Merge pull request #80 from Illumina/release-to-public

Refactor of C++ and SWIG code

CMakeLists.txt

@@ -17,6 +17,7 @@ set(INTEROP_DL_LIB interop_fpic_lib)
 option(ENABLE_BACKWARDS_COMPATIBILITY "Compile code for c++98" ON)
 option(ENABLE_DOCS "Build documentation with Doxygen" ON)
 option(ENABLE_SWIG "Build third-party language bindings, e.g. C#" ON)
+option(ENABLE_CSHARP "Build C# language bindings" ON)
 option(ENABLE_TEST "Build unit tests (depends on Boost)" ON)
 option(ENABLE_APPS "Build command line programs" ON)
 option(ENABLE_EXAMPLES "Build example programs" ON)
@@ -75,6 +76,7 @@ if(ENABLE_DOCS)
     add_subdirectory("docs")
 endif()
 install(DIRECTORY interop DESTINATION include)
+install(FILES README.md docs/src/changes.md DESTINATION .)
 
 find_package(Git)
 if(GIT_FOUND)

cmake/InternalUtils.cmake

@@ -42,8 +42,10 @@ macro(interop_config_compiler_and_linker)
 
     include(CheckIsNaN)
 
-    if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang" OR CMAKE_COMPILER_IS_GNUCC)
+    if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "AppleClang" OR CMAKE_COMPILER_IS_GNUCC OR "${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
         set(COMPILER_IS_GNUCC_OR_CLANG ON)
+    else()
+        set(COMPILER_IS_GNUCC_OR_CLANG OFF)
     endif()
 
     if(CMAKE_SIZEOF_VOID_P EQUAL "4")
@@ -72,7 +74,7 @@ macro(interop_config_compiler_and_linker)
     if(IS_INT64_LONG)
         add_definitions(-DHAVE_LONG64)
     endif()
-
+    check_type_size(size_t SIZE_T)
     if(MINGW)
         set(CXX11_FLAG_ "-std=gnu++11")
     else()
@@ -101,12 +103,17 @@ macro(interop_config_compiler_and_linker)
             message(FATAL_ERROR "Unsupported compiler")
         endif()
     endif()
-    if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "AppleClang" OR CMAKE_COMPILER_IS_GNUCC)
+    if(COMPILER_IS_GNUCC_OR_CLANG)
         SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Werror -Wno-c++0x-compat -Wno-error=c++0x-compat -Wextra")
+        if(WIN32 AND MINGW)
+            # Add big object support to Windows Compilers
+            SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wa,-mbig-obj")
+        endif()
     elseif(MSVC)
         # Visual Studio Complains about not being able to create an assignment operator and copy constructor
         # -wd4511 and -wd4512 disable these pointless warnings
-        SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /WX -wd4511 -wd4512")
+        # Add big object support to Windows Compilers
+        SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /WX -wd4511 -wd4512 /bigobj")
     elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
         if(WIN32)
             set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /WX")
@@ -115,7 +122,7 @@ macro(interop_config_compiler_and_linker)
         endif()
     endif()
     if(NOT ENABLE_BACKWARDS_COMPATIBILITY)
-        if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "AppleClang" OR CMAKE_COMPILER_IS_GNUCC)
+        if(COMPILER_IS_GNUCC_OR_CLANG)
             set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CXX_CX11_FLAG}")
         endif()
     elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "AppleClang")

cmake/Modules/FindGMock.cmake

@@ -31,11 +31,24 @@ find_library(GMOCK_LIBRARY
         PATH_SUFFIXES . lib lib64
         )
 find_library(GMOCK_MAIN_LIBRARY
-        NAMES gmock_main$
+        NAMES gmock_main
         HINTS ${PC_GMOCK_INCLUDEDIR} ${PC_GMOCK_INCLUDE_DIRS} ${GMOCK_ROOT} $ENV{GMOCK_DIR}
         PATH_SUFFIXES . lib lib64
         )
 
