]; - tbinptr _treebins[NTREEBINS]; -public: - size_t _footprint; - size_t _max_footprint; - size_t _footprint_limit; // zero means no limit - flag_t _mflags; - - msegment _seg; - -private: - void* _extp; // Unused but available for extensions - size_t _exts; -}; - -typedef malloc_state* mstate; - -/* ------------- end malloc_state ------------------- */ - -#if SPP_FOOTERS -static malloc_state* get_mstate_for(malloc_chunk_header *p) -{ - return (malloc_state*)(((mchunkptr)((char*)(p) + - (p->chunksize())))->prev_foot ^ mparams._magic); -} -#endif - -/* -------------------------- system alloc setup ------------------------- */ - - - -// For mmap, use granularity alignment on windows, else page-align -#ifdef WIN32 - #define mmap_align(S) mparams.granularity_align(S) -#else - #define mmap_align(S) mparams.page_align(S) -#endif - -// True if segment S holds address A -static bool segment_holds(msegmentptr S, mchunkptr A) -{ - return (char*)A >= S->_base && (char*)A < S->_base + S->_size; -} - -/* - top_foot_size is padding at the end of a segment, including space - that may be needed to place segment records and fenceposts when new - noncontiguous segments are added. -*/ -static SPP_FORCEINLINE size_t top_foot_size() -{ - return align_offset(chunk2mem((void *)0)) + - pad_request(sizeof(struct malloc_segment)) + - MIN_CHUNK_SIZE; -} - - -// For sys_alloc, enough padding to ensure can malloc request on success -static SPP_FORCEINLINE size_t sys_alloc_padding() -{ - return top_foot_size() + SPP_MALLOC_ALIGNMENT; -} - - -#define SPP_USAGE_ERROR_ACTION(m,p) SPP_ABORT - -/* ---------------------------- setting mparams -------------------------- */ - -// Initialize mparams -int malloc_params::_init() -{ -#ifdef NEED_GLOBAL_LOCK_INIT - if (malloc_global_mutex_status <= 0) - init_malloc_global_mutex(); -#endif - - if (_magic == 0) - { - size_t magic; - size_t psize; - size_t gsize; - -#ifndef WIN32 - psize = malloc_getpagesize; - gsize = ((SPP_DEFAULT_GRANULARITY != 0) ? SPP_DEFAULT_GRANULARITY : psize); -#else - { - SYSTEM_INFO system_info; - GetSystemInfo(&system_info); - psize = system_info.dwPageSize; - gsize = ((SPP_DEFAULT_GRANULARITY != 0) ? - SPP_DEFAULT_GRANULARITY : system_info.dwAllocationGranularity); - } -#endif - - /* Sanity-check configuration: - size_t must be unsigned and as wide as pointer type. - ints must be at least 4 bytes. - alignment must be at least 8. - Alignment, min chunk size, and page size must all be powers of 2. - */ - if ((sizeof(size_t) != sizeof(char*)) || - (spp_max_size_t < MIN_CHUNK_SIZE) || - (sizeof(int) < 4) || - (SPP_MALLOC_ALIGNMENT < (size_t)8U) || - ((SPP_MALLOC_ALIGNMENT & (SPP_MALLOC_ALIGNMENT - 1)) != 0) || - ((MCHUNK_SIZE & (MCHUNK_SIZE - 1)) != 0) || - ((gsize & (gsize - 1)) != 0) || - ((psize & (psize - 1)) != 0)) - SPP_ABORT; - _granularity = gsize; - _page_size = psize; - _mmap_threshold = SPP_DEFAULT_MMAP_THRESHOLD; - _trim_threshold = SPP_DEFAULT_TRIM_THRESHOLD; - _default_mflags = USE_MMAP_BIT | USE_NONCONTIGUOUS_BIT; - - { -#if SPP_USE_DEV_RANDOM - int fd; - unsigned char buf[sizeof(size_t)]; - // Try to use /dev/urandom, else fall back on using time - if ((fd = open("/dev/urandom", O_RDONLY)) >= 0 && - read(fd, buf, sizeof(buf)) == sizeof(buf)) - { - magic = *((size_t *) buf); - close(fd); - } - else -#endif - { -#ifdef WIN32 - magic = (size_t)(GetTickCount() ^ (size_t)0x55555555U); -#elif defined(SPP_LACKS_TIME_H) - magic = (size_t)&magic ^ (size_t)0x55555555U; -#else - magic = (size_t)(time(0) ^ (size_t)0x55555555U); -#endif - } - magic |= (size_t)8U; // ensure nonzero - magic &= ~(size_t)7U; // improve chances of fault for bad values - // Until memory modes commonly available, use volatile-write - (*(volatile size_t *)(&(_magic))) = magic; - } - } - - return 1; -} - -/* - mallopt tuning options. SVID/XPG defines four standard parameter - numbers for mallopt, normally defined in malloc.h. None of these - are used in this malloc, so setting them has no effect. But this - malloc does support the following options. -*/ -static const int m_trim_threshold = -1; -static const int m_granularity = -2; -static const int m_mmap_threshold = -3; - -// support for mallopt -int malloc_params::change(int param_number, int value) -{ - size_t val; - ensure_initialization(); - val = (value == -1) ? spp_max_size_t : (size_t)value; - - switch (param_number) - { - case m_trim_threshold: - _trim_threshold = val; - return 1; - - case m_granularity: - if (val >= _page_size && ((val & (val - 1)) == 0)) - { - _granularity = val; - return 1; - } - else - return 0; - - case m_mmap_threshold: - _mmap_threshold = val; - return 1; - - default: - return 0; - } -} - -#if SPP_DEBUG -/* ------------------------- Debugging Support --------------------------- */ - -// Check properties of any chunk, whether free, inuse, mmapped etc -void malloc_state::do_check_any_chunk(mchunkptr p) const -{ - assert((spp_is_aligned(chunk2mem(p))) || (p->_head == FENCEPOST_HEAD)); - assert(ok_address(p)); -} - -// Check properties of top chunk -void malloc_state::do_check_top_chunk(mchunkptr p) const -{ - msegmentptr sp = segment_holding((char*)p); - size_t sz = p->_head & ~INUSE_BITS; // third-lowest bit can be set! - assert(sp != 0); - assert((spp_is_aligned(chunk2mem(p))) || (p->_head == FENCEPOST_HEAD)); - assert(ok_address(p)); - assert(sz == _topsize); - assert(sz > 0); - assert(sz == ((sp->_base + sp->_size) - (char*)p) - top_foot_size()); - assert(p->pinuse()); - assert(!p->chunk_plus_offset(sz)->pinuse()); -} - -// Check properties of (inuse) mmapped chunks -void malloc_state::do_check_mmapped_chunk(mchunkptr p) const -{ - size_t sz = p->chunksize(); - size_t len = (sz + (p->_prev_foot) + SPP_MMAP_FOOT_PAD); - assert(p->is_mmapped()); - assert(use_mmap()); - assert((spp_is_aligned(chunk2mem(p))) || (p->_head == FENCEPOST_HEAD)); - assert(ok_address(p)); - assert(!is_small(sz)); - assert((len & (mparams._page_size - 1)) == 0); - assert(p->chunk_plus_offset(sz)->_head == FENCEPOST_HEAD); - assert(p->chunk_plus_offset(sz + sizeof(size_t))->_head == 0); -} - -// Check properties of inuse chunks -void malloc_state::do_check_inuse_chunk(mchunkptr p) const -{ - do_check_any_chunk(p); - assert(p->is_inuse()); - assert(p->next_pinuse()); - // If not pinuse and not mmapped, previous chunk has OK offset - assert(p->is_mmapped() || p->pinuse() || (mchunkptr)p->prev_chunk()->next_chunk() == p); - if (p->is_mmapped()) - do_check_mmapped_chunk(p); -} - -// Check properties of free chunks -void malloc_state::do_check_free_chunk(mchunkptr p) const -{ - size_t sz = p->chunksize(); - mchunkptr next = (mchunkptr)p->chunk_plus_offset(sz); - do_check_any_chunk(p); - assert(!p->is_inuse()); - assert(!p->next_pinuse()); - assert(!p->is_mmapped()); - if (p != _dv && p != _top) - { - if (sz >= MIN_CHUNK_SIZE) - { - assert((sz & spp_chunk_align_mask) == 0); - assert(spp_is_aligned(chunk2mem(p))); - assert(next->_prev_foot == sz); - assert(p->pinuse()); - assert(next == _top || next->is_inuse()); - assert(p->_fd->_bk == p); - assert(p->_bk->_fd == p); - } - else // markers are always of size sizeof(size_t) - assert(sz == sizeof(size_t)); - } -} - -// Check properties of malloced chunks at the point they are malloced -void malloc_state::do_check_malloced_chunk(void* mem, size_t s) const -{ - if (mem != 0) - { - mchunkptr p = mem2chunk(mem); - size_t sz = p->_head & ~INUSE_BITS; - do_check_inuse_chunk(p); - assert((sz & spp_chunk_align_mask) == 0); - assert(sz >= MIN_CHUNK_SIZE); - assert(sz >= s); - // unless mmapped, size is less than MIN_CHUNK_SIZE more than request - assert(p->is_mmapped() || sz < (s + MIN_CHUNK_SIZE)); - } -} - -// Check a tree and its subtrees. -void malloc_state::do_check_tree(tchunkptr t) -{ - tchunkptr head = 0; - tchunkptr u = t; - bindex_t tindex = t->_index; - size_t tsize = t->chunksize(); - bindex_t idx = compute_tree_index(tsize); - assert(tindex == idx); - assert(tsize >= MIN_LARGE_SIZE); - assert(tsize >= minsize_for_tree_index(idx)); - assert((idx == NTREEBINS - 1) || (tsize < minsize_for_tree_index((idx + 1)))); - - do - { - // traverse through chain of same-sized nodes - do_check_any_chunk((mchunkptr)u); - assert(u->_index == tindex); - assert(u->chunksize() == tsize); - assert(!u->is_inuse()); - assert(!u->next_pinuse()); - assert(u->_fd->_bk == u); - assert(u->_bk->_fd == u); - if (u->_parent == 0) - { - assert(u->_child[0] == 0); - assert(u->_child[1] == 0); - } - else - { - assert(head == 0); // only one node on chain has parent - head = u; - assert(u->_parent != u); - assert(u->_parent->_child[0] == u || - u->_parent->_child[1] == u || - *((tbinptr*)(u->_parent)) == u); - if (u->_child[0] != 0) - { - assert(u->_child[0]->_parent == u); - assert(u->_child[0] != u); - do_check_tree(u->_child[0]); - } - if (u->_child[1] != 0) - { - assert(u->_child[1]->_parent == u); - assert(u->_child[1] != u); - do_check_tree(u->_child[1]); - } - if (u->_child[0] != 0 && u->_child[1] != 0) - assert(u->_child[0]->chunksize() < u->_child[1]->chunksize()); - } - u = u->_fd; - } - while (u != t); - assert(head != 0); -} - -// Check all the chunks in a treebin. -void malloc_state::do_check_treebin(bindex_t i) -{ - tbinptr* tb = (tbinptr*)treebin_at(i); - tchunkptr t = *tb; - int empty = (_treemap & (1U << i)) == 0; - if (t == 0) - assert(empty); - if (!empty) - do_check_tree(t); -} - -// Check all the chunks in a smallbin. -void malloc_state::do_check_smallbin(bindex_t i) -{ - sbinptr b = smallbin_at(i); - mchunkptr p = b->_bk; - unsigned int empty = (_smallmap & (1U << i)) == 0; - if (p == b) - assert(empty); - if (!empty) - { - for (; p != b; p = p->_bk) - { - size_t size = p->chunksize(); - mchunkptr q; - // each chunk claims to be free - do_check_free_chunk(p); - // chunk belongs in bin - assert(small_index(size) == i); - assert(p->_bk == b || p->_bk->chunksize() == p->chunksize()); - // chunk is followed by an inuse chunk - q = (mchunkptr)p->next_chunk(); - if (q->_head != FENCEPOST_HEAD) - do_check_inuse_chunk(q); - } - } -} - -// Find x in a bin. Used in other check functions. -int malloc_state::bin_find(mchunkptr x) -{ - size_t size = x->chunksize(); - if (is_small(size)) - { - bindex_t sidx = small_index(size); - sbinptr b = smallbin_at(sidx); - if (smallmap_is_marked(sidx)) - { - mchunkptr p = b; - do - { - if (p == x) - return 1; - } - while ((p = p->_fd) != b); - } - } - else - { - bindex_t tidx = compute_tree_index(size); - if (treemap_is_marked(tidx)) - { - tchunkptr t = *treebin_at(tidx); - size_t sizebits = size << leftshift_for_tree_index(tidx); - while (t != 0 && t->chunksize() != size) - { - t = t->_child[(sizebits >> (spp_size_t_bitsize - 1)) & 1]; - sizebits <<= 1; - } - if (t != 0) - { - tchunkptr u = t; - do - { - if (u == (tchunkptr)x) - return 1; - } - while ((u = u->_fd) != t); - } - } - } - return 0; -} - -// Traverse each chunk and check it; return total -size_t malloc_state::traverse_and_check() -{ - size_t sum = 0; - if (is_initialized()) - { - msegmentptr s = (msegmentptr)&_seg; - sum += _topsize + top_foot_size(); - while (s != 0) - { - mchunkptr q = align_as_chunk(s->_base); - mchunkptr lastq = 0; - assert(q->pinuse()); - while (segment_holds(s, q) && - q != _top && q->_head != FENCEPOST_HEAD) - { - sum += q->chunksize(); - if (q->is_inuse()) - { - assert(!bin_find(q)); - do_check_inuse_chunk(q); - } - else - { - assert(q == _dv || bin_find(q)); - assert(lastq == 0 || lastq->is_inuse()); // Not 2 consecutive free - do_check_free_chunk(q); - } - lastq = q; - q = (mchunkptr)q->next_chunk(); - } - s = s->_next; - } - } - return sum; -} - - -// Check all properties of malloc_state. -void malloc_state::do_check_malloc_state() -{ - bindex_t i; - size_t total; - // check bins - for (i = 0; i < NSMALLBINS; ++i) - do_check_smallbin(i); - for (i = 0; i < NTREEBINS; ++i) - do_check_treebin(i); - - if (_dvsize != 0) - { - // check dv chunk - do_check_any_chunk(_dv); - assert(_dvsize == _dv->chunksize()); - assert(_dvsize >= MIN_CHUNK_SIZE); - assert(bin_find(_dv) == 0); - } - - if (_top != 0) - { - // check top chunk - do_check_top_chunk(_top); - //assert(topsize == top->chunksize()); redundant - assert(_topsize > 0); - assert(bin_find(_top) == 0); - } - - total = traverse_and_check(); - assert(total <= _footprint); - assert(_footprint <= _max_footprint); -} -#endif // SPP_DEBUG - -/* ----------------------- Operations on smallbins ----------------------- */ - -/* - Various forms of linking and unlinking are defined as macros. Even - the ones for trees, which are very long but have very short typical - paths. This is ugly but reduces reliance on inlining support of - compilers. -*/ - -// Link a free chunk into a smallbin -void malloc_state::insert_small_chunk(mchunkptr p, size_t s) -{ - bindex_t I = small_index(s); - mchunkptr B = smallbin_at(I); - mchunkptr F = B; - assert(s >= MIN_CHUNK_SIZE); - if (!smallmap_is_marked(I)) - mark_smallmap(I); - else if (rtcheck(ok_address(B->_fd))) - F = B->_fd; - else - SPP_ABORT; - B->_fd = p; - F->_bk = p; - p->_fd = F; - p->_bk = B; -} - -// Unlink a chunk from a smallbin -void malloc_state::unlink_small_chunk(mchunkptr p, size_t s) -{ - mchunkptr F = p->_fd; - mchunkptr B = p->_bk; - bindex_t I = small_index(s); - assert(p != B); - assert(p != F); - assert(p->chunksize() == small_index2size(I)); - if (rtcheck(F == smallbin_at(I) || (ok_address(F) && F->_bk == p))) - { - if (B == F) - clear_smallmap(I); - else if (rtcheck(B == smallbin_at(I) || - (ok_address(B) && B->_fd == p))) - { - F->_bk = B; - B->_fd = F; - } - else - SPP_ABORT; - } - else - SPP_ABORT; -} - -// Unlink the first chunk from a smallbin -void malloc_state::unlink_first_small_chunk(mchunkptr B, mchunkptr p, bindex_t I) -{ - mchunkptr F = p->_fd; - assert(p != B); - assert(p != F); - assert(p->chunksize() == small_index2size(I)); - if (B == F) - clear_smallmap(I); - else if (rtcheck(ok_address(F) && F->_bk == p)) - { - F->_bk = B; - B->_fd = F; - } - else - SPP_ABORT; -} - -// Replace dv node, binning the old one -// Used only when dvsize known to be small -void malloc_state::replace_dv(mchunkptr p, size_t s) -{ - size_t DVS = _dvsize; - assert(is_small(DVS)); - if (DVS != 0) - { - mchunkptr DV = _dv; - insert_small_chunk(DV, DVS); - } - _dvsize = s; - _dv = p; -} - -/* ------------------------- Operations on trees ------------------------- */ - -// Insert chunk into tree -void malloc_state::insert_large_chunk(tchunkptr X, size_t s) -{ - tbinptr* H; - bindex_t I = compute_tree_index(s); - H = treebin_at(I); - X->_index = I; - X->_child[0] = X->_child[1] = 0; - if (!treemap_is_marked(I)) - { - mark_treemap(I); - *H = X; - X->_parent = (tchunkptr)H; - X->_fd = X->_bk = X; - } - else - { - tchunkptr T = *H; - size_t K = s << leftshift_for_tree_index(I); - for (;;) - { - if (T->chunksize() != s) - { - tchunkptr* C = &(T->_child[(K >> (spp_size_t_bitsize - 1)) & 1]); - K <<= 1; - if (*C != 0) - T = *C; - else if (rtcheck(ok_address(C))) - { - *C = X; - X->_parent = T; - X->_fd = X->_bk = X; - break; - } - else - { - SPP_ABORT; - break; - } - } - else - { - tchunkptr F = T->_fd; - if (rtcheck(ok_address(T) && ok_address(F))) - { - T->_fd = F->_bk = X; - X->_fd = F; - X->_bk = T; - X->_parent = 0; - break; - } - else - { - SPP_ABORT; - break; - } - } - } - } -} - -/* - Unlink steps: - - 1. If x is a chained node, unlink it from its same-sized fd/bk links - and choose its bk node as its replacement. - 2. If x was the last node of its size, but not a leaf node, it must - be replaced with a leaf node (not merely one with an open left or - right), to make sure that lefts and rights of descendents - correspond properly to bit masks. We use the rightmost descendent - of x. We could use any other leaf, but this is easy to locate and - tends to counteract removal of leftmosts elsewhere, and so keeps - paths shorter than minimally guaranteed. This doesn't loop much - because on average a node in a tree is near the bottom. - 3. If x is the base of a chain (i.e., has parent links) relink - x's parent and children to x's replacement (or null if none). -*/ - -void malloc_state::unlink_large_chunk(tchunkptr X) -{ - tchunkptr XP = X->_parent; - tchunkptr R; - if (X->_bk != X) - { - tchunkptr F = X->_fd; - R = X->_bk; - if (rtcheck(ok_address(F) && F->_bk == X && R->_fd == X)) - { - F->_bk = R; - R->_fd = F; - } - else - SPP_ABORT; - } - else - { - tchunkptr* RP; - if (((R = *(RP = &(X->_child[1]))) != 0) || - ((R = *(RP = &(X->_child[0]))) != 0)) - { - tchunkptr* CP; - while ((*(CP = &(R->_child[1])) != 0) || - (*(CP = &(R->_child[0])) != 0)) - R = *(RP = CP); - if (rtcheck(ok_address(RP))) - *RP = 0; - else - SPP_ABORT; - } - } - if (XP != 0) - { - tbinptr* H = treebin_at(X->_index); - if (X == *H) - { - if ((*H = R) == 0) - clear_treemap(X->_index); - } - else if (rtcheck(ok_address(XP))) - { - if (XP->_child[0] == X) - XP->_child[0] = R; - else - XP->_child[1] = R; - } - else - SPP_ABORT; - if (R != 0) - { - if (rtcheck(ok_address(R))) - { - tchunkptr C0, C1; - R->_parent = XP; - if ((C0 = X->_child[0]) != 0) - { - if (rtcheck(ok_address(C0))) - { - R->_child[0] = C0; - C0->_parent = R; - } - else - SPP_ABORT; - } - if ((C1 = X->_child[1]) != 0) - { - if (rtcheck(ok_address(C1))) - { - R->_child[1] = C1; - C1->_parent = R; - } - else - SPP_ABORT; - } - } - else - SPP_ABORT; - } - } -} - -// Relays to large vs small bin operations - -void malloc_state::insert_chunk(mchunkptr p, size_t s) -{ - if (is_small(s)) - insert_small_chunk(p, s); - else - { - tchunkptr tp = (tchunkptr)(p); - insert_large_chunk(tp, s); - } -} - -void malloc_state::unlink_chunk(mchunkptr p, size_t s) -{ - if (is_small(s)) - unlink_small_chunk(p, s); - else - { - tchunkptr tp = (tchunkptr)(p); - unlink_large_chunk(tp); - } -} - - -/* ----------------------- Direct-mmapping chunks ----------------------- */ - -/* - Directly mmapped chunks are set up with an offset to the start of - the mmapped region stored in the prev_foot field of the chunk. This - allows reconstruction of the required argument to MUNMAP when freed, - and also allows adjustment of the returned chunk to meet alignment - requirements (especially in memalign). -*/ - -// Malloc using mmap -void* malloc_state::mmap_alloc(size_t nb) -{ - size_t mmsize = mmap_align(nb + 6 * sizeof(size_t) + spp_chunk_align_mask); - if (_footprint_limit != 0) - { - size_t fp = _footprint + mmsize; - if (fp <= _footprint || fp > _footprint_limit) - return 0; - } - if (mmsize > nb) - { - // Check for wrap around 0 - char* mm = (char*)(SPP_CALL_DIRECT_MMAP(mmsize)); - if (mm != cmfail) - { - size_t offset = align_offset(chunk2mem(mm)); - size_t psize = mmsize - offset - SPP_MMAP_FOOT_PAD; - mchunkptr p = (mchunkptr)(mm + offset); - p->_prev_foot = offset; - p->_head = psize; - mark_inuse_foot(p, psize); - p->chunk_plus_offset(psize)->_head = FENCEPOST_HEAD; - p->chunk_plus_offset(psize + sizeof(size_t))->_head = 0; - - if (_least_addr == 0 || mm < _least_addr) - _least_addr = mm; - if ((_footprint += mmsize) > _max_footprint) - _max_footprint = _footprint; - assert(spp_is_aligned(chunk2mem(p))); - check_mmapped_chunk(p); - return chunk2mem(p); - } - } - return 0; -} - -// Realloc using mmap -mchunkptr malloc_state::mmap_resize(mchunkptr oldp, size_t nb, int flags) -{ - size_t oldsize = oldp->chunksize(); - (void)flags; // placate people compiling -Wunused - if (is_small(nb)) // Can't shrink mmap regions below small size - return 0; - - // Keep old chunk if big enough but not too big - if (oldsize >= nb + sizeof(size_t) && - (oldsize - nb) <= (mparams._granularity << 1)) - return oldp; - else - { - size_t offset = oldp->_prev_foot; - size_t oldmmsize = oldsize + offset + SPP_MMAP_FOOT_PAD; - size_t newmmsize = mmap_align(nb + 6 * sizeof(size_t) + spp_chunk_align_mask); - char* cp = (char*)SPP_CALL_MREMAP((char*)oldp - offset, - oldmmsize, newmmsize, flags); - if (cp != cmfail) - { - mchunkptr newp = (mchunkptr)(cp + offset); - size_t psize = newmmsize - offset - SPP_MMAP_FOOT_PAD; - newp->_head = psize; - mark_inuse_foot(newp, psize); - newp->chunk_plus_offset(psize)->_head = FENCEPOST_HEAD; - newp->chunk_plus_offset(psize + sizeof(size_t))->_head = 0; - - if (cp < _least_addr) - _least_addr = cp; - if ((_footprint += newmmsize - oldmmsize) > _max_footprint) - _max_footprint = _footprint; - check_mmapped_chunk(newp); - return newp; - } - } - return 0; -} - - -/* -------------------------- mspace management -------------------------- */ - -// Initialize top chunk and its size -void malloc_state::init_top(mchunkptr p, size_t psize) -{ - // Ensure alignment - size_t offset = align_offset(chunk2mem(p)); - p = (mchunkptr)((char*)p + offset); - psize -= offset; - - _top = p; - _topsize = psize; - p->_head = psize | PINUSE_BIT; - // set size of fake trailing chunk holding overhead space only once - p->chunk_plus_offset(psize)->_head = top_foot_size(); - _trim_check = mparams._trim_threshold; // reset on each update -} - -// Initialize bins for a new mstate that is otherwise zeroed out -void malloc_state::init_bins() -{ - // Establish circular links for smallbins - bindex_t i; - for (i = 0; i < NSMALLBINS; ++i) - { - sbinptr bin = smallbin_at(i); - bin->_fd = bin->_bk = bin; - } -} - -#if SPP_PROCEED_ON_ERROR - -// default corruption action -void malloc_state::reset_on_error() -{ - int i; - ++malloc_corruption_error_count; - // Reinitialize fields to forget about all memory - _smallmap = _treemap = 0; - _dvsize = _topsize = 0; - _seg._base = 0; - _seg._size = 0; - _seg._next = 0; - _top = _dv = 0; - for (i = 0; i < NTREEBINS; ++i) - *treebin_at(i) = 0; - init_bins(); -} -#endif - -/* Allocate chunk and prepend remainder with chunk in successor base. */ -void* malloc_state::prepend_alloc(char* newbase, char* oldbase, size_t nb) -{ - mchunkptr p = align_as_chunk(newbase); - mchunkptr oldfirst = align_as_chunk(oldbase); - size_t psize = (char*)oldfirst - (char*)p; - mchunkptr q = (mchunkptr)p->chunk_plus_offset(nb); - size_t qsize = psize - nb; - set_size_and_pinuse_of_inuse_chunk(p, nb); - - assert((char*)oldfirst > (char*)q); - assert(oldfirst->pinuse()); - assert(qsize >= MIN_CHUNK_SIZE); - - // consolidate remainder with first chunk of old base - if (oldfirst == _top) - { - size_t tsize = _topsize += qsize; - _top = q; - q->_head = tsize | PINUSE_BIT; - check_top_chunk(q); - } - else if (oldfirst == _dv) - { - size_t dsize = _dvsize += qsize; - _dv = q; - q->set_size_and_pinuse_of_free_chunk(dsize); - } - else - { - if (!oldfirst->is_inuse()) - { - size_t nsize = oldfirst->chunksize(); - unlink_chunk(oldfirst, nsize); - oldfirst = (mchunkptr)oldfirst->chunk_plus_offset(nsize); - qsize += nsize; - } - q->set_free_with_pinuse(qsize, oldfirst); - insert_chunk(q, qsize); - check_free_chunk(q); - } - - check_malloced_chunk(chunk2mem(p), nb); - return chunk2mem(p); -} - -// Add a segment to hold a new noncontiguous region -void malloc_state::add_segment(char* tbase, size_t tsize, flag_t mmapped) -{ - // Determine locations and sizes of segment, fenceposts, old top - char* old_top = (char*)_top; - msegmentptr oldsp = segment_holding(old_top); - char* old_end = oldsp->_base + oldsp->_size; - size_t ssize = pad_request(sizeof(struct malloc_segment)); - char* rawsp = old_end - (ssize + 4 * sizeof(size_t) + spp_chunk_align_mask); - size_t offset = align_offset(chunk2mem(rawsp)); - char* asp = rawsp + offset; - char* csp = (asp < (old_top + MIN_CHUNK_SIZE)) ? old_top : asp; - mchunkptr sp = (mchunkptr)csp; - msegmentptr ss = (msegmentptr)(chunk2mem(sp)); - mchunkptr tnext = (mchunkptr)sp->chunk_plus_offset(ssize); - mchunkptr p = tnext; - int nfences = 0; - - // reset top to new space - init_top((mchunkptr)tbase, tsize - top_foot_size()); - - // Set up segment record - assert(spp_is_aligned(ss)); - set_size_and_pinuse_of_inuse_chunk(sp, ssize); - *ss = _seg; // Push current record - _seg._base = tbase; - _seg._size = tsize; - _seg._sflags = mmapped; - _seg._next = ss; - - // Insert trailing fenceposts - for (;;) - { - mchunkptr nextp = (mchunkptr)p->chunk_plus_offset(sizeof(size_t)); - p->_head = FENCEPOST_HEAD; - ++nfences; - if ((char*)(&(nextp->_head)) < old_end) - p = nextp; - else - break; - } - assert(nfences >= 2); - - // Insert the rest of old top into a bin as an ordinary free chunk - if (csp != old_top) - { - mchunkptr q = (mchunkptr)old_top; - size_t psize = csp - old_top; - mchunkptr tn = (mchunkptr)q->chunk_plus_offset(psize); - q->set_free_with_pinuse(psize, tn); - insert_chunk(q, psize); - } - - check_top_chunk(_top); -} - -/* -------------------------- System allocation -------------------------- */ - -// Get memory from system using MMAP -void* malloc_state::sys_alloc(size_t nb) -{ - char* tbase = cmfail; - size_t tsize = 0; - flag_t mmap_flag = 0; - size_t asize; // allocation size - - mparams.ensure_initialization(); - - // Directly map large chunks, but only if already initialized - if (use_mmap() && nb >= mparams._mmap_threshold && _topsize != 0) - { - void* mem = mmap_alloc(nb); - if (mem != 0) - return mem; - } - - asize = mparams.granularity_align(nb + sys_alloc_padding()); - if (asize <= nb) - return 0; // wraparound - if (_footprint_limit != 0) - { - size_t fp = _footprint + asize; - if (fp <= _footprint || fp > _footprint_limit) - return 0; - } - - /* - Try getting memory with a call to MMAP new space (disabled if not SPP_HAVE_MMAP). - We need to request enough bytes from system to ensure - we can malloc nb bytes upon success, so pad with enough space for - top_foot, plus alignment-pad to make sure we don't lose bytes if - not on boundary, and round this up to a granularity unit. - */ - - if (SPP_HAVE_MMAP && tbase == cmfail) - { - // Try MMAP - char* mp = (char*)(SPP_CALL_MMAP(asize)); - if (mp != cmfail) - { - tbase = mp; - tsize = asize; - mmap_flag = USE_MMAP_BIT; - } - } - - if (tbase != cmfail) - { - - if ((_footprint += tsize) > _max_footprint) - _max_footprint = _footprint; - - if (!is_initialized()) - { - // first-time initialization - if (_least_addr == 0 || tbase < _least_addr) - _least_addr = tbase; - _seg._base = tbase; - _seg._size = tsize; - _seg._sflags = mmap_flag; - _magic = mparams._magic; - _release_checks = SPP_MAX_RELEASE_CHECK_RATE; - init_bins(); - - // Offset top by embedded malloc_state - mchunkptr mn = (mchunkptr)mem2chunk(this)->next_chunk(); - init_top(mn, (size_t)((tbase + tsize) - (char*)mn) - top_foot_size()); - } - - else - { - // Try to merge with an existing segment - msegmentptr sp = &_seg; - // Only consider most recent segment if traversal suppressed - while (sp != 0 && tbase != sp->_base + sp->_size) - sp = (SPP_NO_SEGMENT_TRAVERSAL) ? 0 : sp->_next; - if (sp != 0 && - !sp->is_extern_segment() && - (sp->_sflags & USE_MMAP_BIT) == mmap_flag && - segment_holds(sp, _top)) - { - // append - sp->_size += tsize; - init_top(_top, _topsize + tsize); - } - else - { - if (tbase < _least_addr) - _least_addr = tbase; - sp = &_seg; - while (sp != 0 && sp->_base != tbase + tsize) - sp = (SPP_NO_SEGMENT_TRAVERSAL) ? 0 : sp->_next; - if (sp != 0 && - !sp->is_extern_segment() && - (sp->_sflags & USE_MMAP_BIT) == mmap_flag) - { - char* oldbase = sp->_base; - sp->_base = tbase; - sp->_size += tsize; - return prepend_alloc(tbase, oldbase, nb); - } - else - add_segment(tbase, tsize, mmap_flag); - } - } - - if (nb < _topsize) - { - // Allocate from new or extended top space - size_t rsize = _topsize -= nb; - mchunkptr p = _top; - mchunkptr r = _top = (mchunkptr)p->chunk_plus_offset(nb); - r->_head = rsize | PINUSE_BIT; - set_size_and_pinuse_of_inuse_chunk(p, nb); - check_top_chunk(_top); - check_malloced_chunk(chunk2mem(p), nb); - return chunk2mem(p); - } - } - - SPP_MALLOC_FAILURE_ACTION; - return 0; -} - -/* ----------------------- system deallocation -------------------------- */ - -// Unmap and unlink any mmapped segments that don't contain used chunks -size_t malloc_state::release_unused_segments() -{ - size_t released = 0; - int nsegs = 0; - msegmentptr pred = &_seg; - msegmentptr sp = pred->_next; - while (sp != 0) - { - char* base = sp->_base; - size_t size = sp->_size; - msegmentptr next = sp->_next; - ++nsegs; - if (sp->is_mmapped_segment() && !sp->is_extern_segment()) - { - mchunkptr p = align_as_chunk(base); - size_t psize = p->chunksize(); - // Can unmap if first chunk holds entire segment and not pinned - if (!p->is_inuse() && (char*)p + psize >= base + size - top_foot_size()) - { - tchunkptr tp = (tchunkptr)p; - assert(segment_holds(sp, p)); - if (p == _dv) - { - _dv = 0; - _dvsize = 0; - } - else - unlink_large_chunk(tp); - if (SPP_CALL_MUNMAP(base, size) == 0) - { - released += size; - _footprint -= size; - // unlink obsoleted record - sp = pred; - sp->_next = next; - } - else - { - // back out if cannot unmap - insert_large_chunk(tp, psize); - } - } - } - if (SPP_NO_SEGMENT_TRAVERSAL) // scan only first segment - break; - pred = sp; - sp = next; - } - // Reset check counter - _release_checks = (((size_t) nsegs > (size_t) SPP_MAX_RELEASE_CHECK_RATE) ? - (size_t) nsegs : (size_t) SPP_MAX_RELEASE_CHECK_RATE); - return released; -} - -int malloc_state::sys_trim(size_t pad) -{ - size_t released = 0; - mparams.ensure_initialization(); - if (pad < MAX_REQUEST && is_initialized()) - { - pad += top_foot_size(); // ensure enough room for segment overhead - - if (_topsize > pad) - { - // Shrink top space in _granularity - size units, keeping at least one - size_t unit = mparams._granularity; - size_t extra = ((_topsize - pad + (unit - 1)) / unit - - 1) * unit; - msegmentptr sp = segment_holding((char*)_top); - - if (!sp->is_extern_segment()) - { - if (sp->is_mmapped_segment()) - { - if (SPP_HAVE_MMAP && - sp->_size >= extra && - !has_segment_link(sp)) - { - // can't shrink if pinned - size_t newsize = sp->_size - extra; - (void)newsize; // placate people compiling -Wunused-variable - // Prefer mremap, fall back to munmap - if ((SPP_CALL_MREMAP(sp->_base, sp->_size, newsize, 0) != mfail) || - (SPP_CALL_MUNMAP(sp->_base + newsize, extra) == 0)) - released = extra; - } - } - } - - if (released != 0) - { - sp->_size -= released; - _footprint -= released; - init_top(_top, _topsize - released); - check_top_chunk(_top); - } - } - - // Unmap any unused mmapped segments - if (SPP_HAVE_MMAP) - released += release_unused_segments(); - - // On failure, disable autotrim to avoid repeated failed future calls - if (released == 0 && _topsize > _trim_check) - _trim_check = spp_max_size_t; - } - - return (released != 0) ? 1 : 0; -} - -/* Consolidate and bin a chunk. Differs from exported versions - of free mainly in that the chunk need not be marked as inuse. -*/ -void malloc_state::dispose_chunk(mchunkptr p, size_t psize) -{ - mchunkptr next = (mchunkptr)p->chunk_plus_offset(psize); - if (!p->pinuse()) - { - mchunkptr prev; - size_t prevsize = p->_prev_foot; - if (p->is_mmapped()) - { - psize += prevsize + SPP_MMAP_FOOT_PAD; - if (SPP_CALL_MUNMAP((char*)p - prevsize, psize) == 0) - _footprint -= psize; - return; - } - prev = (mchunkptr)p->chunk_minus_offset(prevsize); - psize += prevsize; - p = prev; - if (rtcheck(ok_address(prev))) - { - // consolidate backward - if (p != _dv) - unlink_chunk(p, prevsize); - else if ((next->_head & INUSE_BITS) == INUSE_BITS) - { - _dvsize = psize; - p->set_free_with_pinuse(psize, next); - return; - } - } - else - { - SPP_ABORT; - return; - } - } - if (rtcheck(ok_address(next))) - { - if (!next->cinuse()) - { - // consolidate forward - if (next == _top) - { - size_t tsize = _topsize += psize; - _top = p; - p->_head = tsize | PINUSE_BIT; - if (p == _dv) - { - _dv = 0; - _dvsize = 0; - } - return; - } - else if (next == _dv) - { - size_t dsize = _dvsize += psize; - _dv = p; - p->set_size_and_pinuse_of_free_chunk(dsize); - return; - } - else - { - size_t nsize = next->chunksize(); - psize += nsize; - unlink_chunk(next, nsize); - p->set_size_and_pinuse_of_free_chunk(psize); - if (p == _dv) - { - _dvsize = psize; - return; - } - } - } - else - p->set_free_with_pinuse(psize, next); - insert_chunk(p, psize); - } - else - SPP_ABORT; -} - -/* ---------------------------- malloc --------------------------- */ - -// allocate a large request from the best fitting chunk in a treebin -void* malloc_state::tmalloc_large(size_t nb) -{ - tchunkptr v = 0; - size_t rsize = -nb; // Unsigned negation - tchunkptr t; - bindex_t idx = compute_tree_index(nb); - if ((t = *treebin_at(idx)) != 0) - { - // Traverse tree for this bin looking for node with size == nb - size_t sizebits = nb << leftshift_for_tree_index(idx); - tchunkptr rst = 0; // The deepest untaken right subtree - for (;;) - { - tchunkptr rt; - size_t trem = t->chunksize() - nb; - if (trem < rsize) - { - v = t; - if ((rsize = trem) == 0) - break; - } - rt = t->_child[1]; - t = t->_child[(sizebits >> (spp_size_t_bitsize - 1)) & 1]; - if (rt != 0 && rt != t) - rst = rt; - if (t == 0) - { - t = rst; // set t to least subtree holding sizes > nb - break; - } - sizebits <<= 1; - } - } - if (t == 0 && v == 0) - { - // set t to root of next non-empty treebin - binmap_t leftbits = left_bits(idx2bit(idx)) & _treemap; - if (leftbits != 0) - { - binmap_t leastbit = least_bit(leftbits); - bindex_t i = compute_bit2idx(leastbit); - t = *treebin_at(i); - } - } - - while (t != 0) - { - // find smallest of tree or subtree - size_t trem = t->chunksize() - nb; - if (trem < rsize) - { - rsize = trem; - v = t; - } - t = t->leftmost_child(); - } - - // If dv is a better fit, return 0 so malloc will use it - if (v != 0 && rsize < (size_t)(_dvsize - nb)) - { - if (rtcheck(ok_address(v))) - { - // split - mchunkptr r = (mchunkptr)v->chunk_plus_offset(nb); - assert(v->chunksize() == rsize + nb); - if (rtcheck(ok_next(v, r))) - { - unlink_large_chunk(v); - if (rsize < MIN_CHUNK_SIZE) - set_inuse_and_pinuse(v, (rsize + nb)); - else - { - set_size_and_pinuse_of_inuse_chunk(v, nb); - r->set_size_and_pinuse_of_free_chunk(rsize); - insert_chunk(r, rsize); - } - return chunk2mem(v); - } - } - SPP_ABORT; - } - return 0; -} - -// allocate a small request from the best fitting chunk in a treebin -void* malloc_state::tmalloc_small(size_t nb) -{ - tchunkptr t, v; - size_t rsize; - binmap_t leastbit = least_bit(_treemap); - bindex_t i = compute_bit2idx(leastbit); - v = t = *treebin_at(i); - rsize = t->chunksize() - nb; - - while ((t = t->leftmost_child()) != 0) - { - size_t trem = t->chunksize() - nb; - if (trem < rsize) - { - rsize = trem; - v = t; - } - } - - if (rtcheck(ok_address(v))) - { - mchunkptr r = (mchunkptr)v->chunk_plus_offset(nb); - assert(v->chunksize() == rsize + nb); - if (rtcheck(ok_next(v, r))) - { - unlink_large_chunk(v); - if (rsize < MIN_CHUNK_SIZE) - set_inuse_and_pinuse(v, (rsize + nb)); - else - { - set_size_and_pinuse_of_inuse_chunk(v, nb); - r->set_size_and_pinuse_of_free_chunk(rsize); - replace_dv(r, rsize); - } - return chunk2mem(v); - } - } - - SPP_ABORT; - return 0; -} - -/* ---------------------------- malloc --------------------------- */ - -void* malloc_state::_malloc(size_t bytes) -{ - if (1) - { - void* mem; - size_t nb; - if (bytes <= MAX_SMALL_REQUEST) - { - bindex_t idx; - binmap_t smallbits; - nb = (bytes < MIN_REQUEST) ? MIN_CHUNK_SIZE : pad_request(bytes); - idx = small_index(nb); - smallbits = _smallmap >> idx; - - if ((smallbits & 0x3U) != 0) - { - // Remainderless fit to a smallbin. - mchunkptr b, p; - idx += ~smallbits & 1; // Uses next bin if idx empty - b = smallbin_at(idx); - p = b->_fd; - assert(p->chunksize() == small_index2size(idx)); - unlink_first_small_chunk(b, p, idx); - set_inuse_and_pinuse(p, small_index2size(idx)); - mem = chunk2mem(p); - check_malloced_chunk(mem, nb); - goto postaction; - } - - else if (nb > _dvsize) - { - if (smallbits != 0) - { - // Use chunk in next nonempty smallbin - mchunkptr b, p, r; - size_t rsize; - binmap_t leftbits = (smallbits << idx) & left_bits(malloc_state::idx2bit(idx)); - binmap_t leastbit = least_bit(leftbits); - bindex_t i = compute_bit2idx(leastbit); - b = smallbin_at(i); - p = b->_fd; - assert(p->chunksize() == small_index2size(i)); - unlink_first_small_chunk(b, p, i); - rsize = small_index2size(i) - nb; - // Fit here cannot be remainderless if 4byte sizes - if (sizeof(size_t) != 4 && rsize < MIN_CHUNK_SIZE) - set_inuse_and_pinuse(p, small_index2size(i)); - else - { - set_size_and_pinuse_of_inuse_chunk(p, nb); - r = (mchunkptr)p->chunk_plus_offset(nb); - r->set_size_and_pinuse_of_free_chunk(rsize); - replace_dv(r, rsize); - } - mem = chunk2mem(p); - check_malloced_chunk(mem, nb); - goto postaction; - } - - else if (_treemap != 0 && (mem = tmalloc_small(nb)) != 0) - { - check_malloced_chunk(mem, nb); - goto postaction; - } - } - } - else if (bytes >= MAX_REQUEST) - nb = spp_max_size_t; // Too big to allocate. Force failure (in sys alloc) - else - { - nb = pad_request(bytes); - if (_treemap != 0 && (mem = tmalloc_large(nb)) != 0) - { - check_malloced_chunk(mem, nb); - goto postaction; - } - } - - if (nb <= _dvsize) - { - size_t rsize = _dvsize - nb; - mchunkptr p = _dv; - if (rsize >= MIN_CHUNK_SIZE) - { - // split dv - mchunkptr r = _dv = (mchunkptr)p->chunk_plus_offset(nb); - _dvsize = rsize; - r->set_size_and_pinuse_of_free_chunk(rsize); - set_size_and_pinuse_of_inuse_chunk(p, nb); - } - else // exhaust dv - { - size_t dvs = _dvsize; - _dvsize = 0; - _dv = 0; - set_inuse_and_pinuse(p, dvs); - } - mem = chunk2mem(p); - check_malloced_chunk(mem, nb); - goto postaction; - } - - else if (nb < _topsize) - { - // Split top - size_t rsize = _topsize -= nb; - mchunkptr p = _top; - mchunkptr r = _top = (mchunkptr)p->chunk_plus_offset(nb); - r->_head = rsize | PINUSE_BIT; - set_size_and_pinuse_of_inuse_chunk(p, nb); - mem = chunk2mem(p); - check_top_chunk(_top); - check_malloced_chunk(mem, nb); - goto postaction; - } - - mem = sys_alloc(nb); - -postaction: - return mem; - } - - return 0; -} - -/* ---------------------------- free --------------------------- */ - -void malloc_state::_free(mchunkptr p) -{ - if (1) - { - check_inuse_chunk(p); - if (rtcheck(ok_address(p) && ok_inuse(p))) - { - size_t psize = p->chunksize(); - mchunkptr next = (mchunkptr)p->chunk_plus_offset(psize); - if (!p->pinuse()) - { - size_t prevsize = p->_prev_foot; - if (p->is_mmapped()) - { - psize += prevsize + SPP_MMAP_FOOT_PAD; - if (SPP_CALL_MUNMAP((char*)p - prevsize, psize) == 0) - _footprint -= psize; - goto postaction; - } - else - { - mchunkptr prev = (mchunkptr)p->chunk_minus_offset(prevsize); - psize += prevsize; - p = prev; - if (rtcheck(ok_address(prev))) - { - // consolidate backward - if (p != _dv) - unlink_chunk(p, prevsize); - else if ((next->_head & INUSE_BITS) == INUSE_BITS) - { - _dvsize = psize; - p->set_free_with_pinuse(psize, next); - goto postaction; - } - } - else - goto erroraction; - } - } - - if (rtcheck(ok_next(p, next) && ok_pinuse(next))) - { - if (!next->cinuse()) - { - // consolidate forward - if (next == _top) - { - size_t tsize = _topsize += psize; - _top = p; - p->_head = tsize | PINUSE_BIT; - if (p == _dv) - { - _dv = 0; - _dvsize = 0; - } - if (should_trim(tsize)) - sys_trim(0); - goto postaction; - } - else if (next == _dv) - { - size_t dsize = _dvsize += psize; - _dv = p; - p->set_size_and_pinuse_of_free_chunk(dsize); - goto postaction; - } - else - { - size_t nsize = next->chunksize(); - psize += nsize; - unlink_chunk(next, nsize); - p->set_size_and_pinuse_of_free_chunk(psize); - if (p == _dv) - { - _dvsize = psize; - goto postaction; - } - } - } - else - p->set_free_with_pinuse(psize, next); - - if (is_small(psize)) - { - insert_small_chunk(p, psize); - check_free_chunk(p); - } - else - { - tchunkptr tp = (tchunkptr)p; - insert_large_chunk(tp, psize); - check_free_chunk(p); - if (--_release_checks == 0) - release_unused_segments(); - } - goto postaction; - } - } -erroraction: - SPP_USAGE_ERROR_ACTION(this, p); -postaction: - ; - } -} - -/* ------------ Internal support for realloc, memalign, etc -------------- */ - -// Try to realloc; only in-place unless can_move true -mchunkptr malloc_state::try_realloc_chunk(mchunkptr p, size_t nb, int can_move) -{ - mchunkptr newp = 0; - size_t oldsize = p->chunksize(); - mchunkptr next = (mchunkptr)p->chunk_plus_offset(oldsize); - if (rtcheck(ok_address(p) && ok_inuse(p) && - ok_next(p, next) && ok_pinuse(next))) - { - if (p->is_mmapped()) - newp = mmap_resize(p, nb, can_move); - else if (oldsize >= nb) - { - // already big enough - size_t rsize = oldsize - nb; - if (rsize >= MIN_CHUNK_SIZE) - { - // split off remainder - mchunkptr r = (mchunkptr)p->chunk_plus_offset(nb); - set_inuse(p, nb); - set_inuse(r, rsize); - dispose_chunk(r, rsize); - } - newp = p; - } - else if (next == _top) - { - // extend into top - if (oldsize + _topsize > nb) - { - size_t newsize = oldsize + _topsize; - size_t newtopsize = newsize - nb; - mchunkptr newtop = (mchunkptr)p->chunk_plus_offset(nb); - set_inuse(p, nb); - newtop->_head = newtopsize | PINUSE_BIT; - _top = newtop; - _topsize = newtopsize; - newp = p; - } - } - else if (next == _dv) - { - // extend into dv - size_t dvs = _dvsize; - if (oldsize + dvs >= nb) - { - size_t dsize = oldsize + dvs - nb; - if (dsize >= MIN_CHUNK_SIZE) - { - mchunkptr r = (mchunkptr)p->chunk_plus_offset(nb); - mchunkptr n = (mchunkptr)r->chunk_plus_offset(dsize); - set_inuse(p, nb); - r->set_size_and_pinuse_of_free_chunk(dsize); - n->clear_pinuse(); - _dvsize = dsize; - _dv = r; - } - else - { - // exhaust dv - size_t newsize = oldsize + dvs; - set_inuse(p, newsize); - _dvsize = 0; - _dv = 0; - } - newp = p; - } - } - else if (!next->cinuse()) - { - // extend into next free chunk - size_t nextsize = next->chunksize(); - if (oldsize + nextsize >= nb) - { - size_t rsize = oldsize + nextsize - nb; - unlink_chunk(next, nextsize); - if (rsize < MIN_CHUNK_SIZE) - { - size_t newsize = oldsize + nextsize; - set_inuse(p, newsize); - } - else - { - mchunkptr r = (mchunkptr)p->chunk_plus_offset(nb); - set_inuse(p, nb); - set_inuse(r, rsize); - dispose_chunk(r, rsize); - } - newp = p; - } - } - } - else - SPP_USAGE_ERROR_ACTION(m, chunk2mem(p)); - return newp; -} - -void* malloc_state::internal_memalign(size_t alignment, size_t bytes) -{ - void* mem = 0; - if (alignment < MIN_CHUNK_SIZE) // must be at least a minimum chunk size - alignment = MIN_CHUNK_SIZE; - if ((alignment & (alignment - 1)) != 0) - { - // Ensure a power of 2 - size_t a = SPP_MALLOC_ALIGNMENT << 1; - while (a < alignment) - a <<= 1; - alignment = a; - } - if (bytes >= MAX_REQUEST - alignment) - SPP_MALLOC_FAILURE_ACTION; - else - { - size_t nb = request2size(bytes); - size_t req = nb + alignment + MIN_CHUNK_SIZE - CHUNK_OVERHEAD; - mem = internal_malloc(req); - if (mem != 0) - { - mchunkptr p = mem2chunk(mem); - if ((((size_t)(mem)) & (alignment - 1)) != 0) - { - // misaligned - /* - Find an aligned spot inside chunk. Since we need to give - back leading space in a chunk of at least MIN_CHUNK_SIZE, if - the first calculation places us at a spot with less than - MIN_CHUNK_SIZE leader, we can move to the next aligned spot. - We've allocated enough total room so that this is always - possible. - */ - char* br = (char*)mem2chunk((void *)(((size_t)((char*)mem + alignment - 1)) & - -alignment)); - char* pos = ((size_t)(br - (char*)(p)) >= MIN_CHUNK_SIZE) ? - br : br + alignment; - mchunkptr newp = (mchunkptr)pos; - size_t leadsize = pos - (char*)(p); - size_t newsize = p->chunksize() - leadsize; - - if (p->is_mmapped()) - { - // For mmapped chunks, just adjust offset - newp->_prev_foot = p->_prev_foot + leadsize; - newp->_head = newsize; - } - else - { - // Otherwise, give back leader, use the rest - set_inuse(newp, newsize); - set_inuse(p, leadsize); - dispose_chunk(p, leadsize); - } - p = newp; - } - - // Give back spare room at the end - if (!p->is_mmapped()) - { - size_t size = p->chunksize(); - if (size > nb + MIN_CHUNK_SIZE) - { - size_t remainder_size = size - nb; - mchunkptr remainder = (mchunkptr)p->chunk_plus_offset(nb); - set_inuse(p, nb); - set_inuse(remainder, remainder_size); - dispose_chunk(remainder, remainder_size); - } - } - - mem = chunk2mem(p); - assert(p->chunksize() >= nb); - assert(((size_t)mem & (alignment - 1)) == 0); - check_inuse_chunk(p); - } - } - return mem; -} - -/* - Common support for independent_X routines, handling - all of the combinations that can result. - The opts arg has: - bit 0 set if all elements are same size (using sizes[0]) - bit 1 set if elements should be zeroed -*/ -void** malloc_state::ialloc(size_t n_elements, size_t* sizes, int opts, - void* chunks[]) -{ - - size_t element_size; // chunksize of each element, if all same - size_t contents_size; // total size of elements - size_t array_size; // request size of pointer array - void* mem; // malloced aggregate space - mchunkptr p; // corresponding chunk - size_t remainder_size; // remaining bytes while splitting - void** marray; // either "chunks" or malloced ptr array - mchunkptr array_chunk; // chunk for malloced ptr array - flag_t was_enabled; // to disable mmap - size_t size; - size_t i; - - mparams.ensure_initialization(); - // compute array length, if needed - if (chunks != 0) - { - if (n_elements == 0) - return chunks; // nothing to do - marray = chunks; - array_size = 0; - } - else - { - // if empty req, must still return chunk representing empty array - if (n_elements == 0) - return (void**)internal_malloc(0); - marray = 0; - array_size = request2size(n_elements * (sizeof(void*))); - } - - // compute total element size - if (opts & 0x1) - { - // all-same-size - element_size = request2size(*sizes); - contents_size = n_elements * element_size; - } - else - { - // add up all the sizes - element_size = 0; - contents_size = 0; - for (i = 0; i != n_elements; ++i) - contents_size += request2size(sizes[i]); - } - - size = contents_size + array_size; - - /* - Allocate the aggregate chunk. First disable direct-mmapping so - malloc won't use it, since we would not be able to later - free/realloc space internal to a segregated mmap region. - */ - was_enabled = use_mmap(); - disable_mmap(); - mem = internal_malloc(size - CHUNK_OVERHEAD); - if (was_enabled) - enable_mmap(); - if (mem == 0) - return 0; - - p = mem2chunk(mem); - remainder_size = p->chunksize(); - - assert(!p->is_mmapped()); - - if (opts & 0x2) - { - // optionally clear the elements - memset((size_t*)mem, 0, remainder_size - sizeof(size_t) - array_size); - } - - // If not provided, allocate the pointer array as final part of chunk - if (marray == 0) - { - size_t array_chunk_size; - array_chunk = (mchunkptr)p->chunk_plus_offset(contents_size); - array_chunk_size = remainder_size - contents_size; - marray = (void**)(chunk2mem(array_chunk)); - set_size_and_pinuse_of_inuse_chunk(array_chunk, array_chunk_size); - remainder_size = contents_size; - } - - // split out elements - for (i = 0; ; ++i) - { - marray[i] = chunk2mem(p); - if (i != n_elements - 1) - { - if (element_size != 0) - size = element_size; - else - size = request2size(sizes[i]); - remainder_size -= size; - set_size_and_pinuse_of_inuse_chunk(p, size); - p = (mchunkptr)p->chunk_plus_offset(size); - } - else - { - // the final element absorbs any overallocation slop - set_size_and_pinuse_of_inuse_chunk(p, remainder_size); - break; - } - } - -#if SPP_DEBUG - if (marray != chunks) - { - // final element must have exactly exhausted chunk - if (element_size != 0) - assert(remainder_size == element_size); - else - assert(remainder_size == request2size(sizes[i])); - check_inuse_chunk(mem2chunk(marray)); - } - for (i = 0; i != n_elements; ++i) - check_inuse_chunk(mem2chunk(marray[i])); - -#endif - - return marray; -} - -/* Try to free all pointers in the given array. - Note: this could be made faster, by delaying consolidation, - at the price of disabling some user integrity checks, We - still optimize some consolidations by combining adjacent - chunks before freeing, which will occur often if allocated - with ialloc or the array is sorted. -*/ -size_t malloc_state::internal_bulk_free(void* array[], size_t nelem) -{ - size_t unfreed = 0; - if (1) - { - void** a; - void** fence = &(array[nelem]); - for (a = array; a != fence; ++a) - { - void* mem = *a; - if (mem != 0) - { - mchunkptr p = mem2chunk(mem); - size_t psize = p->chunksize(); -#if SPP_FOOTERS - if (get_mstate_for(p) != m) - { - ++unfreed; - continue; - } -#endif - check_inuse_chunk(p); - *a = 0; - if (rtcheck(ok_address(p) && ok_inuse(p))) - { - void ** b = a + 1; // try to merge with next chunk - mchunkptr next = (mchunkptr)p->next_chunk(); - if (b != fence && *b == chunk2mem(next)) - { - size_t newsize = next->chunksize() + psize; - set_inuse(p, newsize); - *b = chunk2mem(p); - } - else - dispose_chunk(p, psize); - } - else - { - SPP_ABORT; - break; - } - } - } - if (should_trim(_topsize)) - sys_trim(0); - } - return unfreed; -} - -void malloc_state::init(char* tbase, size_t tsize) -{ - _seg._base = _least_addr = tbase; - _seg._size = _footprint = _max_footprint = tsize; - _magic = mparams._magic; - _release_checks = SPP_MAX_RELEASE_CHECK_RATE; - _mflags = mparams._default_mflags; - _extp = 0; - _exts = 0; - disable_contiguous(); - init_bins(); - mchunkptr mn = (mchunkptr)mem2chunk(this)->next_chunk(); - init_top(mn, (size_t)((tbase + tsize) - (char*)mn) - top_foot_size()); - check_top_chunk(_top); -} - -/* Traversal */ -#if SPP_MALLOC_INSPECT_ALL -void malloc_state::internal_inspect_all(void(*handler)(void *start, void *end, - size_t used_bytes, - void* callback_arg), - void* arg) -{ - if (is_initialized()) - { - mchunkptr top = top; - msegmentptr s; - for (s = &seg; s != 0; s = s->next) - { - mchunkptr q = align_as_chunk(s->base); - while (segment_holds(s, q) && q->head != FENCEPOST_HEAD) - { - mchunkptr next = (mchunkptr)q->next_chunk(); - size_t sz = q->chunksize(); - size_t used; - void* start; - if (q->is_inuse()) - { - used = sz - CHUNK_OVERHEAD; // must not be mmapped - start = chunk2mem(q); - } - else - { - used = 0; - if (is_small(sz)) - { - // offset by possible bookkeeping - start = (void*)((char*)q + sizeof(struct malloc_chunk)); - } - else - start = (void*)((char*)q + sizeof(struct malloc_tree_chunk)); - } - if (start < (void*)next) // skip if all space is bookkeeping - handler(start, next, used, arg); - if (q == top) - break; - q = next; - } - } - } -} -#endif // SPP_MALLOC_INSPECT_ALL - - - -/* ----------------------------- user mspaces ---------------------------- */ - -static mstate init_user_mstate(char* tbase, size_t tsize) -{ - size_t msize = pad_request(sizeof(malloc_state)); - mchunkptr msp = align_as_chunk(tbase); - mstate m = (mstate)(chunk2mem(msp)); - memset(m, 0, msize); - msp->_head = (msize | INUSE_BITS); - m->init(tbase, tsize); - return m; -} - -SPP_API mspace create_mspace(size_t capacity, int locked) -{ - mstate m = 0; - size_t msize; - mparams.ensure_initialization(); - msize = pad_request(sizeof(malloc_state)); - if (capacity < (size_t) - (msize + top_foot_size() + mparams._page_size)) - { - size_t rs = ((capacity == 0) ? mparams._granularity : - (capacity + top_foot_size() + msize)); - size_t tsize = mparams.granularity_align(rs); - char* tbase = (char*)(SPP_CALL_MMAP(tsize)); - if (tbase != cmfail) - { - m = init_user_mstate(tbase, tsize); - m->_seg._sflags = USE_MMAP_BIT; - m->set_lock(locked); - } - } - return (mspace)m; -} - -SPP_API size_t destroy_mspace(mspace msp) -{ - size_t freed = 0; - mstate ms = (mstate)msp; - if (ms->ok_magic()) - { - msegmentptr sp = &ms->_seg; - while (sp != 0) - { - char* base = sp->_base; - size_t size = sp->_size; - flag_t flag = sp->_sflags; - (void)base; // placate people compiling -Wunused-variable - sp = sp->_next; - if ((flag & USE_MMAP_BIT) && !(flag & EXTERN_BIT) && - SPP_CALL_MUNMAP(base, size) == 0) - freed += size; - } - } - else - SPP_USAGE_ERROR_ACTION(ms, ms); - return freed; -} - -/* ---------------------------- mspace versions of malloc/calloc/free routines -------------------- */ -SPP_API void* mspace_malloc(mspace msp, size_t bytes) -{ - mstate ms = (mstate)msp; - if (!ms->ok_magic()) - { - SPP_USAGE_ERROR_ACTION(ms, ms); - return 0; - } - return ms->_malloc(bytes); -} - -SPP_API void mspace_free(mspace msp, void* mem) -{ - if (mem != 0) - { - mchunkptr p = mem2chunk(mem); -#if SPP_FOOTERS - mstate fm = get_mstate_for(p); - (void)msp; // placate people compiling -Wunused -#else - mstate fm = (mstate)msp; -#endif - if (!fm->ok_magic()) - { - SPP_USAGE_ERROR_ACTION(fm, p); - return; - } - fm->_free(p); - } -} - -SPP_API inline void* mspace_calloc(mspace msp, size_t n_elements, size_t elem_size) -{ - void* mem; - size_t req = 0; - mstate ms = (mstate)msp; - if (!ms->ok_magic()) - { - SPP_USAGE_ERROR_ACTION(ms, ms); - return 0; - } - if (n_elements != 0) - { - req = n_elements * elem_size; - if (((n_elements | elem_size) & ~(size_t)0xffff) && - (req / n_elements != elem_size)) - req = spp_max_size_t; // force downstream failure on overflow - } - mem = ms->internal_malloc(req); - if (mem != 0 && mem2chunk(mem)->calloc_must_clear()) - memset(mem, 0, req); - return mem; -} - -SPP_API inline void* mspace_realloc(mspace msp, void* oldmem, size_t bytes) -{ - void* mem = 0; - if (oldmem == 0) - mem = mspace_malloc(msp, bytes); - else if (bytes >= MAX_REQUEST) - SPP_MALLOC_FAILURE_ACTION; -#ifdef REALLOC_ZERO_BYTES_FREES - else if (bytes == 0) - mspace_free(msp, oldmem); -#endif - else - { - size_t nb = request2size(bytes); - mchunkptr oldp = mem2chunk(oldmem); -#if ! SPP_FOOTERS - mstate m = (mstate)msp; -#else - mstate m = get_mstate_for(oldp); - if (!m->ok_magic()) - { - SPP_USAGE_ERROR_ACTION(m, oldmem); - return 0; - } -#endif - if (1) - { - mchunkptr newp = m->try_realloc_chunk(oldp, nb, 1); - if (newp != 0) - { - m->check_inuse_chunk(newp); - mem = chunk2mem(newp); - } - else - { - mem = mspace_malloc(m, bytes); - if (mem != 0) - { - size_t oc = oldp->chunksize() - oldp->overhead_for(); - memcpy(mem, oldmem, (oc < bytes) ? oc : bytes); - mspace_free(m, oldmem); - } - } - } - } - return mem; -} - -#if 0 - -SPP_API mspace create_mspace_with_base(void* base, size_t capacity, int locked) -{ - mstate m = 0; - size_t msize; - mparams.ensure_initialization(); - msize = pad_request(sizeof(malloc_state)); - if (capacity > msize + top_foot_size() && - capacity < (size_t) - (msize + top_foot_size() + mparams._page_size)) - { - m = init_user_mstate((char*)base, capacity); - m->_seg._sflags = EXTERN_BIT; - m->set_lock(locked); - } - return (mspace)m; -} - -SPP_API int mspace_track_large_chunks(mspace msp, int enable) -{ - int ret = 0; - mstate ms = (mstate)msp; - if (1) - { - if (!ms->use_mmap()) - ret = 1; - if (!enable) - ms->enable_mmap(); - else - ms->disable_mmap(); - } - return ret; -} - -SPP_API void* mspace_realloc_in_place(mspace msp, void* oldmem, size_t bytes) -{ - void* mem = 0; - if (oldmem != 0) - { - if (bytes >= MAX_REQUEST) - SPP_MALLOC_FAILURE_ACTION; - else - { - size_t nb = request2size(bytes); - mchunkptr oldp = mem2chunk(oldmem); -#if ! SPP_FOOTERS - mstate m = (mstate)msp; -#else - mstate m = get_mstate_for(oldp); - (void)msp; // placate people compiling -Wunused - if (!m->ok_magic()) - { - SPP_USAGE_ERROR_ACTION(m, oldmem); - return 0; - } -#endif - if (1) - { - mchunkptr newp = m->try_realloc_chunk(oldp, nb, 0); - if (newp == oldp) - { - m->check_inuse_chunk(newp); - mem = oldmem; - } - } - } - } - return mem; -} - -SPP_API void* mspace_memalign(mspace msp, size_t alignment, size_t bytes) -{ - mstate ms = (mstate)msp; - if (!ms->ok_magic()) - { - SPP_USAGE_ERROR_ACTION(ms, ms); - return 0; - } - if (alignment <= SPP_MALLOC_ALIGNMENT) - return mspace_malloc(msp, bytes); - return ms->internal_memalign(alignment, bytes); -} - -SPP_API void** mspace_independent_calloc(mspace msp, size_t n_elements, - size_t elem_size, void* chunks[]) -{ - size_t sz = elem_size; // serves as 1-element array - mstate ms = (mstate)msp; - if (!ms->ok_magic()) - { - SPP_USAGE_ERROR_ACTION(ms, ms); - return 0; - } - return ms->ialloc(n_elements, &sz, 3, chunks); -} - -SPP_API void** mspace_independent_comalloc(mspace msp, size_t n_elements, - size_t sizes[], void* chunks[]) -{ - mstate ms = (mstate)msp; - if (!ms->ok_magic()) - { - SPP_USAGE_ERROR_ACTION(ms, ms); - return 0; - } - return ms->ialloc(n_elements, sizes, 0, chunks); -} - -#endif - -SPP_API inline size_t mspace_bulk_free(mspace msp, void* array[], size_t nelem) -{ - return ((mstate)msp)->internal_bulk_free(array, nelem); -} - -#if SPP_MALLOC_INSPECT_ALL -SPP_API void mspace_inspect_all(mspace msp, - void(*handler)(void *start, - void *end, - size_t used_bytes, - void* callback_arg), - void* arg) -{ - mstate ms = (mstate)msp; - if (ms->ok_magic()) - internal_inspect_all(ms, handler, arg); - else - SPP_USAGE_ERROR_ACTION(ms, ms); -} -#endif - -SPP_API inline int mspace_trim(mspace msp, size_t pad) -{ - int result = 0; - mstate ms = (mstate)msp; - if (ms->ok_magic()) - result = ms->sys_trim(pad); - else - SPP_USAGE_ERROR_ACTION(ms, ms); - return result; -} - -SPP_API inline size_t mspace_footprint(mspace msp) -{ - size_t result = 0; - mstate ms = (mstate)msp; - if (ms->ok_magic()) - result = ms->_footprint; - else - SPP_USAGE_ERROR_ACTION(ms, ms); - return result; -} - -SPP_API inline size_t mspace_max_footprint(mspace msp) -{ - size_t result = 0; - mstate ms = (mstate)msp; - if (ms->ok_magic()) - result = ms->_max_footprint; - else - SPP_USAGE_ERROR_ACTION(ms, ms); - return result; -} - -SPP_API inline size_t mspace_footprint_limit(mspace msp) -{ - size_t result = 0; - mstate ms = (mstate)msp; - if (ms->ok_magic()) - { - size_t maf = ms->_footprint_limit; - result = (maf == 0) ? spp_max_size_t : maf; - } - else - SPP_USAGE_ERROR_ACTION(ms, ms); - return result; -} - -SPP_API inline size_t mspace_set_footprint_limit(mspace msp, size_t bytes) -{ - size_t result = 0; - mstate ms = (mstate)msp; - if (ms->ok_magic()) - { - if (bytes == 0) - result = mparams.granularity_align(1); // Use minimal size - if (bytes == spp_max_size_t) - result = 0; // disable - else - result = mparams.granularity_align(bytes); - ms->_footprint_limit = result; - } - else - SPP_USAGE_ERROR_ACTION(ms, ms); - return result; -} - -SPP_API inline size_t mspace_usable_size(const void* mem) -{ - if (mem != 0) - { - mchunkptr p = mem2chunk(mem); - if (p->is_inuse()) - return p->chunksize() - p->overhead_for(); - } - return 0; -} - -SPP_API inline int mspace_mallopt(int param_number, int value) -{ - return mparams.change(param_number, value); -} - -} // spp_ namespace - - -#endif // SPP_EXCLUDE_IMPLEMENTATION - -#endif // spp_dlalloc__h_ diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp_memory.h b/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp_memory.h deleted file mode 100644 index cfaa108..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp_memory.h +++ /dev/null @@ -1,190 +0,0 @@ -#if !defined(spp_memory_h_guard) -#define spp_memory_h_guard - -#include -#include -#include - -#if defined(_WIN32) || defined( __CYGWIN__) - #define SPP_WIN -#endif - -#ifdef SPP_WIN - #include - #include - #undef min - #undef max -#elif defined(__linux__) - #include - #include -#elif defined(__FreeBSD__) - #include - #include - #include - #include - #include - #include -#endif - -namespace spp -{ - uint64_t GetSystemMemory() - { -#ifdef SPP_WIN - MEMORYSTATUSEX memInfo; - memInfo.dwLength = sizeof(MEMORYSTATUSEX); - GlobalMemoryStatusEx(&memInfo); - return static_cast(memInfo.ullTotalPageFile); -#elif defined(__linux__) - struct sysinfo memInfo; - sysinfo (&memInfo); - auto totalVirtualMem = memInfo.totalram; - - totalVirtualMem += memInfo.totalswap; - totalVirtualMem *= memInfo.mem_unit; - return static_cast(totalVirtualMem); -#elif defined(__FreeBSD__) - kvm_t *kd; - u_int pageCnt; - size_t pageCntLen = sizeof(pageCnt); - u_int pageSize; - struct kvm_swap kswap; - uint64_t totalVirtualMem; - - pageSize = static_cast(getpagesize()); - - sysctlbyname("vm.stats.vm.v_page_count", &pageCnt, &pageCntLen, NULL, 0); - totalVirtualMem = pageCnt * pageSize; - - kd = kvm_open(NULL, _PATH_DEVNULL, NULL, O_RDONLY, "kvm_open"); - kvm_getswapinfo(kd, &kswap, 1, 0); - kvm_close(kd); - totalVirtualMem += kswap.ksw_total * pageSize; - - return totalVirtualMem; -#else - return 0; -#endif - } - - uint64_t GetTotalMemoryUsed() - { -#ifdef SPP_WIN - MEMORYSTATUSEX memInfo; - memInfo.dwLength = sizeof(MEMORYSTATUSEX); - GlobalMemoryStatusEx(&memInfo); - return static_cast(memInfo.ullTotalPageFile - memInfo.ullAvailPageFile); -#elif defined(__linux__) - struct sysinfo memInfo; - sysinfo(&memInfo); - auto virtualMemUsed = memInfo.totalram - memInfo.freeram; - - virtualMemUsed += memInfo.totalswap - memInfo.freeswap; - virtualMemUsed *= memInfo.mem_unit; - - return static_cast(virtualMemUsed); -#elif defined(__FreeBSD__) - kvm_t *kd; - u_int pageSize; - u_int pageCnt, freeCnt; - size_t pageCntLen = sizeof(pageCnt); - size_t freeCntLen = sizeof(freeCnt); - struct kvm_swap kswap; - uint64_t virtualMemUsed; - - pageSize = static_cast(getpagesize()); - - sysctlbyname("vm.stats.vm.v_page_count", &pageCnt, &pageCntLen, NULL, 0); - sysctlbyname("vm.stats.vm.v_free_count", &freeCnt, &freeCntLen, NULL, 0); - virtualMemUsed = (pageCnt - freeCnt) * pageSize; - - kd = kvm_open(NULL, _PATH_DEVNULL, NULL, O_RDONLY, "kvm_open"); - kvm_getswapinfo(kd, &kswap, 1, 0); - kvm_close(kd); - virtualMemUsed += kswap.ksw_used * pageSize; - - return virtualMemUsed; -#else - return 0; -#endif - } - - uint64_t GetProcessMemoryUsed() - { -#ifdef SPP_WIN - PROCESS_MEMORY_COUNTERS_EX pmc; - GetProcessMemoryInfo(GetCurrentProcess(), reinterpret_cast(&pmc), sizeof(pmc)); - return static_cast(pmc.PrivateUsage); -#elif defined(__linux__) - auto parseLine = - [](char* line)->int - { - auto i = strlen(line); - - while(*line < '0' || *line > '9') - { - line++; - } - - line[i-3] = '\0'; - i = atoi(line); - return i; - }; - - auto file = fopen("/proc/self/status", "r"); - auto result = -1; - char line[128]; - - while(fgets(line, 128, file) != nullptr) - { - if(strncmp(line, "VmSize:", 7) == 0) - { - result = parseLine(line); - break; - } - } - - fclose(file); - return static_cast(result) * 1024; -#elif defined(__FreeBSD__) - struct kinfo_proc info; - size_t infoLen = sizeof(info); - int mib[] = { CTL_KERN, KERN_PROC, KERN_PROC_PID, getpid() }; - - sysctl(mib, sizeof(mib) / sizeof(*mib), &info, &infoLen, NULL, 0); - return static_cast(info.ki_rssize * getpagesize()); -#else - return 0; -#endif - } - - uint64_t GetPhysicalMemory() - { -#ifdef SPP_WIN - MEMORYSTATUSEX memInfo; - memInfo.dwLength = sizeof(MEMORYSTATUSEX); - GlobalMemoryStatusEx(&memInfo); - return static_cast(memInfo.ullTotalPhys); -#elif defined(__linux__) - struct sysinfo memInfo; - sysinfo(&memInfo); - - auto totalPhysMem = memInfo.totalram; - - totalPhysMem *= memInfo.mem_unit; - return static_cast(totalPhysMem); -#elif defined(__FreeBSD__) - u_long physMem; - size_t physMemLen = sizeof(physMem); - int mib[] = { CTL_HW, HW_PHYSMEM }; - - sysctl(mib, sizeof(mib) / sizeof(*mib), &physMem, &physMemLen, NULL, 0); - return physMem; -#else - return 0; -#endif - } - -} - -#endif // spp_memory_h_guard diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp_smartptr.h b/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp_smartptr.h deleted file mode 100644 index fba3acf..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp_smartptr.h +++ /dev/null @@ -1,71 +0,0 @@ -#if !defined(spp_smartptr_h_guard) -#define spp_smartptr_h_guard - - -/* ----------------------------------------------------------------------------------------------- - * quick version of intrusive_ptr - * ----------------------------------------------------------------------------------------------- - */ - -#include -#include "spp_config.h" - -// ------------------------------------------------------------------------ -class spp_rc -{ -public: - spp_rc() : _cnt(0) {} - spp_rc(const spp_rc &) : _cnt(0) {} - void increment() const { ++_cnt; } - void decrement() const { assert(_cnt); if (--_cnt == 0) delete this; } - unsigned count() const { return _cnt; } - -protected: - virtual ~spp_rc() {} - -private: - mutable unsigned _cnt; -}; - -// ------------------------------------------------------------------------ -template -class spp_sptr -{ -public: - spp_sptr() : _p(0) {} - spp_sptr(T *p) : _p(p) { if (_p) _p->increment(); } - spp_sptr(const spp_sptr &o) : _p(o._p) { if (_p) _p->increment(); } -#ifndef SPP_NO_CXX11_RVALUE_REFERENCES - spp_sptr(spp_sptr &&o) : _p(o._p) { o._p = (T *)0; } - spp_sptr& operator=(spp_sptr &&o) { this->swap(o); return *this; } -#endif - ~spp_sptr() { if (_p) _p->decrement(); } - spp_sptr& operator=(const spp_sptr &o) { reset(o._p); return *this; } - T* get() const { return _p; } - void swap(spp_sptr &o) { T *tmp = _p; _p = o._p; o._p = tmp; } - void reset(const T *p = 0) - { - if (p == _p) - return; - if (_p) _p->decrement(); - _p = (T *)p; - if (_p) _p->increment(); - } - T* operator->() const { return const_cast(_p); } - bool operator!() const { return _p == 0; } - -private: - T *_p; -}; - -// ------------------------------------------------------------------------ -namespace std -{ - template - inline void swap(spp_sptr &a, spp_sptr &b) - { - a.swap(b); - } -} - -#endif // spp_smartptr_h_guard diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp_stdint.h b/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp_stdint.h deleted file mode 100644 index 3adced9..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp_stdint.h +++ /dev/null @@ -1,16 +0,0 @@ -#if !defined(spp_stdint_h_guard) -#define spp_stdint_h_guard - -#include "spp_config.h" - -#if defined(SPP_HAS_CSTDINT) && (__cplusplus >= 201103) - #include -#else - #if defined(__FreeBSD__) || defined(__IBMCPP__) || defined(_AIX) - #include - #else - #include - #endif -#endif - -#endif // spp_stdint_h_guard diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp_timer.h b/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp_timer.h deleted file mode 100644 index 48180f4..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp_timer.h +++ /dev/null @@ -1,58 +0,0 @@ -/** - Copyright (c) 2016 Mariano Gonzalez - - Permission is hereby granted, free of charge, to any person obtaining a copy - of this software and associated documentation files (the "Software"), to deal - in the Software without restriction, including without limitation the rights - to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - copies of the Software, and to permit persons to whom the Software is - furnished to do so, subject to the following conditions: - - The above copyright notice and this permission notice shall be included in all - copies or substantial portions of the Software. - - THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - SOFTWARE. -*/ - -#ifndef spp_timer_h_guard -#define spp_timer_h_guard - -#include - -namespace spp -{ - template - class Timer - { - public: - Timer() { reset(); } - void reset() { _start = _snap = clock::now(); } - void snap() { _snap = clock::now(); } - - float get_total() const { return get_diff(_start, clock::now()); } - float get_delta() const { return get_diff(_snap, clock::now()); } - - private: - using clock = std::chrono::high_resolution_clock; - using point = std::chrono::time_point; - - template - static T get_diff(const point& start, const point& end) - { - using duration_t = std::chrono::duration; - - return std::chrono::duration_cast(end - start).count(); - } - - point _start; - point _snap; - }; -} - -#endif // spp_timer_h_guard diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp_traits.h b/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp_traits.h deleted file mode 100644 index 792f52f..