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> biojava-1.6-bin.jar.zip
标签:biojava-1.6-bin.jar.zip,biojava,1.6,bin,jar.zip包下载,依赖包
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  • >>> Java Explorer <2.6.8>
    • META-INF
      • MANIFEST.MF
      • services
        • org.biojava.bio.program.formats.Format
        • org.biojava.directory.SequenceDBProvider
    • obda
      • naming
        • core.xml
    • org
      • biojava
        • bibliography
          • BiblioArticle.java
          • BiblioBook.java
          • BiblioBookArticle.java
          • BiblioCriterion.java
          • BiblioDescription.java
          • BiblioEntryStatus.java
          • BiblioJournal.java
          • BiblioJournalArticle.java
          • BiblioOrganisation.java
          • BiblioPatent.java
          • BiblioPerson.java
          • BiblioProceeding.java
          • BiblioProvider.java
          • BiblioScope.java
          • BiblioService.java
          • BiblioSubject.java
          • BiblioTechReport.java
          • BiblioThesis.java
          • BiblioWebResource.java
          • BibRef.java
          • BibRefException.java
          • BibRefQuery.java
          • BibRefSupport.java
        • bio
          • AbstractAnnotation.java
          • alignment
            • AbstractULAlignment.java
            • AlignmentElement.java
            • ARAlignment.java
            • EditableAlignment.java
            • FlexibleAlignment.java
            • IllegalAlignmentEditException.java
            • NeedlemanWunsch.java
            • QualitativeAlignment.java
            • SequenceAlignment.java
            • SimpleAlignmentElement.java
            • SmithWaterman.java
            • SubstitutionMatrix.java
            • UnequalLengthAlignment.java
          • annodb
            • AnnotationDB.java
            • EmptyAnnotationDB.java
            • IndexedAnnotationDB.java
            • LazyFilteredAnnotationDB.java
            • LazySearchedAnnotationDB.java
            • MergingAnnotationDB.java
            • SimpleAnnotationDB.java
          • Annotatable.java
          • Annotation.java
          • AnnotationChanger.java
          • AnnotationRenamer.java
          • AnnotationTools.java
          • AnnotationType.java
          • AnyPropertyConstraint.java
          • BeanAsAnnotation.java
          • BioError.java
          • BioException.java
          • BioRuntimeException.java
          • CardinalityConstraint.java
          • chromatogram
            • AbstractChromatogram.java
            • Chromatogram.java
            • ChromatogramFactory.java
            • ChromatogramTools.java
            • graphic
              • ChromatogramGraphic.java
              • ChromatogramNonlinearScaler.java
              • FixedBaseWidthScaler.java
            • SimpleChromatogram.java
            • UnsupportedChromatogramFormatException.java
          • CollectionConstraint.java
          • dist
            • AbstractDistribution.java
            • AbstractOrderNDistribution.java
            • Count.java
            • Distribution.java
            • DistributionFactory.java
            • DistributionTools.java
            • DistributionTrainer.java
            • DistributionTrainerContext.java
            • GapDistribution.java
            • GeneralNthOrderDistribution.java
            • IgnoreCountsTrainer.java
            • IndexedCount.java
            • IndexedNthOrderDistribution.java
            • OrderNDistribution.java
            • OrderNDistributionFactory.java
            • PairDistribution.java
            • SimpleDistribution.java
            • SimpleDistributionTrainer.java
            • SimpleDistributionTrainerContext.java
            • TranslatedDistribution.java
            • UniformDistribution.java
            • UntrainableDistribution.java
            • XMLDistributionReader.java
            • XMLDistributionWriter.java
          • dp
            • AbstractTrainer.java
            • BackPointer.java
            • BaumWelchSampler.java
            • BaumWelchTrainer.java
            • DotState.java
            • DP.java
            • DPFactory.java
            • DPMatrix.java
            • EmissionState.java
            • FlatModel.java
            • HMMTrainer.java
            • IllegalTransitionException.java
            • MagicalState.java
            • MarkovModel.java
            • ModelInState.java
            • ModelTrainer.java
            • onehead
              • AbstractCursor.java
              • DPCursor.java
              • MatrixCursor.java
              • SingleDP.java
              • SingleDPMatrix.java
              • SmallCursor.java
            • ProfileHMM.java
            • ScoreType.java
            • SimpleDotState.java
            • SimpleEmissionState.java
            • SimpleHMMTrainer.java
            • SimpleMarkovModel.java
            • SimpleModelInState.java
            • SimpleModelTrainer.java
            • SimpleStatePath.java
            • SimpleWeightMatrix.java
            • State.java
            • StatePath.java
            • StoppingCriteria.java
            • Trainable.java
            • TrainerTransition.java
            • TrainingAlgorithm.java
            • Transition.java
            • TransitionTrainer.java
            • twohead
              • AbstractMatrixPairDPCursor.java
              • BackMatrixPairDPCursor.java
              • Cell.java
              • CellCalculator.java
              • CellCalculatorFactory.java
              • CellCalculatorFactoryMaker.java
              • DPCompiler.java
              • DPInterpreter.java
              • EmissionCache.java
              • LightPairDPCursor.java
              • MatrixPairDPCursor.java
              • PairDPCursor.java
              • PairDPMatrix.java
              • PairwiseDP.java
            • WeightMatrix.java
            • WeightMatrixAnnotator.java
            • WMAsMM.java
            • XmlMarkovModel.java
          • EcNumber.java
          • EmptyAnnotation.java
          • gui
            • BarLogoPainter.java
            • BlockPainter.java
            • DistributionLogo.java
            • DNAStyle.java
            • FeatureTree.java
            • glyph
              • ArrowGlyph.java
              • Glyph.java
              • GlyphUtils.java
              • HelixGlyph.java
              • RectangleGlyph.java
              • TurnGlyph.java
              • TwoHeadedArrowGlyph.java
            • LogoContext.java
            • LogoPainter.java
            • PlainBlock.java
            • PlainStyle.java
            • sequence
              • AbiTraceRenderer.java
              • AbstractBeadRenderer.java
              • AbstractPeptideDigestRenderer.java
              • AlignmentRenderer.java
              • aprDesc.html
              • aprExamp.apr
              • ArrowedFeatureRenderer.java
              • BasicFeatureRenderer.java
              • BasicImapRenderer.java