+
+find_library(GMOCK_LIBRARY_DEBUG
+        NAMES gmock-d
+        HINTS ${PC_GMOCK_INCLUDEDIR} ${PC_GMOCK_INCLUDE_DIRS} ${GMOCK_ROOT} $ENV{GMOCK_DIR}
+        PATH_SUFFIXES . lib lib64
+)
+find_library(GMOCK_MAIN_LIBRARY_DEBUG
+        NAMES gmock_main-d
+        HINTS ${PC_GMOCK_INCLUDEDIR} ${PC_GMOCK_INCLUDE_DIRS} ${GMOCK_ROOT} $ENV{GMOCK_DIR}
+        PATH_SUFFIXES . lib lib64
+)
+
+
 if(NOT GMOCK_INCLUDE_DIR OR NOT GMOCK_LIBRARY OR NOT GMOCK_MAIN_LIBRARY)
 
     if(NOT GMOCK_INCLUDE_DIR)
@@ -82,7 +95,20 @@ if(NOT GMOCK_INCLUDE_DIR OR NOT GMOCK_LIBRARY OR NOT GMOCK_MAIN_LIBRARY)
     set(GMOCK_TARGET googlemock)
 endif()
 
-
+if(GMOCK_LIBRARY AND GMOCK_LIBRARY_DEBUG)
+    get_filename_component(GMOCK_RELEASE_EXT ${GMOCK_LIBRARY} EXT)
+    get_filename_component(GMOCK_DEBUG_EXT ${GMOCK_LIBRARY_DEBUG} EXT)
+    if(GMOCK_RELEASE_EXT STREQUAL GMOCK_DEBUG_EXT)
+        set(GMOCK_LIBRARY optimized ${GMOCK_LIBRARY} debug ${GMOCK_LIBRARY_DEBUG})
+    endif()
+endif()
+if(GMOCK_MAIN_LIBRARY AND GMOCK_MAIN_LIBRARY_DEBUG)
+    get_filename_component(GMOCK_RELEASE_EXT ${GMOCK_MAIN_LIBRARY} EXT)
+    get_filename_component(GMOCK_DEBUG_EXT ${GMOCK_MAIN_LIBRARY_DEBUG} EXT)
+    if(GMOCK_RELEASE_EXT STREQUAL GMOCK_DEBUG_EXT)
+        set(GMOCK_MAIN_LIBRARY optimized ${GMOCK_MAIN_LIBRARY} debug ${GMOCK_MAIN_LIBRARY_DEBUG})
+    endif()
+endif()
 
 set(GMOCK_LIBRARIES ${GMOCK_LIBRARY} )
 set(GMOCK_INCLUDE_DIRS ${GMOCK_INCLUDE_DIR} )

cmake/Modules/FindGTest.cmake

@@ -31,12 +31,40 @@ find_library(GTEST_LIBRARY
         PATH_SUFFIXES . lib lib64
 )
 find_library(GTEST_MAIN_LIBRARY
-        NAMES gtest_main$
+        NAMES gtest_main
         HINTS ${PC_GTEST_INCLUDEDIR} ${PC_GTEST_INCLUDE_DIRS} ${GTEST_ROOT} $ENV{GTEST_DIR}
         PATH_SUFFIXES . lib lib64
         )
 
-if(NOT GTEST_INCLUDE_DIR OR NOT GTEST_LIBRARY OR NOT GTEST_MAIN_LIBRARY)
+find_library(GTEST_LIBRARY_DEBUG
+        NAMES gtest-d
+        HINTS ${PC_GTEST_INCLUDEDIR} ${PC_GTEST_INCLUDE_DIRS} ${GTEST_ROOT} $ENV{GTEST_DIR}
+        PATH_SUFFIXES . lib lib64
+        )
+find_library(GTEST_MAIN_LIBRARY_DEBUG
+        NAMES gtest_main-d
+        HINTS ${PC_GTEST_INCLUDEDIR} ${PC_GTEST_INCLUDE_DIRS} ${GTEST_ROOT} $ENV{GTEST_DIR}
+        PATH_SUFFIXES . lib lib64
+        )
+
+find_path(GMOCK_INCLUDE_DIR_TEST
+        NAMES gmock/gmock.h
+        HINTS ${PC_GMOCK_INCLUDEDIR} ${PC_GMOCK_INCLUDE_DIRS} ${GMOCK_ROOT} $ENV{GMOCK_DIR}
+        PATH_SUFFIXES . include
+        )
+
+find_library(GMOCK_LIBRARY_TEST
+        NAMES gmock
+        HINTS ${PC_GMOCK_INCLUDEDIR} ${PC_GMOCK_INCLUDE_DIRS} ${GMOCK_ROOT} $ENV{GMOCK_DIR}
+        PATH_SUFFIXES . lib lib64
+        )
+find_library(GMOCK_MAIN_LIBRARY_TEST
+        NAMES gmock_main
+        HINTS ${PC_GMOCK_INCLUDEDIR} ${PC_GMOCK_INCLUDE_DIRS} ${GMOCK_ROOT} $ENV{GMOCK_DIR}
+        PATH_SUFFIXES . lib lib64
+        )
+
+if(NOT GTEST_INCLUDE_DIR OR NOT GTEST_LIBRARY OR NOT GTEST_MAIN_LIBRARY OR NOT GMOCK_INCLUDE_DIR_TEST OR NOT GMOCK_LIBRARY_TEST OR NOT GMOCK_MAIN_LIBRARY_TEST)
 