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp_traits.h +++ /dev/null @@ -1,125 +0,0 @@ -#if !defined(spp_traits_h_guard) -#define spp_traits_h_guard - -#include "spp_config.h" - -template class HashObject; // for Google's benchmark, not in spp namespace! - -namespace spp_ -{ - -// --------------------------------------------------------------------------- -// type_traits we need -// --------------------------------------------------------------------------- -template -struct integral_constant { static const T value = v; }; - -template const T integral_constant::value; - -typedef integral_constant true_type; -typedef integral_constant false_type; - -typedef integral_constant zero_type; -typedef integral_constant one_type; -typedef integral_constant two_type; -typedef integral_constant three_type; - -template struct is_same : public false_type { }; -template struct is_same : public true_type { }; - -template struct remove_const { typedef T type; }; -template struct remove_const { typedef T type; }; - -template struct remove_volatile { typedef T type; }; -template struct remove_volatile { typedef T type; }; - -template struct remove_cv -{ - typedef typename remove_const::type>::type type; -}; - -// ---------------- is_integral ---------------------------------------- -template struct is_integral; -template struct is_integral : false_type { }; -template<> struct is_integral : true_type { }; -template<> struct is_integral : true_type { }; -template<> struct is_integral : true_type { }; -template<> struct is_integral : true_type { }; -template<> struct is_integral : true_type { }; -template<> struct is_integral : true_type { }; -template<> struct is_integral : true_type { }; -template<> struct is_integral : true_type { }; -template<> struct is_integral : true_type { }; -template<> struct is_integral : true_type { }; -#ifdef SPP_HAS_LONG_LONG - template<> struct is_integral : true_type { }; - template<> struct is_integral : true_type { }; -#endif -template struct is_integral : is_integral { }; -template struct is_integral : is_integral { }; -template struct is_integral : is_integral { }; - -// ---------------- is_floating_point ---------------------------------------- -template struct is_floating_point; -template struct is_floating_point : false_type { }; -template<> struct is_floating_point : true_type { }; -template<> struct is_floating_point : true_type { }; -template<> struct is_floating_point : true_type { }; -template struct is_floating_point : is_floating_point { }; -template struct is_floating_point : is_floating_point { }; -template struct is_floating_point : is_floating_point { }; - -// ---------------- is_pointer ---------------------------------------- -template struct is_pointer; -template struct is_pointer : false_type { }; -template struct is_pointer : true_type { }; -template struct is_pointer : is_pointer { }; -template struct is_pointer : is_pointer { }; -template struct is_pointer : is_pointer { }; - -// ---------------- is_reference ---------------------------------------- -template struct is_reference; -template struct is_reference : false_type {}; -template struct is_reference : true_type {}; - -// ---------------- is_relocatable ---------------------------------------- -// relocatable values can be moved around in memory using memcpy and remain -// correct. Most types are relocatable, an example of a type who is not would -// be a struct which contains a pointer to a buffer inside itself - this is the -// case for std::string in gcc 5. -// ------------------------------------------------------------------------ -template struct is_relocatable; -template struct is_relocatable : - integral_constant::value || - is_floating_point::value || - is_pointer::value - )> -{ }; - -template struct is_relocatable > : true_type { }; - -template struct is_relocatable : is_relocatable { }; -template struct is_relocatable : is_relocatable { }; -template struct is_relocatable : is_relocatable { }; -template struct is_relocatable : is_relocatable { }; -template struct is_relocatable > : - integral_constant::value && is_relocatable::value)> -{ }; - -// A template helper used to select A or B based on a condition. -// ------------------------------------------------------------ -template -struct if_ -{ - typedef A type; -}; - -template -struct if_ -{ - typedef B type; -}; - -} // spp_ namespace - -#endif // spp_traits_h_guard diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp_utils.h b/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp_utils.h deleted file mode 100644 index 4f2e925..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp_utils.h +++ /dev/null @@ -1,477 +0,0 @@ -// ---------------------------------------------------------------------- -// Copyright (c) 2016, Steven Gregory Popovitch - greg7mdp@gmail.com -// All rights reserved. -// -// Code derived derived from Boost libraries. -// Boost software licence reproduced below. -// -// Redistribution and use in source and binary forms, with or without -// modification, are permitted provided that the following conditions are -// met: -// -// * Redistributions of source code must retain the above copyright -// notice, this list of conditions and the following disclaimer. -// * Redistributions in binary form must reproduce the above -// copyright notice, this list of conditions and the following disclaimer -// in the documentation and/or other materials provided with the -// distribution. -// * The name of Steven Gregory Popovitch may not be used to -// endorse or promote products derived from this software without -// specific prior written permission. -// -// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS -// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT -// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR -// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT -// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, -// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT -// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, -// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY -// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE -// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -// ---------------------------------------------------------------------- - -// --------------------------------------------------------------------------- -// Boost Software License - Version 1.0 - August 17th, 2003 -// -// Permission is hereby granted, free of charge, to any person or organization -// obtaining a copy of the software and accompanying documentation covered by -// this license (the "Software") to use, reproduce, display, distribute, -// execute, and transmit the Software, and to prepare derivative works of the -// Software, and to permit third-parties to whom the Software is furnished to -// do so, all subject to the following: -// -// The copyright notices in the Software and this entire statement, including -// the above license grant, this restriction and the following disclaimer, -// must be included in all copies of the Software, in whole or in part, and -// all derivative works of the Software, unless such copies or derivative -// works are solely in the form of machine-executable object code generated by -// a source language processor. -// -// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -// FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT -// SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE -// FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE, -// ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER -// DEALINGS IN THE SOFTWARE. -// --------------------------------------------------------------------------- - -// ---------------------------------------------------------------------- -// H A S H F U N C T I O N S -// ---------------------------- -// -// Implements spp::spp_hash() and spp::hash_combine() -// ---------------------------------------------------------------------- - -#if !defined(spp_utils_h_guard_) -#define spp_utils_h_guard_ - -#if defined(_MSC_VER) - #if (_MSC_VER >= 1600 ) // vs2010 (1900 is vs2015) - #include - #define SPP_HASH_CLASS std::hash - #else - #include - #define SPP_HASH_CLASS stdext::hash_compare - #endif - #if (_MSC_FULL_VER < 190021730) - #define SPP_NO_CXX11_NOEXCEPT - #endif -#elif defined __clang__ - #if __has_feature(cxx_noexcept) || defined(SPP_CXX11) // define SPP_CXX11 if your compiler has - #include - #define SPP_HASH_CLASS std::hash - #else - #include - #define SPP_HASH_CLASS std::tr1::hash - #endif - - #if !__has_feature(cxx_noexcept) - #define SPP_NO_CXX11_NOEXCEPT - #endif -#elif defined(__GNUC__) - #if defined(__GXX_EXPERIMENTAL_CXX0X__) || (__cplusplus >= 201103L) - #include - #define SPP_HASH_CLASS std::hash - - #if (__GNUC__ * 10000 + __GNUC_MINOR__ * 100) < 40600 - #define SPP_NO_CXX11_NOEXCEPT - #endif - #else - #include - #define SPP_HASH_CLASS std::tr1::hash - #define SPP_NO_CXX11_NOEXCEPT - #endif -#else - #include - #define SPP_HASH_CLASS std::hash -#endif - -#ifdef SPP_NO_CXX11_NOEXCEPT - #define SPP_NOEXCEPT -#else - #define SPP_NOEXCEPT noexcept -#endif - -#ifdef SPP_NO_CXX11_CONSTEXPR - #define SPP_CONSTEXPR -#else - #define SPP_CONSTEXPR constexpr -#endif - -#ifdef SPP_NO_CXX14_CONSTEXPR - #define SPP_CXX14_CONSTEXPR -#else - #define SPP_CXX14_CONSTEXPR constexpr -#endif - -#define SPP_INLINE - -#ifndef spp_ - #define spp_ spp -#endif - -namespace spp_ -{ - -template T spp_min(T a, T b) { return a < b ? a : b; } -template T spp_max(T a, T b) { return a >= b ? a : b; } - -template -struct spp_hash -{ - SPP_INLINE size_t operator()(const T &__v) const SPP_NOEXCEPT - { - SPP_HASH_CLASS hasher; - return hasher(__v); - } -}; - -template -struct spp_hash -{ - static size_t spp_log2 (size_t val) SPP_NOEXCEPT - { - size_t res = 0; - while (val > 1) - { - val >>= 1; - res++; - } - return res; - } - - SPP_INLINE size_t operator()(const T *__v) const SPP_NOEXCEPT - { - static const size_t shift = 3; // spp_log2(1 + sizeof(T)); // T might be incomplete! - const uintptr_t i = (const uintptr_t)__v; - return static_cast(i >> shift); - } -}; - -// from http://burtleburtle.net/bob/hash/integer.html -// fast and efficient for power of two table sizes where we always -// consider the last bits. -// --------------------------------------------------------------- -inline size_t spp_mix_32(uint32_t a) -{ - a = a ^ (a >> 4); - a = (a ^ 0xdeadbeef) + (a << 5); - a = a ^ (a >> 11); - return static_cast(a); -} - -// More thorough scrambling as described in -// https://gist.github.com/badboy/6267743 -// ---------------------------------------- -inline size_t spp_mix_64(uint64_t a) -{ - a = (~a) + (a << 21); // a = (a << 21) - a - 1; - a = a ^ (a >> 24); - a = (a + (a << 3)) + (a << 8); // a * 265 - a = a ^ (a >> 14); - a = (a + (a << 2)) + (a << 4); // a * 21 - a = a ^ (a >> 28); - a = a + (a << 31); - return static_cast(a); -} - -template -struct spp_unary_function -{ - typedef ArgumentType argument_type; - typedef ResultType result_type; -}; - -template <> -struct spp_hash : public spp_unary_function -{ - SPP_INLINE size_t operator()(bool __v) const SPP_NOEXCEPT - { return static_cast(__v); } -}; - -template <> -struct spp_hash : public spp_unary_function -{ - SPP_INLINE size_t operator()(char __v) const SPP_NOEXCEPT - { return static_cast(__v); } -}; - -template <> -struct spp_hash : public spp_unary_function -{ - SPP_INLINE size_t operator()(signed char __v) const SPP_NOEXCEPT - { return static_cast(__v); } -}; - -template <> -struct spp_hash : public spp_unary_function -{ - SPP_INLINE size_t operator()(unsigned char __v) const SPP_NOEXCEPT - { return static_cast(__v); } -}; - -template <> -struct spp_hash : public spp_unary_function -{ - SPP_INLINE size_t operator()(wchar_t __v) const SPP_NOEXCEPT - { return static_cast(__v); } -}; - -template <> -struct spp_hash : public spp_unary_function -{ - SPP_INLINE size_t operator()(int16_t __v) const SPP_NOEXCEPT - { return spp_mix_32(static_cast(__v)); } -}; - -template <> -struct spp_hash : public spp_unary_function -{ - SPP_INLINE size_t operator()(uint16_t __v) const SPP_NOEXCEPT - { return spp_mix_32(static_cast(__v)); } -}; - -template <> -struct spp_hash : public spp_unary_function -{ - SPP_INLINE size_t operator()(int32_t __v) const SPP_NOEXCEPT - { return spp_mix_32(static_cast(__v)); } -}; - -template <> -struct spp_hash : public spp_unary_function -{ - SPP_INLINE size_t operator()(uint32_t __v) const SPP_NOEXCEPT - { return spp_mix_32(static_cast(__v)); } -}; - -template <> -struct spp_hash : public spp_unary_function -{ - SPP_INLINE size_t operator()(int64_t __v) const SPP_NOEXCEPT - { return spp_mix_64(static_cast(__v)); } -}; - -template <> -struct spp_hash : public spp_unary_function -{ - SPP_INLINE size_t operator()(uint64_t __v) const SPP_NOEXCEPT - { return spp_mix_64(static_cast(__v)); } -}; - -template <> -struct spp_hash : public spp_unary_function -{ - SPP_INLINE size_t operator()(float __v) const SPP_NOEXCEPT - { - // -0.0 and 0.0 should return same hash - uint32_t *as_int = reinterpret_cast(&__v); - return (__v == 0) ? static_cast(0) : spp_mix_32(*as_int); - } -}; - -template <> -struct spp_hash : public spp_unary_function -{ - SPP_INLINE size_t operator()(double __v) const SPP_NOEXCEPT - { - // -0.0 and 0.0 should return same hash - uint64_t *as_int = reinterpret_cast(&__v); - return (__v == 0) ? static_cast(0) : spp_mix_64(*as_int); - } -}; - -template struct Combiner -{ - inline void operator()(T& seed, T value); -}; - -template struct Combiner -{ - inline void operator()(T& seed, T value) - { - seed ^= value + 0x9e3779b9 + (seed << 6) + (seed >> 2); - } -}; - -template struct Combiner -{ - inline void operator()(T& seed, T value) - { - seed ^= value + T(0xc6a4a7935bd1e995) + (seed << 6) + (seed >> 2); - } -}; - -template -inline void hash_combine(std::size_t& seed, T const& v) -{ - spp_::spp_hash hasher; - Combiner combiner; - - combiner(seed, hasher(v)); -} - -static inline uint32_t s_spp_popcount_default(uint32_t i) SPP_NOEXCEPT -{ - i = i - ((i >> 1) & 0x55555555); - i = (i & 0x33333333) + ((i >> 2) & 0x33333333); - return (((i + (i >> 4)) & 0x0F0F0F0F) * 0x01010101) >> 24; -} - -static inline uint32_t s_spp_popcount_default(uint64_t x) SPP_NOEXCEPT -{ - const uint64_t m1 = uint64_t(0x5555555555555555); // binary: 0101... - const uint64_t m2 = uint64_t(0x3333333333333333); // binary: 00110011.. - const uint64_t m4 = uint64_t(0x0f0f0f0f0f0f0f0f); // binary: 4 zeros, 4 ones ... - const uint64_t h01 = uint64_t(0x0101010101010101); // the sum of 256 to the power of 0,1,2,3... - - x -= (x >> 1) & m1; // put count of each 2 bits into those 2 bits - x = (x & m2) + ((x >> 2) & m2); // put count of each 4 bits into those 4 bits - x = (x + (x >> 4)) & m4; // put count of each 8 bits into those 8 bits - return (x * h01)>>56; // returns left 8 bits of x + (x<<8) + (x<<16) + (x<<24)+... -} - -#ifdef __APPLE__ - static inline uint32_t count_trailing_zeroes(size_t v) SPP_NOEXCEPT - { - size_t x = (v & -v) - 1; - // sadly sizeof() required to build on macos - return sizeof(size_t) == 8 ? s_spp_popcount_default((uint64_t)x) : s_spp_popcount_default((uint32_t)x); - } - - static inline uint32_t s_popcount(size_t v) SPP_NOEXCEPT - { - // sadly sizeof() required to build on macos - return sizeof(size_t) == 8 ? s_spp_popcount_default((uint64_t)v) : s_spp_popcount_default((uint32_t)v); - } -#else - static inline uint32_t count_trailing_zeroes(size_t v) SPP_NOEXCEPT - { - return s_spp_popcount_default((v & -(intptr_t)v) - 1); - } - - static inline uint32_t s_popcount(size_t v) SPP_NOEXCEPT - { - return s_spp_popcount_default(v); - } -#endif - -// ----------------------------------------------------------- -// ----------------------------------------------------------- -template -class libc_allocator -{ -public: - typedef T value_type; - typedef T* pointer; - typedef ptrdiff_t difference_type; - typedef const T* const_pointer; - typedef size_t size_type; - - libc_allocator() {} - libc_allocator(const libc_allocator&) {} - - template - libc_allocator(const libc_allocator &) {} - - libc_allocator& operator=(const libc_allocator &) { return *this; } - - template - libc_allocator& operator=(const libc_allocator &) { return *this; } - -#ifndef SPP_NO_CXX11_RVALUE_REFERENCES - libc_allocator(libc_allocator &&) {} - libc_allocator& operator=(libc_allocator &&) { return *this; } -#endif - - pointer allocate(size_t n, const_pointer /* unused */= 0) - { - pointer res = static_cast(malloc(n * sizeof(T))); - if (!res) - throw std::bad_alloc(); - return res; - } - - void deallocate(pointer p, size_t /* unused */) - { - free(p); - } - - pointer reallocate(pointer p, size_t new_size) - { - pointer res = static_cast(realloc(p, new_size * sizeof(T))); - if (!res) - throw std::bad_alloc(); - return res; - } - - // extra API to match spp_allocator interface - pointer reallocate(pointer p, size_t /* old_size */, size_t new_size) - { - return static_cast(realloc(p, new_size * sizeof(T))); - } - - size_type max_size() const - { - return static_cast(-1) / sizeof(value_type); - } - - void construct(pointer p, const value_type& val) - { - new(p) value_type(val); - } - - void destroy(pointer p) { p->~value_type(); } - - template - struct rebind - { - typedef spp_::libc_allocator other; - }; - -}; - -// forward declaration -// ------------------- -template -class spp_allocator; - -} - -template -inline bool operator==(const spp_::libc_allocator &, const spp_::libc_allocator &) -{ - return true; -} - -template -inline bool operator!=(const spp_::libc_allocator &, const spp_::libc_allocator &) -{ - return false; -} - -#endif // spp_utils_h_guard_ - diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/DagAlignerAffine.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/DagAlignerAffine.hh deleted file mode 100644 index b795877..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/DagAlignerAffine.hh +++ /dev/null @@ -1,387 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Roman Petrovski -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include -#include -#include - -#include -#include - -#include "dagAligner/AffineAlignMatrix.hh" -#include "dagAligner/AffineAlignMatrixVectorized.hh" -#include "dagAligner/PenaltyMatrix.hh" - -namespace graphalign -{ - -namespace dagAligner -{ - /** - * Performs global alignment of query against DAG of target nodes. - * \param clipFront true instructs to represent insertions at the start of CIGAR as soft clips - */ - template class Aligner - { - AlignMatrix alignMatrix_; - - // max number of best paths to backtrack - const std::size_t maxRepeats_; - - public: - Aligner( - const typename AlignMatrix::PenaltyMatrix& penaltyMatrix, Score gapOpen, Score gapExt, - std::size_t maxRepeats = 10) - : alignMatrix_(penaltyMatrix, gapOpen, gapExt) - , maxRepeats_(maxRepeats) - { - } - - template - void __attribute((noinline)) - align(QueryIt queryBegin, QueryIt queryEnd, TargetIt targetBegin, TargetIt targetEnd, const EdgeMap& edgeMap) - { - alignMatrix_.init(queryBegin, queryEnd, targetBegin, targetEnd, edgeMap); - } - - struct Step - { - Cigar::OpCode operation_; - int q_; - int t_; - }; - - static bool removeDuplicateCigars(std::vector& cigars) - { - std::sort(cigars.begin(), cigars.end()); - std::vector::iterator uniq = std::unique(cigars.begin(), cigars.end()); - if (cigars.end() != uniq) - { - cigars.erase(uniq, cigars.end()); - return true; - } - - return false; - } - template - Score __attribute((noinline)) - backtrackAllPaths(const EdgeMap& edgeMap, std::vector& cigars, Score& secondBestScore) const - { - Score bestScore = SCORE_MIN; - secondBestScore = SCORE_MIN; - typename AlignMatrix::const_iterator bestCell - = alignMatrix_.template nextBestAlign(alignMatrix_.alignBegin(), secondBestScore); - for (; alignMatrix_.alignEnd() != bestCell && bestScore <= secondBestScore; - bestCell = alignMatrix_.template nextBestAlign(bestCell + 1, secondBestScore)) - { - bestScore = secondBestScore; - const int t = alignMatrix_.targetOffset(bestCell); - const int q = alignMatrix_.queryOffset(bestCell); - const int softClip = alignMatrix_.queryLen() - 1 - q; - - std::size_t firstNodeId = edgeMap.getNodeId(t); - Cigar start; - start.push_back(Cigar::Operation(Cigar::NODE_START, firstNodeId)); - if (softClip) - { - start.push_back(Cigar::Operation(Cigar::SOFT_CLIP, softClip)); - } - - if (!backtrackPath(edgeMap, start, firstNodeId, q, t, cigars)) - { - // ran out of cigars buffer - return bestScore; - } - } - - removeDuplicateCigars(cigars); - if (1 < cigars.size()) - { - // at least one duplicate, reset secondBestScore - secondBestScore = bestScore; - } - else if (alignMatrix_.alignEnd() == bestCell) - { - // one candidate only, no second best. Might had some duplicates, reset secondBestScore - secondBestScore = SCORE_MIN; - } - // else scondBest is set properly - return bestScore; - } - - template - Cigar __attribute((noinline)) - backtrackBestPath(const EdgeMap& edgeMap, Score& bestScore, Score& secondBestScore) const - { - bestScore = SCORE_MIN; - secondBestScore = SCORE_MIN; - typename AlignMatrix::const_iterator bestCell - = alignMatrix_.template nextBestAlign(alignMatrix_.alignBegin(), bestScore); - if (alignMatrix_.alignEnd() == bestCell) - { - throw std::logic_error("No best path available"); - } - std::vector ret; - const int t = alignMatrix_.targetOffset(bestCell); - const int q = alignMatrix_.queryOffset(bestCell); - const int softClip = alignMatrix_.queryLen() - 1 - q; - - std::size_t firstNodeId = edgeMap.getNodeId(t); - Cigar start; - start.push_back(Cigar::Operation(Cigar::NODE_START, firstNodeId)); - if (softClip) - { - start.push_back(Cigar::Operation(Cigar::SOFT_CLIP, softClip)); - } - - backtrackPath(edgeMap, start, firstNodeId, q, t, ret); - alignMatrix_.template nextBestAlign(bestCell + 1, secondBestScore); - return ret.front(); - } - - private: - template - Step __attribute((noinline)) stepBack( - const EdgeMap& edgeMap, const Cigar& base, std::size_t lastNodeId, int q, int t, - std::vector& cigars) const - { - Step ret = { Cigar::UNKNOWN, q, t }; - - if (alignMatrix_.isInsertion(q, t)) - { - const Cigar::OpCode code - = (1 == base.length() && Cigar::NODE_START == base.lastOp()) || Cigar::SOFT_CLIP == base.lastOp() - ? Cigar::SOFT_CLIP - : Cigar::INSERT; - ret = Step{ code, q - 1, t }; - } - - EdgeMap::OffsetEdges::const_iterator prevNodeIndexIt = edgeMap.prevNodesBegin(t); - while (prevNodeIndexIt != edgeMap.prevNodesEnd(t)) - { - const int p = *prevNodeIndexIt; - if (alignMatrix_.isDeletion(q, t, p)) - { - if (Cigar::UNKNOWN != ret.operation_ && exploreAllPaths) - { - // recurse if more than one path is possible - if (!backtrackPath(edgeMap, base + Cigar::DELETE, lastNodeId, q, p, cigars)) - { - return Step{ Cigar::UNKNOWN, q, t }; - } - } - else - { - ret = Step{ Cigar::DELETE, q, p }; - } - } - - if (alignMatrix_.isMatch(q, t, p)) - { - if (Cigar::UNKNOWN != ret.operation_ && exploreAllPaths) - { - // recurse if more than one path is possible - if (!backtrackPath(edgeMap, base + Cigar::MATCH, lastNodeId, q - 1, p, cigars)) - { - return Step{ Cigar::UNKNOWN, q, t }; - } - } - else - { - ret = Step{ Cigar::MATCH, q - 1, p }; - } - } - else if (alignMatrix_.isMismatch(q, t, p)) - { - const Cigar::OpCode code = (1 == base.length() && Cigar::NODE_START == base.lastOp()) - || Cigar::SOFT_CLIP == base.lastOp() - ? Cigar::SOFT_CLIP - : Cigar::MISMATCH; - if (Cigar::UNKNOWN != ret.operation_ && exploreAllPaths) - { - // recurse if more than one path is possible - if (!backtrackPath(edgeMap, base + code, lastNodeId, q - 1, p, cigars)) - { - return Step{ Cigar::UNKNOWN, q, t }; - } - } - else - { - ret = Step{ code, q - 1, p }; - } - } - - ++prevNodeIndexIt; - } - - if (Cigar::UNKNOWN == ret.operation_) - { - throw std::logic_error("backtracking failure: no nodes found on best path!"); - } - - // Return the one we have not recursed for. If only one path is possible, no recursion occurs - return ret; - } - - template - bool backtrackPath( - const EdgeMap& edgeMap, const Cigar& base, std::size_t lastNodeId, int q, int t, - std::vector& cigars) const - { - Cigar ret = base; - while (-1 != t) - { - const std::size_t curNodeId = edgeMap.getNodeId(t); - if (lastNodeId != curNodeId) - { - ret.push_back(Cigar::Operation(Cigar::NODE_END, lastNodeId)); - ret.push_back(Cigar::Operation(Cigar::NODE_START, curNodeId)); - lastNodeId = curNodeId; - } - - Step step = stepBack(edgeMap, ret, lastNodeId, q, t, cigars); - if (Cigar::UNKNOWN == step.operation_) - { - // ran out of cigars buffer - return false; - } - - ret.append(step.operation_); - q = step.q_; - t = step.t_; - } - - if (-1 != q) - { - if (Cigar::DELETE == ret.lastOp()) - { - const Cigar::Operation del = ret.pop_back(); - ret.push_back(Cigar::Operation(Cigar::INSERT, q + 1)); - ret.push_back(del); - } - else - { - ret.push_back(Cigar::Operation(Cigar::INSERT, q + 1)); - } - } - // TODO: according to while loop above, this cannot happen. Code below is legacy for - // the original termination condition of while loop - else if (-1 != t) // we're either on -1 row or -1 column - { - // count number of bases to the start of the last node - const std::size_t nodeId = edgeMap.getNodeId(t + 1); - int cur = t + 1; - while (cur && edgeMap.getNodeId(cur - 1) == nodeId) - { - --cur; - } - if (t + 1 != cur) - { - ret.push_back(Cigar::Operation(Cigar::DELETE, t + 1 - cur)); - } - } - - if (clipFront && Cigar::INSERT == ret.lastOp()) - { - ret.lastOp() = Cigar::SOFT_CLIP; - } - ret.push_back(Cigar::Operation(Cigar::NODE_END, lastNodeId)); - - ret.collapseLastEmptyNode(); - ret.reverse(); - if (cigars.size() == maxRepeats_ && !removeDuplicateCigars(cigars)) - { - return false; - } - cigars.push_back(ret); - return true; - } - - friend std::ostream& operator<<(std::ostream& os, const Aligner& aligner) - { - return os << "Aligner(" << aligner.alignMatrix_ << ")"; - } - }; - -} // namespace dagAligner - -// template -// class DagAligner -// : public dagAligner::Aligner> -// { -// public: -// DagAligner(const dagAligner::FixedPenaltyMatrix& penaltyMatrix, dagAligner::Score gapOpen, dagAligner::Score gapExt) -// : dagAligner::Aligner>( -// penaltyMatrix, gapOpen, gapExt) -// { -// } -// -// DagAligner(dagAligner::Score match, dagAligner::Score mismatch, dagAligner::Score gapOpen, dagAligner::Score gapExt) -// : dagAligner::Aligner>( -// dagAligner::FixedPenaltyMatrix(match, mismatch), gapOpen, gapExt) -// { -// } -// }; - -template -class DagAligner : public dagAligner::Aligner< - dagAligner::AffineAlignMatrixVectorized< - dagAligner::FixedPenaltyMatrix, penalizeMove>, - clipFront> -{ - typedef dagAligner::FixedPenaltyMatrix PenaltyMatrix; - -public: - DagAligner(const PenaltyMatrix& penaltyMatrix, dagAligner::Score gapOpen, dagAligner::Score gapExt) - : dagAligner::Aligner, clipFront>( - penaltyMatrix, gapOpen, gapExt) - { - } - - DagAligner(dagAligner::Score match, dagAligner::Score mismatch, dagAligner::Score gapOpen, dagAligner::Score gapExt) - : dagAligner::Aligner, clipFront>( - PenaltyMatrix(match, mismatch), gapOpen, gapExt) - { - } -}; - -// template -// class DagAligner -// : public dagAligner::Aligner> -// { -// public: -// DagAligner(const dagAligner::FreePenaltyMatrix& penaltyMatrix, dagAligner::Score gapOpen, dagAligner::Score -// gapExt) -// : dagAligner::Aligner>( -// penaltyMatrix, gapOpen, gapExt) -// { -// } -// -// DagAligner(dagAligner::Score match, dagAligner::Score mismatch, dagAligner::Score gapOpen, dagAligner::Score -// gapExt) -// : dagAligner::Aligner>( -// dagAligner::FreePenaltyMatrix(match, mismatch), gapOpen, gapExt) -// { -// } -// }; - -} // namespace graphalign diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/GappedAligner.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/GappedAligner.hh deleted file mode 100644 index 504011e..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/GappedAligner.hh +++ /dev/null @@ -1,179 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko , -// Roman Petrovski -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include -#include -#include -#include - -#include - -#include "graphalign/GraphAligner.hh" -#include "graphalign/GraphAlignment.hh" -#include "graphalign/KmerIndex.hh" -#include "graphalign/LinearAlignment.hh" -#include "graphalign/LinearAlignmentParameters.hh" -#include "graphalign/PinnedDagAligner.hh" -#include "graphalign/PinnedPathAligner.hh" -#include "graphcore/Graph.hh" -#include "graphcore/Path.hh" - -namespace graphtools -{ - -enum class AlignerType -{ - PATH_ALIGNER, - DAG_ALIGNER -}; - -/// Implements alignment details that are independent of the graph -class AlignerSelector -{ - std::shared_ptr ptrPathAligner_; - mutable std::shared_ptr ptrDagAligner_; - -public: - explicit AlignerSelector( - const AlignerType alignerType, const LinearAlignmentParameters& alignerParameters = LinearAlignmentParameters()) - { - if (alignerType == AlignerType::PATH_ALIGNER) - { - ptrPathAligner_ = std::make_shared( - alignerParameters.matchScore, alignerParameters.mismatchScore, alignerParameters.gapOpenScore); - } - else if (alignerType == AlignerType::DAG_ALIGNER) - { - ptrDagAligner_ = std::make_shared( - alignerParameters.matchScore, alignerParameters.mismatchScore, alignerParameters.gapOpenScore, - alignerParameters.gapExtendScore); - } - else - { - throw std::invalid_argument( - "AlignerType " + std::to_string(static_cast(alignerType)) + " is not available"); - } - } - - std::list - suffixAlign(const Path& seed_path, const std::string& query_piece, size_t extension_len, int& score) const - { - return ptrPathAligner_ ? ptrPathAligner_->suffixAlign(seed_path, query_piece, extension_len, score) - : ptrDagAligner_->suffixAlign(seed_path, query_piece, extension_len, score); - } - - std::list - prefixAlign(const Path& seed_path, const std::string& query_piece, size_t extension_len, int& score) const - { - return ptrPathAligner_ ? ptrPathAligner_->prefixAlign(seed_path, query_piece, extension_len, score) - : ptrDagAligner_->prefixAlign(seed_path, query_piece, extension_len, score); - } -}; - -using PathAndAlignment = std::pair; - -/** - * General graph aligner supporting linear gaps. - */ -class GappedGraphAligner -{ -public: - /** - * @param graph: A graph possibly containing loops (but no cycles) - * @param kmer_len: Kmer length for kmer index - * @param padding_len: Elongate paths by this much during path kmer extension step to allow for gaps - * @param seed_affix_trim_len: Trim length for the prefix and suffix (=affix) of the path - */ - GappedGraphAligner(const Graph* graph_ptr, size_t kmer_len, size_t padding_len, size_t seed_affix_trim_len) - : kmer_len_(kmer_len) - , padding_len_(padding_len) - , seed_affix_trim_len_(seed_affix_trim_len) - , kmer_index_(*graph_ptr, kmer_len) - { - } - - /** - * Aligns a read to the graph - * - * @param query: Query sequence - * @return List of top-scoring graph alignments - */ - std::list align(const std::string& query, AlignerSelector& alignerSelector) const; - - /** - * Extends a seed path corresponding to a perfect match to the query sequence to full-length alignments - * - * @param seed_path: Seed path - * @param query: Query sequence - * @param seed_start_on_query: Position of the left-most base of the seed on the query sequence - * @return List of top-scoring graph alignments going through the seed path - */ - std::list extendSeedToFullAlignments( - Path seed_path, const std::string& query, size_t seed_start_on_query, AlignerSelector& alignerSelector) const; - - /** - * Aligns query suffix to all suffix-extensions of a given path - * - * @param query_piece: Query suffix to align - * @param seed_path: Path from whose suffix the alignments should start - * @param extension_len: Length of suffix-extensions - * @return List of top-scoring alignments and their paths; each path is extended to contain the seed path - */ - std::list extendAlignmentPrefix( - const Path& seed_path, const std::string& query_piece, size_t extension_len, - AlignerSelector& alignerSelector) const; - - /** - * Aligns query prefix to all prefix-extensions of a given path - * - * @param query_piece: Query prefix to align - * @param seed_path: Path at whose prefix the alignments should end - * @param extension_len: Length of prefix-extensions - * @return List of top-scoring alignments and their paths; each path is extended to contain the seed path - */ - std::list extendAlignmentSuffix( - const Path& seed_path, const std::string& query_piece, size_t extension_len, - AlignerSelector& alignerSelector) const; - -private: - const size_t kmer_len_; - const size_t padding_len_; - const int32_t seed_affix_trim_len_; - const KmerIndex kmer_index_; - - // An alignment seed is a path whose sequence is a perfect match to the query starting from a given position - struct AlignmentSeed - { - AlignmentSeed(Path path, int start_on_query) - : path(std::move(path)) - , start_on_query(start_on_query) - { - } - Path path; - int start_on_query = -1; - }; - - // Performs a search for an alignment seed - boost::optional searchForAlignmentSeed(const std::string& query) const; -}; -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/GraphAligner.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/GraphAligner.hh deleted file mode 100644 index 7e2cb24..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/GraphAligner.hh +++ /dev/null @@ -1,39 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include -#include - -#include "graphalign/GraphAlignment.hh" - -namespace graphtools -{ -/** - * Interface class for graph aligners - */ -class GraphAligner -{ -public: - virtual ~GraphAligner(){}; - virtual std::list align(const std::string& query) const = 0; -}; -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/GraphAlignment.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/GraphAlignment.hh deleted file mode 100644 index 2d6ca36..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/GraphAlignment.hh +++ /dev/null @@ -1,95 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include -#include -#include -#include -#include -#include -#include -#include -#include - -#include "graphalign/LinearAlignment.hh" -#include "graphcore/Graph.hh" -#include "graphcore/Path.hh" - -namespace graphtools -{ -/** - * Represents an alignment of a sequence to a graph. Graph alignment consists of a path and linear alignments for each - * node of the path. - */ -class GraphAlignment -{ -public: - typedef size_t size_type; - typedef std::vector NodeAlignments; - typedef NodeAlignments::const_iterator const_iterator; - GraphAlignment(const Path& path, const std::vector& alignments) - : path_(path) - , alignments_(alignments) - { - assertValidity(); - } - - uint32_t queryLength() const; - uint32_t referenceLength() const; - uint32_t numMatches() const; - const Path& path() const { return path_; } - bool overlapsNode(NodeId node_id) const; - NodeId getNodeIdByIndex(int32_t node_index) const { return path_.getNodeIdByIndex(node_index); } - std::list getIndexesOfNode(NodeId node_id) const; - - // Removes the specified number of reference bases from the beginning of the alignment while softclipping as many - // query bases as required - void shrinkStart(int reference_length); - - // Removes the specified number of reference bases from the end of the alignment while softclipping as many query - // bases as required - void shrinkEnd(int reference_length); - - const_iterator begin() const { return alignments_.begin(); } - const_iterator end() const { return alignments_.end(); } - const Alignment& front() const { return alignments_.front(); } - const Alignment& back() const { return alignments_.back(); } - size_type size() const { return alignments_.size(); } - const Alignment& operator[](size_t index) const { return alignments_[index]; } - const std::vector& alignments() const { return alignments_; } - bool operator==(const GraphAlignment& other) const - { - return path_ == other.path_ && alignments_ == other.alignments_; - } - bool operator<(const GraphAlignment& other) const; - std::string generateCigar() const; - - friend std::ostream& operator<<(std::ostream& os, const GraphAlignment& graph_alignment); - -private: - void assertValidity() const; - Path path_; - std::vector alignments_; -}; - -std::ostream& operator<<(std::ostream& os, const GraphAlignment& graph_alignment); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/GraphAlignmentOperations.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/GraphAlignmentOperations.hh deleted file mode 100644 index 890576e..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/GraphAlignmentOperations.hh +++ /dev/null @@ -1,70 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include -#include - -#include "graphalign/GraphAlignment.hh" -#include "graphalign/LinearAlignment.hh" -#include "graphcore/Graph.hh" - -namespace graphtools -{ - -// Checks if graph alignment is consistent with the given query sequence -bool checkConsistency(const GraphAlignment& graph_alignment, const std::string& query); - -// Returns true if (disregarding soft clipping) the alignment starts and ends with a match -bool isLocalAlignment(const GraphAlignment& graph_alignment); - -// A node CIGAR is a string of the form "[linear alignment CIGAR]". This function extracts node_id and -// linear alignment CIGAR from the node CIGAR. -void splitNodeCigar(const std::string& node_cigar, std::string& cigar, NodeId& node_id); - -/** - * Converts graph CIGAR string to a graph alignment - * - * @param first_node_start Start position of the alignment on the first node - * @param graph_cigar Graph CIGAR string - * @param query Query sequence - * @param graph_ptr Pointer to the graph - * @return GraphAlignment - */ -GraphAlignment decodeGraphAlignment(int32_t first_node_start, const std::string& graph_cigar, const Graph* graph_ptr); - -/** - * Convert linear alignment to graph alignment by projecting it onto a compatible path - * - * @param linear_alignment: Linear alignment - * @param path: Path to project the alignment onto; sequence of the path must be equal to alignment's reference sequence - * @return Graph alignment composed of the input linear alignment and the (appropriately shrunk) path - */ -GraphAlignment projectAlignmentOntoGraph(Alignment linear_alignment, Path path); - -// Splits query into pieces corresponding to each node that the alignment spans -std::list getQuerySequencesForEachNode(const GraphAlignment& graph_alignment, const std::string& query); - -// Encodes alignment as a three-row strings where the top corresponds to the query sequence, the bottom to the sequence -// of alignment's path, and the middle contains a "|" for each pair of matching bases; gaps are indicated by "-"; ends -// of nodes are denoted by ":" -std::string prettyPrint(const GraphAlignment& graph_alignment, const std::string& query); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/KmerIndex.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/KmerIndex.hh deleted file mode 100644 index 9809b9b..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/KmerIndex.hh +++ /dev/null @@ -1,65 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko , -// Peter Krusche -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include -#include -#include - -#include "graphcore/Graph.hh" -#include "graphcore/Path.hh" - -namespace graphtools -{ - -// Kmer index holds paths that correspond to each kmer that appears in the graph and supports a few standard operations. -class KmerIndex -{ -public: - explicit KmerIndex(const Graph& graph, int32_t kmer_len = 12); - KmerIndex(const KmerIndex& other); - KmerIndex(KmerIndex&& other) noexcept; - KmerIndex& operator=(const KmerIndex& other); - KmerIndex& operator=(KmerIndex&& other) noexcept; - ~KmerIndex(); - bool operator==(const KmerIndex& other) const; - std::string encode() const; - - /// \brief Return all paths for kmer - /// - /// Calling this with kmer that isn't contained in the index triggers a runtime error - std::vector getPaths(const std::string& kmer) const; - bool contains(const std::string& kmer) const; - size_t numPaths(const std::string& kmer) const; - std::unordered_set kmers() const; - size_t kmerLength() const; - - size_t numUniqueKmersOverlappingNode(NodeId node_id) const; - size_t numUniqueKmersOverlappingEdge(NodeId from, NodeId to) const; - -private: - struct Impl; - std::unique_ptr pimpl_; -}; - -std::ostream& operator<<(std::ostream& os, const KmerIndex& kmer_index); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/KmerIndexOperations.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/KmerIndexOperations.hh deleted file mode 100644 index dc9e518..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/KmerIndexOperations.hh +++ /dev/null @@ -1,42 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Peter Krusche , -// Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include - -#include "graphalign/KmerIndex.hh" - -namespace graphtools -{ - -// Returns true if the sequence is in graph's (forward) orientation -bool checkIfForwardOriented(const KmerIndex& kmer_index, const std::string& sequence); - -/** - * Find minimum kmer length that covers each node with a unique kmer - * @param graph a graph - * @param min_unique_kmers_per_edge min number of unique kmers to cover each edge - * @param min_unique_kmers_per_node min number of unique kmers to cover each node - * @return - */ -int findMinCoveringKmerLength(Graph const* graph, size_t min_unique_kmers_per_edge, size_t min_unique_kmers_per_node); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/LinearAlignment.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/LinearAlignment.hh deleted file mode 100644 index 5b945f3..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/LinearAlignment.hh +++ /dev/null @@ -1,100 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include -#include - -#include "graphalign/Operation.hh" - -namespace graphtools -{ - -// Represents a linear alignment -class Alignment -{ -public: - using size_type = size_t; - using const_iterator = std::list::const_iterator; - - Alignment(int32_t reference_start, std::list operations) - : reference_start_(reference_start) - , operations_(std::move(operations)) - { - updateCounts(); - } - Alignment(uint32_t reference_start, const std::string& cigar); - const std::list& operations() const { return operations_; } - size_type numOperations() const { return operations_.size(); } - uint32_t queryLength() const; - uint32_t referenceLength() const; - uint32_t referenceStart() const { return reference_start_; } - void setReferenceStart(uint32_t reference_start) { reference_start_ = reference_start; } - - const_iterator begin() const { return operations_.begin(); } - const_iterator end() const { return operations_.end(); } - const Operation& front() const { return operations_.front(); } - const Operation& back() const { return operations_.back(); } - size_type size() const { return operations_.size(); } - bool operator==(const Alignment& other) const - { - return operations_ == other.operations_ && reference_start_ == other.reference_start_; - } - bool operator<(const Alignment& other) const; - - size_t numMatched() const { return matched_; } - size_t numMismatched() const { return mismatched_; } - size_t numClipped() const { return clipped_; } - size_t numInserted() const { return inserted_; } - size_t numDeleted() const { return deleted_; } - std::string generateCigar() const; - /** - * Reverses an alignment - * - * @param reference_length: Total length of the reference sequence - */ - void reverse(size_t reference_length); - - /** - * Splits off a piece of the alignment at the given reference position - * - * @param reference_position: Position at which the alignment is to be split - * @return Suffix alignment - */ - Alignment splitAtReferencePosition(size_t reference_position); - -protected: - void decodeCigar(const std::string& encoding); - void updateCounts(); - -private: - size_t matched_ = 0; - size_t mismatched_ = 0; - size_t clipped_ = 0; - size_t inserted_ = 0; - size_t deleted_ = 0; - size_t missing_ = 0; - int32_t reference_start_ = 0; - std::list operations_; -}; - -std::ostream& operator<<(std::ostream& os, const Alignment& alignment); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/LinearAlignmentOperations.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/LinearAlignmentOperations.hh deleted file mode 100644 index 21558c3..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/LinearAlignmentOperations.hh +++ /dev/null @@ -1,85 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include -#include -#include -#include - -#include "graphalign/LinearAlignment.hh" -#include "graphutils/SequenceOperations.hh" - -namespace graphtools -{ - -// Checks if a given linear alignment is consistent with the given query and reference sequences -bool checkConsistency(const Alignment& alignment, const std::string& reference, const std::string& query); - -/** - * Splits query and reference into pieces corresponding to operations that the alignment is made of - * - * @param alignment: Any linear alignment - * @param query: Any query sequence - * @param reference: Any reference sequence - * @return: List of pairs of sequences corresponding to each operation in the alignment - */ -std::list -getSequencesForEachOperation(const Alignment& alignment, const std::string& reference, const std::string& query); - -/** - * Checks if two alignments are bookended - * - * Two alignments are considered bookended if - * - Positions of first alignment end and second alignment start are adjacent and - * - First alignment does not end in softclipped bases (unless all of its bases are softclipped) - * - Second alignment does not start in softclipped bases (unless all of its bases are softclipped) - * - * @param first_alignment: Any linear alignment - * @param second_alignment: Any linear alignment - * @return true if alignment are bookended - */ -bool checkIfBookended(const Alignment& first_alignment, const Alignment& second_alignment); - -/** - * Merges two bookended alignments into a longer alignment - * - * @param first_alignment: Any linear alignment - * @param second_alignment: Any linear alignment that is bookeneded with the first - * @return Merged alignment - */ -Alignment mergeAlignments(const Alignment& first_alignment, const Alignment& second_alignment); - -/** - * Calculates alignment score - * - * @param alignment: Any linear alignment - * @param match_score: Score of a match - * @param mismatch_score: Score of a mismatch - * @param gap_score: Score of a gap - * @return Alignment score - */ -int32_t scoreAlignment(const Alignment& alignment, int32_t match_score, int32_t mismatch_score, int32_t gap_score); - -// Encodes alignment as a three-row strings where the top corresponds to the query sequence, the bottom to the reference -// sequence, and the middle contains a "|" for each pair of matching bases; gaps are indicated by "-" -std::string prettyPrint(const Alignment& alignment, const std::string& reference, const std::string& query); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/LinearAlignmentParameters.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/LinearAlignmentParameters.hh deleted file mode 100644 index 1529eec..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/LinearAlignmentParameters.hh +++ /dev/null @@ -1,49 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include -#include -/** - * Holds scores for linear sequence alignment algorithms - */ -struct LinearAlignmentParameters -{ - LinearAlignmentParameters() { assertThatScoresAreValid(); } - LinearAlignmentParameters(int32_t matchScore, int32_t mismatchScore, int32_t gapOpenScore, int32_t gapExtendScore) - : matchScore(matchScore) - , mismatchScore(mismatchScore) - , gapOpenScore(gapOpenScore) - , gapExtendScore(gapExtendScore) - { - assertThatScoresAreValid(); - } - - void assertThatScoresAreValid() - { - assert(0 <= matchScore && mismatchScore <= 0 && gapOpenScore <= 0 && gapExtendScore <= 0); - } - - const int32_t matchScore = 5; - const int32_t mismatchScore = -4; - const int32_t gapOpenScore = -8; - const int32_t gapExtendScore = -2; -}; diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/Operation.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/Operation.hh deleted file mode 100644 index 861b7ff..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/Operation.hh +++ /dev/null @@ -1,68 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include -#include - -namespace graphtools -{ -enum class OperationType -{ - kMatch, - kMismatch, - kInsertionToRef, - kDeletionFromRef, - kSoftclip, - kMissingBases -}; - -// Represents a single alignment operation -class Operation -{ -public: - Operation(OperationType type, uint32_t length) - : type_(type) - , length_(length) - { - } - explicit Operation(std::string cigar); - - OperationType type() const { return type_; } - uint32_t length() const { return length_; } - uint32_t referenceLength() const; - uint32_t queryLength() const; - - bool operator==(const Operation& other) const { return type_ == other.type_ && length_ == other.length_; } - bool operator<(const Operation& other) const; - - std::string generateCigar() const; - -private: - OperationType type_; - uint32_t length_; -}; - -OperationType decodeOperationType(char type_encoding); - -std::ostream& operator<<(std::ostream& os, OperationType operation_type); -std::ostream& operator<<(std::ostream& os, const Operation& operation); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/OperationOperations.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/OperationOperations.hh deleted file mode 100644 index 764504e..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/OperationOperations.hh +++ /dev/null @@ -1,42 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphalign/Operation.hh" - -#include -#include - -namespace graphtools -{ - -// Returns true if a given operation is consistent with the given query and reference sequences -bool checkConsistency(const Operation& operation, const std::string& reference, const std::string& query); - -using OperationPair = std::pair; - -/** - * Splits a given operation by reference length - * - * @param operation: Any operation that spans over one base of the reference - * @param prefix_reference_length: Length of the first piece (prefix) - * @return A pair of operations produced by the split - */ -OperationPair splitByReferenceLength(const Operation& operation, uint32_t prefix_reference_length); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/PinnedAligner.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/PinnedAligner.hh deleted file mode 100644 index d94faa8..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/PinnedAligner.hh +++ /dev/null @@ -1,63 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include -#include - -#include "graphalign/LinearAlignment.hh" -#include "graphalign/TracebackMatrix.hh" - -namespace graphtools -{ - -/** - * Performs local alignment of a pair of sequences that starts at the beginning or the end of both sequences - */ -class PinnedAligner -{ -public: - PinnedAligner(int32_t match_score, int32_t mismatch_score, int32_t gap_score) - : match_score_(match_score) - , mismatch_score_(mismatch_score) - , gap_score_(gap_score) - { - } - TracebackMatrix populateTracebackMatrix(const std::string& reference, const std::string& query); - // Calculates a top-scoring local alignment of a query to the reference that starts at left-most position of both - // sequences - Alignment prefixAlign(const std::string& reference, const std::string& query); - // Calculates a top-scoring local alignment of a query to the reference that starts at right-most position of both - // sequences - Alignment suffixAlign(std::string query, std::string reference); - -private: - void fillTopLeft(TracebackMatrix& matrix); - void fillTopRow(TracebackMatrix& matrix); - void fillLeftColumn(TracebackMatrix& matrix); - void fillBody(const std::string& reference, const std::string& query, TracebackMatrix& matrix); - void fillBodyCell(TracebackMatrix& matrix, size_t row_index, size_t col_index, bool do_bases_match); - - int32_t match_score_; - int32_t mismatch_score_; - int32_t gap_score_; -}; -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/PinnedDagAligner.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/PinnedDagAligner.hh deleted file mode 100644 index 22ce556..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/PinnedDagAligner.hh +++ /dev/null @@ -1,620 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Roman Petrovski -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include -#include -#include - -#include - -#include "graphalign/DagAlignerAffine.hh" -#include "graphalign/GraphAlignment.hh" -#include "graphalign/Operation.hh" -#include "graphalign/dagAligner/BaseMatchingPenaltyMatrix.hh" -#include "graphcore/Graph.hh" -#include "graphcore/Path.hh" - -namespace graphtools -{ - -using PathAndAlignment = std::pair; - -template -class BaseMatchingDagAligner : public graphalign::dagAligner::Aligner< - graphalign::dagAligner::AffineAlignMatrixVectorized< - graphalign::dagAligner::BaseMatchingPenaltyMatrix, penalizeMove>, - clipFront> -{ - typedef graphalign::dagAligner::BaseMatchingPenaltyMatrix PenaltyMatrix; - typedef graphalign::dagAligner::Score Score; - -public: - BaseMatchingDagAligner(const PenaltyMatrix& penaltyMatrix, Score gapOpen, Score gapExt) - : graphalign::dagAligner::Aligner< - graphalign::dagAligner::AffineAlignMatrixVectorized, clipFront>( - penaltyMatrix, gapOpen, gapExt) - { - } - - BaseMatchingDagAligner(graphalign::dagAligner::Score match, Score mismatch, Score gapOpen, Score gapExt) - : graphalign::dagAligner::Aligner< - graphalign::dagAligner::AffineAlignMatrixVectorized, clipFront>( - PenaltyMatrix(match, mismatch), gapOpen, gapExt) - { - } -}; - -/** - * Performs alignment of query pieces that start or end at the seed in the graph - */ -class PinnedDagAligner -{ - typedef std::pair Edge; - typedef std::vector Edges; - typedef graphalign::dagAligner::Cigar Cigar; - BaseMatchingDagAligner aligner_; - - static void appendOperation(OperationType type, uint32_t length, std::list& operations) - { - if (operations.empty() || operations.back().type() != type) - { - operations.push_back(Operation(type, length)); - } - else - { - operations.back() = Operation(type, operations.back().length() + length); - } - } - - template - static void parseGraphCigar( - const GraphT& graph, const graphalign::dagAligner::Cigar& cigar, PathT& path, std::list& operations) - { - using namespace graphalign::dagAligner; - for (const Cigar::Operation& op : cigar) - { - if (Cigar::NODE_START == op.code_) - { - if (path.lastNodeId() != op.value_ - || std::size_t(path.endPosition()) == graph.nodeSeq(op.value_).length()) - { - path.extendEndToNode(op.value_); - } - } - else if (Cigar::NODE_END == op.code_) - { - } - else - switch (op.code_) - { - case Cigar::MATCH: - { - appendOperation(OperationType::kMatch, op.value_, operations); - path.shiftEndAlongNode(op.value_); - break; - } - case Cigar::MISMATCH: - { - appendOperation(OperationType::kMismatch, op.value_, operations); - path.shiftEndAlongNode(op.value_); - break; - } - case Cigar::INSERT: - { - appendOperation(OperationType::kInsertionToRef, op.value_, operations); - break; - } - case Cigar::SOFT_CLIP: - { - appendOperation(OperationType::kSoftclip, op.value_, operations); - break; - } - case Cigar::DELETE: - { - appendOperation(OperationType::kDeletionFromRef, op.value_, operations); - path.shiftEndAlongNode(op.value_); - break; - } - default: - { - throw std::logic_error(std::string("Unexpected graph cigar operation:") + std::to_string(op.code_)); - } - } - } - } - - typedef int MappedId; - - void unmapNodeIds(const std::map& originalIds, graphalign::dagAligner::Cigar& cigar) - { - using namespace graphalign::dagAligner; - for (Cigar::Operation& op : cigar) - { - if (Cigar::NODE_START == op.code_ || Cigar::NODE_END == op.code_) - { - op.value_ = originalIds.at(op.value_); - } - } - } - - /** - * \brief Tests if the cigar first node is a repeat expansion and corrects - * cigar to ensure that fraction of the first expansion is interpreted correctly - */ - template - void fixFirstNodeExpansion( - const std::vector& nodeIds, const std::map& originalIds, const PathT& seedPath, - graphalign::dagAligner::Cigar& cigar) - { - using namespace graphalign::dagAligner; - - if (seedPath.lastNodeId() != originalIds.at(cigar.firstNode()) || MappedId(cigar.firstNode()) != nodeIds[0]) - { - const int skipLen - = seedPath.graphRawPtr()->nodeSeq(seedPath.lastNodeId()).length() - seedPath.endPosition(); - if (0 > skipLen) - { - throw std::logic_error("invalid distance to skip"); - } - if (skipLen) - { - const Cigar::Operation skipFirstNode[] - = { Cigar::Operation( - Cigar::NODE_START, nodeIds[0]), // endPosition is on the base that belongs to the path... - Cigar::Operation(Cigar::DELETE, skipLen), Cigar::Operation(Cigar::NODE_END, nodeIds[0]) }; - - cigar.insert( - cigar.begin(), skipFirstNode, skipFirstNode + sizeof(skipFirstNode) / sizeof(skipFirstNode[0])); - } - } - } - -public: - explicit PinnedDagAligner( - const int32_t matchScore, const int32_t mismatchScore, const int32_t gapOpenScore, const int32_t gapExtendScore) - : aligner_(matchScore, mismatchScore, gapOpenScore, gapExtendScore) - { - } - - std::list - prefixAlign(const Path& seedPath, const std::string& queryPiece, size_t extensionLen, int& score) - { - using namespace graphalign::dagAligner; - std::vector nodeIds; - Edges edges; - std::string target; - - // when repeat expansions are unrolled each copy gets a unique id, so, all - // ids have to be remapped - std::map originalIds; - - bfsDiscoverEdges( - *seedPath.graphRawPtr(), seedPath.nodeIds().back(), seedPath.endPosition(), extensionLen, nodeIds, edges, - target, originalIds); - edges.push_back(Edge(target.length(), target.length())); - - std::list ret; - if (!target.empty()) - { - const EdgeMap alignerEdges(edges, nodeIds); - - aligner_.align(queryPiece.begin(), queryPiece.end(), target.begin(), target.end(), alignerEdges); - - std::vector cigars; - Score secondBestScore = 0; - Score bestScore = aligner_.backtrackAllPaths(alignerEdges, cigars, secondBestScore); - - score = bestScore; - for (Cigar& cigar : cigars) - { - fixFirstNodeExpansion(nodeIds, originalIds, seedPath, cigar); - - unmapNodeIds(originalIds, cigar); - - Path path = seedPath; - std::list operations; - parseGraphCigar(*seedPath.graphRawPtr(), cigar, path, operations); - - ret.push_back(PathAndAlignment(path, Alignment(seedPath.seq().length(), operations))); - } - } - - return ret; - } - - std::list - suffixAlign(const Path& seedPath, std::string queryPiece, size_t extensionLen, int& score) - { - using namespace graphalign::dagAligner; - std::vector nodeIds; - Edges edges; - std::string target; - - // when repeat expansions are unrolled each copy gets a unique id, so, all - // ids have to be remapped - std::map originalIds; - - ReverseGraph rg(*seedPath.graphRawPtr()); - bfsDiscoverEdges( - rg, seedPath.nodeIds().front(), - // endPosition is on the base that belongs to the path... - ConstReversePath(seedPath).endPosition(), extensionLen, nodeIds, edges, target, originalIds); - edges.push_back(Edge(target.length(), target.length())); - - std::list ret; - if (!target.empty()) - { - const EdgeMap alignerEdges(edges, nodeIds); - - std::reverse(queryPiece.begin(), queryPiece.end()); - aligner_.align(queryPiece.begin(), queryPiece.end(), target.begin(), target.end(), alignerEdges); - - std::vector cigars; - Score secondBestScore = 0; - Score bestScore = aligner_.backtrackAllPaths(alignerEdges, cigars, secondBestScore); - - score = bestScore; - for (Cigar& cigar : cigars) - { - fixFirstNodeExpansion(nodeIds, originalIds, ConstReversePath(seedPath), cigar); - - unmapNodeIds(originalIds, cigar); - - Path path = seedPath; - ReversePath rp(path); - std::list operations; - parseGraphCigar(rg, cigar, rp, operations); - operations.reverse(); - - // reversed alignments always start at the beginning of the path because - // the seed path gets start-extended to incorporate them - ret.push_back(PathAndAlignment(path, Alignment(0, operations))); - } - } - - return ret; - } - -private: - template - static std::map extractSubgraph( - const GraphT& graph, const NodeId startNodeId, const std::size_t startNodeOffset, const std::size_t seqLen) - { - std::map nodeStartSeqOffset; - - if (graph.nodeSeq(startNodeId).length() == startNodeOffset) - { - // flag empty start node in a special way - nodeStartSeqOffset[startNodeId] = -1; - } - else - { - // first node start is at the start of the sequence - nodeStartSeqOffset[startNodeId] = 0; - } - - // nodes to be visited by bfs - std::deque shouldVisit(1, startNodeId); - - // extract longest subgraph of nodes such that each node begins within - // seqLen from the start of the start node - while (!shouldVisit.empty()) - { - const NodeId currentNodeId = shouldVisit.front(); - shouldVisit.pop_front(); - - const std::string& currentNodeSeq = graph.nodeSeq(currentNodeId); - const int currentNodeSeqOffset = nodeStartSeqOffset[currentNodeId]; - - // avoid dealing with individual node startNodeOffset (only start node has it) - // by pretending the sequence starts at the start node start - if (seqLen + startNodeOffset - std::max(0, currentNodeSeqOffset) > currentNodeSeq.length()) - { - const int successorSeqOffset - = -1 == currentNodeSeqOffset ? 0 : currentNodeSeqOffset + currentNodeSeq.length(); - // sequence does not terminate at this node, enqueue successors - const std::set& successors = graph.successors(currentNodeId); - for (const NodeId successorId : successors) - { - const auto seenSuccessor = nodeStartSeqOffset.find(successorId); - if (nodeStartSeqOffset.end() == seenSuccessor || seenSuccessor->second > successorSeqOffset) - { - // some successors will end up listed in shouldVisit more than once at a time - shouldVisit.push_back(successorId); - nodeStartSeqOffset[successorId] = successorSeqOffset; - } - } - } - } - - return nodeStartSeqOffset; - } - - typedef std::pair IdEdge; - typedef std::vector IdEdges; - - /** - * \brief expands repeats up to remainder of sequnce length - * \return pairs of mapped node ids indicating an edge between them. - * \postcondition result array is ordered by successor id then by predecessor id - */ - template - static IdEdges unrollRepeats( - const GraphT& graph, const std::size_t seqLen, const std::map& nodeStartSeqOffset, - std::map& originalIds, std::multimap& mappedIds) - { - IdEdges idEdges; - for (const auto& nodeIdOffset : nodeStartSeqOffset) - { - if (int(seqLen) <= nodeIdOffset.second) - { - throw std::logic_error("node should not be in the subgraph"); - } - - const std::set& successors = graph.successors(nodeIdOffset.first); - if (successors.end() != successors.find(nodeIdOffset.first)) - { - const std::size_t nodeSeqLen = graph.nodeSeq(nodeIdOffset.first).length(); - // don't forget empty repeat start node has special sequence offset -1 - for (std::size_t lenLeft = seqLen - std::max(0, nodeIdOffset.second); lenLeft;) - { - // chain unrolled repeat nodes together - IdEdge edge(mappedIds.size(), mappedIds.size() + 1); - idEdges.push_back(edge); - mappedIds.emplace(nodeIdOffset.first, originalIds.size()); - originalIds.emplace(originalIds.size(), nodeIdOffset.first); - lenLeft -= std::min(lenLeft, nodeSeqLen); - } - - // since edges point forward, above loop always produces one more edge than we need - idEdges.pop_back(); - } - else - { - mappedIds.emplace(nodeIdOffset.first, originalIds.size()); - originalIds.emplace(originalIds.size(), nodeIdOffset.first); - } - } - - linkPredecessors(graph, originalIds, mappedIds, idEdges); - - // group edges by successor node - std::sort(idEdges.begin(), idEdges.end(), [](const IdEdge& left, const IdEdge& right) { - return left.second < right.second || (left.second == right.second && left.first < right.first); - }); - - return idEdges; - } - - static void dfsExtractOrderedNodeIds( - const MappedId currentId, const IdEdges& idEdges, const std::vector& idEdgesIndex, - std::vector& seenNodes, std::vector& nodeIds) - { - if (!seenNodes.at(currentId)) - { - seenNodes[currentId] = true; - for (std::size_t predOffset = idEdgesIndex.at(currentId); idEdgesIndex.at(currentId + 1) != predOffset; - ++predOffset) - { - if (idEdges.at(predOffset).second != currentId) - { - throw std::logic_error( - "dfsExtractOrderedNodeIds: Invalid edge for node " + std::to_string(currentId)); - } - - dfsExtractOrderedNodeIds(idEdges[predOffset].first, idEdges, idEdgesIndex, seenNodes, nodeIds); - } - nodeIds.push_back(currentId); - } - } - /** - * \brief dfs in order to produce the topological ordering with start node on top - */ - static std::vector - extractOrderedNodeIds(const IdEdges& idEdges, const std::vector& idEdgesIndex) - { - std::vector nodeIds; - std::vector seenNodes(idEdgesIndex.size(), false); - for (std::size_t mappedId = 0; idEdgesIndex.size() - 1 != mappedId; ++mappedId) - { - dfsExtractOrderedNodeIds(mappedId, idEdges, idEdgesIndex, seenNodes, nodeIds); - } - - return nodeIds; - } - - /** - * \brief self-repeat edges already in idEdges, add all mapped predecessor edges to each first expansion - * and non-repeat nodes - */ - template - static void linkPredecessors( - const GraphT& graph, const std::map& originalIds, - const std::multimap& mappedIds, IdEdges& idEdges) - { - for (MappedId mappedId = 0; MappedId(mappedIds.size()) != mappedId;) - { - const NodeId originalId = originalIds.at(mappedId); - - bool selfRepeat = false; - for (const NodeId& predecessorId : graph.predecessors(originalId)) - { - if (predecessorId != originalId) - { - auto mappedPredIds = mappedIds.equal_range(predecessorId); - - // other nodes, insert edges for each predecessor instance - // empty ranges indicate predecessors that are not part of subgraph - while (mappedPredIds.second != mappedPredIds.first) - { - IdEdge edge(mappedPredIds.first->second, mappedId); - idEdges.push_back(edge); - ++mappedPredIds.first; - } - } - else - { - selfRepeat = true; - } - } - - if (selfRepeat) - { - // skip all instances of self repeat so that only first node gets edges - // from predecessors - auto mappedIdsRange = mappedIds.equal_range(originalId); - mappedId += std::distance(mappedIdsRange.first, mappedIdsRange.second); - } - else - { - ++mappedId; - } - } - } - - static std::vector indexEdges(const IdEdges& idEdges, const std::map& originalIds) - { - std::vector index; - index.reserve(idEdges.size() + 1); - index.push_back(0); - if (!idEdges.size()) - { - // no edges. Single-node graph, just close the index - index.push_back(0); - } - else - { - MappedId lastId = -1; - for (const IdEdge& edge : idEdges) - { - while (lastId != edge.second) - { - index.push_back(index.back()); - ++lastId; - } - ++index.back(); - } - // add nodes without predecessors to index - while (lastId != MappedId(originalIds.rbegin()->first)) - { - index.push_back(index.back()); - ++lastId; - } - } - - return index; - } - - template - static std::string buildTargetSequence( - const GraphT& graph, const std::size_t startNodeOffset, const std::vector& nodeIds, - const std::map& originalIds, const std::map& nodeStartSeqOffset, - const std::vector& idEdgesIndex, const IdEdges& idEdges, std::vector& edges) - { - std::string target; - std::vector mappedIdEndOffset(nodeIds.size(), 0); - // when first node is a repeat expansion fully consumed by seed, just pretend that query start - // at the beginning of the node rather than after the end... - std::size_t startOffset = startNodeOffset; - for (const MappedId mappedId : nodeIds) - { - const NodeId originalId = originalIds.at(mappedId); - const std::string& nodeSeq = graph.nodeSeq(originalId); - if (!startOffset || -1 != nodeStartSeqOffset.at(originalId)) - { - const std::size_t nodePartLen = nodeSeq.length() - startOffset; - if (!nodePartLen) - { - throw std::logic_error("Empty node in expanded subgraph and it is not the first one"); - } - - for (std::size_t predOffset = idEdgesIndex[mappedId]; idEdgesIndex[mappedId + 1] != predOffset; - ++predOffset) - { - if (idEdges[predOffset].second != mappedId) - { - throw std::logic_error("bfsDiscoverEdges: Invalid edge"); - } - Edge edge(mappedIdEndOffset.at(idEdges[predOffset].first), target.length()); - edges.push_back(edge); - } - target += nodeSeq.substr(startOffset, nodePartLen); - } - mappedIdEndOffset[mappedId] = target.length() - 1; - startOffset = 0; - } - - return target; - } - - /** - * \param seqLen extensionLen + offset in the first node. This simplifies - * the process - * by assuming that sequence starts at the node start - */ - template - static void bfsDiscoverEdges( - const GraphT& graph, const NodeId startNodeId, const std::size_t startNodeOffset, const std::size_t seqLen, - std::vector& nodeIds, std::vector& edges, std::string& target, - std::map& originalIds) - { - // length of shortest path to the first node character - const std::map nodeStartSeqOffset = extractSubgraph(graph, startNodeId, startNodeOffset, seqLen); - - // Repeat expansions need to be unrolled, so we create unique id for each unrolled instance and map - // them to original ids - std::multimap mappedIds; - const IdEdges idEdges - = unrollRepeats(graph, startNodeOffset + seqLen, nodeStartSeqOffset, originalIds, mappedIds); - - // index the edge array so that for each mappedId there is a pair of entries index[mappedId], - // index[mappedId+1] which contains offsets of all predecessor edges in the idEdges; - const std::vector idEdgesIndex = indexEdges(idEdges, originalIds); - - nodeIds = extractOrderedNodeIds(idEdges, idEdgesIndex); - if (nodeIds.size() != mappedIds.size()) - { - throw std::logic_error( - "Invalid number of nodeIds entries " + std::to_string(nodeIds.size()) + " expected " - + std::to_string(mappedIds.size())); - } - - if (originalIds.at(nodeIds.at(0)) != startNodeId) - { - // nodeIds must be topologically sorted. Since we're discovering our subgraph from the - // start node, its first expansion must sort to the top. - throw std::logic_error("First expansion of start node must be the first node"); - } - - // extract target sequence in the proper order - target = buildTargetSequence( - graph, startNodeOffset, nodeIds, originalIds, nodeStartSeqOffset, idEdgesIndex, idEdges, edges); - - if (-1 == nodeStartSeqOffset.at(startNodeId)) - { - // if the first node is an empty repeat expansion (consumed by seed), remove it as it has no - // corresponding sequence in the target. - nodeIds.erase(nodeIds.begin()); - } - } -}; -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/PinnedPathAligner.