              • BeadFeatureRenderer.java
              • BumpedRenderer.java
              • CircularFeatureFilteringRenderer.java
              • CircularFeatureRenderer.java
              • CircularFeaturesRenderer.java
              • CircularMLR.java
              • CircularPaddedRenderer.java
              • CircularRenderer.java
              • CircularRendererContext.java
              • CircularRendererPanel.java
              • CrosshairRenderer.java
              • EllipticalBeadRenderer.java
              • fastaDesc.html
              • fastaExamp.fasta
              • FeatureBlockSequenceRenderer.java
              • FeatureLabelRenderer.java
              • FeatureRenderer.java
              • FeatureSource.java
              • FilteringRenderer.java
              • GappedRenderer.java
              • GlyphFeatureRenderer.java
              • GUITools.java
              • HeadlessRenderContext.java
              • ImageMap.java
              • ImageMapRenderer.java
              • LabelledSequenceRenderer.java
              • LabelRenderer.java
              • LayeredRenderer.java
              • LineInfo.java
              • msfDesc.html
              • msfExamp.msf
              • MultiLineRenderer.java
              • NoDesc.html
              • NoSample.txt
              • OffsetRulerRenderer.java
              • OverlayMarker.java
              • OverlayRendererWrapper.java
              • PaddingRenderer.java
              • PairwiseDiagonalRenderer.java
              • PairwiseFilteringRenderer.java
              • PairwiseOverlayRenderer.java
              • PairwiseRenderContext.java
              • PairwiseSequencePanel.java
              • PairwiseSequenceRenderer.java
              • PeptideDigestRenderer.java
              • RectangularBeadRenderer.java
              • RectangularImapRenderer.java
              • RoundRectangularBeadRenderer.java
              • RulerRenderer.java
              • SecondaryStructureFeatureRenderer.java
              • SequencePanel.java
              • SequencePanelWrapper.java
              • SequencePoster.java
              • SequenceRenderContext.java
              • SequenceRenderer.java
              • SequenceRendererWrapper.java
              • SequenceViewerEvent.java
              • SequenceViewerListener.java
              • SequenceViewerMotionListener.java
              • SequenceViewerMotionSupport.java
              • SequenceViewerSupport.java
              • SimpleLabelRenderer.java
              • SixFrameRenderer.java
              • SixFrameZiggyRenderer.java
              • StackedFeatureRenderer.java
              • StopRenderer.java
              • SubCircularRendererContext.java
              • SubPairwiseRenderContext.java
              • SubSequenceRenderContext.java
              • SymbolSequenceRenderer.java
              • TickFeatureRenderer.java
              • tracklayout
                • SimpleTrackLayout.java
                • TrackLayout.java
                • UserDefinedTrackLayout.java
              • TranslatedSequencePanel.java
              • ZiggyFeatureRenderer.java
              • ZiggyImapRenderer.java
            • SimpleSymbolStyle.java
            • StackedLogoPainter.java
            • SymbolStyle.java
            • TextBlock.java
            • TextLogoPainter.java
          • MergeAnnotation.java
          • molbio
            • Composition.java
            • DNAComposition.java
            • rebase_common.dat
            • RestrictionEnzyme.java
            • RestrictionEnzymeManager.java
            • RestrictionEnzymeManager.properties
            • RestrictionMapper.java
            • RestrictionSite.java
            • RestrictionSiteFinder.java
          • NoneCollectionConstraint.java
          • NonePropertyConstraint.java
          • OverlayAnnotation.java
          • program
            • abi
              • ABIFChromatogram.java
              • ABIFParser.java
              • ABITools.java
              • ABITrace.java
            • blast2html
              • AbstractAlignmentStyler.java
              • AlignmentMarker.java
              • AlignmentStyler.java
              • Blast2HTMLHandler.java
              • BlastLikeAlignment.java
              • BlastMatrixAlignmentStyler.java
              • ColourCommand.java
              • DatabaseURLGenerator.java
              • DefaultURLGeneratorFactory.java
              • DetailHit.java
              • EbiDatabaseURLGenerator.java
              • HitDescription.java
              • HitId.java
              • HitSummary.java
              • HSP.java
              • HSPSummary.java
              • HTMLRenderer.java
              • NcbiDatabaseURLGenerator.java
              • Sequence.java
              • SimpleAlignmentStyler.java
              • URLGeneratorFactory.java
            • BlastLikeToXMLConverter.java
            • das
              • ComponentFeatureHandler.java
              • DAS.java
              • dasalignment
                • Alignment.java
                • DASAlignmentCall.java
                • DASAlignmentClient.java
                • DASAlignmentXMLResponseParser.java
                • DASException.java
              • DASAnnotationDistDataSource.java
              • DASCapabilities.java
              • DASComponentFeature.java
              • DASDistDataSource.java
              • DASFeatureSet.java
              • DASGFFFeatureHandler.java
              • DASLink.java
              • DASLinkHandler.java
              • DASRawSymbolList.java
              • DASSequence.java
              • DASSequenceDB.java
              • DASSequenceDBProvider.java
              • DASSequenceI.java
              • dasstructure
                • DASStructureCall.java
                • DASStructureXMLResponseParser.java
              • DataSource.java
              • FeatureFetcher.java
              • FeatureRequestManager.java
              • Fetcher.java
              • RawAnnotationSequence.java
              • ReferenceServer.java
              • Segment.java
              • TypesFetcher.java
              • TypesListener.java
            • formats
              • Embl.java
              • Enzyme.java
              • Format.java
              • FormatTools.java
              • Ligand.java
              • Swissprot.java
            • gff
              • GFFComparator.java
              • GFFDocumentHandler.java
              • GFFEntrySet.java
              • GFFErrorHandler.java
              • GFFFilterer.java
              • GFFParser.java
              • GFFRecord.java
              • GFFRecordFilter.java
              • GFFTools.java
              • GFFWriter.java
              • IgnoreRecordException.java
              • SequencesAsGFF.java
              • SimpleGFFRecord.java
            • gff3
              • GFF3DocumentHandler.java
              • GFF3Parser.java
              • GFF3Record.java
            • hmmer
