Download biojava Free Java Code

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biojava3-aa-prop/pom.xml
biojava3-aa-prop/src/main/assembly/assembly.xml
biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/CommandPrompt.java
biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/Constraints.java
biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/IPeptideProperties.java
biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/PeptideProperties.java
biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/PeptidePropertiesImpl.java
biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/Utils.java
biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/package-info.java
biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/profeat/IProfeatProperties.java
biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/profeat/ProfeatProperties.java
biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/profeat/ProfeatPropertiesImpl.java
biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/profeat/convertor/Convert2Charge.java
biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/profeat/convertor/Convert2Hydrophobicity.java
biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/profeat/convertor/Convert2NormalizedVanDerWaalsVolume.java
biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/profeat/convertor/Convert2Polarity.java
biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/profeat/convertor/Convert2Polarizability.java
biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/profeat/convertor/Convert2SecondaryStructure.java
biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/profeat/convertor/Convert2SolventAccessibility.java
biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/profeat/convertor/Convertor.java
biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/profeat/convertor/package-info.java
biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/profeat/package-info.java
biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/xml/AminoAcidComposition.java
biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/xml/AminoAcidCompositionTable.java
biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/xml/CaseFreeAminoAcidCompoundSet.java
biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/xml/Element.java
biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/xml/ElementTable.java
biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/xml/Isotope.java
biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/xml/ModifiedAminoAcidCompoundSet.java
biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/xml/MyValidationEventHandler.java
biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/xml/Name2Count.java
biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/xml/SchemaGenerator.java
biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/xml/package-info.java
biojava3-aa-prop/src/main/resources/AdvancedAminoAcidComposition.xml
biojava3-aa-prop/src/main/resources/AdvancedElementMass.xml
biojava3-aa-prop/src/main/resources/AminoAcidComposition.xml
biojava3-aa-prop/src/main/resources/AminoAcidComposition.xsd
biojava3-aa-prop/src/main/resources/AminoAcidCompositionWithID.xml
biojava3-aa-prop/src/main/resources/ElementMass.xml
biojava3-aa-prop/src/main/resources/ElementMass.xsd
biojava3-aa-prop/src/main/resources/MinAminoAcidComposition.xml
biojava3-aa-prop/src/main/resources/MinElementMass.xml
biojava3-aa-prop/src/main/resources/Simplified_compound.xml
biojava3-aa-prop/src/test/java/org/biojava3/aaproperties/CommandPromptTester.java
biojava3-aa-prop/src/test/java/org/biojava3/aaproperties/CookBookTester.java
biojava3-aa-prop/src/test/java/org/biojava3/aaproperties/GenbankCommandPromptTester.java
biojava3-aa-prop/src/test/java/org/biojava3/aaproperties/PeptidePropertiesImplTester.java
biojava3-aa-prop/src/test/java/org/biojava3/aaproperties/ProfeatPropertiesImplTester.java
biojava3-aa-prop/src/test/java/org/biojava3/aaproperties/profeat/CookBookTester.java
biojava3-aa-prop/src/test/java/org/biojava3/aaproperties/xml/AminoAcidTester.java
biojava3-aa-prop/src/test/java/org/biojava3/aaproperties/xml/ElementTester.java
biojava3-aa-prop/src/test/java/org/biojava3/aaproperties/xml/GenerateJavaCodesFromText.java
biojava3-aa-prop/src/test/resources/BondFeature.gb
biojava3-aa-prop/src/test/resources/Symbol2Name.txt
biojava3-aa-prop/src/test/resources/Symbol2Weight.txt
biojava3-aa-prop/src/test/resources/modifiedTest.csv
biojava3-aa-prop/src/test/resources/modifiedTest.fasta
biojava3-aa-prop/src/test/resources/modifiedTestGB.csv
biojava3-aa-prop/src/test/resources/test.csv
biojava3-aa-prop/src/test/resources/test.fasta
biojava3-aa-prop/src/test/resources/test.tsv
biojava3-aa-prop/src/test/resources/testWithCases.fasta
biojava3-aa-prop/src/test/resources/testgb.csv
biojava3-aa-prop/src/test/resources/testgb.tsv
biojava3-alignment/pom.xml
biojava3-alignment/src/main/java/demo/CookbookMSA.java
biojava3-alignment/src/main/java/demo/DemoAlignProteins.java
biojava3-alignment/src/main/java/demo/DemoLoadSubstMax.java
biojava3-alignment/src/main/java/demo/TestDNANeedlemanWunsch.java
biojava3-alignment/src/main/java/org/biojava3/alignment/Alignments.java
biojava3-alignment/src/main/java/org/biojava3/alignment/FractionalIdentityInProfileScorer.java
biojava3-alignment/src/main/java/org/biojava3/alignment/FractionalIdentityScorer.java
biojava3-alignment/src/main/java/org/biojava3/alignment/FractionalSimilarityInProfileScorer.java
biojava3-alignment/src/main/java/org/biojava3/alignment/FractionalSimilarityScorer.java
biojava3-alignment/src/main/java/org/biojava3/alignment/GuideTree.java
biojava3-alignment/src/main/java/org/biojava3/alignment/NeedlemanWunsch.java
biojava3-alignment/src/main/java/org/biojava3/alignment/SimpleAlignedSequence.java
biojava3-alignment/src/main/java/org/biojava3/alignment/SimpleGapPenalty.java
biojava3-alignment/src/main/java/org/biojava3/alignment/SimpleProfile.java
biojava3-alignment/src/main/java/org/biojava3/alignment/SimpleProfilePair.java
biojava3-alignment/src/main/java/org/biojava3/alignment/SimpleProfileProfileAligner.java
biojava3-alignment/src/main/java/org/biojava3/alignment/SimpleSequencePair.java
biojava3-alignment/src/main/java/org/biojava3/alignment/SimpleSubstitutionMatrix.java
biojava3-alignment/src/main/java/org/biojava3/alignment/SmithWaterman.java
biojava3-alignment/src/main/java/org/biojava3/alignment/StandardRescoreRefiner.java
biojava3-alignment/src/main/java/org/biojava3/alignment/SubstitutionMatrixHelper.java
biojava3-alignment/src/main/java/org/biojava3/alignment/aaindex/AAIndexFileParser.java
biojava3-alignment/src/main/java/org/biojava3/alignment/aaindex/AAIndexProvider.java
biojava3-alignment/src/main/java/org/biojava3/alignment/aaindex/AAindexFactory.java
biojava3-alignment/src/main/java/org/biojava3/alignment/aaindex/DefaultAAIndexProvider.java
biojava3-alignment/src/main/java/org/biojava3/alignment/aaindex/ScaledSubstitutionMatrix.java
biojava3-alignment/src/main/java/org/biojava3/alignment/io/StockholmConsensusAnnotation.java
biojava3-alignment/src/main/java/org/biojava3/alignment/io/StockholmFileAnnotation.java
biojava3-alignment/src/main/java/org/biojava3/alignment/io/StockholmFileParser.java
biojava3-alignment/src/main/java/org/biojava3/alignment/io/StockholmResidueAnnotation.java
biojava3-alignment/src/main/java/org/biojava3/alignment/io/StockholmSequenceAnnotation.java
biojava3-alignment/src/main/java/org/biojava3/alignment/io/StockholmStructure.java
biojava3-alignment/src/main/java/org/biojava3/alignment/routines/AlignerHelper.java
biojava3-alignment/src/main/java/org/biojava3/alignment/routines/AnchoredPairwiseSequenceAligner.java
biojava3-alignment/src/main/java/org/biojava3/alignment/routines/GuanUberbacher.java
biojava3-alignment/src/main/java/org/biojava3/alignment/template/AbstractMatrixAligner.java
biojava3-alignment/src/main/java/org/biojava3/alignment/template/AbstractPairwiseSequenceAligner.java
biojava3-alignment/src/main/java/org/biojava3/alignment/template/AbstractProfileProfileAligner.java
biojava3-alignment/src/main/java/org/biojava3/alignment/template/AbstractScorer.java
biojava3-alignment/src/main/java/org/biojava3/alignment/template/AlignedSequence.java
biojava3-alignment/src/main/java/org/biojava3/alignment/template/Aligner.java
biojava3-alignment/src/main/java/org/biojava3/alignment/template/CallablePairwiseSequenceAligner.java
biojava3-alignment/src/main/java/org/biojava3/alignment/template/CallablePairwiseSequenceScorer.java
biojava3-alignment/src/main/java/org/biojava3/alignment/template/CallableProfileProfileAligner.java
biojava3-alignment/src/main/java/org/biojava3/alignment/template/GapPenalty.java
biojava3-alignment/src/main/java/org/biojava3/alignment/template/GuideTreeNode.java
biojava3-alignment/src/main/java/org/biojava3/alignment/template/HierarchicalClusterer.java
biojava3-alignment/src/main/java/org/biojava3/alignment/template/MatrixAligner.java
biojava3-alignment/src/main/java/org/biojava3/alignment/template/MutableAlignedSequence.java
biojava3-alignment/src/main/java/org/biojava3/alignment/template/MutableProfile.java
biojava3-alignment/src/main/java/org/biojava3/alignment/template/MutableProfilePair.java
biojava3-alignment/src/main/java/org/biojava3/alignment/template/MutableSequencePair.java
biojava3-alignment/src/main/java/org/biojava3/alignment/template/PairInProfileScorer.java
biojava3-alignment/src/main/java/org/biojava3/alignment/template/PairwiseSequenceAligner.java
biojava3-alignment/src/main/java/org/biojava3/alignment/template/PairwiseSequenceScorer.java
biojava3-alignment/src/main/java/org/biojava3/alignment/template/PartitionRefiner.java
biojava3-alignment/src/main/java/org/biojava3/alignment/template/Profile.java