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/PinnedPathAligner.hh deleted file mode 100644 index c4ddd80..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/PinnedPathAligner.hh +++ /dev/null @@ -1,117 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include -#include - -#include "graphalign/GraphAlignment.hh" -#include "graphalign/LinearAlignmentOperations.hh" -#include "graphalign/PinnedAligner.hh" -#include "graphcore/PathOperations.hh" - -namespace graphtools -{ - -using PathAndAlignment = std::pair; - -class PinnedPathAligner -{ - const int32_t matchScore_; - const int32_t mismatchScore_; - const int32_t gapOpenScore_; - - mutable PinnedAligner pinnedAligner_; - -public: - PinnedPathAligner(int32_t matchScore = 5, int32_t mismatchScore = -4, int32_t gapOpenScore = -8) - : matchScore_(matchScore) - , mismatchScore_(mismatchScore) - , gapOpenScore_(gapOpenScore) - , pinnedAligner_(matchScore_, mismatchScore_, gapOpenScore_) - { - } - std::list - suffixAlign(const Path& seed_path, const std::string& query_piece, size_t extension_len, int& score) const; - std::list - prefixAlign(const Path& seed_path, const std::string& query_piece, size_t extension_len, int& score) const; - -private: - int32_t scoreAlignment(const Alignment& alignment) const - { - return graphtools::scoreAlignment(alignment, matchScore_, mismatchScore_, gapOpenScore_); - } -}; - -inline std::list PinnedPathAligner::suffixAlign( - const Path& seed_path, const std::string& query_piece, size_t extension_len, int& top_alignment_score) const -{ - std::list top_paths_and_alignments; - top_alignment_score = INT32_MIN; - - const std::list path_extensions = extendPathStart(seed_path, extension_len); - for (const auto& path : path_extensions) - { - Alignment alignment = pinnedAligner_.suffixAlign(path.seq(), query_piece); - const int32_t alignment_score = scoreAlignment(alignment); - - if (top_alignment_score < alignment_score) - { - top_paths_and_alignments.clear(); - top_alignment_score = alignment_score; - } - - if (top_alignment_score == alignment_score) - { - top_paths_and_alignments.push_back(std::make_pair(path, alignment)); - } - } - - return top_paths_and_alignments; -} - -inline std::list PinnedPathAligner::prefixAlign( - const Path& seed_path, const std::string& query_piece, size_t extension_len, int& top_alignment_score) const -{ - std::list top_paths_and_alignments; - top_alignment_score = INT32_MIN; - - const std::list path_extensions = extendPathEnd(seed_path, extension_len); - for (const auto& path : path_extensions) - { - Alignment alignment = pinnedAligner_.prefixAlign(path.seq(), query_piece); - const int32_t alignment_score = scoreAlignment(alignment); - - if (top_alignment_score < alignment_score) - { - top_paths_and_alignments.clear(); - top_alignment_score = alignment_score; - } - - if (top_alignment_score == alignment_score) - { - top_paths_and_alignments.push_back(std::make_pair(path, alignment)); - } - } - - return top_paths_and_alignments; -} -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/TracebackMatrix.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/TracebackMatrix.hh deleted file mode 100644 index f692855..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/TracebackMatrix.hh +++ /dev/null @@ -1,104 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include -#include -#include - -namespace graphtools -{ -enum class TracebackStep -{ - kStop, - kTop, - kLeft, - kDiagonalMatch, - kDiagonalMismatch -}; - -std::ostream& operator<<(std::ostream& out, const TracebackStep& trace_dir); - -struct TracebackMatrixCell -{ - TracebackMatrixCell() - : direction(TracebackStep::kStop) - , score(INT32_MIN) - { - } - TracebackMatrixCell(TracebackStep new_direction, int32_t new_score) - : direction(new_direction) - , score(new_score) - { - } - bool operator==(const TracebackMatrixCell& other) const - { - return direction == other.direction && score == other.score; - } - TracebackStep direction; - int32_t score; -}; - -std::ostream& operator<<(std::ostream& out, const TracebackMatrixCell& cell); - -/** - * Implementation of traceback matrix abstraction; each cell of the matrix contains traceback direction and alignment - * score - */ -class TracebackMatrix -{ -public: - TracebackMatrix(size_t num_rows, size_t num_cols) - : num_rows_(num_rows) - , num_cols_(num_cols) - { - cells_.resize(num_rows_ * num_cols_); - }; - explicit TracebackMatrix(const std::string& encoding); - - size_t numRows() const { return num_rows_; } - size_t numCols() const { return num_cols_; } - int32_t score(size_t row_index, size_t col_index) const; - void setScore(size_t row_index, size_t col_index, int32_t score); - TracebackStep tracebackStep(size_t row_index, size_t col_index) const; - void setTracebackStep(size_t row_index, size_t col_index, TracebackStep direction); - - void locateTopScoringCell(size_t& top_row_index, size_t& top_col_index) const; - - bool operator==(const TracebackMatrix& other) const; - -private: - inline const TracebackMatrixCell& getCell(size_t row_index, size_t col_index) const - { - return cells_[row_index * num_cols_ + col_index]; - } - inline TracebackMatrixCell& getCell(size_t row_index, size_t col_index) - { - return cells_[row_index * num_cols_ + col_index]; - } - - size_t num_rows_; - size_t num_cols_; - std::vector cells_; -}; - -std::ostream& operator<<(std::ostream& out, const TracebackMatrix& matrix); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/TracebackRunner.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/TracebackRunner.hh deleted file mode 100644 index f383b25..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/TracebackRunner.hh +++ /dev/null @@ -1,60 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include -#include - -#include "graphalign/LinearAlignment.hh" -#include "graphalign/TracebackMatrix.hh" - -namespace graphtools -{ -/** - * Implements traceback of dynamic programming matrices generated by local and global alignment algorithms - */ -class TracebackRunner -{ -public: - explicit TracebackRunner(const TracebackMatrix& matrix) - : matrix_(matrix) - { - } - - // Performs traceback starting from a given cell of the matrix - Alignment runTraceback(size_t row_index, size_t col_index); - -private: - void computeTracebackRunForAlignmentOperation(size_t row_index, size_t col_index); - void tracebackPosition(size_t& row_index, size_t& col_index); - void convertCurrentRunToAlignmentOperation(); - void softclipQuerySuffix(size_t& row_index); - void softclipQueryPrefix(size_t& row_index); - - const TracebackMatrix& matrix_; - - std::list operations_; - TracebackStep run_traceback_step; - size_t run_length = 0; - size_t run_last_row_index = 0; - size_t run_last_col_index = 0; -}; -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/dagAligner/AffineAlignMatrix.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/dagAligner/AffineAlignMatrix.hh deleted file mode 100644 index cdb4f17..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/dagAligner/AffineAlignMatrix.hh +++ /dev/null @@ -1,285 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Roman Petrovski -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include -#include - -#include "Details.hh" - -namespace graphalign -{ - -namespace dagAligner -{ - - // the 2-d table of scores filled during the alignment - template class AffineAlignMatrix - { - public: - typedef PenaltyMatrixT PenaltyMatrix; - - private: - const PenaltyMatrix penaltyMatrix_; - const Score gapOpen_; - const Score gapExt_; - - AlignMatrix v_; - AlignMatrix g_; - AlignMatrix f_; - AlignMatrix e_; - - std::vector query_; - std::vector target_; - - public: - AffineAlignMatrix(const PenaltyMatrix& penaltyMatrix, Score gapOpen, Score gapExt) - : penaltyMatrix_(penaltyMatrix) - , gapOpen_(gapOpen) - , gapExt_(gapExt) - { - } - - template - void - init(QueryIt queryBegin, QueryIt queryEnd, TargetIt targetBegin, TargetIt targetEnd, const EdgeMap& edgeMap) - { - if (queryEnd == queryBegin) - { - throw std::logic_error("Empty query is not allowed."); - } - - if (targetEnd == targetBegin) - { - throw std::logic_error("Empty target is not allowed."); - } - - query_.clear(); - penaltyMatrix_.translateQuery(queryBegin, queryEnd, std::back_inserter(query_)); - target_.clear(); - penaltyMatrix_.translateTarget(targetBegin, targetEnd, std::back_inserter(target_)); - - reset(edgeMap); - - fill(edgeMap); - } - - typedef AlignMatrix::const_iterator const_iterator; - template const_iterator nextBestAlign(const_iterator start, Score& bestScore) const - { - return !localAlign ? v_.nextBestAlign(start, queryLen() - 1, bestScore) - : v_.nextBestAlign(start, bestScore); - } - - const_iterator alignBegin() const { return v_.cellOneOne(); } - const_iterator alignEnd() const { return v_.end(); } - int targetOffset(const_iterator cell) const { return std::distance(v_.cellOneOne(), cell) / v_.paddedRowLen(); } - int queryOffset(const_iterator cell) const { return std::distance(v_.cellOneOne(), cell) % v_.paddedRowLen(); } - int queryLen() const { return query_.size(); } - - bool isInsertion(int q, int t) const - { - if (-1 == q) - { - return false; - } - const Score insExtScore = v_.at(q, t) - f_.at(q - 1, t); - const Score insOpenScore = v_.at(q, t) - v_.at(q - 1, t); - return gapExt_ == insExtScore || gapOpen_ + gapExt_ == insOpenScore; - } - - bool isDeletion(int q, int t, int p) const - { - // q == -1 is ok here, just check the score match as usual - const Score delExtScore = v_.at(q, t) - e_.at(q, p); - const Score delOpenScore = v_.at(q, t) - v_.at(q, p); - return gapExt_ == delExtScore || gapOpen_ + gapExt_ == delOpenScore; - } - - bool isMatch(int q, int t, int p) const - { - if (-1 == q) - { - return false; - } - - typename PenaltyMatrix::QueryChar queryChar = query_[q]; - typename PenaltyMatrix::TargetChar targetChar = target_[t]; - const Score alnScore = v_.at(q, t) - v_.at(q - 1, p); - return penaltyMatrix_.isMatch(queryChar, targetChar) && penaltyMatrix_(queryChar, targetChar) == alnScore; - } - - bool isMismatch(int q, int t, int p) const - { - if (-1 == q) - { - return false; - } - - typename PenaltyMatrix::QueryChar queryChar = query_[q]; - typename PenaltyMatrix::TargetChar targetChar = target_[t]; - const Score alnScore = v_.at(q, t) - v_.at(q - 1, p); - return !penaltyMatrix_.isMatch(queryChar, targetChar) && penaltyMatrix_(queryChar, targetChar) == alnScore; - } - - private: - void computeAlignPenalties(int q, typename PenaltyMatrix::TargetChar tc, Score penalties[16]) - { - const typename PenaltyMatrix::QueryChar* query = &query_[q]; - for (int i = 0; i < 16; ++i) - { - penalties[i] = penaltyMatrix_(query[i], tc); - } - } - - void reset(const EdgeMap& edgeMap) - { - const int qLen = query_.size(); - const int tLen = target_.size(); - - v_.reset(qLen, tLen); - g_.reset(qLen, tLen); - f_.reset(qLen, tLen); - e_.reset(qLen, tLen); - - // top left must be 0 and never change - if (v_.at(-1, -1)) - { - throw std::logic_error("Incorrectly initialized v_"); - } - if (g_.at(-1, -1)) - { - throw std::logic_error("Incorrectly initialized g_"); - } - if (f_.at(-1, -1)) - { - throw std::logic_error("Incorrectly initialized f_"); - } - if (e_.at(-1, -1)) - { - throw std::logic_error("Incorrectly initialized e_"); - } - - // first column penalises for deletion - for (int t = 0; t < tLen; ++t) - { - if (penalizeMove) - { - for (EdgeMap::OffsetEdges::const_iterator prevNodeIndexIt = edgeMap.prevNodesBegin(t); - prevNodeIndexIt != edgeMap.prevNodesEnd(t); ++prevNodeIndexIt) - { - const int p = *prevNodeIndexIt; - v_.at(-1, t) = std::max(v_.at(-1, t), Score(v_.at(-1, p) + gapOpen_ + gapExt_)); - f_.at(-1, t) = std::max(v_.at(-1, t), Score(f_.at(-1, p) + gapOpen_ + gapExt_)); - } - } - else - { - v_.at(-1, t) = 0; - f_.at(-1, t) = 0; - } - } - - // first row penalises for insertion - for (int q = 0; q < qLen; ++q) - { - v_.at(q, -1) = v_.at(q - 1, -1) + gapOpen_ + gapExt_; - e_.at(q, -1) = e_.at(q - 1, -1) + gapOpen_ + gapExt_; - } - } - - void fill(const EdgeMap& edgeMap) - { - const int qLen = query_.size(); - const int tLen = target_.size(); - - for (int t = 0; t < tLen; ++t) - { - for (EdgeMap::OffsetEdges::const_iterator prevNodeIndexIt = edgeMap.prevNodesBegin(t); - edgeMap.prevNodesEnd(t) != prevNodeIndexIt; ++prevNodeIndexIt) - { - const int p = *prevNodeIndexIt; - recomputeForDeletion(qLen, t, p); - recomputeForAlign(qLen, t, p); - } - - consolidate(qLen, t); - recomputeForInsertion(qLen, t); - } - } - - void recomputeForDeletion(int qLen, int t, int p) - { - Score* ep = e_.row(0, p); - Score* v = v_.row(0, p); - Score* et = e_.row(0, t); - for (int i = 0; i < qLen; ++i) - { - et[i] = std::max(et[i], std::max(ep[i] + gapExt_, v[i] + gapOpen_ + gapExt_)); - } - } - - void recomputeForAlign(int qLen, int t, int p) - { - const typename PenaltyMatrix::QueryChar* query = &query_[0]; - - Score* g = g_.row(0, t); - Score* v = v_.row(-1, p); - for (int i = 0; i < qLen; ++i) - { - g[i] = std::max(g[i], v[i] + penaltyMatrix_(query[i], target_[t])); - } - } - - void consolidate(int qLen, int t) - { - Score* e = e_.row(0, t); - Score* g = g_.row(0, t); - Score* v = v_.row(0, t); - for (int i = 0; i < qLen; ++i) - { - v[i] = std::max(v[i], std::max(g[i], e[i])); - } - } - - void recomputeForInsertion(int qLen, int t) - { - Score* v = v_.row(0, t); - Score* f = f_.row(0, t); - Score* fp = f_.row(-1, t); - Score* vp = v_.row(-1, t); - - for (int i = 0; i < qLen; ++i) - { - f[i] = std::max(f[i], std::max((fp[i] + gapExt_), (vp[i] + gapOpen_ + gapExt_))); - v[i] = std::max(v[i], f[i]); - } - } - - friend std::ostream& operator<<(std::ostream& os, const AffineAlignMatrix& matrix) - { - return os << "AffineAlignMatrix(" << matrix.v_ << ")"; - } - }; - -} // namespace dagAligner - -} // namespace graphalign diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/dagAligner/AffineAlignMatrixVectorized.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/dagAligner/AffineAlignMatrixVectorized.hh deleted file mode 100644 index c56ea9c..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/dagAligner/AffineAlignMatrixVectorized.hh +++ /dev/null @@ -1,341 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Roman Petrovski -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include -#include - -#include "Details.hh" - -namespace graphalign -{ - -namespace dagAligner -{ - - // the 2-d table of scores filled during the alignment - template class AffineAlignMatrixVectorized - { - public: - typedef PenaltyMatrixT PenaltyMatrix; - - private: - const PenaltyMatrix penaltyMatrix_; - const Score gapOpen_; - const Score gapExt_; - - PaddedAlignMatrix v_; - PaddedAlignMatrix g_; - PaddedAlignMatrix f_; - PaddedAlignMatrix e_; - - std::vector query_; - std::vector target_; - std::vector alignmentPenalties_[PenaltyMatrix::TARGET_CHAR_MAX_ + 1]; - - public: - AffineAlignMatrixVectorized(const PenaltyMatrix& penaltyMatrix, Score gapOpen, Score gapExt) - : penaltyMatrix_(penaltyMatrix) - , gapOpen_(gapOpen) - , gapExt_(gapExt) - { - } - - template - void - init(QueryIt queryBegin, QueryIt queryEnd, TargetIt targetBegin, TargetIt targetEnd, const EdgeMap& edgeMap) - { - if (queryEnd == queryBegin) - { - throw std::logic_error("Empty query is not allowed."); - } - - if (targetEnd == targetBegin) - { - throw std::logic_error("Empty target is not allowed."); - } - - // avoid "uninitialized read" complaints from valgrind - query_.resize((std::distance(queryBegin, queryEnd) + step - 1) / step * step); - query_.clear(); - penaltyMatrix_.translateQuery(queryBegin, queryEnd, std::back_inserter(query_)); - target_.clear(); - penaltyMatrix_.translateTarget(targetBegin, targetEnd, std::back_inserter(target_)); - - reset(edgeMap); - - fill(edgeMap); - } - - typedef AlignMatrix::const_iterator const_iterator; - template const_iterator nextBestAlign(const_iterator start, Score& bestScore) const - { - return !localAlign ? v_.nextBestAlign(start, queryLen() - 1, bestScore) - : v_.nextBestAlign(start, bestScore); - } - const_iterator alignBegin() const { return v_.cellOneOne(); } - const_iterator alignEnd() const { return v_.end(); } - int targetOffset(const_iterator cell) const { return std::distance(v_.cellOneOne(), cell) / v_.paddedRowLen(); } - int queryOffset(const_iterator cell) const { return std::distance(v_.cellOneOne(), cell) % v_.paddedRowLen(); } - int queryLen() const { return query_.size(); } - - bool isInsertion(int q, int t) const - { - if (-1 == q) - { - return false; - } - - const Score insExtScore = v_.at(q, t) - f_.at(q - 1, t); - const Score insOpenScore = v_.at(q, t) - v_.at(q - 1, t); - return gapExt_ == insExtScore || gapOpen_ + gapExt_ == insOpenScore; - } - - bool isDeletion(int q, int t, int p) const - { - // q == -1 is ok here, just check the score match as usual - const Score delExtScore = v_.at(q, t) - e_.at(q, p); - const Score delOpenScore = v_.at(q, t) - v_.at(q, p); - return gapExt_ == delExtScore || gapOpen_ + gapExt_ == delOpenScore; - } - - bool isMatch(int q, int t, int p) const - { - if (-1 == q) - { - return false; - } - - typename PenaltyMatrix::QueryChar queryChar = query_[q]; - typename PenaltyMatrix::TargetChar targetChar = target_[t]; - const Score alnScore = v_.at(q, t) - v_.at(q - 1, p); - return penaltyMatrix_.isMatch(queryChar, targetChar) && penaltyMatrix_(queryChar, targetChar) == alnScore; - } - - bool isMismatch(int q, int t, int p) const - { - if (-1 == q) - { - return false; - } - - typename PenaltyMatrix::QueryChar queryChar = query_[q]; - typename PenaltyMatrix::TargetChar targetChar = target_[t]; - const Score alnScore = v_.at(q, t) - v_.at(q - 1, p); - return !penaltyMatrix_.isMatch(queryChar, targetChar) && penaltyMatrix_(queryChar, targetChar) == alnScore; - } - - private: - // __attribute((noinline)) - void reset(const EdgeMap& edgeMap) - { - const int qLen = query_.size(); - const int tLen = target_.size(); - - for (typename PenaltyMatrix::TargetChar tc = 0; tc <= PenaltyMatrix::TARGET_CHAR_MAX_; ++tc) - { - alignmentPenalties_[tc].resize((qLen + step - 1) / step * step, 0); - for (int q = 0; q < qLen; q += step) - { - computeAlignPenalties(q, tc, &alignmentPenalties_[tc].front() + q); - } - } - - v_.reset(qLen, tLen); - g_.reset(qLen, tLen); - f_.reset(qLen, tLen); - e_.reset(qLen, tLen); - - // top left must be 0 and never change - if (v_.at(-1, -1)) - { - throw std::logic_error("Incorrectly initialized v_"); - } - if (g_.at(-1, -1)) - { - throw std::logic_error("Incorrectly initialized g_"); - } - if (f_.at(-1, -1)) - { - throw std::logic_error("Incorrectly initialized f_"); - } - if (e_.at(-1, -1)) - { - throw std::logic_error("Incorrectly initialized e_"); - } - - // first column penalises for deletion - for (int t = 0; t < tLen; ++t) - { - if (penalizeMove) - { - for (EdgeMap::OffsetEdges::const_iterator prevNodeIndexIt = edgeMap.prevNodesBegin(t); - prevNodeIndexIt != edgeMap.prevNodesEnd(t); ++prevNodeIndexIt) - { - const int p = *prevNodeIndexIt; - v_.at(-1, t) = std::max(v_.at(-1, t), Score(v_.at(-1, p) + gapOpen_ + gapExt_)); - f_.at(-1, t) = std::max(v_.at(-1, t), Score(f_.at(-1, p) + gapOpen_ + gapExt_)); - } - } - else - { - v_.at(-1, t) = 0; - f_.at(-1, t) = 0; - } - } - - // first row penalizes for insertion - for (int q = 0; q < queryLen(); ++q) - { - v_.at(q, -1) = v_.at(q - 1, -1) + gapOpen_ + gapExt_; - e_.at(q, -1) = e_.at(q - 1, -1) + gapOpen_ + gapExt_; - } - } - - // __attribute((noinline)) - void fill(const EdgeMap& edgeMap) - { - const int qLen = query_.size(); - const int tLen = target_.size(); - - for (int t = 0; t < tLen; ++t) - { - const typename PenaltyMatrix::TargetChar tc = target_[t]; - const Score* const penalties = &alignmentPenalties_[tc].front(); - for (EdgeMap::OffsetEdges::const_iterator prevNodeIndexIt = edgeMap.prevNodesBegin(t); - edgeMap.prevNodesEnd(t) != prevNodeIndexIt; ++prevNodeIndexIt) - { - const int p = *prevNodeIndexIt; - for (int q = 0; q < qLen; q += step) - { - recomputeForDeletion(q, t, p); - recomputeForAlign(q, t, p, penalties + q); - } - } - - for (int q = 0; q < qLen; q += step) - { - consolidate(q, t); - } - recomputeForInsertion(qLen, t); - } - } - - // __attribute((noinline)) - void computeAlignPenalties(int q, typename PenaltyMatrix::TargetChar tc, Score penalties[step]) - { - const typename PenaltyMatrix::QueryChar* query = &query_[q]; - for (int i = 0; i < step; ++i) - { - penalties[i] = penaltyMatrix_(query[i], tc); - } - } - - // __attribute((noinline)) - void recomputeForAlign(int q, int t, int p, const Score penalties[step]) - { - Score tmp[step]; - Score* v = v_.row(q - 1, p); - for (int i = 0; i < step; ++i) - { - tmp[i] = v[i] + penalties[i]; - } - - Score* g = g_.row(q, t); - for (int i = 0; i < step; ++i) - { - g[i] = g[i] > tmp[i] ? g[i] : tmp[i]; - } - } - - // __attribute((noinline)) - void recomputeForDeletion(int q, int t, int p) - { - Score* ep = e_.row(q, p); - Score tmpEp[step]; - for (int i = 0; i < step; ++i) - { - tmpEp[i] = ep[i] + gapExt_; - } - - Score* vp = v_.row(q, p); - Score tmpVp[step]; - for (int i = 0; i < step; ++i) - { - tmpVp[i] = vp[i] + gapOpen_ + gapExt_; - } - - Score tmp[step]; - for (int i = 0; i < step; ++i) - { - tmp[i] = tmpEp[i] > tmpVp[i] ? tmpEp[i] : tmpVp[i]; - } - - Score* e = e_.row(q, t); - for (int i = 0; i < step; ++i) - { - e[i] = e[i] > tmp[i] ? e[i] : tmp[i]; - } - } - - // __attribute((noinline)) - void recomputeForInsertion(int qLen, int t) - { - Score* v = v_.row(0, t); - Score* f = f_.row(0, t); - Score* fp = f_.row(-1, t); - Score* vp = v_.row(-1, t); - - // cannot be vectorized since insertion is computed horisontally - for (int i = 0; i < qLen; ++i) - { - f[i] = std::max(f[i], std::max((fp[i] + gapExt_), (vp[i] + gapOpen_ + gapExt_))); - v[i] = std::max(v[i], f[i]); - } - } - - // __attribute((noinline)) - void consolidate(int q, int t) - { - Score tmp[step]; - Score* e = e_.row(q, t); - Score* g = g_.row(q, t); - for (int i = 0; i < step; ++i) - { - tmp[i] = g[i] > e[i] ? g[i] : e[i]; - } - - Score* v = v_.row(q, t); - for (int i = 0; i < step; ++i) - { - v[i] = v[i] > tmp[i] ? v[i] : tmp[i]; - } - } - - friend std::ostream& operator<<(std::ostream& os, const AffineAlignMatrixVectorized& matrix) - { - return os << "AffineAlignMatrix(" << matrix.v_ << ")"; - } - }; - -} // namespace dagAligner - -} // namespace graphalign diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/dagAligner/BaseMatchingPenaltyMatrix.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/dagAligner/BaseMatchingPenaltyMatrix.hh deleted file mode 100644 index d71ce6e..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/dagAligner/BaseMatchingPenaltyMatrix.hh +++ /dev/null @@ -1,119 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Roman Petrovski -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include - -#include "graphalign/dagAligner/Details.hh" -#include "graphutils/BaseMatching.hh" - -namespace graphalign -{ - -namespace dagAligner -{ - - class BaseMatchingPenaltyMatrix - { - typedef graphtools::codes::BaseCode Oligo; - typedef graphalign::dagAligner::Score Score; - - public: - typedef Oligo QueryChar; - typedef Oligo TargetChar; - - // test constructor, since this is a free-form penalty matrix, the one - // that accepts an actual matrix is expected - BaseMatchingPenaltyMatrix(const Score match = 2, const Score mismatch = -2) - { - int row = 0; - for (const auto& r : graphtools::codes::kReferenceQueryCodeMatchLookupTable) - { - int col = 0; - for (const auto& c : r) - { - matrix_[row][col] = c ? match : mismatch; - ++col; - } - ++row; - } - } - - Score operator()(QueryChar q, TargetChar t) const - { - if (t >= ROWS_) - { - throw std::logic_error("Invalid row request from BaseMatchingPenaltyMatrix"); - } - if (q >= COLUMNS_) - { - throw std::logic_error("Invalid column request from BaseMatchingPenaltyMatrix"); - } - - return matrix_[t][q]; - } - - bool isMatch(QueryChar q, TargetChar t) const - { - return graphtools::codes::kReferenceQueryCodeMatchLookupTable[t][q]; - } - - template - static void translateTarget(InputIterator targetBegin, InputIterator targetEnd, OutputIterator output) - { - std::transform(targetBegin, targetEnd, output, [](unsigned char tc) { - return graphtools::codes::kReferenceBaseEncodingTable[tc]; - }); - } - - template - static void translateQuery(InputIterator queryBegin, InputIterator queryEnd, OutputIterator output) - { - std::transform(queryBegin, queryEnd, output, [](unsigned char tc) { - return graphtools::codes::kQueryBaseEncodingTable[tc]; - }); - } - - friend std::ostream& operator<<(std::ostream& os, const BaseMatchingPenaltyMatrix& matrix) - { - os << "BaseMatchingPenaltyMatrix(\n"; - for (int r = 0; r < ROWS_; ++r) - { - for (int c = 0; c < COLUMNS_; ++c) - { - os << (c ? "\t" : "[") << int(matrix.matrix_[r][c]); - } - os << "]\n"; - } - return os << ")"; - } - - static const int ROWS_ = graphtools::codes::kMaxReferenceBaseCode + 1; - static const int COLUMNS_ = graphtools::codes::kMaxQueryBaseCode + 1; - static const Oligo TARGET_CHAR_MAX_ = graphtools::codes::kMaxReferenceBaseCode; - - private: - graphalign::dagAligner::Score matrix_[ROWS_][COLUMNS_]; - }; - -} // namespace dagAligner - -} // namespace graphalign diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/dagAligner/Details.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/dagAligner/Details.hh deleted file mode 100644 index 0531f9b..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/dagAligner/Details.hh +++ /dev/null @@ -1,505 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Roman Petrovski -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include -#include - -#include -#include -#include -#include - -#include -#include - -// avoid boost lambda issues with boost::adaptors::transformed on boost 1.53 -#define BOOST_RESULT_OF_USE_DECLTYPE - -#include - -namespace graphalign -{ - -namespace dagAligner -{ - - typedef signed short Score; - static const Score SCORE_MIN = std::numeric_limits::min(); - - /** - * \brief Contains information about graph edges between the target sequence characters - */ - class EdgeMap - { - public: - typedef int NodeId; - typedef std::vector OffsetNodeIds; - typedef std::vector OffsetEdges; - - private: - // for target character, an id of the node to which the character belongs - OffsetNodeIds offsetNodeIds_; - - // [index_[t], index_[t+1]) contains range in prevOffsets_ that point to base preceding t in the target graph - std::vector index_; - - OffsetEdges prevOffsets_; - - public: - EdgeMap( - const OffsetNodeIds& offsetNodeIds, const std::vector& index, - const std::vector& prevOffsets) - : offsetNodeIds_(offsetNodeIds) - , index_(index) - , prevOffsets_(prevOffsets) - { - if (index.back() != prevOffsets_.size()) - { - throw std::out_of_range("index.back() != edges.size()"); - } - } - - /** - * \brief construct EdgeMap from list of unique node identifiers and edges as pairs of offsets - * \param edges offset pairs in form of {from,to} describing the connectivity in the graph - * \param nodeIds unique identifier of nodes in the same order as offsets appear in the edges - * Edges have to be sorted by 'to' position and cannot create cycles ('from' < 'to') - * Edges starting from offset -1 are ways to enter the graph. An edge from {-1,0} is implied, - * i.e. alignments can always start at position 0. - * For a (graph) sequence of length n, a dummy sequence of form {n,n} must be present as a marker - * of sequence length. - */ - EdgeMap(const std::vector>& edges, const std::vector& nodeIds) - { - typedef std::vector> Edges; - if (edges.back().second != edges.back().first) - { - throw std::invalid_argument( - "last pair of offsets must point to itself and last character in the graph"); - } - std::vector::const_iterator nodeIdIt = nodeIds.begin(); - - index_.push_back(0); - // root node offset is -1 - prevOffsets_.push_back(-1); - index_.push_back(prevOffsets_.size()); - - Edges::const_iterator edge = edges.begin(); - if (!edges.front().second) - { - if (-1 == edges.front().first) - { - // first node edge from -1 is optional - ++edge; - } - } - - for (; edges.end() != edge;) - { - // fill regular offsets to previous character within the node - while (int(offsetNodeIds_.size()) < edge->second - 1) - { - prevOffsets_.push_back(int(offsetNodeIds_.size())); - index_.push_back(prevOffsets_.size()); - offsetNodeIds_.push_back(*nodeIdIt); - } - - offsetNodeIds_.push_back(*nodeIdIt); - - // insert graph edges, all incoming edges for the same target offset - const int lastEdge = edge->second; - do - { - prevOffsets_.push_back(edge->first); - ++edge; - } while (edges.end() != edge && lastEdge == edge->second); - - index_.push_back(prevOffsets_.size()); - - // Now we're on a new node - ++nodeIdIt; - } - // remove closing offset reference to itself - prevOffsets_.pop_back(); - index_.pop_back(); - } - - /* - * \param t offset of character in target character sequence - * \return iterator to the first offset of the predecessor character. Could be on the same or a different node - */ - OffsetEdges::const_iterator prevNodesBegin(std::size_t t) const - { - assert(t < index_.size()); - return prevOffsets_.begin() + index_[t]; - } - - /* - * \param t offset of character in target character sequence - * \return iterator to the one after last offset of the predecessor character. Could be on the same or a - * different node - */ - OffsetEdges::const_iterator prevNodesEnd(std::size_t t) const - { - return prevOffsets_.begin() + index_.at(t + 1); - } - - std::size_t getNodeId(std::size_t t) const { return offsetNodeIds_.at(t); } - - friend std::ostream& operator<<(std::ostream& os, const EdgeMap& edgeMap) - { - return os << "EdgeMap(" - << "nodeIds(" - << boost::algorithm::join( - edgeMap.offsetNodeIds_ - | boost::adaptors::transformed([](std::size_t d) { return std::to_string(d); }), - ",") - << ")," - << "index(" - << boost::algorithm::join( - edgeMap.index_ - | boost::adaptors::transformed([](std::size_t d) { return std::to_string(d); }), - ",") - << ")," - << "prevOffsets(" - << boost::algorithm::join( - edgeMap.prevOffsets_ - | boost::adaptors::transformed([](int d) { return std::to_string(d); }), - ",") - << "))"; - } - }; - - // the 2-d table of scores filled during the alignment - template class PaddedAlignMatrix - { - std::size_t rowLen_; - typedef std::vector Matrix; - Matrix matrix_; - - public: - PaddedAlignMatrix() - : rowLen_(1) - , matrix_(rowLen_, 0) - { - } - - void reset(std::size_t qLen, std::size_t tLen) - { - // + 1 for gap row and gap column - rowLen_ = qLen + 1; - matrix_.resize(paddedRowLen() * (tLen + 1)); - std::fill(matrix_.begin() + 1, matrix_.end(), SCORE_MIN); - } - - int paddedRowLen() const { return 1 + (rowLen_ - 1 + pad - 1) / pad * pad; } - int rowLen() const { return rowLen_; } - Score at(int q, int t) const { return *(cellOneOne() + t * paddedRowLen() + q); } - Score& at(int q, int t) { return *(cellOneOne() + t * paddedRowLen() + q); } - Score* row(int q, int t) { return &(*(cellOneOne() + t * paddedRowLen() + q)); } - - typedef Matrix::iterator iterator; - iterator cellZeroZero() { return matrix_.begin(); } - iterator cellOneOne() { return matrix_.begin() + 1 + paddedRowLen(); } - iterator cellOneZero() { return matrix_.begin() + 1; } - iterator cellZeroOne() { return matrix_.begin() + paddedRowLen(); } - typedef Matrix::const_iterator const_iterator; - const_iterator cellOneOne() const { return matrix_.begin() + 1 + paddedRowLen(); } - const_iterator begin() const { return matrix_.begin(); } - const_iterator end() const { return matrix_.end() - paddedRowLen() + rowLen(); } - const_iterator last(int q) const { return matrix_.end() - paddedRowLen() + q + 1; } - // find best alignment after the line indicated by start iterator - const_iterator nextBestAlign(const_iterator start, int q, Score& bestScore) const - { - const_iterator rowStart = begin() - + (std::distance(begin(), start) + paddedRowLen() - 1 - q - 1) / paddedRowLen() * paddedRowLen(); - if (matrix_.end() == rowStart) - { - // current line is the end, no more good scores - return end(); - } - const_iterator rowEnd = rowStart + q + 1; - bestScore = *rowEnd; - const_iterator ret = rowEnd; - - while (last(q) != rowEnd) - { - rowEnd += paddedRowLen(); - if (bestScore < *rowEnd) - { - bestScore = *rowEnd; - ret = rowEnd; - } - } - return ret; - } - - const_iterator nextBestAlign(const_iterator start, Score& bestScore) const - { - const_iterator it = start; - if (end() == it) - { - // next line is the end, no more good scores - return end(); - } - if (!(std::distance(begin(), it) % paddedRowLen())) - { - ++it; - } - - if (rowLen() == (std::distance(begin(), it) % paddedRowLen())) - { - it += paddedRowLen() - rowLen() + 1; - } - const_iterator ret = it; - bestScore = *(it++); - - // - while (end() != it) - { - if (rowLen() == (std::distance(begin(), it) % paddedRowLen())) - { - it += paddedRowLen() - rowLen() + 1; - } - if (bestScore < *it) - { - bestScore = *it; - ret = it; - } - ++it; - } - return ret; - } - - int targetOffset(const_iterator cell) const { return std::distance(cellOneOne(), cell) / paddedRowLen(); } - int queryOffset(const_iterator cell) const { return std::distance(cellOneOne(), cell) % paddedRowLen(); } - - friend std::ostream& operator<<(std::ostream& os, const PaddedAlignMatrix& matrix) - { - os << "AlignMatrix(\n"; - for (const_iterator it = matrix.begin(); matrix.end() > it; it += matrix.paddedRowLen()) - { - for (std::size_t i = 0; i < matrix.rowLen_; ++i) - { - os << (i ? "\t" : "[") << int(*(it + i)); - } - os << "]\n"; - } - return os << ")"; - } - }; - - typedef PaddedAlignMatrix<1> AlignMatrix; - - class Cigar - { - public: - enum OpCode - { - ALIGN = 0, // 'M' - INSERT = 1, // 'I' - DELETE = 2, // 'D' - SKIP = 3, // 'N' Essentially same as 'D' but not treated as a deletion. - // Can be used for intron when aligning RNA sample against whole genome reference - SOFT_CLIP = 4, // 'S' - HARD_CLIP = 5, // 'H' - PAD = 6, // 'P' - MATCH = 7, // '=' - MISMATCH = 8, // 'X' - UNKNOWN, // '?' - NODE_START, // Non-standard. Indicates change of the node in graph cigar - NODE_END // Non-standard. Indicates change of the node in graph cigar - }; - - struct Operation - { - typedef std::size_t ValueType; - Operation(OpCode code, ValueType value) - : code_(code) - , value_(value) - { - } - OpCode code_; - ValueType value_; // normally the operation length, but for NODE contains nodeId - - char getCharCode(const char matchChar = '=', const char mismatchChar = 'X') const - { - const std::vector CIGAR_CHARS - = { 'M', 'I', 'D', 'N', 'S', 'H', 'P', matchChar, mismatchChar, '?', '[', ']' }; - if (CIGAR_CHARS.size() > code_) - { - return CIGAR_CHARS[code_]; - } - throw std::out_of_range(std::string("invalid code '") + std::to_string(code_) + "'"); - } - - bool operator<(const Operation& that) const - { - return code_ < that.code_ || (code_ == that.code_ && value_ < that.value_); - } - - bool operator==(const Operation& that) const { return code_ == that.code_ && value_ == that.value_; } - - friend std::ostream& operator<<(std::ostream& os, const Operation& op) - { - return os << "Operation(" << op.getCharCode() << op.value_ << ")"; - } - }; - - typedef std::vector Operations; - - typedef Operations::iterator iterator; - iterator begin() { return cigar_.begin(); } - iterator end() { return cigar_.end(); } - - typedef Operations::const_iterator const_iterator; - const_iterator begin() const { return cigar_.begin(); } - const_iterator end() const { return cigar_.end(); } - void push_back(const Operation& op) { cigar_.push_back(op); } - Operation pop_back() - { - const Operation ret = cigar_.back(); - cigar_.pop_back(); - return ret; - } - iterator erase(const_iterator from, const_iterator to) { return cigar_.erase(from, to); } - - template void insert(const_iterator before, IteratorT b, IteratorT e) - { - cigar_.insert(before, b, e); - } - - Operation back() const { return cigar_.back(); } - - std::size_t firstNode() const - { - if (Cigar::NODE_START != cigar_.front().code_) - { - throw std::logic_error("First CIGAR op is expected to be a node start"); - } - return cigar_.front().value_; - } - - bool empty() const { return cigar_.empty(); } - std::size_t length() const { return cigar_.size(); } - - OpCode lastOp() const { return cigar_.back().code_; } - OpCode& lastOp() { return cigar_.back().code_; } - std::size_t& lastValue() { return cigar_.back().value_; } - void append(OpCode op) - { - if (lastOp() != op) - { - push_back(Cigar::Operation(op, 1)); - } - else - { - ++lastValue(); - } - } - - Cigar operator+(OpCode op) const - { - Cigar ret = *this; - ret.append(op); - return ret; - } - - void reverse() - { - std::reverse(cigar_.begin(), cigar_.end()); - for (Operation& op : cigar_) - { - if (NODE_START == op.code_) - { - op.code_ = NODE_END; - } - else if (NODE_END == op.code_) - { - op.code_ = NODE_START; - } - } - } - - void collapseLastEmptyNode() - { - if (4 < cigar_.size() && cigar_[cigar_.size() - 1].code_ == Cigar::NODE_END - && cigar_[cigar_.size() - 4].code_ == Cigar::NODE_START - && Cigar::SOFT_CLIP == cigar_[cigar_.size() - 3].code_ - && Cigar::DELETE == cigar_[cigar_.size() - 2].code_) - { - Cigar::Operation op = cigar_[cigar_.size() - 3]; - cigar_.pop_back(); - cigar_.pop_back(); - cigar_.pop_back(); - cigar_.pop_back(); - std::swap(cigar_.back(), op); - cigar_.push_back(op); - } - else if ( - 3 < cigar_.size() && cigar_[cigar_.size() - 1].code_ == Cigar::NODE_END - && cigar_[cigar_.size() - 3].code_ == Cigar::NODE_START - && Cigar::SOFT_CLIP == cigar_[cigar_.size() - 2].code_) - { - Cigar::Operation op = cigar_[cigar_.size() - 2]; - cigar_.pop_back(); - cigar_.pop_back(); - cigar_.pop_back(); - std::swap(cigar_.back(), op); - cigar_.push_back(op); - } - } - - friend std::ostream& operator<<(std::ostream& os, const Cigar& cigar) - { - for (const Operation& op : cigar.cigar_) - { - if (NODE_START == op.code_) - { - os << op.value_ << '['; - } - else if (NODE_END == op.code_) - { - os << ']'; - } - else - { - os << op.value_ << op.getCharCode(); - } - } - return os; - } - - bool operator<(const Cigar& that) const - { - return std::lexicographical_compare(begin(), end(), that.begin(), that.end()); - } - - bool operator==(const Cigar& that) const { return cigar_ == that.cigar_; } - - private: - Operations cigar_; - }; - -} // namespace dagAligner - -} // namespace graphalign diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/dagAligner/PenaltyMatrix.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/dagAligner/PenaltyMatrix.hh deleted file mode 100644 index 07bdef9..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphalign/dagAligner/PenaltyMatrix.hh +++ /dev/null @@ -1,228 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Roman Petrovski -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include -#include - -#include -#include - -#include - -#include "graphalign/dagAligner/Details.hh" - -namespace graphalign -{ - -namespace dagAligner -{ - - class FreePenaltyMatrix - { - typedef unsigned char Oligo; - - public: - typedef Oligo QueryChar; - typedef Oligo TargetChar; - - // test constructor, since this is a free-form penalty matrix, the one - // that accepts an actual matrix is expected - FreePenaltyMatrix(const Score match = 2, const Score mismatch = -2) - : matrix_{ - // // a c g t n - // {match, mismatch, mismatch, mismatch, 0}, // a - // {mismatch, match, mismatch, mismatch, 0}, // c - // {mismatch, mismatch, match, mismatch, 0}, // g - // {mismatch, mismatch, mismatch, match, 0}, // t - // {0, 0, 0, 0, 0} // n - - // // a c g t n - // {match, mismatch, mismatch, mismatch, mismatch}, // a - // {mismatch, match, mismatch, mismatch, mismatch}, // c - // {mismatch, mismatch, match, mismatch, mismatch}, // g - // {mismatch, mismatch, mismatch, match, mismatch}, // t - // {mismatch, mismatch, mismatch, mismatch, match} // n - - // // a c g t n - // { match, mismatch, mismatch, mismatch, match }, // a - // { mismatch, match, mismatch, mismatch, match }, // c - // { mismatch, mismatch, match, mismatch, match }, // g - // { mismatch, mismatch, mismatch, match, match }, // t - // - - // a c g t n - { match, mismatch, mismatch, mismatch, match }, // a - { mismatch, match, mismatch, mismatch, match }, // c - { mismatch, mismatch, match, mismatch, match }, // g - { mismatch, mismatch, mismatch, match, match }, // t - { match, match, match, match, match } // n - - } - { - } - //__attribute__ ((noinline)) - Score operator()(QueryChar q, TargetChar t) const - { - if (q >= ROWS_) - { - throw std::logic_error("Invalid row request from FreePenaltyMatrix"); - } - if (t >= COLUMNS_) - { - throw std::logic_error("Invalid column request from FreePenaltyMatrix"); - } - - return matrix_[q][t]; - } - - bool isMatch(QueryChar q, TargetChar t) const { return (*this)(q, q) == (*this)(q, t); } - - template - static void translateTarget(InputIterator targetBegin, InputIterator targetEnd, OutputIterator output) - { - std::transform(targetBegin, targetEnd, output, &translateOligo); - } - - template - static void translateQuery(InputIterator queryBegin, InputIterator queryEnd, OutputIterator output) - { - std::transform(queryBegin, queryEnd, output, &translateOligo); - } - - friend std::ostream& operator<<(std::ostream& os, const FreePenaltyMatrix& matrix) - { - os << "FreePenaltyMatrix(\n"; - for (int r = 0; r < ROWS_; ++r) - { - for (int c = 0; c < COLUMNS_; ++c) - { - os << (c ? "\t" : "[") << int(matrix.matrix_[r][c]); - } - os << "]\n"; - } - return os << ")"; - } - - static const Oligo A = 0; - static const Oligo C = 1; - static const Oligo G = 2; - static const Oligo T = 3; - static const Oligo N = 4; - static const Oligo TARGET_CHAR_MAX_ = N; - - static const int ROWS_ = 5; - static const int COLUMNS_ = 5; - - private: - const Score matrix_[ROWS_][COLUMNS_]; - static const std::size_t OLIGO_MAX_CHAR = 255; - static const Oligo TRANSLATION_TABLE_[OLIGO_MAX_CHAR + 1]; - - static Oligo translateOligo(unsigned char tc) { return TRANSLATION_TABLE_[tc]; } - }; - - template class FixedPenaltyMatrix - { - typedef unsigned char Oligo; - - public: - typedef Oligo QueryChar; - typedef Oligo TargetChar; - - FixedPenaltyMatrix(const Score match = 2, const Score mismatch = -2) - : match_(match) - , mismatch_(mismatch) - { - } - //__attribute__ ((noinline)) - Score operator()(QueryChar q, TargetChar t) const { return isMatch(q, t) ? match_ : mismatch_; } - - bool isMatch(QueryChar q, TargetChar t) const - { - return q == t || (matchQueryN && N == q) || (matchTargetN && N == t); - } - - template - static void translateTarget(InputIterator targetBegin, InputIterator targetEnd, OutputIterator output) - { - std::transform(targetBegin, targetEnd, output, &translateOligo); - } - - template - static void translateQuery(InputIterator queryBegin, InputIterator queryEnd, OutputIterator output) - { - std::transform(queryBegin, queryEnd, output, &translateOligo); - } - - friend std::ostream& operator<<(std::ostream& os, const FixedPenaltyMatrix& matrix) - { - return os << "FixedPenaltyMatrix(" << matrix.match_ << "," << matrix.mismatch_ << ")"; - } - static const Oligo A = 0; - static const Oligo C = 1; - static const Oligo G = 2; - static const Oligo T = 3; - static const Oligo N = 4; - static const Oligo X = 5; - static const Oligo TARGET_CHAR_MAX_ = 5; - - private: - const Score match_; - const Score mismatch_; - static const std::size_t OLIGO_MAX_CHAR = 255; - static const Oligo TRANSLATION_TABLE_[OLIGO_MAX_CHAR + 1]; - static Oligo translateOligo(unsigned char tc) { return TRANSLATION_TABLE_[tc]; } - }; - // clang-format off - template - const typename FixedPenaltyMatrix::Oligo - FixedPenaltyMatrix::TRANSLATION_TABLE_[OLIGO_MAX_CHAR + 1] - = { - N, N, N, N, N, N, N, N, N, N, - N, N, N, N, N, N, N, N, N, N, - N, N, N, N, N, N, N, N, N, N, - N, N, N, N, N, N, N, N, N, N, - N, N, N, N, N, N, N, N, N, N, - N, N, N, N, N, N, N, N, N, N, - N, N, N, N, N, - // capitals - A, N, C, N, N, N, G, N, N, N, - N, N, N, N, N, N, N, N, N, T, - N, N, N, X, N, N, - // rubbish - N, N, N, N, N, N, - // lowercase - A, N, C, N, N, N, G, N, N, N, - N, N, N, N, N, N, N, N, N, T, - N, N, N, X, N, N, - // padding - N, N, N, N, - N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, - N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, - N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, - N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, - }; - // clang-format on - -} // namespace dagAligner - -} // namespace graphalign diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphcore/Graph.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphcore/Graph.hh deleted file mode 100644 index 03ad232..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphcore/Graph.hh +++ /dev/null @@ -1,136 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko , -// Peter Krusche , -// Felix Schlesinger - -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include -#include -#include -#include -#include -#include -#include -#include - -#include "graphutils/PairHashing.hh" - -namespace graphtools -{ - -using NodeId = uint32_t; -using NodeIdPair = std::pair; -using SortedLabels = std::set; -using Labels = std::unordered_set; -using AdjacencyList = std::vector>; - -struct Node -{ - std::string name; - std::string sequence; - std::vector sequence_expansion; -}; - -/** - * Sequence graph that can hold degenerate nucleotide sequences - */ -class Graph -{ -public: - explicit Graph(size_t num_nodes = 0, std::string const& id = "") - : graphId(id) - { - init(num_nodes); - } - - virtual ~Graph() = default; - - size_t numNodes() const { return nodes_.size(); } - size_t numEdges() const { return edge_labels_.size(); } - const std::string& nodeName(NodeId node_id) const; - void setNodeName(NodeId node_id, const std::string& node_name); - const std::string& nodeSeq(NodeId node_id) const; - void setNodeSeq(NodeId node_id, const std::string& sequence); - const std::vector& nodeSeqExpansion(NodeId node_id) const; - void addEdge(NodeId source_node_id, NodeId sink_node_id); - bool hasEdge(NodeId source_node_id, NodeId sink_node_id) const; - - SortedLabels allLabels() const; - const Labels& edgeLabels(NodeId source_node_id, NodeId sink_node_id) const; - // All edges in the graph with this label - std::set edgesWithLabel(const std::string& label) const; - /** - * All label to an existing edge - * @throws if source -> sink is not an edge in the graph - */ - void addLabelToEdge(NodeId source_node_id, NodeId sink_node_id, const std::string& label); - // Remove this label from all edges - void eraseLabel(const std::string& label); - - // this cannot be const if graphs are to be assigned. Currently this happens in unit tests. - std::string graphId; - const std::set& successors(NodeId node_id) const; - const std::set& predecessors(NodeId node_id) const; - -private: - void init(size_t num_nodes); - void assertNodeExists(NodeId node_id) const; - void assertEdgeExists(NodeIdPair edge) const; - std::vector nodes_; - std::unordered_map edge_labels_; - AdjacencyList adjacency_list_; - AdjacencyList reverse_adjacency_list_; -}; - -class ReverseGraph -{ - const Graph& graph_; - -public: - explicit ReverseGraph(const Graph& graph) - : graph_(graph) - { - } - - size_t numNodes() const { return graph_.numNodes(); } - size_t numEdges() const { return graph_.numEdges(); } - const std::string& nodeName(NodeId nodeId) const { return graph_.nodeName(nodeId); } - const std::string nodeSeq(NodeId nodeId) const - { - std::string ret = graph_.nodeSeq(nodeId); - std::reverse(ret.begin(), ret.end()); - return ret; - } - bool hasEdge(NodeId sourceNodeId, NodeId sinkNodeId) const { return graph_.hasEdge(sourceNodeId, sinkNodeId); } - - SortedLabels allLabels() const { return graph_.allLabels(); } - const Labels& edgeLabels(NodeId sourceNodeId, NodeId sinkNodeId) const - { - return graph_.edgeLabels(sourceNodeId, sinkNodeId); - } - - // All edges in the graph with this label - std::set edgesWithLabel(const std::string& label) const { return graph_.edgesWithLabel(label); } - - const std::set& successors(NodeId nodeId) const { return graph_.predecessors(nodeId); } - const std::set& predecessors(NodeId nodeId) const { return graph_.successors(nodeId); } -}; -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphcore/GraphBuilders.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphcore/GraphBuilders.hh deleted file mode 100644 index 54cefb3..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphcore/GraphBuilders.hh +++ /dev/null @@ -1,104 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko , -// Peter Krusche - -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include - -#include "graphcore/Graph.hh" - -namespace graphtools -{ - -/** - * Construct a graph representing deletion of a sequence from a reference - * - * The node ids are assigned in order specified by the function paramters. - * - * @param left_flank Sequence of the left flank - * @param deletion Sequence deleted from the reference - * @param right_flank Sequence of the right flank - * @return Deletion graph - */ -Graph makeDeletionGraph(const std::string& left_flank, const std::string& deletion, const std::string& right_flank); - -/** - * Construct a graph representing replacement of a piece of a reference by another sequence - * - * The node ids are assigned in order specified by the function paramters. - * - * @param left_flank Sequence of the left flank - * @param deletion Sequence deleted from the reference - * @param insertion Sequence inserted into the reference - * @param right_flank Sequence of the right flank - * @return Swap graph - */ -Graph makeSwapGraph( - const std::string& left_flank, const std::string& deletion, const std::string& insertion, - const std::string& right_flank); - -/** - * Construct a graph representing two sequence swaps separated by another sequence - * - * The node ids are assigned in order specified by the function paramters. - * - * @param left_flank Sequence of the left flank - * @param deletion1 Deleted sequence of the first swap - * @param insertion1 Inserted sequence of the first swap - * @param middle Sequence separating the swaps - * @param deletion2 Deleted sequence of the second swap - * @param insertion2 Inserted sequence of the second swap - * @param right_flank Sequence of the right flank - * @return Double-swap graph - */ -Graph makeDoubleSwapGraph( - const std::string& left_flank, const std::string& deletion1, const std::string& insertion1, - const std::string& middle, const std::string& deletion2, const std::string& insertion2, - const std::string& right_flank); - -/** - * Construct a graph representing an STR repeat with the loop separated into multiple nodes to keep the graph acyclic - * - * The first and the last nodes correspond to the left and the right flanks respectively. The internal nodes correspond - * to the repeat unit. The number of repeat unit nodes is given by ceiling(read length/unit length). - * - * @param read_len Length of the sequenced reads - * @param left_flank Sequence of the left flank - * @param repeat_unit Repeat unit - * @param right_flank Sequence of the right flank - * @return Loopless STR graph - */ -Graph makeLooplessStrGraph( - size_t read_len, const std::string& left_flank, const std::string& repeat_unit, const std::string& right_flank); - -/** - * Construct a graph representing an STR repeat - * - * The graph consists of the repeat flanks separated by the loop corresponding to multiple repetitions of the repeat - * unit. The node ids are assigned in order specified by the function paramters. - * - * @param left_flank Sequence of the left flank - * @param repeat_unit Repeat unit - * @param right_flank Sequence of the right flank - * @return STR graph - */ -Graph makeStrGraph(const std::string& left_flank, const std::string& repeat_unit, const std::string& right_flank); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphcore/GraphCoordinates.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphcore/GraphCoordinates.hh deleted file mode 100644 index 7768312..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphcore/GraphCoordinates.hh +++ /dev/null @@ -1,92 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Peter Krusche - -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include "graphalign/GraphAlignment.hh" - -#include - -namespace graphtools -{ - -/** - * Class to translate between different ways to index nucleotides on the graph - */ -class GraphCoordinates -{ -public: - explicit GraphCoordinates(graphtools::Graph const* g); - virtual ~GraphCoordinates(); - GraphCoordinates(GraphCoordinates const&) = delete; - GraphCoordinates& operator=(GraphCoordinates const&) = delete; - - GraphCoordinates(GraphCoordinates&& rhs) noexcept; - GraphCoordinates& operator=(GraphCoordinates&& rhs) noexcept; - - /** - * Get a "canonical" / linearized position -- every base on the graph has such a position - * Positions within the same node are guaranteed to be consecutive - * @param node node name - * @param offset offset relative to start of node - * @return canonical position - */ - uint64_t canonicalPos(std::string const& node, uint64_t offset = 0) const; - - /** - * Calculated canonical start and end positions for a graph mapping - * @param mapping - * @return start and end - */ - std::pair canonicalStartAndEnd(graphtools::Path const& mapping) const; - - /** - * Reverse lookup : get node and offset from a canonical pos - * @param canonical_pos canonical position - * @param node output variable for node name - * @param offset output variable for offset - */ - void nodeAndOffset(uint64_t canonical_pos, std::string& node, uint64_t& offset) const; - - /** - * Calculate the minimum distance in bp between two canonical positions - * @param pos1 start pos - * @param pos2 end pos - * @return basepairs between pos1 and pos2 - */ - uint64_t distance(uint64_t pos1, uint64_t pos2) const; - - /** - * Return the node id for a node name - * @param node_name name of node - * @return node id for the node - */ - NodeId nodeId(const std::string& node_name) const; - - /** - * @return the graph for these coordinates - */ - Graph const& getGraph() const; - -private: - struct GraphCoordinatesImpl; - std::unique_ptr _impl; -}; -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphcore/GraphOperations.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphcore/GraphOperations.hh deleted file mode 100644 index 6fbe3ad..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphcore/GraphOperations.hh +++ /dev/null @@ -1,34 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko , -// Peter Krusche - -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include "Graph.hh" - -namespace graphtools -{ -/** - * Reverse (and optionally complement) a graph - * @param graph the graph to reverse - * @param complement true to also reverse-complement all sequences - */ -Graph reverseGraph(Graph const& graph, bool complement = false); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphcore/GraphReferenceMapping.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphcore/GraphReferenceMapping.hh deleted file mode 100644 index e477d60..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphcore/GraphReferenceMapping.hh +++ /dev/null @@ -1,128 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Felix Schlesinger - -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include -#include -#include - -#include "Graph.hh" -#include "Path.hh" - -namespace graphtools -{ -typedef std::string ContigId; // Identifier of a contig (chromosome) within a reference -typedef int32_t Position; // 0-based position in a reference sequence - -/** - * Defines an interval on a (genomic) reference sequence - */ -class ReferenceInterval -{ -public: - ReferenceInterval(ContigId contig, Position start, Position end); - /** - * Create a 0-length interval with start=stop=pos. - * Represents the position right before base 'pos' (0-based) - */ - static ReferenceInterval makePosition(ContigId const& contig, Position pos); - /** - * Create a region by parsing it from a region string - * @param region string: :-. 0-based Half-open interval - * @return ReferenceInterval matching the region - * @throws If not a valid region string - */ - static ReferenceInterval parseRegion(std::string const& regionString); - friend bool operator<(ReferenceInterval const&, ReferenceInterval const&); - friend bool operator==(ReferenceInterval const&, ReferenceInterval const&); - friend std::ostream& operator<<(std::ostream&, ReferenceInterval const&); - - /** - * Length (number of bases covered) of the interval - */ - int32_t length() const; - - // Reference sequence (chromosome) name - ContigId const contig; - // Start 0-based closed (i.e. included) - Position const start; - // End 0-based open (i.e. excluded) - Position const end; -}; - -/** - * Map a node to a single piece of reference sequence - * Very simple 1-1 mapping for now - */ -class NodeReferenceMapping -{ -public: - /** - * Create a mapping from a node to a reference interval - * The reference interval must have the same length as the sequence of the node - */ - NodeReferenceMapping(Graph const&, NodeId, ReferenceInterval const&); - - /** - * Map a position within a node to a reference position using the NodeReferenceMapping - * @param offset Position within the node. Must be < node length - * @return 0-length interval at mapped position - */ - ReferenceInterval map(int32_t offset) const; - -private: - int32_t const nodeLength_; - ReferenceInterval const ref_; -}; - -/** - * Mapping of (a subset of) nodes in a graph to a reference sequence - * At most one mapping per node for now - */ -class GraphReferenceMapping -{ -public: - explicit GraphReferenceMapping(Graph const*); - - /** - * Map a node to a reference interval - * ReferenceInterval must have the same length as node sequence - */ - void addMapping(NodeId, ReferenceInterval const&); - /** - * Map a position within a node to a reference position - * @param node in the graph this GraphReferenceMapping is based on - * @param offset Position within the node. Must be < node length - * @return 0-length interval at mapped position if the node is mapped, nothing otherwise - */ - boost::optional map(NodeId node, int32_t offset) const; - /** - * Map the first mappable position in a path to a reference position - * I.e. the start position of the path in the first node that has a reference mapping - * @return 0-length interval at mapped position if the node is mapped, nothing otherwise - */ - boost::optional map(Path const&) const; - -private: - Graph const* const graph_; - std::unordered_map mappings_; -}; -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphcore/Path.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphcore/Path.hh deleted file mode 100644 index ddf3528..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphcore/Path.hh +++ /dev/null @@ -1,193 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include -#include -#include -#include - -#include "graphcore/Graph.hh" - -namespace graphtools -{ - -/** - * A path in a sequence graph is given by (1) a sequence of nodes and (2) start/end position on the first/last node. The - * start/end positions are 0-based and form a half-open interval. - */ -class Path -{ -public: - typedef std::vector::const_iterator const_iterator; - - /// Checks if the inputs define a well-formed path. - Path(const Graph* graph_raw_ptr, int32_t start_position, const std::vector& nodes, int32_t end_position); - ~Path() = default; - - bool operator==(const Path& other) const; - bool operator<(const Path& path) const; - - const_iterator begin() const { return nodes_.begin(); } - const_iterator end() const { return nodes_.end(); } - - /// Ids of nodes overlapped by the path - const std::vector& nodeIds() const { return nodes_; } - size_t numNodes() const { return nodeIds().size(); } - - /// Sequence of the entire path - std::string seq() const; - - /// Piece of node sequence that the path overlaps - std::string getNodeSeq(size_t node_index) const; - const Graph* graphRawPtr() const { return graph_raw_ptr_; } - std::string encode() const; - int32_t startPosition() const { return start_position_; } - int32_t endPosition() const { return end_position_; } - size_t length() const; - NodeId getNodeIdByIndex(const size_t node_index) const { return nodes_[node_index]; } - int32_t getStartPositionOnNodeByIndex(size_t node_index) const; - int32_t getEndPositionOnNodeByIndex(size_t node_index) const; - size_t getNodeOverlapLengthByIndex(size_t node_index) const; - - bool checkOverlapWithNode(NodeId node_id) const; - int32_t getDistanceFromPathStart(NodeId node, int32_t offset) const; - - // Path modifiers - // Moves start position by a specified length; the path gets longer/shorter if shift_len is positive/negative - // respectively. - void shiftStartAlongNode(int32_t shift_len); - // Moves end position by a specified length; the path gets longer/shorter if shift_len is positive/negative - // respectively. - void shiftEndAlongNode(int32_t shift_len); - // Moves path start to the end of the specified node. The new node must be a predecessor of the previous start node. - void extendStartToNode(NodeId node_id); - // Moves path start to the start of the specified node. The new node must be a predecessor of the previous start - // node. - void extendStartToIncludeNode(NodeId node_id); - // Moves path end to the start of the specified node. The new node must be a successor of the previous start node. - void extendEndToNode(NodeId node_id); - // Moves path end to the end of the specified node. The new node must be a successor of the previous start node. - void extendEndToIncludeNode(NodeId node_id); - // Moves path start to the start of the next node in the path. - void removeStartNode(); - // Moves path end to the end of the previous node in the path. - void removeEndNode(); - // Moves path start to the start of the next node if the start has zero-length overlap with the corresponding node; - // does nothing if path spans only one node. - void removeZeroLengthStart(); - // Moves path end to the end of the end of the previous node if the end of the path has zero-length overlap with the - // corresponding node; does nothing if path spans only one node. - void removeZeroLengthEnd(); - // Shortens the start of the path by a specified length. - void shrinkStartBy(int32_t shrink_len); - // Shortens the end of the path by a specified length. - void shrinkEndBy(int32_t shrink_len); - // Shortens the path by the specified lengths from each direction. - void shrinkBy(int32_t start_shrink_len, int32_t end_shrink_len); - - NodeId firstNodeId() const { return nodeIds().front(); } - NodeId lastNodeId() const { return nodeIds().back(); } - -private: - void assertValidity() const; - bool isNodePositionValid(NodeId node_id, int32_t position) const; - void assertPositionsOrdered() const; - void assertNonEmpty() const; - void assertFirstNodePosValid() const; - void assertLastNodePosValid() const; - void assertConnected() const; - void assertThatIndexIsValid(int32_t node_index) const; - - const Graph* graph_raw_ptr_; - int32_t start_position_; - int32_t end_position_; - std::vector nodes_; -}; - -std::ostream& operator<<(std::ostream& os, const Path& path); - -class ReversePath -{ - Path& path_; - -public: - explicit ReversePath(Path& path) - : path_(path) - { - } - - // TODO: add methods as needed - - NodeId firstNodeId() const { return path_.lastNodeId(); } - NodeId lastNodeId() const { return path_.firstNodeId(); } - - int32_t startPosition() const - { - return path_.graphRawPtr()->nodeSeq(path_.lastNodeId()).length() - path_.endPosition(); - } - - int32_t endPosition() const - { - return path_.graphRawPtr()->nodeSeq(path_.firstNodeId()).length() - path_.startPosition(); - } - - std::string seq() const - { - std::string ret = path_.seq(); - std::reverse(ret.begin(), ret.end()); - return ret; - } - - void shiftEndAlongNode(int32_t shift_len) { path_.shiftStartAlongNode(shift_len); } - void extendEndToNode(NodeId node_id) { path_.extendStartToNode(node_id); } - - friend std::ostream& operator<<(std::ostream& os, const ReversePath& path); -}; - -class ConstReversePath -{ - const Path& path_; - -public: - explicit ConstReversePath(const Path& path) - : path_(path) - { - } - - // TODO: add methods as needed - - NodeId firstNodeId() const { return path_.lastNodeId(); } - NodeId lastNodeId() const { return path_.firstNodeId(); } - - int32_t startPosition() const - { - return path_.graphRawPtr()->nodeSeq(path_.lastNodeId()).length() - path_.endPosition(); - } - - int32_t endPosition() const - { - return path_.graphRawPtr()->nodeSeq(path_.firstNodeId()).length() - path_.startPosition(); - } - - const Graph* graphRawPtr() const { return path_.graphRawPtr(); } -}; -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphcore/PathFamily.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphcore/PathFamily.hh deleted file mode 100644 index e53fc10..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphcore/PathFamily.hh +++ /dev/null @@ -1,74 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Felix Schlesinger , -// Peter Krusche -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include -#include -#include -#include -#include -#include - -#include "graphcore/Graph.hh" -#include "graphcore/Path.hh" - -namespace graphtools -{ - -/** - * Defines a Path Family (a set of paths) from a set of edges. - * Briefly, a path is part of a path family F if - * - it uses at least one edge in F - * - it uses an edge in F into or out-of any node where such an edge is present - */ -class PathFamily -{ -public: - explicit PathFamily(Graph*); - // Path family from all edges with the given label - PathFamily(Graph* graph, const std::string& label); - PathFamily(const PathFamily&); - PathFamily(PathFamily&&) noexcept; - ~PathFamily() noexcept; - - bool operator==(const PathFamily&) const; - bool operator!=(const PathFamily&) const; - - std::unordered_set const& edges() const; - const Graph& graph() const; - - // Check if a path in contained in (consistent with) F - bool containsPath(const Path&) const; - // Check if another path family contains a subset of edges in F - bool includes(const PathFamily&) const; - - void addEdge(NodeId first, NodeId second); - // Apply the given label on the graph to on all edges in F (and delete from others) - void setLabel(const std::string&); - -private: - struct Impl; - std::unique_ptr pimpl_; -}; - -std::ostream& operator<<(std::ostream& os, const PathFamily& path); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphcore/PathFamilyOperations.