              • FullHmmerProfileHMM.java
              • HmmerProfileHMM.java
              • HmmerProfileParser.java
              • ProfileEmissionState.java
            • homologene
              • AbstractOrthologueSet.java
              • AbstractOrthoPairCollection.java
              • AbstractOrthoPairSet.java
              • DuplicateTaxonException.java
              • HomologeneBuilder.java
              • HomologeneDB.java
              • HomologeneTools.java
              • Orthologue.java
              • OrthologueFilter.java
              • OrthologueSet.java
              • OrthoPair.java
              • OrthoPairCollection.java
              • OrthoPairFilter.java
              • OrthoPairSet.java
              • OrthoPairSetFilter.java
              • SimilarityType.java
              • SimpleHomologeneBuilder.java
              • SimpleHomologeneDB.java
              • SimpleOrthologue.java
              • SimpleOrthologueSet.java
              • SimpleOrthoPair.java
              • SimpleOrthoPairCollection.java
              • SimpleOrthoPairSet.java
              • Taxon.java
            • indexdb
              • BioStore.java
              • BioStoreFactory.java
              • CacheList.java
              • ConfigFile.java
              • IndexStore.java
              • IndexTools.java
              • KeyPair.java
              • PrimaryIDList.java
              • PropertiesAnnotation.java
              • Record.java
              • SearchableFileAsList.java
              • SearchableList.java
              • SecondaryFileAsList.java
            • Meme.java
            • PdbToXMLConverter.java
            • phred
              • PhredFormat.java
              • PhredSequence.java
              • PhredTools.java
              • Qualitative.java
            • sax
              • AbstractNativeAppSAXParser.java
              • BaseXMLWriterTestHelper.java
              • BlastLikeAlignmentSAXParser.java
              • BlastLikeSAXParser.java
              • BlastLikeVersionSupport.java
              • BlastSAXParser.java
              • blastxml
                • BlastAggregator.java
                • BlastOutputHandler.java
                • BlastOutputIterationsHandler.java
                • BlastXMLParser.java
                • BlastXMLParserFacade.java
                • HitHandler.java
                • HitHspsHandler.java
                • HspHandler.java
                • IterationHandler.java
                • IterationHitsHandler.java
                • NCBI_BlastOutput.dtd
                • NCBI_BlastOutput.mod
                • NCBI_Entity.mod
                • StAXFeatureHandler.java
                • StAXFeatureHandlerMod.java
                • StAXHandlerFactory.java
              • ClustalWAlignmentSAXParser.java
              • DomainSectionSAXParser.java
              • FastaSearchParser.java
              • FastaSearchSAXParser.java
              • FastaSequenceSAXParser.java
              • GCGBlastSummaryLineHelper.java
              • GenericSAXParserTest.java
              • HitSectionSAXParser.java
              • HmmerAlignmentSAXParser.java
              • HmmerSummaryLineHelper.java
              • HSPSummaryHelper.java
              • NamespaceConfigurationIF.java
              • NcbiBlastSummaryLineHelper.java
              • NeedleAlignmentSAXParser.java
              • PdbSAXParser.java
              • QName.java
              • SequenceAlignmentSAXParser.java
              • SimpleXMLEmitterTestHelper.java
              • SummaryLineHelperIF.java
              • WuBlastSummaryLineHelper.java
            • scf
              • SCF.java
            • ssaha
              • CompactedDataStore.java
              • CompactedDataStoreFactory.java
              • DataStore.java
              • DataStoreFactory.java
              • HitMerger.java
              • MappedDataStore.java
              • MappedDataStoreFactory.java
              • NIODataStore.java
              • NIODataStoreFactory.java
              • SearchException.java
              • SearchListener.java
              • SequenceStreamer.java
            • ssbind
              • AlignmentStAXHandler.java
              • AlphabetResolver.java
              • AnnotationFactory.java
              • BlastLikeHomologyBuilder.java
              • BlastLikeSearchBuilder.java
              • HeaderStAXHandler.java
              • HitStAXHandler.java
              • HSPStAXHandler.java
              • HSPSummaryStAXHandler.java
              • SeqSimilarityAdapter.java
              • SeqSimilarityStAXAdapter.java
              • SeqSimilarityStAXHandler.java
              • SimilarityPairBuilder.java
              • StAXHandlerBinding.java
              • StAXHandlerFactory.java
              • ViewSequenceFactory.java
            • tagvalue
              • AbstractWrapper.java
              • Aggregator.java
              • AnnotationBuilder.java
              • BoundaryFinder.java
              • ChangeTable.java
              • Echo.java
              • Formats.java
              • Index2Model.java
              • Indexer.java
              • Indexer2.java
              • LineSplitParser.java
              • MultiTagger.java
              • Parser.java
              • ParserListener.java
              • PropertyChanger.java
              • RegexChanger.java
              • RegexFieldFinder.java
              • RegexParser.java
              • RegexSplitter.java
              • SimpleTagValueWrapper.java
              • StateMachine.java
              • TagDelegator.java
              • TagDropper.java
              • TagMapper.java
              • TagRenamer.java
              • TagValue.java
              • TagValueContext.java
              • TagValueListener.java
              • TagValueParser.java
              • TagValueWrapper.java
              • ValueChanger.java
            • unigene
              • createUnigene.sql
              • FlatFileUnigeneDB.java
              • FlatFileUnigeneFactory.java
              • SQLUnigeneDB.java
              • SQLUnigeneFactory.java
              • UnigeneCluster.java
              • UnigeneDB.java
              • UnigeneFactory.java
              • UnigeneTools.java
            • xff
              • BasicXFFHelper.java
              • ElementRecognizer.java
              • FeatureHandler.java
              • LocationHandlerBase.java
              • PropDetailHandler.java
              • PropertyWriter.java
              • StrandedFeatureHandler.java
              • XFFFeatureSetHandler.java
              • XFFHelper.java
              • XFFPartHandlerFactory.java
              • XFFTools.java
              • XFFWriter.java
            • xml
              • BaseXMLWriter.java
              • SimpleXMLEmitter.java
          • PropertyConstraint.java
          • proteomics
            • aaindex
              • AAindex.java
              • AAindexStreamReader.java
