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.gitignore
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/build
*.swp
/GBfileNoFeats.ape~
/invalidGBfile.ape~
/libs/biojava-1.7.1/LICENSE
/libs/biojava-1.7.1/LICENSE.COMMONS
/libs/biojava-1.7.1/README
/libs/biojava-1.7.1/README.biosql
/libs/biojava-1.7.1/apps/org/biojava/app/BioFlatIndex.java
/libs/biojava-1.7.1/apps/org/biojava/app/BioGetSeq.java
/libs/biojava-1.7.1/build.xml
/libs/biojava-1.7.1/demos-1.7.1.jar
/libs/biojava-1.7.1/demos/CircLocTest/CircularLocationTester.java
/libs/biojava-1.7.1/demos/CircLocTest/TestFrame.java
/libs/biojava-1.7.1/demos/ListChangeTypes.java
/libs/biojava-1.7.1/demos/RFetch.java
/libs/biojava-1.7.1/demos/annodb/CreateIndexDB.java
/libs/biojava-1.7.1/demos/biosql/DummyFromGFF.java
/libs/biojava-1.7.1/demos/biosql/LargeSequenceTest.java
/libs/biojava-1.7.1/demos/biosql/SeqDumper.java
/libs/biojava-1.7.1/demos/biosql/SeqEMBL.java
/libs/biojava-1.7.1/demos/biosql/SeqGFF.java
/libs/biojava-1.7.1/demos/biosql/SequenceTest.java
/libs/biojava-1.7.1/demos/biosql/UploadFlat.java
/libs/biojava-1.7.1/demos/blastxml/BlastParser.java
/libs/biojava-1.7.1/demos/blastxml/input.xml
/libs/biojava-1.7.1/demos/das/TestDAS.java
/libs/biojava-1.7.1/demos/das/TestDASG.java
/libs/biojava-1.7.1/demos/das/TestDASH.java
/libs/biojava-1.7.1/demos/das/TestDSN.java
/libs/biojava-1.7.1/demos/dist/TestDistribution.java
/libs/biojava-1.7.1/demos/dist/TestOrderNAlphabet.java
/libs/biojava-1.7.1/demos/dist/TestOrderNDistribution.java
/libs/biojava-1.7.1/demos/dist/Tools.java
/libs/biojava-1.7.1/demos/dp/Dice.java
/libs/biojava-1.7.1/demos/dp/PairwiseAlignment.java
/libs/biojava-1.7.1/demos/dp/PatternFinder.java
/libs/biojava-1.7.1/demos/dp/SearchProfile.java
/libs/biojava-1.7.1/demos/dp/ViterbiAlign.java
/libs/biojava-1.7.1/demos/dp/fake.fasta
/libs/biojava-1.7.1/demos/dp/fakepromoter.xml
/libs/biojava-1.7.1/demos/dp/package.html
/libs/biojava-1.7.1/demos/eventbasedparsing/Blast2HTML.java
/libs/biojava-1.7.1/demos/eventbasedparsing/BlastLike2XML.java
/libs/biojava-1.7.1/demos/eventbasedparsing/Fasta2XML.java
/libs/biojava-1.7.1/demos/eventbasedparsing/Pdb2XML.java
/libs/biojava-1.7.1/demos/eventbasedparsing/TutorialEx1.java
/libs/biojava-1.7.1/demos/eventbasedparsing/TutorialEx1Handler.java
/libs/biojava-1.7.1/demos/eventbasedparsing/stylesheets/copyall.xsl
/libs/biojava-1.7.1/demos/eventbasedparsing/stylesheets/hitlisthtml.xsl
/libs/biojava-1.7.1/demos/files/ACTN_HUMAN.uniprot
/libs/biojava-1.7.1/demos/files/AF438419.embl
/libs/biojava-1.7.1/demos/files/AL121903.embl
/libs/biojava-1.7.1/demos/files/AL121903.genbank
/libs/biojava-1.7.1/demos/files/ChrI.prom.fasta
/libs/biojava-1.7.1/demos/files/GCG/blast.report
/libs/biojava-1.7.1/demos/files/NP_001307.gp
/libs/biojava-1.7.1/demos/files/clustal/keratin.aln
/libs/biojava-1.7.1/demos/files/fake.fasta
/libs/biojava-1.7.1/demos/files/fakepromoter.xml
/libs/biojava-1.7.1/demos/files/fp_demo.db
/libs/biojava-1.7.1/demos/files/fp_demo.m10
/libs/biojava-1.7.1/demos/files/fp_queries.db
/libs/biojava-1.7.1/demos/files/hmmer/plus_tot.out
/libs/biojava-1.7.1/demos/files/ncbiblast/Massive.out
/libs/biojava-1.7.1/demos/files/ncbiblast/ReadMe
/libs/biojava-1.7.1/demos/files/ncbiblast/blastn.out
/libs/biojava-1.7.1/demos/files/ncbiblast/blastp.out
/libs/biojava-1.7.1/demos/files/ncbiblast/blastx.out