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphcore/PathFamilyOperations.hh deleted file mode 100644 index e67dfbe..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphcore/PathFamilyOperations.hh +++ /dev/null @@ -1,92 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Felix Schlesinger , -// Peter Krusche , -// Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include "Path.hh" -#include "PathFamily.hh" - -#include -#include -#include - -namespace graphtools -{ - -/** - * Generate path segments in a family which can be combined into longer paths. - * - * These segments are built by concatenating family edges into paths whenever - * this is possible uniquely, ignoring repeat / self-loop edges. - * - * @param family the path family - * @return a list of path segments - */ -std::list getPathSegmentsForFamily(graphtools::PathFamily const& family); - -/** - * Enumerate path segment combinations in family. - * - * Two path segments can be combined if they overlap or are adjacent and - * (if adjacent on different nodes) their linking edge is in the family. - * - * @param family a path family - * @param segments a set of path segments - * @param[out] paths output list of paths - * @param maxPaths maximum number of paths to generate - * @return true if all paths were generated, false if maxPaths was used to limit the number of paths - */ -bool enumeratePathCombinationsInFamily( - PathFamily const& family, std::list const& segments, std::list* paths, size_t maxPaths); - -/** - * Get all maximal paths in a path family, exhaustively - * - * Note that this function can generate an number of paths that is - * exponential in the number of nodes. - * - * @param family the path family - * @param[out] paths output list of paths - * @param maxPaths limit the number of paths - * @return true if all paths were enumerated, false if additional paths can be generated - * - * Note this will ignore self-edges / loops. - * - */ -bool getMaximalPathsForFamily( - graphtools::PathFamily const& family, std::list* paths, size_t maxPaths = std::numeric_limits::max()); - -/** - * Convert path to path family - * @param graph must match the graph used by path - * @param path a path on graph - * @return a path family containing all edges in path - */ -graphtools::PathFamily pathToPathFamily(graphtools::Graph& graph, graphtools::Path const& path); - -/** - * Get all path families from edge labels on a graph - * @param graph a graph (not const because path families are constructed from a non-const graph) - * @return mapping of label -> path family - */ -std::map getPathFamiliesFromGraph(graphtools::Graph& graph); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphcore/PathOperations.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphcore/PathOperations.hh deleted file mode 100644 index d3dc4c0..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphcore/PathOperations.hh +++ /dev/null @@ -1,175 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko , -// Peter Krusche -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include - -#include "graphcore/Path.hh" - -namespace graphtools -{ - -/** - * Computes all possible extensions of the path by the specified length in both directions - * - * @param start_extension_len Extension length of the start posision - * @param end_extension_len Extension length of the end position - * @return List of extended paths - */ -std::list extendPath(const Path& path, int32_t start_extension_len, int32_t end_extension_len); - -// Computes all possible extensions of the start of the path by the specified length -std::list extendPathStart(const Path& path, int32_t extension_len); - -// Computes all possible extensions of the end of the path by the specified length -std::list extendPathEnd(const Path& path, int32_t extension_len); - -/** - * Extend a path matching a query sequence to produce maximum exact + unique matches - * - * The path is extended at the end while the query string matches uniquely. - * - * @param path the path. We must have path.length() <= query.size() - qpos - * @param query query string. - * @param qpos position where path starts in query - * @return extended path - */ -Path extendPathEndMatching(Path path, const std::string& query, size_t qpos); - -/** - * Extend a path matching a query sequence to produce maximum exact + unique matches - * - * The path is extended at the start while the query string matches uniquely. - * - * @param path the path. We must have path.length() <= query.size() - qpos - * @param query query string. - * @param[out] qpos position where path starts in query -- updated as path is extended at start - * @return extended path - */ -Path extendPathStartMatching(Path path, const std::string& query, size_t& pos_in_query); - -/** - * Extend a path matching a query sequence to produce maximum exact + unique matches - * - * The path is extended at the start and end while the query string matches uniquely. - * - * @param path the path. We must have path.length() <= query.size() - qpos - * @param query query string. - * @param[out] qpos position where path starts in query -- updated as path is extended at start - * @return extended path - */ -Path extendPathMatching(Path path, const std::string& query, size_t& pos_in_query); - -/** - * Splits sequence into segments corresponding to the path - * - * @param path Any path - * @param sequence A string having the same length as the path - * @return Segments of the sequence corresponding to nodes spanned by the path - */ -std::vector splitSequenceByPath(const Path& path, const std::string& sequence); - -/** - * Return true if two paths are exactly adjacent - * (i.e. p1 starts just before p2, or the other way around) - * - * @param p1 first path - * @param p2 second path - * @return true if the paths are adjacent - */ -bool checkIfPathsAdjacent(Path const& p1, Path const& p2); - -/** - * Return true if two paths overlap either prefix - suffix or suffix-prefix - * @param p1 first path - * @param p2 second path - * @return true if the paths overlap - */ -bool checkPathPrefixSuffixOverlap(Path const& p1, Path const& p2); - -/** - * Paths can be merged if they overlap prefix-suffix / suffix-prefix. - * - * @param p1 first path - * @param p2 second path - * @return merged path - */ -Path mergePaths(Path const& p1, Path const& p2); - -/** - * Merge a set of paths - * - * This will merge paths iteratively until none of the resulting paths overlap - * - * @param paths a list of paths - */ -void greedyMerge(std::list& paths); - -/** - * Merge a set of paths - * - * This will merge paths exhaustively, each path is merged with all - * paths it overlaps until we cannot merge anymore - * - * @param paths a list of paths - */ -void exhaustiveMerge(std::list& paths); - -/** - * Return the intersection(s) between two paths - * - * Multiple paths may be returned when paths diverge and re-join. - * - * @param p1 first path - * @param p2 second path - * @return merged path - */ -std::list intersectPaths(Path const& p1, Path const& p2); - -/** - * Returns subpaths corresponding to overlap of the input path with each node it passes through - * - * @param path: any path - * @return single-node subpaths - */ -std::list generateSubpathForEachNode(const Path& path); - -/** - * Checks if two paths are bookended - * - * Two paths are considered bookended if positions of first path end and second path start are adjacent on the graph - * - * @param first_alignment: Any path - * @param second_alignment: Any path on same graph - * @return true if paths are bookended - */ -bool checkIfBookended(const Path& first_path, const Path& second_path); - -/** - * Concatenates two bookended paths into a longer path - * - * @param first_alignment: Any path - * @param second_alignment: Any path that is bookended with the first - * @return Concatenated path - */ -Path concatenatePaths(const Path& first_path, const Path& second_path); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphio/AlignmentWriter.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphio/AlignmentWriter.hh deleted file mode 100644 index e075b9a..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphio/AlignmentWriter.hh +++ /dev/null @@ -1,52 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Felix Schlesinger , -// Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include -#include -#include - -#include "graphalign/GraphAlignment.hh" -#include "graphcore/GraphReferenceMapping.hh" - -namespace graphtools -{ - -class AlignmentWriter -{ -public: - virtual ~AlignmentWriter() = default; - virtual void write( - const std::string& locusId, const std::string& fragmentName, const std::string& query, bool isFirstMate, - bool isReversed, bool isMateReversed, const GraphAlignment& alignment) - = 0; -}; - -class BlankAlignmentWriter : public AlignmentWriter -{ -public: - ~BlankAlignmentWriter() override = default; - void write( - const std::string& locusId, const std::string& fragmentName, const std::string& query, bool isFirstMate, - bool isReversed, bool isMateReversed, const GraphAlignment& alignment) override; -}; -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphio/GraphJson.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphio/GraphJson.hh deleted file mode 100644 index 8ad6c63..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphio/GraphJson.hh +++ /dev/null @@ -1,60 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Felix Schlesinger -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -// cppcheck-suppress missingInclude -#include "nlohmann/json.hpp" - -#include "graphcore/Graph.hh" -#include "graphcore/GraphReferenceMapping.hh" - -using namespace graphtools; - -namespace graphtools -{ - -using Json = nlohmann::json; - -/** - * Load JSON from file and parse Graph. - * Graph can be either directly the top-level object in the json or under 'graph' - */ -Graph loadGraph(std::string const& jsonPath); - -/** - * Create graph from Json representation. - * @throws if the Json does not represent a valid graph - */ -Graph parseGraph(Json const& jsonGraph); - -/** - * Create Json representation of the graph - */ -Json graphToJson(Graph const& graph); - -/** - * Load Reference mapping from graph description - * @param jRefmap Json representation of referenceMapping. Must match the graph - * @param graph Graph to map to reference. - * @throws if the Json does not represent a valid reference map or does not match the graph - */ -GraphReferenceMapping parseReferenceMapping(Json const& jRefmap, Graph const& graph); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphutils/BaseMatching.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphutils/BaseMatching.hh deleted file mode 100644 index dafcbaf..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphutils/BaseMatching.hh +++ /dev/null @@ -1,164 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include -#include -#include - -namespace graphtools -{ - -namespace codes -{ - using BaseCode = unsigned char; - const int kMaxBaseCode = 15; - - // Core base codes - const BaseCode A = 0; - const BaseCode C = 1; - const BaseCode G = 2; - const BaseCode T = 3; - const BaseCode X = 4; - - // Degenerate base codes - const BaseCode B = 5; - const BaseCode D = 6; - const BaseCode H = 7; - const BaseCode K = 8; - const BaseCode M = 9; - const BaseCode N = 10; - const BaseCode R = 11; - const BaseCode S = 12; - const BaseCode V = 13; - const BaseCode W = 14; - const BaseCode Y = 15; - - const int kMaxQueryBaseCode = 4; - const int kMaxReferenceBaseCode = 15; - - const int maxBaseAscii = 255; - - // Currently, low-quality (lower case) bases get the same encoding as their high-quality counterparts. We should - // extend the coding scheme when we are ready to deal with base-quality in the alignment. - - // Core bases A, C, G, T and degenerate bases B, D, H, K, M, N, S, R, V, W, Y all receive distinct codes. All other - // base symbols are coded as X, which is the code intended to mismatch everything. - const std::array kReferenceBaseEncodingTable - = { X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, - X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, - X, A, B, C, D, X, X, G, H, X, X, K, X, M, N, X, X, X, R, S, T, X, V, W, X, Y, X, X, X, X, X, X, - X, A, X, C, X, X, X, G, X, X, X, X, X, X, X, X, X, X, X, X, T, X, X, X, X, X, X, X, X, X, X, X, - X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, - X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, - X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, - X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X }; - - // Core bases A, C, G, T all recieve distinct codes. All other base symbols are coded as X. - const std::array kQueryBaseEncodingTable - = { X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, - X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, - X, A, X, C, X, X, X, G, X, X, X, X, X, X, X, X, X, X, X, X, T, X, X, X, X, X, X, X, X, X, X, X, - X, A, X, C, X, X, X, G, X, X, X, X, X, X, X, X, X, X, X, X, T, X, X, X, X, X, X, X, X, X, X, X, - X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, - X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, - X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, - X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X, X }; - - // We use the standard matching rules for degenerate bases. The X symbol corresponds to a mismatch - const std::array, codes::kMaxReferenceBaseCode + 1> - kReferenceQueryCodeMatchLookupTable = { - // clang-format off - // A C G T X - { { true, false, false, false, false }, // A - { false, true, false, false, false }, // C - { false, false, true, false, false }, // G - { false, false, false, true, false }, // T - { false, false, false, false, false }, // X - { false, true, true, true, false }, // B - { true, false, true, true, false }, // D - { true, true, false, true, false }, // H - { false, false, true, true, false }, // K - { true, true, false, false, false }, // M - { true, true, true, true, false }, // N - { true, false, true, false, false }, // R - { false, true, true, false, false }, // S - { true, true, true, false, false }, // V - { true, false, false, true, false }, // W - { false, true, false, true, false } // Y - } - // clang-format on - }; -} - -inline codes::BaseCode encodeReferenceBase(char base) { return codes::kReferenceBaseEncodingTable[base]; } - -inline codes::BaseCode encodeQueryBase(char base) { return codes::kQueryBaseEncodingTable[base]; } - -/** - * Checks if a pair of reference and query base codes corresponds to matching bases - * - * Examples: - * checkIfReferenceBaseCodeMatchesQueryBaseCode(encodeReferenceBase('C'), encodeQueryBase('c')) == true - * checkIfReferenceBaseCodeMatchesQueryBaseCode(encodeReferenceBase('T'), encodeQueryBase('Y')) == true - * checkIfReferenceBaseCodeMatchesQueryBaseCode(encodeReferenceBase('a'), encodeQueryBase('W')) == true - * checkIfReferenceBaseCodeMatchesQueryBaseCode(encodeReferenceBase('C'), encodeQueryBase('G')) == false - * - */ -inline bool checkIfReferenceBaseCodeMatchesQueryBaseCode(codes::BaseCode referenceCode, codes::BaseCode queryCode) -{ - // Temporary asserts until we add validation code for reference/query strings. - assert(referenceCode <= codes::kMaxReferenceBaseCode); - assert(queryCode <= codes::kMaxQueryBaseCode); - - return codes::kReferenceQueryCodeMatchLookupTable[referenceCode][queryCode]; -} - -inline bool checkIfReferenceBaseMatchesQueryBase(char referenceBase, char queryBase) -{ - return checkIfReferenceBaseCodeMatchesQueryBaseCode(encodeReferenceBase(referenceBase), encodeQueryBase(queryBase)); -} - -/** - * Checks if a reference sequence matches a query sequence - * - * @param reference And reference sequence - * @param query Any query sequence - * @return True if the sequences match - */ -inline bool checkIfReferenceAndQuerySequencesMatch(const std::string& reference, const std::string& query) -{ - if (reference.length() != query.length()) - { - return false; - } - - for (size_t index = 0; index != reference.length(); ++index) - { - if (!checkIfReferenceBaseMatchesQueryBase(reference[index], query[index])) - { - return false; - } - } - - return true; -} -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphutils/DepthTest.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphutils/DepthTest.hh deleted file mode 100644 index d1debc7..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphutils/DepthTest.hh +++ /dev/null @@ -1,54 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Sai Chen , -// Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include -#include - -using boost::math::normal_distribution; - -class DepthTest -{ -public: - /** - * Set up depth test - * @param expectedNumReads The mean number of reads when the coverage is as expected - * @param stdDeviation The standard deviation of the number of reads - * @param lowerSignificanceThreshold P value cutoff at the lower tail of the distribution - * @param upperSignificanceThreshold P value cutoff at the upper tail of the distribution - */ - DepthTest( - int32_t expectedNumReads, double stdDeviation, double lowerSignificanceThreshold, - double upperSignificanceThreshold); - - /** - * Given observed number of reads, return true if pass depth test - */ - bool testReadCount(int32_t observedNumReads); - -private: - int32_t expectedNumReads_; - double stdDeviation_; - double lowerSignificanceThreshold_; - double upperSignificanceThreshold_; - const normal_distribution<> coverageDistribution_; -}; diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphutils/IntervalBuffer.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphutils/IntervalBuffer.hh deleted file mode 100644 index 382b270..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphutils/IntervalBuffer.hh +++ /dev/null @@ -1,77 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Peter Krusche -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include -#include -#include -#include -#include - -namespace intervals -{ - -class IntervalBuffer -{ -public: - /** tracks intervals over a number of lanes */ - IntervalBuffer(); - IntervalBuffer(IntervalBuffer const& rhs); - virtual ~IntervalBuffer(); - IntervalBuffer& operator=(IntervalBuffer const& rhs); - - /** - * @brief Add an interval to a lane - * - * @param start interval coordinates - * @param end interval coordinates - * @param lane lane to add to - */ - void addInterval(int64_t start, int64_t end, size_t lane); - - /** - * @brief Advance buffer, discarding all intervals with end < to - * - * @param to interval minimum end position; pass -1 to clear buffer - */ - void advance(int64_t to); - - /** - * @brief Check if interval is fully covered in a given lane - */ - bool isCovered(int64_t start, int64_t end, size_t lane) const; - - /** - * @brief Check if interval is partially covered in a given lane - */ - bool hasOverlap(int64_t start, int64_t end, size_t lane) const; - - /** - * Get the intervals for a particular lane - * @return intervals for a particular lane - */ - std::list> getIntervals(size_t lane) const; - -private: - struct Impl; - std::unique_ptr pimpl_; -}; -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphutils/IntervalList.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphutils/IntervalList.hh deleted file mode 100644 index b394042..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphutils/IntervalList.hh +++ /dev/null @@ -1,278 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Peter Krusche -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -/** - * \brief Store a list of non-intersecting intervals - * - * - * \file IntervalList.hh - * \author Peter Krusche - * \email pkrusche@illumina.com - * - */ - -#pragma once - -#include -#include -#include -#include -#include -#include -#include - -namespace intervals -{ - -/** interval interface */ -struct interval -{ - explicit interval(int64_t _start = -1, int64_t _end = -1) - : start(_start) - , end(_end) - { - } - virtual ~interval() = default; - - // merge two intervals - virtual void merge(interval const& rhs) - { - if (start < 0) - { - start = rhs.start; - } - else - { - start = std::min(rhs.start, start); - } - if (end < 0) - { - end = rhs.end; - } - else - { - end = std::max(rhs.end, end); - } - } - - virtual void resize(int64_t _start, int64_t _end) - { - if (_start >= 0) - { - start = _start; - } - if (_end >= 0) - { - end = _end; - } - } - - int64_t start, end; -}; - -template class IntervalList -{ -public: - virtual ~IntervalList() = default; - - void add(interval_t const& iv) - { - if (iv.start > iv.end) - { - return; - } - - // find first interval that ends after start - 1 (so we join adjacent intervals) - auto ivr = intervals.lower_bound(iv.start - 1); - if (ivr == intervals.end()) - { - // no interval ends after start => prepend - intervals[iv.end] = iv; - } - else - { - // first interval that ends after start - // check overlap - - // do they overlap - // we know ivr->first >= start - if (ivr->second.start <= iv.end) - { - // overlap => merge - interval_t tmp = ivr->second; - tmp.merge(iv); - intervals.erase(ivr); - add(tmp); - } - else - { - // no overlap: - // x y s f - //-[---]--------[-------]------- - // |----| - // start end - // (y must be < start because otherwise we'd have found it with lower_bound) - // => insert interval - intervals[iv.end] = iv; - } - } - } - - /** get all intervals that overlap a range */ - interval_t query(int64_t start, int64_t end) const - { - interval_t ivs; - - if (end < start) - { - return ivs; - } - - // find first interval that ends after start - auto it = intervals.cbegin(); - - int x = 0; - while (it != intervals.cend() && it->second.end < start && x < 3) - { - ++it; - ++x; - } - - // if using advance, we don't need to search -- the first interval will - // already be the one we're looking for - if (it != intervals.cend() && it->second.end < start) - { - it = intervals.lower_bound(start); - } - - // overlap if it->second.start <= end - while (it != intervals.cend() && - // check if overlap - it->second.start <= end) - { - ivs.merge(it->second); - ++it; - } - return ivs; - } - - /** get all intervals that overlap a range */ - template > void get(int64_t start, int64_t end, container_t& output) - { - if (end < start) - { - return; - } - - // find first interval that ends after start - auto it = intervals.lower_bound(start); - - // overlap if it->second.start <= end - while (it != intervals.end() && - // check if overlap - it->second.start <= end) - { - output.push_back(it->second); - ++it; - } - } - - /** reset / remove interval range */ - void remove_from(int64_t start) - { - // find first interval that ends after start - auto it = intervals.lower_bound(start); - - // keep all intervals that end before start - // know: - // it->second.start <= it->second.end && - // start <= it->second.end && - // start <= end - // region to delete starts inside interval? - // (if interval starts exactly at start, we can remove it) - if (it != intervals.end() && it->second.start < start) - { - interval_t tmp = it->second; - intervals.erase(it, intervals.end()); - // start is > end if end == -1 - tmp.resize(tmp.start, start - 1); - intervals[tmp.end] = tmp; - } - else - { - // remove stuff that ends afterwards, if any - intervals.erase(it, intervals.end()); - } - } - - /** reset / remove interval range */ - void remove_to(int64_t end) - { - if (end < 0) - { - intervals.clear(); - return; - } - - // find first interval that ends after end - auto it = intervals.lower_bound(end); - if (it != intervals.end() && it->second.start <= end) - { - if (it->first > end) - { - it->second.resize(end + 1, it->first); - } - else // fully contained => also remove - { - ++it; - } - } - intervals.erase(intervals.begin(), it); - } - - /** remove values outside region */ - void keep_only(int64_t _start, int64_t _end) - { - remove_to(_start - 1); - remove_from(_end + 1); - } - - /** return intervals in arbitrary container */ - template > container_t getIntervals() const - { - container_t t; - for (auto const& iv : intervals) - { - t.push_back(iv.second); - } - return t; - } - -protected: - std::map intervals; - - void ensure_is_interval() - { - // make sure interval_t is derived from interval - interval* iv = new interval_t(); - delete iv; - } -}; -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphutils/KmerEncoding.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphutils/KmerEncoding.hh deleted file mode 100644 index cecb366..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphutils/KmerEncoding.hh +++ /dev/null @@ -1,103 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Chris Saunders -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include -#include -#include - -namespace graphtools -{ - -struct TwoBitKmerEncoder -{ - using KmerKey_t = uint32_t; - - explicit TwoBitKmerEncoder(const size_t kmerLength) - : kmerLength_(kmerLength) - { - const size_t maxKeyBitCount(8 * sizeof(KmerKey_t)); - if (maxKeyBitCount < (kmerLength_ * 2)) - { - throw std::logic_error( - "Can't support kmer size of " + std::to_string(kmerLength_) + " with a " - + std::to_string(maxKeyBitCount) + "bit key type."); - } - } - - KmerKey_t encode(const std::string& kmer) const - { - if (kmer.size() != kmerLength_) - { - throw std::logic_error( - "kmer size (" + std::to_string(kmer.size()) + ") does not match expected size (" - + std::to_string(kmerLength_) + "), for kmer '" + kmer + "'."); - } - - KmerKey_t kmerKey(0); - for (unsigned i(0); i < kmerLength_; ++i) - { - kmerKey = (kmerKey << 2) | baseToIndex(kmer[i]); - } - return kmerKey; - } - - std::string decode(KmerKey_t kmerKey) const - { - std::string kmer(kmerLength_, 'N'); - for (unsigned i(0); i < kmerLength_; ++i) - { - kmer[kmerLength_ - (i + 1)] = indexToBase(kmerKey & 0x3); - kmerKey >>= 2; - } - return kmer; - } - -private: - static uint8_t baseToIndex(const char c) { return baseToIndex_.table[static_cast(c)]; } - - static char indexToBase(const uint8_t i) - { - static const char bases[] = "ACGT"; - if (i > 3) - { - throw std::logic_error("Unexpected kmer index: '" + std::to_string(i) + "'"); - } - return bases[i]; - } - - struct BaseToIndex - { - BaseToIndex() - { - std::fill(table, table + 256, 0); - table[static_cast('C')] = 1; - table[static_cast('G')] = 2; - table[static_cast('T')] = 3; - } - - uint8_t table[256]; - }; - - static BaseToIndex baseToIndex_; - size_t kmerLength_; -}; -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphutils/PairHashing.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphutils/PairHashing.hh deleted file mode 100644 index 49651a2..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphutils/PairHashing.hh +++ /dev/null @@ -1,49 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Peter Krusche -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include - -namespace graphtools -{ - -static inline void hash_combine(std::size_t& /*seed*/) {} - -template inline void hash_combine(std::size_t& seed, const T& v, Rest... rest) -{ - std::hash hasher; - seed ^= hasher(v) + 0x9e3779b9 + (seed << 6) + (seed >> 2); - hash_combine(seed, rest...); -} -} - -namespace std -{ -template struct hash> -{ - std::size_t operator()(const std::pair& t) const - { - std::size_t result = 0; - graphtools::hash_combine(result, t.first, t.second); - return result; - } -}; -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphutils/SequenceOperations.hh b/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphutils/SequenceOperations.hh deleted file mode 100644 index 36f2e60..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/include/graphutils/SequenceOperations.hh +++ /dev/null @@ -1,82 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#pragma once - -#include -#include -#include - -namespace graphtools -{ - -using StringPair = std::pair; - -/** - * Splits a string by the specified delimiter - */ -std::vector splitStringByDelimiter(const std::string& str, char sep = ' '); - -/** - * Splits a string by whitespace - */ -std::vector splitStringByWhitespace(const std::string& str); - -/** - * Return reversed sequence - * @param seq sequence to reverse - * @return reversed sequence - */ -static inline std::string reverseString(std::string seq) -{ - std::reverse(seq.begin(), seq.end()); - return seq; -} - -/** - * Return reverse complemented sequence - * @param seq sequence to reverse-complement - * @return reverse complemented sequence - */ -std::string reverseComplement(std::string seq); - -/** - * Returns true if sequence consists of uppercase symbols over extended nucleotide alphabet - */ -bool checkIfReferenceSequence(const std::string& sequence); - -/** - * Checks if sequence consists of uppercase As, Ts, Cs, and Gs - */ -bool checkIfNucleotideReferenceSequence(const std::string& sequence); - -/** - * Expands reference symbol into strings made up of matching nucleotides - */ -std::string const& expandReferenceSymbol(char reference_symbol); - -/** - * Expands reference sequence by expanding each degenerate symbol - * - * @param sequence Reference sequence to expand - * @return All nucleotide sequences matching the input sequence - */ -void expandReferenceSequence(const std::string& sequence, std::vector& target); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/GappedAligner.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/GappedAligner.cpp deleted file mode 100644 index 268fd3a..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/GappedAligner.cpp +++ /dev/null @@ -1,348 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko , -// Roman Petrovski -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphalign/GappedAligner.hh" - -#include -#include - -#include -#include - -#include "graphalign/GraphAlignmentOperations.hh" -#include "graphalign/LinearAlignmentOperations.hh" -#include "graphcore/PathOperations.hh" - -using boost::optional; -using std::list; -using std::logic_error; -using std::make_pair; -using std::string; -using std::to_string; - -namespace graphtools -{ - -/** - * Trim prefix of a path if it is close to node edge - * - * @param requested_trim_len: length of the prefix to attempt to trim by - * @param min_path_len: minimal length of the trimmed path - * @param[in|out] path: any path - * @return: actual trim length - */ -static int32_t trimPrefixNearNodeEdge(int32_t requested_trim_len, int32_t min_path_len, Path& path) -{ - if (path.numNodes() == 1 || static_cast(path.length()) <= min_path_len) - { - return 0; - } - - const int32_t overlap_len_with_first_node = path.getNodeOverlapLengthByIndex(0); - if (overlap_len_with_first_node > requested_trim_len) - { - return 0; - } - - const bool can_be_fully_trimmed = static_cast(path.length()) >= requested_trim_len + min_path_len; - const int32_t actual_trim_len = can_be_fully_trimmed ? requested_trim_len : path.length() - min_path_len; - - path.shrinkStartBy(actual_trim_len); - return actual_trim_len; -} - -/** - * Trim suffix of a path if it is close to node edge - * - * @param requested_trim_len: length of the suffix to attempt to trim by - * @param min_path_len: minimal length of the shrank path - * @param[in|out] path: any path - * @return: the length by which the path's end was trimmed - */ -static int32_t trimSuffixNearNodeEdge(int32_t requested_trim_len, int32_t min_path_len, Path& path) -{ - if (path.numNodes() == 1 || static_cast(path.length()) <= min_path_len) - { - return 0; - } - - const int32_t overlap_len_with_last_node = path.getNodeOverlapLengthByIndex(path.numNodes() - 1); - if (overlap_len_with_last_node > requested_trim_len) - { - return 0; - } - - const bool can_be_fully_trimmed = static_cast(path.length()) >= requested_trim_len + min_path_len; - const int32_t actual_trim_len = can_be_fully_trimmed ? requested_trim_len : path.length() - min_path_len; - - path.shrinkEndBy(actual_trim_len); - return actual_trim_len; -} - -list GappedGraphAligner::align(const string& query, AlignerSelector& alignerSelector) const -{ - try - { - optional optional_seed = searchForAlignmentSeed(query); - - if (optional_seed) - { - Path& seed_path = optional_seed->path; - int seed_start_on_query = optional_seed->start_on_query; - - const int kMinPathLength = 2; - trimSuffixNearNodeEdge(seed_affix_trim_len_, kMinPathLength, seed_path); - const int trimmed_prefix_len = trimPrefixNearNodeEdge(seed_affix_trim_len_, kMinPathLength, seed_path); - return extendSeedToFullAlignments( - seed_path, query, seed_start_on_query + trimmed_prefix_len, alignerSelector); - } - else - { - return {}; - } - } - catch (const std::exception& e) - { - throw logic_error("Unable to align " + query + ": " + e.what()); - } -} - -optional GappedGraphAligner::searchForAlignmentSeed(const string& query) const -{ - string upperQuery = query; - boost::to_upper(upperQuery); - - optional optional_seed; - - bool found_multipath_kmer = false; - size_t kmer_start_position = 0; - while (kmer_start_position + kmer_len_ <= upperQuery.length()) - { - const string kmer = upperQuery.substr(kmer_start_position, static_cast(kmer_len_)); - - // Initiate seed construction from a unique kmer - auto num_kmer_paths = kmer_index_.numPaths(kmer); - if (num_kmer_paths > 1) - { - found_multipath_kmer = true; - } - - if (num_kmer_paths == 1) - { - const Path kmer_path = kmer_index_.getPaths(kmer).front(); - // This call updates kmer_start_position to the start of the extended path - Path extended_path = extendPathMatching(kmer_path, upperQuery, kmer_start_position); - - if (!optional_seed || extended_path.length() > optional_seed->path.length()) - { - optional_seed = AlignmentSeed(extended_path, kmer_start_position); - } - - kmer_start_position += extended_path.length(); - } - else - { - ++kmer_start_position; - } - } - - if (optional_seed || !found_multipath_kmer) - { - return optional_seed; - } - - // If the search for unique kmer failed, consider kmers that correspond to multiple paths - const int kMaxPathCount = 10; - kmer_start_position = 0; - while (kmer_start_position + kmer_len_ <= upperQuery.length()) - { - const string kmer = upperQuery.substr(kmer_start_position, static_cast(kmer_len_)); - - const int numPaths = kmer_index_.numPaths(kmer); - if (0 < numPaths && numPaths <= kMaxPathCount) - { - size_t longest_kmer_path_extension = 0; - size_t kmer_start_position_for_longest_extension = 0; - for (const Path& kmer_path : kmer_index_.getPaths(kmer)) - { - size_t kmer_start_position_for_kmer_path = kmer_start_position; - Path extended_path = extendPathMatching(kmer_path, upperQuery, kmer_start_position_for_kmer_path); - - if (longest_kmer_path_extension < extended_path.length()) - { - longest_kmer_path_extension = extended_path.length(); - kmer_start_position_for_longest_extension = kmer_start_position_for_kmer_path; - } - - if (!optional_seed || extended_path.length() > optional_seed->path.length()) - { - optional_seed = AlignmentSeed(extended_path, kmer_start_position_for_kmer_path); - } - } - - kmer_start_position = kmer_start_position_for_longest_extension + longest_kmer_path_extension; - } - else - { - ++kmer_start_position; - } - } - - return optional_seed; -} - -list GappedGraphAligner::extendSeedToFullAlignments( - Path seed_path, const string& query, size_t seed_start_on_query, AlignerSelector& alignerSelector) const -{ - assert(seed_path.length() > 1); - - // Generate prefix extensions - list prefix_extensions; - size_t query_prefix_len = seed_start_on_query; - if (query_prefix_len != 0) - { - const string query_prefix = query.substr(0, query_prefix_len); - Path prefix_seed_path = seed_path; - prefix_seed_path.shrinkEndBy(seed_path.length()); - prefix_extensions - = extendAlignmentPrefix(prefix_seed_path, query_prefix, query_prefix_len + padding_len_, alignerSelector); - } - else - { - // Because (a) empty alignments are currently disallowed and (b) we don't want to deal with an empty list of - // prefix_extensions we create a 1bp prefix artificially. - query_prefix_len = 1; - Path prefix_path = seed_path; - prefix_path.shrinkEndBy(prefix_path.length() - 1); - prefix_extensions = { make_pair(prefix_path, Alignment(0, "1M")) }; - seed_path.shrinkStartBy(1); - } - - // Generate suffix extensions - list suffix_extensions; - size_t query_suffix_len = query.length() - seed_path.length() - query_prefix_len; - if (query_suffix_len != 0) - { - const string query_suffix = query.substr(query_prefix_len + seed_path.length(), query_suffix_len); - Path suffix_seed_path = seed_path; - suffix_seed_path.shrinkStartBy(seed_path.length()); - suffix_extensions - = extendAlignmentSuffix(suffix_seed_path, query_suffix, query_suffix_len + padding_len_, alignerSelector); - } - else - { - // Because (a) empty alignments are currently disallowed and (b) we don't want to deal with an empty list of - // suffix_extensions we create a 1bp suffix artificially. - Path suffix_path = seed_path; - suffix_path.shrinkStartBy(suffix_path.length() - 1); - suffix_extensions = { make_pair(suffix_path, Alignment(0, "1M")) }; - seed_path.shrinkEndBy(1); - } - - // Merge alignments together - list top_paths_and_alignments; - for (PathAndAlignment& prefix_path_and_alignment : prefix_extensions) - { - Path& prefix_path = prefix_path_and_alignment.first; - Path prefix_plus_seed_path = concatenatePaths(prefix_path, seed_path); - - Alignment& prefix_alignment = prefix_path_and_alignment.second; - Alignment kmer_alignment(prefix_alignment.referenceLength(), to_string(seed_path.length()) + "M"); - Alignment prefix_plus_kmer_alignment = mergeAlignments(prefix_alignment, kmer_alignment); - - for (PathAndAlignment& suffix_path_and_alignment : suffix_extensions) - { - Path& suffix_path = suffix_path_and_alignment.first; - Alignment& suffix_alignment = suffix_path_and_alignment.second; - Path full_path = concatenatePaths(prefix_plus_seed_path, suffix_path); - - suffix_alignment.setReferenceStart(prefix_plus_seed_path.length()); - Alignment full_alignment = mergeAlignments(prefix_plus_kmer_alignment, suffix_alignment); - top_paths_and_alignments.push_back(make_pair(full_path, full_alignment)); - } - } - - list top_graph_alignments; - for (PathAndAlignment& path_and_alignment : top_paths_and_alignments) - { - Path& path = path_and_alignment.first; - Alignment& alignment = path_and_alignment.second; - top_graph_alignments.push_back(projectAlignmentOntoGraph(alignment, path)); - } - - top_graph_alignments.sort(); - top_graph_alignments.unique(); - return top_graph_alignments; -} - -list GappedGraphAligner::extendAlignmentPrefix( - const Path& seed_path, const string& query_piece, size_t extension_len, AlignerSelector& alignerSelector) const -{ - assert(seed_path.length() == 0); - - int32_t top_alignment_score = INT32_MIN; - list top_paths_and_alignments - = alignerSelector.suffixAlign(seed_path, query_piece, extension_len, top_alignment_score); - - for (PathAndAlignment& path_and_alignment : top_paths_and_alignments) - { - Path& path = path_and_alignment.first; - Alignment& alignment = path_and_alignment.second; - alignment.setReferenceStart(0); - - const int32_t overhang = path.length() - alignment.referenceLength(); - path.shrinkStartBy(overhang); - - if (!checkConsistency(path_and_alignment.second, path.seq(), query_piece)) - { - throw std::logic_error("Inconsistent prefix"); - } - } - - return top_paths_and_alignments; -} - -list GappedGraphAligner::extendAlignmentSuffix( - const Path& seed_path, const string& query_piece, size_t extension_len, AlignerSelector& alignerSelector) const -{ - assert(seed_path.length() == 0); - - int32_t top_alignment_score = INT32_MIN; - list top_paths_and_alignments - = alignerSelector.prefixAlign(seed_path, query_piece, extension_len, top_alignment_score); - - for (PathAndAlignment& path_and_alignment : top_paths_and_alignments) - { - if (!checkConsistency(path_and_alignment.second, path_and_alignment.first.seq(), query_piece)) - { - throw std::logic_error("Inconsistent suffix"); - } - - Path& path = path_and_alignment.first; - Alignment& alignment = path_and_alignment.second; - - const int32_t overhang = path.length() - alignment.referenceLength(); - path.shrinkEndBy(overhang); - } - - return top_paths_and_alignments; -} -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/GraphAlignment.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/GraphAlignment.cpp deleted file mode 100644 index 5280757..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/GraphAlignment.cpp +++ /dev/null @@ -1,220 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include -#include -#include - -#include "graphalign/GraphAlignment.hh" -#include "graphalign/LinearAlignmentOperations.hh" -#include "graphcore/PathOperations.hh" - -using std::list; -using std::map; -using std::string; -using std::to_string; - -namespace graphtools -{ -void GraphAlignment::assertValidity() const -{ - for (size_t node_index = 0; node_index != path_.numNodes(); ++node_index) - { - const Alignment& node_alignment = alignments_[node_index]; - - const bool is_start_wrong - = path_.getStartPositionOnNodeByIndex(node_index) != (int32_t)node_alignment.referenceStart(); - - const int32_t node_alignment_end = node_alignment.referenceLength() + node_alignment.referenceStart(); - const bool is_end_wrong = path_.getEndPositionOnNodeByIndex(node_index) != node_alignment_end; - - if (is_start_wrong || is_end_wrong) - { - std::ostringstream graph_alignment_encoding; - graph_alignment_encoding << *this; - throw std::logic_error( - "Path " + path_.encode() + " is not compatible with graph alignment " + graph_alignment_encoding.str()); - } - } -} - -uint32_t GraphAlignment::queryLength() const -{ - uint32_t query_span = 0; - for (const auto& alignment : alignments_) - { - query_span += alignment.queryLength(); - } - return query_span; -} - -uint32_t GraphAlignment::referenceLength() const -{ - uint32_t reference_span = 0; - for (const auto& alignment : alignments_) - { - reference_span += alignment.referenceLength(); - } - return reference_span; -} - -uint32_t GraphAlignment::numMatches() const -{ - uint32_t num_matches = 0; - for (const auto& alignment : alignments_) - { - num_matches += alignment.numMatched(); - } - return num_matches; -} - -bool GraphAlignment::overlapsNode(NodeId node_id) const -{ - return path_.checkOverlapWithNode(static_cast(node_id)); -} - -list GraphAlignment::getIndexesOfNode(NodeId node_id) const -{ - list indexes; - const auto num_alignments = static_cast(alignments_.size()); - for (int32_t node_index = 0; node_index != num_alignments; ++node_index) - { - const NodeId cur_node_id = path_.getNodeIdByIndex(static_cast(node_index)); - if (cur_node_id == node_id) - { - indexes.push_back(node_index); - } - } - return indexes; -} - -string GraphAlignment::generateCigar() const -{ - string graph_cigar; - for (int32_t index = 0; index != (int32_t)size(); ++index) - { - const int32_t node_id = path_.getNodeIdByIndex(static_cast(index)); - graph_cigar += std::to_string(node_id); - const Alignment& alignment = alignments_[index]; - graph_cigar += "[" + alignment.generateCigar() + "]"; - } - return graph_cigar; -} - -bool GraphAlignment::operator<(const GraphAlignment& other) const -{ - if (!(path_ == other.path_)) - { - return path_ < other.path_; - } - - return alignments_ < other.alignments_; -} - -void GraphAlignment::shrinkStart(int reference_length) -{ - int prefix_query_length = 0; - - if (reference_length >= (int)referenceLength()) - { - std::stringstream string_stream; - string_stream << "Cannot shrink start of " << *this << " by " << reference_length; - throw std::logic_error(string_stream.str()); - } - - path_.shrinkStartBy(reference_length); - - size_t leftover_reference_length = reference_length; - - auto first_suffix_alignment_iter = alignments_.begin(); - while (leftover_reference_length >= first_suffix_alignment_iter->referenceLength()) - { - leftover_reference_length -= first_suffix_alignment_iter->referenceLength(); - prefix_query_length += first_suffix_alignment_iter->queryLength(); - ++first_suffix_alignment_iter; - } - - if (leftover_reference_length != 0) - { - const int split_position = first_suffix_alignment_iter->referenceStart() + leftover_reference_length; - Alignment suffix = first_suffix_alignment_iter->splitAtReferencePosition(split_position); - prefix_query_length += first_suffix_alignment_iter->queryLength(); - *first_suffix_alignment_iter = suffix; - } - - Alignment softclipAlignment(first_suffix_alignment_iter->referenceStart(), to_string(prefix_query_length) + "S"); - *first_suffix_alignment_iter = mergeAlignments(softclipAlignment, *first_suffix_alignment_iter); - - alignments_.erase(alignments_.begin(), first_suffix_alignment_iter); - - assertValidity(); -} - -void GraphAlignment::shrinkEnd(int reference_length) -{ - int suffix_query_length = 0; - - if (reference_length >= (int)referenceLength()) - { - std::stringstream string_stream; - string_stream << "Cannot shrink start of " << *this << " by " << reference_length; - throw std::logic_error(string_stream.str()); - } - - path_.shrinkEndBy(reference_length); - - size_t leftover_reference_length = reference_length; - - auto last_prefix_alignment_iter = alignments_.end() - 1; - while (leftover_reference_length >= last_prefix_alignment_iter->referenceLength()) - { - leftover_reference_length -= last_prefix_alignment_iter->referenceLength(); - suffix_query_length += last_prefix_alignment_iter->queryLength(); - --last_prefix_alignment_iter; - } - - if (leftover_reference_length != 0) - { - const int split_position = last_prefix_alignment_iter->referenceStart() - + last_prefix_alignment_iter->referenceLength() - leftover_reference_length; - Alignment suffix = last_prefix_alignment_iter->splitAtReferencePosition(split_position); - suffix_query_length += suffix.queryLength(); - } - - auto last_prefix_alignment_reference_end - = last_prefix_alignment_iter->referenceStart() + last_prefix_alignment_iter->referenceLength(); - Alignment softclip_alignment(last_prefix_alignment_reference_end, to_string(suffix_query_length) + "S"); - *last_prefix_alignment_iter = mergeAlignments(*last_prefix_alignment_iter, softclip_alignment); - - alignments_.erase(last_prefix_alignment_iter + 1, alignments_.end()); - - assertValidity(); -} - -std::ostream& operator<<(std::ostream& out, const GraphAlignment& graph_alignment) -{ - for (int32_t node_index = 0; node_index != (int32_t)graph_alignment.size(); ++node_index) - { - const int32_t node_id = graph_alignment.getNodeIdByIndex(node_index); - out << node_id << "[" << graph_alignment[node_index] << "]"; - } - return out; -} -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/GraphAlignmentOperations.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/GraphAlignmentOperations.cpp deleted file mode 100644 index 4c2e8d5..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/GraphAlignmentOperations.cpp +++ /dev/null @@ -1,261 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphalign/GraphAlignmentOperations.hh" - -#include - -#include - -#include "graphalign/LinearAlignmentOperations.hh" - -using std::list; -using std::string; -using std::vector; - -namespace graphtools -{ - -bool checkConsistency(const GraphAlignment& graph_alignment, const string& query) -{ - NodeId node_index = 0; - uint32_t query_pos = 0; - const Graph* graph_ptr = graph_alignment.path().graphRawPtr(); - for (const auto& linear_alignment : graph_alignment) - { - if (query.length() < query_pos + linear_alignment.queryLength()) - { - return false; - } - const string query_piece = query.substr(query_pos, linear_alignment.queryLength()); - query_pos += linear_alignment.queryLength(); - - NodeId node_id = graph_alignment.getNodeIdByIndex(node_index); - const string& node_seq = graph_ptr->nodeSeq(node_id); - if (!checkConsistency(linear_alignment, node_seq, query_piece)) - { - return false; - } - - const bool query_or_reference_length_is_zero - = linear_alignment.referenceLength() == 0 || linear_alignment.queryLength() == 0; - - if (graph_alignment.path().numNodes() != 1 && query_or_reference_length_is_zero) - { - return false; - } - - ++node_index; - } - - return true; -} - -static bool startsWithMatch(const Alignment& alignment) -{ - for (const auto& operation : alignment) - { - if (operation.type() != OperationType::kSoftclip) - { - return operation.type() == OperationType::kMatch; - } - } - - return false; -} - -static bool endsWithMatch(const Alignment& alignment) -{ - for (const auto& operation : boost::adaptors::reverse(alignment)) - { - if (operation.type() != OperationType::kSoftclip) - { - return operation.type() == OperationType::kMatch; - } - } - - return false; -} - -bool isLocalAlignment(const GraphAlignment& graph_alignment) -{ - return startsWithMatch(graph_alignment.front()) && endsWithMatch(graph_alignment.back()); -} - -static vector splitGraphCigar(const string& graph_cigar) -{ - vector node_cigars; - string node_cigar; - for (size_t index = 0; index != graph_cigar.length(); ++index) - { - node_cigar += graph_cigar[index]; - if (node_cigar.back() == ']') - { - node_cigars.push_back(node_cigar); - node_cigar.clear(); - } - } - - return node_cigars; -} - -GraphAlignment decodeGraphAlignment(int32_t first_node_start, const string& graph_cigar, const Graph* graph_ptr) -{ - vector node_ids; - vector alignments; - vector node_cigars = splitGraphCigar(graph_cigar); - for (const string& node_cigar : node_cigars) - { - int32_t ref_pos = alignments.empty() ? first_node_start : 0; - - string cigar; - NodeId node_id; - splitNodeCigar(node_cigar, cigar, node_id); - node_ids.push_back(node_id); - - Alignment alignment(ref_pos, cigar); - alignments.push_back(alignment); - } - - // Convert to 0-based coordinates - int32_t last_node_end = alignments.back().referenceStart() + alignments.back().referenceLength(); - Path path(graph_ptr, first_node_start, node_ids, last_node_end); - return GraphAlignment(path, alignments); -} - -void splitNodeCigar(const string& node_cigar, string& cigar, NodeId& node_id) -{ - node_id = static_cast(-1); - string nodeid_encoding; - for (size_t index = 0; index != node_cigar.length(); ++index) - { - if (node_cigar[index] == '[') - { - node_id = static_cast(std::stoull(nodeid_encoding)); - cigar = node_cigar.substr(index + 1); - cigar.pop_back(); - return; - } - if (isdigit(node_cigar[index]) == 0) - { - throw std::logic_error(node_cigar + " is a malformed node CIGAR"); - } - nodeid_encoding += node_cigar[index]; - } -} - -// Implementation note: Unless stated otherwise, all calculations are performed in path coordinates. -GraphAlignment projectAlignmentOntoGraph(Alignment linear_alignment, Path path) -{ - vector alignments; - - path.shrinkBy( - linear_alignment.referenceStart(), - path.length() - linear_alignment.referenceStart() - linear_alignment.referenceLength()); - linear_alignment.setReferenceStart(0); - - for (size_t node_index = 0; node_index != path.numNodes(); ++node_index) - { - const size_t last_position_of_path_on_this_node = path.getNodeOverlapLengthByIndex(node_index); - - const size_t linear_alignment_last_position - = linear_alignment.referenceStart() + linear_alignment.referenceLength(); - - if (linear_alignment_last_position <= last_position_of_path_on_this_node) - { - alignments.push_back(linear_alignment); - break; - } - else - { - Alignment suffix = linear_alignment.splitAtReferencePosition(last_position_of_path_on_this_node); - alignments.push_back(linear_alignment); - linear_alignment = suffix; - linear_alignment.setReferenceStart(0); - } - } - - Alignment& first_alignment = alignments.front(); - first_alignment.setReferenceStart(path.startPosition()); - - return GraphAlignment(path, alignments); -} - -list getQuerySequencesForEachNode(const GraphAlignment& graph_alignment, const string& query) -{ - list sequence_pieces; - - uint32_t query_pos = 0; - for (const auto& linear_alignment : graph_alignment) - { - const string query_piece = query.substr(query_pos, linear_alignment.queryLength()); - sequence_pieces.push_back(query_piece); - query_pos += linear_alignment.queryLength(); - } - - return sequence_pieces; -} - -static string joinLinearAlignmentEncodings(const vector& linear_alignment_encodings) -{ - string graph_query_encoding, graph_match_pattern_encoding, graph_reference_encoding; - - for (const string& linear_alignment_encoding : linear_alignment_encodings) - { - if (!graph_query_encoding.empty()) - { - graph_query_encoding += ':'; - graph_match_pattern_encoding += ':'; - graph_reference_encoding += ':'; - } - - const vector query_pattern_reference_encodings - = splitStringByDelimiter(linear_alignment_encoding, '\n'); - - graph_query_encoding += query_pattern_reference_encodings[0]; - graph_match_pattern_encoding += query_pattern_reference_encodings[1]; - graph_reference_encoding += query_pattern_reference_encodings[2]; - } - - return graph_query_encoding + '\n' + graph_match_pattern_encoding + '\n' + graph_reference_encoding; -} - -string prettyPrint(const GraphAlignment& graph_alignment, const string& query) -{ - const list node_queries = getQuerySequencesForEachNode(graph_alignment, query); - - const Graph* graph_ptr = graph_alignment.path().graphRawPtr(); - - vector linear_alignment_encodings; - size_t node_index = 0; - for (const string& node_query : node_queries) - { - NodeId node_id = graph_alignment.getNodeIdByIndex(node_index); - const string& node_seq = graph_ptr->nodeSeq(node_id); - - const auto& linear_alignment = graph_alignment[node_index]; - linear_alignment_encodings.push_back(prettyPrint(linear_alignment, node_seq, node_query)); - - ++node_index; - } - - return joinLinearAlignmentEncodings(linear_alignment_encodings); -} -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/KmerIndex.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/KmerIndex.cpp deleted file mode 100644 index ce2ea3a..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/KmerIndex.cpp +++ /dev/null @@ -1,347 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko , -// Peter Krusche -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphalign/KmerIndex.hh" - -#include -#include -#include -#include -#include - -#include -#include - -#include "graphcore/PathOperations.hh" -#include "graphutils/KmerEncoding.hh" -#include "graphutils/PairHashing.hh" -#include "graphutils/SequenceOperations.hh" - -using std::list; -using std::string; -using std::unordered_set; -using std::vector; - -namespace graphtools -{ - -struct MiniPath -{ - bool operator==(const MiniPath& other) const - { - return (start_position == other.start_position) and (node_id == other.node_id); - } - - using pos_t = uint16_t; - using node_t = uint16_t; - pos_t start_position; - node_t node_id; -}; - -using KmerKey_t = uint32_t; - -typedef spp::sparse_hash_map StringToMiniPathsMap; -typedef spp::sparse_hash_map> StringToPathsMap; - -struct KmerIndex::Impl -{ - explicit Impl(const Graph& graph, size_t kmer_len_); - void addKmerPathsStartingAtNode(NodeId node_id); - void addKmerPaths(const std::list& kmer_paths); - void updateKmerCounts(); - Path MiniPathToPath(const MiniPath& miniPath) const; - -private: - const Graph& graph_; - -public: - size_t kmer_len; - TwoBitKmerEncoder kmer_coder; - StringToMiniPathsMap kmer_to_minipaths_map; - StringToPathsMap kmer_to_paths_map; - std::unordered_map node_kmer_counts; - std::unordered_map edge_kmer_counts; -}; - -KmerIndex::Impl::Impl(const Graph& graph, size_t kmer_len_) - : graph_(graph) - , kmer_len(kmer_len_) - , kmer_coder(kmer_len) -{ - for (NodeId node_id = 0; node_id != graph.numNodes(); ++node_id) - { - addKmerPathsStartingAtNode(node_id); - } - updateKmerCounts(); -} - -void KmerIndex::Impl::addKmerPathsStartingAtNode(NodeId node_id) -{ - const string node_seq = graph_.nodeSeq(node_id); - vector node_list; - node_list.push_back(node_id); - for (size_t pos = 0; pos != node_seq.length(); ++pos) - { - Path path(&graph_, static_cast(pos), node_list, static_cast(pos)); - addKmerPaths(extendPathEnd(path, static_cast(kmer_len))); - } -} - -Path KmerIndex::Impl::MiniPathToPath(const MiniPath& miniPath) const -{ - return Path(&graph_, miniPath.start_position, { miniPath.node_id }, miniPath.start_position + kmer_len); -} - -void KmerIndex::Impl::addKmerPaths(const list& kmer_paths) -{ - for (const Path& kmer_path : kmer_paths) - { - vector expanded_sequences; - expandReferenceSequence(kmer_path.seq(), expanded_sequences); - for (const auto& expanded_kmer_seq : expanded_sequences) - { - const auto expanded_kmer_key = kmer_coder.encode(expanded_kmer_seq); - auto pathIter(kmer_to_paths_map.find(expanded_kmer_key)); - if (pathIter != kmer_to_paths_map.end()) - { - pathIter->second.push_back(kmer_path); - continue; - } - - auto miniPathIter(kmer_to_minipaths_map.find(expanded_kmer_key)); - if (miniPathIter != kmer_to_minipaths_map.end()) - { - kmer_to_paths_map[expanded_kmer_key] = { MiniPathToPath(miniPathIter->second), kmer_path }; - kmer_to_minipaths_map.erase(miniPathIter); - } - else - { - if ((kmer_path.numNodes() == 1) - and ((kmer_path.endPosition() - kmer_path.startPosition()) == static_cast(kmer_len)) - and (kmer_path.startPosition() >= 0) - and (kmer_path.startPosition() <= std::numeric_limits::max()) - and (kmer_path.nodeIds().front() <= std::numeric_limits::max())) - { - MiniPath miniPath{ static_cast(kmer_path.startPosition()), - static_cast(kmer_path.nodeIds().front()) }; - kmer_to_minipaths_map.emplace(expanded_kmer_key, miniPath); - continue; - } - else - { - kmer_to_paths_map[expanded_kmer_key] = { kmer_path }; - } - } - } - } -} - -void KmerIndex::Impl::updateKmerCounts() -{ - node_kmer_counts.clear(); - edge_kmer_counts.clear(); - for (const auto& kmer_and_paths : kmer_to_minipaths_map) - { - auto const path_node_id(kmer_and_paths.second.node_id); - node_kmer_counts[path_node_id] += 1; - } - - for (const auto& kmer_and_paths : kmer_to_paths_map) - { - // kmer is unique - if (kmer_and_paths.second.size() == 1) - { - bool has_previous = false; - NodeId previous_node = 0; - for (auto const& path_node_id : kmer_and_paths.second.front().nodeIds()) - { - node_kmer_counts[path_node_id] += 1; - if (has_previous) - { - edge_kmer_counts[std::make_pair(previous_node, path_node_id)] += 1; - } - has_previous = true; - previous_node = path_node_id; - } - } - } -} - -KmerIndex::KmerIndex(const Graph& graph, int32_t kmer_len) - : pimpl_(new Impl(graph, static_cast(kmer_len))) -{ -} - -KmerIndex::KmerIndex(const KmerIndex& other) - : pimpl_(new Impl(*other.pimpl_)) -{ -} - -KmerIndex::KmerIndex(KmerIndex&& other) noexcept - : pimpl_(std::move(other.pimpl_)) -{ -} - -KmerIndex& KmerIndex::operator=(const KmerIndex& other) -{ - if (this != &other) - { - pimpl_.reset(new Impl(*other.pimpl_)); - } - return *this; -} - -KmerIndex& KmerIndex::operator=(KmerIndex&& other) noexcept -{ - pimpl_ = std::move(other.pimpl_); - return *this; -} - -KmerIndex::~KmerIndex() = default; - -bool KmerIndex::operator==(const KmerIndex& other) const -{ - return ( - pimpl_->kmer_to_minipaths_map == other.pimpl_->kmer_to_minipaths_map - and pimpl_->kmer_to_paths_map == other.pimpl_->kmer_to_paths_map && pimpl_->kmer_len == other.pimpl_->kmer_len); -} - -static string encodePaths(const std::vector& paths) -{ - std::vector path_encodings; - for (const auto& path : paths) - { - path_encodings.push_back(path.encode()); - } - return boost::algorithm::join(path_encodings, ","); -} - -size_t KmerIndex::kmerLength() const { return pimpl_->kmer_len; } - -string KmerIndex::encode() const -{ - std::vector kv_encodings; - for (const auto& kv : pimpl_->kmer_to_minipaths_map) - { - const string encoding_of_paths = encodePaths({ pimpl_->MiniPathToPath(kv.second) }); - kv_encodings.emplace_back("{" + pimpl_->kmer_coder.decode(kv.first) + "->" + encoding_of_paths + "}"); - } - for (const auto& kv : pimpl_->kmer_to_paths_map) - { - const string encoding_of_paths = encodePaths(kv.second); - kv_encodings.emplace_back("{" + pimpl_->kmer_coder.decode(kv.first) + "->" + encoding_of_paths + "}"); - } - return boost::algorithm::join(kv_encodings, ","); -} - -bool KmerIndex::contains(const std::string& kmer) const -{ - if ((kmer.size() != pimpl_->kmer_len) or (kmer.find_last_not_of("ACGT") != std::string::npos)) - { - return false; - } - - const auto kmer_key = pimpl_->kmer_coder.encode(kmer); - return ( - (pimpl_->kmer_to_minipaths_map.find(kmer_key) != pimpl_->kmer_to_minipaths_map.end()) - or (pimpl_->kmer_to_paths_map.find(kmer_key) != pimpl_->kmer_to_paths_map.end())); -} - -size_t KmerIndex::numPaths(const std::string& kmer) const -{ - if ((kmer.size() != pimpl_->kmer_len) or (kmer.find_last_not_of("ACGT") != std::string::npos)) - { - return 0; - } - - const auto kmer_key = pimpl_->kmer_coder.encode(kmer); - if (pimpl_->kmer_to_minipaths_map.find(kmer_key) != pimpl_->kmer_to_minipaths_map.end()) - { - return 1; - } - else - { - const auto pathIter(pimpl_->kmer_to_paths_map.find(kmer_key)); - if (pathIter == pimpl_->kmer_to_paths_map.end()) - { - return 0; - } - else - { - return pathIter->second.size(); - } - } -} - -std::vector KmerIndex::getPaths(const std::string& kmer) const -{ - const auto kmer_key = pimpl_->kmer_coder.encode(kmer); - const auto miniPathIter(pimpl_->kmer_to_minipaths_map.find(kmer_key)); - if (miniPathIter != pimpl_->kmer_to_minipaths_map.end()) - { - return { pimpl_->MiniPathToPath(miniPathIter->second) }; - } - else - { - return pimpl_->kmer_to_paths_map.at(kmer_key); - } -} - -unordered_set KmerIndex::kmers() const -{ - unordered_set kmers; - for (const auto& kv : pimpl_->kmer_to_minipaths_map) - { - kmers.insert(pimpl_->kmer_coder.decode(kv.first)); - } - for (const auto& kv : pimpl_->kmer_to_paths_map) - { - kmers.insert(pimpl_->kmer_coder.decode(kv.first)); - } - return kmers; -} - -size_t KmerIndex::numUniqueKmersOverlappingNode(NodeId node_id) const -{ - auto node_it = pimpl_->node_kmer_counts.find(node_id); - if (node_it != pimpl_->node_kmer_counts.end()) - { - return node_it->second; - } - return 0; -} - -size_t KmerIndex::numUniqueKmersOverlappingEdge(NodeId from, NodeId to) const -{ - auto edge_it = pimpl_->edge_kmer_counts.find(std::make_pair(from, to)); - if (edge_it != pimpl_->edge_kmer_counts.end()) - { - return edge_it->second; - } - return 0; -} - -std::ostream& operator<<(std::ostream& os, const KmerIndex& kmer_index) -{ - os << kmer_index.encode(); - return os; -} -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/KmerIndexOperations.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/KmerIndexOperations.cpp deleted file mode 100644 index bfbccac..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/KmerIndexOperations.cpp +++ /dev/null @@ -1,113 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko , -// Peter Krusche -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphalign/KmerIndexOperations.hh" - -#include - -#include - -#include "graphutils/SequenceOperations.hh" - -using std::list; -using std::string; - -namespace graphtools -{ -list extractKmersFromAllPositions(const string& sequence, int32_t kmer_len) -{ - list kmers; - for (size_t pos = 0; pos + kmer_len <= sequence.length(); ++pos) - { - string kmer = sequence.substr(pos, static_cast(kmer_len)); - boost::to_upper(kmer); - kmers.push_back(kmer); - } - return kmers; -} - -int32_t countKmerMatches(const KmerIndex& kmer_index, const std::string& seq) -{ - const list kmers = extractKmersFromAllPositions(seq, kmer_index.kmerLength()); - int32_t num_kmer_matches = 0; - - for (const string& kmer : kmers) - { - if (kmer_index.numPaths(kmer) != 0) - { - ++num_kmer_matches; - } - } - return num_kmer_matches; -} - -bool checkIfForwardOriented(const KmerIndex& kmer_index, const std::string& sequence) -{ - const int32_t num_forward_matches = countKmerMatches(kmer_index, sequence); - const int32_t num_revcomp_matches = countKmerMatches(kmer_index, reverseComplement(sequence)); - return num_forward_matches >= num_revcomp_matches; -} - -/** - * Find minimum kmer length that covers each node with a unique kmer - * @param graph a graph - * @param min_unique_kmers_per_edge min number of unique kmers to cover each edge - * @param min_unique_kmers_per_node min number of unique kmers to cover each node - * @return - */ -int findMinCoveringKmerLength(Graph const* graph, size_t min_unique_kmers_per_edge, size_t min_unique_kmers_per_node) -{ - for (int32_t k = 10; k < 64; ++k) - { - KmerIndex index(*graph, k); - - bool any_below = false; - for (NodeId node_id = 0; node_id != graph->numNodes(); ++node_id) - { - if (index.numUniqueKmersOverlappingNode(node_id) < min_unique_kmers_per_node) - { - any_below = true; - break; - } - // this will enumerate all edges - for (const auto succ : graph->successors(node_id)) - { - if (index.numUniqueKmersOverlappingEdge(node_id, succ) < min_unique_kmers_per_edge) - { - any_below = true; - break; - } - } - if (any_below) - { - break; - } - } - if (any_below) - { - continue; - } - - return k; - } - return -1; -} -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/LinearAlignment.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/LinearAlignment.cpp deleted file mode 100644 index 29ae693..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/LinearAlignment.cpp +++ /dev/null @@ -1,222 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphalign/LinearAlignment.hh" - -#include -#include -#include -#include -#include -#include - -#include "graphalign/OperationOperations.hh" -#include "graphutils/BaseMatching.hh" - -using std::list; -using std::logic_error; -using std::map; -using std::string; -using std::to_string; -using std::vector; - -namespace graphtools -{ - -Alignment::Alignment(uint32_t reference_start, const string& cigar) - : reference_start_(reference_start) -{ - decodeCigar(cigar); - updateCounts(); -} - -void Alignment::updateCounts() -{ - clipped_ = 0; - matched_ = 0; - mismatched_ = 0; - missing_ = 0; - inserted_ = 0; - deleted_ = 0; - for (const Operation& operation : operations_) - { - switch (operation.type()) - { - case OperationType::kSoftclip: - clipped_ += operation.length(); - break; - case OperationType::kMatch: - matched_ += operation.length(); - break; - case OperationType::kMismatch: - mismatched_ += operation.length(); - break; - case OperationType::kMissingBases: - missing_ += operation.length(); - break; - case OperationType::kInsertionToRef: - inserted_ += operation.length(); - break; - case OperationType::kDeletionFromRef: - deleted_ += operation.length(); - break; - } - } -} - -void Alignment::decodeCigar(const string& cigar) -{ - string length_encoding; - for (char c : cigar) - { - if (isalpha(c) != 0) - { - uint32_t operation_length = std::stoi(length_encoding); - OperationType operation_type = decodeOperationType(c); - operations_.emplace_back(operation_type, operation_length); - length_encoding.clear(); - } - else - { - if (isdigit(c) == 0) - { - throw logic_error(cigar + " is malformed CIGAR string"); - } - length_encoding += c; - } - } -} - -uint32_t Alignment::queryLength() const -{ - int32_t query_span = 0; - for (const auto& operation : operations_) - { - query_span += operation.queryLength(); - } - return query_span; -} - -uint32_t Alignment::referenceLength() const -{ - int32_t reference_span = 0; - for (const auto& operation : operations_) - { - reference_span += operation.referenceLength(); - } - return reference_span; -} - -string Alignment::generateCigar() const -{ - string cigar_string; - for (const auto& operation : operations_) - { - cigar_string += operation.generateCigar(); - } - return cigar_string; -} - -Alignment Alignment::splitAtReferencePosition(size_t reference_position) -{ - const size_t end_of_reference_positions = referenceStart() + referenceLength(); - if (reference_position == 0 || end_of_reference_positions <= reference_position) - { - std::ostringstream os; - os << *this; - throw logic_error("Cannot split " + os.str() + " at reference position " + to_string(reference_position)); - } - - size_t first_unused_position = reference_start_; - - list::const_iterator operation_it = operations_.begin(); - - while (operation_it != operations_.end()) - { - const size_t first_unused_position_after_applying_operation - = first_unused_position + operation_it->referenceLength(); - if (first_unused_position_after_applying_operation <= reference_position) - { - ++operation_it; - first_unused_position = first_unused_position_after_applying_operation; - } - else - { - break; - } - } - - if (operation_it == operations_.end()) - { - // Throw error (test first) - } - - if (first_unused_position == reference_position) - { - list suffix_operations; - suffix_operations.splice(suffix_operations.begin(), operations_, operation_it, operations_.end()); - - updateCounts(); - return Alignment(first_unused_position, suffix_operations); - } - else - { - const size_t first_piece_reference_length = reference_position - first_unused_position; - OperationPair prefix_suffix = splitByReferenceLength(*operation_it, first_piece_reference_length); - - list suffix_operations; - suffix_operations.splice(suffix_operations.begin(), operations_, ++operation_it, operations_.end()); - suffix_operations.push_front(prefix_suffix.second); - - operations_.pop_back(); - operations_.push_back(prefix_suffix.first); - - updateCounts(); - return Alignment(reference_position, suffix_operations); - } -} - -void Alignment::reverse(size_t reference_length) -{ - reference_start_ = reference_length - reference_start_ - referenceLength(); - std::reverse(operations_.begin(), operations_.end()); -} - -bool Alignment::operator<(const Alignment& other) const -{ - if (reference_start_ != other.reference_start_) - { - return reference_start_ < other.reference_start_; - } - - return operations_ < other.operations_; -} - -std::ostream& operator<<(std::ostream& os, const Alignment& alignment) -{ - os << "Ref start: " << alignment.referenceStart() << ", "; - for (const Operation& operation : alignment) - { - os << operation; - } - - return os; -} -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/LinearAlignmentOperations.