              • SimpleSymbolPropertyTableDB.java
              • SymbolPropertyTableDB.java
              • SymbolPropertyTableIterator.java
            • Digest.java
            • IsoelectricPointCalc.java
            • MassCalc.java
            • Protease.java
            • ProteaseManager.java
            • ProteaseManager.xml
            • StructureTools.java
          • search
            • BioMatcher.java
            • BioPattern.java
            • BlastLikeSearchFilter.java
            • FilteringContentHandler.java
            • FilterTest.java
            • KnuthMorrisPrattSearch.java
            • MaxMismatchMatcher.java
            • MaxMismatchPattern.java
            • SearchBuilder.java
            • SearchContentAdapter.java
            • SearchContentFilter.java
            • SearchContentHandler.java
            • SearchContentHandlerDebugger.java
            • SeqContentMatcher.java
            • SeqContentPattern.java
            • SeqSimilaritySearcher.java
            • SeqSimilaritySearchHit.java
            • SeqSimilaritySearchResult.java
            • SeqSimilaritySearchSubHit.java
            • SequenceDBSearchHit.java
            • SequenceDBSearchResult.java
            • SequenceDBSearchSubHit.java
            • SimpleSeqSimilaritySearchHit.java
            • SimpleSeqSimilaritySearchResult.java
            • SimpleSeqSimilaritySearchSubHit.java
          • seq
            • AbstractFeatureHolder.java
            • AcceptAllFilter.java
            • AcceptNoneFilter.java
            • ByHierarchy.java
            • ByLocationMinMaxComparator.java
            • ByLocationMinMaxFeatureComparator.java
            • CircularView.java
            • ComponentFeature.java
            • db
              • AbstractSequenceDB.java
              • AnnotatedSequenceDB.java
              • biofetch
                • BioFetchSequenceDB.java
                • BioFetchSequenceDBProvider.java
              • BioIndex.java
              • biosql
                • BioSQLAllFeatures.java
                • BioSQLAssembly.java
                • BioSQLComponentFeature.java
                • BioSQLEntryAnnotationChangeHub.java
                • BioSQLEntryChangeHub.java
                • BioSQLFeature.java
                • BioSQLFeatureAnnotation.java
                • BioSQLFeatureAnnotationChangeHub.java
                • BioSQLFeatureChangeHub.java
                • BioSQLFeatureReceiver.java
                • BioSQLSequence.java
                • BioSQLSequenceAnnotation.java
                • BioSQLSequenceDB.java
                • BioSQLSequenceDBProvider.java
                • BioSQLSequenceI.java
                • BioSQLStrandedFeature.java
                • BioSQLTiledFeatures.java
                • DBHelper.java
                • FeaturesSQL.java
                • HypersonicDBHelper.java
                • MySQLDBHelper.java
                • OntologySQL.java
                • OracleDBHelper.java
                • PostgreSQLDBHelper.java
                • TaxonSQL.java
                • UnknownDBHelper.java
              • CachingSequenceDB.java
              • DummySequenceDB.java
              • DummySequenceDBInstallation.java
              • emblcd
                • AcnumHitReader.java
                • AcnumTrgReader.java
                • DivisionLkpReader.java
                • EmblCDROMIndexReader.java
                • EmblCDROMRandomAccess.java
                • EntryNamIdxReader.java
                • EntryNamRandomAccess.java
                • RecordParser.java
              • EmblCDROMIndexStore.java
              • FetchURL.java
              • flat
                • FlatSequenceDB.java
                • FlatSequenceDBProvider.java
              • GenbankSequenceDB.java
              • GenpeptSequenceDB.java
              • HashSequenceDB.java
              • IDMaker.java
              • IllegalIDException.java
              • Index.java
              • IndexedSequenceDB.java
              • IndexStore.java
              • NCBISequenceDB.java
              • SequenceDB.java
              • SequenceDBInstallation.java
              • SequenceDBLite.java
              • SequenceDBWrapper.java
              • SimpleIndex.java
              • SimpleSequenceDBInstallation.java
              • SubSequenceDB.java
              • SwissprotSequenceDB.java
              • TabIndexStore.java
              • ViewingSequenceDB.java
              • WebSequenceDB.java
            • distributed
              • DistComponentFeature.java
              • DistDataSource.java
              • DistProjectionContext.java
              • DistributedSequence.java
              • DistributedSequenceDB.java
              • GFFDataSource.java
              • SequenceDBDataSource.java
            • DNATools.java
            • Down.java
            • Feature.java
            • FeatureFilter.java
            • FeatureHolder.java
            • FeatureHolderUtils.java
            • FeatureRealizer.java
            • FeatureTypes.java
            • filter
              • FilterTransformer.java
            • FilterUtils.java
            • Frame.java
            • FramedFeature.java
            • GappedSequence.java
            • GeneticCodes.java
            • homol
              • Homology.java
              • HomologyDB.java
              • HomologyFeature.java
              • SimilarityPairFeature.java
              • SimpleHomology.java
            • impl
              • AssembledSymbolList.java
              • DummySequence.java
              • FeatureImpl.java
              • LazyFilterFeatureHolder.java
              • NewAssembledSymbolList.java
              • RevCompSequence.java
              • SimpleFeature.java
              • SimpleFramedFeature.java
              • SimpleGappedSequence.java
              • SimpleHomologyFeature.java
              • SimpleRemoteFeature.java
              • SimpleRestrictionSite.java
              • SimpleSequence.java
              • SimpleSequenceFactory.java
              • SimpleSimilarityPairFeature.java
              • SimpleStrandedFeature.java
              • SubSequence.java
              • TemplateUtils.java
              • ViewSequence.java
            • io
              • AbstractGenEmblFileFormer.java
              • agave
                • Agave2AgaveAnnotFilter.java
                • AGAVEAltIdsPropHandler.java
                • AGAVEAnnotationsHandler.java
                • AGAVEAnnotFilter.java
                • AGAVEAnnotFilterFactory.java
                • AGAVEAssemblyHandler.java
                • AGAVEBioSeqCallbackItf.java
                • AGAVEBioSeqHandler.java
                • AGAVEBioSequenceHandler.java
                • AGAVECallbackItf.java
                • AGAVECdsHandler.java
                • AGAVEChromosomeCallbackItf.java
                • AGAVEChromosomeHandler.java
                • AGAVEClassificationHandler.java
                • AGAVECompResultHandler.java