biojava3-alignment/src/main/java/org/biojava3/alignment/template/ProfilePair.java
biojava3-alignment/src/main/java/org/biojava3/alignment/template/ProfileProfileAligner.java
biojava3-alignment/src/main/java/org/biojava3/alignment/template/ProfileProfileScorer.java
biojava3-alignment/src/main/java/org/biojava3/alignment/template/ProfileView.java
biojava3-alignment/src/main/java/org/biojava3/alignment/template/RescoreRefiner.java
biojava3-alignment/src/main/java/org/biojava3/alignment/template/Scorer.java
biojava3-alignment/src/main/java/org/biojava3/alignment/template/SequencePair.java
biojava3-alignment/src/main/java/org/biojava3/alignment/template/SubstitutionMatrix.java
biojava3-alignment/src/main/resources/AAINDEX.txt
biojava3-alignment/src/main/resources/blosum100.txt
biojava3-alignment/src/main/resources/blosum30.txt
biojava3-alignment/src/main/resources/blosum35.txt
biojava3-alignment/src/main/resources/blosum40.txt
biojava3-alignment/src/main/resources/blosum45.txt
biojava3-alignment/src/main/resources/blosum50.txt
biojava3-alignment/src/main/resources/blosum55.txt
biojava3-alignment/src/main/resources/blosum60.txt
biojava3-alignment/src/main/resources/blosum62.txt
biojava3-alignment/src/main/resources/blosum65.txt
biojava3-alignment/src/main/resources/blosum70.txt
biojava3-alignment/src/main/resources/blosum75.txt
biojava3-alignment/src/main/resources/blosum80.txt
biojava3-alignment/src/main/resources/blosum85.txt
biojava3-alignment/src/main/resources/blosum90.txt
biojava3-alignment/src/main/resources/gonnet250.txt
biojava3-alignment/src/main/resources/nuc-4_2.txt
biojava3-alignment/src/main/resources/nuc-4_4.txt
biojava3-alignment/src/main/resources/pam250.txt
biojava3-alignment/src/test/java/org/biojava3/alignment/CookbookAlignAllGlobal.java
biojava3-alignment/src/test/java/org/biojava3/alignment/CookbookAlignAllLocal.java
biojava3-alignment/src/test/java/org/biojava3/alignment/CookbookAlignPairGlobal.java
biojava3-alignment/src/test/java/org/biojava3/alignment/CookbookAlignPairLocal.java
biojava3-alignment/src/test/java/org/biojava3/alignment/CookbookMSA.java
biojava3-alignment/src/test/java/org/biojava3/alignment/CookbookMSAProfiler.java
biojava3-alignment/src/test/java/org/biojava3/alignment/FractionalIdentityScorerTest.java
biojava3-alignment/src/test/java/org/biojava3/alignment/FractionalSimilarityScorerTest.java
biojava3-alignment/src/test/java/org/biojava3/alignment/GuideTreeTest.java
biojava3-alignment/src/test/java/org/biojava3/alignment/NeedlemanWunschTest.java
biojava3-alignment/src/test/java/org/biojava3/alignment/SimpleAlignedSequenceTest.java
biojava3-alignment/src/test/java/org/biojava3/alignment/SimpleGapPenaltyTest.java
biojava3-alignment/src/test/java/org/biojava3/alignment/SimpleProfilePairTest.java
biojava3-alignment/src/test/java/org/biojava3/alignment/SimpleProfileProfileAlignerTest.java
biojava3-alignment/src/test/java/org/biojava3/alignment/SimpleProfileTest.java
biojava3-alignment/src/test/java/org/biojava3/alignment/SimpleSequencePairTest.java
biojava3-alignment/src/test/java/org/biojava3/alignment/SimpleSubstitutionMatrixTest.java
biojava3-alignment/src/test/java/org/biojava3/alignment/SmithWatermanTest.java
biojava3-alignment/src/test/java/org/biojava3/alignment/TestDNAAlignment.java
biojava3-alignment/src/test/java/org/biojava3/alignment/aaindex/TestAAINDEXLoading.java
biojava3-alignment/src/test/java/org/biojava3/alignment/io/TestStockholmParser.java
biojava3-alignment/src/test/java/org/biojava3/alignment/routines/GuanUberbacherTest.java
biojava3-alignment/src/test/resources/dna-fasta.txt
biojava3-alignment/src/test/resources/longTest(Ankyrin repeat).sto
biojava3-alignment/src/test/resources/piwi-aligned-fasta.txt
biojava3-alignment/src/test/resources/piwi-seed-fasta.txt
biojava3-alignment/src/test/resources/piwi.sth.gz
biojava3-alignment/src/test/resources/pkinase.sto
biojava3-alignment/src/test/resources/rrm.sto
biojava3-alignment/src/test/resources/test.sth
biojava3-alignment/src/test/resources/test1.sth
biojava3-core/dir_conflicts.prej
biojava3-core/nbactions.xml
biojava3-core/pom.xml
biojava3-core/src/main/java/org/biojava3/core/exceptions/CompoundNotFoundError.java
biojava3-core/src/main/java/org/biojava3/core/exceptions/FileAccessError.java
biojava3-core/src/main/java/org/biojava3/core/exceptions/HeaderParseException.java
biojava3-core/src/main/java/org/biojava3/core/exceptions/ParserException.java
biojava3-core/src/main/java/org/biojava3/core/exceptions/SequenceLengthError.java
biojava3-core/src/main/java/org/biojava3/core/exceptions/TranslationException.java
biojava3-core/src/main/java/org/biojava3/core/sequence/AccessionID.java
biojava3-core/src/main/java/org/biojava3/core/sequence/BasicSequence.java
biojava3-core/src/main/java/org/biojava3/core/sequence/CDSComparator.java
biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java
biojava3-core/src/main/java/org/biojava3/core/sequence/ChromosomeSequence.java
biojava3-core/src/main/java/org/biojava3/core/sequence/DNASequence.java
biojava3-core/src/main/java/org/biojava3/core/sequence/DataSource.java
biojava3-core/src/main/java/org/biojava3/core/sequence/ExonComparator.java
biojava3-core/src/main/java/org/biojava3/core/sequence/ExonSequence.java
biojava3-core/src/main/java/org/biojava3/core/sequence/GeneSequence.java
biojava3-core/src/main/java/org/biojava3/core/sequence/IntronSequence.java
biojava3-core/src/main/java/org/biojava3/core/sequence/MultipleSequenceAlignment.java
biojava3-core/src/main/java/org/biojava3/core/sequence/ProteinSequence.java
biojava3-core/src/main/java/org/biojava3/core/sequence/RNASequence.java
biojava3-core/src/main/java/org/biojava3/core/sequence/SequenceComparator.java
biojava3-core/src/main/java/org/biojava3/core/sequence/SequenceOptimizationHints.java
biojava3-core/src/main/java/org/biojava3/core/sequence/StartCodonSequence.java
biojava3-core/src/main/java/org/biojava3/core/sequence/StopCodonSequence.java
biojava3-core/src/main/java/org/biojava3/core/sequence/Strand.java
biojava3-core/src/main/java/org/biojava3/core/sequence/TaxonomyID.java
biojava3-core/src/main/java/org/biojava3/core/sequence/TranscriptSequence.java
biojava3-core/src/main/java/org/biojava3/core/sequence/compound/AmbiguityDNACompoundSet.java
biojava3-core/src/main/java/org/biojava3/core/sequence/compound/AmbiguityRNACompoundSet.java
biojava3-core/src/main/java/org/biojava3/core/sequence/compound/AminoAcidCompound.java
biojava3-core/src/main/java/org/biojava3/core/sequence/compound/AminoAcidCompoundSet.java
biojava3-core/src/main/java/org/biojava3/core/sequence/compound/CodonCompound.java
biojava3-core/src/main/java/org/biojava3/core/sequence/compound/DNACompoundSet.java
biojava3-core/src/main/java/org/biojava3/core/sequence/compound/NucleotideCompound.java
biojava3-core/src/main/java/org/biojava3/core/sequence/compound/RNACompoundSet.java
biojava3-core/src/main/java/org/biojava3/core/sequence/edits/Edit.java
biojava3-core/src/main/java/org/biojava3/core/sequence/features/AbstractFeature.java
biojava3-core/src/main/java/org/biojava3/core/sequence/features/DBReferenceInfo.java
biojava3-core/src/main/java/org/biojava3/core/sequence/features/DatabaseReferenceInterface.java
biojava3-core/src/main/java/org/biojava3/core/sequence/features/FeatureInterface.java
biojava3-core/src/main/java/org/biojava3/core/sequence/features/FeaturesKeyWordInterface.java
biojava3-core/src/main/java/org/biojava3/core/sequence/features/Qualifier.java
biojava3-core/src/main/java/org/biojava3/core/sequence/features/QualityFeature.java
biojava3-core/src/main/java/org/biojava3/core/sequence/features/QuantityFeature.java
biojava3-core/src/main/java/org/biojava3/core/sequence/features/TextFeature.java
biojava3-core/src/main/java/org/biojava3/core/sequence/io/BufferedReaderBytesRead.java
biojava3-core/src/main/java/org/biojava3/core/sequence/io/CasePreservingProteinSequenceCreator.java
biojava3-core/src/main/java/org/biojava3/core/sequence/io/DNASequenceCreator.java
biojava3-core/src/main/java/org/biojava3/core/sequence/io/FastaGeneWriter.java
biojava3-core/src/main/java/org/biojava3/core/sequence/io/FastaReader.java
biojava3-core/src/main/java/org/biojava3/core/sequence/io/FastaReaderHelper.java
biojava3-core/src/main/java/org/biojava3/core/sequence/io/FastaSequenceParser.java
biojava3-core/src/main/java/org/biojava3/core/sequence/io/FastaWriter.java
biojava3-core/src/main/java/org/biojava3/core/sequence/io/FastaWriterHelper.java
biojava3-core/src/main/java/org/biojava3/core/sequence/io/FileProxyDNASequenceCreator.java
biojava3-core/src/main/java/org/biojava3/core/sequence/io/FileProxyProteinSequenceCreator.java
biojava3-core/src/main/java/org/biojava3/core/sequence/io/GenbankReader.java
biojava3-core/src/main/java/org/biojava3/core/sequence/io/GenbankReaderHelper.java
biojava3-core/src/main/java/org/biojava3/core/sequence/io/GenbankSequenceParser.java
biojava3-core/src/main/java/org/biojava3/core/sequence/io/GenbankWriter.java
biojava3-core/src/main/java/org/biojava3/core/sequence/io/GenbankWriterHelper.java
biojava3-core/src/main/java/org/biojava3/core/sequence/io/GenericFastaHeaderFormat.java
biojava3-core/src/main/java/org/biojava3/core/sequence/io/GenericFastaHeaderParser.java
biojava3-core/src/main/java/org/biojava3/core/sequence/io/GenericGenbankHeaderFormat.java
biojava3-core/src/main/java/org/biojava3/core/sequence/io/GenericGenbankHeaderParser.java
biojava3-core/src/main/java/org/biojava3/core/sequence/io/GenericInsdcHeaderFormat.java
biojava3-core/src/main/java/org/biojava3/core/sequence/io/IUPACParser.java
biojava3-core/src/main/java/org/biojava3/core/sequence/io/PlainFastaHeaderParser.java