/libs/biojava-1.7.1/demos/files/ncbiblast/shortBlastn.out
/libs/biojava-1.7.1/demos/files/ncbiblast/tblastn.out
/libs/biojava-1.7.1/demos/files/ncbiblast/tblastx.out
/libs/biojava-1.7.1/demos/files/ncbiblast/unsuppVersionBlastn.out
/libs/biojava-1.7.1/demos/files/ontology/biosapiens.obo
/libs/biojava-1.7.1/demos/files/ontology/evidence_code.obo
/libs/biojava-1.7.1/demos/files/ontology/so.obo
/libs/biojava-1.7.1/demos/files/out.gff
/libs/biojava-1.7.1/demos/files/pdb/12E8.pdb
/libs/biojava-1.7.1/demos/files/pdb/hgh_ori.pdb
/libs/biojava-1.7.1/demos/files/pdb/hmga_1.pdb
/libs/biojava-1.7.1/demos/files/pdb/tnf.pdb
/libs/biojava-1.7.1/demos/files/scoptest.fa
/libs/biojava-1.7.1/demos/files/test.hmm
/libs/biojava-1.7.1/demos/files/varC4-2.dna
/libs/biojava-1.7.1/demos/files/varC4-2.gff
/libs/biojava-1.7.1/demos/files/wublast/blastn.out
/libs/biojava-1.7.1/demos/files/wublast/blastp.out
/libs/biojava-1.7.1/demos/files/wublast/blastx.out
/libs/biojava-1.7.1/demos/files/wublast/sh_blastn.out
/libs/biojava-1.7.1/demos/files/wublast/sh_blastp.out
/libs/biojava-1.7.1/demos/files/wublast/sh_blastx.out
/libs/biojava-1.7.1/demos/files/wublast/sh_tblastx.out
/libs/biojava-1.7.1/demos/files/wublast/tblastn.out
/libs/biojava-1.7.1/demos/files/wublast/tblastx.out
/libs/biojava-1.7.1/demos/game/AE002734.game
/libs/biojava-1.7.1/demos/game/README.txt
/libs/biojava-1.7.1/demos/game/SeqIOTatler.java
/libs/biojava-1.7.1/demos/game/TestGAME.java
/libs/biojava-1.7.1/demos/gff/AL121903.embl
/libs/biojava-1.7.1/demos/gff/EmblToGffFasta.java
/libs/biojava-1.7.1/demos/gff/GFFCompare.java
/libs/biojava-1.7.1/demos/gff/GFFFilter.java
/libs/biojava-1.7.1/demos/gff/GFFMask.java
/libs/biojava-1.7.1/demos/gff/GFFToFeatures.java
/libs/biojava-1.7.1/demos/gff/GenbankToGffFasta.java
/libs/biojava-1.7.1/demos/gff/SwissprotToGffFasta.java
/libs/biojava-1.7.1/demos/gff/XFF2GFF.java
/libs/biojava-1.7.1/demos/gff/varC4-2.gff
/libs/biojava-1.7.1/demos/indexing/CreateFAIndex.java
/libs/biojava-1.7.1/demos/indexing/CreateIndex.java
/libs/biojava-1.7.1/demos/indexing/CreateSPIndex.java
/libs/biojava-1.7.1/demos/indexing/ListIDs.java
/libs/biojava-1.7.1/demos/indexing/ReadRaw.java
/libs/biojava-1.7.1/demos/indexing/ReadRawSecondary.java
/libs/biojava-1.7.1/demos/nativeapps/BlastLike2XML.java
/libs/biojava-1.7.1/demos/nativeapps/Pdb2XML.java
/libs/biojava-1.7.1/demos/ontology/obo/ParseBioSapiensOntology.java
/libs/biojava-1.7.1/demos/performance/AlignProteins.java
/libs/biojava-1.7.1/demos/performance/ReadFasta.java
/libs/biojava-1.7.1/demos/performance/ReadFastaX.java
/libs/biojava-1.7.1/demos/performance/ReadFastaX2.java
/libs/biojava-1.7.1/demos/performance/ReverseComplement.java
/libs/biojava-1.7.1/demos/performance/SmithWatermanExample.java
/libs/biojava-1.7.1/demos/performance/UserDisplay.java
/libs/biojava-1.7.1/demos/performance/package.html
/libs/biojava-1.7.1/demos/process/ProcessToolsTest.java
/libs/biojava-1.7.1/demos/prot/TestDigestIO.java
/libs/biojava-1.7.1/demos/search/IndexFastaDB.java
/libs/biojava-1.7.1/demos/seq/AL121903.embl
/libs/biojava-1.7.1/demos/seq/AL121903.genbank
/libs/biojava-1.7.1/demos/seq/FetchSeq.java
/libs/biojava-1.7.1/demos/seq/GCContent.java
/libs/biojava-1.7.1/demos/seq/MotifFinder2.java
/libs/biojava-1.7.1/demos/seq/ReverseComplement.java