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/LinearAlignmentOperations.cpp deleted file mode 100644 index 5f69c8c..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/LinearAlignmentOperations.cpp +++ /dev/null @@ -1,226 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphalign/LinearAlignmentOperations.hh" - -#include -#include -#include -#include -#include - -#include "graphalign/OperationOperations.hh" - -using std::list; -using std::logic_error; -using std::string; - -namespace graphtools -{ - -bool checkConsistency(const Alignment& alignment, const string& reference, const string& query) -{ - const bool does_alignment_span_whole_query = alignment.queryLength() == query.length(); - const bool is_alignment_within_reference - = alignment.referenceStart() + alignment.referenceLength() <= reference.length(); - - if (!does_alignment_span_whole_query || !is_alignment_within_reference) - { - return false; - } - - uint32_t query_pos = 0; - uint32_t ref_pos = alignment.referenceStart(); - - for (const auto& operation : alignment) - { - const string query_piece = query.substr(query_pos, operation.queryLength()); - const string reference_piece = reference.substr(ref_pos, operation.referenceLength()); - - if (!checkConsistency(operation, reference_piece, query_piece)) - { - return false; - } - - query_pos += operation.queryLength(); - ref_pos += operation.referenceLength(); - } - - return true; -} - -list getSequencesForEachOperation(const Alignment& alignment, const string& reference, const string& query) -{ - list sequence_pieces; - - uint32_t query_pos = 0; - uint32_t ref_pos = alignment.referenceStart(); - - for (const auto& operation : alignment) - { - const string reference_piece = reference.substr(ref_pos, operation.referenceLength()); - const string query_piece = query.substr(query_pos, operation.queryLength()); - sequence_pieces.emplace_back(reference_piece, query_piece); - - query_pos += operation.queryLength(); - ref_pos += operation.referenceLength(); - } - - return sequence_pieces; -} - -bool checkIfBookended(const Alignment& first_alignment, const Alignment& second_alignment) -{ - const size_t position_after_first_alignment_end - = first_alignment.referenceStart() + first_alignment.referenceLength(); - const bool are_adjacent = position_after_first_alignment_end == (size_t)second_alignment.referenceStart(); - - if (!are_adjacent) - { - return false; - } - - const bool is_first_alignment_ends_with_softclip = first_alignment.back().type() == OperationType::kSoftclip; - const bool is_second_alignment_starts_with_softclip = second_alignment.front().type() == OperationType::kSoftclip; - - if (is_first_alignment_ends_with_softclip || is_second_alignment_starts_with_softclip) - { - const bool is_first_alignment_fully_softclipped - = first_alignment.numOperations() == 1 && is_first_alignment_ends_with_softclip; - const bool is_second_alignment_fully_softclipped - = second_alignment.numOperations() == 1 && is_second_alignment_starts_with_softclip; - - return is_first_alignment_fully_softclipped || is_second_alignment_fully_softclipped; - } - - return true; -} - -Alignment mergeAlignments(const Alignment& first_alignment, const Alignment& second_alignment) -{ - if (!checkIfBookended(first_alignment, second_alignment)) - { - std::ostringstream msg; - msg << "Alignments " << first_alignment << " and " << second_alignment << " are not bookended"; - throw std::logic_error(msg.str()); - } - - list first_alignment_operations = first_alignment.operations(); - list second_alignment_operations = second_alignment.operations(); - - if (first_alignment_operations.back().type() == second_alignment_operations.front().type()) - { - const Operation last_operation_of_first_alignment = first_alignment_operations.back(); - first_alignment_operations.pop_back(); - - const Operation first_operations_of_second_alignment = second_alignment_operations.front(); - second_alignment_operations.pop_front(); - - uint32_t merged_operation_length - = last_operation_of_first_alignment.length() + first_operations_of_second_alignment.length(); - - first_alignment_operations.emplace_back(last_operation_of_first_alignment.type(), merged_operation_length); - } - - first_alignment_operations.splice(first_alignment_operations.end(), second_alignment_operations); - - return Alignment(first_alignment.referenceStart(), first_alignment_operations); -} - -int32_t scoreAlignment(const Alignment& alignment, int32_t match_score, int32_t mismatch_score, int32_t gap_score) -{ - int32_t score = 0; - - for (const Operation& operation : alignment) - { - switch (operation.type()) - { - case OperationType::kMatch: - score += match_score * operation.referenceLength(); - break; - case OperationType::kMismatch: - score += mismatch_score * operation.referenceLength(); - break; - case OperationType::kInsertionToRef: - score += gap_score * operation.queryLength(); - break; - case OperationType::kDeletionFromRef: - score += gap_score * operation.referenceLength(); - break; - default: - break; - } - } - - return score; -} - -string prettyPrint(const Alignment& alignment, const string& reference, const string& query) -{ - string reference_encoding, match_patten, query_encoding; - - const list sequence_pieces = getSequencesForEachOperation(alignment, reference, query); - auto matched_sequences_it = sequence_pieces.begin(); - - for (const auto& operation : alignment) - { - const string& operation_reference = matched_sequences_it->first; - const string& operation_query = matched_sequences_it->second; - - switch (operation.type()) - { - case OperationType::kDeletionFromRef: - reference_encoding += operation_reference; - query_encoding += string(operation.referenceLength(), '-'); - match_patten += string(operation.referenceLength(), ' '); - break; - - case OperationType::kInsertionToRef: - reference_encoding += string(operation.queryLength(), '-'); - match_patten += string(operation.queryLength(), ' '); - query_encoding += operation_query; - break; - - case OperationType::kMatch: - reference_encoding += operation_reference; - match_patten += string(operation.queryLength(), '|'); - query_encoding += operation_query; - break; - - case OperationType::kMismatch: - case OperationType::kMissingBases: - reference_encoding += operation_reference; - match_patten += string(operation.queryLength(), ' '); - query_encoding += operation_query; - break; - - case OperationType::kSoftclip: - reference_encoding += string(operation.queryLength(), '-'); - match_patten += string(operation.queryLength(), ' '); - query_encoding += operation_query; - break; - } - - ++matched_sequences_it; - } - - return reference_encoding + '\n' + match_patten + '\n' + query_encoding; -} -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/Operation.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/Operation.cpp deleted file mode 100644 index dca6205..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/Operation.cpp +++ /dev/null @@ -1,147 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphalign/Operation.hh" - -#include -#include -#include -#include -#include -#include - -using std::logic_error; -using std::map; -using std::string; -using std::to_string; - -namespace graphtools -{ - -string Operation::generateCigar() const -{ - string cigar_string = to_string(length_); - - std::ostringstream os; - os << type_; - cigar_string += os.str(); - - return cigar_string; -} - -OperationType decodeOperationType(char type_encoding) -{ - switch (type_encoding) - { - case 'M': - return OperationType::kMatch; - case 'N': - return OperationType::kMissingBases; - case 'X': - return OperationType::kMismatch; - case 'I': - return OperationType::kInsertionToRef; - case 'D': - return OperationType::kDeletionFromRef; - case 'S': - return OperationType::kSoftclip; - default: - throw logic_error(to_string(type_encoding) + " is unknown CIGAR operation"); - } -} - -Operation::Operation(string cigar) -{ - type_ = decodeOperationType(cigar.back()); - cigar.pop_back(); - length_ = std::stoi(cigar); -} - -uint32_t Operation::referenceLength() const -{ - switch (type_) - { - case OperationType::kMatch: - case OperationType::kMismatch: - case OperationType::kMissingBases: - case OperationType::kDeletionFromRef: - return length_; - default: - return 0; - } -} - -uint32_t Operation::queryLength() const -{ - switch (type_) - { - case OperationType::kMatch: - case OperationType::kMismatch: - case OperationType::kMissingBases: - case OperationType::kInsertionToRef: - case OperationType::kSoftclip: - return length_; - default: - return 0; - } -} - -bool Operation::operator<(const Operation& other) const -{ - if (type_ != other.type_) - { - return type_ < other.type_; - } - - return length_ < other.length_; -} - -std::ostream& operator<<(std::ostream& os, OperationType operation_type) -{ - switch (operation_type) - { - case OperationType::kMatch: - os << 'M'; - break; - case OperationType::kMismatch: - os << 'X'; - break; - case OperationType::kInsertionToRef: - os << 'I'; - break; - case OperationType::kDeletionFromRef: - os << 'D'; - break; - case OperationType::kSoftclip: - os << 'S'; - break; - case OperationType::kMissingBases: - os << 'N'; - } - - return os; -} - -std::ostream& operator<<(std::ostream& os, const Operation& operation) -{ - os << operation.length() << operation.type(); - return os; -} -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/OperationOperations.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/OperationOperations.cpp deleted file mode 100644 index f552742..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/OperationOperations.cpp +++ /dev/null @@ -1,115 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphalign/OperationOperations.hh" - -#include -#include - -#include "graphutils/BaseMatching.hh" - -using std::string; - -namespace graphtools -{ -bool checkConsistency(const Operation& operation, const std::string& reference, const std::string& query) -{ - const bool is_query_full_length = query.length() == operation.length(); - const bool is_ref_full_length = reference.length() == operation.length(); - - switch (operation.type()) - { - case OperationType::kMatch: - if (is_query_full_length && checkIfReferenceAndQuerySequencesMatch(reference, query)) - return true; - return false; - - case OperationType::kMismatch: - if (is_query_full_length && query.length() == reference.length()) - { - bool found_matching_base = false; - for (size_t index = 0; index != query.length(); ++index) - { - if (checkIfReferenceBaseMatchesQueryBase(reference[index], query[index])) - { - found_matching_base = true; - } - } - if (!found_matching_base) - { - return true; - } - } - return false; - - case OperationType::kMissingBases: - if (query.length() == reference.length() && is_query_full_length) - { - bool found_non_n_base_in_query = false; - for (size_t index = 0; index != query.length(); ++index) - { - if (query[index] != 'N') - { - found_non_n_base_in_query = true; - } - } - if (!found_non_n_base_in_query) - { - return true; - } - } - return false; - - case OperationType::kDeletionFromRef: - if (query.empty() && !reference.empty() && is_ref_full_length) - return true; - return false; - - case OperationType::kInsertionToRef: - if (!query.empty() && reference.empty() && is_query_full_length) - return true; - return false; - - case OperationType::kSoftclip: - if (!query.empty() && reference.empty() && is_query_full_length) - return true; - return false; - } - - return false; -} - -OperationPair splitByReferenceLength(const Operation& operation, uint32_t prefix_reference_length) -{ - if (prefix_reference_length == 0 || operation.referenceLength() <= prefix_reference_length) - { - std::ostringstream os; - os << operation; - const string msg = os.str() + " cannot be split by reference length " + std::to_string(prefix_reference_length); - throw std::logic_error(msg); - } - - uint32_t suffix_reference_length = operation.referenceLength() - prefix_reference_length; - Operation prefix_operation(operation.type(), prefix_reference_length); - Operation suffix_operation(operation.type(), suffix_reference_length); - - return std::make_pair(prefix_operation, suffix_operation); -} -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/PinnedAligner.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/PinnedAligner.cpp deleted file mode 100644 index aa6e01c..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/PinnedAligner.cpp +++ /dev/null @@ -1,131 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphalign/PinnedAligner.hh" - -#include - -#include "graphalign/TracebackRunner.hh" -#include "graphutils/BaseMatching.hh" - -using std::string; - -namespace graphtools -{ -TracebackMatrix PinnedAligner::populateTracebackMatrix(const string& reference, const string& query) -{ - const size_t num_rows = query.length() + 1; - const size_t num_cols = reference.length() + 1; - - TracebackMatrix matrix(num_rows, num_cols); - - fillTopLeft(matrix); - fillTopRow(matrix); - fillLeftColumn(matrix); - fillBody(reference, query, matrix); - - return matrix; -} - -void PinnedAligner::fillTopLeft(TracebackMatrix& matrix) -{ - matrix.setScore(0, 0, 0); - matrix.setTracebackStep(0, 0, TracebackStep::kStop); -} - -void PinnedAligner::fillTopRow(TracebackMatrix& matrix) -{ - for (size_t col_index = 1; col_index != matrix.numCols(); ++col_index) - { - matrix.setScore(0, col_index, col_index * gap_score_); - matrix.setTracebackStep(0, col_index, TracebackStep::kLeft); - } -} - -void PinnedAligner::fillLeftColumn(TracebackMatrix& matrix) -{ - for (size_t row_index = 1; row_index != matrix.numRows(); ++row_index) - { - matrix.setScore(row_index, 0, row_index * gap_score_); - matrix.setTracebackStep(row_index, 0, TracebackStep::kTop); - } -} - -void PinnedAligner::fillBody(const string& reference, const string& query, TracebackMatrix& matrix) -{ - for (size_t row_index = 1; row_index != matrix.numRows(); ++row_index) - { - for (size_t col_index = 1; col_index != matrix.numCols(); ++col_index) - { - const bool do_bases_match - = checkIfReferenceBaseMatchesQueryBase(reference[col_index - 1], query[row_index - 1]); - fillBodyCell(matrix, row_index, col_index, do_bases_match); - } - } -} - -void PinnedAligner::fillBodyCell(TracebackMatrix& matrix, size_t row_index, size_t col_index, bool do_bases_match) -{ - const int32_t match_mismatch_score = do_bases_match ? match_score_ : mismatch_score_; - const TracebackStep traceback_step - = do_bases_match ? TracebackStep::kDiagonalMatch : TracebackStep::kDiagonalMismatch; - const int32_t no_gap_score = matrix.score(row_index - 1, col_index - 1) + match_mismatch_score; - matrix.setScore(row_index, col_index, no_gap_score); - matrix.setTracebackStep(row_index, col_index, traceback_step); - - const int32_t query_gap_score = matrix.score(row_index, col_index - 1) + gap_score_; - if (query_gap_score > matrix.score(row_index, col_index)) - { - matrix.setScore(row_index, col_index, query_gap_score); - matrix.setTracebackStep(row_index, col_index, TracebackStep::kLeft); - } - - const int32_t reference_gap_score = matrix.score(row_index - 1, col_index) + gap_score_; - if (reference_gap_score > matrix.score(row_index, col_index)) - { - matrix.setScore(row_index, col_index, reference_gap_score); - matrix.setTracebackStep(row_index, col_index, TracebackStep::kTop); - } -} - -Alignment PinnedAligner::prefixAlign(const string& reference, const string& query) -{ - TracebackMatrix matrix = populateTracebackMatrix(reference, query); - - size_t top_row_index, top_col_index; - matrix.locateTopScoringCell(top_row_index, top_col_index); - - TracebackRunner traceback_runner(matrix); - Alignment alignment = traceback_runner.runTraceback(top_row_index, top_col_index); - - return alignment; -} - -Alignment PinnedAligner::suffixAlign(string reference, string query) -{ - std::reverse(query.begin(), query.end()); - std::reverse(reference.begin(), reference.end()); - - Alignment alignment = prefixAlign(reference, query); - alignment.reverse(reference.length()); - - return alignment; -} -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/TracebackMatrix.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/TracebackMatrix.cpp deleted file mode 100644 index de8b6f7..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/TracebackMatrix.cpp +++ /dev/null @@ -1,178 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphalign/TracebackMatrix.hh" - -#include -#include -#include -#include - -#include "graphutils/SequenceOperations.hh" - -using std::string; -using std::vector; - -namespace graphtools -{ - -TracebackStep decodeTracebackDirection(std::string encoding) -{ - if (encoding == "S") - { - return TracebackStep::kStop; - } - else if (encoding == "I") - { - return TracebackStep::kTop; - } - else if (encoding == "D") - { - return TracebackStep::kLeft; - } - else if (encoding == "M") - { - return TracebackStep::kDiagonalMatch; - } - else if (encoding == "X") - { - return TracebackStep::kDiagonalMismatch; - } - throw std::logic_error(encoding + " is an unknown traceback"); -} - -TracebackMatrix::TracebackMatrix(const string& encoding) -{ - vector lines = splitStringByDelimiter(encoding, '\n'); - num_rows_ = lines.size(); - num_cols_ = std::count(lines.front().begin(), lines.front().end(), '/'); - cells_.resize(num_rows_ * num_cols_); - - for (size_t row_index = 0; row_index != num_rows_; ++row_index) - { - const std::string& line = lines[row_index]; - std::vector words = splitStringByWhitespace(line); - for (size_t col_index = 0; col_index != num_cols_; ++col_index) - { - const std::string& word = words[col_index]; - std::vector tracedir_score_encodings = splitStringByDelimiter(word, '/'); - assert(tracedir_score_encodings.size() == 2); - const TracebackStep trace_dir = decodeTracebackDirection(tracedir_score_encodings.front()); - const int32_t score = std::stoi(tracedir_score_encodings.back()); - getCell(row_index, col_index) = TracebackMatrixCell(trace_dir, score); - } - } -} - -int32_t TracebackMatrix::score(size_t row_index, size_t col_index) const { return getCell(row_index, col_index).score; } - -void TracebackMatrix::setScore(size_t row_index, size_t col_index, int32_t score) -{ - getCell(row_index, col_index).score = score; -} - -TracebackStep TracebackMatrix::tracebackStep(size_t row_index, size_t col_index) const -{ - return getCell(row_index, col_index).direction; -} - -void TracebackMatrix::setTracebackStep(size_t row_index, size_t col_index, TracebackStep direction) -{ - getCell(row_index, col_index).direction = direction; -} - -void TracebackMatrix::locateTopScoringCell(size_t& top_row_index, size_t& top_col_index) const -{ - int32_t top_score = INT32_MIN; - - for (size_t row_index = 0; row_index != num_rows_; ++row_index) - { - for (size_t col_index = 0; col_index != num_cols_; ++col_index) - { - const int32_t cell_score = score(row_index, col_index); - if (top_score <= cell_score) - { - top_score = cell_score; - top_row_index = row_index; - top_col_index = col_index; - } - } - } -} - -bool TracebackMatrix::operator==(const TracebackMatrix& other) const -{ - return (num_rows_ == other.num_rows_ && num_cols_ == other.num_cols_ && cells_ == other.cells_); -} - -std::ostream& operator<<(std::ostream& out, const TracebackStep& trace_dir) -{ - switch (trace_dir) - { - case TracebackStep::kStop: - out << "S"; - break; - case TracebackStep::kTop: - out << "I"; - break; - case TracebackStep::kLeft: - out << "D"; - break; - case TracebackStep::kDiagonalMatch: - out << "M"; - break; - case TracebackStep::kDiagonalMismatch: - out << "X"; - break; - default: - out << "?"; - } - return out; -} - -std::ostream& operator<<(std::ostream& out, const TracebackMatrixCell& cell) -{ - out << cell.direction << "/" << cell.score; - return out; -} - -std::ostream& operator<<(std::ostream& out, const TracebackMatrix& matrix) -{ - out << "{"; - for (size_t row_index = 0; row_index != matrix.numRows(); ++row_index) - { - out << "{"; - for (size_t col_index = 0; col_index != matrix.numCols(); ++col_index) - { - out << matrix.tracebackStep(row_index, col_index) << "/" << matrix.score(row_index, col_index); - if (col_index != matrix.numCols() - 1) - { - out << ", "; - } - } - if (row_index != matrix.numRows() - 1) - { - out << "}, "; - } - } - out << "}}"; - return out; -} -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/TracebackRunner.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/TracebackRunner.cpp deleted file mode 100644 index 369fb48..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/TracebackRunner.cpp +++ /dev/null @@ -1,136 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphalign/TracebackRunner.hh" - -#include -#include -#include -#include - -using std::string; -using std::vector; - -namespace graphtools -{ - -Alignment TracebackRunner::runTraceback(size_t row_index, size_t col_index) -{ - operations_.clear(); - - if (row_index != matrix_.numRows() - 1) - { - softclipQuerySuffix(row_index); - } - - while (matrix_.tracebackStep(row_index, col_index) != TracebackStep::kStop) - { - computeTracebackRunForAlignmentOperation(row_index, col_index); - convertCurrentRunToAlignmentOperation(); - row_index = run_last_row_index; - col_index = run_last_col_index; - tracebackPosition(row_index, col_index); - } - - if (row_index != 0) - { - softclipQueryPrefix(row_index); - } - - std::reverse(operations_.begin(), operations_.end()); - return Alignment(col_index, operations_); -} - -void TracebackRunner::computeTracebackRunForAlignmentOperation(size_t row_index, size_t col_index) -{ - TracebackStep cur_traceback_step = matrix_.tracebackStep(row_index, col_index); - run_traceback_step = cur_traceback_step; - run_length = 0; - - while (run_traceback_step == cur_traceback_step) - { - run_last_col_index = col_index; - run_last_row_index = row_index; - ++run_length; - tracebackPosition(row_index, col_index); - cur_traceback_step = matrix_.tracebackStep(row_index, col_index); - } -} - -void TracebackRunner::tracebackPosition(size_t& row_index, size_t& col_index) -{ - TracebackStep traceback_step = matrix_.tracebackStep(row_index, col_index); - switch (traceback_step) - { - case TracebackStep::kDiagonalMatch: - case TracebackStep::kDiagonalMismatch: - --row_index; - --col_index; - break; - case TracebackStep::kLeft: - --col_index; - break; - case TracebackStep::kTop: - --row_index; - break; - case TracebackStep::kStop: - break; - } -} - -void TracebackRunner::convertCurrentRunToAlignmentOperation() -{ - OperationType operation_type; - - switch (run_traceback_step) - { - case TracebackStep::kDiagonalMatch: - operation_type = OperationType::kMatch; - break; - case TracebackStep::kDiagonalMismatch: - operation_type = OperationType::kMismatch; - break; - case TracebackStep::kLeft: - operation_type = OperationType::kDeletionFromRef; - break; - case TracebackStep::kTop: - operation_type = OperationType::kInsertionToRef; - break; - case TracebackStep::kStop: - default: - throw std::logic_error("Attempted invalid traceback run decoding"); - } - - operations_.emplace_back(operation_type, run_length); -} - -void TracebackRunner::softclipQuerySuffix(size_t& row_index) -{ - - const uint32_t softclip_len = matrix_.numRows() - row_index - 1; - - operations_.emplace_back(OperationType::kSoftclip, softclip_len); -} - -void TracebackRunner::softclipQueryPrefix(size_t& row_index) -{ - operations_.emplace_back(OperationType::kSoftclip, row_index); -} -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/dagAligner/PenaltyMatrix.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/dagAligner/PenaltyMatrix.cpp deleted file mode 100644 index d1c7bba..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/dagAligner/PenaltyMatrix.cpp +++ /dev/null @@ -1,60 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Roman Petrovski -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphalign/dagAligner/PenaltyMatrix.hh" - -namespace graphalign -{ - -namespace dagAligner -{ - - // clang-format off -// Notice: this one does not support X at the moment -const FreePenaltyMatrix::Oligo FreePenaltyMatrix::TRANSLATION_TABLE_[OLIGO_MAX_CHAR + 1] = { - N, N, N, N, N, N, N, N, N, N, - N, N, N, N, N, N, N, N, N, N, - N, N, N, N, N, N, N, N, N, N, - N, N, N, N, N, N, N, N, N, N, - N, N, N, N, N, N, N, N, N, N, - N, N, N, N, N, N, N, N, N, N, - N, N, N, N, N, - // capitals - A, N, C, N, N, N, G, N, N, N, - N, N, N, N, N, N, N, N, N, T, - N, N, N, N, N, N, - // rubbish - N, N, N, N, N, N, - // lowercase - A, N, C, N, N, N, G, N, N, N, - N, N, N, N, N, N, N, N, N, T, - N, N, N, N, N, N, - // padding - N, N, N, N, - N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, - N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, - N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, - N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, N, -}; - // clang-format on - -} // namespace dagAligner - -} // namespace graphalign diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphcore/Graph.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphcore/Graph.cpp deleted file mode 100644 index bdeabe3..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphcore/Graph.cpp +++ /dev/null @@ -1,186 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko , -// Peter Krusche , -// Felix Schlesinger -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphcore/Graph.hh" - -#include - -#include "graphutils/SequenceOperations.hh" - -using std::set; -using std::string; -using std::to_string; -using std::vector; - -namespace graphtools -{ - -void Graph::init(size_t numnodes_) -{ - nodes_.resize(numnodes_); - adjacency_list_.resize(numnodes_); - reverse_adjacency_list_.resize(numnodes_); -} - -void Graph::assertNodeExists(NodeId node_id) const -{ - if (node_id >= nodes_.size()) - { - throw std::logic_error("Node with id " + to_string(node_id) + " does not exist"); - } -} - -void Graph::assertEdgeExists(NodeIdPair node_id_pair) const -{ - if (!hasEdge(node_id_pair.first, node_id_pair.second)) - { - throw std::logic_error( - "There is no edge between " + to_string(node_id_pair.first) + " and " + to_string(node_id_pair.second)); - } -} - -void assertValidSequence(string const& seq) -{ - if (seq.empty()) - { - throw std::logic_error("Invalid node sequence " + seq); - } -} - -const string& Graph::nodeName(NodeId node_id) const -{ - assertNodeExists(node_id); - return nodes_[node_id].name; -} -void Graph::setNodeName(NodeId node_id, const std::string& node_name) -{ - assertNodeExists(node_id); - nodes_[node_id].name = node_name; -} - -const string& Graph::nodeSeq(const NodeId node_id) const -{ - assertNodeExists(node_id); - return nodes_[node_id].sequence; -} - -const vector& Graph::nodeSeqExpansion(NodeId node_id) const -{ - assertNodeExists(node_id); - return nodes_[node_id].sequence_expansion; -} - -void Graph::setNodeSeq(NodeId node_id, const string& sequence) -{ - assertNodeExists(node_id); - assertValidSequence(sequence); - nodes_[node_id].sequence = sequence; - expandReferenceSequence(sequence, nodes_[node_id].sequence_expansion); -} - -void Graph::addEdge(NodeId source_id, NodeId sink_id) -{ - assertNodeExists(source_id); - assertNodeExists(sink_id); - - const string edge_encoding = "(" + to_string(source_id) + " ," + to_string(sink_id) + ")"; - if (hasEdge(source_id, sink_id)) - { - throw std::logic_error("Graph already contains edge " + edge_encoding); - } - - if (source_id > sink_id) - { - throw std::logic_error("Edge " + edge_encoding + " breaks topological order"); - } - - NodeIdPair node_id_pair = std::make_pair(source_id, sink_id); - edge_labels_[node_id_pair]; - - adjacency_list_[source_id].emplace(sink_id); - reverse_adjacency_list_[sink_id].emplace(source_id); -} - -bool Graph::hasEdge(NodeId source_id, NodeId sink_id) const -{ - assertNodeExists(source_id); - assertNodeExists(sink_id); - NodeIdPair node_id_pair(source_id, sink_id); - return edge_labels_.find(node_id_pair) != edge_labels_.end(); -} - -void Graph::addLabelToEdge(NodeId source_id, NodeId sink_id, const std::string& label) -{ - NodeIdPair node_pair = std::make_pair(source_id, sink_id); - assertEdgeExists(node_pair); - edge_labels_[node_pair].insert(label); -} - -SortedLabels Graph::allLabels() const -{ - SortedLabels labels; - for (const auto& single_edge_labels_ : edge_labels_) - { - labels.insert(single_edge_labels_.second.begin(), single_edge_labels_.second.end()); - } - return labels; -} - -const Labels& Graph::edgeLabels(NodeId source_id, NodeId sink_id) const -{ - NodeIdPair node_id_pair = std::make_pair(source_id, sink_id); - return edge_labels_.at(node_id_pair); -} - -std::set Graph::edgesWithLabel(const std::string& label) const -{ - std::set result; - for (const auto& pair : edge_labels_) - { - if (pair.second.count(label)) - { - result.insert(pair.first); - } - } - return result; -} - -void Graph::eraseLabel(const std::string& label) -{ - for (auto& pair : edge_labels_) - { - pair.second.erase(label); - } -} - -const set& Graph::successors(NodeId node_id) const -{ - assertNodeExists(node_id); - return adjacency_list_[node_id]; -} - -const std::set& Graph::predecessors(NodeId node_id) const -{ - assertNodeExists(node_id); - return reverse_adjacency_list_[node_id]; -} -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphcore/GraphBuilders.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphcore/GraphBuilders.cpp deleted file mode 100644 index dd31318..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphcore/GraphBuilders.cpp +++ /dev/null @@ -1,126 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko , -// Peter Krusche -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphcore/GraphBuilders.hh" - -// needed in gcc 5 -#include - -using std::string; - -namespace graphtools -{ - -Graph makeDeletionGraph(const string& left_flank, const string& deletion, const string& right_flank) -{ - Graph graph(3); - - graph.setNodeSeq(0, left_flank); - graph.setNodeSeq(1, deletion); - graph.setNodeSeq(2, right_flank); - graph.addEdge(0, 1); - graph.addEdge(0, 2); - graph.addEdge(1, 2); - - return graph; -} - -Graph makeSwapGraph( - const string& left_flank, const string& deletion, const string& insertion, const string& right_flank) -{ - Graph graph(4); - - graph.setNodeSeq(0, left_flank); - graph.setNodeSeq(1, deletion); - graph.setNodeSeq(2, insertion); - graph.setNodeSeq(3, right_flank); - graph.addEdge(0, 1); - graph.addEdge(0, 2); - graph.addEdge(1, 3); - graph.addEdge(2, 3); - - return graph; -} - -Graph makeDoubleSwapGraph( - const string& left_flank, const string& deletion1, const string& insertion1, const string& middle, - const string& deletion2, const string& insertion2, const string& right_flank) -{ - Graph graph(7); - - graph.setNodeSeq(0, left_flank); - graph.setNodeSeq(1, deletion1); - graph.setNodeSeq(2, insertion1); - graph.setNodeSeq(3, middle); - graph.setNodeSeq(4, deletion2); - graph.setNodeSeq(5, insertion2); - graph.setNodeSeq(6, right_flank); - graph.addEdge(0, 1); - graph.addEdge(0, 2); - graph.addEdge(1, 3); - graph.addEdge(2, 3); - graph.addEdge(3, 4); - graph.addEdge(3, 5); - graph.addEdge(4, 6); - graph.addEdge(5, 6); - - return graph; -} - -Graph makeLooplessStrGraph( - size_t read_len, const string& left_flank, const string& repeat_unit, const string& right_flank) -{ - const auto num_repeat_unit_nodes = (size_t)std::ceil(read_len / (double)repeat_unit.length()); - const size_t num_nodes = num_repeat_unit_nodes + 2; // Account for flanks - - Graph graph(num_nodes); - - NodeId right_flank_node_id = static_cast(num_nodes - 1); - - graph.setNodeSeq(0, left_flank); - graph.setNodeSeq(right_flank_node_id, right_flank); - graph.addEdge(0, right_flank_node_id); - - for (NodeId node_id = 0; node_id != num_repeat_unit_nodes; ++node_id) - { - graph.setNodeSeq(node_id + 1, repeat_unit); - graph.addEdge(node_id, node_id + 1); - graph.addEdge(node_id + 1, right_flank_node_id); - } - - return graph; -} - -Graph makeStrGraph(const string& left_flank, const string& repeat_unit, const string& right_flank) -{ - Graph graph(3); - graph.setNodeSeq(0, left_flank); - graph.setNodeSeq(1, repeat_unit); - graph.setNodeSeq(2, right_flank); - - graph.addEdge(0, 1); - graph.addEdge(0, 2); - graph.addEdge(1, 1); - graph.addEdge(1, 2); - - return graph; -} -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphcore/GraphCoordinates.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphcore/GraphCoordinates.cpp deleted file mode 100644 index 2550eda..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphcore/GraphCoordinates.cpp +++ /dev/null @@ -1,229 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Peter Krusche -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphcore/GraphCoordinates.hh" -#include "graphutils/PairHashing.hh" - -#include - -namespace graphtools -{ - -struct GraphCoordinates::GraphCoordinatesImpl -{ - explicit GraphCoordinatesImpl(Graph const* graph_) - : graph(graph_) - { - uint64_t canonical_offset = 0; - for (NodeId n_id = 0; n_id < (NodeId)graph_->numNodes(); ++n_id) - { - node_name_to_id[graph_->nodeName(n_id)] = n_id; - auto const& n_name = graph_->nodeName(n_id); - canonical_offsets[n_name] = canonical_offset; - node_starts[canonical_offset] = n_name; - canonical_offset += std::max((size_t)1, graph_->nodeSeq(n_id).size()); - - // nodes are sorted in topological order, so we can compute distances as min over all predecessors - for (NodeId n_source = 0; n_source < (NodeId)graph_->numNodes(); ++n_source) - { - // distance = zero in these cases - if (n_id == n_source || graph_->hasEdge(n_source, n_id)) - { - continue; - } - - size_t min_dist = std::numeric_limits::max(); - for (auto pred : graph_->predecessors(n_id)) - { - auto pred_distance_it = node_end_to_start_distance.find(std::make_pair(n_source, pred)); - if (pred_distance_it != node_end_to_start_distance.end()) - { - // minimal distance via that predecessor - min_dist = std::min(min_dist, pred_distance_it->second + graph_->nodeSeq(pred).size()); - } - else if (graph_->hasEdge(n_source, pred)) - { - min_dist = std::min(min_dist, graph_->nodeSeq(pred).size()); - } - } - - if (min_dist != std::numeric_limits::max()) - { - node_end_to_start_distance[std::make_pair(n_source, n_id)] = min_dist; - } - } - } - } - - Graph const* graph; - - std::unordered_map canonical_offsets; - std::map node_starts; - std::map node_name_to_id; - - std::unordered_map, size_t> node_end_to_start_distance; -}; - -GraphCoordinates::GraphCoordinates(Graph const* g) - : _impl(new GraphCoordinatesImpl(g)) -{ -} -GraphCoordinates::~GraphCoordinates() = default; - -GraphCoordinates::GraphCoordinates(GraphCoordinates&& rhs) noexcept - : _impl(std::move(rhs._impl)) -{ -} - -GraphCoordinates& GraphCoordinates::operator=(GraphCoordinates&& rhs) noexcept -{ - _impl = std::move(rhs._impl); - return *this; -} - -/** - * Get a "canonical" / linearized position -- every base on the graph has such a position - * @param node node name - * @param offset offset relative to start of node - * @return canonical position - */ -uint64_t GraphCoordinates::canonicalPos(std::string const& node, uint64_t offset) const -{ - auto ioffset = _impl->canonical_offsets.find(node); - assert(ioffset != _impl->canonical_offsets.end()); - return ioffset->second + offset; -} - -/** - * Calculated canonical start and end positions for a graph mapping - * @param mapping - * @return start and end - */ -std::pair GraphCoordinates::canonicalStartAndEnd(Path const& path) const -{ - std::pair start_end{ -1, -1 }; - - start_end.first - = canonicalPos(_impl->graph->nodeName(path.nodeIds().front()), static_cast(path.startPosition())); - - auto end_offset = static_cast(path.endPosition()); - if (path.numNodes() > 0 && end_offset > 0) - { - start_end.second = canonicalPos(_impl->graph->nodeName(path.nodeIds().back()), end_offset); - } - - if (start_end.first > start_end.second) - { - std::swap(start_end.first, start_end.second); - } - - return start_end; -} - -/** - * Reverse lookup : get node and offset from a canonical pos - * @param canonical_pos canonical position - * @param node output variable for node name - * @param offset output variable for offset - */ -void GraphCoordinates::nodeAndOffset(uint64_t canonical_pos, std::string& node, uint64_t& offset) const -{ - auto lb = _impl->node_starts.lower_bound(canonical_pos); - if (lb != _impl->node_starts.end()) - { - if (lb != _impl->node_starts.begin() && canonical_pos < lb->first) - { - lb = std::prev(lb); - } - node = lb->second; - offset = canonical_pos - lb->first; - } - else - { - node = _impl->node_starts.rbegin()->second; - offset = canonical_pos - _impl->node_starts.rbegin()->first; - } -} - -/** - * Calculate the minimum distance in bp between two canonical positions - * @param pos1 start pos - * @param pos2 end pos - * @return basepairs between pos1 and pos2 - */ -uint64_t GraphCoordinates::distance(uint64_t pos1, uint64_t pos2) const -{ - if (pos1 == pos2) - { - return 0; - } - if (pos2 < pos1) - { - std::swap(pos1, pos2); - } - - std::string n1, n2; - uint64_t offset1, offset2; - nodeAndOffset(pos1, n1, offset1); - nodeAndOffset(pos2, n2, offset2); - - // on on the same node-> can compute distance directly - if (n1 == n2) - { - return pos2 - pos1; - } - - const NodeId n1_id = _impl->node_name_to_id[n1]; - const NodeId n2_id = _impl->node_name_to_id[n2]; - const size_t n1_length = _impl->graph->nodeSeq(n1_id).size(); - - uint64_t result = std::numeric_limits::max(); - if (_impl->graph->hasEdge(n1_id, n2_id)) - { - result = n1_length - offset1 + offset2; - } - else - { - auto dist_it = _impl->node_end_to_start_distance.find(std::make_pair(n1_id, n2_id)); - - if (dist_it != _impl->node_end_to_start_distance.end()) - { - result = n1_length - offset1 + offset2 + dist_it->second; - } - } - return result; -} - -/** - * Return the node id for a node name - * @param node_name name of node - * @return node id for the node - */ -NodeId GraphCoordinates::nodeId(const std::string& node_name) const -{ - assert(_impl->node_name_to_id.count(node_name) != 0); - return _impl->node_name_to_id[node_name]; -} - -/** - * @return the graph for these coordinates - */ -Graph const& GraphCoordinates::getGraph() const { return *(_impl->graph); } -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphcore/GraphOperations.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphcore/GraphOperations.cpp deleted file mode 100644 index 54357ef..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphcore/GraphOperations.cpp +++ /dev/null @@ -1,56 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko , -// Peter Krusche -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphcore/GraphOperations.hh" - -#include "graphutils/SequenceOperations.hh" - -namespace graphtools -{ -/** - * Reverse (and optionally complement) a graph - * @param graph the graph to reverse - * @param complement true to also reverse-complement all sequences - */ -Graph reverseGraph(Graph const& graph, bool complement) -{ - Graph reversed(graph.numNodes(), ""); - - for (NodeId node_id = 0; node_id != graph.numNodes(); ++node_id) - { - reversed.setNodeSeq( - static_cast(graph.numNodes() - 1 - node_id), - complement ? reverseComplement(graph.nodeSeq(node_id)) : reverseString(graph.nodeSeq(node_id))); - - for (auto succ : graph.successors(node_id)) - { - const auto to_new = static_cast(graph.numNodes() - 1 - node_id); - const auto from_new = static_cast(graph.numNodes() - 1 - succ); - reversed.addEdge(from_new, to_new); - for (const auto& label : graph.edgeLabels(node_id, succ)) - { - reversed.addLabelToEdge(from_new, to_new, label); - } - } - } - return reversed; -} -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphcore/GraphReferenceMapping.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphcore/GraphReferenceMapping.cpp deleted file mode 100644 index 6b4f2fa..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphcore/GraphReferenceMapping.cpp +++ /dev/null @@ -1,143 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Felix Schlesinger -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphcore/GraphReferenceMapping.hh" - -#include -#include - -#include "graphcore/GraphCoordinates.hh" -#include "graphcore/PathOperations.hh" -#include "graphutils/IntervalList.hh" - -using std::string; - -namespace graphtools -{ - -ReferenceInterval::ReferenceInterval(ContigId const contig, Position const start, Position const end) - : contig(contig) - , start(start) - , end(end) -{ - if ((start < 0) || (start > end)) - { - throw std::logic_error("Invalid Interval"); - } -} -ReferenceInterval ReferenceInterval::makePosition(ContigId const& contig, Position const pos) -{ - return ReferenceInterval(contig, pos, pos); -} - -ReferenceInterval ReferenceInterval::parseRegion(std::string const& regionString) -{ - std::vector spl; - boost::split(spl, regionString, boost::is_any_of(":")); - if (spl.size() != 2) - { - throw std::runtime_error("Invalid region string: " + regionString); - } - string const contig = spl[0]; - boost::replace_all(spl[1], ",", ""); - boost::split(spl, spl[1], boost::is_any_of("-")); - if (spl.size() != 2) - { - throw std::runtime_error("Invalid region string: " + regionString); - } - int const start = std::stoll(spl[0]); - int const end = std::stoll(spl[1]); - return ReferenceInterval(contig, start, end); -} - -bool operator<(ReferenceInterval const& lhs, ReferenceInterval const& rhs) -{ - return lhs.contig < rhs.contig || (lhs.contig == rhs.contig && lhs.start < rhs.start) - || (lhs.contig == rhs.contig && lhs.start == rhs.start && lhs.end < rhs.end); -} -bool operator==(ReferenceInterval const& lhs, ReferenceInterval const& rhs) -{ - return lhs.contig == rhs.contig && lhs.start == rhs.start && lhs.end == rhs.end; -} -std::ostream& operator<<(std::ostream& output, ReferenceInterval const& ri) -{ - output << ri.contig << ":" << ri.start << "-" << ri.end; - return output; -} - -int32_t ReferenceInterval::length() const { return end - start; } - -NodeReferenceMapping::NodeReferenceMapping(Graph const& graph, NodeId const node, ReferenceInterval const& ref) - : nodeLength_(graph.nodeSeq(node).length()) - , ref_(ref) -{ - if (nodeLength_ != ref.length()) - { - throw std::logic_error("Length of node sequence does not match reference map length " + graph.nodeName(node)); - } -} - -ReferenceInterval NodeReferenceMapping::map(int32_t const offset) const -{ - if (offset >= nodeLength_) - { - throw std::logic_error("Cannot map position outside node"); - } - return ReferenceInterval::makePosition(ref_.contig, ref_.start + offset); -} - -GraphReferenceMapping::GraphReferenceMapping(Graph const* graph) - : graph_(graph) -{ -} - -void GraphReferenceMapping::addMapping(NodeId node, ReferenceInterval const& ref) -{ - NodeReferenceMapping const nodeMapping(*graph_, node, ref); - mappings_.insert({ node, nodeMapping }); -} - -boost::optional GraphReferenceMapping::map(NodeId node, int32_t offset) const -{ - if (node >= graph_->numNodes()) - { - throw std::logic_error("Invalid node " + std::to_string(node)); - } - auto const& mapping = mappings_.find(node); - if (mapping != mappings_.end()) - { - return mapping->second.map(offset); - } - return boost::optional(); -} - -boost::optional GraphReferenceMapping::map(Path const& path) const -{ - for (auto const& nodePath : generateSubpathForEachNode(path)) - { - auto const mapped = map(*nodePath.nodeIds().begin(), nodePath.startPosition()); - if (mapped) - { - return mapped; - } - } - return boost::optional(); -} -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphcore/Path.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphcore/Path.cpp deleted file mode 100644 index 7043175..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphcore/Path.cpp +++ /dev/null @@ -1,496 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphcore/Path.hh" - -#include -#include -#include - -using std::logic_error; -using std::ostream; -using std::string; -using std::to_string; -using std::vector; - -namespace graphtools -{ - -void Path::assertValidity() const -{ - assertNonEmpty(); - assertFirstNodePosValid(); - assertLastNodePosValid(); - assertPositionsOrdered(); - assertConnected(); -} - -void Path::assertPositionsOrdered() const -{ - const bool positionsOrdered = nodes_.size() != 1 || start_position_ <= end_position_; - if (!positionsOrdered) - { - throw logic_error("Positions are not ordered"); - } -} - -bool Path::isNodePositionValid(const NodeId node_id, const int32_t position) const -{ - if (position < 0) - { - return false; - } - const string& node_seq = graph_raw_ptr_->nodeSeq(node_id); - return (unsigned)position <= node_seq.length(); -} - -void Path::assertNonEmpty() const -{ - if (nodes_.empty()) - { - throw logic_error("Path is empty"); - } -} - -void Path::assertFirstNodePosValid() const -{ - const NodeId first_node_id = nodes_.front(); - if (!isNodePositionValid(first_node_id, start_position_)) - { - throw logic_error("Position of first node is invalid"); - } -} - -void Path::assertLastNodePosValid() const -{ - const NodeId last_node_id = nodes_.back(); - if (!isNodePositionValid(last_node_id, end_position_)) - { - throw logic_error("Position of last node is invalid"); - } -} - -void Path::assertConnected() const -{ - const unsigned nodeCount(nodes_.size()); - for (unsigned nodeIndex(0); (nodeIndex + 1) < nodeCount; ++nodeIndex) - { - if (!graph_raw_ptr_->hasEdge(nodes_[nodeIndex], nodes_[nodeIndex + 1])) - { - throw logic_error("Path is not connected"); - } - } -} - -void Path::assertThatIndexIsValid(const int32_t node_index) const -{ - if (node_index < 0 || node_index >= (signed)nodes_.size()) - { - const string msg = "Node index " + to_string(node_index) + "is out of bounds for path " + encode(); - throw std::logic_error(msg); - } -} - -string Path::encode() const -{ - string path_encoding; - - size_t node_index = 0; - const size_t last_index = nodes_.size() - 1; - for (NodeId node_id : nodes_) - { - const string node_name = to_string(node_id); - string node_encoding; - if (node_index == 0) // Encoding first node. - { - node_encoding = "(" + node_name + "@" + to_string(start_position_) + ")"; - } - if (node_index == last_index) // Encoding last node. - { - node_encoding += "-(" + node_name + "@" + to_string(end_position_) + ")"; - } - if (node_index != 0 && node_index != last_index) // Encoding intermediate node. - { - node_encoding = "-(" + node_name + ")"; - } - path_encoding += node_encoding; - ++node_index; - } - - return path_encoding; -} - -Path::Path(const Graph* graph_raw_ptr, int32_t start_position, const vector& nodes, int32_t end_position) - : graph_raw_ptr_(graph_raw_ptr) - , start_position_(start_position) - , end_position_(end_position) - , nodes_(nodes) -{ - try - { - assertValidity(); - } - catch (const std::exception& e) - { - throw logic_error("Unable to create path " + encode() + ": " + e.what()); - } -} - -bool Path::checkOverlapWithNode(const NodeId node_id) const -{ - return std::find(nodes_.begin(), nodes_.end(), node_id) != nodes_.end(); -} - -int32_t Path::getStartPositionOnNodeByIndex(size_t node_index) const -{ - assertThatIndexIsValid(static_cast(node_index)); - - if (node_index == 0) - { - return startPosition(); - } - - return 0; -} - -int32_t Path::getEndPositionOnNodeByIndex(size_t node_index) const -{ - assertThatIndexIsValid(static_cast(node_index)); - - if (node_index == (numNodes() - 1)) - { - return endPosition(); - } - - return graphRawPtr()->nodeSeq(nodes_[node_index]).length(); -} - -size_t Path::getNodeOverlapLengthByIndex(size_t node_index) const -{ - assertThatIndexIsValid(static_cast(node_index)); - const size_t node_length = graphRawPtr()->nodeSeq(nodes_[node_index]).length(); - auto length_on_node = (int32_t)node_length; // This is the length of all intermediate nodes. - - const bool is_first_node = node_index == 0; - const bool is_last_node = node_index + 1 == numNodes(); - - if (is_first_node && is_last_node) - { - length_on_node = end_position_ - start_position_; - } - else if (is_first_node) - { - length_on_node = static_cast(node_length - start_position_); - } - else if (is_last_node) - { - length_on_node = end_position_; - } - - return static_cast(length_on_node); -} - -int32_t Path::getDistanceFromPathStart(const NodeId node, const int32_t offset) const -{ - int32_t distance = 0; - bool found = false; - const size_t nodeCount(numNodes()); - for (size_t nodeIndex(0); nodeIndex < nodeCount; ++nodeIndex) - { - const auto node_id = nodes_[nodeIndex]; - const int32_t node_start = nodeIndex == 0 ? start_position_ : 0; - const int32_t node_end - = (nodeIndex + 1) == nodeCount ? end_position_ : (int32_t)graph_raw_ptr_->nodeSeq(node_id).size() - 1; - - if (node_id == node && offset >= node_start && offset <= node_end) - { - distance += offset - node_start; - found = true; - break; - } - - distance += node_end - node_start + 1; - } - if (!found) - { - throw std::logic_error(std::to_string(node) + "@" + std::to_string(offset) + " is not on path " + encode()); - } - return distance; -} - -size_t Path::length() const -{ - size_t path_length = 0; - const size_t nodeCount(numNodes()); - for (size_t node_index = 0; node_index != nodeCount; ++node_index) - { - path_length += getNodeOverlapLengthByIndex(node_index); - } - - return path_length; -} - -string Path::getNodeSeq(const size_t node_index) const -{ - const string& sequence = graph_raw_ptr_->nodeSeq(nodes_[node_index]); - - if (node_index == 0) - { - const size_t node_overlap_len = getNodeOverlapLengthByIndex(node_index); - return sequence.substr(static_cast(start_position_), node_overlap_len); - } - else if ((node_index + 1) == numNodes()) - { - const size_t node_overlap_len = getNodeOverlapLengthByIndex(node_index); - return sequence.substr(0, node_overlap_len); - } - else - { - return sequence; - } -} - -string Path::seq() const -{ - string path_seq; - const size_t nodeCount(numNodes()); - for (size_t node_index = 0; node_index != nodeCount; ++node_index) - { - const std::string& node_seq(graph_raw_ptr_->nodeSeq(nodes_[node_index])); - if ((node_index == 0) or ((node_index + 1) == nodeCount)) - { - const size_t pos((node_index == 0) ? start_position_ : 0); - const size_t len(((node_index + 1) == nodeCount) ? (end_position_ - pos) : std::string::npos); - path_seq += node_seq.substr(pos, len); - } - else - { - path_seq += node_seq; - } - } - return path_seq; -} - -ostream& operator<<(ostream& os, const Path& path) { return os << path.encode(); } - -void Path::shiftStartAlongNode(const int32_t shift_len) -{ - start_position_ -= shift_len; - - try - { - assertValidity(); - } - catch (const std::exception& e) - { - throw logic_error("Unable to shift start of " + encode() + " by " + to_string(shift_len) + ": " + e.what()); - } -} - -void Path::shiftEndAlongNode(const int32_t shift_len) -{ - end_position_ += shift_len; - - try - { - assertValidity(); - } - catch (const std::exception& e) - { - throw logic_error("Unable to shift end of " + encode() + " by " + to_string(shift_len) + ": " + e.what()); - } -} - -void Path::extendStartToNode(const NodeId node_id) -{ - nodes_.insert(nodes_.begin(), node_id); - const auto new_node_seq_len = static_cast(graph_raw_ptr_->nodeSeq(node_id).length()); - start_position_ = new_node_seq_len; - - try - { - assertValidity(); - } - catch (const std::exception& e) - { - throw logic_error("Unable to extend " + encode() + " to node " + to_string(node_id) + ": " + e.what()); - } -} - -void Path::extendStartToIncludeNode(const NodeId node_id) -{ - nodes_.insert(nodes_.begin(), node_id); - start_position_ = 0; - - try - { - assertValidity(); - } - catch (const std::exception& e) - { - throw logic_error("Unable to extend " + encode() + " to node " + to_string(node_id) + ": " + e.what()); - } -} - -void Path::removeStartNode() -{ - nodes_.erase(nodes_.begin()); - start_position_ = 0; - - try - { - assertValidity(); - } - catch (const std::exception& e) - { - throw logic_error("Unable to remove start node of " + encode() + ": " + e.what()); - } -} - -void Path::removeZeroLengthStart() -{ - if (numNodes() > 1 && getNodeOverlapLengthByIndex(0) == 0) - { - removeStartNode(); - } -} - -void Path::removeZeroLengthEnd() -{ - const size_t index_of_last_node = numNodes() - 1; - if (numNodes() > 1 && getNodeOverlapLengthByIndex(index_of_last_node) == 0) - { - removeEndNode(); - } -} - -void Path::extendEndToNode(const NodeId node_id) -{ - nodes_.push_back(node_id); - end_position_ = 0; - - try - { - assertValidity(); - } - catch (const std::exception& e) - { - throw logic_error("Unable to extend " + encode() + " right to node " + to_string(node_id) + ": " + e.what()); - } -} - -void Path::extendEndToIncludeNode(const NodeId node_id) -{ - nodes_.push_back(node_id); - const auto new_node_seq_len = static_cast(graph_raw_ptr_->nodeSeq(node_id).length()); - end_position_ = new_node_seq_len; - - try - { - assertValidity(); - } - catch (const std::exception& e) - { - throw logic_error("Unable to extend " + encode() + " right to node " + to_string(node_id) + ": " + e.what()); - } -} - -void Path::removeEndNode() -{ - nodes_.erase(nodes_.end() - 1); - NodeId new_last_node_id = nodes_.back(); - auto new_last_node_len = static_cast(graph_raw_ptr_->nodeSeq(new_last_node_id).length()); - end_position_ = new_last_node_len; - - try - { - assertValidity(); - } - catch (const std::exception& e) - { - throw logic_error("Unable to remove end node of " + encode() + ": " + e.what()); - } -} - -void Path::shrinkStartBy(const int32_t shrink_len) -{ - const int32_t node_len_left = getNodeOverlapLengthByIndex(0); - - if (shrink_len <= node_len_left) - { - shiftStartAlongNode(-shrink_len); - removeZeroLengthStart(); - } - else - { - removeStartNode(); - - const int32_t leftover_len = shrink_len - node_len_left; - shrinkStartBy(leftover_len); - } -} - -void Path::shrinkEndBy(const int32_t shrink_len) -{ - const int32_t node_len_left = end_position_; - - if (shrink_len <= node_len_left) - { - shiftEndAlongNode(-shrink_len); - removeZeroLengthEnd(); - } - else - { - removeEndNode(); - - const int32_t leftover_len = shrink_len - node_len_left; - shrinkEndBy(leftover_len); - } -} - -void Path::shrinkBy(const int32_t start_shrink_len, const int32_t end_shrink_len) -{ - shrinkStartBy(start_shrink_len); - shrinkEndBy(end_shrink_len); -} - -bool Path::operator==(const Path& other) const -{ - return (graph_raw_ptr_ == other.graph_raw_ptr_) && (start_position_ == other.start_position_) - && (end_position_ == other.end_position_) && (nodes_ == other.nodes_); -} - -bool Path::operator<(const Path& other) const -{ - if (start_position_ != other.start_position_) - { - return start_position_ < other.start_position_; - } - - if (nodes_ != other.nodes_) - { - return nodes_ < other.nodes_; - } - - return end_position_ < other.end_position_; -} - -std::ostream& operator<<(std::ostream& os, const ReversePath& path) { return os << "reverse path of: " << path.path_; } -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphcore/PathFamily.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphcore/PathFamily.cpp deleted file mode 100644 index a3a8bfd..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphcore/PathFamily.cpp +++ /dev/null @@ -1,141 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Felix Schlesinger , -// Peter Krusche -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphcore/PathFamily.hh" - -#include -#include -#include -#include -#include -#include - -#include "graphcore/Path.hh" - -namespace graphtools -{ -struct PathFamily::Impl -{ - explicit Impl(Graph* const graph) - : graph_(graph) - { - } - - Graph* const graph_; - std::unordered_set edges_; - std::unordered_set inNodes_; - std::unordered_set outNodes_; -}; - -PathFamily::PathFamily(Graph* const graph) - : pimpl_(new PathFamily::Impl(graph)) -{ -} - -PathFamily::PathFamily(Graph* const graph, const std::string& label) - : pimpl_(new PathFamily::Impl(graph)) -{ - for (const auto& edge : graph->edgesWithLabel(label)) - { - addEdge(edge.first, edge.second); - } -} - -PathFamily::PathFamily(const PathFamily& other) - : pimpl_(new Impl(*other.pimpl_)) -{ -} - -PathFamily::PathFamily(PathFamily&& other) noexcept - : pimpl_(std::move(other.pimpl_)) -{ -} - -PathFamily::~PathFamily() noexcept = default; - -const Graph& PathFamily::graph() const { return *(pimpl_->graph_); } -const std::unordered_set& PathFamily::edges() const { return pimpl_->edges_; } - -bool PathFamily::operator==(const PathFamily& other) const -{ - return ((edges() == other.edges()) && (pimpl_->graph_ == other.pimpl_->graph_)); -} - -bool PathFamily::operator!=(const PathFamily& other) const { return !(*this == other); } - -bool PathFamily::containsPath(const Path& path) const -{ - int matched(0); - for (auto start = path.begin(); start != std::prev(path.end()); ++start) - { - auto end = std::next(start); - if (edges().count(NodeIdPair(*start, *end))) - { - ++matched; - } - else - { - if (pimpl_->outNodes_.count(*start) || pimpl_->inNodes_.count(*end)) - { - return false; - } - } - } - return matched > 0; -} - -bool PathFamily::includes(const PathFamily& other) const -{ - return std::all_of( - other.edges().begin(), other.edges().end(), [&](const NodeIdPair& e) { return edges().count(e); }); -} - -void PathFamily::addEdge(NodeId first, NodeId second) -{ - if (!graph().hasEdge(first, second)) - { - throw std::logic_error("Edges added to path family is not in the graph."); - } - pimpl_->edges_.emplace(first, second); - pimpl_->outNodes_.insert(first); - pimpl_->inNodes_.insert(second); -} - -void PathFamily::setLabel(const std::string& label) -{ - pimpl_->graph_->eraseLabel(label); - for (const auto& edge : edges()) - { - pimpl_->graph_->addLabelToEdge(edge.first, edge.second, label); - } -} - -std::ostream& operator<<(std::ostream& os, const PathFamily& path) -{ - os << "{"; - for (const auto& edge : path.edges()) - { - os << "(" << edge.first << ", " << edge.second << "), "; - } - os << "}"; - return os; -} -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphcore/PathFamilyOperations.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphcore/PathFamilyOperations.cpp deleted file mode 100644 index f3a75af..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphcore/PathFamilyOperations.cpp +++ /dev/null @@ -1,205 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Felix Schlesinger , -// Peter Krusche -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphcore/Path.hh" -#include "graphcore/PathFamily.hh" -#include "graphcore/PathOperations.hh" - -#include -#include -#include -#include -#include -#include - -using std::list; -using std::map; -using std::set; -using std::vector; - -namespace graphtools -{ - -std::list getPathSegmentsForFamily(graphtools::PathFamily const& family) -{ - std::list segments; - Graph const& graph = family.graph(); - - // sort edges to have their start nodes in topological order - vector edges{ family.edges().begin(), family.edges().end() }; - std::sort(edges.begin(), edges.end(), [](NodeIdPair const& a, NodeIdPair const& b) -> bool { - return a.first == b.first ? a.second < b.second : a.first < b.first; - }); - - // compute in and out degree of nodes for subgraph given by path family edges - map in_count; - map out_count; - for (const auto& edge : edges) - { - out_count[edge.first]++; - in_count[edge.second]++; - } - - // concatenate path segments within the family - for (const auto& edge : edges) - { - if (edge.first == edge.second) - { - continue; - } - - bool any_path_extended_by_edge = false; - for (auto& prefix : segments) - { - // only extend when we can do so uniquely - if (prefix.nodeIds().back() == edge.first && in_count[edge.first] == 1 && out_count[edge.first] == 1) - { - prefix.extendEndToIncludeNode(edge.second); - any_path_extended_by_edge = true; - } - } - if (!any_path_extended_by_edge) - { - segments.emplace_back(Path{ - &graph, 0, { edge.first, edge.second }, static_cast(graph.nodeSeq(edge.second).size()) }); - } - } - - return segments; -} - -bool enumeratePathCombinationsInFamily( - PathFamily const& family, std::list const& segments, std::list* paths, size_t maxPaths) -{ - if (paths == nullptr) - { - throw std::logic_error("paths cannot be null."); - } - paths->clear(); - - bool complete = true; - map> segmentsStartingAt; - map> segmentsEndingAt; - for (const auto& segment : segments) - { - segmentsStartingAt[segment.nodeIds().front()].insert(segment); - segmentsEndingAt[segment.nodeIds().back()].insert(segment); - } - - bool any_merged = true; - while (any_merged) - { - any_merged = false; - set merged_subpaths; - for (const auto& edge : family.edges()) - { - auto check_and_merge = [&](std::set const& prefixes, std::set const& suffixes) { - for (const auto& prefix : prefixes) - { - for (const auto& suffix : suffixes) - { - if (checkPathPrefixSuffixOverlap(prefix, suffix) || checkIfPathsAdjacent(prefix, suffix)) - { - Path segment = mergePaths(prefix, suffix); - segmentsStartingAt[segment.nodeIds().front()].insert(segment); - segmentsEndingAt[segment.nodeIds().back()].insert(segment); - - merged_subpaths.insert(prefix); - merged_subpaths.insert(suffix); - any_merged = true; - } - } - } - }; - - check_and_merge(segmentsEndingAt[edge.first], segmentsStartingAt[edge.first]); - check_and_merge(segmentsEndingAt[edge.second], segmentsStartingAt[edge.second]); - check_and_merge(segmentsEndingAt[edge.first], segmentsStartingAt[edge.second]); - } - for (const auto& path : merged_subpaths) - { - segmentsStartingAt[path.nodeIds().front()].erase(path); - segmentsEndingAt[path.nodeIds().back()].erase(path); - } - - // check we're not over the maximum count - size_t count = 0; - for (const auto& start_list : segmentsStartingAt) - { - count += start_list.second.size(); - } - if (count > maxPaths) - { - complete = false; - break; - } - } - - for (const auto& start_list : segmentsStartingAt) - { - for (const auto& path : start_list.second) - { - paths->push_back(path); - if (paths->size() > maxPaths) - { - complete = false; - break; - } - } - if (paths->size() > maxPaths) - { - break; - } - } - - return complete; -} - -bool getMaximalPathsForFamily(graphtools::PathFamily const& family, std::list* paths, size_t maxPaths) -{ - const auto segments = getPathSegmentsForFamily(family); - return enumeratePathCombinationsInFamily(family, segments, paths, maxPaths); -} - -std::map getPathFamiliesFromGraph(graphtools::Graph& graph) -{ - std::map families; - - for (const auto& label : graph.allLabels()) - { - families.insert(std::make_pair(label, PathFamily(&graph, label))); - } - - return families; -} - -graphtools::PathFamily pathToPathFamily(graphtools::Graph& graph, graphtools::Path const& path) -{ - graphtools::PathFamily family(&graph); - - for (size_t i = 1; i < path.numNodes(); ++i) - { - family.addEdge(path.getNodeIdByIndex(i - 1), path.getNodeIdByIndex(i)); - } - - return family; -} -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphcore/PathOperations.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphcore/PathOperations.cpp deleted file mode 100644 index 29a6e53..