biojava3-core/src/main/java/org/biojava3/core/sequence/io/ProteinSequenceCreator.java
biojava3-core/src/main/java/org/biojava3/core/sequence/io/RNASequenceCreator.java
biojava3-core/src/main/java/org/biojava3/core/sequence/io/template/FastaHeaderFormatInterface.java
biojava3-core/src/main/java/org/biojava3/core/sequence/io/template/GenbankHeaderFormatInterface.java
biojava3-core/src/main/java/org/biojava3/core/sequence/io/template/SequenceCreatorInterface.java
biojava3-core/src/main/java/org/biojava3/core/sequence/io/template/SequenceHeaderParserInterface.java
biojava3-core/src/main/java/org/biojava3/core/sequence/io/template/SequenceParserInterface.java
biojava3-core/src/main/java/org/biojava3/core/sequence/io/util/ClasspathResource.java
biojava3-core/src/main/java/org/biojava3/core/sequence/io/util/IOUtils.java
biojava3-core/src/main/java/org/biojava3/core/sequence/loader/ArrayListProxySequenceReader.java
biojava3-core/src/main/java/org/biojava3/core/sequence/loader/GenbankProxySequenceReader.java
biojava3-core/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java
biojava3-core/src/main/java/org/biojava3/core/sequence/loader/StringProxySequenceReader.java
biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java
biojava3-core/src/main/java/org/biojava3/core/sequence/location/FuzzyPoint.java
biojava3-core/src/main/java/org/biojava3/core/sequence/location/InsdcLocations.java
biojava3-core/src/main/java/org/biojava3/core/sequence/location/InsdcParser.java
biojava3-core/src/main/java/org/biojava3/core/sequence/location/LocationHelper.java
biojava3-core/src/main/java/org/biojava3/core/sequence/location/SequenceLocation.java
biojava3-core/src/main/java/org/biojava3/core/sequence/location/SimpleLocation.java
biojava3-core/src/main/java/org/biojava3/core/sequence/location/SimplePoint.java
biojava3-core/src/main/java/org/biojava3/core/sequence/location/template/AbstractLocation.java
biojava3-core/src/main/java/org/biojava3/core/sequence/location/template/AccesionedLocation.java
biojava3-core/src/main/java/org/biojava3/core/sequence/location/template/Location.java
biojava3-core/src/main/java/org/biojava3/core/sequence/location/template/Point.java
biojava3-core/src/main/java/org/biojava3/core/sequence/storage/ArrayListSequenceReader.java
biojava3-core/src/main/java/org/biojava3/core/sequence/storage/BitSequenceReader.java
biojava3-core/src/main/java/org/biojava3/core/sequence/storage/FourBitSequenceReader.java
biojava3-core/src/main/java/org/biojava3/core/sequence/storage/JoiningSequenceReader.java
biojava3-core/src/main/java/org/biojava3/core/sequence/storage/SequenceAsStringHelper.java
biojava3-core/src/main/java/org/biojava3/core/sequence/storage/SingleCompoundSequenceReader.java
biojava3-core/src/main/java/org/biojava3/core/sequence/storage/TwoBitSequenceReader.java
biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractCompound.java
biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractCompoundSet.java
biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractCompoundTranslator.java
biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractNucleotideCompoundSet.java
biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java
biojava3-core/src/main/java/org/biojava3/core/sequence/template/Accessioned.java
biojava3-core/src/main/java/org/biojava3/core/sequence/template/ComplementCompound.java
biojava3-core/src/main/java/org/biojava3/core/sequence/template/Compound.java
biojava3-core/src/main/java/org/biojava3/core/sequence/template/CompoundSet.java
biojava3-core/src/main/java/org/biojava3/core/sequence/template/CompoundTranslator.java
biojava3-core/src/main/java/org/biojava3/core/sequence/template/LightweightProfile.java
biojava3-core/src/main/java/org/biojava3/core/sequence/template/ProxySequenceReader.java
biojava3-core/src/main/java/org/biojava3/core/sequence/template/Sequence.java
biojava3-core/src/main/java/org/biojava3/core/sequence/template/SequenceMixin.java
biojava3-core/src/main/java/org/biojava3/core/sequence/template/SequenceProxyView.java
biojava3-core/src/main/java/org/biojava3/core/sequence/template/SequenceReader.java
biojava3-core/src/main/java/org/biojava3/core/sequence/template/SequenceView.java
biojava3-core/src/main/java/org/biojava3/core/sequence/transcription/CaseInsensitiveCompound.java
biojava3-core/src/main/java/org/biojava3/core/sequence/transcription/DNAToRNATranslator.java
biojava3-core/src/main/java/org/biojava3/core/sequence/transcription/Frame.java
biojava3-core/src/main/java/org/biojava3/core/sequence/transcription/RNAToAminoAcidTranslator.java
biojava3-core/src/main/java/org/biojava3/core/sequence/transcription/Table.java
biojava3-core/src/main/java/org/biojava3/core/sequence/transcription/TranscriptionEngine.java
biojava3-core/src/main/java/org/biojava3/core/sequence/views/ComplementSequenceView.java
biojava3-core/src/main/java/org/biojava3/core/sequence/views/ReversedSequenceView.java
biojava3-core/src/main/java/org/biojava3/core/sequence/views/RnaSequenceView.java
biojava3-core/src/main/java/org/biojava3/core/sequence/views/WindowedSequence.java
biojava3-core/src/main/java/org/biojava3/core/util/CRC64Checksum.java
biojava3-core/src/main/java/org/biojava3/core/util/ConcurrencyTools.java
biojava3-core/src/main/java/org/biojava3/core/util/Equals.java
biojava3-core/src/main/java/org/biojava3/core/util/FlatFileCache.java
biojava3-core/src/main/java/org/biojava3/core/util/Hashcoder.java
biojava3-core/src/main/java/org/biojava3/core/util/InputStreamProvider.java
biojava3-core/src/main/java/org/biojava3/core/util/PrettyXMLWriter.java
biojava3-core/src/main/java/org/biojava3/core/util/SequenceTools.java
biojava3-core/src/main/java/org/biojava3/core/util/SoftHashMap.java
biojava3-core/src/main/java/org/biojava3/core/util/StringManipulationHelper.java
biojava3-core/src/main/java/org/biojava3/core/util/UncompressInputStream.java
biojava3-core/src/main/java/org/biojava3/core/util/XMLHelper.java
biojava3-core/src/main/java/org/biojava3/core/util/XMLWriter.java
biojava3-core/src/main/resources/org/biojava3/core/sequence/iupac.txt
biojava3-core/src/test/java/org/biojava3/core/sequence/DNATest.java
biojava3-core/src/test/java/org/biojava3/core/sequence/EditSequenceTest.java
biojava3-core/src/test/java/org/biojava3/core/sequence/JoiningSequenceReaderTest.java
biojava3-core/src/test/java/org/biojava3/core/sequence/MultipleSequenceAlignmentTest.java
biojava3-core/src/test/java/org/biojava3/core/sequence/SequenceViewTest.java
biojava3-core/src/test/java/org/biojava3/core/sequence/TranslationTest.java
biojava3-core/src/test/java/org/biojava3/core/sequence/compound/AmbiguityDNACompoundTest.java
biojava3-core/src/test/java/org/biojava3/core/sequence/io/CasePreservingProteinSequenceCreatorTest.java
biojava3-core/src/test/java/org/biojava3/core/sequence/io/FastaReaderTest.java
biojava3-core/src/test/java/org/biojava3/core/sequence/io/FastaWriterTest.java
biojava3-core/src/test/java/org/biojava3/core/sequence/io/GenbankCookbookTest.java
biojava3-core/src/test/java/org/biojava3/core/sequence/io/GenbankReaderTest.java
biojava3-core/src/test/java/org/biojava3/core/sequence/io/GenbankWriterTest.java
biojava3-core/src/test/java/org/biojava3/core/sequence/io/GenericFastaHeaderParserTest.java
biojava3-core/src/test/java/org/biojava3/core/sequence/location/LocationParserTest.java
biojava3-core/src/test/java/org/biojava3/core/sequence/location/LocationTest.java
biojava3-core/src/test/java/org/biojava3/core/sequence/views/WindowViewTests.java
biojava3-core/src/test/resources/BondFeature.gb
biojava3-core/src/test/resources/NM_000266.gb
biojava3-core/src/test/resources/PF00070.selex
biojava3-core/src/test/resources/PF00104_small.fasta
biojava3-core/src/test/resources/org/biojava3/core/sequence/BRCA2-cds.fasta
biojava3-core/src/test/resources/org/biojava3/core/sequence/BRCA2-peptide.fasta
biojava3-core/src/test/resources/org/biojava3/core/sequence/volvox-cds.fasta
biojava3-core/src/test/resources/org/biojava3/core/sequence/volvox-peptide.fasta
biojava3-genome/nb-configuration.xml
biojava3-genome/nbactions.xml
biojava3-genome/pom.xml
biojava3-genome/src/main/java/org/biojava3/genome/App.java
biojava3-genome/src/main/java/org/biojava3/genome/GeneFeatureHelper.java
biojava3-genome/src/main/java/org/biojava3/genome/homology/BlastHomologyHits.java
biojava3-genome/src/main/java/org/biojava3/genome/homology/GFF3FromUniprotBlastHits.java
biojava3-genome/src/main/java/org/biojava3/genome/parsers/geneid/GeneIDXMLReader.java
biojava3-genome/src/main/java/org/biojava3/genome/parsers/gff/Feature.java
biojava3-genome/src/main/java/org/biojava3/genome/parsers/gff/FeatureHelper.java
biojava3-genome/src/main/java/org/biojava3/genome/parsers/gff/FeatureI.java
biojava3-genome/src/main/java/org/biojava3/genome/parsers/gff/FeatureList.java
biojava3-genome/src/main/java/org/biojava3/genome/parsers/gff/GCStats.java
biojava3-genome/src/main/java/org/biojava3/genome/parsers/gff/GFF3Reader.java
biojava3-genome/src/main/java/org/biojava3/genome/parsers/gff/GFF3Writer.java
biojava3-genome/src/main/java/org/biojava3/genome/parsers/gff/GeneIDGFF2Reader.java
biojava3-genome/src/main/java/org/biojava3/genome/parsers/gff/GeneMarkGTFReader.java
biojava3-genome/src/main/java/org/biojava3/genome/parsers/gff/LocIterator.java
biojava3-genome/src/main/java/org/biojava3/genome/parsers/gff/Location.java
biojava3-genome/src/main/java/org/biojava3/genome/query/BlastXMLQuery.java
biojava3-genome/src/main/java/org/biojava3/genome/query/OutputHitsGFF.java
biojava3-genome/src/main/java/org/biojava3/genome/uniprot/UniprotToFasta.java
biojava3-genome/src/main/java/org/biojava3/genome/util/SplitFasta.java
biojava3-genome/src/test/java/org/biojava3/genome/AppTest.java