     if(NOT GTEST_INCLUDE_DIR)
         message(STATUS "GTest include directory not found")
@@ -82,7 +110,20 @@ if(NOT GTEST_INCLUDE_DIR OR NOT GTEST_LIBRARY OR NOT GTEST_MAIN_LIBRARY)
     set(GTEST_TARGET gtest)
 endif()
 
-
+if(GTEST_LIBRARY AND GTEST_LIBRARY_DEBUG)
+    get_filename_component(GTEST_RELEASE_EXT ${GTEST_LIBRARY} EXT)
+    get_filename_component(GTEST_DEBUG_EXT ${GTEST_LIBRARY_DEBUG} EXT)
+    if(GTEST_RELEASE_EXT STREQUAL GTEST_DEBUG_EXT)
+        set(GTEST_LIBRARY optimized ${GTEST_LIBRARY} debug ${GTEST_LIBRARY_DEBUG})
+    endif()
+endif()
+if(GTEST_MAIN_LIBRARY AND GTEST_MAIN_LIBRARY_DEBUG)
+    get_filename_component(GTEST_RELEASE_EXT ${GTEST_MAIN_LIBRARY} EXT)
+    get_filename_component(GTEST_DEBUG_EXT ${GTEST_MAIN_LIBRARY_DEBUG} EXT)
+    if(GTEST_RELEASE_EXT STREQUAL GTEST_DEBUG_EXT)
+        set(GTEST_MAIN_LIBRARY optimized ${GTEST_MAIN_LIBRARY} debug ${GTEST_MAIN_LIBRARY_DEBUG})
+    endif()
+endif()
 
 set(GTEST_LIBRARIES ${GTEST_LIBRARY} )
 set(GTEST_INCLUDE_DIRS ${GTEST_INCLUDE_DIR} )

cmake/Modules/UseCSharp.cmake

@@ -92,7 +92,6 @@ macro( CSHARP_ADD_PROJECT type name )
   #endif ()
   #list( SORT sources_dep )
 
-  set(CSHARP_OUTPUT_DIR ${CMAKE_RUNTIME_OUTPUT_DIRECTORY})
   set(CSHARP_OUTPUT_DIR ${CMAKE_CURRENT_BINARY_DIR})
 
   string (REPLACE ";" "," source_list "${sources}")
@@ -101,17 +100,17 @@ macro( CSHARP_ADD_PROJECT type name )
   # Add custom target and command
   MESSAGE( STATUS "Adding C# ${type} ${name}: '${CSHARP_COMPILER} /t:${type} /out:${name}.${output} /platform:${CSHARP_PLATFORM} ${CSHARP_SDK} ${refs} ${sources}'" )
   add_custom_command(
-    COMMENT "Compiling C# ${type} ${name}: '${CSHARP_COMPILER} /unsafe /t:${type} /out:${CSHARP_OUTPUT_DIR}/${name}.${output} /platform:${CSHARP_PLATFORM} ${CSHARP_SDK} ${refs} ${sources}'"
-    OUTPUT ${CMAKE_BINARY_DIR}/${name}.${output}
-    COMMAND ${CMAKE_COMMAND} -DFILES_TO_COPY="${source_list}" -DDESTINATION_DIR="${CMAKE_BINARY_DIR}" -P "${CMAKE_SOURCE_DIR}/cmake/CopyListOfFiles.cmake"
+    COMMENT "Compiling C# ${type} ${name}: '${CSHARP_COMPILER} /unsafe /t:${type} /out:${CMAKE_CURRENT_BINARY_DIR}/${name}.${output} /platform:${CSHARP_PLATFORM} ${CSHARP_SDK} ${refs} ${sources}'"
+    OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/${name}.${output}
+    COMMAND ${CMAKE_COMMAND} -DFILES_TO_COPY="${source_list}" -DDESTINATION_DIR="${CMAKE_CURRENT_BINARY_DIR}" -P "${CMAKE_SOURCE_DIR}/cmake/CopyListOfFiles.cmake"
     COMMAND ${CSHARP_COMPILER}
     ARGS /t:${type} /out:${CSHARP_OUTPUT_DIR}/${name}.${output} /unsafe /platform:${CSHARP_PLATFORM} ${CSHARP_SDK} ${refs} ${sources}
-    WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+    WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     DEPENDS ${sources_dep}
   )
   add_custom_target(
     ${name} ALL
-    DEPENDS ${CMAKE_BINARY_DIR}/${name}.${output}
+    DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/${name}.${output}
     SOURCES ${sources_dep}
   )
 endmacro( CSHARP_ADD_PROJECT )