                • AGAVEComputationHandler.java
                • AGAVEContigCallbackItf.java
                • AGAVEContigHandler.java
                • AGAVEDbId.java
                • AGAVEDbIdCallbackItf.java
                • AGAVEDbIdPropCallbackItf.java
                • AGAVEDbIdPropHandler.java
                • AGAVEDescPropHandler.java
                • AGAVEElementIdPropHandler.java
                • AGAVEEvidenceCallbackItf.java
                • AGAVEEvidenceHandler.java
                • AGAVEExonsPropHandler.java
                • AGAVEFeatureCallbackItf.java
                • AGAVEFragmentOrderHandler.java
                • AGAVEFragmentOrientationHandler.java
                • AGAVEGeneHandler.java
                • AGAVEHandler.java
                • AGAVEIdAlias.java
                • AGAVEIdAliasCallbackItf.java
                • AGAVEIdAliasPropHandler.java
                • AGAVEKeywordPropHandler.java
                • AGAVEMapLocation.java
                • AGAVEMapLocationPropHandler.java
                • AGAVEMapPosition.java
                • AGAVEMapPositionPropHandler.java
                • AGAVEMatchAlignPropHandler.java
                • AGAVEMatchDescPropHandler.java
                • AGAVEMatchRegion.java
                • AGAVEMatchRegionPropHandler.java
                • AGAVEMrnaHandler.java
                • AGAVENotePropHandler.java
                • AGAVEPredictedProteinHandler.java
                • AGAVEProperty.java
                • AGAVEQualifierPropHandler.java
                • AGAVEQueryRegion.java
                • AGAVEQueryRegionPropHandler.java
                • AGAVERelatedAnnot.java
                • AGAVERelatedAnnotPropHandler.java
                • AGAVEResultGroupHandler.java
                • AGAVEResultPropertyPropHandler.java
                • AGAVESciPropertyPropHandler.java
                • AGAVESeqFeatureHandler.java
                • AGAVESeqLocationPropHandler.java
                • AGAVESeqMapHandler.java
                • AGAVESeqPropHandler.java
                • AGAVETranscriptHandler.java
                • AGAVEUnorderedFragmentsHandler.java
                • AGAVEViewPropHandler.java
                • AgaveWriter.java
                • AGAVEXref.java
                • AGAVEXrefCallbackItf.java
                • AGAVEXrefPropHandler.java
                • AGAVEXrefPropPropHandler.java
                • AGAVEXrefs.java
                • AGAVEXrefsPropHandler.java
                • DelegationManager.java
                • ElementRecognizer.java
                • Embl2AgaveAnnotFilter.java
                • PCDATAFilterWriter.java
                • SAX2StAXAdaptor.java
                • SequenceHandler.java
                • SimpleAnnotFilter.java
                • StAXContentHandler.java
                • StAXContentHandlerBase.java
                • StAXFeatureHandler.java
                • StAXHandlerFactory.java
                • StAXPropertyHandler.java
                • UtilHelper.java
              • AlignIOConstants.java
              • AlignmentFormat.java
              • AlternateTokenization.java
              • CharacterTokenization.java
              • ChunkedSymbolListFactory.java
              • CrossProductTokenization.java
              • DoubleTokenization.java
              • EmblFileFormer.java
              • EmblLikeFormat.java
              • EmblLikeLocationParser.java
              • EmblProcessor.java
              • EmblReferenceComparator.java
              • FastaAlignmentFormat.java
              • FastaDescriptionLineParser.java
              • FastaFormat.java
              • FeatureQualifier.xml
              • FeatureTableParser.java
              • filterxml
                • QName.java
                • XMLAnnotationTypeHandler.java
                • XMLAnnotationTypeWriter.java
                • XMLFilterHandler.java
                • XMLFilterWriter.java
              • game
                • ElementRecognizer.java
                • GAMEAnnotationHandler.java
                • GAMEAspectPropHandler.java
                • GAMEDbxrefPropHandler.java
                • GAMEDescriptionPropHandler.java
                • GAMEFeatureCallbackItf.java
                • GAMEFeatureSetHandler.java
                • GAMEFeatureSetPropHandler.java
                • GAMEFeatureSpanHandler.java
                • GAMEGenePropHandler.java
                • GAMEHandler.java
                • GAMEMapPosPropHandler.java
                • GAMENameCallbackItf.java
                • GAMENamePropHandler.java
                • GAMEResiduesPropHandler.java
                • GAMESeqPropHandler.java
                • GAMESeqRelPropHandler.java
                • GAMESpanPropHandler.java
                • GAMETranscriptCallbackItf.java
                • GAMETypePropHandler.java
                • SequenceContentHandlerBase.java
                • StAXFeatureHandler.java
                • StAXHandlerFactory.java
                • StAXPropertyHandler.java
              • game12
                • GAMEAnnotationHandler.java
                • GAMEAspectHandler.java
                • GAMEDbxrefHandler.java
                • GAMEFeatureSetHandler.java
                • GAMEFeatureSpanHandler.java
                • GAMEGeneHandler.java
                • GAMEHandler.java
                • GAMEPropertyHandler.java
                • GAMESeqHandler.java
                • GAMESeqRelHandler.java
                • GAMESpanHandler.java
                • StAXFeatureHandler.java
                • StAXHandlerFactory.java
              • GAMEFormat.java
              • GenbankContext.java
              • GenbankFileFormer.java
              • GenbankFormat.java
              • GenbankProcessor.java
              • GenbankXmlFormat.java
              • GenEmblFeatureComparator.java
              • GenEmblPropertyComparator.java
              • GenpeptFileFormer.java
              • GenpeptFormat.java
              • IntegerTokenization.java
              • MSFAlignmentFormat.java
              • NameTokenization.java
              • OrganismParser.java
              • ParseException.java
              • ProteinRefSeqFileFormer.java
              • ProteinRefSeqProcessor.java
              • ReferenceAnnotation.java
              • SeqFileFormer.java
              • SeqIOAdapter.java
              • SeqIOConstants.java
              • SeqIOEventEmitter.java
              • SeqIOFilter.java
              • SeqIOListener.java
              • SeqIOTools.java
              • SequenceBuilder.java
              • SequenceBuilderBase.java
              • SequenceBuilderFactory.java
              • SequenceBuilderFilter.java
              • SequenceDBSequenceBuilder.java
              • SequenceFormat.java
              • SimpleAssemblyBuilder.java
              • SimpleSequenceBuilder.java
              • SmartSequenceBuilder.java