biojava3-genome/src/test/java/org/biojava3/genome/GeneFeatureHelperTest.java
biojava3-genome/src/test/resources/amphimedon.gff3
biojava3-genome/src/test/resources/volvox.gff3
biojava3-genome/src/test/resources/volvox_all.faa
biojava3-genome/src/test/resources/volvox_all.fna
biojava3-genome/src/test/resources/volvox_all_genes_exon_uppercase.fna
biojava3-genome/src/test/resources/volvox_all_reference.faa
biojava3-genome/src/test/resources/volvox_length.gff3
biojava3-genome/src/test/resources/volvox_length_reference.gff3
biojava3-modfinder/pom.xml
biojava3-modfinder/src/main/java/org/biojava3/protmod/Component.java
biojava3-modfinder/src/main/java/org/biojava3/protmod/ModificationCategory.java
biojava3-modfinder/src/main/java/org/biojava3/protmod/ModificationCondition.java
biojava3-modfinder/src/main/java/org/biojava3/protmod/ModificationConditionImpl.java
biojava3-modfinder/src/main/java/org/biojava3/protmod/ModificationLinkage.java
biojava3-modfinder/src/main/java/org/biojava3/protmod/ModificationOccurrenceType.java
biojava3-modfinder/src/main/java/org/biojava3/protmod/ProteinModification.java
biojava3-modfinder/src/main/java/org/biojava3/protmod/ProteinModificationImpl.java
biojava3-modfinder/src/main/java/org/biojava3/protmod/ProteinModificationRegistry.java
biojava3-modfinder/src/main/java/org/biojava3/protmod/io/ComponentXMLConverter.java
biojava3-modfinder/src/main/java/org/biojava3/protmod/io/ModifiedCompoundXMLConverter.java
biojava3-modfinder/src/main/java/org/biojava3/protmod/io/ProteinModificationXmlReader.java
biojava3-modfinder/src/main/java/org/biojava3/protmod/io/StructureAtomXMLConverter.java
biojava3-modfinder/src/main/java/org/biojava3/protmod/io/StructureGroupXMLConverter.java
biojava3-modfinder/src/main/java/org/biojava3/protmod/structure/ModifiedCompound.java
biojava3-modfinder/src/main/java/org/biojava3/protmod/structure/ModifiedCompoundImpl.java
biojava3-modfinder/src/main/java/org/biojava3/protmod/structure/ProteinModificationIdentifier.java
biojava3-modfinder/src/main/java/org/biojava3/protmod/structure/StructureAtom.java
biojava3-modfinder/src/main/java/org/biojava3/protmod/structure/StructureAtomLinkage.java
biojava3-modfinder/src/main/java/org/biojava3/protmod/structure/StructureGroup.java
biojava3-modfinder/src/main/java/org/biojava3/protmod/structure/StructureUtil.java
biojava3-modfinder/src/main/resources/org/biojava3/protmod/ptm_list.xml
biojava3-modfinder/src/test/java/org/biojava3/protmod/structure/ModifiedCompoundSerializationTest.java
biojava3-modfinder/src/test/java/org/biojava3/protmod/structure/ProteinModificationParserTest.java
biojava3-modfinder/src/test/java/org/biojava3/protmod/structure/ProteinModificationRegistryTest.java
biojava3-modfinder/src/test/java/org/biojava3/protmod/structure/TmpAtomCache.java
biojava3-modfinder/src/test/resources/org/biojava3/protmod/parser/modifiedCompound.xml
biojava3-phylo/pom.xml
biojava3-phylo/src/main/java/org/biojava3/phylo/App.java
biojava3-phylo/src/main/java/org/biojava3/phylo/CheckTreeAccuracy.java
biojava3-phylo/src/main/java/org/biojava3/phylo/Comparison.java
biojava3-phylo/src/main/java/org/biojava3/phylo/NJTreeProgressListener.java
biojava3-phylo/src/main/java/org/biojava3/phylo/ProgessListenerStub.java
biojava3-phylo/src/main/java/org/biojava3/phylo/ResidueProperties.java
biojava3-phylo/src/main/java/org/biojava3/phylo/ScoreMatrix.java
biojava3-phylo/src/main/java/org/biojava3/phylo/TreeConstructionAlgorithm.java
biojava3-phylo/src/main/java/org/biojava3/phylo/TreeConstructor.java
biojava3-phylo/src/main/java/org/biojava3/phylo/TreeType.java
biojava3-phylo/src/main/resources/PF00104_small.fasta
biojava3-phylo/src/test/java/org/biojava3/phylo/AppTest.java
biojava3-protein-disorder/pom.xml
biojava3-protein-disorder/src/main/java/demo/PredictDisorder.java
biojava3-protein-disorder/src/main/java/org/biojava3/data/sequence/FastaSequence.java
biojava3-protein-disorder/src/main/java/org/biojava3/data/sequence/SequenceUtil.java
biojava3-protein-disorder/src/main/java/org/biojava3/data/sequence/package-info.java
biojava3-protein-disorder/src/main/java/org/biojava3/print_usage.txt
biojava3-protein-disorder/src/main/java/org/biojava3/ronn/InputParameters.java
biojava3-protein-disorder/src/main/java/org/biojava3/ronn/Jronn.java
biojava3-protein-disorder/src/main/java/org/biojava3/ronn/ModelLoader.java
biojava3-protein-disorder/src/main/java/org/biojava3/ronn/NullOutputStream.java
biojava3-protein-disorder/src/main/java/org/biojava3/ronn/ORonn.java
biojava3-protein-disorder/src/main/java/org/biojava3/ronn/ORonnModel.java
biojava3-protein-disorder/src/main/java/org/biojava3/ronn/RonnConstraint.java
biojava3-protein-disorder/src/main/java/org/biojava3/ronn/Timer.java
biojava3-protein-disorder/src/main/java/org/biojava3/ronn/package-info.java
biojava3-protein-disorder/src/main/resources/org/biojava3/ronn/model0.rec
biojava3-protein-disorder/src/main/resources/org/biojava3/ronn/model1.rec
biojava3-protein-disorder/src/main/resources/org/biojava3/ronn/model2.rec
biojava3-protein-disorder/src/main/resources/org/biojava3/ronn/model3.rec
biojava3-protein-disorder/src/main/resources/org/biojava3/ronn/model4.rec
biojava3-protein-disorder/src/main/resources/org/biojava3/ronn/model5.rec
biojava3-protein-disorder/src/main/resources/org/biojava3/ronn/model6.rec
biojava3-protein-disorder/src/main/resources/org/biojava3/ronn/model7.rec
biojava3-protein-disorder/src/main/resources/org/biojava3/ronn/model8.rec
biojava3-protein-disorder/src/main/resources/org/biojava3/ronn/model9.rec
biojava3-protein-disorder/src/test/java/org/biojava3/ronn/JronnExample.java
biojava3-protein-disorder/src/test/java/org/biojava3/ronn/JronnTest.java
biojava3-protein-disorder/src/test/java/org/biojava3/ronn/NonstandardProteinCompoundTest.java
biojava3-protein-disorder/src/test/resources/fasta.in
biojava3-sequencing/pom.xml
biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/AbstractFastqReader.java
biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/AbstractFastqWriter.java
biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/Fastq.java
biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/FastqBuilder.java
biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/FastqParser.java
biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/FastqReader.java
biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/FastqTools.java
biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/FastqVariant.java
biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/FastqWriter.java
biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/IlluminaFastqReader.java
biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/IlluminaFastqWriter.java
biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/ParseListener.java
biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/SangerFastqReader.java
biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/SangerFastqWriter.java
biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/SolexaFastqReader.java
biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/SolexaFastqWriter.java
biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/StreamListener.java
biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/StreamingFastqParser.java
biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/package-info.java
biojava3-sequencing/src/test/java/org/biojava3/sequencing/io/fastq/AbstractFastqReaderTest.java
biojava3-sequencing/src/test/java/org/biojava3/sequencing/io/fastq/AbstractFastqWriterTest.java
biojava3-sequencing/src/test/java/org/biojava3/sequencing/io/fastq/FastqBuilderTest.java
biojava3-sequencing/src/test/java/org/biojava3/sequencing/io/fastq/FastqTest.java
biojava3-sequencing/src/test/java/org/biojava3/sequencing/io/fastq/FastqToolsTest.java
biojava3-sequencing/src/test/java/org/biojava3/sequencing/io/fastq/FastqVariantTest.java
biojava3-sequencing/src/test/java/org/biojava3/sequencing/io/fastq/IlluminaFastqReaderTest.java
biojava3-sequencing/src/test/java/org/biojava3/sequencing/io/fastq/IlluminaFastqWriterTest.java
biojava3-sequencing/src/test/java/org/biojava3/sequencing/io/fastq/SangerFastqReaderTest.java
biojava3-sequencing/src/test/java/org/biojava3/sequencing/io/fastq/SangerFastqWriterTest.java
biojava3-sequencing/src/test/java/org/biojava3/sequencing/io/fastq/SolexaFastqReaderTest.java
biojava3-sequencing/src/test/java/org/biojava3/sequencing/io/fastq/SolexaFastqWriterTest.java
biojava3-sequencing/src/test/java/org/biojava3/sequencing/io/fastq/StreamingFastqParserTest.java