docs/Doxyfile.in

@@ -416,7 +416,7 @@ LOOKUP_CACHE_SIZE      = 0
 # normally produced when WARNINGS is set to YES.
 # The default value is: NO.
 
-EXTRACT_ALL            = NO
+EXTRACT_ALL            = YES
 
 # If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will
 # be included in the documentation.
@@ -654,7 +654,7 @@ SHOW_USED_FILES        = YES
 # (if specified).
 # The default value is: YES.
 
-SHOW_FILES             = NO
+SHOW_FILES             = YES
 
 # Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces
 # page. This will remove the Namespaces entry from the Quick Index and from the
@@ -716,6 +716,9 @@ QUIET                  = NO
 
 WARNINGS               = YES
 
+# Treat warnings as errors
+#WARN_AS_ERROR = YES
+
 # If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate
 # warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag
 # will automatically be disabled.
@@ -737,7 +740,7 @@ WARN_IF_DOC_ERROR      = YES
 # parameter documentation, but not about the absence of documentation.
 # The default value is: NO.
 
-WARN_NO_PARAMDOC       = NO
+WARN_NO_PARAMDOC       = YES
 
 # The WARN_FORMAT tag determines the format of the warning messages that doxygen
 # can produce. The string should contain the $file, $line, and $text tags, which

docs/src/changes.md

@@ -1,10 +1,32 @@
 # Changes                                               {#changes}
 
 
-## Trunk
-
-Commit     | Description
--------    | -----------
+## v1.0.9
+
+Date       | Description
+---------- | -----------
+2016-08-26 | Refactor CSharp code into additional library
+2016-08-26 | IPA-5028: Add RunInfo and InterOp validation
+2016-08-19 | Fix sorting in imaging table
+2016-08-18 | Cleanup code
+2016-08-17 | Fix the read ID
+2016-08-16 | IPA-5009: Add sorting to imaging table
+2016-08-16 | IPA-5007: Fix combo boxes on analysis tab
+2016-08-16 | Fix msvc warning and some script differences
+2016-08-15 | Add clear function to run metrics
+2016-08-15 | IPA-4799: Create Internal Coverity Build
+2016-08-11 | Refactor unit tests to make more flexible for regression testing
+2016-08-08 | IPA-4922: Move logic code from header to cpp
+2016-08-05 | IPA-4827: Make run info parsing more robust
+2016-08-03 | Refactor code and add test build script
+2016-08-02 | Add big object support for unit tests
+2016-08-02 | Clean buffers in the heatmap and flowcell
+2016-08-02 | Update travis-ci to GCC-5
+2016-07-28 | Added float array backing to heat map
+2016-07-25 | IPA-4752: Replace InterOp 1.x Code with InterOp 2.x Code - Imaging Tab
+2016-07-22 | Fix camel case
+2016-07-22 | IPA-4751: Integrated InterOp2.x with Analysis Tab
+2016-07-22 | Github Issue 74: Compiler warning as error unsigned/signed comp
 2016-07-21 | Bug fixes for flowcell chart and more recent versions of GCC
 2016-07-17 | Added coverity online scan and fixed some issues found
 

docs/src/performance.md

@@ -63,6 +63,6 @@ Direct Call 1 | 38
 Direct Call 2 | 45
 Indirect Call | < 1
 
-The results show that everytime we make a call from the native language to C++, we pay a hefty price. In many applications
-this is a price we are willing to pay. However, for those applications were performance is a concern, it pays to add
-methods like `copy_focus`, which limit the number of times we have to jump between C# (or another language) and C++.
+The results show that everytime we make a call from the native language to C++, we pay a hefty price. In many applications,
+this is a price we are willing to pay. However, for those applications where performance is a concern, it pays to add
+methods like `copy_focus`, which limit the number of times we have to jump between C# (or another language) and C++.