              • StreamParser.java
              • StreamReader.java
              • StreamWriter.java
              • SubIntegerTokenization.java
              • SwissprotFeatureTableParser.java
              • SwissprotFileFormer.java
              • SwissprotProcessor.java
              • SymbolListCharSequence.java
              • SymbolReader.java
              • SymbolTokenization.java
              • WordTokenization.java
            • IsLeaf.java
            • IsTopLevel.java
            • LazyFeatureHolder.java
            • MergeFeatureHolder.java
            • NewSimpleAssembly.java
            • NucleotideTools.java
            • OptimizableFilter.java
            • projection
              • ProjectedFeature.java
              • ProjectedFeatureHolder.java
              • Projection.java
              • ProjectionContext.java
              • ProjectionEngine.java
              • ProjectionUtils.java
              • ReparentContext.java
              • TranslateFlipContext.java
            • ProteinTools.java
            • RealizingFeatureHolder.java
            • RemoteFeature.java
            • RNATools.java
            • Sequence.java
            • SequenceAnnotator.java
            • SequenceFactory.java
            • SequenceIterator.java
            • SequenceTools.java
            • SimpleAssembly.java
            • SimpleComponentFeature.java
            • SimpleFeatureHolder.java
            • SimpleFeatureRealizer.java
            • StrandedFeature.java
            • StrandParser.java
            • TranslationTables.xml
            • Up.java
          • SimpleAnnotation.java
          • SmallAnnotation.java
          • structure
            • align
              • ClusterAltAligs.java
              • helper
                • AligMatEl.java
                • AlignTools.java
                • GapArray.java
                • IndexPair.java
                • JointFragments.java
              • pairwise
                • Alignable.java
                • AligNPE.java
                • AltAligComparator.java
                • AlternativeAlignment.java
                • FragmentJoiner.java
                • FragmentPair.java
                • Gotoh.java
                • JointFragmentsComparator.java
                • StrCompAlignment.java
              • StrucAligParameters.java
              • StructurePairAligner.java
            • AlphaCTools.java
            • AminoAcid.java
            • AminoAcidImpl.java
            • Atom.java
            • AtomImpl.java
            • AtomIterator.java
            • blosum62.mat
            • Calc.java
            • Chain.java
            • ChainImpl.java
            • Compound.java
            • DBRef.java
            • Group.java
            • GroupIterator.java
            • gui
              • BiojavaJmol.java
              • JMatrixPanel.java
              • RasmolCommandListener.java
              • ScaleableMatrixPanel.java
            • HetatomImpl.java
            • io
              • CAConverter.java
              • DASStructureClient.java
              • FileConvert.java
              • PDBFileParser.java
              • PDBFileReader.java
              • PDBMSDReader.java
              • PDBParseException.java
              • PDBSRSReader.java
              • SeqRes2AtomAligner.java
              • StructureIO.java
              • StructureIOFile.java
            • jama
              • CholeskyDecomposition.java
              • EigenvalueDecomposition.java
              • LUDecomposition.java
              • Maths.java
              • Matrix.java
              • QRDecomposition.java
              • SingularValueDecomposition.java
            • Mutator.java
            • NucleotideImpl.java
            • PDBHeader.java
            • server
              • DemoStructureServer.java
              • FlatFileInstallation.java
              • PDBFilter.java
              • PDBInstallation.java
              • PrepareIndexFile.java
              • SimpleStructureServer.java
              • StructureEvent.java
              • StructureEventImpl.java
              • StructureFetcherRunnable.java
              • StructureListener.java
              • StructureServer.java
            • SSBond.java
            • StandardAminoAcid.java
            • standardaminos.pdb
            • Structure.java
            • StructureException.java
            • StructureImpl.java
            • StructureTools.java
            • SVDSuperimposer.java
          • symbol
            • AbstractAlphabet.java
            • AbstractLocation.java
            • AbstractLocationDecorator.java
            • AbstractManyToOneTranslationTable.java
            • AbstractRangeLocation.java
            • AbstractReversibleTranslationTable.java
            • AbstractSimpleBasisSymbol.java
            • AbstractSymbol.java
            • AbstractSymbolList.java
            • AbstractTranslationTable.java
            • Alignment.java
            • Alphabet.java
            • AlphabetIndex.java
            • AlphabetManager.java
            • AlphabetManager.xml
            • AtomicSymbol.java
            • BasisSymbol.java
            • BetweenLocation.java
            • BetweenLocationTools.java
            • ChunkedSymbolList.java
            • CircularLocation.java
            • CircularLocationTools.java
            • CodonPref.java
            • CodonPrefFilter.java
            • CodonPrefTables.xml
            • CodonPrefTools.java
            • CompoundLocation.java
            • CrossProductAlphabetIndex.java
            • DNAAmbPack.java
            • DNANoAmbPack.java
            • DoubleAlphabet.java
            • DummySymbolList.java
            • Edit.java
            • EmptyAlphabet.java
            • EmptyLocation.java
            • EmptySymbolList.java
            • FiniteAlphabet.java
            • FullDnaAlphabetIndex.java
            • FundamentalAtomicSymbol.java
            • FuzzyLocation.java
            • FuzzyPointLocation.java
            • GappedSymbolList.java
            • HashedAlphabetIndex.java
            • IllegalAlphabetException.java
            • IllegalSymbolException.java
            • IndexedNoAmbPack.java
            • InfiniteCrossProductAlphabet.java
            • IntegerAlphabet.java
            • LinearAlphabetIndex.java
            • Location.java
            • LocationComparator.java
            • LocationTools.java
            • ManyToOneTranslationTable.java
            • MergeLocation.java
            • MotifTools.java
            • OrderNSymbolList.java
            • PackedSymbolList.java
            • PackedSymbolListFactory.java
            • Packing.java
            • PackingFactory.java
            • PointLocation.java
            • RangeLocation.java
            • RelabeledAlignment.java
            • ResidueProperties.xml
            • ReverseSymbolList.java
            • ReversibleTranslationTable.java
            • SimpleAlignment.java