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/bug2335.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/empty.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/error_diff_ids.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/error_double_qual.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/error_double_seq.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/error_long_qual.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/error_no_qual.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/error_qual_del.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/error_qual_escape.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/error_qual_null.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/error_qual_space.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/error_qual_tab.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/error_qual_unit_sep.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/error_qual_vtab.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/error_short_qual.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/error_spaces.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/error_tabs.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/error_trunc_at_plus.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/error_trunc_at_qual.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/error_trunc_at_seq.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/error_trunc_in_plus.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/error_trunc_in_qual.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/error_trunc_in_seq.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/error_trunc_in_title.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/evil_wrapping.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/example.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/illumina-invalid-description.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/illumina-invalid-repeat-description.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/illumina_example.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/illumina_faked.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/illumina_full_range_as_illumina.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/illumina_full_range_as_sanger.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/illumina_full_range_as_solexa.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/illumina_full_range_original_illumina.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/longreads_as_illumina.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/longreads_as_sanger.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/longreads_as_solexa.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/longreads_original_sanger.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/misc_dna_as_illumina.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/misc_dna_as_sanger.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/misc_dna_as_solexa.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/misc_dna_original_sanger.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/misc_rna_as_illumina.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/misc_rna_as_sanger.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/misc_rna_as_solexa.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/misc_rna_original_sanger.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/multiple-wrapped-quality.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/sanger-invalid-description.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/sanger-invalid-repeat-description.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/sanger_93.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/sanger_faked.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/sanger_full_range_as_illumina.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/sanger_full_range_as_sanger.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/sanger_full_range_as_solexa.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/sanger_full_range_original_sanger.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/solexa-invalid-description.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/solexa-invalid-repeat-description.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/solexa_example.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/solexa_faked.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/solexa_full_range_as_illumina.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/solexa_full_range_as_sanger.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/solexa_full_range_as_solexa.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/solexa_full_range_original_solexa.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/test1_sanger.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/test2_solexa.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/test3_illumina.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/tricky.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/wrapped-quality.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/wrapped-sequence.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/wrapping_as_illumina.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/wrapping_as_sanger.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/wrapping_as_solexa.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/wrapping_issues.fastq
biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/wrapping_original_sanger.fastq
biojava3-structure-gui/pom.xml
biojava3-structure-gui/src/main/java/demo/AFPFromFasta.java
biojava3-structure-gui/src/main/java/demo/AlignmentGuiDemo.java
biojava3-structure-gui/src/main/java/demo/CookBook.java
biojava3-structure-gui/src/main/java/demo/DemoAlignmentFromFasta.java
biojava3-structure-gui/src/main/java/demo/DemoCE.java
biojava3-structure-gui/src/main/java/demo/DemoFATCAT.java
biojava3-structure-gui/src/main/java/demo/DemoRotationAxis.java
biojava3-structure-gui/src/main/java/demo/DemoSW3DAligner.java
biojava3-structure-gui/src/main/java/demo/DemoShowBiolAssembly.java
biojava3-structure-gui/src/main/java/demo/DemoShowCATHDomain.java
biojava3-structure-gui/src/main/java/demo/DemoShowLargeAssembly.java
biojava3-structure-gui/src/main/java/demo/DemoShowValidationResults.java
biojava3-structure-gui/src/main/java/demo/DemoStructureFromFasta.java
biojava3-structure-gui/src/main/java/demo/ShowStructureInJmol.java
biojava3-structure-gui/src/main/java/demo/WebStartClientDemo.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/AboutDialog.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/AlignmentCalc.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/AlignmentCalcDB.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/AlignmentCalculationRunnable.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/AlignmentGui.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/AlignmentTextPanel.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/ChooseDirAction.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/ConfigPDBInstallPanel.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/DBResultTable.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/DBSearchGUI.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/DisplayAFP.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/DotPlotPanel.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/GUIAlignmentProgressListener.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/GUIFarmJobRunnable.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/HelpDialog.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/JPrintPanel.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/MemoryMonitor.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/MenuCreator.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/MyAlignmentLoadListener.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/MyDistMaxListener.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/MyExportListener.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/MyOpenPdbFileListener.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/MySaveFileListener.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/MyTableRowSorter.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/ParameterGUI.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/SelectPDBPanel.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/ShowPDBIDListener.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/StructureAlignmentDisplay.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/StructureLoaderThread.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/SystemInfo.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/aligpanel/AFPChainCoordManager.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/aligpanel/AligPanel.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/aligpanel/AligPanelMouseMotionListener.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/aligpanel/StatusDisplay.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/autosuggest/AutoSuggestProvider.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/autosuggest/DefaultAutoSuggestProvider.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/autosuggest/JAutoSuggest.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/autosuggest/SCOPAutoSuggestProvider.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/jmol/AtomInfo.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/jmol/AtomInfoParser.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/jmol/JmolPanel.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/jmol/JmolTools.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/jmol/MyJmolStatusListener.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/jmol/RasmolCommandListener.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/jmol/StructureAlignmentJmol.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/jmol/package.html
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/webstart/AligUIManager.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/webstart/BrowserOpener.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/webstart/ConfigXMLHandler.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/webstart/JNLPProxy.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/webstart/PersistentConfig.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/webstart/WebStartDBSearch.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/webstart/WebStartDBSearchResults.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/webstart/WebStartMain.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/webstart/package.html