interop/constants/enums.h

@@ -24,6 +24,7 @@
         INTEROP_TUPLE2(ChannelFeature, 0x10), \
         INTEROP_TUPLE1(UnknownMetricFeature)
 
+
 /** Enumeration of each metric type
  *
  * @note This macro requires the macro INTEROP_TUPLE3 to be defined before use
@@ -34,6 +35,7 @@
         INTEROP_TUPLE4(FWHM, "FWHM", Extraction, CycleFeature|ChannelFeature),\
         /*INTEROP_TUPLE4(PercentBase, "% Base", CorrectedInt, CycleFeature|BaseFeature), */\
         INTEROP_TUPLE4(BasePercent, "% Base", CorrectedInt, CycleFeature|BaseFeature),\
+        INTEROP_TUPLE4(PercentNoCall, "% NoCall", CorrectedInt, CycleFeature),\
         /*INTEROP_TUPLE4(PercentQ20, "% >=Q20", Q, CycleFeature),*/\
         INTEROP_TUPLE4(Q20Percent, "% >=Q20", Q, CycleFeature),\
         /*INTEROP_TUPLE4(PercentQ30, "% >=Q30", Q, CycleFeature),*/\
@@ -45,7 +47,7 @@
         /*INTEROP_TUPLE4(Density, "Density (K/mm2)", Tile, TileFeature),*/ \
         INTEROP_TUPLE4(ClustersPF, "Density PF", Tile, TileFeature),\
         /*INTEROP_TUPLE4(DensityPF, "Density PF", Tile, TileFeature),*/\
-        INTEROP_TUPLE4(ClusterCount, "Clusters", Tile, TileFeature),\
+        INTEROP_TUPLE4(ClusterCount, "Cluster Count", Tile, TileFeature),\
         /*INTEROP_TUPLE4(ClusterCount, "Cluster Count", Tile, TileFeature),*/\
         INTEROP_TUPLE4(ClusterCountPF, "Clusters PF", Tile, TileFeature),\
         INTEROP_TUPLE4(ErrorRate, "Error Rate", Error, CycleFeature),\
@@ -157,10 +159,10 @@
         INTEROP_TUPLE1(InstrumentCount), \
         INTEROP_TUPLE1(UnknownInstrument)
 
-/** Enumeration of instrument types
+/** Enumeration of metric types
  *
  * @note This macro requires the macro INTEROP_TUPLE1 to be defined before use
- * @see illumina::interop::constants::instrument_type
+ * @see illumina::interop::constants::metric_base_type
  */
 #define INTEROP_ENUM_METRIC_BASE_TYPES \
         /** Tile base types are written out once for each tile */\
@@ -169,6 +171,8 @@
         INTEROP_TUPLE1(BaseCycleType),\
         /** Read base types are written out once for each tile and read */\
         INTEROP_TUPLE1(BaseReadType),\
+        /** Lane base types are written out once for each lane and cycle */\
+        INTEROP_TUPLE1(BaseLaneType),\
         INTEROP_TUPLE1(BaseMetricCount),\
         INTEROP_TUPLE1(UnknownBaseType)
 
@@ -201,6 +205,7 @@
         INTEROP_TUPLE1(Shifted),\
         INTEROP_TUPLE1(UnknownBarPlotOption)
 
+/** Sentinel for an unknown enum type */
 #define INTEROP_UNKNOWN 0xff
 /** This temp macro converts a enum/description pair into the an enum (first element of the pair) */
 #define INTEROP_TUPLE4(X, Y, Z, A) X
@@ -211,6 +216,8 @@
 /** This temp macro converts an enum/value pair to an enum */
 #define INTEROP_TUPLE2(X, V) X=V
 
+
+
 namespace illumina { namespace interop { namespace constants
 {
     /** Common codes for all enums */

interop/constants/typedefs.h

@@ -19,5 +19,7 @@ namespace illumina { namespace interop { namespace constants {
     typedef constant_type<metric_base_type, BaseCycleType> base_cycle_t;
     /** Define base type for read metrics */
     typedef constant_type<metric_base_type, BaseReadType> base_read_t;
+    /** Define base type for lane metrics */
+    typedef constant_type<metric_base_type, BaseLaneType> base_lane_t;
 
 }}}

interop/interop.h

@@ -18,7 +18,8 @@
 #include "interop/logic/summary/index_summary.h"
 #include "interop/logic/summary/run_summary.h"
 
-namespace illumina { namespace interop{
+namespace illumina { namespace interop
+{
     /** Get the version of the library
      *
      * @return library version