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphcore/PathOperations.cpp +++ /dev/null @@ -1,794 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko , -// Peter Krusche -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphcore/PathOperations.hh" - -#include -#include -#include -#include -#include -#include - -#include "graphutils/BaseMatching.hh" - -using std::list; -using std::set; -using std::string; -using std::vector; - -namespace graphtools -{ - -list extendPathStart(const Path& path, int32_t extension_len) -{ - list extended_paths; - - const NodeId start_node_id = path.nodeIds().front(); - - // Start position gives the maximum extension. - if (extension_len <= path.startPosition()) - { - Path extended_path(path); - extended_path.shiftStartAlongNode(extension_len); - extended_paths.push_back(extended_path); - } - else - { - const set pred_node_ids = path.graphRawPtr()->predecessors(start_node_id); - const int32_t leftover_length = extension_len - path.startPosition(); - for (NodeId pred_node_id : pred_node_ids) - { - Path path_with_this_node(path); - path_with_this_node.extendStartToNode(pred_node_id); - list extensions_of_path_with_this_node = extendPathStart(path_with_this_node, leftover_length); - - extended_paths.splice(extended_paths.end(), extensions_of_path_with_this_node); - } - } - - return extended_paths; -} - -list extendPathEnd(const Path& path, int32_t extension_len) -{ - list extended_paths; - - const NodeId end_node_id = path.nodeIds().back(); - - const auto end_node_length = static_cast(path.graphRawPtr()->nodeSeq(end_node_id).length()); - const int32_t max_extension_at_end_node = end_node_length - path.endPosition(); - - if (extension_len <= max_extension_at_end_node) - { - Path extended_path(path); - extended_path.shiftEndAlongNode(extension_len); - extended_paths.push_back(extended_path); - } - else - { - const set succ_node_ids = path.graphRawPtr()->successors(end_node_id); - const int32_t leftover_length = extension_len - max_extension_at_end_node; - for (NodeId succ_node_id : succ_node_ids) - { - Path path_with_this_node(path); - path_with_this_node.extendEndToNode(succ_node_id); - - list extensions_of_path_with_this_node = extendPathEnd(path_with_this_node, leftover_length); - extended_paths.splice(extended_paths.end(), extensions_of_path_with_this_node); - } - } - - return extended_paths; -} - -list extendPath(const Path& path, int32_t start_extension_len, int32_t end_extension_len) -{ - list extended_paths; - list start_extended_paths = extendPathStart(path, start_extension_len); - for (const Path& start_extended_path : start_extended_paths) - { - list end_extended_paths = extendPathEnd(start_extended_path, end_extension_len); - extended_paths.splice(extended_paths.end(), end_extended_paths); - } - return extended_paths; -} - -Path extendPathEndMatching(Path path, const std::string& query, size_t qpos) -{ - const Graph& graph = *path.graphRawPtr(); - size_t pos_in_query = qpos + path.length(); - NodeId node_in_graph = path.nodeIds().back(); - size_t pos_in_node = (size_t)path.endPosition(); - - std::vector nodes = path.nodeIds(); - bool moved = true; - - while (moved) - { - moved = false; - const std::string& node_sequence = graph.nodeSeq(node_in_graph); - - while (pos_in_query < query.size() && pos_in_node < node_sequence.size() - && checkIfReferenceBaseMatchesQueryBase(node_sequence.at(pos_in_node), query.at(pos_in_query))) - { - moved = true; - ++pos_in_node; - ++pos_in_query; - } - - if (pos_in_node >= node_sequence.size()) - { - const auto& successors = graph.successors(node_in_graph); - - size_t num_longest_matches = 0; - size_t current_longest_match = 0; - NodeId current_successor = 0; - - size_t successor_min_size = std::numeric_limits::max(); - for (auto successor : successors) - { - successor_min_size = std::min(successor_min_size, graph.nodeSeq(successor).size()); - } - - for (auto successor : successors) - { - size_t pos_in_successor = 0; - const std::string& successor_sequence = graph.nodeSeq(successor); - while (pos_in_successor < successor_min_size && pos_in_query + pos_in_successor < query.size() - && checkIfReferenceBaseMatchesQueryBase( - successor_sequence.at(pos_in_successor), query[pos_in_query + pos_in_successor])) - { - ++pos_in_successor; - } - - if (pos_in_successor > current_longest_match) - { - current_longest_match = pos_in_successor; - current_successor = successor; - num_longest_matches = 1; - } - else if (pos_in_successor == current_longest_match) - { - ++num_longest_matches; - } - } - - if (current_longest_match == 0 || num_longest_matches != 1) - { - break; - } - - nodes.push_back(current_successor); - pos_in_query += current_longest_match; - pos_in_node = current_longest_match; - node_in_graph = current_successor; - moved = true; - } - } - return Path{ &graph, path.startPosition(), nodes, static_cast(pos_in_node) }; -} - -Path extendPathStartMatching(Path path, const std::string& query, size_t& pos_in_query) -{ - const Graph& graph = *path.graphRawPtr(); - NodeId node_in_graph = path.nodeIds().front(); - auto pos_in_node = (size_t)path.startPosition(); - - std::vector nodes = path.nodeIds(); - bool moved = true; - - while (moved) - { - moved = false; - - const std::string& node_sequence = graph.nodeSeq(node_in_graph); - - while (pos_in_query > 0 && pos_in_node > 0 - && checkIfReferenceBaseMatchesQueryBase(node_sequence.at(pos_in_node - 1), query.at(pos_in_query - 1))) - { - moved = true; - --pos_in_node; - --pos_in_query; - } - - if (pos_in_node == 0) - { - const auto& predecessors = graph.predecessors(node_in_graph); - - size_t num_longest_matches = 0; - size_t current_longest_match = 0; - NodeId current_predecessor = 0; - - size_t predecessor_min_size = std::numeric_limits::max(); - for (auto predecessor : predecessors) - { - predecessor_min_size = std::min(predecessor_min_size, graph.nodeSeq(predecessor).size()); - } - for (auto predecessor : predecessors) - { - const std::string& predecessor_sequence = graph.nodeSeq(predecessor); - size_t pos_in_predecessor = predecessor_sequence.size(); - size_t match_length = 0; - while (pos_in_predecessor > (predecessor_sequence.size() - predecessor_min_size) - && pos_in_query - match_length > 0 - && checkIfReferenceBaseMatchesQueryBase( - predecessor_sequence.at(pos_in_predecessor - 1), query[pos_in_query - match_length - 1])) - { - --pos_in_predecessor; - ++match_length; - } - - if (match_length > current_longest_match) - { - current_longest_match = match_length; - current_predecessor = predecessor; - num_longest_matches = 1; - } - else if (match_length == current_longest_match) - { - ++num_longest_matches; - } - } - - if (current_longest_match == 0 - || num_longest_matches != 1) // also gets the case where current_longest_match == 0 - { - break; - } - - nodes.insert(nodes.begin(), current_predecessor); - pos_in_query -= current_longest_match; - node_in_graph = current_predecessor; - pos_in_node = graph.nodeSeq(node_in_graph).size() - current_longest_match; - moved = true; - } - } - - return Path{ &graph, static_cast(pos_in_node), nodes, path.endPosition() }; -} - -Path extendPathMatching(Path path, const std::string& query, size_t& pos_in_query) -{ - return extendPathStartMatching(extendPathEndMatching(std::move(path), query, pos_in_query), query, pos_in_query); -} - -vector splitSequenceByPath(const Path& path, const string& sequence) -{ - if (path.length() != sequence.length()) - { - throw std::logic_error( - "Split operation requires that " + path.encode() + " and " + sequence + " have same length"); - } - - vector split_seq; - size_t cur_position = 0; - for (int32_t node_index = 0; node_index != (signed)path.numNodes(); ++node_index) - { - const size_t length_on_node = path.getNodeOverlapLengthByIndex(static_cast(node_index)); - split_seq.push_back(sequence.substr(cur_position, length_on_node)); - cur_position += length_on_node; - } - return split_seq; -} - -/** - * Return true if two paths are exactly adjacent - * (i.e. p1 starts just before p2, or the other way around) - * - * @param p1 first path - * @param p2 second path - * @return true if the paths are adjacent - */ -bool checkIfPathsAdjacent(Path const& p1, Path const& p2) -{ - // if p1 ends after p2 starts, try the other way around - if (p1.nodeIds().back() > p2.nodeIds().front()) - { - return checkIfPathsAdjacent(p2, p1); - } - - // now p1.nodeIds().back() <= p2.nodeIds().front() - const auto& graph = *p1.graphRawPtr(); - - const auto p1_end_node = p1.nodeIds().back(); - const auto p2_start_node = p2.nodeIds().front(); - - if (p1_end_node != p2_start_node && !graph.hasEdge(p1_end_node, p2_start_node)) - { - return false; - } - - // now we are left with two cases: - // p1 ends on node before p2 - // p1 ends on same node as p2 - - // adjacent nodes -- check if graph has an edge + if the start / end positions are compatible - if (p1_end_node != p2_start_node) - { - assert(graph.hasEdge(p1_end_node, p2_start_node)); - return p2.startPosition() == 0 && p1.endPosition() == (int32_t)graph.nodeSeq(p1_end_node).size() - 1; - } - - assert(p1_end_node == p2_start_node); - return p1.endPosition() + 1 == p2.startPosition(); -} - -/** - * Return true if two paths overlap either prefix - suffix or suffix-prefix - * @param p1 first path - * @param p2 second path - * @return true if the paths overlap - */ -bool checkPathPrefixSuffixOverlap(Path const& p1, Path const& p2) -{ - // technically we'd want to check that the two graphs match also - if (p1.numNodes() == 0 || p2.numNodes() == 0) - { - return false; - } - if (p1.nodeIds().back() < p2.nodeIds().front() || // p1 ends before p2 - p1.nodeIds().front() > p2.nodeIds().back()) // p1 starts after p2 - { - return false; - } - - auto p1_it = p1.nodeIds().begin(); - auto p2_it = p2.nodeIds().begin(); - - int shared_nodes = 0; - while (p1_it != p1.nodeIds().end() && p2_it != p2.nodeIds().end()) - { - if (*p1_it < *p2_it) - { - if (p2_it != p2.nodeIds().begin()) - { - // paths diverged - return false; - } - // --> ignore non-matching prefix of p1 until paths meet - ++p1_it; - } - else if (*p1_it > *p2_it) - { - if (p1_it != p1.nodeIds().begin()) - { - // paths diverged - return false; - } - // --> ignore non-matching prefix of p2 until paths meet - ++p2_it; - } - else - { // *p1_it == *p2_it - // paths have met. They must now match until one of them ends - ++shared_nodes; - ++p1_it; - ++p2_it; - } - } - - if (shared_nodes == 0) - { - return false; - } - - // if we only share one node, the paths may not overlap on that node - if (shared_nodes == 1) - { - if (p1_it == p1.nodeIds().end() && p2_it == p2.nodeIds().end()) - { - if (p1.numNodes() > 1 && p2.numNodes() > 1) - { - // if they both have > 1 nodes, they should also share more than one of them; - // otherwise they cannot both end here - assert(false); - } - else if (p1.numNodes() == 1 && p2.numNodes() > 1) - { - // p1 starts here, p2 ends here - if (p2.endPosition() < p1.startPosition()) - { - return false; - } - } - else if (p1.numNodes() > 1 && p2.numNodes() == 1) - { - // p2 starts here, p1 ends here - if (p1.endPosition() < p2.startPosition()) - { - return false; - } - } - else if (p1.numNodes() == 1 && p2.numNodes() == 1) - { - // both paths on same node, check if they overlap there - return p1.endPosition() >= p2.startPosition() && p2.endPosition() >= p1.startPosition(); - } - } - else if (p1_it != p1.nodeIds().end() && p2_it == p2.nodeIds().end()) - { - // p2 starts+ends on this node p1 starts -- check that p1 starts before p2 ends - if (p2.endPosition() < p1.startPosition()) - { - return false; - } - } - else if (p1_it == p1.nodeIds().end() && p2_it != p2.nodeIds().end()) - { - // p1 starts+ends on this node p2 starts -- check that p2 starts before p1 ends - if (p1.endPosition() < p2.startPosition()) - { - return false; - } - } - else - { - // this shouldn't happen. we iterate until one of them reaches end() above - assert(false); - } - } - - return true; -} - -/** - * Paths can be merged if they overlap prefix-suffix / suffix-prefix. - * - * @param p1 first path - * @param p2 second path - * @return merged path - */ -Path mergePaths(Path const& p1, Path const& p2) -{ - assert(checkPathPrefixSuffixOverlap(p1, p2) || checkIfPathsAdjacent(p1, p2)); - - int32_t start = -1; - int32_t end = -1; - std::vector nodes; - auto p1_it = p1.nodeIds().begin(); - auto p2_it = p2.nodeIds().begin(); - while ((p1_it != p1.nodeIds().end()) && (p2_it != p2.nodeIds().end())) - { - if (*p1_it < *p2_it) - { - if (start < 0) - { - start = p1.startPosition(); - } - nodes.push_back(*p1_it); - ++p1_it; - } - else if (*p1_it > *p2_it) - { - if (start < 0) - { - start = p2.startPosition(); - } - nodes.push_back(*p2_it); - ++p2_it; - } - else - { // *p1_it == *p2_it - if (start < 0) - { - start = std::min(p1.startPosition(), p2.startPosition()); - } - nodes.push_back(*p1_it); - ++p1_it; - ++p2_it; - } - } - if (p1_it == p1.nodeIds().end() && p2_it == p2.nodeIds().end()) - { - end = std::max(p1.endPosition(), p2.endPosition()); - } - else if (p1_it != p1.nodeIds().end() && p2_it == p2.nodeIds().end()) - { - nodes.insert(nodes.end(), p1_it, p1.nodeIds().end()); - end = p1.endPosition(); - } - else if (p1_it == p1.nodeIds().end() && p2_it != p2.nodeIds().end()) - { - nodes.insert(nodes.end(), p2_it, p2.nodeIds().end()); - end = p2.endPosition(); - } - assert(start >= 0 && end >= 0); - return Path(p1.graphRawPtr(), start, nodes, end); -} - -/** - * Merge a set of paths - * - * This will merge paths until none of the resulting paths overlap - * - * @param paths a list of paths - */ -void greedyMerge(std::list& paths) -{ - bool has_merged = true; - while (has_merged && paths.size() > 1) - { - auto path_a = paths.begin(); - has_merged = false; - while (path_a != paths.end()) - { - auto path_b = std::next(path_a); - while (path_b != paths.end()) - { - if (checkPathPrefixSuffixOverlap(*path_a, *path_b)) - { - const Path merged_a_b{ mergePaths(*path_a, *path_b) }; - paths.erase(path_a); - paths.erase(path_b); - paths.push_back(merged_a_b); - has_merged = true; - break; - } - ++path_b; - } - if (has_merged) - { - break; - } - ++path_a; - } - } -} - -/** - * Merge a set of paths - * - * This will merge paths exhaustively, each path is merged with all - * paths it overlaps until we cannot merge anymore - * - * @param paths a list of paths - */ -void exhaustiveMerge(std::list& paths) -{ - bool has_merged = true; - while (has_merged && paths.size() > 1) - { - auto path_a = paths.begin(); - has_merged = false; - - list new_paths; - while (path_a != paths.end()) - { - auto path_b = paths.begin(); - while (path_b != paths.end()) - { - if (path_a == path_b) - { - ++path_b; - continue; - } - if (checkPathPrefixSuffixOverlap(*path_a, *path_b)) - { - const Path merged_a_b{ mergePaths(*path_a, *path_b) }; - const bool a_contained_in_b = merged_a_b.encode() == path_b->encode(); - const bool b_contained_in_a = merged_a_b.encode() == path_a->encode(); - const bool a_eq_b = a_contained_in_b && b_contained_in_a; - - if (a_eq_b) - { - // keep only one of them - new_paths.push_back(*path_b); - } - else if (a_contained_in_b || b_contained_in_a) - { - new_paths.push_back(merged_a_b); - } - else - { - new_paths.push_back(merged_a_b); - new_paths.push_back(*path_a); - new_paths.push_back(*path_b); - } - ++path_b; - has_merged = true; - } - else - { - new_paths.push_back(*path_b); - ++path_b; - } - } - if (has_merged) - { - break; - } - new_paths.push_back(*path_a); - ++path_a; - } - if (has_merged) - { - paths = new_paths; - } - } -} - -std::list intersectPaths(Path const& p1, Path const& p2) -{ - std::list result; - - int32_t start = -1; - int32_t end = -1; - std::vector nodes; - - const auto savePath = [&p1, &start, &end, &nodes, &result]() { - if (!nodes.empty()) - { - result.emplace_back(p1.graphRawPtr(), start, nodes, end); - nodes.clear(); - start = -1; - end = -1; - } - }; - - auto p1_it = p1.nodeIds().begin(); - auto p2_it = p2.nodeIds().begin(); - while ((p1_it != p1.nodeIds().end()) && (p2_it != p2.nodeIds().end())) - { - if (*p1_it < *p2_it) - { - savePath(); - ++p1_it; - } - else if (*p1_it > *p2_it) - { - savePath(); - ++p2_it; - } - else - { // *p1_it == *p2_it - const auto p1_nodesize = (int32_t)p1.graphRawPtr()->nodeSeq(*p1_it).size(); - const auto p2_nodesize = (int32_t)p2.graphRawPtr()->nodeSeq(*p2_it).size(); - if (p1_nodesize != p2_nodesize) - { - throw std::logic_error("Intersecting paths on different graphs is not possible."); - } - - const int32_t start_p1 = p1_it == p1.nodeIds().begin() ? p1.startPosition() : 0; - const int32_t start_p2 = p2_it == p2.nodeIds().begin() ? p2.startPosition() : 0; - const int32_t end_p1 = std::next(p1_it) == p1.nodeIds().end() ? p1.endPosition() : p1_nodesize; - const int32_t end_p2 = std::next(p2_it) == p2.nodeIds().end() ? p2.endPosition() : p2_nodesize; - - const int32_t start_pos = std::max(start_p1, start_p2); - const int32_t end_pos = std::min(end_p1, end_p2); - - if (start_pos <= end_pos) - { - // start within the node => cannot extend previous matched path - if (start_pos > 0) - { - savePath(); - } - - if (nodes.empty()) - { - // Not sure why cppcheck complains here. start will be read when we call savePath in line 503 - // cppcheck-suppress unreadVariable - start = start_pos; - } - else if (!p1.graphRawPtr()->hasEdge(nodes.back(), *p1_it)) - { - savePath(); - } - - // Not sure why cppcheck complains here. end will be read when we call savePath in line 503 - // cppcheck-suppress unreadVariable - end = end_pos; - nodes.push_back(*p1_it); - - // ends before end of node => cannot combine with match on next node - if (end_pos + 1 < p1_nodesize) - { - savePath(); - } - } - else if (!nodes.empty()) - { - savePath(); - } - - ++p1_it; - ++p2_it; - } - } - savePath(); - - return result; -} - -list generateSubpathForEachNode(const Path& path) -{ - list subpaths; - - for (size_t node_index = 0; node_index != path.numNodes(); ++node_index) - { - const vector subpath_nodes = { path.getNodeIdByIndex(node_index) }; - const int32_t subpath_start = path.getStartPositionOnNodeByIndex(node_index); - const int32_t subpath_end = path.getEndPositionOnNodeByIndex(node_index); - - subpaths.emplace_back(path.graphRawPtr(), subpath_start, subpath_nodes, subpath_end); - } - - return subpaths; -} - -bool checkIfBookended(const Path& first_path, const Path& second_path) -{ - const NodeId first_path_end_node = first_path.getNodeIdByIndex(first_path.numNodes() - 1); - const NodeId second_path_start_node = second_path.getNodeIdByIndex(0); - const bool are_ends_on_same_node = first_path_end_node == second_path_start_node; - const bool are_positions_adjacent = first_path.endPosition() == second_path.startPosition(); - - if (are_ends_on_same_node && are_positions_adjacent) - { - return true; - } - - const Graph& graph = *first_path.graphRawPtr(); - const auto& successors = graph.successors(first_path_end_node); - const bool are_ends_on_neighboring_nodes = successors.find(second_path_start_node) != successors.end(); - const auto first_paths_last_node_length = static_cast(graph.nodeSeq(first_path_end_node).length()); - const bool is_first_path_ends_at_node_end = first_path.endPosition() == first_paths_last_node_length; - const bool is_second_path_starts_at_node_start = second_path.startPosition() == 0; - - if (are_ends_on_neighboring_nodes && is_first_path_ends_at_node_end && is_second_path_starts_at_node_start) - { - return true; - } - - return false; -} - -Path concatenatePaths(const Path& first_path, const Path& second_path) -{ - if (!checkIfBookended(first_path, second_path)) - { - std::ostringstream msg; - msg << "Paths " << first_path << " and " << second_path << " are not bookended"; - throw std::logic_error(msg.str()); - } - - const NodeId first_path_end_node = first_path.getNodeIdByIndex(first_path.numNodes() - 1); - const NodeId second_path_start_node = second_path.getNodeIdByIndex(0); - const bool are_ends_on_same_node = first_path_end_node == second_path_start_node; - const bool are_positions_adjacent = first_path.endPosition() == second_path.startPosition(); - - vector merged_node_ids; - merged_node_ids.reserve(first_path.nodeIds().size() + second_path.nodeIds().size()); - merged_node_ids.insert(merged_node_ids.end(), first_path.nodeIds().begin(), first_path.nodeIds().end()); - - if (are_ends_on_same_node && are_positions_adjacent) - { - merged_node_ids.insert(merged_node_ids.end(), second_path.nodeIds().begin() + 1, second_path.nodeIds().end()); - } - else - { - merged_node_ids.insert(merged_node_ids.end(), second_path.nodeIds().begin(), second_path.nodeIds().end()); - } - - return Path(first_path.graphRawPtr(), first_path.startPosition(), merged_node_ids, second_path.endPosition()); -} -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphio/AlignmentWriter.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphio/AlignmentWriter.cpp deleted file mode 100644 index e457f32..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphio/AlignmentWriter.cpp +++ /dev/null @@ -1,39 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Felix Schlesinger -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphio/AlignmentWriter.hh" - -#include -#include -#include - -#include - -using std::string; - -namespace graphtools -{ - -void BlankAlignmentWriter::write( - const std::string& /*locusId*/, const std::string& /*fragmentName*/, const std::string& /*query*/, - bool /*isFirstMate*/, bool /*isReversed*/, bool /*isMateReversed*/, const GraphAlignment& /*alignment*/) -{ -} -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphio/GraphJson.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphio/GraphJson.cpp deleted file mode 100644 index 1dfb2e4..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphio/GraphJson.cpp +++ /dev/null @@ -1,149 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Felix Schlesinger -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphio/GraphJson.hh" - -#include -#include - -using std::string; - -namespace graphtools -{ - -Graph loadGraph(string const& jsonPath) -{ - std::ifstream jsonFile(jsonPath); - assert(jsonFile.good()); - Json json; - jsonFile >> json; - return parseGraph((json.count("graph") == 1) ? json["graph"] : json); -} - -Graph parseGraph(Json const& jsonGraph) -{ - // boost::optional genome; - // const auto refFasta = jsonGraph.find("reference_genome"); - // if (refFasta != jsonGraph.end()) - //{ - // genome.emplace(refFasta->get()); - //} - - Json::array_t nodes = jsonGraph.value("nodes", Json::array()); - auto const nNodes = nodes.size(); - string const& graphId = jsonGraph.value("graph_id", ""); - Graph graph(nNodes, graphId); - - std::unordered_map nodeIds; // NodeName -> NameID - NodeId nodeIndex = 0; - for (auto const& jsonNode : nodes) - { - string const name = jsonNode.at("name"); - graph.setNodeName(nodeIndex, name); - auto const seq = jsonNode.find("sequence"); - if (seq != jsonNode.end()) - { - graph.setNodeSeq(nodeIndex, *seq); - } - else - { - throw std::runtime_error("Node has an invalid sequence: " + graph.nodeName(nodeIndex)); - // auto const refRegion = jsonNode.find("reference"); - // if (refRegion == jsonNode.end()) - //{ - // throw std::runtime_error("Node has no sequence: " + graph.nodeName(nodeIndex)); - //} - // if (!genome) - //{ - // throw std::runtime_error("Need 'referenceGenome' FASTA file to use reference nodes"); - //} - // auto const interval = ReferenceInterval::parseRegion(*refRegion); - // graph.setNodeSeq(nodeIndex, genome->extractSeq(interval)); - } - assert(nodeIds.count(name) == 0); - nodeIds[name] = nodeIndex; - nodeIndex++; - } - for (auto const& jsonEdge : jsonGraph.value("edges", Json::array())) - { - NodeId const sourceNode = nodeIds.at(jsonEdge.at("from")); - NodeId const sinkNode = nodeIds.at(jsonEdge.at("to")); - graph.addEdge(sourceNode, sinkNode); - const auto labels = jsonEdge.find("labels"); - if (labels != jsonEdge.end()) - { - for (auto const& label : *labels) - { - graph.addLabelToEdge(sourceNode, sinkNode, label.get()); - } - } - } - return graph; -} - -Json graphToJson(Graph const& graph) -{ - Json json; - if (!graph.graphId.empty()) - { - json["graph_id"] = graph.graphId; - } - json["nodes"] = Json::array(); - for (size_t i = 0; i != graph.numNodes(); ++i) - { - json["nodes"].push_back({ { "name", graph.nodeName(i) }, { "sequence", graph.nodeSeq(i) } }); - } - json["edges"] = Json::array(); - for (size_t n1 = 0; n1 < graph.numNodes(); ++n1) - { - for (NodeId n2 : graph.successors(n1)) - { - Json edge = { { "from", graph.nodeName(n1) }, { "to", graph.nodeName(n2) } }; - auto const& labels = graph.edgeLabels(n1, n2); - if (labels.size() > 0) - { - edge["labels"] = labels; - } - - json["edges"].push_back(std::move(edge)); - } - } - return json; -} - -GraphReferenceMapping parseReferenceMapping(Json const& jRefmap, Graph const& graph) -{ - Json::array_t nodes = jRefmap.value("nodes", Json::array()); - - GraphReferenceMapping refmap(&graph); - NodeId nodeIndex = 0; - for (auto const& jNode : nodes) - { - const auto refInterval = jNode.find("reference"); - if (refInterval != jNode.end()) - { - auto const region = ReferenceInterval::parseRegion(*refInterval); - refmap.addMapping(nodeIndex, region); - } - ++nodeIndex; - } - return refmap; -} -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphutils/DepthTest.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphutils/DepthTest.cpp deleted file mode 100644 index dd17882..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphutils/DepthTest.cpp +++ /dev/null @@ -1,47 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Sai Chen , -// Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphutils/DepthTest.hh" - -DepthTest::DepthTest( - int32_t expectedNumReads, double stdDeviation, double lowerSignificanceThreshold, double upperSignificanceThreshold) - : expectedNumReads_(expectedNumReads) - , stdDeviation_(stdDeviation) - , lowerSignificanceThreshold_(lowerSignificanceThreshold) - , upperSignificanceThreshold_(upperSignificanceThreshold) - , coverageDistribution_(expectedNumReads_, stdDeviation_) -{ -} - -bool DepthTest::testReadCount(int32_t observedNumReads) -{ - double coverageTestPvalue = cdf(coverageDistribution_, observedNumReads); - - if (coverageTestPvalue <= 0.5) - { - return coverageTestPvalue < lowerSignificanceThreshold_ ? false : true; - } - else - { - coverageTestPvalue = 1 - coverageTestPvalue; - return coverageTestPvalue < upperSignificanceThreshold_ ? false : true; - } -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphutils/IntervalBuffer.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphutils/IntervalBuffer.cpp deleted file mode 100644 index 250cbd6..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphutils/IntervalBuffer.cpp +++ /dev/null @@ -1,176 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Peter Krusche -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphutils/IntervalBuffer.hh" -#include "graphutils/IntervalList.hh" - -#include -#include -#include -#include -#include -#include - -namespace intervals -{ - -struct IntervalBuffer::Impl -{ - Impl() = default; - Impl(Impl const& rhs) = default; - Impl& operator=(Impl const& rhs) = default; - Impl(Impl&& rhs) = delete; - Impl& operator=(Impl&& rhs) = delete; - ~Impl() = default; - - typedef IntervalList ivmap_t; - - std::vector lanes; -}; - -/** tracks intervals over a number of lanes */ -IntervalBuffer::IntervalBuffer() - : pimpl_(new Impl()) -{ -} - -IntervalBuffer::~IntervalBuffer() = default; - -IntervalBuffer::IntervalBuffer(IntervalBuffer const& rhs) - : pimpl_(new Impl(*rhs.pimpl_)) -{ -} - -IntervalBuffer& IntervalBuffer::operator=(IntervalBuffer const& rhs) -{ - if (&rhs == this) - { - return *this; - } - pimpl_.reset(new Impl(*rhs.pimpl_)); - return *this; -} - -/** - * @brief Add an interval to a lane - * - * @param start interval coordinates - * @param end interval coordinates - * @param lane lane to add to - * @return Interval identifier - */ -void IntervalBuffer::addInterval(int64_t start, int64_t end, size_t lane) -{ - if (start > end) - { - return; - } - if (pimpl_->lanes.size() <= lane) - { - pimpl_->lanes.resize(lane + 1); - } - pimpl_->lanes[lane].add(interval(start, end)); -} - -/** - * @brief Advance buffer, discarding all intervals with start < to - * - * @param to interval minimum end position - */ -void IntervalBuffer::advance(int64_t to) -{ - if (to < 0) - { - pimpl_->lanes.clear(); - return; - } - - for (auto& lane : pimpl_->lanes) - { - lane.remove_to(to - 1); - } -} - -/** - * @brief Check if interval is fully covered in a given lane - */ -bool IntervalBuffer::isCovered(int64_t start, int64_t end, size_t lane) const -{ - if (lane >= pimpl_->lanes.size()) - { - return false; - } - - // intervals of zero length count as covered - if (end < start) - { - return true; - } - - std::list is; - pimpl_->lanes[lane].get(start, end, is); - if (is.size() != 1) - { - // if we overlap with more than one interval, then there must be a gap - return false; - } - - interval& it = is.front(); - return it.start <= start && it.end >= end; -} - -/** - * @brief Check if interval is partially covered in a given lane - */ -bool IntervalBuffer::hasOverlap(int64_t start, int64_t end, size_t lane) const -{ - if (lane >= pimpl_->lanes.size()) - { - return false; - } - - // intervals of zero length count as covered - if (end < start) - { - return true; - } - - interval it = pimpl_->lanes[lane].query(start, end); - return it.start >= 0 && it.end >= 0 && it.end - it.start + 1 > 0; -} - -/** - * Get the intervals for a particular lane - * @return intervals for a particular lane - */ -std::list> IntervalBuffer::getIntervals(size_t lane) const -{ - if (lane >= pimpl_->lanes.size()) - { - throw std::logic_error(std::string("Unknown lane: ") + std::to_string(lane)); - } - std::list> result; - for (auto const& iv : pimpl_->lanes[lane].getIntervals()) - { - result.emplace_back(iv.start, iv.end); - } - return result; -} -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphutils/KmerEncoding.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphutils/KmerEncoding.cpp deleted file mode 100644 index d2956cd..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphutils/KmerEncoding.cpp +++ /dev/null @@ -1,27 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Chris Saunders -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphutils/KmerEncoding.hh" - -namespace graphtools -{ - -TwoBitKmerEncoder::BaseToIndex TwoBitKmerEncoder::baseToIndex_; -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphutils/SequenceOperations.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphutils/SequenceOperations.cpp deleted file mode 100644 index 04608b7..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphutils/SequenceOperations.cpp +++ /dev/null @@ -1,213 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphutils/SequenceOperations.hh" - -#include -#include -#include -#include - -using std::string; -using std::unordered_map; -using std::vector; - -namespace graphtools -{ - -vector splitStringByDelimiter(const std::string& str, char sep) -{ - vector words; - std::stringstream sstream(str); - string word; - while (std::getline(sstream, word, sep)) - { - words.push_back(word); - } - - return words; -} - -vector splitStringByWhitespace(const std::string& str) -{ - vector words; - std::stringstream sstream(str); - string word; - while (sstream >> word) - { - words.push_back(word); - } - return words; -} - -static char complementBase(char base) -{ - switch (base) - { - case 'A': - return 'T'; - case 'a': - return 't'; - case 'C': - return 'G'; - case 'c': - return 'g'; - case 'G': - return 'C'; - case 'g': - return 'c'; - case 'T': - return 'A'; - case 't': - return 'a'; - case 'R': - return 'Y'; - case 'Y': - return 'R'; - case 'K': - return 'M'; - case 'M': - return 'K'; - case 'S': - return 'S'; - case 'W': - return 'W'; - case 'B': - return 'V'; - case 'D': - return 'H'; - case 'H': - return 'D'; - case 'V': - return 'B'; - default: - return 'N'; - } -} - -string reverseComplement(string seq) -{ - std::transform(seq.begin(), seq.end(), seq.begin(), complementBase); - std::reverse(seq.begin(), seq.end()); - return seq; -} - -const unordered_map kSymbolExpansion - = { { 'A', "A" }, { 'C', "C" }, { 'T', "T" }, { 'G', "G" }, { 'R', "AG" }, { 'Y', "CT" }, - { 'K', "GT" }, { 'M', "AC" }, { 'S', "CG" }, { 'W', "AT" }, { 'B', "CGT" }, { 'D', "AGT" }, - { 'H', "ACT" }, { 'V', "ACG" }, { 'N', "ACGT" }, { 'X', "X" } }; - -static bool checkIfNucleotideReferenceSymbol(char symbol) -{ - return (symbol == 'A') || (symbol == 'C') || (symbol == 'T') || (symbol == 'G'); -} - -static bool hasExpandableSymbols(const std::string& s) -{ - static const struct ExpandableSyms - { - ExpandableSyms() - { - for (const auto& sym : kSymbolExpansion) - { - if (sym.second.size() > 1) - { - value.push_back(sym.first); - } - } - } - string value; - } expandableSyms; - return s.find_first_of(expandableSyms.value) != string::npos; -} - -bool checkIfNucleotideReferenceSequence(const std::string& sequence) -{ - for (char symbol : sequence) - { - if (!checkIfNucleotideReferenceSymbol(symbol)) - { - return false; - } - } - return true; -} - -static bool checkIfReferenceSymbol(char symbol) { return kSymbolExpansion.find(symbol) != kSymbolExpansion.end(); } - -bool checkIfReferenceSequence(const std::string& sequence) -{ - for (char symbol : sequence) - { - if (!checkIfReferenceSymbol(symbol)) - { - return false; - } - } - return true; -} - -string const& expandReferenceSymbol(char symbol) -{ - if (!checkIfReferenceSymbol(symbol)) - { - const string symbol_encoding(1, symbol); - throw std::logic_error("Symbol " + symbol_encoding + " is not a valid reference symbol"); - } - return kSymbolExpansion.at(symbol); -} - -void expandReferenceSequence(const string& sequence, vector& expanded_sequences) -{ - if (!hasExpandableSymbols(sequence)) - { - expanded_sequences = { sequence }; - return; - } - expanded_sequences.resize(1); - expanded_sequences.front().clear(); - expanded_sequences.front().reserve(2 * sequence.size()); - - for (char symbol : sequence) - { - const auto& expansions = expandReferenceSymbol(symbol); - - // first expansion: append to all - for (auto& expanded_sequence : expanded_sequences) - { - expanded_sequence.push_back(expansions.front()); - } - - size_t sequences_to_expand = expanded_sequences.size(); - size_t exp_pos = 1; - while (exp_pos < expansions.size()) - { - // more than one expansion: create expanded copy for each of them - for (size_t to_copy_pos = 0; to_copy_pos < sequences_to_expand; ++to_copy_pos) - { - string to_copy = expanded_sequences[to_copy_pos]; - to_copy.back() = expansions[exp_pos]; - expanded_sequences.emplace_back(std::move(to_copy)); - } - exp_pos++; - } - } -} -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/src/sh/check-format.sh b/ehunter/thirdparty/graph-tools-master-f421f4c/src/sh/check-format.sh deleted file mode 100755 index 9850365..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/src/sh/check-format.sh +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env bash - -DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" -SOURCE_DIR="${DIR}/../../src" -export CLANG_FORMAT=clang-format-5.0 - -set +e -DIFFS=0 -for x in $(find ${SOURCE_DIR} -iname *.h -o -iname *.hh -o -iname *.cpp); do - ${CLANG_FORMAT} -style=file ${x} | diff --ignore-blank-lines --strip-trailing-cr ${x} - - if [[ $? != 0 ]]; then - echo "Differences found in $x" - DIFFS=1 - fi -done - -if [[ ${DIFFS} == 0 ]]; then - echo "No formatting issues found." - exit 0 -else - echo "Some formatting issues were found." - exit 1 -fi diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/src/sh/docker-build.sh b/ehunter/thirdparty/graph-tools-master-f421f4c/src/sh/docker-build.sh deleted file mode 100755 index 52d2ad1..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/src/sh/docker-build.sh +++ /dev/null @@ -1,62 +0,0 @@ -#!/usr/bin/env bash - -# Make a build using Docker -DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" - -set -e - -PULL=1 -CLANG=0 -CLANG_ASAN=0 -CLANG_MSAN=0 -VALGRIND=0 -while test $# -gt 0 -do - case "$1" in - --no-pull) echo "Not pulling image."; PULL=0 - ;; - --valgrind) echo "Using valgrind"; VALGRIND=1 - ;; - --clang) echo "Using CLang"; CLANG=1 - ;; - --clang-asan) echo "Using CLang+Address Sanitizer"; CLANG_ASAN=1; CLANG=1 - ;; - --clang-msan) echo "Using CLang+Memory Sanitizer"; CLANG_MSAN=1; CLANG=1 - ;; - *) echo "Unknown argument $1"; exit 1 - ;; - esac - shift -done - -if [[ ${PULL} -ne 0 ]]; then - docker pull ilmncgrpmi/cpp-dev:latest -fi - -EXTRA_CMAKE="" -if [[ ${CLANG} -ne 0 ]]; then - EXTRA_CMAKE="-DCMAKE_CXX_COMPILER=clang++" -fi -if [[ ${CLANG_ASAN} -ne 0 ]]; then - EXTRA_CMAKE="${EXTRA_CMAKE} -DUSE_ASAN=ON" -fi -if [[ ${CLANG_MSAN} -ne 0 ]]; then - EXTRA_CMAKE="${EXTRA_CMAKE} -DUSE_MSAN=ON" -fi - -if [[ ${VALGRIND} -ne 0 ]]; then - VALGRIND='for x in `find /graphtools-build/tests -executable -type f`; do valgrind --leak-check=full --xml=yes --xml-file=/graphtools-source/valgrind_`basename ${x}`.xml $x ; done && find /graphtools-source/valgrind_*.xml | xargs -n1 python /graphtools-source/src/sh/valgrind-check.py &&' -else - VALGRIND="" -fi - -docker run -v ${DIR}/../..:/graphtools-source --rm ilmncgrpmi/cpp-dev:latest /bin/bash -c "mkdir -p /graphtools-build && \ - cd /graphtools-build && \ - cmake ../graphtools-source -DBUILD_TESTS=ON -DCMAKE_INSTALL_PREFIX=/graphtools-install ${EXTRA_CMAKE} && \ - make -j8 && \ - make test && \ - make install && \ - ${VALGRIND} \ - cd /graphtools-install && \ - tar czf /graphtools-source/graphtools-install.tar.gz * " - diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/src/sh/docker-check-format.sh b/ehunter/thirdparty/graph-tools-master-f421f4c/src/sh/docker-check-format.sh deleted file mode 100755 index a0cb90c..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/src/sh/docker-check-format.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/usr/bin/env bash - -DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" - -set -e - -PULL=1 -while test $# -gt 0 -do - case "$1" in - --no-pull) echo "Not pulling image."; PULL=0 - ;; - *) echo "Unknown argument $1"; exit 1 - ;; - esac - shift -done - -if [[ ${PULL} -ne 0 ]]; then - docker pull ilmncgrpmi/cpp-dev:latest -fi - -LOGFILE=$(mktemp) -docker run -v ${DIR}/../..:/graphtools-source --rm ilmncgrpmi/cpp-dev:latest /bin/bash -c "cd /graphtools-source && \ - /graphtools-source/src/sh/check-format.sh" diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/src/sh/docker-cppcheck.sh b/ehunter/thirdparty/graph-tools-master-f421f4c/src/sh/docker-cppcheck.sh deleted file mode 100755 index 280bcf6..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/src/sh/docker-cppcheck.sh +++ /dev/null @@ -1,35 +0,0 @@ -#!/usr/bin/env bash - -DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" - -set -e - -PULL=1 -while test $# -gt 0 -do - case "$1" in - --no-pull) echo "Not pulling image."; PULL=0 - ;; - *) echo "Unknown argument $1"; exit 1 - ;; - esac - shift -done - -if [[ ${PULL} -ne 0 ]]; then - docker pull ilmncgrpmi/cpp-dev:latest -fi - -LOGFILE=$(mktemp) -docker run -v ${DIR}/../..:/graphtools-source --rm ilmncgrpmi/cpp-dev:latest /bin/bash -c "cd /graphtools-source && \ - cppcheck --enable=all --suppress=missingIncludeSystem --suppress=unusedFunction --inline-suppr -I/graphtools-source/include /graphtools-source/src > /dev/null" &> ${LOGFILE} - -cat ${LOGFILE} - -MESSAGES=$(cat ${LOGFILE} | wc -l) -if [[ ${MESSAGES} -ne 0 ]]; then - echo "$MESSAGES cppcheck errors were found!" - exit 1 -fi - -exit 0 diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/src/sh/docker-format-everything.sh b/ehunter/thirdparty/graph-tools-master-f421f4c/src/sh/docker-format-everything.sh deleted file mode 100755 index aaac3eb..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/src/sh/docker-format-everything.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/usr/bin/env bash - -DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" - -set -e - -PULL=1 -while test $# -gt 0 -do - case "$1" in - --no-pull) echo "Not pulling image."; PULL=0 - ;; - *) echo "Unknown argument $1"; exit 1 - ;; - esac - shift -done - -if [[ ${PULL} -ne 0 ]]; then - docker pull ilmncgrpmi/cpp-dev:latest -fi - -LOGFILE=$(mktemp) -docker run -v ${DIR}/../..:/graphtools-source --rm ilmncgrpmi/cpp-dev:latest /bin/bash -c "cd /graphtools-source && \ - /graphtools-source/src/sh/format-everything.sh" \ No newline at end of file diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/src/sh/format-everything.sh b/ehunter/thirdparty/graph-tools-master-f421f4c/src/sh/format-everything.sh deleted file mode 100755 index d6c9d8e..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/src/sh/format-everything.sh +++ /dev/null @@ -1,27 +0,0 @@ -#!/usr/bin/env bash - -DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" - -CLANG_FORMAT=clang-format - -if [ ! -x "$(command -v ${CLANG_FORMAT})" ]; then - CLANG_FORMAT=clang-format-5.0 -fi - -if [ ! -x "$(command -v ${CLANG_FORMAT})" ]; then - CLANG_FORMAT=clang-format-mp-5.0 -fi - -if [ ! -x "$(command -v ${CLANG_FORMAT})" ]; then - echo "Clang-format not found, please install as clang-format or clang-format-mp-5.0" - exit 1 -fi - -if [[ -z "$(${CLANG_FORMAT} --version | grep 'version 5')" ]]; then - echo "Clang-format has the wrong version, please install as clang-format version 5.0" - exit 1 -fi - -find ${DIR}/../../src -iname *.h -o -iname *.hh -o -iname *.cpp | xargs ${CLANG_FORMAT} -i -style=file -find ${DIR}/../../include -iname *.h -o -iname *.hh -o -iname *.cpp | xargs ${CLANG_FORMAT} -i -style=file -find ${DIR}/../../tests -iname *.h -o -iname *.hh -o -iname *.cpp | xargs ${CLANG_FORMAT} -i -style=file diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/src/sh/valgrind-check.py b/ehunter/thirdparty/graph-tools-master-f421f4c/src/sh/valgrind-check.py deleted file mode 100644 index c78516c..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/src/sh/valgrind-check.py +++ /dev/null @@ -1,18 +0,0 @@ -#!/usr/bin/env python -# Simple checker for whether valgrind found errors - -import sys -import xml.etree.ElementTree as ElementTree - -e = ElementTree.parse(sys.argv[1]) - -states = [x.find('state').text for x in e.findall('status')] -errors = [x.find('kind').text for x in e.findall('error')] - -if "RUNNING" not in states or "FINISHED" not in states: - raise Exception("Valgrind didn't run successfully, states seen: %s" % str(states)) - -if errors: - raise Exception("Valgrind found some errors in %s: %s" % (sys.argv[1], str(errors))) - -sys.exit(0) diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/BaseMatchingTest.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/tests/BaseMatchingTest.cpp deleted file mode 100644 index 066dc16..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/BaseMatchingTest.cpp +++ /dev/null @@ -1,52 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphutils/BaseMatching.hh" - -#include "gtest/gtest.h" - -using namespace graphtools; - -TEST(MatchingBases, CoreBases_Matched) -{ - EXPECT_TRUE(checkIfReferenceBaseMatchesQueryBase('A', 'A')); - EXPECT_TRUE(checkIfReferenceBaseMatchesQueryBase('T', 't')); - EXPECT_TRUE(checkIfReferenceBaseMatchesQueryBase('c', 'C')); - EXPECT_TRUE(checkIfReferenceBaseMatchesQueryBase('G', 'g')); - - EXPECT_FALSE(checkIfReferenceBaseMatchesQueryBase('T', 'c')); -} - -TEST(MatchingBases, DegenerateBases_Matched) -{ - EXPECT_TRUE(checkIfReferenceBaseMatchesQueryBase('Y', 'c')); - EXPECT_TRUE(checkIfReferenceBaseMatchesQueryBase('Y', 'T')); - EXPECT_TRUE(checkIfReferenceBaseMatchesQueryBase('W', 'a')); - EXPECT_TRUE(checkIfReferenceBaseMatchesQueryBase('N', 'A')); - - EXPECT_FALSE(checkIfReferenceBaseMatchesQueryBase('Y', 'a')); -} - -TEST(MatchingStrings, TypicalStrings_Matched) -{ - EXPECT_TRUE(checkIfReferenceAndQuerySequencesMatch("RRTCS", "AaTCG")); - EXPECT_FALSE(checkIfReferenceAndQuerySequencesMatch("WG", "CG")); - EXPECT_FALSE(checkIfReferenceAndQuerySequencesMatch("CC", "CCC")); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/CMakeLists.txt b/ehunter/thirdparty/graph-tools-master-f421f4c/tests/CMakeLists.txt deleted file mode 100644 index a3e73e4..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/CMakeLists.txt +++ /dev/null @@ -1,119 +0,0 @@ -add_executable(SequenceOperationsTest SequenceOperationsTest.cpp) -target_link_libraries(SequenceOperationsTest graphtools gtest_main) -add_test(NAME SequenceOperationsTest COMMAND SequenceOperationsTest) - -add_executable(BaseMatchingTest BaseMatchingTest.cpp) -target_link_libraries(BaseMatchingTest graphtools gtest_main) -add_test(NAME BaseMatchingTest COMMAND BaseMatchingTest) - -add_executable(OperationTest OperationTest.cpp) -target_link_libraries(OperationTest graphtools gtest_main) -add_test(NAME OperationTest COMMAND OperationTest) - -add_executable(OperationOperationsTest OperationOperationsTest.cpp) -target_link_libraries(OperationOperationsTest graphtools gtest_main) -add_test(NAME OperationOperationsTest COMMAND OperationOperationsTest) - -add_executable(LinearAlignmentTest LinearAlignmentTest.cpp) -target_link_libraries(LinearAlignmentTest graphtools gtest_main) -add_test(NAME LinearAlignmentTest COMMAND LinearAlignmentTest) - -add_executable(LinearAlignmentOperationsTest LinearAlignmentOperationsTest.cpp) -target_link_libraries(LinearAlignmentOperationsTest graphtools gtest_main) -add_test(NAME LinearAlignmentOperationsTest COMMAND LinearAlignmentOperationsTest) - -add_executable(TracebackMatrixTest TracebackMatrixTest.cpp) -target_link_libraries(TracebackMatrixTest graphtools gtest_main) -add_test(NAME TracebackMatrixTest COMMAND TracebackMatrixTest) - -add_executable(TracebackRunnerTest TracebackRunnerTest.cpp) -target_link_libraries(TracebackRunnerTest graphtools gtest_main) -add_test(NAME TracebackRunnerTest COMMAND TracebackRunnerTest) - -add_executable(PinnedAlignerTest PinnedAlignerTest.cpp) -target_link_libraries(PinnedAlignerTest graphtools gtest_main) -add_test(NAME PinnedAlignerTest COMMAND PinnedAlignerTest) - -add_executable(DagAlignerTest DagAlignerTest.cpp) -target_link_libraries(DagAlignerTest graphtools gtest_main) -add_test(NAME DagAlignerTest COMMAND DagAlignerTest) - -add_executable(PinnedDagAlignerTest PinnedDagAlignerTest.cpp) -target_link_libraries(PinnedDagAlignerTest graphtools gtest_main) -add_test(NAME PinnedDagAlignerTest COMMAND PinnedDagAlignerTest) - -add_executable(GraphAlignmentTest GraphAlignmentTest.cpp) -target_link_libraries(GraphAlignmentTest graphtools gtest_main) -add_test(NAME GraphAlignmentTest COMMAND GraphAlignmentTest) - -add_executable(GraphAlignmentOperationsTest GraphAlignmentOperationsTest.cpp) -target_link_libraries(GraphAlignmentOperationsTest graphtools gtest_main) -add_test(NAME GraphAlignmentOperationsTest COMMAND GraphAlignmentOperationsTest) - -add_executable(GraphTest GraphTest.cpp) -target_link_libraries(GraphTest graphtools gtest_main) -add_test(NAME GraphTest COMMAND GraphTest) - -add_executable(GraphBuildersTest GraphBuildersTest.cpp) -target_link_libraries(GraphBuildersTest graphtools gtest_main) -add_test(NAME GraphBuildersTest COMMAND GraphBuildersTest) - -add_executable(PathTest PathTest.cpp) -target_link_libraries(PathTest graphtools gtest_main) -add_test(NAME PathTest COMMAND PathTest) - -add_executable(PathOperationsTest PathOperationsTest.cpp) -target_link_libraries(PathOperationsTest graphtools gtest_main) -add_test(NAME PathOperationsTest COMMAND PathOperationsTest) - -add_executable(KmerEncodingTest KmerEncodingTest.cpp) -target_link_libraries(KmerEncodingTest graphtools gtest_main) -add_test(NAME KmerEncodingTest COMMAND KmerEncodingTest) - -add_executable(KmerIndexTest KmerIndexTest.cpp) -target_link_libraries(KmerIndexTest graphtools gtest_main) -add_test(NAME KmerIndexTest COMMAND KmerIndexTest) - -add_executable(KmerIndexOperationsTest KmerIndexOperationsTest.cpp) -target_link_libraries(KmerIndexOperationsTest graphtools gtest_main) -add_test(NAME KmerIndexOperationsTest COMMAND KmerIndexOperationsTest) - -add_executable(GappedAlignerTest GappedAlignerTest.cpp) -target_link_libraries(GappedAlignerTest graphtools gtest_main) -add_test(NAME GappedAlignerTest COMMAND GappedAlignerTest) - -add_executable(GraphCoordinatesTest GraphCoordinatesTest.cpp) -target_link_libraries(GraphCoordinatesTest graphtools gtest_main) -add_test(NAME GraphCoordinatesTest COMMAND GraphCoordinatesTest) - -add_executable(GraphOperationsTest GraphOperationsTest.cpp) -target_link_libraries(GraphOperationsTest graphtools gtest_main) -add_test(NAME GraphOperationsTest COMMAND GraphOperationsTest) - -add_executable(PathFamilyTest PathFamilyTest.cpp) -target_link_libraries(PathFamilyTest graphtools gtest_main) -add_test(NAME PathFamilyTest COMMAND PathFamilyTest) - -add_executable(PathFamilyOperationsTest PathFamilyOperationsTest.cpp) -target_link_libraries(PathFamilyOperationsTest graphtools gtest_main) -add_test(NAME PathFamilyOperationsTest COMMAND PathFamilyOperationsTest) - -add_executable(IntervalBufferTest IntervalBufferTest.cpp) -target_link_libraries(IntervalBufferTest graphtools gtest_main) -add_test(NAME IntervalBufferTest COMMAND IntervalBufferTest) - -add_executable(IntervalListTest IntervalListTest.cpp) -target_link_libraries(IntervalListTest graphtools gtest_main) -add_test(NAME IntervalListTest COMMAND IntervalListTest) - -add_executable(GraphReferenceMappingTest GraphReferenceMappingTest.cpp) -target_link_libraries(GraphReferenceMappingTest graphtools gtest_main) -add_test(NAME GraphReferenceMappingTest COMMAND GraphReferenceMappingTest) - -add_executable(DepthTestTest DepthTestTest.cpp) -target_link_libraries(DepthTestTest graphtools gtest_main) -add_test(NAME DepthTestTest COMMAND DepthTestTest) - -add_executable(GraphJsonTest GraphJsonTest.cpp) -target_link_libraries(GraphJsonTest graphtools gtest_main) -add_test(NAME GraphJsonTest COMMAND GraphJsonTest) diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/DagAlignerTest.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/tests/DagAlignerTest.cpp deleted file mode 100644 index 1ec68ee..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/DagAlignerTest.cpp +++ /dev/null @@ -1,775 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Roman Petrovski -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphalign/DagAlignerAffine.hh" - -#include "gtest/gtest.h" - -using std::string; - -using namespace graphalign; -using namespace graphalign::dagAligner; - -template std::string toString(const T& obj) -{ - std::stringstream ss; - ss << obj; - return ss.str(); -} - -TEST(SimpleAlignment, Short_to_short) -{ - DagAligner aligner({ 5, -4 }, 0, -8); - - EdgeMap edges(std::vector>({ { 151, 151 } }), std::vector({ 0 })); - - const string query = "tgCccgcCCcCCCCcccC"; - - const string reference = "TGCAGTCCCGCCCCGTCCC"; - aligner.align(query.begin(), query.end(), reference.begin(), reference.end(), edges); - - Score secondBestScore = 0; - std::vector cigars; - const Score bestScore = aligner.backtrackAllPaths(edges, cigars, secondBestScore); - - EXPECT_EQ(std::size_t(3), cigars.size()); - EXPECT_EQ("0[3=3X3=1X4=1X1D3=]", toString(cigars.at(2))); - EXPECT_EQ("0[3=3X3=1X4=1D1X3=]", toString(cigars.at(1))); - EXPECT_EQ("0[3=3X3=1D4=2X3=]", toString(cigars.at(0))); - EXPECT_EQ(37, bestScore); -} - -TEST(SimpleAlignment, Long_to_Long) -{ - DagAligner aligner({ 5, -4 }, 0, -8); - - EdgeMap edges(std::vector>({ { 151, 151 } }), std::vector({ 0 })); - - const string query = "TCTCGCCCCGCCCCTCAGGCGGCCTCCCTGCtgtgCCCCGCCCCGGCCcCGCCCCgCCCCcCCCCCcCCaCgCCCCCCcCccCcCCCCgCCCC" - "CCCCctCcCCCCccctCCCCtccCCtgCccgcCCcCCCCcccC"; - const string reference = "CCGCCCCGCCCCCGTCTCGCCCCGCCCCTCAGGCGGCCTCCCTGCTGTGCCCCGCCCCGGCCTCGCCACGCCCCTACCTCACCACGCCC" - "CCCGCATCGCCACGCCCCCCGCATCGCCACGCCTCCCTTACCATGCAGTCCCGCCCCGTCCC"; - aligner.align(query.begin(), query.end(), reference.begin(), reference.end(), edges); - - Score secondBestScore = 0; - std::vector cigars; - const Score bestScore = aligner.backtrackAllPaths(edges, cigars, secondBestScore); - EXPECT_EQ(std::size_t(3), cigars.size()); - - EXPECT_EQ( - "0[14D48=1X4=1X6=2X2=1X1=1X11=1X1=2X1=1X2=1X8=1X1=1X2=1X2=1X1=1X6=1X1=1X2=1X3=3X3=1X4=1X1D3=]", - toString(cigars.at(2))); - EXPECT_EQ( - "0[14D48=1X4=1X6=2X2=1X1=1X11=1X1=2X1=1X2=1X8=1X1=1X2=1X2=1X1=1X6=1X1=1X2=1X3=3X3=1X4=1D1X3=]", - toString(cigars.at(1))); - EXPECT_EQ( - "0[14D48=1X4=1X6=2X2=1X1=1X11=1X1=2X1=1X2=1X8=1X1=1X2=1X2=1X1=1X6=1X1=1X2=1X3=3X3=1D4=2X3=]", - toString(cigars.at(0))); - EXPECT_EQ(344, bestScore); -} - -TEST(SimpleAlignment, AAAC_to_AGC) -{ - DagAligner aligner({ 1, -1 }, 0, -2); - - EdgeMap edges(std::vector>({ { 3, 3 } }), std::vector({ 0 })); - - const string query = "AAAC"; - const string reference = "AGC"; - aligner.align(query.begin(), query.end(), reference.begin(), reference.end(), edges); - - Score secondBestScore = 0; - - std::vector cigars; - Score bestScore = aligner.backtrackAllPaths(edges, cigars, secondBestScore); - EXPECT_EQ(std::size_t(3), cigars.size()); - EXPECT_EQ("0[1S1=1X1=]", toString(cigars.at(0))); - EXPECT_EQ("0[1=1I1X1=]", toString(cigars.at(1))); - EXPECT_EQ("0[1=1X1I1=]", toString(cigars.at(2))); - - Cigar cigar = aligner.backtrackBestPath(edges, bestScore, secondBestScore); - EXPECT_EQ("0[1S1=1X1=]", toString(cigar)); -} - -TEST(SimpleAlignment, ATGC_to_AGC) -{ - DagAligner aligner({ 1, -1 }, 0, -2); - - const string query = "ATGC"; - const string reference = "AGC"; - - EdgeMap edges(std::vector>({ { 3, 3 } }), std::vector({ 0 })); - - aligner.align(query.begin(), query.end(), reference.begin(), reference.end(), edges); - - Score bestScore = 0; - Score secondBestScore = 0; - Cigar cigar = aligner.backtrackBestPath(edges, bestScore, secondBestScore); - EXPECT_EQ("0[1=1I2=]", toString(cigar)); -} - -TEST(SimpleAlignment, TAACTTTTGGG_to_TGCTTTTAA) -{ - // query: TAACTTTTGGG - // |x |||||xx - // reference: TG-CTTTTAA- - - const string query = "TAACTTTTGGG"; - const string reference = "TGCTTTTAA"; - - DagAligner aligner({ 1, -1 }, 0, -2); - - EdgeMap edges(std::vector>({ { 9, 9 } }), std::vector({ 0 })); - - aligner.align(query.begin(), query.end(), reference.begin(), reference.end(), edges); - - std::vector cigars; - Score secondBestScore = 0; - Score bestScore = aligner.backtrackAllPaths(edges, cigars, secondBestScore); - EXPECT_EQ(std::size_t(2), cigars.size()); - EXPECT_EQ("0[1=1I1X5=3S]", toString(cigars.at(0))); - EXPECT_EQ("0[1=1X1I5=3S]", toString(cigars.at(1))); - - Cigar cigar = aligner.backtrackBestPath(edges, bestScore, secondBestScore); - - EXPECT_EQ("0[1=1I1X5=3S]", toString(cigar)); -} - -TEST(SimpleAlignment, TCACGGAGA_to_TACGAGAG) -{ - // TCACGGAGA - // | ||| ||| - // T-ACG-AGAG - - const string query = "TCACGGAGA"; - const string reference = "TACGAGAG"; - - DagAligner aligner({ 5, -4 }, 0, -8); - - EdgeMap edges(std::vector>({ { 8, 8 } }), std::vector({ 0 })); - - aligner.align(query.begin(), query.end(), reference.begin(), reference.end(), edges); - - std::vector cigars; - Score secondBestScore = 0; - Score bestScore = aligner.backtrackAllPaths(edges, cigars, secondBestScore); - EXPECT_EQ(std::size_t(2), cigars.size()); - EXPECT_EQ("0[1=1I2=1I4=]", toString(cigars.at(0))); - EXPECT_EQ("0[1=1I3=1I3=]", toString(cigars.at(1))); - - Cigar cigar = aligner.backtrackBestPath(edges, bestScore, secondBestScore); - EXPECT_EQ("0[1=1I2=1I4=]", toString(cigar)); -} - -TEST(ForkAlignment, AAAC_to_AAC_fork_AAC) -{ - DagAligner aligner({ 1, -1 }, 0, -2); - - const string query = "AAAC"; - const string reference = "AAC" - "AAC"; - - EdgeMap edges(std::vector>({ { -1, 3 }, { 6, 6 } }), std::vector({ 0, 1 })); - - aligner.align(query.begin(), query.end(), reference.begin(), reference.end(), edges); - - std::vector cigars; - Score secondBestScore = 0; - Score bestScore = aligner.backtrackAllPaths(edges, cigars, secondBestScore); - EXPECT_EQ(std::size_t(6), cigars.size()); - EXPECT_EQ("0[1S3=]", toString(cigars.at(0))); - EXPECT_EQ("0[1=1I2=]", toString(cigars.at(1))); - EXPECT_EQ("0[2=1I1=]", toString(cigars.at(2))); - EXPECT_EQ("1[1S3=]", toString(cigars.at(3))); - EXPECT_EQ("1[1=1I2=]", toString(cigars.at(4))); - EXPECT_EQ("1[2=1I1=]", toString(cigars.at(5))); - - Cigar cigar = aligner.backtrackBestPath(edges, bestScore, secondBestScore); - EXPECT_EQ("0[1S3=]", toString(cigar)); -} - -TEST(ForkAlignment, AAAC_to_AGC_fork_AAC) -{ - DagAligner aligner({ 1, -1 }, 0, -2); - - const string query = "AAAC"; - const string reference = "AGC" - "AAC"; - EdgeMap edges(std::vector>({ { -1, 3 }, { 6, 6 } }), std::vector({ 0, 1 })); - - aligner.align(query.begin(), query.end(), reference.begin(), reference.end(), edges); - - std::vector cigars; - Score secondBestScore = 0; - Score bestScore = aligner.backtrackAllPaths(edges, cigars, secondBestScore); - EXPECT_EQ(std::size_t(3), cigars.size()); - EXPECT_EQ("1[1S3=]", toString(cigars.at(0))); - EXPECT_EQ("1[1=1I2=]", toString(cigars.at(1))); - EXPECT_EQ("1[2=1I1=]", toString(cigars.at(2))); - - Cigar cigar = aligner.backtrackBestPath(edges, bestScore, secondBestScore); - EXPECT_EQ("1[1S3=]", toString(cigar)); -} - -TEST(Fork, AAC_to_AGC_AAC) -{ - DagAligner aligner({ 1, -1 }, 0, -2); - - const string query = "AAC"; - const string reference = "AGC" - "AAC"; - - EdgeMap edges(std::vector>({ { -1, 3 }, { 6, 6 } }), std::vector({ 0, 1 })); - - aligner.align(query.begin(), query.end(), reference.begin(), reference.end(), edges); - - Score bestScore = 0; - Score secondBestScore = 0; - Cigar cigar = aligner.backtrackBestPath(edges, bestScore, secondBestScore); - EXPECT_EQ("1[3=]", toString(cigar)); -} - -/* - * A - * / \ - * A C - * \ / - * G - */ -TEST(ForkJoin1Base, AAC_to_AGC_AAC) -{ - DagAligner aligner({ 1, -1 }, 0, -2); - - const string query = "AAC"; - const string reference = "A" - "A" - "G" - "C"; - - EdgeMap edges( - std::vector>({ { 0, 1 }, { 0, 2 }, { 1, 3 }, { 2, 3 }, { 4, 4 } }), - std::vector({ 0, 1, 2, 3 })); - - aligner.align(query.begin(), query.end(), reference.begin(), reference.end(), edges); - - Score bestScore = 0; - Score secondBestScore = 0; - Cigar cigar = aligner.backtrackBestPath(edges, bestScore, secondBestScore); - EXPECT_EQ("0[1=]1[1=]3[1=]", toString(cigar)); -} - -/* - * AA - * / \ - * A C - * \ / - * AG - */ -TEST(ForkJoin2Base, AAGC_to_AAGC_AAAC) -{ - DagAligner aligner({ 1, -1 }, 0, -2); - - const string query = "AAGC"; - const string reference = "A" - "AA" - "AG" - "C"; - - EdgeMap edges( - std::vector>({ { 0, 1 }, { 0, 3 }, { 2, 5 }, { 4, 5 }, { 6, 6 } }), - std::vector({ 0, 1, 2, 3 })); - - aligner.align(query.begin(), query.end(), reference.begin(), reference.end(), edges); - - Score bestScore = 0; - Score secondBestScore = 0; - Cigar cigar = aligner.backtrackBestPath(edges, bestScore, secondBestScore); - EXPECT_EQ("0[1=]2[2=]3[1=]", toString(cigar)); -} - -/* - * AA - * / \ - * A C - * \ / - * AC - */ -TEST(ForkJoin2Base, AAGC_to_AAAC_AACC) -{ - DagAligner aligner({ 1, -1 }, 0, -2); - - const string query = "AAGC"; - const string reference = "A" - "AA" - "AC" - "C"; - EdgeMap edges( - std::vector>({ { 0, 1 }, { 0, 3 }, { 2, 5 }, { 4, 5 }, { 6, 6 } }), - std::vector({ 0, 1, 2, 3 })); - aligner.align(query.begin(), query.end(), reference.begin(), reference.end(), edges); - - std::vector cigars; - Score secondBestScore = 0; - Score bestScore = aligner.backtrackAllPaths(edges, cigars, secondBestScore); - EXPECT_EQ(std::size_t(2), cigars.size()); - EXPECT_EQ("0[1=]1[1=1X]3[1=]", toString(cigars.at(0))); - EXPECT_EQ("0[1=]2[1=1X]3[1=]", toString(cigars.at(1))); - - Cigar cigar = aligner.backtrackBestPath(edges, bestScore, secondBestScore); - EXPECT_EQ("0[1=]2[1=1X]3[1=]", toString(cigar)); -} - -/* - * AA - * / \ - * A C - * \ / - * AC - */ -TEST(ForkJoin2Base, AAC_to_AAAC_AACC) -{ - DagAligner aligner({ 1, -1 }, 0, -2); - - const string query = "AAC"; - const string reference = "A" - "AA" - "AC" - "C"; - EdgeMap edges( - std::vector>({ { 0, 1 }, { 0, 3 }, { 2, 5 }, { 4, 5 }, { 6, 6 } }), - std::vector({ 0, 1, 2, 3 })); - - aligner.align(query.begin(), query.end(), reference.begin(), reference.end(), edges); - - Score bestScore = 0; - Score secondBestScore = 0; - Cigar cigar = aligner.backtrackBestPath(edges, bestScore, secondBestScore); - EXPECT_EQ("0[1=]2[2=]", toString(cigar)); -} - -/* - * AAAA - * \ - * T - * / - * GACC - */ -TEST(JoinStartAtOffset, ACCT_to_AAAAT_GACCT) -{ - DagAligner aligner({ 1, -1 }, 0, -2); - - const string query = "ACCT"; - const string reference = "AAAA" - "GACC" - "T"; - - EdgeMap edges( - std::vector>({ { -1, 4 }, { 3, 8 }, { 7, 8 }, { 9, 9 } }), std::vector({ 0, 1, 2 })); - - aligner.align(query.begin(), query.end(), reference.begin(), reference.end(), edges); - - Score bestScore = 0; - Score secondBestScore = 0; - Cigar cigar = aligner.backtrackBestPath(edges, bestScore, secondBestScore); - EXPECT_EQ("1[1D3=]2[1=]", toString(cigar)); -} - -/* - * AA - * \ - * T - * / - * C - */ -TEST(JoinStartAtOffset, AAT_to_AAT_CT) -{ - DagAligner aligner({ 1, -1 }, 0, -2); - - const string query = "AAT"; - const string reference = "AA" - "C" - "T"; - - EdgeMap edges( - std::vector>({ { -1, 2 }, { 1, 3 }, { 2, 3 }, { 4, 4 } }), std::vector({ 0, 1, 2 })); - - aligner.align(query.begin(), query.end(), reference.begin(), reference.end(), edges); - - EXPECT_EQ( - "Aligner(AffineAlignMatrix(AlignMatrix(\n" - "[0\t-2\t-4\t-6]\n" - "[-2\t1\t-1\t-3]\n" - "[-4\t-1\t2\t0]\n" - "[-2\t-1\t-3\t-5]\n" - "[-4\t-3\t0\t3]\n" - ")))", - toString(aligner)); - - Score bestScore = 0; - Score secondBestScore = 0; - Cigar cigar = aligner.backtrackBestPath(edges, bestScore, secondBestScore); - EXPECT_EQ("0[2=]2[1=]", toString(cigar)); -} - -/* - * C - * \ - * T - * / - * AA - */ -TEST(JoinStartAtOffset, AAT_to_CT_AAT) -{ - DagAligner aligner({ 1, -1 }, 0, -2); - - const string query = "AAT"; - const string reference = "C" - "AA" - "T"; - - EdgeMap edges( - std::vector>({ { -1, 1 }, { 0, 3 }, { 2, 3 }, { 4, 4 } }), std::vector({ 0, 1, 2 })); - - aligner.align(query.begin(), query.end(), reference.begin(), reference.end(), edges); - - EXPECT_EQ( - "Aligner(AffineAlignMatrix(AlignMatrix(\n" - "[0\t-2\t-4\t-6]\n" - "[-2\t-1\t-3\t-5]\n" - "[-2\t1\t-1\t-3]\n" - "[-4\t-1\t2\t0]\n" - "[-4\t-3\t0\t3]\n" - ")))", - toString(aligner)); - - Score bestScore = 0; - Score secondBestScore = 0; - Cigar cigar = aligner.backtrackBestPath(edges, bestScore, secondBestScore); - EXPECT_EQ("1[2=]2[1=]", toString(cigar)); -} - -/* - * AA - * / \ - * TCGTGTAA CCCCCCCCTTTTT - * \ / - * GC - */ -TEST(ForkJoinLong, AAGCCCCCCCCCTTTTT_to_TCGTGTAACCCCCCCCTTTTT_TCGTGTGCCCCCCCCCTTTTT) -{ - DagAligner aligner({ 1, -1 }, 0, -2); - - const string query = "AAGCCCCCCCCCTTTTT"; - const string reference = "TCGTGTAA" - "AA" - "GC" - "CCCCCCCCTTTTT"; - - EdgeMap edges( - std::vector>({ { 7, 8 }, { 7, 10 }, { 9, 12 }, { 11, 12 }, { 25, 25 } }), - std::vector({ 0, 1, 2, 3 })); - - aligner.align(query.begin(), query.end(), reference.begin(), reference.end(), edges); - - Score bestScore = 0; - Score secondBestScore = 0; - Cigar cigar = aligner.backtrackBestPath(edges, bestScore, secondBestScore); - EXPECT_EQ("0[6D2=]2[2=]3[13=]", toString(cigar)); -} - -/* - * AAA - * / \ - * TCGTGTAA CCCCCCCCTTTTT - * \ / - * GC - */ -TEST(ForkJoinLong, AAGCCCCCCCCCTTTTT_to_TCGTGTAAAAACCCCCCCCTTTTT_TCGTGTAAGCCCCCCCCCTTTTT) -{ - DagAligner aligner({ 1, -1 }, 0, -2); - - const string query = "AAGCCCCCCCCCTTTTT"; - const string reference = "TCGTGTAA" - "AAA" - "GC" - "CCCCCCCCTTTTT"; - - EdgeMap edges( - std::vector>({ { 7, 8 }, { 7, 11 }, { 10, 13 }, { 12, 13 }, { 26, 26 } }), - std::vector({ 0, 1, 2, 3 })); - - aligner.align(query.begin(), query.end(), reference.begin(), reference.end(), edges); - - Score bestScore = 0; - Score secondBestScore = 0; - Cigar cigar = aligner.backtrackBestPath(edges, bestScore, secondBestScore); - EXPECT_EQ("0[6D2=]2[2=]3[13=]", toString(cigar)); -} - -/* - * A--- TT - * \ / - * T - * / \ - * GACC C - */ -class SimpleGraphTest : public testing::Test -{ -protected: - string reference; - EdgeMap edges; - DagAligner aligner; - Score bestScore = 0; - Score secondBestScore = 0; - - SimpleGraphTest() - : reference("A" - "GACC" - "T" - "TT" - "C") - , edges( - std::vector>({ { -1, 1 }, { 0, 5 }, { 4, 5 }, { 5, 6 }, { 5, 8 }, { 9, 9 } }), - std::vector({ 0, 1, 2, 3, 4 })) - , aligner({ 1, -1 }, 0, -2) - { - } -}; - -TEST_F(SimpleGraphTest, OffEnd) -{ - string query = "ATCTG"; - aligner.align(query.begin(), query.end(), reference.begin(), reference.end(), edges); - - std::vector cigars; - bestScore = aligner.backtrackAllPaths(edges, cigars, secondBestScore); - EXPECT_EQ(std::size_t(2), cigars.size()); - EXPECT_EQ("0[1=]2[1=1I]3[1=1S]", toString(cigars.at(0))); - EXPECT_EQ("0[1=]2[1=]3[1X1=1S]", toString(cigars.at(1))); - - Cigar cigar = aligner.backtrackBestPath(edges, bestScore, secondBestScore); - EXPECT_EQ(0, bestScore); - EXPECT_EQ("0[1=]2[1=1I]3[1=1S]", toString(cigar)); -} -// -TEST_F(SimpleGraphTest, QueryAllN) -{ - string query = "N"; - aligner.align(query.begin(), query.end(), reference.begin(), reference.end(), edges); - - std::vector cigars; - bestScore = aligner.backtrackAllPaths(edges, cigars, secondBestScore); - EXPECT_EQ(std::size_t(2), cigars.size()); - EXPECT_EQ("0[1=]", toString(cigars.at(0))); - EXPECT_EQ("1[1=]", toString(cigars.at(1))); - - Cigar cigar = aligner.backtrackBestPath(edges, bestScore, secondBestScore); - EXPECT_EQ(1, bestScore); - EXPECT_EQ("0[1=]", toString(cigar)); - - cigar = aligner.backtrackBestPath(edges, bestScore, secondBestScore); - EXPECT_EQ(1, bestScore); - EXPECT_EQ("0[1=]", toString(cigar)); - - query = "NNNNNNNNNN"; - aligner.align(query.begin(), query.end(), reference.begin(), reference.end(), edges); - - cigars.clear(); - bestScore = aligner.backtrackAllPaths(edges, cigars, secondBestScore); - EXPECT_EQ(std::size_t(1), cigars.size()); - EXPECT_EQ("1[4=]2[1=]3[2=3S]", toString(cigars.at(0))); - - cigar = aligner.backtrackBestPath(edges, bestScore, secondBestScore); - EXPECT_EQ(7, bestScore); - EXPECT_EQ("1[4=]2[1=]3[2=3S]", toString(cigar)); - - cigar = aligner.backtrackBestPath(edges, bestScore, secondBestScore); - EXPECT_EQ(1, bestScore); - EXPECT_EQ("1[3S4=]2[1=]3[2=]", toString(cigar)); -} - -TEST_F(SimpleGraphTest, QuerySomeN) -{ - string query = "GANCNC"; - aligner.align(query.begin(), query.end(), reference.begin(), reference.end(), edges); - Cigar cigar = aligner.backtrackBestPath(edges, bestScore, secondBestScore); - EXPECT_EQ(6, bestScore); - EXPECT_EQ("1[4=]2[1=]4[1=]", toString(cigar)); -} - -TEST_F(SimpleGraphTest, EmptyQuery) -{ - string query = ""; - EXPECT_ANY_THROW(aligner.align(query.begin(), query.end(), reference.begin(), reference.end(), edges)); -} - -TEST_F(SimpleGraphTest, BadQualities) -{ - string query = "gACc"; - aligner.align(query.begin(), query.end(), reference.begin(), reference.end(), edges); - Cigar cigar = aligner.backtrackBestPath(edges, bestScore, secondBestScore); - EXPECT_EQ(4, bestScore); - EXPECT_EQ("1[4=]", toString(cigar)); -} - -/* - * _ - * / \ - * G-TCC-AAAAA - */ -TEST(RepeatExpansion, SimpleRepeat) -{ - DagAligner aligner({ 1, -1 }, 0, -2); - - const string reference = "G" - "TCC" - "TCC" - "TCC" - "AAAAA"; - - EdgeMap edges( - std::vector>({ { 0, 1 }, - { 3, 4 }, - { 6, 7 }, - { 3, 10 }, - { 6, 10 }, - { 9, 10 }, - { reference.length(), reference.length() } }), - std::vector({ 0, 1, 2, 3, 4 })); - - string query = "TCCTCCAA"; - aligner.align(query.begin(), query.end(), reference.begin(), reference.end(), edges); - Score bestScore = 0; - Score secondBestScore = 0; - Cigar cigar = aligner.backtrackBestPath(edges, bestScore, secondBestScore); - EXPECT_EQ(6, bestScore); - EXPECT_EQ("0[1D]1[3=]2[3=]4[2=]", toString(cigar)); - - query = "GTCTCCCCAA"; - aligner.align(query.begin(), query.end(), reference.begin(), reference.end(), edges); - - std::vector cigars; - bestScore = aligner.backtrackAllPaths(edges, cigars, secondBestScore); - EXPECT_EQ(std::size_t(2), cigars.size()); - EXPECT_EQ("0[1=]1[1=1D1=]2[3=]3[1D2=]4[2=]", toString(cigars.at(0))); - EXPECT_EQ("0[1=]1[2=1D]2[3=]3[1D2=]4[2=]", toString(cigars.at(1))); - - cigar = aligner.backtrackBestPath(edges, bestScore, secondBestScore); - EXPECT_EQ(6, bestScore); - EXPECT_EQ("0[1=]1[1=1D1=]2[3=]3[1D2=]4[2=]", toString(cigar)); -} - -/* - * |\ |\ - * G--TCC-C - */ -TEST(RepeatExpansion, HomoPolymers) -{ - DagAligner aligner({ 1, -1 }, 0, -2); - - const string query = "GGTCCGC"; - const string reference = "G" - "G" - "G" - "TCC" - "C" - "C"; - - EdgeMap edges( - std::vector>({ { 0, 1 }, - { 1, 2 }, - { 0, 3 }, - { 1, 3 }, - { 2, 3 }, - { 5, 6 }, - { 6, 7 }, - { reference.length(), reference.length() } }), - std::vector({ 0, 1, 2, 3, 4, 5 })); - - aligner.align(query.begin(), query.end(), reference.begin(), reference.end(), edges); - - Score bestScore = 0; - Score secondBestScore = 0; - Cigar cigar = aligner.backtrackBestPath(edges, bestScore, secondBestScore); - EXPECT_EQ(5, bestScore); - EXPECT_EQ("0[1=]1[1=]3[3=]4[1X]5[1=]", toString(cigar)); -} - -/* - * --- - * / \ - * C-GCC-GACAAC-GAC-CTTCCTGAACT - * \ / \ / - * - - - */ -TEST(RepeatExpansion, two_repeats) -{ - DagAligner aligner({ 5, -4 }, 0, -8); - - const string query = "CgCCGCCA"; - const string reference = "C" - "GCC" - "GCC" - "GCC" - "GCC" - "GCC" - "GCC" - "GACAAC" - "GAC" - "GAC" - "GAC" - "GAC" - "CTTCCTGAACT"; - - EdgeMap edges( - std::vector>({ { 0, 1 }, - { 3, 4 }, - { 6, 7 }, - { 9, 10 }, - { 12, 13 }, - { 15, 16 }, - { 0, 19 }, - { 3, 19 }, - { 6, 19 }, - { 9, 19 }, - { 12, 19 }, - { 15, 19 }, - { 18, 19 }, - { 24, 25 }, - { 27, 28 }, - { 30, 31 }, - { 33, 34 }, - { 27, 37 }, - { 30, 37 }, - { 33, 37 }, - { 36, 37 }, - { 24, 37 }, - { reference.length(), reference.length() } }), - std::vector({ 6, 7, 8, 9, 10, 11, 12, 5, 1, 2, 3, 4, 0 })); - - aligner.align(query.begin(), query.end(), reference.begin(), reference.end(), edges); - - Score secondBestScore = 0; - std::vector cigars; - const Score bestScore = aligner.backtrackAllPaths(edges, cigars, secondBestScore); - - EXPECT_EQ(32, bestScore); - EXPECT_EQ("6[1=]7[3=]8[3=]5[1D1=]", toString(cigars.at(0))); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/DepthTestTest.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/tests/DepthTestTest.cpp deleted file mode 100644 index add5680..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/DepthTestTest.cpp +++ /dev/null @@ -1,38 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Sai Chen , -// Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphutils/DepthTest.hh" - -#include "gtest/gtest.h" - -TEST(TestingCoverageDepth, ReasonableCoverage_TestPasses) -{ - DepthTest depth_test(20, 5, 0.05, 0.001); - EXPECT_TRUE(depth_test.testReadCount(15)); - EXPECT_TRUE(depth_test.testReadCount(30)); -} - -TEST(TestingCoverageDepth, PoorCoverage_TestFails) -{ - DepthTest depth_test(20, 5, 0.05, 0.001); - EXPECT_FALSE(depth_test.testReadCount(10)); - EXPECT_FALSE(depth_test.testReadCount(40)); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/GappedAlignerTest.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/tests/GappedAlignerTest.cpp deleted file mode 100644 index 4bbc449..