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/BiojavaJmol.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/JMatrixPanel.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/RasmolCommandListener.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/ScaleableMatrixPanel.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/SequenceDisplay.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/events/AlignmentPositionListener.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/events/JmolAlignedPositionListener.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/events/package.html
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/package.html
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/AlignedPosition.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/AlignmentCalc.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/AlternativeAlignmentFrame.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/CoordManager.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/JButtonTableCellRenderer.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/JTableDataButtonModel.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/JTableMouseButtonListener.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/MenuCreator.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/PDBDirPanel.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/PDBServerPanel.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/PDBUploadPanel.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/ScopInstallationInstance.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/ScopSelectPanel.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/SequenceMouseListener.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/SequenceScalePanel.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/StructurePairSelector.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/ColorInterpolator.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/ColorUtils.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/ContinuousColorMapper.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/ContinuousColorMapperTransform.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/DefaultMatrixMapper.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/GradientMapper.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/GradientPanel.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/HSVColorSpace.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/LinearColorInterpolator.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/LogColorMapper.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/SqrtColorMapper.java
biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/package.html
biojava3-structure-gui/src/main/java/org/biojava3/structure/gui/JmolViewerImpl.java
biojava3-structure-gui/src/main/java/org/biojava3/structure/gui/OpenAstexViewerImpl.java
biojava3-structure-gui/src/main/java/org/biojava3/structure/gui/RenderStyle.java
biojava3-structure-gui/src/main/java/org/biojava3/structure/gui/Selection.java
biojava3-structure-gui/src/main/java/org/biojava3/structure/gui/SelectionImpl.java
biojava3-structure-gui/src/main/java/org/biojava3/structure/gui/StructureViewer.java
biojava3-structure-gui/src/main/java/org/biojava3/structure/gui/package.html
biojava3-structure-gui/src/main/resources/3vtq-valdata.xml.gz
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biojava3-structure-gui/src/main/resources/3zpy-valdata.xml.gz
biojava3-structure-gui/src/main/resources/icons/background.png
biojava3-structure-gui/src/main/resources/icons/compfile.png
biojava3-structure-gui/src/main/resources/icons/configure.png
biojava3-structure-gui/src/main/resources/icons/editdelete.png
biojava3-structure-gui/src/main/resources/icons/exit.png
biojava3-structure-gui/src/main/resources/icons/fileprint.png
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biojava3-structure-gui/src/main/resources/icons/help.png
biojava3-structure-gui/src/main/resources/icons/kpdf.png
biojava3-structure-gui/src/main/resources/icons/print_printer.png
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biojava3-structure-gui/src/main/resources/icons/window_new.png
biojava3-structure-gui/src/test/java/org/biojava/bio/structure/gui/TestAtomInfo.java
biojava3-structure-gui/src/test/java/org/biojava/structure/gui/JmolViewerImplTest.java
biojava3-structure-gui/src/test/java/org/biojava/structure/gui/OpenAstexViewerImplTest.java
biojava3-structure-gui/src/test/java/org/biojava/structure/gui/RenderStyleTest.java
biojava3-structure-gui/src/test/java/org/biojava/structure/gui/StructureViewerTest.java
biojava3-structure-gui/src/test/java/org/biojava/structure/gui/ViewerTest.java
biojava3-structure/.gitignore
biojava3-structure/pom.xml
biojava3-structure/src/main/java/META-INF/MANIFEST.MF
biojava3-structure/src/main/java/demo/ChemCompDistribution.java
biojava3-structure/src/main/java/demo/DemoAtomCache.java
biojava3-structure/src/main/java/demo/DemoBerkeleyScop.java
biojava3-structure/src/main/java/demo/DemoCATH.java
biojava3-structure/src/main/java/demo/DemoCE.java
biojava3-structure/src/main/java/demo/DemoChangeChemCompProvider.java
biojava3-structure/src/main/java/demo/DemoCommandLineStartup.java
biojava3-structure/src/main/java/demo/DemoDomainsplit.java
biojava3-structure/src/main/java/demo/DemoFATCAT.java
biojava3-structure/src/main/java/demo/DemoLoadSecStruc.java
biojava3-structure/src/main/java/demo/DemoLoadStructure.java
biojava3-structure/src/main/java/demo/DemoMMCIFReader.java
biojava3-structure/src/main/java/demo/DemoSCOP.java
biojava3-structure/src/main/java/org/biojava/bio/structure/AminoAcid.java
biojava3-structure/src/main/java/org/biojava/bio/structure/AminoAcidImpl.java
biojava3-structure/src/main/java/org/biojava/bio/structure/Atom.java
biojava3-structure/src/main/java/org/biojava/bio/structure/AtomImpl.java
biojava3-structure/src/main/java/org/biojava/bio/structure/AtomIterator.java
biojava3-structure/src/main/java/org/biojava/bio/structure/AtomPositionMap.java
biojava3-structure/src/main/java/org/biojava/bio/structure/Author.java
biojava3-structure/src/main/java/org/biojava/bio/structure/Bond.java
biojava3-structure/src/main/java/org/biojava/bio/structure/BondType.java
biojava3-structure/src/main/java/org/biojava/bio/structure/Calc.java
biojava3-structure/src/main/java/org/biojava/bio/structure/Chain.java
biojava3-structure/src/main/java/org/biojava/bio/structure/ChainImpl.java
biojava3-structure/src/main/java/org/biojava/bio/structure/Compound.java
biojava3-structure/src/main/java/org/biojava/bio/structure/DBRef.java
biojava3-structure/src/main/java/org/biojava/bio/structure/Element.java
biojava3-structure/src/main/java/org/biojava/bio/structure/ElementType.java
biojava3-structure/src/main/java/org/biojava/bio/structure/Group.java
biojava3-structure/src/main/java/org/biojava/bio/structure/GroupIterator.java
biojava3-structure/src/main/java/org/biojava/bio/structure/GroupType.java
biojava3-structure/src/main/java/org/biojava/bio/structure/HetatomImpl.java
biojava3-structure/src/main/java/org/biojava/bio/structure/JournalArticle.java
biojava3-structure/src/main/java/org/biojava/bio/structure/Mutator.java
biojava3-structure/src/main/java/org/biojava/bio/structure/NucleotideImpl.java
biojava3-structure/src/main/java/org/biojava/bio/structure/PDBCrystallographicInfo.java
biojava3-structure/src/main/java/org/biojava/bio/structure/PDBHeader.java
biojava3-structure/src/main/java/org/biojava/bio/structure/PDBRecord.java
biojava3-structure/src/main/java/org/biojava/bio/structure/PDBStatus.java
biojava3-structure/src/main/java/org/biojava/bio/structure/ResidueNumber.java
biojava3-structure/src/main/java/org/biojava/bio/structure/ResidueRange.java
biojava3-structure/src/main/java/org/biojava/bio/structure/SSBond.java
biojava3-structure/src/main/java/org/biojava/bio/structure/SVDSuperimposer.java
biojava3-structure/src/main/java/org/biojava/bio/structure/Site.java
biojava3-structure/src/main/java/org/biojava/bio/structure/StandardAminoAcid.java
biojava3-structure/src/main/java/org/biojava/bio/structure/Structure.java
biojava3-structure/src/main/java/org/biojava/bio/structure/StructureException.java
biojava3-structure/src/main/java/org/biojava/bio/structure/StructureImpl.java
biojava3-structure/src/main/java/org/biojava/bio/structure/StructureTools.java
biojava3-structure/src/main/java/org/biojava/bio/structure/UnknownPdbAminoAcidException.java
biojava3-structure/src/main/java/org/biojava/bio/structure/align/AFPTwister.java
biojava3-structure/src/main/java/org/biojava/bio/structure/align/AbstractStructureAlignment.java
biojava3-structure/src/main/java/org/biojava/bio/structure/align/BioJavaStructureAlignment.java
biojava3-structure/src/main/java/org/biojava/bio/structure/align/CallableStructureAlignment.java
biojava3-structure/src/main/java/org/biojava/bio/structure/align/ClusterAltAligs.java
biojava3-structure/src/main/java/org/biojava/bio/structure/align/FarmJob.java
biojava3-structure/src/main/java/org/biojava/bio/structure/align/MultiThreadedDBSearch.java
biojava3-structure/src/main/java/org/biojava/bio/structure/align/StrucAligParameters.java
biojava3-structure/src/main/java/org/biojava/bio/structure/align/StructureAlignment.java
biojava3-structure/src/main/java/org/biojava/bio/structure/align/StructureAlignmentFactory.java
biojava3-structure/src/main/java/org/biojava/bio/structure/align/StructurePairAligner.java
biojava3-structure/src/main/java/org/biojava/bio/structure/align/ce/AbstractUserArgumentProcessor.java
biojava3-structure/src/main/java/org/biojava/bio/structure/align/ce/CECalculator.java
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biojava3-structure/src/main/java/org/biojava/bio/structure/secstruc/BigSqrt.java
biojava3-structure/src/main/java/org/biojava/bio/structure/secstruc/BridgeType.java
biojava3-structure/src/main/java/org/biojava/bio/structure/secstruc/DistEn.java