            • SimpleAlphabet.java
            • SimpleAtomicSymbol.java
            • SimpleBasisSymbol.java
            • SimpleCodonPref.java
            • SimpleCrossProductAlphabet.java
            • SimpleGappedSymbolList.java
            • SimpleGeneticCodeTable.java
            • SimpleManyToOneTranslationTable.java
            • SimpleReversibleTranslationTable.java
            • SimpleSymbol.java
            • SimpleSymbolList.java
            • SimpleSymbolListFactory.java
            • SimpleSymbolPropertyTable.java
            • SimpleTranslationTable.java
            • SimpleWobbleDistribution.java
            • SingletonAlphabet.java
            • SoftMaskedAlphabet.java
            • SparseCrossProductAlphabet.java
            • SubList.java
            • SuffixTree.java
            • Symbol.java
            • SymbolList.java
            • SymbolListFactory.java
            • SymbolListViews.java
            • SymbolPropertyTable.java
            • TranslatedSymbolList.java
            • TranslationTable.java
            • UkkonenSuffixTree.java
            • WindowedSymbolList.java
            • WobbleDistribution.java
          • taxa
            • AbstractTaxon.java
            • CircularReferenceException.java
            • EbiFormat.java
            • SimpleTaxon.java
            • SimpleTaxonFactory.java
            • Taxon.java
            • TaxonFactory.java
            • TaxonParser.java
            • WeakTaxon.java
            • WeakTaxonFactory.java
        • directory
          • OBDARegistryParser.java
          • ProviderNotFoundException.java
          • Registry.java
          • RegistryConfiguration.java
          • RegistryException.java
          • SequenceDBProvider.java
          • SystemRegistry.java
        • naming
          • ObdaContext.java
          • ObdaInitialContextFactory.java
          • ObdaUriParser.java
        • ontology
          • AbstractTerm.java
          • AlreadyExistsException.java
          • colonel-west.pred
          • core.agregate.pred
          • core.list.pred
          • core.onto
          • core.pred
          • core.set.pred
          • DefaultOps.java
          • IntegerOntology.java
          • InvalidTermException.java
          • io
            • GOParser.java
            • TabDelimParser.java
          • Ontology.java
          • ontology.pred
          • OntologyException.java
          • OntologyFactory.java
          • OntologyOps.java
          • OntologyTerm.java
          • OntoTools.java
          • RemoteTerm.java
          • Term.java
          • Triple.java
          • Variable.java
        • stats
          • svm
            • AbstractSVMClassifierModel.java
            • AbstractSVMTarget.java
            • CachingKernel.java
            • DiagonalAddKernel.java
            • DiagonalCachingKernel.java
            • ItemValue.java
            • LinearKernel.java
            • ListSumKernel.java
            • NestedKernel.java
            • NormalizingKernel.java
            • PolynomialKernel.java
            • RadialBaseKernel.java
            • SigmoidKernel.java
            • SimpleItemValue.java
            • SimpleSVMClassifierModel.java
            • SimpleSVMTarget.java
            • SMORegressionTrainer.java
            • SMOTrainer.java
            • SparseVector.java
            • SVMClassifierModel.java
            • SVMKernel.java
            • SVMRegressionModel.java
            • SVMTarget.java
            • tools
              • ClassifierExample.java
              • Classify.java
              • SuffixTreeKernel.java
              • SVM_Light.java
              • Train.java
              • TrainRegression.java
            • TrainingContext.java
            • TrainingEvent.java
            • TrainingListener.java
        • utils
          • AbstractChangeable.java
          • ActivityListener.java
          • AssertionFailure.java
          • automata
            • ArrayStateMachineToolkit.java
            • AutomatonException.java
            • DfaBuilder.java
            • FiniteAutomaton.java
            • Nfa.java
            • NfaBuilder.java
            • NfaSubModel.java
            • PatternBlitz.java
            • PatternListener.java
            • PatternMaker.java
            • StateMachineFactory.java
            • StateMachineInstance.java
            • StateMachineToolkit.java
          • BeanAsMap.java
          • cache
            • Cache.java
            • CacheMap.java
            • CacheReference.java
            • ChangeableCache.java
            • FixedSizeCache.java
            • FixedSizeMap.java
            • KeyedWeakReference.java
            • SoftReferenceCache.java
            • WeakCacheMap.java
            • WeakValueHashMap.java
          • candy
            • CandyEntry.java
            • CandyException.java
            • CandyFinder.java
            • CandyVocabulary.java
          • Changeable.java
          • ChangeAdapter.java
          • ChangeEvent.java
          • ChangeForwarder.java
          • ChangeHub.java
          • ChangeListener.java
          • ChangeSupport.java
          • ChangeType.java
          • ChangeVetoException.java
          • ClassTools.java
          • Commitable.java
          • CommitFailure.java
          • Constants.java
          • ExecRunner.java
          • FileAsList.java
          • IndexedChangeHub.java
          • io
            • CachingInputStream.java
            • CountedBufferedReader.java
            • InputStreamProvider.java
            • LargeBuffer.java
            • RAF.java
            • RandomAccessReader.java
            • Seekable.java
            • UncompressInputStream.java
          • JDBCConnectionPool.java
          • JDBCPooledDataSource.java
          • ListTools.java
          • lsid
            • Identifiable.java
            • LifeScienceIdentifier.java
            • LifeScienceIdentifierParseException.java
          • math
            • BinarySearch.java
            • ComputeObject.java
          • MergingIterator.java
          • MergingSet.java
          • net
            • URLFactory.java
          • ObjectUtil.java
          • OverlayMap.java
          • ParseErrorEvent.java
          • ParseErrorListener.java
          • ParseErrorSource.java
          • ParserException.java
          • process
            • ExternalProcess.java
            • InputHandler.java
            • OutputHandler.java
            • ReaderInputHandler.java
            • ReaderWriterPipe.java
            • SimpleInputHandler.java
            • SimpleOutputHandler.java
            • StreamPipe.java
            • WriterOutputHandler.java
          • ProcessTimeoutException.java
          • ProcessTools.java
          • regex
            • Matcher.java
            • Pattern.java
            • PatternChecker.java
            • PatternFactory.java
            • RegexException.java
            • Search.java
          • RepeatedCharSequence.java