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/GappedAlignerTest.cpp +++ /dev/null @@ -1,333 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphalign/GappedAligner.hh" - -#include "gtest/gtest.h" - -#include "graphalign/GraphAlignmentOperations.hh" -#include "graphalign/LinearAlignment.hh" -#include "graphcore/Graph.hh" -#include "graphcore/GraphBuilders.hh" -#include "graphcore/Path.hh" - -using std::list; -using std::make_pair; -using std::string; - -using namespace graphtools; - -TEST(DISABLED_ExtendingAlignmentSuffix, UniquelyMappingQuery_AlignmentExtended) -{ - Graph graph = makeStrGraph("ATA", "CG", "TATTTTTTTTT"); - - const size_t kmer_len = 3; - const size_t padding_len = 5; - const int32_t seed_affix_trim_len = 0; - GappedGraphAligner aligner(&graph, kmer_len, padding_len, seed_affix_trim_len); - AlignerSelector alignerSelector(AlignerType::PATH_ALIGNER); - - // -> CGCGCGTA - // | |||||| - // -> C-CGCGTA - // 11111122 - - Path seed_path(&graph, 3, { 0 }, 3); - const size_t extension_len = 12; - list extensions - = aligner.extendAlignmentSuffix(seed_path, "CCGCGTA", extension_len, alignerSelector); - - Alignment expected_alignment(0, "1M1D6M"); - Path expected_path(&graph, 3, { 0, 1, 1, 1, 2 }, 2); - list expected_extensions = { make_pair(expected_path, expected_alignment) }; - - EXPECT_EQ(expected_extensions, extensions); -} - -TEST(DISABLED_ExtendingAlignmentSuffix, MultiMappingQuery_AlignmentExtended) -{ - Graph graph = makeStrGraph("AAA", "C", "CCA"); - - const size_t kmer_len = 3; - const size_t padding_len = 0; - const int32_t seed_affix_trim_len = 0; - GappedGraphAligner aligner(&graph, kmer_len, padding_len, seed_affix_trim_len); - AlignerSelector alignerSelector(AlignerType::PATH_ALIGNER); - - Path seed_path(&graph, 3, { 0 }, 3); - list extensions = aligner.extendAlignmentSuffix(seed_path, "CCC", 3, alignerSelector); - - Alignment expected_alignment_a = Alignment(0, "3M"); - Path expected_path_a(&graph, 3, { 0, 1, 1, 1 }, 1); - - Alignment expected_alignment_b = Alignment(0, "3M"); - Path expected_path_b(&graph, 3, { 0, 1, 1, 2 }, 1); - - Alignment expected_alignment_c = Alignment(0, "3M"); - Path expected_path_c(&graph, 3, { 0, 1, 2 }, 2); - - list expected_extensions - = { make_pair(expected_path_a, expected_alignment_a), make_pair(expected_path_b, expected_alignment_b), - make_pair(expected_path_c, expected_alignment_c) }; - - EXPECT_EQ(expected_extensions, extensions); -} - -class AlignerTests : public ::testing::TestWithParam -{ -}; - -// TODO: Throw an error if there are no valid extensions? -TEST_P(AlignerTests, ExtendingAlignmentPrefix_TypicalSequences_AlignmentExtended) -{ - Graph graph = makeStrGraph("ATATTA", "CG", "TATTT"); - - const size_t kmer_len = 3; - const size_t padding_len = 5; - const size_t seed_affix_trim_len = 0; - GappedGraphAligner aligner(&graph, kmer_len, padding_len, seed_affix_trim_len); - AlignerSelector alignerSelector(GetParam()); - - // ATTAC-GCGC <- - // || || ||| - // ATAACAGCGG <- - // 00001 1111 - - Path seed_path(&graph, 1, { 1 }, 1); - const size_t extension_len = 10; - list extensions - = aligner.extendAlignmentPrefix(seed_path, "ATAACAGCGG", extension_len, alignerSelector); - - Alignment expected_alignment(0, "2M1X2M1I3M1X"); - Path expected_path(&graph, 2, { 0, 1, 1, 1 }, 1); - list expected_extensions = { make_pair(expected_path, expected_alignment) }; - - EXPECT_EQ(expected_extensions, extensions); -} - -TEST_P(AlignerTests, PerformingGappedAlignment_UniquelyMappingQuery_AlignmentPerformed) -{ - Graph graph = makeStrGraph("ATATTA", "CG", "TATTT"); - - const size_t kmer_len = 3; - const size_t padding_len = 2; - const int32_t seed_affix_trim_len = 0; - GappedGraphAligner aligner(&graph, kmer_len, padding_len, seed_affix_trim_len); - AlignerSelector alignerSelector(GetParam(), LinearAlignmentParameters(5, -4, -8, 0)); - - { - // TTA-CG-CG-TAT - // || || | ||| - // TT--CG-C--TAT - - list alignments = aligner.align("TTCGCTAT", alignerSelector); - - list expected_alignments = { decodeGraphAlignment(3, "0[2M1D]1[2M]1[1M1D]2[3M]", &graph) }; - // with default m=5,mm=-4,go=-8,ge=-2 2M1D=10-8-2=0, 1M1X=5-4=1, so, test needs an update: - // list expected_alignments = { decodeGraphAlignment(4, "0[1M1X]1[2M]1[1M1D]2[3M]", &graph) }; - EXPECT_EQ(expected_alignments, alignments); - } - - { - list alignments = aligner.align("ATTCGCTAT", alignerSelector); - - list expected_alignments = { decodeGraphAlignment(2, "0[3M1D]1[2M]1[1M1D]2[3M]", &graph) }; - // with default m=5,mm=-4,go=-8,ge=-2 2M1D=10-8-2=0, 1M1X=5-4=1, so, test needs an update: - // list expected_alignments = { decodeGraphAlignment(4, "0[1M1X]1[2M]1[1M1D]2[3M]", &graph) }; - EXPECT_EQ(expected_alignments, alignments); - } -} - -TEST_P(AlignerTests, PerformingGappedAlignment_MultimappingQuery_BestAlignmentsComputed) -{ - Graph graph = makeStrGraph("AAG", "CGG", "CTT"); - GappedGraphAligner aligner(&graph, 3, 0, 0); - AlignerSelector alignerSelector(GetParam()); - - // G-CG-C - // 0-11-1 - // 1-11-1 - - list alignments = aligner.align("GCGGC", alignerSelector); - - list expected_alignments - = { decodeGraphAlignment(2, "0[1M]1[3M]1[1M]", &graph), decodeGraphAlignment(2, "0[1M]1[3M]2[1M]", &graph), - decodeGraphAlignment(2, "1[1M]1[3M]1[1M]", &graph), decodeGraphAlignment(2, "1[1M]1[3M]2[1M]", &graph) }; - EXPECT_EQ(expected_alignments, alignments); -} - -TEST_P(AlignerTests, PerformingGappedAlignment_KmerExtensionInBothDirectionsNotNeeded_BestAlignmentsComputed) -{ - Graph graph = makeStrGraph("AAG", "CGG", "CTT"); - GappedGraphAligner aligner(&graph, 3, 0, 0); - AlignerSelector alignerSelector(GetParam()); - - { - list alignments = aligner.align("CGGCT", alignerSelector); - list expected_alignments = { decodeGraphAlignment(0, "1[3M]2[2M]", &graph) }; - EXPECT_EQ(expected_alignments, alignments); - } - - { - list alignments = aligner.align("AATCGG", alignerSelector); - list expected_alignments = { decodeGraphAlignment(0, "0[2M1X]1[3M]", &graph) }; - EXPECT_EQ(expected_alignments, alignments); - } - - { - list alignments = aligner.align("CTT", alignerSelector); - list expected_alignments = { decodeGraphAlignment(0, "2[3M]", &graph) }; - EXPECT_EQ(expected_alignments, alignments); - } -} - -TEST_P(AlignerTests, PerformingGappedAlignment_KmerExtensionIsUnalignable_BestAlignmentsComputed) -{ - Graph graph = makeStrGraph("AAG", "CGG", "CTT"); - GappedGraphAligner aligner(&graph, 3, 0, 0); - AlignerSelector alignerSelector(GetParam()); - - { - list alignments = aligner.align("CGGAA", alignerSelector); - list expected_alignments = { decodeGraphAlignment(0, "1[3M2S]", &graph) }; - EXPECT_EQ(expected_alignments, alignments); - } - - { - list alignments = aligner.align("TTCGG", alignerSelector); - list expected_alignments = { decodeGraphAlignment(0, "1[2S3M]", &graph) }; - EXPECT_EQ(expected_alignments, alignments); - } - - { - list alignments = aligner.align("TCGGA", alignerSelector); - list expected_alignments = { decodeGraphAlignment(0, "1[1S3M1S]", &graph) }; - EXPECT_EQ(expected_alignments, alignments); - } -} - -TEST_P(AlignerTests, PerformingGappedAlignment_PolyalanineRepeat_ReadAligned) -{ - Graph graph = makeStrGraph("AAG", "GCN", "ATT"); - GappedGraphAligner aligner(&graph, 4, 0, 0); - AlignerSelector alignerSelector(GetParam()); - - list alignments = aligner.align("AGGCCGTGGCAATT", alignerSelector); - list expected_alignments = { decodeGraphAlignment(1, "0[2M]1[3M]1[1M1X1M]1[3M]2[3M]", &graph) }; - - EXPECT_EQ(expected_alignments, alignments); -} - -TEST_P(AlignerTests, PerformingGappedAlignment_ReadWithLowqualityBases_ReadAligned) -{ - Graph graph = makeStrGraph("AAG", "CGG", "CTT"); - GappedGraphAligner aligner(&graph, 4, 0, 0); - AlignerSelector alignerSelector(GetParam()); - - list alignments = aligner.align("aagcggctt", alignerSelector); - list expected_alignments = { decodeGraphAlignment(0, "0[3M]1[3M]2[3M]", &graph) }; - - EXPECT_EQ(expected_alignments, alignments); -} - -TEST_P(AlignerTests, PerformingGappedAlignment_IncorrectSeedKmer_ReadAligned) -{ - Graph graph = makeStrGraph("AAAA", "CCG", "TTTT"); - const int32_t seed_affix_trim_len = 2; - GappedGraphAligner aligner(&graph, 4, 0, seed_affix_trim_len); - AlignerSelector alignerSelector(GetParam()); - - { - list alignments = aligner.align("CCACCGTTTT", alignerSelector); - list expected_alignments = { decodeGraphAlignment(0, "1[2M1X]1[3M]2[4M]", &graph) }; - - EXPECT_EQ(expected_alignments, alignments); - } - - { - list alignments = aligner.align("CCGTCG", alignerSelector); - list expected_alignments = { decodeGraphAlignment(0, "1[3M]1[1X2M]", &graph) }; - - EXPECT_EQ(expected_alignments, alignments); - } -} - -TEST_P(AlignerTests, PerformingGappedAlignment_NoExceptionThrown) -{ - // 0 1 2 3 4 5 6 7 - //(AT)*(GATATATATATATAT)*G(AT)*TTATATATG(AT)* - Graph graph(8); - graph.setNodeSeq(0, "AGGATGACAGTAATATTATCTTACTATCTTACTATGTGTTACTTTATTAGTTTTTCCCTTATATGTTTGTTTTGGGATATATGACTTGGCTC"); - graph.setNodeSeq(1, "AT"); - graph.setNodeSeq(2, "GATATATATATATAT"); - graph.setNodeSeq(3, "G"); - graph.setNodeSeq(4, "AT"); - graph.setNodeSeq(5, "TTATATATG"); - graph.setNodeSeq(6, "AT"); - graph.setNodeSeq(7, "GATATATATTTATATTAAAAGGTGCTTTGTTCTTTGCAAAACAGTCTCCTATGTTATTTCCTCATTTTATTAAAATGTAACCTAAAACTGTT"); - - graph.addEdge(0, 1); - graph.addEdge(1, 2); - graph.addEdge(2, 3); - graph.addEdge(3, 4); - graph.addEdge(4, 5); - graph.addEdge(5, 6); - graph.addEdge(6, 7); - - graph.addEdge(1, 1); - graph.addEdge(0, 2); - graph.addEdge(0, 3); - - graph.addEdge(2, 2); - graph.addEdge(1, 3); - - graph.addEdge(4, 4); - graph.addEdge(3, 5); - - graph.addEdge(6, 6); - graph.addEdge(5, 7); - - const size_t kmer_len = 14; - const size_t padding_len = 10; - const int32_t seed_affix_trim_len = 14; - GappedGraphAligner aligner(&graph, kmer_len, padding_len, seed_affix_trim_len); - AlignerSelector alignerSelector(GetParam()); - - const string query = "ctTTttgaTTTtttccctcacatgTTTTTtatatGataTtTctcTtCtCtcataTAtttaTAtAtAttAtATtTAtAtataTctttTAtATAT" - "AtaATaTaTaTATatCATATAtATaTATGATATATATATATATCATATATATATATG"; - - ASSERT_NO_THROW(aligner.align(query, alignerSelector)); -} - -TEST_P(AlignerTests, PerformingGappedAlignment_FlankWithStrKmer_ReadAligned) -{ - Graph graph = makeStrGraph("AAAA", "CGG", "TTCGGCGGTT"); - const int32_t seed_affix_trim_len = 2; - GappedGraphAligner aligner(&graph, 4, 0, seed_affix_trim_len); - AlignerSelector alignerSelector(GetParam()); - - list alignments = aligner.align("CGGCGGCGGCGGCGG", alignerSelector); - list expected_alignments = { decodeGraphAlignment(0, "1[3M]1[3M]1[3M]1[3M]1[3M]", &graph) }; - - EXPECT_EQ(expected_alignments, alignments); -} - -INSTANTIATE_TEST_SUITE_P( - AlignerTestsInst, AlignerTests, ::testing::Values(AlignerType::PATH_ALIGNER, AlignerType::DAG_ALIGNER)); diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/GraphAlignmentOperationsTest.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/tests/GraphAlignmentOperationsTest.cpp deleted file mode 100644 index 92ae73d..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/GraphAlignmentOperationsTest.cpp +++ /dev/null @@ -1,168 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphalign/GraphAlignmentOperations.hh" - -#include - -#include "gtest/gtest.h" - -#include "graphcore/Graph.hh" -#include "graphcore/GraphBuilders.hh" -#include "graphcore/Path.hh" - -using std::list; -using std::string; - -using namespace graphtools; - -TEST(SplitingNodeCigarEncoding, TypicalCigarEncoding_CigarAndNodeIdExtracted) -{ - string cigar; - NodeId node_id; - splitNodeCigar("1[4M5S]", cigar, node_id); - EXPECT_EQ(1ul, node_id); - EXPECT_EQ("4M5S", cigar); -} - -TEST(DecodingGraphAlignment, SinglenodeGraphAlignment_Decoded) -{ - Graph graph = makeDeletionGraph("AAAA", "TTGG", "TTTT"); - GraphAlignment alignment = decodeGraphAlignment(1, "1[2M]", &graph); - - GraphAlignment expected_alignment(Path(&graph, 1, { 1 }, 3), { Alignment(1, "2M") }); - EXPECT_EQ(expected_alignment, alignment); -} - -TEST(DecodingGraphAlignment, MultinodeGraphAlignment_Decoded) -{ - Graph graph = makeDeletionGraph("AAAA", "TTGG", "TTTT"); - GraphAlignment alignment = decodeGraphAlignment(0, "0[4M]1[2M3S]", &graph); - - GraphAlignment expected_alignment(Path(&graph, 0, { 0, 1 }, 2), { Alignment(0, "4M"), Alignment(0, "2M3S") }); - EXPECT_EQ(expected_alignment, alignment); -} - -TEST(CheckingConsistencyOfAlignments, ConsistentAlignment_CheckPassed) -{ - Graph graph = makeDeletionGraph("AAAA", "TTGG", "TTTT"); - GraphAlignment alignment = decodeGraphAlignment(0, "0[4M]1[2M3S]", &graph); - - const string query = "AAAATTCCC"; - ASSERT_TRUE(checkConsistency(alignment, query)); -} - -TEST(CheckingConsistencyOfAlignments, QueryIsShorterThanAlignment_CheckFailed) -{ - Graph graph = makeDeletionGraph("AAAA", "TTGG", "TTTT"); - GraphAlignment alignment = decodeGraphAlignment(0, "0[4M]1[2M3S]", &graph); - - const string query = "AAAATT"; - ASSERT_FALSE(checkConsistency(alignment, query)); -} - -TEST(CheckingConsistencyOfAlignments, GraphAlignmentWithInconsistentLinearAlignment_CheckFailed) -{ - Graph graph = makeDeletionGraph("AAAA", "TTGG", "TTTT"); - GraphAlignment alignment = decodeGraphAlignment(0, "0[4M]1[2M3S]", &graph); - - const string query = "AAAAGGCCC"; - ASSERT_FALSE(checkConsistency(alignment, query)); -} - -TEST(CheckingConsistencyOfAlignments, UnderlyingPathCanBeShortened_CheckFailed) -{ - Graph graph = makeDeletionGraph("AAAA", "TTGG", "TTTT"); - - GraphAlignment alignment(Path(&graph, 4, { 0, 1 }, 2), { Alignment(4, "3S"), Alignment(0, "2M") }); - ASSERT_FALSE(checkConsistency(alignment, "GGGTT")); -} - -TEST(CheckingIfAlignmentIsLocal, AlignmentsThatStartAndEndWithMatch_CheckPassed) -{ - Graph graph = makeDeletionGraph("AAAA", "TTGG", "TTTT"); - - ASSERT_TRUE(isLocalAlignment(decodeGraphAlignment(0, "0[4M]1[2M]", &graph))); - ASSERT_TRUE(isLocalAlignment(decodeGraphAlignment(0, "0[4M]1[2M3S]", &graph))); - ASSERT_TRUE(isLocalAlignment(decodeGraphAlignment(0, "0[3S4M]1[2M]", &graph))); -} - -TEST(CheckingIfAlignmentIsLocal, AlignmentsWithoutTerminalMatch_CheckFailed) -{ - Graph graph = makeDeletionGraph("AAAA", "TTGG", "TTTT"); - - ASSERT_FALSE(isLocalAlignment(decodeGraphAlignment(0, "0[1D3M]1[2M3S]", &graph))); - ASSERT_FALSE(isLocalAlignment(decodeGraphAlignment(1, "0[3M]1[2M1X3S]", &graph))); - ASSERT_FALSE(isLocalAlignment(decodeGraphAlignment(0, "0[1X3M]1[2M1I3S]", &graph))); -} - -TEST(GettingQuerySequencesForEachNode, TypicalAlignment_SequencePairs) -{ - // AAA:CGG:CGG:TG - // |: :|||:|| - // TTTA:C--:CGG:TGGTTT - - Graph graph = makeStrGraph("AAA", "CGG", "TG"); - GraphAlignment alignment = decodeGraphAlignment(2, "0[3S1M]1[1M2D]1[3M]2[2M4S]", &graph); - - const string query = "TTTACCGGTGGTTT"; - const list query_pieces = getQuerySequencesForEachNode(alignment, query); - - const list expected_pieces = { "TTTA", "C", "CGG", "TGGTTT" }; - ASSERT_EQ(expected_pieces, query_pieces); -} - -TEST(PrettyPrintingAlignments, TypicalAlignment_PrettyPrinted) -{ - // AAA:CGG:CGG:TG - // |: :|||:|| - // TTTA:C--:CGG:TGGTTT - - Graph graph = makeStrGraph("AAA", "CGG", "TG"); - GraphAlignment alignment = decodeGraphAlignment(2, "0[3S1M]1[1M2D]1[3M]2[2M4S]", &graph); - - const string query = "TTTACCGGTGGTTT"; - const string encoding = prettyPrint(alignment, query); - - const string expected_encoding = "---A:CGG:CGG:TG----\n" - " |:| :|||:|| \n" - "TTTA:C--:CGG:TGGTTT"; - ASSERT_EQ(expected_encoding, encoding); -} - -TEST(ProjectingLinearAlignmentOntoPath, TypicalLinearAlignment_GraphAlignment) -{ - // CATAC - // || | - // GGAT-CGAA - // 00122 - const string query = "GGATCGAA"; - const string reference = "CAWAC"; - Alignment linear_alignment(1, "2S2M1D1M3S"); - - Graph graph = makeStrGraph("AACA", "W", "ACTTT"); - Path path(&graph, 2, { 0, 1, 2 }, 1); - - GraphAlignment graph_alignment = projectAlignmentOntoGraph(linear_alignment, path); - - GraphAlignment expected_graph_alignment = decodeGraphAlignment(3, "0[2S1M]1[1M]2[1D1M3S]", &graph); - - ASSERT_EQ(expected_graph_alignment, graph_alignment); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/GraphAlignmentTest.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/tests/GraphAlignmentTest.cpp deleted file mode 100644 index 14aa897..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/GraphAlignmentTest.cpp +++ /dev/null @@ -1,251 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphalign/GraphAlignment.hh" - -#include "gtest/gtest.h" - -#include "graphalign/GraphAlignmentOperations.hh" -#include "graphcore/Graph.hh" -#include "graphcore/GraphBuilders.hh" -#include "graphcore/Path.hh" - -using std::list; -using std::string; -using std::vector; - -using namespace graphtools; - -TEST(InitializingGraphAlignment, CompatiblePath_GraphAlignmentCreated) -{ - Graph graph = makeDeletionGraph("AAAA", "TTGG", "TTTT"); - - { - Path path(&graph, 3, { 0, 1, 2 }, 3); - vector alignments = { Alignment(3, "1M"), Alignment(0, "4M"), Alignment(0, "3M") }; - EXPECT_NO_THROW(GraphAlignment(path, alignments)); - } - - { - Path path(&graph, 2, { 1 }, 3); - vector alignments = { Alignment(2, "1M") }; - EXPECT_NO_THROW(GraphAlignment(path, alignments)); - } -} - -TEST(InitializingGraphAlignment, IncompatiblePath_ExceptionThrown) -{ - Graph graph = makeDeletionGraph("AAAA", "TTGG", "TTTT"); - Path path(&graph, 2, { 0, 1, 2 }, 3); - - { - vector alignments = { Alignment(3, "1M"), Alignment(0, "4M"), Alignment(0, "3M") }; - EXPECT_ANY_THROW(GraphAlignment(path, alignments)); - } - - { - vector alignments = { Alignment(2, "2M"), Alignment(0, "4M"), Alignment(0, "4M") }; - EXPECT_ANY_THROW(GraphAlignment(path, alignments)); - } - - { - vector alignments = { Alignment(2, "2M"), Alignment(0, "3M"), Alignment(0, "3M") }; - EXPECT_ANY_THROW(GraphAlignment(path, alignments)); - } - - { - vector alignments = { Alignment(2, "2M"), Alignment(1, "4M"), Alignment(0, "3M") }; - EXPECT_ANY_THROW(GraphAlignment(path, alignments)); - } -} - -TEST(GettingNumMatchesInGraphAlignment, TypicalGraphAlignment_GotNumMatches) -{ - Graph graph = makeDeletionGraph("AAAA", "TTGG", "TTTT"); - const string query = "AAAATTCCC"; - GraphAlignment graph_alignment = decodeGraphAlignment(0, "0[4M]1[2M3S]", &graph); - EXPECT_EQ(6u, graph_alignment.numMatches()); -} - -TEST(GettingGraphAlignmentSpans, TypicalGraphAlignment_GotQueryAndReferenceSpans) -{ - Graph graph = makeDeletionGraph("AAAA", "TTGG", "TTTT"); - const string query = "AAAATTCCC"; - GraphAlignment graph_alignment = decodeGraphAlignment(0, "0[4M]1[2M3S]", &graph); - EXPECT_EQ(9u, graph_alignment.queryLength()); - EXPECT_EQ(6u, graph_alignment.referenceLength()); -} - -TEST(AccessingNodeAlignmentsByIndex, TypicalGraphAlignment_NodeAlignmentsAccessed) -{ - Graph graph = makeDeletionGraph("AAAA", "TTGC", "TTTT"); - const string query = "AAAATTCCC"; - GraphAlignment graph_alignment = decodeGraphAlignment(0, "0[4M]1[2M3S]", &graph); - EXPECT_EQ(Alignment(0, "4M"), graph_alignment[0]); - EXPECT_EQ(Alignment(0, "2M3S"), graph_alignment[1]); -} - -TEST(GettingIndexesOfNode, TypicalAlignment_IndexesObtained) -{ - Graph graph = makeStrGraph("AAAACC", "CCG", "ATTT"); - const string read = "CCCCGCCGAT"; - GraphAlignment alignment = decodeGraphAlignment(4, "0[2M]1[3M]1[3M]2[2M]", &graph); - const list left_flank_indexes = { 0 }; - const list repeat_unit_indexes = { 1, 2 }; - const list right_flank_indexes = { 3 }; - EXPECT_EQ(left_flank_indexes, alignment.getIndexesOfNode(0)); - EXPECT_EQ(repeat_unit_indexes, alignment.getIndexesOfNode(1)); - EXPECT_EQ(right_flank_indexes, alignment.getIndexesOfNode(2)); -} - -TEST(GettingIndexesOfNode, NodeNotInAlignment_EmptyListReturned) -{ - Graph graph = makeStrGraph("AAAACC", "CCG", "ATTT"); - const string read = "ACCCCG"; - GraphAlignment alignment = decodeGraphAlignment(3, "0[3M]1[3M]", &graph); - const list empty_list; - EXPECT_EQ(empty_list, alignment.getIndexesOfNode(2)); - EXPECT_EQ(empty_list, alignment.getIndexesOfNode(4)); -} - -TEST(CheckingIfAlignmentOverlapsNode, TypicalAlignment_ChecksPerformed) -{ - Graph graph = makeStrGraph("AAAACC", "CCG", "ATTT"); - const string read = "ACCCCG"; - GraphAlignment alignment = decodeGraphAlignment(3, "0[3M]1[3M]", &graph); - EXPECT_TRUE(alignment.overlapsNode(0)); - EXPECT_TRUE(alignment.overlapsNode(1)); - EXPECT_FALSE(alignment.overlapsNode(2)); - EXPECT_FALSE(alignment.overlapsNode(3)); -} - -TEST(EncodingGraphAlignment, TypicalGraphAlignment_CigarStringObtained) -{ - Graph graph = makeStrGraph("AAAACC", "CCG", "ATTT"); - const string read = "CCCCGCCGAT"; - const string cigar_string = "0[2M]1[3M]1[3M]2[2M]"; - GraphAlignment alignment = decodeGraphAlignment(4, cigar_string, &graph); - - ASSERT_EQ(cigar_string, alignment.generateCigar()); -} - -TEST(ComparingGraphAlignments, TypicalGraphAlignments_Compared) -{ - Graph graph = makeStrGraph("ATT", "CCG", "CTTT"); - - GraphAlignment alignment_a = decodeGraphAlignment(1, "0[2M]1[3M]1[1M]", &graph); - GraphAlignment alignment_b = decodeGraphAlignment(1, "0[2M]1[3M]2[1M]", &graph); - - EXPECT_TRUE(alignment_a < alignment_b); - EXPECT_FALSE(alignment_b < alignment_a); - EXPECT_FALSE(alignment_a == alignment_b); -} - -TEST(ShrinkingGraphAlignmentStarts, TypicalGraphAlignment_Shrank) -{ - Graph graph = makeStrGraph("ATT", "CCG", "CTTT"); - - { - GraphAlignment alignment = decodeGraphAlignment(1, "0[2M]1[3M]1[1M]", &graph); - alignment.shrinkStart(1); - GraphAlignment expectedAlignment = decodeGraphAlignment(2, "0[1S1M]1[3M]1[1M]", &graph); - - EXPECT_EQ(alignment, expectedAlignment); - } - - { - GraphAlignment alignment = decodeGraphAlignment(1, "0[2M]1[3M]1[1M]", &graph); - alignment.shrinkStart(2); - GraphAlignment expectedAlignment = decodeGraphAlignment(0, "1[2S3M]1[1M]", &graph); - - EXPECT_EQ(alignment, expectedAlignment); - } - - { - GraphAlignment alignment = decodeGraphAlignment(1, "0[2M]1[3M]1[1M]", &graph); - alignment.shrinkStart(5); - GraphAlignment expectedAlignment = decodeGraphAlignment(0, "1[5S1M]", &graph); - - EXPECT_EQ(alignment, expectedAlignment); - } - - { - GraphAlignment alignment = decodeGraphAlignment(1, "0[1S2M]1[3M]1[1M]", &graph); - alignment.shrinkStart(3); - GraphAlignment expectedAlignment = decodeGraphAlignment(1, "1[4S2M]1[1M]", &graph); - - EXPECT_EQ(alignment, expectedAlignment); - } -} - -TEST(ShrinkingGraphAlignmentStarts, ShrinkingByAlignmentLengthOrMore_ExceptionThrown) -{ - Graph graph = makeStrGraph("ATT", "CCG", "CTTT"); - - GraphAlignment alignment = decodeGraphAlignment(1, "0[2M]1[3M]1[1M]", &graph); - EXPECT_ANY_THROW(alignment.shrinkStart(alignment.referenceLength())); - EXPECT_ANY_THROW(alignment.shrinkStart(alignment.referenceLength() + 1)); -} - -TEST(ShrinkingGraphAlignmentEnds, TypicalGraphAlignment_Shrank) -{ - Graph graph = makeStrGraph("ATT", "CCG", "CTTT"); - - { - GraphAlignment alignment = decodeGraphAlignment(1, "0[2M]1[3M]1[1M]", &graph); - alignment.shrinkEnd(1); - GraphAlignment expectedAlignment = decodeGraphAlignment(1, "0[2M]1[3M1S]", &graph); - - EXPECT_EQ(alignment, expectedAlignment); - } - - { - GraphAlignment alignment = decodeGraphAlignment(1, "0[2M]1[3M]1[1M]", &graph); - alignment.shrinkEnd(2); - GraphAlignment expectedAlignment = decodeGraphAlignment(1, "0[2M]1[2M2S]", &graph); - - EXPECT_EQ(alignment, expectedAlignment); - } - - { - GraphAlignment alignment = decodeGraphAlignment(1, "0[2M]1[3M]1[1M]", &graph); - alignment.shrinkEnd(5); - GraphAlignment expectedAlignment = decodeGraphAlignment(1, "0[1M5S]", &graph); - - EXPECT_EQ(alignment, expectedAlignment); - } - - { - GraphAlignment alignment = decodeGraphAlignment(1, "0[1S2M]1[3M]1[1M3S]", &graph); - alignment.shrinkEnd(4); - GraphAlignment expectedAlignment = decodeGraphAlignment(1, "0[1S2M7S]", &graph); - - EXPECT_EQ(alignment, expectedAlignment); - } -} - -TEST(ShrinkingGraphAlignmentEnds, ShrinkingByAlignmentLengthOrMore_ExceptionThrown) -{ - Graph graph = makeStrGraph("ATT", "CCG", "CTTT"); - - GraphAlignment alignment = decodeGraphAlignment(1, "0[2M]1[3M]1[1M]", &graph); - EXPECT_ANY_THROW(alignment.shrinkEnd(alignment.referenceLength())); - EXPECT_ANY_THROW(alignment.shrinkEnd(alignment.referenceLength() + 1)); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/GraphBuildersTest.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/tests/GraphBuildersTest.cpp deleted file mode 100644 index 36c1eab..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/GraphBuildersTest.cpp +++ /dev/null @@ -1,140 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphcore/GraphBuilders.hh" - -#include "gtest/gtest.h" - -using std::string; - -using namespace graphtools; - -TEST(CreatingGraphs, TypicalSequences_DeletionGraphCreated) -{ - const string left_flank = "AATT"; - const string deletion = "CCCC"; - const string right_flank = "GGGCC"; - Graph graph = makeDeletionGraph(left_flank, deletion, right_flank); - - EXPECT_EQ(3ul, graph.numNodes()); - EXPECT_EQ(left_flank, graph.nodeSeq(0)); - EXPECT_EQ(deletion, graph.nodeSeq(1)); - EXPECT_EQ(right_flank, graph.nodeSeq(2)); - EXPECT_TRUE(graph.hasEdge(0, 1)); - EXPECT_TRUE(graph.hasEdge(0, 2)); - EXPECT_TRUE(graph.hasEdge(1, 2)); -} - -TEST(CreatingGraphs, TypicalSequences_SwapGraphCreated) -{ - const string left_flank = "AATT"; - const string deletion = "CCCC"; - const string insertion = "TTTT"; - const string right_flank = "GGGCC"; - Graph graph = makeSwapGraph(left_flank, deletion, insertion, right_flank); - - EXPECT_EQ(4ul, graph.numNodes()); - EXPECT_EQ(left_flank, graph.nodeSeq(0)); - EXPECT_EQ(deletion, graph.nodeSeq(1)); - EXPECT_EQ(insertion, graph.nodeSeq(2)); - EXPECT_EQ(right_flank, graph.nodeSeq(3)); - EXPECT_TRUE(graph.hasEdge(0, 1)); - EXPECT_TRUE(graph.hasEdge(0, 2)); - EXPECT_TRUE(graph.hasEdge(1, 3)); - EXPECT_TRUE(graph.hasEdge(2, 3)); -} - -TEST(CreatingGraphs, TypicalSequences_DoubleSwapGraphCreated) -{ - const string left_flank = "AATT"; - const string deletion1 = "CCCC"; - const string insertion1 = "TTTT"; - const string middle = "CCCC"; - const string deletion2 = "AAAA"; - const string insertion2 = "GGGG"; - const string right_flank = "GGGCC"; - Graph graph = makeDoubleSwapGraph(left_flank, deletion1, insertion1, middle, deletion2, insertion2, right_flank); - - EXPECT_EQ(7ul, graph.numNodes()); - EXPECT_EQ(left_flank, graph.nodeSeq(0)); - EXPECT_EQ(deletion1, graph.nodeSeq(1)); - EXPECT_EQ(insertion1, graph.nodeSeq(2)); - EXPECT_EQ(middle, graph.nodeSeq(3)); - EXPECT_EQ(deletion2, graph.nodeSeq(4)); - EXPECT_EQ(insertion2, graph.nodeSeq(5)); - EXPECT_EQ(right_flank, graph.nodeSeq(6)); - EXPECT_TRUE(graph.hasEdge(0, 1)); - EXPECT_TRUE(graph.hasEdge(0, 2)); - EXPECT_TRUE(graph.hasEdge(1, 3)); - EXPECT_TRUE(graph.hasEdge(2, 3)); - EXPECT_TRUE(graph.hasEdge(3, 4)); - EXPECT_TRUE(graph.hasEdge(3, 5)); - EXPECT_TRUE(graph.hasEdge(4, 6)); - EXPECT_TRUE(graph.hasEdge(5, 6)); -} - -TEST(CreatingGraphs, TypicalSequences_LooplessStrGraphCreated) -{ - const string left_flank = "AATT"; - const string repeat_unit = "CGG"; - const string right_flank = "ATTT"; - const int32_t read_len = 10; - Graph graph = makeLooplessStrGraph(read_len, left_flank, repeat_unit, right_flank); - - ASSERT_EQ(6ul, graph.numNodes()); - EXPECT_EQ(left_flank, graph.nodeSeq(0)); - EXPECT_EQ(repeat_unit, graph.nodeSeq(1)); - EXPECT_EQ(repeat_unit, graph.nodeSeq(2)); - EXPECT_EQ(repeat_unit, graph.nodeSeq(3)); - EXPECT_EQ(repeat_unit, graph.nodeSeq(4)); - EXPECT_EQ(right_flank, graph.nodeSeq(5)); - - EXPECT_TRUE(graph.hasEdge(0, 5)); - - EXPECT_TRUE(graph.hasEdge(0, 1)); - EXPECT_TRUE(graph.hasEdge(1, 5)); - - EXPECT_TRUE(graph.hasEdge(1, 2)); - EXPECT_TRUE(graph.hasEdge(2, 5)); - - EXPECT_TRUE(graph.hasEdge(2, 3)); - EXPECT_TRUE(graph.hasEdge(3, 5)); - - EXPECT_TRUE(graph.hasEdge(3, 4)); - EXPECT_TRUE(graph.hasEdge(4, 5)); -} - -TEST(CreatingGraphs, TypicalSequences_StrGraphCreated) -{ - const string left_flank = "AATT"; - const string repeat_unit = "CGG"; - const string right_flank = "ATTT"; - Graph graph = makeStrGraph(left_flank, repeat_unit, right_flank); - - ASSERT_EQ(3ul, graph.numNodes()); - EXPECT_EQ(left_flank, graph.nodeSeq(0)); - EXPECT_EQ(repeat_unit, graph.nodeSeq(1)); - EXPECT_EQ(right_flank, graph.nodeSeq(2)); - - EXPECT_TRUE(graph.hasEdge(0, 1)); - EXPECT_TRUE(graph.hasEdge(0, 2)); - EXPECT_TRUE(graph.hasEdge(1, 1)); - EXPECT_TRUE(graph.hasEdge(1, 2)); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/GraphCoordinatesTest.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/tests/GraphCoordinatesTest.cpp deleted file mode 100644 index d1cb592..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/GraphCoordinatesTest.cpp +++ /dev/null @@ -1,127 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Peter Krusche -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphcore/GraphCoordinates.hh" - -#include "gtest/gtest.h" - -using namespace testing; -using namespace graphtools; - -class GraphCoordinatesTest : public Test -{ -public: - Graph graph{ 4 }; - - void SetUp() override - { - graph.setNodeName(0, "LF"); - graph.setNodeSeq(0, "AAAAAAAAAAA"); - - graph.setNodeName(1, "P1"); - graph.setNodeSeq(1, "TTTTTT"); - - graph.setNodeName(2, "Q1"); - graph.setNodeSeq(2, "GGGGGGGG"); - - graph.setNodeName(3, "RF"); - graph.setNodeSeq(3, "AAAAAAAAAAA"); - - /** - * - * LF RF - * | ^ - * | | - * *-> P1 -----* - * | | - * *-> Q1 -----* - */ - - graph.addEdge(0, 1); - graph.addEdge(0, 2); - graph.addEdge(1, 3); - graph.addEdge(2, 3); - } -}; - -TEST_F(GraphCoordinatesTest, CanonicalPositionLookup) -{ - GraphCoordinates coordinates(&graph); - - // LF has offset 0 - ASSERT_EQ(static_cast(6), coordinates.canonicalPos("LF", 6)); - ASSERT_EQ(static_cast(11 + 4), coordinates.canonicalPos("P1", 4)); - ASSERT_EQ(static_cast(11 + 6 + 3), coordinates.canonicalPos("Q1", 3)); - ASSERT_EQ(static_cast(11 + 6 + 8 + 2), coordinates.canonicalPos("RF", 2)); -} - -TEST_F(GraphCoordinatesTest, ReverseLookup) -{ - GraphCoordinates coordinates(&graph); - for (size_t j = 0; j < graph.nodeSeq(0).size(); ++j) // node 0 == LF - { - std::string n; - uint64_t offset = static_cast(-1); - coordinates.nodeAndOffset(j, n, offset); - ASSERT_EQ("LF", n); - ASSERT_EQ(static_cast(j), offset); - } - - for (size_t j = 0; j < graph.nodeSeq(1).size(); ++j) // node 1 == P1 - { - std::string n; - uint64_t offset = static_cast(-1); - coordinates.nodeAndOffset(11 + j, n, offset); - ASSERT_EQ("P1", n); - ASSERT_EQ(static_cast(j), offset); - } - for (size_t j = 0; j < graph.nodeSeq(2).size(); ++j) // node 2 == Q1 - { - std::string n; - uint64_t offset = static_cast(-1); - coordinates.nodeAndOffset(11 + 6 + j, n, offset); - ASSERT_EQ("Q1", n); - ASSERT_EQ(static_cast(j), offset); - } - for (size_t j = 0; j < graph.nodeSeq(3).size(); ++j) // node 3 == RF - { - std::string n; - uint64_t offset = static_cast(-1); - coordinates.nodeAndOffset(11 + 6 + 8 + j, n, offset); - ASSERT_EQ("RF", n); - ASSERT_EQ(static_cast(j), offset); - } -} - -TEST_F(GraphCoordinatesTest, DistanceComputation) -{ - GraphCoordinates coordinates(&graph); - - // both on LF - ASSERT_EQ(static_cast(5), coordinates.distance(10, 5)); - ASSERT_EQ(static_cast(5), coordinates.distance(5, 10)); - - // one on LF, one on neighbour (P1 or Q1) - ASSERT_EQ(static_cast(8), coordinates.distance(14, 6)); - ASSERT_EQ(static_cast(8), coordinates.distance(20, 6)); - - // LF -> RF should go via P1 because this is shorter - ASSERT_EQ(static_cast(9 + 6 + 4), coordinates.distance(2, 11 + 6 + 8 + 4)); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/GraphJsonTest.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/tests/GraphJsonTest.cpp deleted file mode 100644 index 387d3da..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/GraphJsonTest.cpp +++ /dev/null @@ -1,194 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Felix Schlesinger -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include - -#include "nlohmann/json.hpp" -#include "gtest/gtest.h" - -#include "graphcore/Graph.hh" -#include "graphcore/GraphBuilders.hh" -#include "graphio/GraphJson.hh" - -using std::string; - -TEST(GraphLoading, ValidGraph_Loaded) -{ - Json jGraph; - jGraph["nodes"] = { { { "name", "n1" }, { "sequence", "AATG" } }, - { { "name", "n2" }, { "sequence", "AA" } }, - { { "name", "n3" }, { "sequence", "TG" } } }; - jGraph["edges"] = { { { "from", "n1" }, { "to", "n2" } }, - { { "from", "n2" }, { "to", "n3" } }, - { { "from", "n2" }, { "to", "n2" } } }; - jGraph["graph_id"] = "TestGraph"; - - Graph const graph = parseGraph(jGraph); - - ASSERT_EQ("TestGraph", graph.graphId); - ASSERT_EQ(jGraph["nodes"].size(), graph.numNodes()); - ASSERT_EQ(jGraph["edges"].size(), graph.numEdges()); - for (size_t i = 0; i != graph.numNodes(); ++i) - { - ASSERT_EQ(jGraph["nodes"][i]["name"], graph.nodeName(i)); - ASSERT_EQ(jGraph["nodes"][i]["sequence"], graph.nodeSeq(i)); - } - ASSERT_TRUE(graph.hasEdge(0, 1)); - ASSERT_TRUE(graph.hasEdge(1, 2)); - ASSERT_TRUE(graph.hasEdge(1, 1)); - ASSERT_FALSE(graph.hasEdge(0, 0)); - ASSERT_FALSE(graph.hasEdge(0, 2)); -} - -TEST(GraphLoading, MissingSequence_Throws) -{ - Json jGraph; - jGraph["nodes"] = { - { { "name", "n1" } }, - }; - jGraph["edges"] = Json::array(); - - ASSERT_ANY_THROW(parseGraph(jGraph)); -} - -TEST(GraphLoading, EmptySequence_Throws) -{ - Json jGraph; - jGraph["nodes"] = { - { { "name", "n1" }, { "sequence", "" } }, - }; - jGraph["edges"] = Json::array(); - - ASSERT_ANY_THROW(parseGraph(jGraph)); -} - -TEST(GraphLoading, InvalidEdgeNode_Throws) -{ - Json jGraph; - jGraph["nodes"] = { - { { "name", "n1" }, { "sequence", "AATG" } }, - }; - jGraph["edges"] = { - { { "from", "n1" }, { "to", "n2" } }, - }; - - ASSERT_ANY_THROW(parseGraph(jGraph)); -} - -TEST(GraphLoading, BackwardsEdge_Throws) -{ - Json jGraph; - jGraph["nodes"] = { - { { "name", "n1" }, { "sequence", "AATG" } }, - { { "name", "n2" }, { "sequence", "AATG" } }, - }; - jGraph["edges"] = { - { { "from", "n2" }, { "to", "n1" } }, - }; - - ASSERT_ANY_THROW(parseGraph(jGraph)); -} - -/* - -TEST(ReferenceGenome, LoadGraphSequence_Success) -{ - Json jGraph; - jGraph["reference_genome"] = fastaPath; - jGraph["nodes"] = { { { "name", "n1" }, { "reference", "chr12:3-7" } } }; - jGraph["edges"] = Json::array(); - - Graph const graph = parseGraph(jGraph); - - ASSERT_EQ("AAGG", graph.nodeSeq(0)); -} - -*/ - -TEST(GraphLoading, MissingReference_Throws) -{ - Json jGraph; - jGraph["nodes"] = { { { "name", "n1" }, { "reference", "chr12:4-7" } } }; - jGraph["edges"] = Json::array(); - - ASSERT_ANY_THROW(parseGraph(jGraph)); -} - -TEST(GraphWriting, EmptyGraph_RoundTrip) -{ - Graph graph(0); - Json jGraph = graphToJson(graph); - Graph newGraph = parseGraph(jGraph); - - ASSERT_EQ((size_t)0, newGraph.numNodes()); -} - -TEST(GraphWriting, Graph_RoundTrip) -{ - Graph graph(2, "Small Graph"); - graph.setNodeName(0, "n0"); - graph.setNodeSeq(0, "AA"); - graph.setNodeName(1, "n1"); - graph.setNodeSeq(1, "TT"); - graph.addEdge(0, 1); - graph.addEdge(1, 1); - graph.addLabelToEdge(1, 1, "foo"); - - Json jGraph = graphToJson(graph); - Graph newGraph = parseGraph(jGraph); - - ASSERT_EQ("Small Graph", graph.graphId); - ASSERT_EQ(graph.numNodes(), newGraph.numNodes()); - ASSERT_EQ(graph.numEdges(), newGraph.numEdges()); - for (size_t i = 0; i != graph.numNodes(); ++i) - { - ASSERT_EQ(graph.nodeName(i), newGraph.nodeName(i)); - ASSERT_EQ(graph.nodeSeq(i), newGraph.nodeSeq(i)); - } - ASSERT_TRUE(newGraph.hasEdge(0, 1)); - ASSERT_TRUE(newGraph.hasEdge(1, 1)); - ASSERT_FALSE(newGraph.hasEdge(0, 0)); - ASSERT_EQ(graph.edgeLabels(1, 1), newGraph.edgeLabels(1, 1)); -} - -/* - -TEST_F(ReferenceGenome, LoadGraphMapping_Success) -{ - Json jGraph; - jGraph["reference_genome"] = fastaPath; - jGraph["nodes"] - = { { { "name", "n1" }, { "reference", "chr12:4-7" } }, { { "name", "n2" }, { "sequence", "TCGA" } } }; - jGraph["edges"] = Json::array(); - - Graph const graph = parseGraph(jGraph); - GraphReferenceMapping const refmap = parseReferenceMapping(jGraph, graph); - - auto const pos = refmap.map(0, 2); - ASSERT_TRUE(pos); - ASSERT_EQ("chr12", pos->contig); - ASSERT_EQ(6, pos->start); - - ASSERT_FALSE(refmap.map(1, 2)); // Node without mapping - ASSERT_ANY_THROW(refmap.map(0, 3)); // Position outside node - ASSERT_ANY_THROW(refmap.map(2, 0)); // Nonexistent node -} - -*/ diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/GraphOperationsTest.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/tests/GraphOperationsTest.cpp deleted file mode 100644 index c8cec14..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/GraphOperationsTest.cpp +++ /dev/null @@ -1,79 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphcore/GraphOperations.hh" -#include "graphcore/Graph.hh" -#include "graphcore/GraphBuilders.hh" - -#include "gtest/gtest.h" - -using std::set; -using std::string; -using std::vector; - -using namespace graphtools; - -TEST(GraphReversal, SwapGraph_Reversed) -{ - Graph graph = makeSwapGraph("CCCC", "AAAA", "GGGG", "TTTT"); - ASSERT_EQ(4ul, graph.numNodes()); - auto reversed_graph = reverseGraph(graph, false); - ASSERT_EQ(4ul, reversed_graph.numNodes()); - ASSERT_EQ("TTTT", reversed_graph.nodeSeq(0)); - ASSERT_EQ("GGGG", reversed_graph.nodeSeq(1)); - ASSERT_EQ("AAAA", reversed_graph.nodeSeq(2)); - ASSERT_EQ("CCCC", reversed_graph.nodeSeq(3)); - ASSERT_EQ((set{ 1, 2 }), reversed_graph.successors(0)); - ASSERT_EQ((set{ 3 }), reversed_graph.successors(1)); - ASSERT_EQ((set{ 3 }), reversed_graph.successors(2)); - ASSERT_TRUE(reversed_graph.successors(3).empty()); -} - -TEST(GraphReversal, SwapGraph_SequenceReversed) -{ - Graph graph = makeSwapGraph("ACCC", "ATAA", "GGTG", "TTTA"); - ASSERT_EQ(4ul, graph.numNodes()); - auto reversed_graph = reverseGraph(graph, false); - ASSERT_EQ(4ul, reversed_graph.numNodes()); - ASSERT_EQ("ATTT", reversed_graph.nodeSeq(0)); - ASSERT_EQ("GTGG", reversed_graph.nodeSeq(1)); - ASSERT_EQ("AATA", reversed_graph.nodeSeq(2)); - ASSERT_EQ("CCCA", reversed_graph.nodeSeq(3)); - ASSERT_EQ((set{ 1, 2 }), reversed_graph.successors(0)); - ASSERT_EQ((set{ 3 }), reversed_graph.successors(1)); - ASSERT_EQ((set{ 3 }), reversed_graph.successors(2)); - ASSERT_TRUE(reversed_graph.successors(3).empty()); -} - -TEST(GraphReversal, SwapGraph_SequenceReverseComplemented) -{ - Graph graph = makeSwapGraph("ACCC", "ATAA", "GGTG", "TTTA"); - ASSERT_EQ(4ul, graph.numNodes()); - auto reversed_graph = reverseGraph(graph, true); - ASSERT_EQ(4ul, reversed_graph.numNodes()); - ASSERT_EQ("TAAA", reversed_graph.nodeSeq(0)); - ASSERT_EQ("CACC", reversed_graph.nodeSeq(1)); - ASSERT_EQ("TTAT", reversed_graph.nodeSeq(2)); - ASSERT_EQ("GGGT", reversed_graph.nodeSeq(3)); - ASSERT_EQ((set{ 1, 2 }), reversed_graph.successors(0)); - ASSERT_EQ((set{ 3 }), reversed_graph.successors(1)); - ASSERT_EQ((set{ 3 }), reversed_graph.successors(2)); - ASSERT_TRUE(reversed_graph.successors(3).empty()); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/GraphReferenceMappingTest.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/tests/GraphReferenceMappingTest.cpp deleted file mode 100644 index 9cd113e..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/GraphReferenceMappingTest.cpp +++ /dev/null @@ -1,74 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Felix Schlesinger -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphcore/GraphReferenceMapping.hh" -#include "graphcore/GraphBuilders.hh" - -#include - -#include "gtest/gtest.h" - -#include "graphcore/Graph.hh" -#include "graphcore/Path.hh" - -using namespace graphtools; - -class GraphMapping : public testing::Test -{ -public: - GraphMapping() - : graph(makeSwapGraph("AAAA", "C", "T", "GGGG")) - , mapping(&graph) - { - mapping.addMapping(0, ReferenceInterval("chr1", 10, 14)); - mapping.addMapping(2, ReferenceInterval("chr1", 15, 16)); - mapping.addMapping(3, ReferenceInterval("chr1", 16, 20)); - } - - Graph graph; - GraphReferenceMapping mapping; -}; -TEST_F(GraphMapping, MapNodePosition_Success) -{ - ASSERT_EQ(ReferenceInterval::makePosition("chr1", 10), mapping.map(0, 0)); - ASSERT_EQ(ReferenceInterval::makePosition("chr1", 13), mapping.map(0, 3)); - ASSERT_EQ(ReferenceInterval::makePosition("chr1", 15), mapping.map(2, 0)); -} -TEST_F(GraphMapping, UnmappedNode_ReturnEmpty) { ASSERT_FALSE(mapping.map(1, 0)); } -TEST_F(GraphMapping, MapInvalidPos_Throws) -{ - ASSERT_ANY_THROW(mapping.map(2, 1)); // Outside Node - ASSERT_ANY_THROW(mapping.map(5, 0)); // Invalid node -} -TEST_F(GraphMapping, MapPath_StartingNode) -{ - auto const map = mapping.map(Path(&graph, 1, { 0, 1, 3 }, 4)); - ASSERT_EQ(ReferenceInterval::makePosition("chr1", 11), map); -} -TEST_F(GraphMapping, MapPath_ExtendingNode) -{ - auto const map = mapping.map(Path(&graph, 0, { 1, 3 }, 4)); - ASSERT_EQ(ReferenceInterval::makePosition("chr1", 16), map); -} -TEST_F(GraphMapping, UnmappedPath_ReturnEmpty) -{ - auto const map = mapping.map(Path(&graph, 0, { 1 }, 1)); - ASSERT_FALSE(map); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/GraphTest.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/tests/GraphTest.cpp deleted file mode 100644 index 680dc01..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/GraphTest.cpp +++ /dev/null @@ -1,176 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphcore/Graph.hh" - -#include "gtest/gtest.h" - -using std::set; -using std::string; -using std::vector; - -using namespace graphtools; - -TEST(GraphConstruction, TypicalNodeCount_GraphConstructed) -{ - Graph graph(3); - ASSERT_EQ(3ul, graph.numNodes()); -} - -TEST(NodeNameManipulation, TypicalNode_NodeNameSet) -{ - Graph graph(3); - graph.setNodeName(1, "LF"); - ASSERT_EQ("LF", graph.nodeName(1)); -} - -TEST(NodeNameManipulation, NonexistingNode_ExceptionRaised) -{ - Graph graph(1); - ASSERT_ANY_THROW(graph.setNodeName(1, "LF")); - ASSERT_ANY_THROW(graph.nodeName(1)); -} - -TEST(NodeSequenceManipulation, TypicalSequence_SequenceSet) -{ - Graph graph(3); - graph.setNodeSeq(1, "ATT"); - EXPECT_EQ("ATT", graph.nodeSeq(1)); -} - -TEST(NodeSequenceManipulation, DegenerateSequence_SequenceExpansionObtained) -{ - Graph graph(3); - graph.setNodeSeq(1, "WC"); - vector expected_expansion = { "AC", "TC" }; - EXPECT_EQ(expected_expansion, graph.nodeSeqExpansion(1)); -} - -TEST(NodeSequenceManipulation, NonexistingNode_ExceptionRaised) -{ - Graph graph(3); - EXPECT_ANY_THROW(graph.setNodeSeq(4, "ATT")); - EXPECT_ANY_THROW(graph.nodeSeq(4)); - EXPECT_ANY_THROW(graph.nodeSeqExpansion(4)); -} - -TEST(NodeSequenceManipulation, EmptySequence_ExceptionRaised) -{ - Graph graph(3); - EXPECT_ANY_THROW(graph.setNodeSeq(1, "")); -} - -TEST(AddingEdges, TypicalEdge_EdgeAdded) -{ - Graph graph(3); - graph.addEdge(0, 1); - graph.addEdge(0, 0); - EXPECT_TRUE(graph.hasEdge(0, 1)); - EXPECT_TRUE(graph.hasEdge(0, 0)); -} - -TEST(AddingEdges, EdgeBreakingTopologicalOrder_ExceptionRaised) -{ - Graph graph(3); - EXPECT_ANY_THROW(graph.addEdge(2, 1)); -} - -TEST(AddingEdges, EdgesBetweenNonexistingNodes_ExceptionRaised) -{ - Graph graph(4); - EXPECT_ANY_THROW(graph.addEdge(-1, 2)); - EXPECT_ANY_THROW(graph.addEdge(1, 4)); - EXPECT_ANY_THROW(graph.addEdge(4, 5)); -} - -TEST(AddingEdges, EdgesThatAlreadyExist_ExceptionRaised) -{ - Graph graph(4); - graph.addEdge(1, 2); - EXPECT_ANY_THROW(graph.addEdge(1, 2)); -} - -TEST(CheckingIfEdgesExist, EdgesBetweenNonexistingNodes_ExceptionRaised) -{ - Graph graph(4); - EXPECT_ANY_THROW(graph.hasEdge(-1, 2)); - EXPECT_ANY_THROW(graph.hasEdge(1, 4)); - EXPECT_ANY_THROW(graph.hasEdge(4, 5)); -} - -TEST(EdgeLabelManipulation, TypicalEdges_EdgesLabeled) -{ - Graph graph(4); - graph.addEdge(0, 2); - graph.addLabelToEdge(0, 2, "ref"); - graph.addLabelToEdge(0, 2, "alt"); - Labels expected_labels = { "ref", "alt" }; - ASSERT_EQ(expected_labels, graph.edgeLabels(0, 2)); -} - -TEST(EdgeLabelManipulation, NonexistingEdges_ExceptionRaised) -{ - Graph graph(4); - EXPECT_ANY_THROW(graph.addLabelToEdge(0, 1, "ref")); - EXPECT_ANY_THROW(graph.addLabelToEdge(0, 4, "ref")); - EXPECT_ANY_THROW(graph.edgeLabels(0, 1)); -} - -TEST(GettingNodeNeighbors, TypicalNode_SuccessorsFound) -{ - Graph graph(4); - graph.addEdge(0, 1); - graph.addEdge(0, 2); - graph.addEdge(0, 3); - graph.addEdge(2, 3); - - const set expected_successors = { 1, 2, 3 }; - ASSERT_EQ(expected_successors, graph.successors(0)); - ASSERT_TRUE(graph.successors(1).empty()); -} - -TEST(GettingNodeNeighbors, LoopAtNode_SuccessorsFound) -{ - Graph graph(4); - graph.addEdge(0, 0); - graph.addEdge(0, 1); - - const set expected_predecessors = { 0, 1 }; - ASSERT_EQ(expected_predecessors, graph.successors(0)); -} - -TEST(GettingNodeNeighbors, TypicalNode_PredecessorsFound) -{ - Graph graph(4); - graph.addEdge(0, 1); - graph.addEdge(0, 2); - graph.addEdge(0, 3); - graph.addEdge(2, 3); - - const set expected_predecessors = { 0, 2 }; - ASSERT_EQ(expected_predecessors, graph.predecessors(3)); -} - -TEST(GettingNodeNeighbors, NeighborsOfNonexistingNode_ExceptionRaised) -{ - Graph graph(4); - EXPECT_ANY_THROW(graph.successors(4)); - EXPECT_ANY_THROW(graph.predecessors(-1)); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/IntervalBufferTest.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/tests/IntervalBufferTest.cpp deleted file mode 100644 index 62f9026..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/IntervalBufferTest.cpp +++ /dev/null @@ -1,249 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Peter Krusche -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphutils/IntervalBuffer.hh" -#include "gtest/gtest.h" - -#include -#include -#include - -using namespace intervals; - -TEST(IntervalBuffer, TestIntervalBuffer) -{ - IntervalBuffer ib; - - ib.addInterval(10, 20, 0); - ib.addInterval(12, 30, 0); - ib.addInterval(10, 30, 1); - ib.addInterval(32, 35, 1); - ib.addInterval(36, 37, 1); - ib.addInterval(38, 40, 1); - ib.addInterval(42, 45, 1); - - IntervalBuffer ib2 = ib; - - ASSERT_TRUE(ib2.isCovered(15, 16, 0)); - ASSERT_TRUE(ib2.isCovered(15, 21, 0)); - ASSERT_TRUE(ib2.isCovered(11, 21, 0)); - ASSERT_TRUE(!ib2.isCovered(11, 31, 0)); - ASSERT_TRUE(!ib2.isCovered(8, 15, 0)); - ASSERT_TRUE(!ib2.isCovered(8, 9, 0)); - - ASSERT_TRUE(ib2.isCovered(15, 16, 1)); - ASSERT_TRUE(ib2.isCovered(32, 39, 1)); - ASSERT_TRUE(!ib2.isCovered(32, 43, 1)); - - ib.advance(30); - - ASSERT_TRUE(!ib.isCovered(10, 11, 0)); - ASSERT_TRUE(!ib.isCovered(15, 16, 0)); - ASSERT_TRUE(!ib.isCovered(15, 21, 0)); - ASSERT_TRUE(!ib.isCovered(11, 21, 0)); - ASSERT_TRUE(ib.isCovered(30, 30, 0)); - ASSERT_TRUE(!ib.isCovered(8, 15, 0)); - ASSERT_TRUE(!ib.isCovered(8, 9, 0)); - - ASSERT_TRUE(!ib.isCovered(15, 16, 1)); - ASSERT_TRUE(ib.isCovered(32, 39, 1)); - ASSERT_TRUE(!ib.isCovered(32, 43, 1)); -} - -TEST(IntervalBuffer, TestIntervalBufferRandom) -{ - static const int count = 2048; - static const int icount = 20; - static const int tcount = 100; - - for (int k = 0; k < tcount; ++k) - { - bool ivs[count]; - - std::vector> ivlist; - - for (int i = 0; i < count; ++i) - { - ivs[i] = false; - } - - for (int i = 0; i < icount; ++i) - { - int64_t start = rand() % count; - int64_t end = std::min(start + rand() % 100, (int64_t)count - 1); - ivlist.push_back(std::pair(start, end)); - for (int j = (int)start; j <= end; ++j) - { - ivs[j] = true; - } - } - - struct random_end_less - { - inline bool operator()(const std::pair& p, const std::pair& q) const - { - return p.first < q.first; - } - }; - - std::sort(ivlist.begin(), ivlist.end(), random_end_less()); - - IntervalBuffer ib; - - for (auto const& p : ivlist) - { - ib.addInterval(p.first, p.second, 2); - } - - for (int i = 0; i < count; ++i) - { - int start = rand() % count; - int end = std::min(start + rand() % 50, (int)count - 1); - - bool is_covered = true; - for (int j = start; j <= end; ++j) - { - if (!ivs[j]) - { - is_covered = false; - break; - } - } - - if (is_covered != ib.isCovered(start, end, 2)) - { - std::cerr << "(c) Interval " << start << "-" << end << ": ivs say " << is_covered << " ib says " - << ib.isCovered(start, end, 2) << "\n"; - } - - ASSERT_EQ(is_covered, ib.isCovered(start, end, 2)); - } - - // check overlaps - for (int i = 0; i < count; ++i) - { - int start = rand() % count; - int end = std::min(start + rand() % 100, (int)count - 1); - - bool is_covered = false; - for (int j = start; j <= end; ++j) - { - if (ivs[j]) - { - is_covered = true; - break; - } - } - - if (is_covered != ib.hasOverlap(start, end, 2)) - { - std::cerr << "(o) Interval " << start << "-" << end << ": ivs say " << is_covered << " ib says " - << ib.hasOverlap(start, end, 2) << "\n"; - } - - ASSERT_EQ(is_covered, ib.hasOverlap(start, end, 2)); - } - -#ifdef _DEBUG - // remember for debugging - IntervalBuffer ib_before = ib; -#endif - ib.advance(count / 2); - - for (int i = 0; i < count / 2; ++i) - { - ivs[i] = false; - } - - for (int i = 0; i < count; ++i) - { - int start = rand() % count; - int end = std::min(start + rand() % 50, (int)count - 1); - - bool is_covered = true; - for (int j = start; j <= end; ++j) - { - if (!ivs[j]) - { - is_covered = false; - break; - } - } - - if (is_covered != ib.isCovered(start, end, 2)) - { - std::cerr << "(c) Interval " << start << "-" << end << ": ivs say " << is_covered << " ib says " - << ib.isCovered(start, end, 2) << "\n"; - } - - ASSERT_EQ(is_covered, ib.isCovered(start, end, 2)); - } - - // check overlaps - for (int i = 0; i < count; ++i) - { - int start = rand() % count; - int end = std::min(start + rand() % 100, (int)count - 1); - - bool is_covered = false; - for (int j = start; j <= end; ++j) - { - if (ivs[j]) - { - is_covered = true; - break; - } - } - - if (is_covered != ib.hasOverlap(start, end, 2)) - { - std::cerr << "(o) Interval " << start << "-" << end << ": ivs say " << is_covered << " ib says " - << ib.hasOverlap(start, end, 2) << "\n"; - } - - ASSERT_EQ(is_covered, ib.hasOverlap(start, end, 2)); - } - } -} - -TEST(IntervalBuffer, TestIntervalBufferIvmerge) -{ - IntervalBuffer ib; - - ib.addInterval(10, 20, 1); - ib.addInterval(12, 30, 1); - ib.addInterval(10, 30, 1); - ib.addInterval(32, 35, 1); - ib.addInterval(36, 37, 1); - ib.addInterval(38, 40, 1); - ib.addInterval(42, 45, 1); - - const std::list> expected = { { 10, 30 }, { 32, 40 }, { 42, 45 } }; - auto ivlist = ib.getIntervals(1); - ASSERT_EQ(expected.size(), ivlist.size()); - auto it1 = expected.cbegin(), it2 = ivlist.cbegin(); - while (it1 != expected.cend() && it2 != ivlist.cend()) - { - ASSERT_EQ(it1->first, it2->first); - ASSERT_EQ(it1->second, it2->second); - ++it1; - ++it2; - } -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/IntervalListTest.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/tests/IntervalListTest.cpp deleted file mode 100644 index 30e7d6e..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/IntervalListTest.cpp +++ /dev/null @@ -1,250 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Peter Krusche -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphutils/IntervalList.hh" -#include "gtest/gtest.h" - -#include -#include -#include -#include - -using namespace intervals; - -template void listcmp(std::list<_t> expected, std::list<_t> actual) -{ - auto i1 = expected.begin(); - auto i2 = actual.begin(); - size_t count = 0; - while (i1 != expected.end() && i2 != actual.end()) - { - ASSERT_EQ(*i1, *i2); - ++count; - ++i1; - ++i2; - } - ASSERT_EQ(count, expected.size()); -} - -template <> void listcmp(std::list> expected, std::list> actual) -{ - auto i1 = expected.begin(); - auto i2 = actual.begin(); - size_t count = 0; - while (i1 != expected.end() && i2 != actual.end()) - { - ASSERT_EQ(i1->first, i2->first); - ASSERT_EQ(i1->second, i2->second); - ++count; - ++i1; - ++i2; - } - ASSERT_EQ(count, expected.size()); -} - -struct ivcount : public interval -{ - ivcount() - : interval() - , count(0) - { - } - ivcount(int64_t _start, int64_t _end, int _count) - : interval(_start, _end) - , count(_count) - { - } - virtual void merge(interval const& rhs) - { - interval::merge(rhs); - count += (dynamic_cast(rhs)).count; - } - - bool operator==(const ivcount& other) const - { - return start == other.start && end == other.end && count == other.count; - } - - bool operator!=(const ivcount& other) const { return !(*this == other); } - - int count; -}; - -std::ostream& operator<<(std::ostream& o, ivcount const& x) -{ - o << x.start << "-" << x.end << ":" << x.count; - return o; -} - -TEST(IntervalList, TestIntervalList) -{ - IntervalList ivl; - - ivl.add(ivcount(10, 20, 1)); - ivl.add(ivcount(12, 30, 1)); - ivl.add(ivcount(32, 35, 1)); - ivl.add(ivcount(36, 37, 1)); - ivl.add(ivcount(38, 40, 1)); - ivl.add(ivcount(42, 45, 1)); - - std::list expected = { ivcount(10, 30, 2), ivcount(32, 40, 3), ivcount(42, 45, 1) }; - - listcmp(expected, ivl.getIntervals()); - - ASSERT_EQ(ivl.query(11, 12).count, 2); - ASSERT_EQ(ivl.query(31, 37).count, 3); - ASSERT_EQ(ivl.query(31, 39).count, 3); - ASSERT_EQ(ivl.query(42, 44).count, 1); - ASSERT_EQ(ivl.query(41, 41).count, 0); - ASSERT_EQ(ivl.query(45, 45).count, 1); - - ivl.keep_only(31, 44); - ASSERT_EQ(ivl.query(11, 12).count, 0); - ASSERT_EQ(ivl.query(31, 37).count, 3); - ASSERT_EQ(ivl.query(31, 39).count, 3); - ASSERT_EQ(ivl.query(42, 44).count, 1); - ASSERT_EQ(ivl.query(41, 41).count, 0); - ASSERT_EQ(ivl.query(45, 45).count, 0); - - expected = { ivcount(32, 40, 3), ivcount(42, 44, 1) }; - - listcmp(expected, ivl.getIntervals()); -} - -TEST(IntervalList, TestIntervalList2) -{ - struct ivlist : public interval - { - ivlist() - : interval() - { - } - ivlist(int64_t _start, int64_t _end) - : interval(_start, _end) - { - contained_ivs.push_back(std::pair(_start, _end)); - } - virtual void merge(interval const& rhs) - { - contained_ivs.insert( - contained_ivs.end(), (dynamic_cast(rhs)).contained_ivs.begin(), - (dynamic_cast(rhs)).contained_ivs.end()); - interval::merge(rhs); - } - - std::list> contained_ivs; - }; - - IntervalList ivl; - - ivl.add(ivlist(10, 20)); - ivl.add(ivlist(12, 30)); - ivl.add(ivlist(32, 35)); - ivl.add(ivlist(36, 37)); - ivl.add(ivlist(38, 40)); - ivl.add(ivlist(42, 45)); - - std::list> expected, actual; - - expected = { std::pair{ 10, 20 }, std::pair{ 12, 30 } }; - actual = ivl.query(11, 12).contained_ivs; - listcmp(expected, actual); - - expected = { std::pair{ 32, 35 }, std::pair{ 36, 37 }, - std::pair{ 38, 40 } }; - actual = ivl.query(31, 37).contained_ivs; - listcmp(expected, actual); -} - -TEST(IntervalList, TestIntervalListRandom) -{ - static const int count = 2048; - static const int icount = 20; - static const int tcount = 300; - - for (int k = 0; k < tcount; ++k) - { - IntervalList ivl; - bool ivs[count]; - std::fill(std::begin(ivs), std::end(ivs), false); - - for (int i = 0; i < icount; ++i) - { - int64_t start = rand() % count; - int64_t end = std::min(start + rand() % 100, (int64_t)count - 1); - std::fill(ivs + start, ivs + end + 1, true); - ivl.add(interval(start, end)); - } - - int64_t iv_start = 0; - int64_t iv_end = count - 1; -#ifdef _DEBUG - // remember for debugging - IntervalList ivl_before = ivl; -#endif - if (k % 3 == 0) - { - iv_end = std::max(0, (rand() % count) - 1); - ivl.remove_to(iv_end); - std::fill(ivs, ivs + iv_end + 1, false); - } - else if (k % 3 == 1) - { - iv_start = std::max(0, (rand() % count) - 1); - ivl.remove_from(iv_start); - std::fill(ivs + iv_start, std::end(ivs), false); - } - - for (int i = 0; i < count; ++i) - { - int64_t start = rand() % count; - int64_t end = std::min(start + rand() % 100, (int64_t)count - 1); - bool iv_ovl = std::any_of(ivs + start, ivs + end + 1, [](bool b) { return b; }); - interval iv = ivl.query(start, end); - bool ivl_ovl = iv.start >= 0 && iv.end >= 0; - if (iv_ovl != ivl_ovl) - { - std::cerr << "IntervalList random test failed" << std::endl; - std::cerr << "Test array:" << std::endl; - std::string ic_str; - ic_str.resize(count); - for (int ic = 0; ic < count; ++ic) - { - if (ivs[ic]) - { - ic_str[ic] = '*'; - } - else - { - ic_str[ic] = '-'; - } - } - std::cerr << ic_str << std::endl; - auto all_intervals = ivl.getIntervals(); - std::cerr << "Intervals: " << all_intervals.size() << std::endl; - for (auto const& iv : all_intervals) - { - std::cerr << "[" << iv.start << ", " << iv.end << "]" << std::endl; - } - } - ASSERT_EQ(iv_ovl, ivl_ovl); - } - } -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/KmerEncodingTest.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/tests/KmerEncodingTest.cpp deleted file mode 100644 index 8f20ce4..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/KmerEncodingTest.cpp +++ /dev/null @@ -1,36 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Chris Saunders -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphutils/KmerEncoding.hh" - -#include "gtest/gtest.h" - -using namespace graphtools; - -TEST(TwoBitKmerEncoder, 1TwoBitKmerEncoder) -{ - TwoBitKmerEncoder ke(4); - - ASSERT_EQ(ke.decode(ke.encode("TAAG")), "TAAG"); - ASSERT_EQ(ke.decode(ke.encode("CTAA")), "CTAA"); - - ASSERT_EQ(ke.encode(ke.decode(12)), 12); - ASSERT_EQ(ke.encode(ke.decode(0)), 0); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/KmerIndexOperationsTest.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/tests/KmerIndexOperationsTest.cpp deleted file mode 100644 index 3380192..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/KmerIndexOperationsTest.cpp +++ /dev/null @@ -1,39 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphalign/KmerIndexOperations.hh" - -#include "gtest/gtest.h" - -#include "graphcore/Graph.hh" -#include "graphcore/GraphBuilders.hh" -#include "graphutils/SequenceOperations.hh" - -using namespace graphtools; - -TEST(StrandClassification, TypicalSequence_StrandDetermined) -{ - Graph graph = makeStrGraph("AAAACC", "CCG", "ATTT"); - KmerIndex kmer_index(graph, 3); - EXPECT_TRUE(checkIfForwardOriented(kmer_index, "CCGCCGCCGCCG")); - EXPECT_FALSE(checkIfForwardOriented(kmer_index, reverseComplement("CCGCCGCCGCCG"))); - EXPECT_TRUE(checkIfForwardOriented(kmer_index, "CCGACGCCTCCG")); - EXPECT_FALSE(checkIfForwardOriented(kmer_index, reverseComplement("CCGACGCCTCCG"))); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/KmerIndexTest.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/tests/KmerIndexTest.cpp deleted file mode 100644 index e7c2b22..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/KmerIndexTest.cpp +++ /dev/null @@ -1,142 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko , -// Peter Krusche -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphalign/KmerIndex.hh" - -#include - -#include "gtest/gtest.h" - -#include "graphcore/GraphBuilders.hh" -#include "graphcore/Path.hh" - -using std::list; -using std::string; -using std::unordered_set; - -using namespace graphtools; - -TEST(KmerIndexInitialization, 1mers_IndexCreated) -{ - Graph graph = makeDeletionGraph("AC", "GG", "CAG"); - - const int32_t kmer_size = 1; - KmerIndex kmer_index(graph, kmer_size); - - const std::vector expected_a_paths = { Path(&graph, 0, { 0 }, 1), Path(&graph, 1, { 2 }, 2) }; - const std::vector expected_c_paths = { Path(&graph, 1, { 0 }, 2), Path(&graph, 0, { 2 }, 1) }; - const std::vector expected_g_paths - = { Path(&graph, 0, { 1 }, 1), Path(&graph, 1, { 1 }, 2), Path(&graph, 2, { 2 }, 3) }; - - ASSERT_EQ(kmer_index.getPaths("A"), expected_a_paths); - ASSERT_EQ(kmer_index.getPaths("C"), expected_c_paths); - ASSERT_EQ(kmer_index.getPaths("G"), expected_g_paths); -} - -TEST(KmerIndexInitialization, 2mers_IndexCreated) -{ - Graph graph = makeDeletionGraph("AK", "GG", "CAG"); - const int32_t kmer_size = 2; - KmerIndex kmer_index(graph, kmer_size); - - const std::vector expected_ag_paths = { Path(&graph, 0, { 0 }, 2), Path(&graph, 1, { 2 }, 3) }; - const std::vector expected_at_paths = { Path(&graph, 0, { 0 }, 2) }; - - const std::vector expected_gg_paths = { Path(&graph, 1, { 0, 1 }, 1), Path(&graph, 0, { 1 }, 2) }; - const std::vector expected_tg_paths = { Path(&graph, 1, { 0, 1 }, 1) }; - - const std::vector expected_gc_paths = { Path(&graph, 1, { 0, 2 }, 1), Path(&graph, 1, { 1, 2 }, 1) }; - const std::vector expected_tc_paths = { Path(&graph, 1, { 0, 2 }, 1) }; - - const std::vector expected_ca_paths = { Path(&graph, 0, { 2 }, 2) }; - - ASSERT_EQ(kmer_index.getPaths("AG"), expected_ag_paths); - ASSERT_EQ(kmer_index.getPaths("AT"), expected_at_paths); - ASSERT_EQ(kmer_index.getPaths("GG"), expected_gg_paths); - ASSERT_EQ(kmer_index.getPaths("TG"), expected_tg_paths); - ASSERT_EQ(kmer_index.getPaths("GC"), expected_gc_paths); - ASSERT_EQ(kmer_index.getPaths("TC"), expected_tc_paths); - ASSERT_EQ(kmer_index.getPaths("CA"), expected_ca_paths); -} - -TEST(KmerExtraction, TypicalIndex_KmersExtracted) -{ - Graph graph = makeDeletionGraph("AC", "GG", "CAG"); - const int32_t kmer_size = 2; - KmerIndex kmer_index(graph, kmer_size); - const unordered_set expected_kmers = { "AC", "CG", "CC", "GG", "GC", "CA", "AG" }; - ASSERT_EQ(expected_kmers, kmer_index.kmers()); -} - -TEST(PathExtraction, TypicalIndex_PathsExtracted) -{ - Graph graph = makeDoubleSwapGraph("AAA", "TTT", "CCC", "AAA", "TTT", "AAA", "TTT"); - const int32_t kmer_size = 4; - KmerIndex kmer_index(graph, kmer_size); - const std::vector paths = kmer_index.getPaths("AATT"); - const std::vector expected_paths - = { Path(&graph, 1, { 0, 1 }, 2), Path(&graph, 1, { 3, 4 }, 2), Path(&graph, 1, { 5, 6 }, 2) }; - ASSERT_EQ(expected_paths, paths); -} - -TEST(CheckingIfKmersArePresent, TypicalKmers_CheckPerformed) -{ - Graph graph = makeDoubleSwapGraph("AAA", "TTT", "CCC", "AAA", "TTT", "AAA", "TTT"); - const int32_t kmer_size = 6; - KmerIndex kmer_index(graph, kmer_size); - EXPECT_TRUE(kmer_index.contains("AAATTT")); - EXPECT_FALSE(kmer_index.contains("AAATTG")); - EXPECT_FALSE(kmer_index.contains("AAA")); -} - -TEST(CountingNumberOfPathsAssociatedWithKmer, TypicalKmers_PathCountObtained) -{ - Graph graph = makeDoubleSwapGraph("AAA", "TTT", "CCC", "AAA", "TTT", "AAA", "TTT"); - { - const int32_t kmer_size = 6; - KmerIndex kmer_index(graph, kmer_size); - EXPECT_EQ(3u, kmer_index.numPaths("AAATTT")); - EXPECT_EQ(0u, kmer_index.numPaths("AAATTG")); - EXPECT_EQ(1u, kmer_index.numPaths("TTTTTT")); - } - { - const int32_t kmer_size = 1; - KmerIndex kmer_index(graph, kmer_size); - EXPECT_EQ(9u, kmer_index.numPaths("A")); - EXPECT_EQ(3u, kmer_index.numPaths("C")); - EXPECT_EQ(9u, kmer_index.numPaths("T")); - EXPECT_EQ(0u, kmer_index.numPaths("G")); - } -} - -TEST(UniqueKmerCounting, TypicalIndex_UniqueKmersCounted) -{ - Graph graph = makeDeletionGraph("AC", "GG", "ACG"); - - const int32_t kmer_size = 3; - KmerIndex kmer_index(graph, kmer_size); - - EXPECT_EQ(1u, kmer_index.numUniqueKmersOverlappingEdge(0, 1)); - EXPECT_EQ(2u, kmer_index.numUniqueKmersOverlappingEdge(1, 2)); - - EXPECT_EQ(3u, kmer_index.numUniqueKmersOverlappingNode(0)); - EXPECT_EQ(4u, kmer_index.numUniqueKmersOverlappingNode(2)); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/LinearAlignmentOperationsTest.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/tests/LinearAlignmentOperationsTest.cpp deleted file mode 100644 index c1d71c4..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/LinearAlignmentOperationsTest.cpp +++ /dev/null @@ -1,232 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphalign/LinearAlignmentOperations.hh" - -#include "gtest/gtest.h" - -#include - -using namespace graphtools; - -using std::list; -using std::make_pair; -using std::string; - -TEST(CheckingConsistencyOfAlignments, ConsistentAlignment_CheckPassed) -{ - // ref: CCCTTCCTTAATT---T---------- - // ||| || || | - // query: ---TTCGNN--TTGGGTCCCCCCCCCC - string reference = "CCCTTCCTTAATTT"; - string query = "TTCGNNTTGGGTCCCCCCCCCC"; - - Alignment alignment(3, "3M1X2N2D2M3I1M10S"); - - EXPECT_TRUE(checkConsistency(alignment, reference, query)); -} - -TEST(CheckingConsistencyOfAlignments, InconsistentAlignment_CheckFailed) -{ - const string query = "AAAT"; - const string reference = "AAAG"; - - EXPECT_FALSE(checkConsistency(Alignment(0, "4M"), reference, query)); - EXPECT_FALSE(checkConsistency(Alignment(0, "3M1X2S"), reference, query)); - EXPECT_FALSE(checkConsistency(Alignment(0, "3M2X"), reference, query)); - EXPECT_FALSE(checkConsistency(Alignment(0, "1M"), reference, query)); -} - -TEST(GettingSequencesForEachOperation, TypicalAlignment_SequencePairs) -{ - // ref: CCCTTCCTTAATT---T---------- - // ||| || || | - // query: ---TTCGNN--TTGGGTCCCCCCCCCC - string reference = "CCCTTCCTTAATTT"; - string query = "TTCGNNTTGGGTCCCCCCCCCC"; - - Alignment alignment(3, "3M1X2N2D2M3I1M10S"); - - list expected_sequence_pieces - = { { "TTC", "TTC" }, { "C", "G" }, { "TT", "NN" }, { "AA", "" }, - { "TT", "TT" }, { "", "GGG" }, { "T", "T" }, { "", "CCCCCCCCCC" } }; - - ASSERT_EQ(expected_sequence_pieces, getSequencesForEachOperation(alignment, reference, query)); -} - -TEST(CheckingIfAlignmentsAreBookended, AdjacentAlignments_AreBookended) -{ - // CCCG--TAG - // || ||| - // ATCGATTAG - Alignment first_alignment(2, "2S2M"); - Alignment second_alignment(4, "2I3M"); - - EXPECT_TRUE(checkIfBookended(first_alignment, second_alignment)); -} - -TEST(CheckingIfAlignmentsAreBookended, NonAdjacentAlignments_NotBookended) -{ - // CCCG--TAG - // || || - // ATCGATTAG - Alignment first_alignment(2, "2S2M"); - Alignment second_alignment(5, "2M"); - - EXPECT_FALSE(checkIfBookended(first_alignment, second_alignment)); -} - -TEST(CheckingIfAlignmentsAreBookended, FirstAlignmentEndsInSoftclip_NotBookended) -{ - Alignment first_alignment(0, "2M2S"); - Alignment second_alignment(2, "2M"); - - EXPECT_FALSE(checkIfBookended(first_alignment, second_alignment)); -} - -TEST(CheckingIfAlignmentsAreBookended, SecondAlignmentStartsInSoftclip_NotBookended) -{ - Alignment first_alignment(0, "2M"); - Alignment second_alignment(2, "2S2M"); - - EXPECT_FALSE(checkIfBookended(first_alignment, second_alignment)); -} - -TEST(CheckingIfAlignmentsAreBookended, OneOfTheAlignmentsEntirelySoftclipped_AreBookended) -{ - { - Alignment first_alignment(0, "2M"); - Alignment second_alignment(2, "4S"); - - EXPECT_TRUE(checkIfBookended(first_alignment, second_alignment)); - } - - { - Alignment first_alignment(0, "2M3S"); - Alignment second_alignment(2, "4S"); - - EXPECT_TRUE(checkIfBookended(first_alignment, second_alignment)); - } - - { - Alignment first_alignment(0, "2S"); - Alignment second_alignment(0, "2M"); - - EXPECT_TRUE(checkIfBookended(first_alignment, second_alignment)); - } - - { - Alignment first_alignment(0, "2S"); - Alignment second_alignment(0, "1S2M"); - - EXPECT_TRUE(checkIfBookended(first_alignment, second_alignment)); - } -} - -TEST(MergingAlignments, NotBookendededAlignments_ExceptionThrown) -{ - Alignment first_alignment(0, "2M"); - Alignment second_alignment(3, "1M"); - EXPECT_ANY_THROW(mergeAlignments(first_alignment, second_alignment)); -} - -TEST(MergingAlignments, AlignmentsWithDifferentBoundaryOperations_Merged) -{ - // CCCG--TAG - // || ||| - // ATCGATTAG - Alignment first_alignment(2, "2S2M"); - Alignment second_alignment(4, "2I3M"); - - Alignment merged_alignment = mergeAlignments(first_alignment, second_alignment); - - Alignment expected_alignment(2, "2S2M2I3M"); - EXPECT_EQ(expected_alignment, merged_alignment); -} - -TEST(MergingAlignments, AlignmentsWithSameBoundaryOperation_Merged) -{ - { - // CCCG---TAG - // || ||| - // ATCGATGTAG - Alignment first_alignment(2, "2S2M1I"); - Alignment second_alignment(4, "2I3M"); - - Alignment merged_alignment = mergeAlignments(first_alignment, second_alignment); - - Alignment expected_alignment(2, "2S2M3I3M"); - EXPECT_EQ(expected_alignment, merged_alignment); - } - - { - Alignment first_alignment(0, "2M3S"); - Alignment second_alignment(2, "4S"); - - Alignment merged_alignment = mergeAlignments(first_alignment, second_alignment); - - Alignment expected_alignment(0, "2M7S"); - EXPECT_EQ(expected_alignment, merged_alignment); - } - - { - - Alignment first_alignment(0, "2S"); - Alignment second_alignment(0, "1S2M"); - - Alignment merged_alignment = mergeAlignments(first_alignment, second_alignment); - - Alignment expected_alignment(0, "3S2M"); - EXPECT_EQ(expected_alignment, merged_alignment); - } -} - -TEST(ScoringAlignment, TypicalAlignment_Scored) -{ - Alignment alignment(3, "2S3M1X2N2D2M3I1M10S"); - const int32_t match_score = 1; - const int32_t mismatch_score = -2; - const int32_t gap_score = -3; - - // 2S 3M 1X 2N 2D 2M 3I 1M 10S - // 2*0 + 3*1 + 1*(-2) + 2*0 + 2*(-3) + 2*1 + 3*(-3) + 1*1 + 10*0 = -11 - const int32_t score = scoreAlignment(alignment, match_score, mismatch_score, gap_score); - - EXPECT_EQ(-11, score); -} - -TEST(PrettyPrintingAlignments, TypicalAlignment_PrettyPrinted) -{ - // ref: CCCTTCCTTAATT---T---------- - // ||| || | - // query: ---TTCGNN--TTGGGTCCCCCCCCCC - string reference = "CCCTTCCTTAATTT"; - string query = "TTCGNNTTGGGTCCCCCCCCCC"; - - Alignment alignment(3, "3M1X2N2D2M3I1M10S"); - - const string alignment_encoding = prettyPrint(alignment, reference, query); - - const string expected_encoding = "TTCCTTAATT---T----------\n" - "||| || | \n" - "TTCGNN--TTGGGTCCCCCCCCCC"; - - ASSERT_EQ(expected_encoding, alignment_encoding); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/LinearAlignmentTest.