biojava3-structure/src/main/java/org/biojava/bio/structure/secstruc/HBond.java
biojava3-structure/src/main/java/org/biojava/bio/structure/secstruc/Ladder.java
biojava3-structure/src/main/java/org/biojava/bio/structure/secstruc/SecStruc.java
biojava3-structure/src/main/java/org/biojava/bio/structure/secstruc/SecStrucGroup.java
biojava3-structure/src/main/java/org/biojava/bio/structure/secstruc/SecStrucState.java
biojava3-structure/src/main/java/org/biojava/bio/structure/secstruc/SecStrucType.java
biojava3-structure/src/main/java/org/biojava/bio/structure/server/FlatFileInstallation.java
biojava3-structure/src/main/java/org/biojava/bio/structure/server/MMCIFFileInstallation.java
biojava3-structure/src/main/java/org/biojava/bio/structure/server/PDBFilter.java
biojava3-structure/src/main/java/org/biojava/bio/structure/server/PDBInstallation.java
biojava3-structure/src/main/java/org/biojava/bio/structure/server/PrepareIndexFile.java
biojava3-structure/src/main/java/org/biojava/bio/structure/server/PrepareMMcifIndexFile.java
biojava3-structure/src/main/java/org/biojava/bio/structure/server/SimpleStructureServer.java
biojava3-structure/src/main/java/org/biojava/bio/structure/server/StructureEvent.java
biojava3-structure/src/main/java/org/biojava/bio/structure/server/StructureEventImpl.java
biojava3-structure/src/main/java/org/biojava/bio/structure/server/StructureFetcherRunnable.java
biojava3-structure/src/main/java/org/biojava/bio/structure/server/StructureListener.java
biojava3-structure/src/main/java/org/biojava/bio/structure/server/StructureServer.java
biojava3-structure/src/main/java/org/biojava/bio/structure/server/package.html
biojava3-structure/src/main/java/org/biojava3/structure/StructureIO.java
biojava3-structure/src/main/java/org/biojava3/structure/validation/AngleOutlier.java
biojava3-structure/src/main/java/org/biojava3/structure/validation/BondOutlier.java
biojava3-structure/src/main/java/org/biojava3/structure/validation/Clash.java
biojava3-structure/src/main/java/org/biojava3/structure/validation/Entry.java
biojava3-structure/src/main/java/org/biojava3/structure/validation/ModelledSubgroup.java
biojava3-structure/src/main/java/org/biojava3/structure/validation/MogAngleOutlier.java
biojava3-structure/src/main/java/org/biojava3/structure/validation/MogBondOutlier.java
biojava3-structure/src/main/java/org/biojava3/structure/validation/ObjectFactory.java
biojava3-structure/src/main/java/org/biojava3/structure/validation/Program.java
biojava3-structure/src/main/java/org/biojava3/structure/validation/Programs.java
biojava3-structure/src/main/java/org/biojava3/structure/validation/WwPDBValidationInformation.java
biojava3-structure/src/main/resources/about.properties
biojava3-structure/src/main/resources/blosum62.mat
biojava3-structure/src/main/resources/ce.properties
biojava3-structure/src/main/resources/chemcomp/2EP.cif.gz
biojava3-structure/src/main/resources/chemcomp/2MD.cif.gz
biojava3-structure/src/main/resources/chemcomp/6MO.cif.gz
biojava3-structure/src/main/resources/chemcomp/A.cif.gz
biojava3-structure/src/main/resources/chemcomp/ACY.cif.gz
biojava3-structure/src/main/resources/chemcomp/ALA.cif.gz
biojava3-structure/src/main/resources/chemcomp/ANS.cif.gz
biojava3-structure/src/main/resources/chemcomp/ARG.cif.gz
biojava3-structure/src/main/resources/chemcomp/ASN.cif.gz
biojava3-structure/src/main/resources/chemcomp/ASP.cif.gz
biojava3-structure/src/main/resources/chemcomp/C.cif.gz
biojava3-structure/src/main/resources/chemcomp/CA.cif.gz
biojava3-structure/src/main/resources/chemcomp/CMP.cif.gz
biojava3-structure/src/main/resources/chemcomp/CSE.cif.gz
biojava3-structure/src/main/resources/chemcomp/CYS.cif.gz
biojava3-structure/src/main/resources/chemcomp/DA.cif.gz
biojava3-structure/src/main/resources/chemcomp/DAR.cif.gz
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biojava3-structure/src/main/resources/chemcomp/DOD.cif.gz
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biojava3-structure/src/main/resources/chemcomp/GLN.cif.gz
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biojava3-structure/src/main/resources/chemcomp/GLY.cif.gz
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biojava3-structure/src/main/resources/chemcomp/HIS.cif.gz
biojava3-structure/src/main/resources/chemcomp/HOH.cif.gz
biojava3-structure/src/main/resources/chemcomp/I.cif.gz
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biojava3-structure/src/main/resources/chemcomp/KTH.cif.gz
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biojava3-structure/src/main/resources/chemcomp/LYS.cif.gz
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biojava3-structure/src/main/resources/chemcomp/NA.cif.gz
biojava3-structure/src/main/resources/chemcomp/PHE.cif.gz
biojava3-structure/src/main/resources/chemcomp/PO4.cif.gz
biojava3-structure/src/main/resources/chemcomp/PRO.cif.gz
biojava3-structure/src/main/resources/chemcomp/SEC.cif.gz
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biojava3-structure/src/main/resources/chemcomp/SF4.cif.gz
biojava3-structure/src/main/resources/chemcomp/SO4.cif.gz
biojava3-structure/src/main/resources/chemcomp/THR.cif.gz
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biojava3-structure/src/main/resources/chemcomp/VAL.cif.gz
biojava3-structure/src/main/resources/chemcomp/ZN.cif.gz
biojava3-structure/src/main/resources/jfatcat.properties
biojava3-structure/src/main/resources/log4j2-test.xml
biojava3-structure/src/main/resources/log4j2.xml
biojava3-structure/src/main/resources/org/biojava/bio/structure/standardaminos.pdb
biojava3-structure/src/test/java/org/biojava/bio/structure/AtomPositionMapTest.java
biojava3-structure/src/test/java/org/biojava/bio/structure/ChemCompTest.java
biojava3-structure/src/test/java/org/biojava/bio/structure/ElementTest.java
biojava3-structure/src/test/java/org/biojava/bio/structure/HetatomImplTest.java
biojava3-structure/src/test/java/org/biojava/bio/structure/PDBStatusTest.java
biojava3-structure/src/test/java/org/biojava/bio/structure/PdbFileFormat30Test.java
biojava3-structure/src/test/java/org/biojava/bio/structure/ResidueNumberTest.java
biojava3-structure/src/test/java/org/biojava/bio/structure/ResidueRangeTest.java
biojava3-structure/src/test/java/org/biojava/bio/structure/SiteTest.java
biojava3-structure/src/test/java/org/biojava/bio/structure/SourceCompoundTest.java
biojava3-structure/src/test/java/org/biojava/bio/structure/StructureIOTest.java
biojava3-structure/src/test/java/org/biojava/bio/structure/Test4hhb.java
biojava3-structure/src/test/java/org/biojava/bio/structure/TestAltLocs.java
biojava3-structure/src/test/java/org/biojava/bio/structure/TestAtomCache.java
biojava3-structure/src/test/java/org/biojava/bio/structure/TestBond.java
biojava3-structure/src/test/java/org/biojava/bio/structure/TestCloning.java
biojava3-structure/src/test/java/org/biojava/bio/structure/TestDNAAlignment.java
biojava3-structure/src/test/java/org/biojava/bio/structure/TestDownloadChemCompProvider.java
biojava3-structure/src/test/java/org/biojava/bio/structure/TestLoadStructureFromURL.java
biojava3-structure/src/test/java/org/biojava/bio/structure/TestNucleotides.java
biojava3-structure/src/test/java/org/biojava/bio/structure/TestParsingCalcium.java
biojava3-structure/src/test/java/org/biojava/bio/structure/TestVeryLongFileName.java
biojava3-structure/src/test/java/org/biojava/bio/structure/align/LoadOldXMLfileTest.java
biojava3-structure/src/test/java/org/biojava/bio/structure/align/TestAlignDBSearchPairs.java
biojava3-structure/src/test/java/org/biojava/bio/structure/align/ce/CeCPMainTest.java
biojava3-structure/src/test/java/org/biojava/bio/structure/align/ce/TestSmallAlignment.java
biojava3-structure/src/test/java/org/biojava/bio/structure/align/ce/TestWebStartClient.java
biojava3-structure/src/test/java/org/biojava/bio/structure/align/util/AlignmentToolsTest.java
biojava3-structure/src/test/java/org/biojava/bio/structure/align/util/AtomCacheTest.java
biojava3-structure/src/test/java/org/biojava/bio/structure/align/util/RotationAxisTest.java
biojava3-structure/src/test/java/org/biojava/bio/structure/io/FastaAFPChainConverterTest.java
biojava3-structure/src/test/java/org/biojava/bio/structure/io/StructureSequenceMatcherTest.java
biojava3-structure/src/test/java/org/biojava/bio/structure/io/TestChemCompProvider.java
biojava3-structure/src/test/java/org/biojava/bio/structure/io/TestHardBioUnits.java
biojava3-structure/src/test/java/org/biojava/bio/structure/io/TestMMcifOrganismParsing.java
biojava3-structure/src/test/java/org/biojava/bio/structure/io/TestQuaternaryStructureProviders.java
biojava3-structure/src/test/java/org/biojava/bio/structure/io/TestSiftsParsing.java
biojava3-structure/src/test/java/org/biojava/bio/structure/rcsb/RCSBDescriptionFactoryTest.java
biojava3-structure/src/test/java/org/biojava/bio/structure/rcsb/RCSBLigandsFactoryTest.java
biojava3-structure/src/test/java/org/biojava/bio/structure/redmine/test1DARSeqAlign.java
biojava3-structure/src/test/java/org/biojava/bio/structure/scop/BerkeleyScopInstallationTest.java
biojava3-structure/src/test/java/org/biojava/bio/structure/scop/RemoteScopInstallationTest.java
biojava3-structure/src/test/java/org/biojava/bio/structure/scop/ScopDatabaseTest.java
biojava3-structure/src/test/java/org/biojava/bio/structure/scop/ScopDescriptionTest.java
biojava3-structure/src/test/java/org/biojava/bio/structure/scop/ScopInstallationTest.java
biojava3-structure/src/test/java/org/biojava3/structure/validation/TestValidationReportParsing.java
biojava3-structure/src/test/resources/104D_v23.pdb
biojava3-structure/src/test/resources/104D_v30.pdb
biojava3-structure/src/test/resources/1w0p_1qdm.xml
biojava3-structure/src/test/resources/2gox.pdb