/libs/biojava-1.7.1/demos/seq/SimpleAssemblyTest.java
/libs/biojava-1.7.1/demos/seq/TestEmbl.java
/libs/biojava-1.7.1/demos/seq/TestEmbl2.java
/libs/biojava-1.7.1/demos/seq/TestGenbank.java
/libs/biojava-1.7.1/demos/seq/TestRefSeqPrt.java
/libs/biojava-1.7.1/demos/seq/TestSubSequence.java
/libs/biojava-1.7.1/demos/seq/TestSwissprot.java
/libs/biojava-1.7.1/demos/seq/TestTranslation.java
/libs/biojava-1.7.1/demos/seq/UniProtDemo.java
/libs/biojava-1.7.1/demos/seq/db/AddFilesToIndex.java
/libs/biojava-1.7.1/demos/seq/db/CreateIndex.java
/libs/biojava-1.7.1/demos/seq/db/FetchSequence.java
/libs/biojava-1.7.1/demos/seq/db/ListSeqsInIndex.java
/libs/biojava-1.7.1/demos/seq/utrs.fa
/libs/biojava-1.7.1/demos/seqviewer/BeadDemo.java
/libs/biojava-1.7.1/demos/seqviewer/CircularEmblViewer.java
/libs/biojava-1.7.1/demos/seqviewer/EmblViewer.java
/libs/biojava-1.7.1/demos/seqviewer/EmblViewer2.java
/libs/biojava-1.7.1/demos/seqviewer/FastBeadDemo.java
/libs/biojava-1.7.1/demos/seqviewer/GappedViewer.java
/libs/biojava-1.7.1/demos/seqviewer/TraceViewer.java
/libs/biojava-1.7.1/demos/seqviewer/test.fa
/libs/biojava-1.7.1/demos/ssaha/CreateDNAFastaHashTable.java
/libs/biojava-1.7.1/demos/ssaha/CreateDNAFastaHashTableCompact.java
/libs/biojava-1.7.1/demos/ssaha/CreateDNAFastaHashTableLarge.java
/libs/biojava-1.7.1/demos/ssaha/CreateEmblHashTable.java
/libs/biojava-1.7.1/demos/ssaha/CreateEmblHashTableLarge.java
/libs/biojava-1.7.1/demos/ssaha/ResultPrinter.java
/libs/biojava-1.7.1/demos/ssaha/SSAHA.java
/libs/biojava-1.7.1/demos/ssaha/SSAHALarge.java
/libs/biojava-1.7.1/demos/ssaha/SSAHASeq.java
/libs/biojava-1.7.1/demos/ssaha/SSAHASeqLarge.java
/libs/biojava-1.7.1/demos/ssbind/AlignmentBuilder.java
/libs/biojava-1.7.1/demos/ssbind/CountHits.java
/libs/biojava-1.7.1/demos/ssbind/CountSubHits.java
/libs/biojava-1.7.1/demos/ssbind/Echoer.java
/libs/biojava-1.7.1/demos/ssbind/FilterByValue.java
/libs/biojava-1.7.1/demos/ssbind/ListQueries.java
/libs/biojava-1.7.1/demos/ssbind/ListSubjects.java
/libs/biojava-1.7.1/demos/ssbind/ProcessBlastReport.java
/libs/biojava-1.7.1/demos/ssbind/PropertyEchoer.java
/libs/biojava-1.7.1/demos/ssbind/SubHitBuilder.java
/libs/biojava-1.7.1/demos/ssbind/SubHitFilter.java
/libs/biojava-1.7.1/demos/structure/LoadStructure.java
/libs/biojava-1.7.1/demos/structure/PDBView.java
/libs/biojava-1.7.1/demos/structure/PhiPsiCalculation.java
/libs/biojava-1.7.1/demos/structure/SuperimposeStructures.java
/libs/biojava-1.7.1/demos/symbol/MatrixValue.java
/libs/biojava-1.7.1/demos/symbol/PatternDemo.java
/libs/biojava-1.7.1/demos/symbol/TestAlphabetIndexers.java
/libs/biojava-1.7.1/demos/symbol/TestAmbiguity.java
/libs/biojava-1.7.1/demos/symbol/TestGappedSymbolList.java
/libs/biojava-1.7.1/demos/symbol/TestIndexedIntegers.java
/libs/biojava-1.7.1/demos/symbol/TestLocation.java
/libs/biojava-1.7.1/demos/symbol/TestOrderNSymbolList.java
/libs/biojava-1.7.1/demos/symbol/TestSimpleAlignment.java
/libs/biojava-1.7.1/demos/symbol/TestWindowedSymbolList.java
/libs/biojava-1.7.1/demos/symbol/Tools.java
/libs/biojava-1.7.1/demos/symbol/WindowCount.java
/libs/biojava-1.7.1/demos/tagvalue/Grep.java
/libs/biojava-1.7.1/demos/tagvalue/Index.java
/libs/biojava-1.7.1/demos/tagvalue/Parse.java
/libs/biojava-1.7.1/demos/tagvalue/ParseEmbl.java
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