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/tests/LinearAlignmentTest.cpp deleted file mode 100644 index f576efc..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/LinearAlignmentTest.cpp +++ /dev/null @@ -1,123 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphalign/LinearAlignment.hh" - -#include "gtest/gtest.h" - -using std::list; -using std::string; - -using namespace graphtools; - -TEST(AlignmentInitialization, TypicalCigarString_AlignmentCreated) -{ - Alignment alignment(3u, "3M1X2N2D2M3I1M10S"); - const list operations = { Operation("3M"), Operation("1X"), Operation("2N"), Operation("2D"), - Operation("2M"), Operation("3I"), Operation("1M"), Operation("10S") }; - - Alignment expected_alignment(3u, operations); - ASSERT_EQ(expected_alignment, alignment); -} - -TEST(GettingAlignmentSpans, TypicalAlignment_QueryAndreferenceSpansObtained) -{ - Alignment alignment(3u, "3M1X2M2D2M3I1M10S"); - EXPECT_EQ(22u, alignment.queryLength()); - EXPECT_EQ(11u, alignment.referenceLength()); -} - -TEST(EncodingAlignment, TypicalAlignment_CigarStringObtained) -{ - const string cigar_string = "3M1X2N2D2M3I1M10S"; - Alignment alignment(3u, cigar_string); - - EXPECT_EQ(cigar_string, alignment.generateCigar()); -} - -TEST(SplittingAlignment, SplitPositionBetweenOperations_PefixAndSuffixAlignments) -{ - // query: -AATTCGTT--TTGGGTCCCCCCCCCC - // ||| || || | - // ref: CCCTTCCNNAATT---T---------- - - const string cigar_string = "2S3M1X2N2D2M3I1M10S"; - Alignment alignment(3, cigar_string); - - Alignment suffix = alignment.splitAtReferencePosition(13); - - Alignment expected_prefix(3, "2S3M1X2N2D2M3I"); - Alignment expected_suffix(13, "1M10S"); - EXPECT_EQ(expected_prefix, alignment); - EXPECT_EQ(expected_suffix, suffix); -} - -TEST(SplittingAlignment, OperationOverlapsSplitPosition_PrefixAndSuffixAlignments) -{ - Alignment alignment(0, "4M1I4M"); - - Alignment suffix = alignment.splitAtReferencePosition(5); - - Alignment expected_prefix(0, "4M1I1M"); - Alignment expected_suffix(5, "3M"); - EXPECT_EQ(alignment, expected_prefix); - EXPECT_EQ(suffix, expected_suffix); -} - -TEST(SplittingAlignment, TypicalAlignments_AlignmentStatsUpdated) -{ - // query: -AATTCGTT--T TGGGTCCCCCCCCCC - // ||| || | | | - // ref: CCCTTCCNNAAT T---T---------- - - Alignment alignment(3, "2S3M1X2M2D2M3I1M10S"); - alignment.splitAtReferencePosition(12); - - EXPECT_EQ(6u, alignment.numMatched()); - EXPECT_EQ(1u, alignment.numMismatched()); - EXPECT_EQ(2u, alignment.numClipped()); - EXPECT_EQ(0u, alignment.numInserted()); - EXPECT_EQ(2u, alignment.numDeleted()); -} - -TEST(SplittingAlignment, InvalidSplitPosition_ExceptionThrown) -{ - Alignment alignment(0, "3M"); - EXPECT_ANY_THROW(alignment.splitAtReferencePosition(0)); - EXPECT_ANY_THROW(alignment.splitAtReferencePosition(3)); - EXPECT_ANY_THROW(alignment.splitAtReferencePosition(4)); -} - -TEST(ReversingAlignment, TypicalAlignment_ReversedAlignment) -{ - // AAC-TCGA - // | || - // TTTTCG-CGCC - Alignment alignment(4, "2S1M1D1I2M1S"); - - const size_t reference_length = 10; - alignment.reverse(reference_length); - - // AGCT-CAA - // || | - // CCGC-GCTTTT - Alignment expected_alignment(2, "1S2M1I1D1M2S"); - EXPECT_EQ(expected_alignment, alignment); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/OperationOperationsTest.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/tests/OperationOperationsTest.cpp deleted file mode 100644 index e84bc7d..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/OperationOperationsTest.cpp +++ /dev/null @@ -1,211 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphalign/OperationOperations.hh" - -#include "gtest/gtest.h" - -using namespace graphtools; - -TEST(CheckingConsistency, MatchOperation_ConsistencyChecked) -{ - { - Operation operation("3M"); - EXPECT_TRUE(checkConsistency(operation, "ATC", "ATC")); - } - - { - Operation operation("4M"); - EXPECT_TRUE(checkConsistency(operation, "ATBB", "AtcG")); - } - - { - Operation operation("4M"); - EXPECT_FALSE(checkConsistency(operation, "AYAA", "AAAA")); - } - - { - Operation operation("4M"); - EXPECT_FALSE(checkConsistency(operation, "ATC", "AAAA")); - } - - { - Operation operation("4M"); - EXPECT_FALSE(checkConsistency(operation, "AAA", "AAA")); - } -} - -TEST(CheckingConsistency, MismatchOperation_ConsistencyChecked) -{ - { - Operation operation("2X"); - EXPECT_TRUE(checkConsistency(operation, "TR", "AT")); - } - - { - Operation operation("2X"); - EXPECT_FALSE(checkConsistency(operation, "TT", "AT")); - } - - { - Operation operation("2X"); - EXPECT_FALSE(checkConsistency(operation, "A", "AT")); - } - - { - Operation operation("1X"); - EXPECT_FALSE(checkConsistency(operation, "W", "T")); - } -} - -TEST(CheckingConsistency, InsertionOperation_ConsistencyChecked) -{ - { - Operation operation("4I"); - EXPECT_TRUE(checkConsistency(operation, "", "ATTG")); - } - - { - Operation operation("2I"); - EXPECT_FALSE(checkConsistency(operation, "T", "AA")); - } -} - -TEST(CheckingConsistency, DeletionOperation_ConsistencyChecked) -{ - - { - Operation operation("3D"); - EXPECT_TRUE(checkConsistency(operation, "TRR", "")); - } - - { - Operation operation("4D"); - EXPECT_FALSE(checkConsistency(operation, "", "AAA")); - } - - { - Operation operation("4D"); - EXPECT_FALSE(checkConsistency(operation, "", "")); - } -} - -TEST(CheckingConsistency, MissingBasesOperation_ConsistencyChecked) -{ - - { - Operation operation("3N"); - EXPECT_TRUE(checkConsistency(operation, "AAN", "NNN")); - } - - { - Operation operation("4N"); - EXPECT_FALSE(checkConsistency(operation, "NNN", "NNN")); - } - - { - Operation operation("2N"); - EXPECT_FALSE(checkConsistency(operation, "NT", "NT")); - } - - { - Operation operation("3N"); - EXPECT_FALSE(checkConsistency(operation, "NNN", "NNA")); // Reference N means degenerate base, not missing base - } -} - -TEST(CheckingConsistency, SoftclipOperation_ConsistencyChecked) -{ - - { - Operation operation("2S"); - EXPECT_TRUE(checkConsistency(operation, "", "AA")); - } - - { - Operation operation("2S"); - EXPECT_FALSE(checkConsistency(operation, "", "TTT")); - } - - { - Operation operation("2S"); - EXPECT_FALSE(checkConsistency(operation, "T", "TT")); - } -} - -TEST(SplittingOperations, MatchOperation_Split) -{ - Operation operation("3M"); - OperationPair operation_parts = splitByReferenceLength(operation, 1); - - EXPECT_EQ(Operation("1M"), operation_parts.first); - EXPECT_EQ(Operation("2M"), operation_parts.second); -} - -TEST(SplittingOperations, MismatchOperation_Split) -{ - Operation operation("4X"); - OperationPair operation_parts = splitByReferenceLength(operation, 3); - - EXPECT_EQ(Operation("3X"), operation_parts.first); - EXPECT_EQ(Operation("1X"), operation_parts.second); -} - -TEST(SplittingOperations, MissingBaseOperation_ExceptionThrown) -{ - Operation operation("7N"); - - OperationPair operation_parts = splitByReferenceLength(operation, 4); - - EXPECT_EQ(Operation("4N"), operation_parts.first); - EXPECT_EQ(Operation("3N"), operation_parts.second); -} - -TEST(SplittingOperations, DeletionOperation_Split) -{ - Operation operation("5D"); - OperationPair operation_parts = splitByReferenceLength(operation, 2); - - EXPECT_EQ(Operation("2D"), operation_parts.first); - EXPECT_EQ(Operation("3D"), operation_parts.second); -} - -TEST(SplittingOperations, InsertionOperation_ExceptionThrown) -{ - Operation operation("7I"); - - ASSERT_ANY_THROW(splitByReferenceLength(operation, 2)); -} - -TEST(SplittingOperations, SoftclipOperation_ExceptionThrown) -{ - Operation operation("10S"); - - ASSERT_ANY_THROW(splitByReferenceLength(operation, 2)); -} - -TEST(SplittingOperations, InvalidReferenceLength_ExceptionThrown) -{ - - Operation operation("3M"); - EXPECT_ANY_THROW(splitByReferenceLength(operation, 0)); - EXPECT_ANY_THROW(splitByReferenceLength(operation, 3)); - EXPECT_ANY_THROW(splitByReferenceLength(operation, 4)); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/OperationTest.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/tests/OperationTest.cpp deleted file mode 100644 index 0e7c58e..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/OperationTest.cpp +++ /dev/null @@ -1,93 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphalign/Operation.hh" - -#include "gtest/gtest.h" - -using namespace graphtools; - -TEST(InitializingOperations, TypicalOperations_QueryAndReferenceSpansObtained) -{ - { - Operation operation("3M"); - EXPECT_EQ(OperationType::kMatch, operation.type()); - EXPECT_EQ(3u, operation.queryLength()); - EXPECT_EQ(3u, operation.referenceLength()); - } - { - Operation operation("4X"); - EXPECT_EQ(OperationType::kMismatch, operation.type()); - EXPECT_EQ(4u, operation.queryLength()); - EXPECT_EQ(4u, operation.referenceLength()); - } - { - Operation operation("5D"); - EXPECT_EQ(OperationType::kDeletionFromRef, operation.type()); - EXPECT_EQ(0u, operation.queryLength()); - EXPECT_EQ(5u, operation.referenceLength()); - } - { - Operation operation("7I"); - EXPECT_EQ(OperationType::kInsertionToRef, operation.type()); - EXPECT_EQ(7u, operation.queryLength()); - EXPECT_EQ(0u, operation.referenceLength()); - } - { - Operation operation("10S"); - EXPECT_EQ(OperationType::kSoftclip, operation.type()); - EXPECT_EQ(10u, operation.queryLength()); - EXPECT_EQ(0u, operation.referenceLength()); - } - { - Operation operation("7N"); - EXPECT_EQ(OperationType::kMissingBases, operation.type()); - EXPECT_EQ(7u, operation.queryLength()); - EXPECT_EQ(7u, operation.referenceLength()); - } -} - -TEST(EncodingOperation, TypicalOperations_CigarStringObtained) -{ - { - Operation operation(OperationType::kMatch, 3); - EXPECT_EQ("3M", operation.generateCigar()); - } - { - Operation operation(OperationType::kMismatch, 4); - EXPECT_EQ("4X", operation.generateCigar()); - } - { - Operation operation(OperationType::kDeletionFromRef, 5); - EXPECT_EQ("5D", operation.generateCigar()); - } - { - Operation operation(OperationType::kInsertionToRef, 7); - EXPECT_EQ("7I", operation.generateCigar()); - } - { - Operation operation(OperationType::kSoftclip, 10); - EXPECT_EQ("10S", operation.generateCigar()); - } - { - Operation operation(OperationType::kMissingBases, 7); - EXPECT_EQ("7N", operation.generateCigar()); - } -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/PathFamilyOperationsTest.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/tests/PathFamilyOperationsTest.cpp deleted file mode 100644 index d6c5d87..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/PathFamilyOperationsTest.cpp +++ /dev/null @@ -1,251 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Felix Schlesinger -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "gtest/gtest.h" - -#include "graphcore/Graph.hh" -#include "graphcore/GraphBuilders.hh" -#include "graphcore/Path.hh" -#include "graphcore/PathFamily.hh" -#include "graphcore/PathFamilyOperations.hh" -#include - -using std::list; -using std::string; - -using namespace graphtools; - -TEST(PathsForPathFamily, GeneratePathsForPathFamily_DisjointPaths) -{ - Graph graph = makeDoubleSwapGraph("AAA", "CCCC", "GGG", "AAAA", "TTTT", "GG", "AA"); - PathFamily family(&graph); - family.addEdge(0, 1); - family.addEdge(1, 3); - family.addEdge(5, 6); - - const list expected_paths{ - Path{ &graph, 0, { 0, 1, 3 }, 4 }, - Path{ &graph, 0, { 5, 6 }, 2 }, - }; - list observed_paths; - ASSERT_TRUE(getMaximalPathsForFamily(family, &observed_paths)); - for (const auto& path : observed_paths) - { - ASSERT_TRUE(family.containsPath(path)); - } - ASSERT_EQ(expected_paths, observed_paths); -} - -TEST(PathsForPathFamily, GeneratePathsForPathFamily_LongPath) -{ - Graph graph = makeDoubleSwapGraph("AAA", "CCCC", "GGG", "AAAA", "TTTT", "GG", "AA"); - PathFamily family(&graph); - family.addEdge(0, 1); - family.addEdge(1, 3); - family.addEdge(3, 4); - family.addEdge(4, 6); - - const list expected_paths{ - Path{ &graph, 0, { 0, 1, 3, 4, 6 }, 2 }, - }; - list observed_paths; - ASSERT_TRUE(getMaximalPathsForFamily(family, &observed_paths)); - for (const auto& path : observed_paths) - { - ASSERT_TRUE(family.containsPath(path)); - } - ASSERT_EQ(expected_paths, observed_paths); -} - -TEST(PathsForPathFamily, GeneratePathsForPathFamily_MultipleExtensions) -{ - Graph graph = makeDoubleSwapGraph("AAA", "CCCC", "GGG", "AAAA", "TTTT", "GG", "AA"); - PathFamily family(&graph); - family.addEdge(1, 3); - family.addEdge(2, 3); - family.addEdge(3, 4); - family.addEdge(3, 5); - family.addEdge(4, 6); - family.addEdge(5, 6); - - const list expected_paths{ - Path{ &graph, 0, { 1, 3, 4, 6 }, 2 }, - Path{ &graph, 0, { 1, 3, 5, 6 }, 2 }, - Path{ &graph, 0, { 2, 3, 4, 6 }, 2 }, - Path{ &graph, 0, { 2, 3, 5, 6 }, 2 }, - }; - list observed_paths; - ASSERT_TRUE(getMaximalPathsForFamily(family, &observed_paths)); - - for (const auto& path : observed_paths) - { - ASSERT_TRUE(family.containsPath(path)); - } - - ASSERT_EQ(expected_paths, observed_paths); -} - -TEST(PathsForPathFamily, GeneratePathsForPathFamily_MultipleExtensionsSingleEdge) -{ - Graph graph(8); - - /* - A E - \ / - C=D - / \ - B F - */ - graph.setNodeName(0, "source"); - graph.setNodeName(1, "A"); - graph.setNodeName(2, "B"); - graph.setNodeName(3, "C"); - graph.setNodeName(4, "D"); - graph.setNodeName(5, "E"); - graph.setNodeName(6, "F"); - graph.setNodeName(7, "sink"); - - graph.setNodeSeq(0, "N"); - graph.setNodeSeq(1, "A"); - graph.setNodeSeq(2, "A"); - graph.setNodeSeq(3, "A"); - graph.setNodeSeq(4, "A"); - graph.setNodeSeq(5, "A"); - graph.setNodeSeq(6, "A"); - graph.setNodeSeq(7, "N"); - - graph.addEdge(0, 1); - graph.addEdge(0, 2); - graph.addEdge(1, 3); - graph.addEdge(2, 3); - graph.addEdge(3, 4); - graph.addEdge(4, 5); - graph.addEdge(4, 6); - graph.addEdge(5, 7); - graph.addEdge(6, 7); - - PathFamily family(&graph); - family.addEdge(3, 4); - - const list expected_paths{ - Path{ &graph, 0, { 3, 4 }, 1 }, - }; - list observed_paths; - ASSERT_TRUE(getMaximalPathsForFamily(family, &observed_paths)); - - for (const auto& path : observed_paths) - { - ASSERT_TRUE(family.containsPath(path)); - } - - ASSERT_EQ(expected_paths, observed_paths); -} - -TEST(PathsForPathFamily, GeneratePathsForPathFamily_LoopGraph) -{ - Graph graph = makeStrGraph("AAA", "TG", "CCC"); - PathFamily family(&graph); - family.addEdge(0, 1); - family.addEdge(1, 1); - family.addEdge(1, 2); - - const list expected_paths{ - Path{ &graph, 0, { 0, 1, 2 }, 3 }, - }; - list observed_paths; - ASSERT_TRUE(getMaximalPathsForFamily(family, &observed_paths, 5)); - for (const auto& path : observed_paths) - { - ASSERT_TRUE(family.containsPath(path)); - } - ASSERT_EQ(expected_paths, observed_paths); -} - -TEST(PathFamilyFromPath, GeneratePathFamilyFromPath_SimplePath) -{ - Graph graph = makeDoubleSwapGraph("A", "C", "T", "A", "G", "C", "T"); - const Path path{ &graph, 0, { 1, 3, 4 }, 0 }; - const PathFamily family = pathToPathFamily(graph, path); - - ASSERT_EQ(2ull, family.edges().size()); - ASSERT_NE(0u, family.edges().count({ 1, 3 })); - ASSERT_NE(0u, family.edges().count({ 3, 4 })); - ASSERT_TRUE(family.containsPath(path)); -} - -TEST(PathFamilyFromGraph, GeneratePathFamilyFromGraph_SimpleGraph) -{ - Graph graph = makeDoubleSwapGraph("A", "C", "T", "A", "G", "T", "C"); - graph.addLabelToEdge(0, 1, "A"); - graph.addLabelToEdge(1, 3, "A"); - graph.addLabelToEdge(3, 5, "A"); - graph.addLabelToEdge(5, 6, "A"); - graph.addLabelToEdge(0, 2, "B"); - graph.addLabelToEdge(2, 3, "B"); - graph.addLabelToEdge(3, 4, "B"); - graph.addLabelToEdge(4, 6, "B"); - - const std::map families = getPathFamiliesFromGraph(graph); - - ASSERT_EQ(2ull, families.size()); - ASSERT_NE(0u, families.count("A")); - ASSERT_NE(0u, families.count("B")); - - const auto a_it = families.find("A"); - const auto b_it = families.find("B"); - ASSERT_EQ(4ull, a_it->second.edges().size()); - ASSERT_EQ(4ull, b_it->second.edges().size()); - - ASSERT_NE(0u, a_it->second.edges().count({ 0, 1 })); - ASSERT_NE(0u, a_it->second.edges().count({ 1, 3 })); - ASSERT_NE(0u, a_it->second.edges().count({ 3, 5 })); - ASSERT_NE(0u, a_it->second.edges().count({ 5, 6 })); - - ASSERT_NE(0u, b_it->second.edges().count({ 0, 2 })); - ASSERT_NE(0u, b_it->second.edges().count({ 2, 3 })); - ASSERT_NE(0u, b_it->second.edges().count({ 3, 4 })); - ASSERT_NE(0u, b_it->second.edges().count({ 4, 6 })); -} - -TEST(PathFamilyFromGraph, GeneratePathFamilyFromGraph_LoopGraph) -{ - Graph graph = makeStrGraph("A", "CT", "G"); - graph.addLabelToEdge(0, 2, "A"); - graph.addLabelToEdge(0, 1, "B"); - graph.addLabelToEdge(1, 1, "B"); - graph.addLabelToEdge(1, 2, "B"); - - const std::map families = getPathFamiliesFromGraph(graph); - - ASSERT_EQ(2ull, families.size()); - ASSERT_NE(0u, families.count("A")); - ASSERT_NE(0u, families.count("B")); - - const auto a_it = families.find("A"); - const auto b_it = families.find("B"); - ASSERT_EQ(1ull, a_it->second.edges().size()); - ASSERT_EQ(3ull, b_it->second.edges().size()); - - ASSERT_NE(0u, a_it->second.edges().count({ 0, 2 })); - - ASSERT_NE(0u, b_it->second.edges().count({ 0, 1 })); - ASSERT_NE(0u, b_it->second.edges().count({ 1, 1 })); - ASSERT_NE(0u, b_it->second.edges().count({ 1, 2 })); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/PathFamilyTest.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/tests/PathFamilyTest.cpp deleted file mode 100644 index 00019ce..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/PathFamilyTest.cpp +++ /dev/null @@ -1,134 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Felix Schlesinger -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "gtest/gtest.h" - -#include "graphcore/Graph.hh" -#include "graphcore/GraphBuilders.hh" -#include "graphcore/Path.hh" -#include "graphcore/PathFamily.hh" -#include - -using std::string; -using std::vector; - -using namespace graphtools; - -TEST(Creation, AddingEdges_ExpectedSize) -{ - Graph graph = makeDeletionGraph("AAAA", "TTGG", "TTTT"); - PathFamily family(&graph); - ASSERT_EQ(0u, family.edges().size()); - family.addEdge(0, 1); - ASSERT_EQ(1u, family.edges().size()); -} - -TEST(Creation, FromLabel_Edgeset) -{ - Graph graph = makeDeletionGraph("AAAA", "TTGG", "TTTT"); - graph.addLabelToEdge(0, 2, "foo"); - PathFamily family(&graph, "foo"); - ASSERT_EQ(1u, family.edges().size()); - family.addEdge(1, 2); - family.setLabel("foo"); - PathFamily family2(&graph, "foo"); - ASSERT_EQ(family, family2); -} - -TEST(Creation, CopyConstructor_Independent) -{ - Graph graph = makeDeletionGraph("AAAA", "TTGG", "TTTT"); - PathFamily fam1(&graph); - fam1.addEdge(0, 1); - PathFamily fam2(fam1); - ASSERT_EQ(fam1, fam2); - fam1.addEdge(0, 2); - ASSERT_NE(fam1, fam2); -} - -TEST(Paths, ContainsPath_MatchFull) -{ - Graph graph = makeDeletionGraph("AAAA", "TTGG", "TTTT"); - PathFamily family(&graph); - family.addEdge(0, 1); - family.addEdge(1, 2); - Path path(&graph, 0, { 0, 1, 2 }, 0); - ASSERT_TRUE(family.containsPath(path)); - Path path2(&graph, 0, { 0, 2 }, 0); - ASSERT_FALSE(family.containsPath(path2)); -} - -TEST(Paths, ContainsPath_MatchPartialPath) -{ - Graph graph = makeDeletionGraph("AAAA", "TTGG", "TTTT"); - PathFamily family(&graph); - family.addEdge(0, 1); - family.addEdge(1, 2); - Path path(&graph, 0, { 0, 1 }, 0); - ASSERT_TRUE(family.containsPath(path)); - Path path2(&graph, 0, { 1, 2 }, 0); - ASSERT_TRUE(family.containsPath(path2)); -} - -TEST(Paths, ContainsPath_MatchPartialFamily) -{ - Graph graph = makeDeletionGraph("AAAA", "TTGG", "TTTT"); - PathFamily family(&graph); - family.addEdge(0, 1); - Path path(&graph, 0, { 0, 1, 2 }, 0); - ASSERT_TRUE(family.containsPath(path)); - Path path2(&graph, 0, { 1, 2 }, 0); - ASSERT_FALSE(family.containsPath(path2)); -} - -TEST(Paths, ContainsPath_MatchAmbiguous) -{ - Graph graph = makeDeletionGraph("AAAA", "TTGG", "TTTT"); - PathFamily family(&graph); - family.addEdge(0, 1); - family.addEdge(0, 2); - Path path2(&graph, 0, { 0, 2 }, 0); - ASSERT_TRUE(family.containsPath(path2)); - Path path(&graph, 0, { 0, 1, 2 }, 0); - ASSERT_FALSE(family.containsPath(path)); -} - -TEST(Compare, AddingEdges_Equality) -{ - Graph graph = makeDeletionGraph("AAAA", "TTGG", "TTTT"); - PathFamily family(&graph); - family.addEdge(0, 1); - PathFamily family2(&graph); - family2.addEdge(0, 1); - ASSERT_EQ(family, family2); - family.addEdge(0, 2); - ASSERT_NE(family, family2); -} -TEST(Compare, AddingEdges_Includes) -{ - Graph graph = makeDeletionGraph("AAAA", "TTGG", "TTTT"); - graph.addLabelToEdge(0, 1, "foo"); - PathFamily fam1(&graph, "foo"); - PathFamily fam2(&graph, "foo"); - ASSERT_TRUE(fam1.includes(fam2)); - fam1.addEdge(0, 2); - ASSERT_TRUE(fam1.includes(fam2)); - ASSERT_FALSE(fam2.includes(fam1)); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/PathOperationsTest.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/tests/PathOperationsTest.cpp deleted file mode 100644 index 9e81801..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/PathOperationsTest.cpp +++ /dev/null @@ -1,676 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphcore/PathOperations.hh" - -#include "gtest/gtest.h" - -#include -#include -#include - -#include "graphcore/Graph.hh" -#include "graphcore/GraphBuilders.hh" -#include "graphcore/Path.hh" - -using std::list; -using std::string; -using std::vector; - -using namespace graphtools; - -TEST(ExtendingPathStarts, TypicalPath_StartExtended) -{ - Graph graph = makeDeletionGraph("AAACC", "TTGGG", "TTAAA"); - - { - Path path(&graph, 4, { 0 }, 4); - list extended_paths = extendPathStart(path, 1); - - list expected_paths = { Path(&graph, 3, { 0 }, 4) }; - ASSERT_EQ(expected_paths, extended_paths); - } - - { - Path path(&graph, 5, { 0, 2 }, 0); - list extended_paths = extendPathStart(path, 2); - - list expected_paths = { Path(&graph, 3, { 0, 2 }, 0) }; - ASSERT_EQ(expected_paths, extended_paths); - } - - { - Path path(&graph, 0, { 2 }, 0); - list extended_paths = extendPathStart(path, 2); - - list expected_paths = { Path(&graph, 3, { 0, 2 }, 0), Path(&graph, 3, { 1, 2 }, 0) }; - ASSERT_EQ(expected_paths, extended_paths); - } -} - -TEST(ExtendingPathEnds, TypicalPath_EndExtended) -{ - Graph graph = makeStrGraph("TTT", "AT", "CCCCC"); - - Path path(&graph, 0, { 0 }, 1); - const list path_extensions = extendPathEnd(path, 6); - - const list expected_path_extensions - = { Path(&graph, 0, { 0, 1, 1 }, 2), Path(&graph, 0, { 0, 1, 2 }, 2), Path(&graph, 0, { 0, 2 }, 4) }; - ASSERT_EQ(expected_path_extensions, path_extensions); -} - -TEST(ExtendingPathsByGivenLength, TypicalPathInStrGraph_PathExtended) -{ - Graph graph = makeStrGraph("TTT", "AT", "CCCCC"); - - Path path(&graph, 0, { 1 }, 2); - const int32_t start_extension = 1; - const int32_t end_extension = 1; - const list path_extensions = extendPath(path, start_extension, end_extension); - - const list expected_path_extensions = { Path(&graph, 2, { 0, 1, 1 }, 1), Path(&graph, 2, { 0, 1, 2 }, 1), - Path(&graph, 1, { 1, 1, 1 }, 1), Path(&graph, 1, { 1, 1, 2 }, 1) }; - ASSERT_EQ(expected_path_extensions, path_extensions); -} - -TEST(ExtendingPathsByGivenLength, TypicalPathInHomopolymerGraph_PathExtended) -{ - Graph graph = makeStrGraph("T", "A", "C"); - - Path path(&graph, 0, { 1 }, 0); - const int32_t start_extension = 3; - const int32_t end_extension = 3; - const list path_extensions = extendPath(path, start_extension, end_extension); - - const list expected_path_extensions - = { Path(&graph, 0, { 0, 1, 1, 1, 1, 1 }, 1), Path(&graph, 0, { 0, 1, 1, 1, 1, 2 }, 1), - Path(&graph, 0, { 1, 1, 1, 1, 1, 1 }, 1), Path(&graph, 0, { 1, 1, 1, 1, 1, 2 }, 1) }; - ASSERT_EQ(expected_path_extensions, path_extensions); -} - -TEST(ExtendingPathsMatching, TypicalPath_ExtendedWithinNode) -{ - Graph graph = makeDeletionGraph("AAACC", "TTGGG", "TTAAA"); - - const Path path(&graph, 2, { 1 }, 2); - const string query = "TTGGG"; - - { - size_t qpos = 2; - const Path extended_path = extendPathStartMatching(path, query, qpos); - const Path expected_path(&graph, 0, { 1 }, 2); - ASSERT_EQ(expected_path, extended_path); - ASSERT_EQ(0ull, qpos); - } - - { - const size_t qpos = 2; - const Path extended_path = extendPathEndMatching(path, query, qpos); - const Path expected_path(&graph, 2, { 1 }, 5); - ASSERT_EQ(expected_path, extended_path); - ASSERT_EQ(2ull, qpos); - } - - { - size_t qpos = 2; - const Path extended_path = extendPathMatching(path, query, qpos); - const Path expected_path(&graph, 0, { 1 }, 5); - ASSERT_EQ(expected_path, extended_path); - ASSERT_EQ(0ull, qpos); - } -} - -TEST(ExtendingPathsMatching, TypicalPath_ExtendedAcrossNodes) -{ - Graph graph = makeDeletionGraph("AAACC", "TTGGG", "TTAAA"); - - const Path path(&graph, 2, { 1 }, 2); - const string query = "CTTGGGT"; - - { - size_t qpos = 3; - const Path extended_path = extendPathStartMatching(path, query, qpos); - const Path expected_path(&graph, 4, { 0, 1 }, 2); - ASSERT_EQ(expected_path, extended_path); - ASSERT_EQ(0ull, qpos); - } - - { - const size_t qpos = 3; - const Path extended_path = extendPathEndMatching(path, query, qpos); - const Path expected_path(&graph, 2, { 1, 2 }, 1); - ASSERT_EQ(expected_path, extended_path); - ASSERT_EQ(3ull, qpos); - } - - { - size_t qpos = 3; - const Path extended_path = extendPathMatching(path, query, qpos); - const Path expected_path(&graph, 4, { 0, 1, 2 }, 1); - ASSERT_EQ(expected_path, extended_path); - ASSERT_EQ(0ull, qpos); - } -} - -TEST(ExtendingPathsMatching, TypicalPath_ExtendedWhenUniqMatch) -{ - { - Graph graph = makeDeletionGraph("AAACC", "TTGGG", "TTAAA"); - const Path path(&graph, 4, { 0 }, 4); - - { - const string query = "CTTGG"; - size_t qpos = 0; - const Path extended_path = extendPathMatching(path, query, qpos); - const Path expected_path(&graph, 4, { 0, 1 }, 4); - ASSERT_EQ(expected_path, extended_path); - ASSERT_EQ(0ull, qpos); - } - - { - const string query = "CTTAA"; - size_t qpos = 0; - const Path extended_path = extendPathMatching(path, query, qpos); - const Path expected_path(&graph, 4, { 0, 2 }, 4); - ASSERT_EQ(expected_path, extended_path); - ASSERT_EQ(qpos, 0ull); - } - } - - { - Graph graph = makeDeletionGraph("AAACC", "ATGCC", "TTAAA"); - const Path path(&graph, 0, { 2 }, 0); - - { - const string query = "TGCCT"; - size_t qpos = 4; - const Path extended_path = extendPathMatching(path, query, qpos); - const Path expected_path(&graph, 1, { 1, 2 }, 1); - ASSERT_EQ(expected_path, extended_path); - ASSERT_EQ(0ull, qpos); - } - - { - const string query = "AACCT"; - size_t qpos = 4; - const Path extended_path = extendPathMatching(path, query, qpos); - const Path expected_path(&graph, 1, { 0, 2 }, 1); - ASSERT_EQ(expected_path, extended_path); - ASSERT_EQ(0ull, qpos); - } - } -} - -TEST(ExtendingPathsMatching, TypicalPath_NotExtendedWhenNonUniqMatch) -{ - { - Graph graph = makeDeletionGraph("AAACC", "TTGGG", "TTAAA"); - const Path path(&graph, 4, { 0 }, 4); - const string query = "CTT"; - size_t qpos = 0; - const Path extended_path = extendPathMatching(path, query, qpos); - const Path expected_path(&graph, 4, { 0 }, 5); - ASSERT_EQ(expected_path, extended_path); - ASSERT_EQ(0ull, qpos); - } - - { - Graph graph = makeDeletionGraph("AAACC", "ATGCC", "TTAAA"); - const Path path(&graph, 0, { 2 }, 0); - const string query = "CCT"; - size_t qpos = 2; - const Path extended_path = extendPathMatching(path, query, qpos); - const Path expected_path(&graph, 0, { 2 }, 1); - ASSERT_EQ(expected_path, extended_path); - ASSERT_EQ(2ull, qpos); - } - - { - Graph graph = makeSwapGraph("AAAG", "AGCC", "A", "GTTT"); - const Path path(&graph, 0, { 0 }, 2); - const string query = "AAAGAG"; - size_t qpos = 0; - const Path extended_path = extendPathEndMatching(path, query, qpos); - const Path expected_path(&graph, 0, { 0 }, 4); - ASSERT_EQ(expected_path, extended_path); - ASSERT_EQ(0ull, qpos); // extending to right doesn't move qpos - } -} - -TEST(SplittingSequenceByPath, SequenceOfDifferentLength_ExceptionRaised) -{ - Graph graph = makeDeletionGraph("AAAACC", "TTTGG", "ATTT"); - Path path(&graph, 3, { 0, 1 }, 2); - const string sequence = "AA"; - EXPECT_ANY_THROW(splitSequenceByPath(path, sequence)); -} - -TEST(SplittingSequenceByPath, SingleNodePath_SequenceSplit) -{ - Graph graph = makeDeletionGraph("AAAACC", "TTTGG", "ATTT"); - Path path(&graph, 1, { 1 }, 4); - const string sequence = "AAT"; - const vector expected_pieces = { sequence }; - EXPECT_EQ(expected_pieces, splitSequenceByPath(path, sequence)); -} - -TEST(SplittingSequenceByPath, MultiNodePath_SequenceSplit) -{ - Graph graph = makeDeletionGraph("AAAACC", "TTTGG", "ATTT"); - { - Path path(&graph, 1, { 0, 1 }, 4); - const string sequence = "AAAAAGGGG"; - const vector expected_pieces = { "AAAAA", "GGGG" }; - EXPECT_EQ(expected_pieces, splitSequenceByPath(path, sequence)); - } - - { - Path path(&graph, 3, { 0, 2 }, 2); - const string sequence = "AAACC"; - const vector expected_pieces = { "AAA", "CC" }; - EXPECT_EQ(expected_pieces, splitSequenceByPath(path, sequence)); - } - - { - Path path(&graph, 3, { 0, 1, 2 }, 2); - const string sequence = "AAAGGGGGCC"; - const vector expected_pieces = { "AAA", "GGGGG", "CC" }; - EXPECT_EQ(expected_pieces, splitSequenceByPath(path, sequence)); - } -} - -TEST(GraphPathOperations, GraphPathsOverlapDetected) -{ - Graph swap = makeSwapGraph("AAAA", "TTTT", "CCCC", "GGGG"); - { - const Path p1(&swap, 0, { 0, 1 }, 3); - const Path p2(&swap, 0, { 1, 3 }, 3); - - ASSERT_TRUE(checkPathPrefixSuffixOverlap(p1, p2)); - ASSERT_TRUE(checkPathPrefixSuffixOverlap(p2, p1)); - - const Path expected_merge(&swap, 0, { 0, 1, 3 }, 3); - ASSERT_EQ(mergePaths(p1, p2), expected_merge); - ASSERT_EQ(mergePaths(p2, p1), expected_merge); - } - - { - const Path p1(&swap, 2, { 0, 1, 3 }, 2); - const Path p2(&swap, 0, { 1, 3 }, 3); - - ASSERT_TRUE(checkPathPrefixSuffixOverlap(p1, p2)); - ASSERT_TRUE(checkPathPrefixSuffixOverlap(p2, p1)); - - const Path expected_merge(&swap, 2, { 0, 1, 3 }, 3); - ASSERT_EQ(mergePaths(p1, p2), expected_merge); - ASSERT_EQ(mergePaths(p2, p1), expected_merge); - } - { - const Path p1(&swap, 2, { 0, 2 }, 1); - const Path p2(&swap, 1, { 2 }, 3); - - ASSERT_TRUE(checkPathPrefixSuffixOverlap(p1, p2)); - ASSERT_TRUE(checkPathPrefixSuffixOverlap(p2, p1)); - - const Path expected_merge(&swap, 2, { 0, 2 }, 3); - ASSERT_EQ(mergePaths(p1, p2), expected_merge); - ASSERT_EQ(mergePaths(p2, p1), expected_merge); - } -} - -TEST(GraphPathOperations, GraphPathsAdjacencyDetected) -{ - Graph graph = makeDoubleSwapGraph("AAAA", "TTTT", "CCCC", "GGGG", "TTTT", "CCCC", "AAAA"); - - { - // p1 ends just before p2 begins - const Path p1(&graph, 0, { 0, 1 }, 1); - const Path p2(&graph, 2, { 1, 3 }, 3); - - ASSERT_TRUE(checkIfPathsAdjacent(p1, p2)); - ASSERT_TRUE(checkIfPathsAdjacent(p2, p1)); - - const Path expected_merge(&graph, 0, { 0, 1, 3 }, 3); - ASSERT_EQ(mergePaths(p1, p2), expected_merge); - ASSERT_EQ(mergePaths(p2, p1), expected_merge); - } - - { - // p1 ends too far before p2 begins - const Path p1(&graph, 0, { 0, 1 }, 0); - const Path p2(&graph, 2, { 1, 3 }, 3); - - ASSERT_FALSE(checkIfPathsAdjacent(p1, p2)); - ASSERT_FALSE(checkIfPathsAdjacent(p2, p1)); - } - { - // p1 ends just before p2 begins - const Path p1(&graph, 0, { 0, 1 }, 3); - const Path p2(&graph, 0, { 3 }, 3); - - ASSERT_TRUE(checkIfPathsAdjacent(p1, p2)); - ASSERT_TRUE(checkIfPathsAdjacent(p2, p1)); - const Path expected_merge(&graph, 0, { 0, 1, 3 }, 3); - ASSERT_EQ(mergePaths(p1, p2), expected_merge); - ASSERT_EQ(mergePaths(p2, p1), expected_merge); - } - - { - // p1 ends too far before p2 begins - const Path p1(&graph, 0, { 0, 1 }, 2); - const Path p2(&graph, 0, { 3 }, 3); - - ASSERT_FALSE(checkIfPathsAdjacent(p1, p2)); - ASSERT_FALSE(checkIfPathsAdjacent(p2, p1)); - } - - { - // p1 ends too far before p2 begins - const Path p1(&graph, 0, { 0, 1 }, 2); - const Path p2(&graph, 0, { 4 }, 3); - - ASSERT_FALSE(checkIfPathsAdjacent(p1, p2)); - ASSERT_FALSE(checkIfPathsAdjacent(p2, p1)); - } -} - -TEST(GraphPathOperations, GraphPathsNoOverlapDetected) -{ - Graph swap = makeSwapGraph("AAAA", "TTTT", "CCCC", "GGGG"); - { - // p1 ends before p2 begins - const Path p1(&swap, 0, { 0, 1 }, 1); - const Path p2(&swap, 2, { 1, 3 }, 3); - - ASSERT_FALSE(checkPathPrefixSuffixOverlap(p1, p2)); - ASSERT_FALSE(checkPathPrefixSuffixOverlap(p2, p1)); - } - - { - // no shared nodes - const Path p1(&swap, 0, { 0 }, 3); - const Path p2(&swap, 2, { 1, 3 }, 3); - - ASSERT_FALSE(checkPathPrefixSuffixOverlap(p1, p2)); - ASSERT_FALSE(checkPathPrefixSuffixOverlap(p2, p1)); - } - - { - // incompatible - const Path p1(&swap, 0, { 0, 1, 3 }, 3); - const Path p2(&swap, 2, { 0, 2, 3 }, 3); - - ASSERT_FALSE(checkPathPrefixSuffixOverlap(p1, p2)); - ASSERT_FALSE(checkPathPrefixSuffixOverlap(p2, p1)); - } - { - // incompatible 2 - const Path p1(&swap, 0, { 0, 1 }, 3); - const Path p2(&swap, 2, { 2, 3 }, 3); - - ASSERT_FALSE(checkPathPrefixSuffixOverlap(p1, p2)); - ASSERT_FALSE(checkPathPrefixSuffixOverlap(p2, p1)); - } -} - -TEST(GraphPathOperations, PathsMergedExhaustively) -{ - Graph swap = makeDoubleSwapGraph("AAAA", "TTTT", "CCCC", "GGGG", "TTTT", "CCCC", "AAAA"); - - { - const Path p0(&swap, 0, { 1, 3 }, 3); - const Path p1(&swap, 0, { 2, 3 }, 3); - const Path p2(&swap, 0, { 3, 4 }, 3); - const Path p3(&swap, 0, { 3, 5 }, 3); - - const list expected_merged_path{ - Path(&swap, 0, { 1, 3, 4 }, 3), - Path(&swap, 0, { 2, 3, 5 }, 3), - Path(&swap, 0, { 2, 3, 4 }, 3), - Path(&swap, 0, { 1, 3, 5 }, 3), - }; - list merged_path{ p0, p1, p2, p3 }; - graphtools::exhaustiveMerge(merged_path); - - ASSERT_EQ(merged_path, expected_merged_path); - } -} - -TEST(GraphPathOperations, IntersectPaths_NoIntersection) -{ - Graph swap = makeDoubleSwapGraph("AAAA", "TTTT", "CCCC", "GGGG", "TTTT", "CCCC", "AAAA"); - - // no shared nodes - { - const Path p0(&swap, 0, { 1 }, 3); - const Path p1(&swap, 0, { 2 }, 3); - - const auto intersection = graphtools::intersectPaths(p0, p1); - ASSERT_TRUE(intersection.empty()); - - const auto intersection_r = graphtools::intersectPaths(p1, p0); - ASSERT_TRUE(intersection_r.empty()); - } - - // one shared node, but no shared sequence - { - const Path p0(&swap, 0, { 1, 3 }, 1); - const Path p1(&swap, 2, { 3, 4 }, 3); - - const auto intersection = graphtools::intersectPaths(p0, p1); - ASSERT_TRUE(intersection.empty()); - - const auto intersection_r = graphtools::intersectPaths(p1, p0); - ASSERT_TRUE(intersection_r.empty()); - } -} - -TEST(GraphPathOperations, IntersectPaths_SimpleIntersection) -{ - Graph swap = makeDoubleSwapGraph("AAAA", "TTTT", "CCCC", "GGGG", "TTTT", "CCCC", "AAAA"); - - // full node is shared - { - const Path p0(&swap, 0, { 1, 3, 5 }, 4); - const Path p1(&swap, 0, { 2, 3, 4 }, 4); - - std::list expected{ - Path(&swap, 0, { 3 }, 4), - - }; - - const auto intersection = graphtools::intersectPaths(p0, p1); - const auto intersection_r = graphtools::intersectPaths(p1, p0); - ASSERT_EQ(expected, intersection); - ASSERT_EQ(expected, intersection_r); - } - - // partial node is shared - { - const Path p0(&swap, 0, { 1, 3 }, 2); - const Path p1(&swap, 1, { 3, 4 }, 3); - - std::list expected{ - Path(&swap, 1, { 3 }, 2), - - }; - - const auto intersection = graphtools::intersectPaths(p0, p1); - const auto intersection_r = graphtools::intersectPaths(p1, p0); - ASSERT_EQ(expected, intersection); - ASSERT_EQ(expected, intersection_r); - } -} - -TEST(GraphPathOperations, IntersectPaths_ComplexIntersection) -{ - Graph swap = makeDoubleSwapGraph("AAAA", "TTTT", "CCCC", "GGGG", "TTTT", "CCCC", "AAAA"); - - // multiple full nodes shared, two resulting paths - { - const Path p0(&swap, 0, { 1, 3, 5, 6 }, 4); - const Path p1(&swap, 0, { 2, 3, 4, 6 }, 4); - - std::list expected{ - Path(&swap, 0, { 3 }, 4), - Path(&swap, 0, { 6 }, 4), - }; - - const auto intersection = graphtools::intersectPaths(p0, p1); - const auto intersection_r = graphtools::intersectPaths(p1, p0); - ASSERT_EQ(expected, intersection); - ASSERT_EQ(expected, intersection_r); - } - - // complex subpath match - { - const Path p0(&swap, 0, { 1, 3, 4 }, 2); - const Path p1(&swap, 0, { 2, 3, 4, 6 }, 3); - - std::list expected{ - Path(&swap, 0, { 3, 4 }, 2), - }; - - const auto intersection = graphtools::intersectPaths(p0, p1); - const auto intersection_r = graphtools::intersectPaths(p1, p0); - ASSERT_EQ(expected, intersection); - ASSERT_EQ(expected, intersection_r); - } - - // complex subpath match - { - const Path p0(&swap, 0, { 1, 3, 4 }, 2); - const Path p1(&swap, 2, { 3, 4, 6 }, 3); - - std::list expected{ - Path(&swap, 2, { 3, 4 }, 2), - }; - - const auto intersection = graphtools::intersectPaths(p0, p1); - const auto intersection_r = graphtools::intersectPaths(p1, p0); - ASSERT_EQ(expected, intersection); - ASSERT_EQ(expected, intersection_r); - } -} - -TEST(GeneratingSubpathForEachNode, TypicalPaths_Split) -{ - Graph graph = makeStrGraph("TTT", "AT", "CCCCC"); - - { - const Path path(&graph, 0, { 0 }, 1); - const list expected_subpaths = { path }; - EXPECT_EQ(expected_subpaths, generateSubpathForEachNode(path)); - } - - { - const Path path(&graph, 3, { 0, 1, 2 }, 0); - const list expected_subpaths - = { Path(&graph, 3, { 0 }, 3), Path(&graph, 0, { 1 }, 2), Path(&graph, 0, { 2 }, 0) }; - EXPECT_EQ(expected_subpaths, generateSubpathForEachNode(path)); - } - - { - const Path path(&graph, 1, { 0, 1, 1, 1, 2 }, 2); - const list expected_subpaths - = { Path(&graph, 1, { 0 }, 3), Path(&graph, 0, { 1 }, 2), Path(&graph, 0, { 1 }, 2), - Path(&graph, 0, { 1 }, 2), Path(&graph, 0, { 2 }, 2) }; - EXPECT_EQ(expected_subpaths, generateSubpathForEachNode(path)); - } -} - -TEST(CheckingIfPathsAreBookended, AdjacentPathsWithEndsOnSameNode_CheckPassed) -{ - Graph graph = makeStrGraph("TTT", "AT", "CCCCC"); - const Path first_path(&graph, 0, { 0, 1 }, 1); - const Path second_path(&graph, 1, { 1, 2 }, 1); - - ASSERT_TRUE(checkIfBookended(first_path, second_path)); -} - -TEST(CheckingIfPathsAreBookended, AdjacentPathsThatEndOnDifferentNodes_CheckPassed) -{ - Graph graph = makeStrGraph("TTT", "AT", "CCCCC"); - const Path first_path(&graph, 0, { 0 }, 3); - const Path second_path(&graph, 0, { 1, 2 }, 1); - - ASSERT_TRUE(checkIfBookended(first_path, second_path)); -} - -TEST(CheckingIfPathsAreBookended, NonadjacentPathsWithEndsOnSameNode_CheckFailed) -{ - Graph graph = makeStrGraph("TTT", "AT", "CCCCC"); - const Path first_path(&graph, 0, { 0, 1 }, 0); - const Path second_path(&graph, 1, { 1, 2 }, 1); - - ASSERT_FALSE(checkIfBookended(first_path, second_path)); -} - -TEST(CheckingIfPathsAreBookended, NonadjacentPathsThatEndOnNeighboringNodes_CheckFailed) -{ - Graph graph = makeStrGraph("TTT", "AT", "CCCCC"); - const Path first_path(&graph, 0, { 0 }, 2); - const Path second_path(&graph, 0, { 1, 2 }, 1); - - ASSERT_FALSE(checkIfBookended(first_path, second_path)); -} - -TEST(CheckingIfPathsAreBookended, NonadjacentPathsThatEndOnNonneighboringNodes_CheckFailed) -{ - Graph graph = makeSwapGraph("TTT", "AT", "CAT", "CCCCC"); - const Path first_path(&graph, 0, { 1 }, 2); - const Path second_path(&graph, 0, { 2 }, 3); - - ASSERT_FALSE(checkIfBookended(first_path, second_path)); -} - -TEST(MergingBookendedPaths, PathsThatAreNotBookended_ExceptionThrown) -{ - Graph graph = makeStrGraph("TTT", "AT", "CCCCC"); - const Path first_path(&graph, 0, { 0 }, 2); - const Path second_path(&graph, 0, { 1, 2 }, 1); - - EXPECT_ANY_THROW(concatenatePaths(first_path, second_path)); -} - -TEST(MergingBookendedPaths, AdjacentPathsWithEndsOnSameNode_Merged) -{ - Graph graph = makeStrGraph("TTT", "AT", "CCCCC"); - const Path first_path(&graph, 0, { 0, 1 }, 1); - const Path second_path(&graph, 1, { 1, 2 }, 1); - - Path merged_path = concatenatePaths(first_path, second_path); - - Path expected_path(&graph, 0, { 0, 1, 2 }, 1); - EXPECT_EQ(expected_path, merged_path); -} - -TEST(MergingBookendedPaths, AdjacentPathsThatEndOnDifferentNodes_Merged) -{ - Graph graph = makeStrGraph("TTT", "AT", "CCCCC"); - const Path first_path(&graph, 0, { 0 }, 3); - const Path second_path(&graph, 0, { 1, 2 }, 1); - - Path merged_path = concatenatePaths(first_path, second_path); - - Path expected_path(&graph, 0, { 0, 1, 2 }, 1); - EXPECT_EQ(expected_path, merged_path); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/PathTest.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/tests/PathTest.cpp deleted file mode 100644 index f87e62c..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/PathTest.cpp +++ /dev/null @@ -1,583 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphcore/Path.hh" - -#include "gtest/gtest.h" - -#include "graphcore/Graph.hh" -#include "graphcore/GraphBuilders.hh" - -using std::string; -using std::vector; - -using namespace graphtools; - -TEST(CreatingPath, WellFormedPath_NoExceptionThrown) -{ - Graph graph = makeStrGraph("TTT", "AT", "CCCCC"); - ASSERT_NO_THROW(Path(&graph, 1, { 0, 1, 1, 2 }, 0)); -} - -TEST(CreatingPath, ZeroLengthPathSpanningAnEdge_NoExceptionThrown) -{ - Graph graph = makeStrGraph("TTT", "AT", "CCCCC"); - ASSERT_NO_THROW(Path(&graph, 3, { 0, 1, 1, 2 }, 0)); -} - -#ifdef _DEBUG - -TEST(CreatingPath, PathWithUnorderedNodes_ExceptionThrown) -{ - Graph graph = makeStrGraph("TTT", "AT", "CCCCC"); - ASSERT_ANY_THROW(Path(&graph, 1, { 2, 1 }, 1)); -} - -TEST(CreatingPath, PathStartingOutsideOfNodesequence_ExceptionThrown) -{ - Graph graph = makeStrGraph("TTT", "AT", "CCCCC"); - ASSERT_ANY_THROW(Path(&graph, 4, { 0, 1, 2 }, 1)); -} - -TEST(CreatingPath, PathEndingOutsideOfNodesequence_ExceptionThrown) -{ - Graph graph = makeStrGraph("TTT", "AT", "CCCCC"); - ASSERT_ANY_THROW(Path(&graph, 3, { 0, 1, 2 }, 10)); -} - -TEST(CreatingPath, PathWithEndBeforeStart_ExceptionThrown) -{ - Graph graph = makeStrGraph("TTT", "AT", "CCCCC"); - ASSERT_ANY_THROW(Path(&graph, 3, { 0 }, 1)); -} - -TEST(CreatingPath, DisconnectedPath_ExceptionThrown) -{ - Graph graph = makeSwapGraph("TTT", "AT", "GG", "CCCCC"); - ASSERT_ANY_THROW(Path(&graph, 0, { 0, 3 }, 0)); -} - -#endif - -TEST(TraversingPath, TypicalPath_NodeIdsTraversed) -{ - Graph graph = makeDeletionGraph("AAAACC", "TTTGG", "ATTT"); - Path path(&graph, 3, { 1, 2 }, 1); - - vector node_ids; - for (NodeId node_id : path) - { - node_ids.push_back(node_id); - } - - ASSERT_EQ(path.nodeIds(), node_ids); -} - -TEST(GettingPathsequence, TypicalPathOnDeletionGraph_SequenceReturned) -{ - Graph graph = makeDeletionGraph("AAAACC", "TTTGG", "ATTT"); - - { - Path path(&graph, 3, { 0 }, 3); - EXPECT_EQ("", path.seq()); - } - - { - Path path(&graph, 3, { 1 }, 4); - EXPECT_EQ("G", path.seq()); - } - - { - Path path(&graph, 3, { 0, 1, 2 }, 1); - EXPECT_EQ("ACCTTTGGA", path.seq()); - } -} - -TEST(GettingPathsequence, TypicalPathOnStrGraph_sequenceReturned) -{ - Graph graph = makeStrGraph("TTT", "AT", "CCCCC"); - Path path(&graph, 1, { 0, 1, 1, 2 }, 0); - EXPECT_EQ("TTATAT", path.seq()); -} - -TEST(CheckingIfPathOverlapsNode, TypicalPath_OverlapChecked) -{ - Graph graph = makeStrGraph("TTT", "AT", "CCCCC"); - Path path(&graph, 1, { 1, 1, 2 }, 0); - EXPECT_TRUE(path.checkOverlapWithNode(1)); - EXPECT_TRUE(path.checkOverlapWithNode(2)); - EXPECT_FALSE(path.checkOverlapWithNode(0)); -} - -TEST(GettingPathBoundsOnNodeByIndex, TypicalPath_BoundsComputed) -{ - Graph graph = makeStrGraph("TTT", "AT", "CCCCC"); - - { - Path path(&graph, 1, { 0 }, 2); - EXPECT_EQ(1, path.getStartPositionOnNodeByIndex(0)); - EXPECT_EQ(2, path.getEndPositionOnNodeByIndex(0)); - } - - { - Path path(&graph, 1, { 1, 1, 2 }, 3); - EXPECT_EQ(1, path.getStartPositionOnNodeByIndex(0)); - EXPECT_EQ(2, path.getEndPositionOnNodeByIndex(0)); - - EXPECT_EQ(0, path.getStartPositionOnNodeByIndex(1)); - EXPECT_EQ(2, path.getEndPositionOnNodeByIndex(1)); - - EXPECT_EQ(0, path.getStartPositionOnNodeByIndex(2)); - EXPECT_EQ(3, path.getEndPositionOnNodeByIndex(2)); - - EXPECT_ANY_THROW(path.getStartPositionOnNodeByIndex(-1)); - EXPECT_ANY_THROW(path.getEndPositionOnNodeByIndex(-1)); - - EXPECT_ANY_THROW(path.getStartPositionOnNodeByIndex(3)); - EXPECT_ANY_THROW(path.getEndPositionOnNodeByIndex(3)); - } -} - -TEST(GettingLengthOfPathOverEachNode, TypicalPathOnStrGraph_LengthReturned) -{ - { - Graph graph = makeStrGraph("TTT", "AT", "CCCCC"); - - Path path(&graph, 2, { 0, 1, 1 }, 0); - - EXPECT_EQ(1ul, path.getNodeOverlapLengthByIndex(0)); - EXPECT_EQ(2ul, path.getNodeOverlapLengthByIndex(1)); - EXPECT_EQ(0ul, path.getNodeOverlapLengthByIndex(2)); - } - - { - Graph graph = makeStrGraph("TTT", "AT", "CCCCC"); - - Path path(&graph, 3, { 0, 1, 1, 2 }, 5); - - EXPECT_EQ(0ul, path.getNodeOverlapLengthByIndex(0)); - EXPECT_EQ(2ul, path.getNodeOverlapLengthByIndex(1)); - EXPECT_EQ(2ul, path.getNodeOverlapLengthByIndex(2)); - EXPECT_EQ(5ul, path.getNodeOverlapLengthByIndex(3)); - } -} - -TEST(GettingLengthOfPathOverEachNode, IndexOutOfBounds_ExceptionRaised) -{ - Graph graph = makeStrGraph("TTT", "AT", "CCCCC"); - - Path path(&graph, 2, { 0, 1, 1 }, 0); - - EXPECT_ANY_THROW(path.getNodeOverlapLengthByIndex(-1)); - EXPECT_ANY_THROW(path.getNodeOverlapLengthByIndex(3)); -} - -TEST(GettingPathLength, TypicalPathOnStrGraph_LengthReturned) -{ - Graph graph = makeStrGraph("TTT", "AT", "CCCCC"); - - { - Path path(&graph, 2, { 0 }, 2); - EXPECT_EQ(0ul, path.length()); - } - - { - Path path(&graph, 0, { 1 }, 1); - EXPECT_EQ(1ul, path.length()); - } - - { - Path path(&graph, 2, { 0, 1, 1 }, 0); - EXPECT_EQ(3ul, path.length()); - } - - { - Path path(&graph, 3, { 0, 1, 1 }, 0); - EXPECT_EQ(2ul, path.length()); - } -} - -TEST(GettingPathsequenceOnNode, TypicalPathOnStrGraph_sequenceReturned) -{ - Graph graph = makeStrGraph("TTT", "AT", "CCCCC"); - - { - Path path(&graph, 1, { 0, 1, 1, 2 }, 0); - EXPECT_EQ("TT", path.getNodeSeq(0)); - EXPECT_EQ("AT", path.getNodeSeq(1)); - EXPECT_EQ("AT", path.getNodeSeq(2)); - EXPECT_EQ("", path.getNodeSeq(3)); - } - - { - Path path(&graph, 1, { 1, 1 }, 1); - EXPECT_EQ("T", path.getNodeSeq(0)); - EXPECT_EQ("A", path.getNodeSeq(1)); - } -} - -TEST(EncodingPaths, TypicalPath_EncodedAsString) -{ - Graph graph = makeStrGraph("TTT", "AT", "CCCCC"); - - { - Path path(&graph, 0, { 0 }, 1); - ASSERT_EQ("(0@0)-(0@1)", path.encode()); - } - - { - Path path(&graph, 1, { 0, 1, 1, 2 }, 0); - ASSERT_EQ("(0@1)-(1)-(1)-(2@0)", path.encode()); - } -} - -TEST(MovePathAlongNode, TypicalPath_StartPositionMoved) -{ - Graph graph = makeStrGraph("TTT", "AT", "CCCCC"); - Path shorter_path(&graph, 3, { 0, 1 }, 1); - Path longer_path(&graph, 0, { 0, 1 }, 1); - - { - Path path(shorter_path); - path.shiftStartAlongNode(3); - EXPECT_EQ(longer_path, path); - } - - { - Path path(longer_path); - path.shiftStartAlongNode(-3); - EXPECT_EQ(shorter_path, path); - } -} - -TEST(MovePathAlongNode, TypicalPath_EndPositionMoved) -{ - Graph graph = makeStrGraph("TTT", "AT", "CCCCC"); - Path shorter_path(&graph, 1, { 0, 1, 1 }, 0); - Path longer_path(&graph, 1, { 0, 1, 1 }, 1); - - { - Path path(shorter_path); - path.shiftEndAlongNode(1); - EXPECT_EQ(longer_path, path); - } - - { - Path path(longer_path); - path.shiftEndAlongNode(-1); - EXPECT_EQ(shorter_path, path); - } -} - -TEST(MovePathAlongNode, ExtensionPastNodeBoundaries_ExceptionRaised) -{ - Graph graph = makeStrGraph("TTT", "AT", "CCCCC"); - - { - Path path(&graph, 2, { 0, 1 }, 1); - EXPECT_ANY_THROW(path.shiftStartAlongNode(3)); - } - - { - Path path(&graph, 2, { 0, 1 }, 1); - EXPECT_ANY_THROW(path.shiftStartAlongNode(-2)); - } - - { - Path path(&graph, 2, { 0, 1 }, 1); - EXPECT_ANY_THROW(path.shiftEndAlongNode(2)); - } - - { - Path path(&graph, 2, { 0, 1 }, 1); - EXPECT_ANY_THROW(path.shiftEndAlongNode(-2)); - } -} - -TEST(ExtendingPathToNode, TypicalPathInSwapGraph_StartPositionMoved) -{ - Graph graph = makeSwapGraph("TTT", "AT", "GG", "CCCCC"); - - { - Path path(&graph, 1, { 1, 3 }, 2); - path.extendStartToNode(0); - Path expected_path(&graph, 3, { 0, 1, 3 }, 2); - EXPECT_EQ(expected_path, path); - } - - { - Path path(&graph, 1, { 1, 3 }, 2); - path.removeStartNode(); - Path expected_path(&graph, 0, { 3 }, 2); - EXPECT_EQ(expected_path, path); - } - - { - Path path(&graph, 1, { 1, 3 }, 2); - path.extendStartToIncludeNode(0); - Path expected_path(&graph, 0, { 0, 1, 3 }, 2); - EXPECT_EQ(expected_path, path); - } -} - -TEST(ExtendingPathToNode, TypicalPathInSwapGraph_EndPositionMoved) -{ - Graph graph = makeSwapGraph("TTT", "AT", "GG", "CCCCC"); - - { - Path path(&graph, 1, { 0, 2 }, 1); - path.extendEndToNode(3); - Path expected_path(&graph, 1, { 0, 2, 3 }, 0); - EXPECT_EQ(expected_path, path); - } - - { - Path path(&graph, 1, { 0, 2 }, 1); - path.removeEndNode(); - Path expected_path(&graph, 1, { 0 }, 3); - EXPECT_EQ(expected_path, path); - } - - { - Path path(&graph, 1, { 0, 2 }, 1); - path.extendEndToIncludeNode(3); - Path expected_path(&graph, 1, { 0, 2, 3 }, 5); - EXPECT_EQ(expected_path, path); - } -} - -TEST(ExtendingPathToNode, ExtendingPathToNonadjacentNode_ExceptionThrown) -{ - Graph graph = makeSwapGraph("TTT", "AT", "GG", "CCCCC"); - - { - Path path(&graph, 1, { 2, 3 }, 1); - EXPECT_ANY_THROW(path.extendStartToNode(1)); - } - - { - Path path(&graph, 1, { 0 }, 2); - EXPECT_ANY_THROW(path.extendEndToNode(3)); - } -} - -TEST(RemovingZeroLengthStarts, TypicalPaths_StartRemovedIfAppropriate) -{ - Graph graph = makeStrGraph("ATAT", "C", "CCTT"); - - { - Path path(&graph, 4, { 0, 1, 2 }, 2); - path.removeZeroLengthStart(); - - Path expected_path(&graph, 0, { 1, 2 }, 2); - - ASSERT_EQ(expected_path, path); - } - - { - Path path(&graph, 3, { 0, 1, 2 }, 2); - path.removeZeroLengthStart(); - - Path expected_path(&graph, 3, { 0, 1, 2 }, 2); - - ASSERT_EQ(expected_path, path); - } - - { - Path path(&graph, 4, { 0 }, 4); - path.removeZeroLengthStart(); - - Path expected_path(&graph, 4, { 0 }, 4); - - ASSERT_EQ(expected_path, path); - } -} - -TEST(RemovingZeroLengthEnds, TypicalPaths_EndRemovedIfAppropriate) -{ - Graph graph = makeStrGraph("ATAT", "C", "CCTT"); - - { - Path path(&graph, 0, { 0, 1, 2 }, 0); - path.removeZeroLengthEnd(); - - Path expected_path(&graph, 0, { 0, 1 }, 1); - - ASSERT_EQ(expected_path, path); - } - - { - Path path(&graph, 0, { 0, 1, 2 }, 1); - path.removeZeroLengthEnd(); - - Path expected_path(&graph, 0, { 0, 1, 2 }, 1); - - ASSERT_EQ(expected_path, path); - } - - { - Path path(&graph, 4, { 0 }, 4); - path.removeZeroLengthEnd(); - - Path expected_path(&graph, 4, { 0 }, 4); - - ASSERT_EQ(expected_path, path); - } -} - -TEST(ShrinkingStartOfPath, TypicalPathInStrGraph_StartShrank) -{ - Graph graph = makeStrGraph("ATAT", "C", "CCTT"); - - { - Path path(&graph, 2, { 0, 1, 2 }, 2); - path.shrinkStartBy(2); - - Path expected_path(&graph, 0, { 1, 2 }, 2); - ASSERT_EQ(expected_path, path); - } - - { - Path path(&graph, 2, { 0, 1 }, 1); - path.shrinkStartBy(3); - - Path expected_path(&graph, 1, { 1 }, 1); - ASSERT_EQ(expected_path, path); - } - - { - Path path(&graph, 4, { 0, 1 }, 1); - path.shrinkStartBy(1); - - Path expected_path(&graph, 1, { 1 }, 1); - ASSERT_EQ(expected_path, path); - } - - { - Path path(&graph, 4, { 0, 1 }, 1); - path.shrinkStartBy(0); - - Path expected_path(&graph, 0, { 1 }, 1); - ASSERT_EQ(expected_path, path); - } -} - -TEST(ShrinkingEndOfPath, TypicalPathInStrGraph_EndShrank) -{ - Graph graph = makeStrGraph("ATAT", "C", "CCTT"); - - { - Path path(&graph, 2, { 0, 1, 2 }, 2); - path.shrinkEndBy(3); - - Path expected_path(&graph, 2, { 0 }, 4); - ASSERT_EQ(expected_path, path); - } - - { - Path path(&graph, 0, { 1, 2 }, 2); - path.shrinkEndBy(3); - - Path expected_path(&graph, 0, { 1 }, 0); - ASSERT_EQ(expected_path, path); - } - - { - Path path(&graph, 0, { 1, 2 }, 0); - path.shrinkEndBy(1); - - Path expected_path(&graph, 0, { 1 }, 0); - ASSERT_EQ(expected_path, path); - } - - { - Path path(&graph, 0, { 1, 2 }, 0); - path.shrinkEndBy(0); - - Path expected_path(&graph, 0, { 1 }, 1); - ASSERT_EQ(expected_path, path); - } -} - -TEST(ShrinkingPathEnds, PathWithLoop_PathShrank) -{ - Graph graph = makeStrGraph("ATA", "CG", "TATTTTTTTTT"); - - Path path(&graph, 1, { 0, 1, 1, 1, 2 }, 3); - path.shrinkEndBy(5); - - Path expected_path(&graph, 1, { 0, 1, 1 }, 2); - ASSERT_EQ(expected_path, path); -} - -TEST(ShrinkingPathsByGivenLength, TypicalPathInStrGraph_PathShrank) -{ - Graph graph = makeStrGraph("TTT", "AC", "CCC"); - - Path path(&graph, 1, { 0, 1, 1, 2 }, 2); - const int32_t start_shrink_len = 5; - const int32_t end_shrink_len = 3; - path.shrinkBy(start_shrink_len, end_shrink_len); - - const Path expected_path(&graph, 1, { 1 }, 1); - ASSERT_EQ(expected_path, path); -} - -TEST(ComputingPathDistance, DistanceFromStart_DistanceReturned) -{ - Graph graph = makeDeletionGraph("TTT", "AC", "CCC"); - - Path path(&graph, 1, { 0, 1, 2 }, 2); - ASSERT_EQ(0, path.getDistanceFromPathStart(0, 1)); - ASSERT_EQ(4, path.getDistanceFromPathStart(2, 0)); - ASSERT_EQ(3, path.getDistanceFromPathStart(1, 1)); -} - -TEST(ComputingPathDistance, DistanceFromStart_ExceptionWhenNodeNotInPath) -{ - Graph graph = makeDeletionGraph("TTT", "AC", "CCCC"); - - Path path(&graph, 1, { 0, 2 }, 2); - - ASSERT_THROW(path.getDistanceFromPathStart(0, 0), std::logic_error); - ASSERT_THROW(path.getDistanceFromPathStart(1, 0), std::logic_error); - ASSERT_THROW(path.getDistanceFromPathStart(2, 3), std::logic_error); -} - -TEST(ComparingPaths, TypicalPaths_Compared) -{ - Graph graph = makeStrGraph("TTT", "AC", "CCC"); - - { - Path path_a(&graph, 1, { 0, 1, 2 }, 1); - Path path_b(&graph, 1, { 0, 1, 2 }, 2); - EXPECT_TRUE(path_a < path_b); - EXPECT_FALSE(path_b < path_a); - EXPECT_FALSE(path_a == path_b); - } - - { - Path path_a(&graph, 0, { 0, 1, 1 }, 1); - Path path_b(&graph, 0, { 0, 1, 2 }, 1); - EXPECT_TRUE(path_a < path_b); - EXPECT_FALSE(path_b < path_a); - EXPECT_FALSE(path_a == path_b); - } -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/PinnedAlignerTest.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/tests/PinnedAlignerTest.cpp deleted file mode 100644 index d02fd51..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/PinnedAlignerTest.cpp +++ /dev/null @@ -1,102 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphalign/PinnedAligner.hh" - -#include "gtest/gtest.h" - -using std::string; - -using namespace graphtools; - -TEST(PopulatingTracebackMatrix, CoreBases_TracebackMatrixPopulated) -{ - const int32_t match_score = 1; - const int32_t mismatch_score = -1; - const int32_t gap_penalty = -2; - PinnedAligner aligner(match_score, mismatch_score, gap_penalty); - - const string query = "AAAC"; - const string reference = "AGC"; - TracebackMatrix matrix = aligner.populateTracebackMatrix(reference, query); - - TracebackMatrix expected_matrix("S/0 D/-2 D/-4 D/-6\n" - "I/-2 M/1 D/-1 D/-3\n" - "I/-4 M/-1 X/0 X/-2\n" - "I/-6 M/-3 X/-2 X/-1\n" - "I/-8 I/-5 X/-4 M/-1"); - EXPECT_EQ(expected_matrix, matrix); -} - -TEST(PerformingPrefixAlignment, CoreBases_Aligned) -{ - // query: TAACTTTTGGG - // | ||||| - // reference: TG-CTTTTAA - - const string query = "TAACTTTTGGG"; - const string reference = "TGCTTTTAA"; - - PinnedAligner aligner(1, -1, -2); - Alignment alignment = aligner.prefixAlign(reference, query); - - Alignment expected_alignment(0, "1M1I1X5M3S"); - EXPECT_EQ(expected_alignment, alignment); -} - -TEST(PerformingPrefixAlignment, NoBasesAlign_SoftclipAlignment) -{ - const string query = "AAAAA"; - const string reference = "TGCTTTT"; - - PinnedAligner aligner(1, -1, -2); - Alignment alignment = aligner.prefixAlign(reference, query); - - Alignment expected_alignment(0, "5S"); - EXPECT_EQ(expected_alignment, alignment); -} - -TEST(PerformingSuffixAlignment, CoreBases_Aligned) -{ - // TCACG-GAGA - // ||| ||| - // TACGAGAG- - - const string query = "TCACGGAGA"; - const string reference = "TACGAGAG"; - - PinnedAligner aligner(5, -4, -8); - Alignment alignment = aligner.suffixAlign(reference, query); - - Alignment expected_alignment(1, "2S3M1D3M1I"); - EXPECT_EQ(expected_alignment, alignment); -} - -TEST(PerformingSuffixAlignment, NoBasesAlign_SoftclipAlignment) -{ - const string query = "CGCGCG"; - const string reference = "TATATATA"; - - PinnedAligner aligner(5, -4, -8); - Alignment alignment = aligner.suffixAlign(reference, query); - - Alignment expected_alignment(8, "6S"); - EXPECT_EQ(expected_alignment, alignment); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/PinnedDagAlignerTest.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/tests/PinnedDagAlignerTest.cpp deleted file mode 100644 index ef7699f..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/PinnedDagAlignerTest.cpp +++ /dev/null @@ -1,75 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Roman Petrovski -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include -#include - -#include "graphalign/DagAlignerAffine.hh" -#include "graphalign/GappedAligner.hh" -#include "graphalign/PinnedDagAligner.hh" -#include "graphcore/Graph.hh" -#include "graphcore/GraphBuilders.hh" -#include "graphcore/Path.hh" - -#include "gtest/gtest.h" - -using std::string; -using namespace testing; -using namespace graphtools; -using namespace graphalign; -using namespace graphalign::dagAligner; - -template std::string toString(const T& obj) -{ - std::stringstream ss; - ss << obj; - return ss.str(); -} - -TEST(SimpleGraph, AlignSuffix) -{ - Graph graph = makeSwapGraph("AAAA", "C", "T", "GGGG"); - graph.addEdge(1, 1); - Path seed( - &graph, 1, - { - 0, - }, - 3); - PinnedDagAligner dag_pinned_aligner(1, -1, 0, -2); - int32_t top_dag_score = INT32_MIN; - std::list> res = dag_pinned_aligner.prefixAlign(seed, "ACGG", 8, top_dag_score); - EXPECT_EQ(4, top_dag_score); - EXPECT_EQ("(0@1)-(1)-(3@2)", toString(res.front().first)); - EXPECT_EQ("4M", res.front().second.generateCigar()); -} - -TEST(SimpleGraph, AlignPrefix) -{ - Graph graph = makeSwapGraph("AAAA", "C", "T", "GGGG"); - graph.addEdge(1, 1); - Path seed(&graph, 0, { 2, 3 }, 2); - PinnedDagAligner dag_pinned_aligner(1, -1, 0, -2); - int32_t top_dag_score = INT32_MIN; - std::list> res = dag_pinned_aligner.suffixAlign(seed, "AA", 8, top_dag_score); - EXPECT_EQ(2, top_dag_score); - EXPECT_EQ("(0@2)-(2)-(3@2)", toString(res.front().first)); - EXPECT_EQ("2M", res.front().second.generateCigar()); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/SequenceOperationsTest.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/tests/SequenceOperationsTest.cpp deleted file mode 100644 index af76f1f..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/SequenceOperationsTest.cpp +++ /dev/null @@ -1,92 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphutils/SequenceOperations.hh" - -#include -#include -#include - -#include "gtest/gtest.h" - -using std::map; -using std::string; -using std::vector; - -using namespace graphtools; - -TEST(CheckingSequenceComposition, TypicalSequences_CompositionDetermined) -{ - const string reference_nucleotide_sequence = "ACTG"; - const string reference_sequence = "ACWG"; - const string nonreference_sequence = "ZZZZ"; - - EXPECT_TRUE(checkIfNucleotideReferenceSequence(reference_nucleotide_sequence)); - EXPECT_FALSE(checkIfNucleotideReferenceSequence(reference_sequence)); - - EXPECT_TRUE(checkIfReferenceSequence(reference_nucleotide_sequence)); - EXPECT_TRUE(checkIfReferenceSequence(reference_sequence)); - EXPECT_FALSE(checkIfReferenceSequence(nonreference_sequence)); -} - -TEST(ExpandingDegenerateSymbols, TypicalSymbol_SymbolExpanded) -{ - map kSymbolExpansion - = { { 'A', "A" }, { 'C', "C" }, { 'T', "T" }, { 'G', "G" }, { 'R', "AG" }, { 'Y', "CT" }, - { 'K', "GT" }, { 'M', "AC" }, { 'S', "CG" }, { 'W', "AT" }, { 'B', "CGT" }, { 'D', "AGT" }, - { 'H', "ACT" }, { 'V', "ACG" }, { 'N', "ACGT" }, { 'X', "X" } }; - - for (const auto& symbol_expansion : kSymbolExpansion) - { - EXPECT_EQ(symbol_expansion.second, expandReferenceSymbol(symbol_expansion.first)); - } -} - -TEST(ExpandingDegenerateSymbols, NonReferenceSymbol_ExceptionThrown) { ASSERT_ANY_THROW(expandReferenceSymbol('a')); } - -TEST(ExpandingDegenerateSequences, SequenceWithDegenerateBases_SequenceExpanded) -{ - string sequence = "RAK"; - const vector expected_expansion = { "AAG", "GAG", "AAT", "GAT" }; - vector observed_expansion = { "AAG", "GAG", "AAT", "GAT" }; - expandReferenceSequence(sequence, observed_expansion); - ASSERT_EQ(expected_expansion, observed_expansion); -} - -TEST(SplittingStrings, WordsDelimitedBySpaces_StringVector) -{ - const string composite_string = "abc /+= ##"; - const vector expected_words = { "abc", "/+=", "##" }; - ASSERT_EQ(expected_words, splitStringByWhitespace(composite_string)); -} - -TEST(SplittingStrings, WordsDelimitedBySlashes_StringVector) -{ - const string string_with_words = "a/b/cd"; - const vector expected_words = { "a", "b", "cd" }; - ASSERT_EQ(expected_words, splitStringByDelimiter(string_with_words, '/')); -} - -TEST(ReverseComplementingSequences, TypicalQueryAndReferenceSequences_ReverseComplemented) -{ - EXPECT_EQ("AAGGCGAT", reverseComplement("ATCGCCTT")); - EXPECT_EQ("aaggcgat", reverseComplement("atcgcctt")); - EXPECT_EQ("RYKMSWBDHVN", reverseComplement("NBDHVWSKMRY")); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/TracebackMatrixTest.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/tests/TracebackMatrixTest.cpp deleted file mode 100644 index 440a050..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/TracebackMatrixTest.cpp +++ /dev/null @@ -1,84 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphalign/TracebackMatrix.hh" - -#include - -#include "gtest/gtest.h" - -using std::string; - -using namespace graphtools; - -TEST(TracebackMatrixInitialization, DefaultInitialization_UnirectedMatrixOfZeros) -{ - TracebackMatrix traceback_matrix(2, 3); - - for (size_t row_index = 0; row_index != 2; ++row_index) - { - for (size_t col_index = 0; col_index != 3; ++col_index) - { - EXPECT_EQ(INT32_MIN, traceback_matrix.score(row_index, col_index)); - EXPECT_EQ(TracebackStep::kStop, traceback_matrix.tracebackStep(row_index, col_index)); - } - } -} - -TEST(TracebackMatrixInitialization, TypicalEncoding_MatrixInitialized) -{ - const std::string encoding = "S/0 D/-2 D/-4\n" - "I/0 M/-1 I/-4"; - - TracebackMatrix traceback_matrix(encoding); - - TracebackMatrix expected_matrix(2, 3); - expected_matrix.setScore(0, 0, 0); - expected_matrix.setTracebackStep(0, 0, TracebackStep::kStop); - - expected_matrix.setScore(0, 1, -2); - expected_matrix.setTracebackStep(0, 1, TracebackStep::kLeft); - - expected_matrix.setScore(0, 2, -4); - expected_matrix.setTracebackStep(0, 2, TracebackStep::kLeft); - - expected_matrix.setScore(1, 0, 0); - expected_matrix.setTracebackStep(1, 0, TracebackStep::kTop); - - expected_matrix.setScore(1, 1, -1); - expected_matrix.setTracebackStep(1, 1, TracebackStep::kDiagonalMatch); - - expected_matrix.setScore(1, 2, -4); - expected_matrix.setTracebackStep(1, 2, TracebackStep::kTop); - - ASSERT_EQ(expected_matrix, traceback_matrix); -} - -TEST(LocatingTopScoringCell, TypicalMatrix_CellLocated) -{ - TracebackMatrix matrix("S/0 S/2 S/10\n" - "S/-1 S/3 S/-1"); - - size_t row_index; - size_t col_index; - matrix.locateTopScoringCell(row_index, col_index); - EXPECT_EQ(0u, row_index); - EXPECT_EQ(2u, col_index); -} diff --git a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/TracebackRunnerTest.cpp b/ehunter/thirdparty/graph-tools-master-f421f4c/tests/TracebackRunnerTest.cpp deleted file mode 100644 index cd1d8e3..0000000 --- a/ehunter/thirdparty/graph-tools-master-f421f4c/tests/TracebackRunnerTest.cpp +++ /dev/null @@ -1,70 +0,0 @@ -// -// GraphTools library -// Copyright 2017-2019 Illumina, Inc. -// All rights reserved. -// -// Author: Egor Dolzhenko -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// - -#include "graphalign/TracebackRunner.hh" - -#include "gtest/gtest.h" - -using std::string; - -using namespace graphtools; - -TEST(PerformingTraceback, NeedlemanWunschMatrixFromCoreBaseAlignment_Traced) -{ - TracebackMatrix matrix("S/0 D/-2 D/-4 D/-6\n" - "I/-2 M/1 D/-1 D/-3\n" - "I/-4 M/-1 X/0 M/-2\n" - "I/-6 M/-3 I/-2 M/-1\n" - "I/-8 I/-5 M/-4 M/-1"); - - const string query = "AAAC"; - const string reference = "AGC"; - - TracebackRunner traceback_runner(matrix); - Alignment alignment = traceback_runner.runTraceback(4, 3); - - Alignment expected_alignment(0, "1M1X1I1M"); - EXPECT_EQ(expected_alignment, alignment); -} - -TEST(PerformingTraceback, LocalAlignmentOfCoreBases_Traced) -{ - // GGAT-CGAA - // || | - // CATAC - TracebackMatrix matrix("S/0 S/0 S/0 S/0 S/0 S/0\n" - "S/0 S/0 S/0 S/0 S/0 S/0\n" - "S/0 S/0 S/0 S/0 S/0 S/0\n" - "S/0 S/0 M/5 D/1 M/5 D/1\n" - "S/0 S/0 I/1 M/10 D/6 D/2\n" - "S/0 M/5 D/1 I/6 M/7 M/11\n" - "S/0 I/1 M/2 I/2 M/3 I/7\n" - "S/0 S/0 M/5 D/1 M/7 I/3\n" - "S/0 S/0 M/5 M/2 M/2 M/4"); - - const string query = "GGATCGAA"; - const string reference = "CATAC"; - - TracebackRunner traceback_runner(matrix); - Alignment alignment = traceback_runner.runTraceback(5, 5); - - Alignment expected_alignment(1, "2S2M1D1M3S"); - EXPECT_EQ(expected_alignment, alignment); -} diff --git a/example/output/repeats.json b/example/output/repeats.json index 5bd044a..1e48001 100644 --- a/example/output/repeats.json +++ b/example/output/repeats.json @@ -2,7 +2,8 @@ "LocusResults": { "SNV_AND_STR": { "AlleleCount": 2, - "Coverage": 99.6486486486486, + "Coverage": 99.64864864864865, + "FragmentLength": 351, "LocusId": "SNV_AND_STR", "ReadLength": 150, "Variants": { @@ -20,9 +21,9 @@ "VariantType": "SmallVariant" }, "SNV_AND_STR_chr1:2005-2008": { - "CountsOfFlankingReads": "(0, 1), (1, 4), (2, 2), (3, 1), (4, 2), (5, 1), (6, 1), (7, 2), (8, 3), (9, 3)", + "CountsOfFlankingReads": "(1, 2), (2, 3), (3, 2), (4, 2), (5, 1), (6, 1), (7, 2), (8, 2), (9, 2), (10, 3)", "CountsOfInrepeatReads": "()", - "CountsOfSpanningReads": "(2, 38), (10, 29)", + "CountsOfSpanningReads": "(2, 47), (10, 35)", "Genotype": "2/10", "GenotypeConfidenceInterval": "2-2/10-10", "ReferenceRegion": "chr1:2005-2008", diff --git a/example/output/repeats.vcf b/example/output/repeats.vcf index 1f13d9d..90fa9e9 100644 --- a/example/output/repeats.vcf +++ b/example/output/repeats.vcf @@ -6,18 +6,19 @@ ##INFO= ##INFO= ##INFO= +##FILTER= ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= -##FORMAT= +##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##ALT= ##ALT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT variants -chr1 2001 . A T . PASS VARID=SNV_AND_STR_chr1:2000-2001 AD:LC:GT 47,39:99.648649:0/1 -chr1 2005 . C , . PASS END=2008;REF=1;RL=1;RU=CAG;VARID=SNV_AND_STR_chr1:2005-2008;REPID=SNV_AND_STR_chr1:2005-2008 GT:SO:REPCN:REPCI:ADSP:ADFL:ADIR:LC 1/2:SPANNING/SPANNING:2/10:2-2/10-10:38/29:7/20:0/0:99.648649 +chr1 2001 . A T . PASS VARID=SNV_AND_STR_chr1:2000-2001 GT:AD:LC 0/1:47,39:99.648649 +chr1 2005 . C , . PASS END=2008;REF=1;RL=3;RU=CAG;VARID=SNV_AND_STR_chr1:2005-2008;REPID=SNV_AND_STR_chr1:2005-2008 GT:SO:REPCN:REPCI:ADSP:ADFL:ADIR:LC 1/2:SPANNING/SPANNING:2/10:2-2/10-10:47/35:5/20:0/0:99.648649 diff --git a/example/run.sh b/example/run.sh index be338a3..42a09b7 100644 --- a/example/run.sh +++ b/example/run.sh @@ -1,8 +1,10 @@ -#!/bin/bash +#!/usr/bin/env bash + +scriptDir=$(cd $(dirname $0) && pwd -P) +cd $scriptDir ../bin/ExpansionHunter \ --reads input/variants.bam \ --reference input/reference.fa \ --variant-catalog input/variants.json \ --output-prefix output/repeats - diff --git a/tools/docker/debug/mallinfo2/Dockerfile b/tools/docker/debug/mallinfo2/Dockerfile index a5137ca..99f9932 100644 --- a/tools/docker/debug/mallinfo2/Dockerfile +++ b/tools/docker/debug/mallinfo2/Dockerfile @@ -12,6 +12,7 @@ RUN yum install -y \ git \ libcurl-devel \ libstdc++-static \ + openssl-devel \ xz-devel \ zlib-devel diff --git a/tools/docker/debug/mallinfo2/setup-docker-image-and-build.bash b/tools/docker/debug/mallinfo2/setup-docker-image-and-build.bash index 5767caa..12ccfe7 100755 --- a/tools/docker/debug/mallinfo2/setup-docker-image-and-build.bash +++ b/tools/docker/debug/mallinfo2/setup-docker-image-and-build.bash @@ -1,31 +1,6 @@ #!/usr/bin/env bash -set -o errexit nounset +scriptDir=$(cd "$(dirname "$0")" && pwd -P) -dockerRoot=/builder -scriptDir=$(cd $(dirname $0) && pwd -P) -rootDir=$(cd $scriptDir && cd ../../../.. && pwd -P) -tag1=ehdebug -tag2=mallinfo2 -tag=${tag1}:${tag2} -buildDirName=build-docker-${tag1}-${tag2} - - -# Build docker image -sudo docker build -t $tag . - -# Run EH build script in docker container -sudo docker run -v $rootDir:$dockerRoot -i $tag bash -<