biojava3-structure/src/test/resources/2gox_v315.pdb
biojava3-structure/src/test/resources/2pos.pdb
biojava3-structure/src/test/resources/388d_v23.pdb
biojava3-structure/src/test/resources/388d_v30.pdb
biojava3-structure/src/test/resources/3cdl.pdb
biojava3-structure/src/test/resources/3cfy.pdb
biojava3-structure/src/test/resources/3dl7_v32.pdb
biojava3-structure/src/test/resources/3mk3.pdb
biojava3-structure/src/test/resources/4hhb.cif.gz
biojava3-structure/src/test/resources/4hhb.pdb.gz
biojava3-structure/src/test/resources/align/1FEZ.A_1O08.A.xml
biojava3-structure/src/test/resources/align/1P80.D_2IUF.E.xml
biojava3-structure/src/test/resources/align/31BI_symm_align.xml
biojava3-structure/src/test/resources/db_search.pairs
biojava3-structure/src/test/resources/describeMol/1w0p.xml
biojava3-structure/src/test/resources/describeMol/4hhb.xml
biojava3-structure/src/test/resources/describeMol/4hhb_ligands.xml
biojava3-structure/src/test/resources/describeMol/almost_empty.xml
biojava3-structure/src/test/resources/describeMol/diff_ecs.xml
biojava3-structure/src/test/resources/describeMol/empty.xml
biojava3-structure/src/test/resources/describeMol/same_ecs.xml
biojava3-structure/src/test/resources/validation/3vtq-valdata.xml.gz
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biojava3-structure/src/test/resources/validation/3wcp-valdata.xml.gz
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biojava3-structure/src/test/resources/validation/3zpy-valdata.xml.gz
biojava3-survival/pom.xml
biojava3-survival/src/main/java/org/biojava3/survival/cox/CoxCC.java
biojava3-survival/src/main/java/org/biojava3/survival/cox/CoxCoefficient.java
biojava3-survival/src/main/java/org/biojava3/survival/cox/CoxHelper.java
biojava3-survival/src/main/java/org/biojava3/survival/cox/CoxInfo.java
biojava3-survival/src/main/java/org/biojava3/survival/cox/CoxMart.java
biojava3-survival/src/main/java/org/biojava3/survival/cox/CoxMethod.java
biojava3-survival/src/main/java/org/biojava3/survival/cox/CoxR.java
biojava3-survival/src/main/java/org/biojava3/survival/cox/CoxScore.java
biojava3-survival/src/main/java/org/biojava3/survival/cox/CoxVariables.java
biojava3-survival/src/main/java/org/biojava3/survival/cox/ResidualsCoxph.java
biojava3-survival/src/main/java/org/biojava3/survival/cox/RiskInfo.java
biojava3-survival/src/main/java/org/biojava3/survival/cox/StrataInfo.java
biojava3-survival/src/main/java/org/biojava3/survival/cox/SurvFitInfo.java
biojava3-survival/src/main/java/org/biojava3/survival/cox/SurvivalInfo.java
biojava3-survival/src/main/java/org/biojava3/survival/cox/SurvivalInfoHelper.java
biojava3-survival/src/main/java/org/biojava3/survival/cox/SurvivalInfoIndex.java
biojava3-survival/src/main/java/org/biojava3/survival/cox/WaldTest.java
biojava3-survival/src/main/java/org/biojava3/survival/cox/WaldTestInfo.java
biojava3-survival/src/main/java/org/biojava3/survival/cox/comparators/CoxVariablesOverallModelFitComparator.java
biojava3-survival/src/main/java/org/biojava3/survival/cox/comparators/CoxVariablesVariableComparator.java
biojava3-survival/src/main/java/org/biojava3/survival/cox/comparators/MeanModelComparator.java
biojava3-survival/src/main/java/org/biojava3/survival/cox/comparators/SurvivalInfoComparator.java
biojava3-survival/src/main/java/org/biojava3/survival/cox/comparators/SurvivalInfoValueComparator.java
biojava3-survival/src/main/java/org/biojava3/survival/cox/matrix/Matrix.java
biojava3-survival/src/main/java/org/biojava3/survival/cox/matrix/StdArrayIO.java
biojava3-survival/src/main/java/org/biojava3/survival/cox/stats/AgScore.java
biojava3-survival/src/main/java/org/biojava3/survival/cox/stats/ChiSq.java
biojava3-survival/src/main/java/org/biojava3/survival/cox/stats/Cholesky2.java
biojava3-survival/src/main/java/org/biojava3/survival/cox/stats/Chsolve2.java
biojava3-survival/src/main/java/org/biojava3/survival/data/ChangeValue.java
biojava3-survival/src/main/java/org/biojava3/survival/data/CompactCharSequence.java
biojava3-survival/src/main/java/org/biojava3/survival/data/HeaderInfo.java
biojava3-survival/src/main/java/org/biojava3/survival/data/WorkSheet.java
biojava3-survival/src/main/java/org/biojava3/survival/kaplanmeier/figure/CensorStatus.java
biojava3-survival/src/main/java/org/biojava3/survival/kaplanmeier/figure/CensorStatusSelect.java
biojava3-survival/src/main/java/org/biojava3/survival/kaplanmeier/figure/ExpressionFigure.java
biojava3-survival/src/main/java/org/biojava3/survival/kaplanmeier/figure/GroupResults.java
biojava3-survival/src/main/java/org/biojava3/survival/kaplanmeier/figure/KMFigureInfo.java
biojava3-survival/src/main/java/org/biojava3/survival/kaplanmeier/figure/KaplanMeierFigure.java
biojava3-survival/src/main/java/org/biojava3/survival/kaplanmeier/figure/SurvFitKM.java
biojava3-survival/src/main/java/org/biojava3/survival/kaplanmeier/metadata/ClinicalMetaDataOutcome.java
biojava3-survival/src/main/java/org/biojava3/survival/kaplanmeier/metadata/DiscreteQuantizerInterface.java
biojava3-survival/src/main/java/org/biojava3/survival/kaplanmeier/metadata/MeanQuantizer.java
biojava3-survival/src/main/java/org/biojava3/survival/kaplanmeier/metadata/MetaDataInfo.java
biojava3-survival/src/main/resources/uis-complete.txt
biojava3-ws/pom.xml
biojava3-ws/src/main/java/demo/HmmerDemo.java
biojava3-ws/src/main/java/demo/NCBIQBlastServiceDemo.java
biojava3-ws/src/main/java/org/biojava3/ws/alignment/RemotePairwiseAlignmentOutputProperties.java
biojava3-ws/src/main/java/org/biojava3/ws/alignment/RemotePairwiseAlignmentProperties.java
biojava3-ws/src/main/java/org/biojava3/ws/alignment/RemotePairwiseAlignmentService.java
biojava3-ws/src/main/java/org/biojava3/ws/alignment/package.html
biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/BlastAlignmentParameterEnum.java
biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/BlastJob.java
biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/BlastMatrixEnum.java
biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/BlastOutputAlignmentFormatEnum.java
biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/BlastOutputFormatEnum.java
biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/BlastOutputParameterEnum.java
biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/BlastProgramEnum.java
biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/MapToStringTransformer.java
biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java
biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/NCBIQBlastOutputProperties.java
biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/NCBIQBlastService.java
biojava3-ws/src/main/java/org/biojava3/ws/hmmer/HmmerDomain.java
biojava3-ws/src/main/java/org/biojava3/ws/hmmer/HmmerResult.java
biojava3-ws/src/main/java/org/biojava3/ws/hmmer/HmmerScan.java
biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java
development/eclipse/biojava-checkstyle.xml
development/eclipse/biojava-cleanup.xml
development/eclipse/biojava-formatter.xml
development/eclipse/biojava-templates.xml
development/hints.md
ignore.txt
integrationtest/pom.xml
integrationtest/src/test/java/org/biojava/bio/structure/HeaderOnlyTest.java
integrationtest/src/test/java/org/biojava/bio/structure/MMcifTest.java
integrationtest/src/test/java/org/biojava/bio/structure/PDBFileParserTest.java
integrationtest/src/test/java/org/biojava/bio/structure/StructurePairAlignerTest.java
integrationtest/src/test/java/org/biojava/bio/structure/StructureTest.java
integrationtest/src/test/java/org/biojava/bio/structure/StructureToolsTest.java
integrationtest/src/test/java/org/biojava/bio/structure/Test1a4w.java
integrationtest/src/test/java/org/biojava/bio/structure/TestSECalignment.java
integrationtest/src/test/java/org/biojava/bio/structure/align/FlipAFPChainTest.java
integrationtest/src/test/java/org/biojava/bio/structure/align/ce/OptimalCECPMainTest.java
integrationtest/src/test/java/org/biojava/bio/structure/align/fatcat/AFPChainSerialisationTest.java
integrationtest/src/test/java/org/biojava/bio/structure/align/fatcat/FlipAFPChainTest.java
integrationtest/src/test/java/org/biojava/bio/structure/align/fatcat/MyTestHelper.java
integrationtest/src/test/java/org/biojava/bio/structure/align/fatcat/TestFlexibleRotationMatrices.java
integrationtest/src/test/java/org/biojava/bio/structure/align/fatcat/TestOutputStrings.java
integrationtest/src/test/java/org/biojava/bio/structure/cath/CathTest.java
integrationtest/src/test/java/org/biojava/bio/structure/scop/ScopTest.java
integrationtest/src/test/java/org/biojava/bio/structure/util/StringManipulationTestsHelper.java
integrationtest/src/test/java/org/integrationtest/AppTest.java
integrationtest/src/test/resources/1a4w.cif
integrationtest/src/test/resources/1a4w.pdb
integrationtest/src/test/resources/1fdo.cif
integrationtest/src/test/resources/1fdo.pdb
integrationtest/src/test/resources/1j59.cif
integrationtest/src/test/resources/1j59.pdb
integrationtest/src/test/resources/1lnl.pdb
integrationtest/src/test/resources/1tap.pdb
integrationtest/src/test/resources/2kc9.cif
integrationtest/src/test/resources/2kc9.pdb
integrationtest/src/test/resources/5pti.cif
integrationtest/src/test/resources/5pti.pdb
integrationtest/src/test/resources/5pti_old.pdb
integrationtest/src/test/resources/ce_1fdo.A_2iv2.X.out
pom.xml
protein-comparison-tool/pom.xml
protein-comparison-tool/src/main/assembly/LICENSE
protein-comparison-tool/src/main/assembly/assembly.xml
protein-comparison-tool/src/main/assembly/db.out
protein-comparison-tool/src/main/assembly/example.lst
protein-comparison-tool/src/main/assembly/runCE.sh
protein-comparison-tool/src/main/assembly/runFATCAT.sh
protein-comparison-tool/src/main/assembly/startFarmJob.sh
readme.md