          • Services.java
          • SimpleThreadPool.java
          • SingletonList.java
          • SmallMap.java
          • SmallSet.java
          • StaticMemberPlaceHolder.java
          • stax
            • BooleanElementHandlerBase.java
            • ByteElementHandlerBase.java
            • CharElementHandlerBase.java
            • DelegationManager.java
            • DoubleElementHandlerBase.java
            • FloatElementHandlerBase.java
            • IntElementHandlerBase.java
            • LongElementHandlerBase.java
            • SAX2StAXAdaptor.java
            • StAXContentHandler.java
            • StAXContentHandlerBase.java
            • StringElementHandlerBase.java
          • StreamGobbler.java
          • ThreadPool.java
          • TriState.java
          • TypedProperties.java
          • Unchangeable.java
          • walker
            • Visitor.java
            • Walker.java
            • WalkerFactory.java
          • xml
            • AppBeanRunner.java
            • AppEntry.java
            • AppException.java
            • FastXMLWriter.java
            • Initializable.java
            • PrettyXMLWriter.java
            • ResourceEntityResolver.java
            • XMLBeans.java
            • XMLWritable.java
            • XMLWriter.java
      • biojavax
        • bio
          • BioEntry.java
          • BioEntryIterator.java
          • BioEntryRelationship.java
          • db
            • AbstractBioEntryDB.java
            • AbstractRichSequenceDB.java
            • BioEntryDB.java
            • BioEntryDBLite.java
            • biosql
              • BioSQLAcceptAllFilter.java
              • BioSQLAcceptNoneFilter.java
              • BioSQLBioEntryDB.java
              • BioSQLCrossReferenceResolver.java
              • BioSQLFeatureFilter.java
              • BioSQLRichObjectBuilder.java
              • BioSQLRichSequenceDB.java
              • BioSQLRichSequenceHandler.java
            • HashBioEntryDB.java
            • HashRichSequenceDB.java
            • ncbi
              • GenbankRichSequenceDB.java
              • GenpeptRichSequenceDB.java
            • RichSequenceDB.java
            • RichSequenceDBLite.java
          • phylo
            • DistanceBasedTreeMethod.java
            • io
              • nexus
                • CharactersBlock.java
                • CharactersBlockBuilder.java
                • CharactersBlockListener.java
                • CharactersBlockParser.java
                • DataBlock.java
                • DataBlockBuilder.java
                • DataBlockListener.java
                • DataBlockParser.java
                • DistancesBlock.java
                • DistancesBlockBuilder.java
                • DistancesBlockListener.java
                • DistancesBlockParser.java
                • NexusBlock.java
                • NexusBlockBuilder.java
                • NexusBlockListener.java
                • NexusBlockParser.java
                • NexusComment.java
                • NexusFile.java
                • NexusFileBuilder.java
                • NexusFileFormat.java
                • NexusFileListener.java
                • NexusObject.java
                • TaxaBlock.java
                • TaxaBlockBuilder.java
                • TaxaBlockListener.java
                • TaxaBlockParser.java
                • TreesBlock.java
                • TreesBlockBuilder.java
                • TreesBlockListener.java
                • TreesBlockParser.java
              • phylip
                • PHYLIPFileBuilder.java
                • PHYLIPFileFormat.java
                • PHYLIPFileListener.java
            • MultipleHitCorrection.java
            • ParsimonyTreeMethod.java
          • seq
            • CompoundRichLocation.java
            • DummyRichSequenceHandler.java
            • EmptyRichLocation.java
            • InfinitelyAmbiguousSymbolList.java
            • io
              • DebuggingRichSeqIOListener.java
              • EMBLFormat.java
              • EMBLxmlFormat.java
              • FastaFormat.java
              • FastaHeader.java
              • GenbankFormat.java
              • GenbankLocationParser.java
              • INSDseqFormat.java
              • RichSeqIOAdapter.java
              • RichSeqIOListener.java
              • RichSequenceBuilder.java
              • RichSequenceBuilderFactory.java
              • RichSequenceFormat.java
              • RichStreamReader.java
              • RichStreamWriter.java
              • SimpleRichSequenceBuilder.java
              • SimpleRichSequenceBuilderFactory.java
              • UniProtCommentParser.java
              • UniProtFormat.java
              • UniProtLocationParser.java
              • UniProtXMLFormat.java
            • MultiSourceCompoundRichLocation.java
            • Position.java
            • PositionResolver.java
            • RichFeature.java
            • RichFeatureRelationship.java
            • RichFeatureRelationshipHolder.java
            • RichLocation.java
            • RichSequence.java
            • RichSequenceHandler.java
            • RichSequenceIterator.java
            • SimplePosition.java
            • SimpleRichFeature.java
            • SimpleRichFeatureRelationship.java
            • SimpleRichLocation.java
            • SimpleRichSequence.java
            • ThinRichSequence.java
          • SimpleBioEntry.java
          • SimpleBioEntryRelationship.java
          • taxa
            • io
              • NCBITaxonomyLoader.java
              • SimpleNCBITaxonomyLoader.java
            • NCBITaxon.java
            • SimpleNCBITaxon.java
            • SimpleNCBITaxonName.java
        • Comment.java
        • CrossRef.java
        • CrossReferenceResolutionException.java
        • CrossReferenceResolver.java
        • DocRef.java
        • DocRefAuthor.java
        • DummyCrossReferenceResolver.java
        • EmptyRichAnnotation.java
        • ga
          • exception
            • IllegalOrganismException.java
          • functions
            • AbstractCrossOverFunction.java
            • AbstractMutationFunction.java
            • CrossOverFunction.java
            • FitnessFunction.java
            • GACross.java
            • GACrossResult.java
            • MutationFunction.java
            • OrderCrossover.java
            • ProportionalSelection.java
            • SelectionFunction.java
            • SimpleCrossOverFunction.java
            • SimpleGACrossResult.java
            • SimpleMutationFunction.java
            • SwapMutationFunction.java
            • TournamentSelection.java
          • GAStoppingCriteria.java
          • GeneticAlgorithm.java
          • impl
            • AbstractGeneticAlgorithm.java
            • AbstractOrganism.java
            • AbstractPopulation.java
            • SimpleGeneticAlgorithm.java
            • SimpleOrganism.java
            • SimplePopulation.java
          • Organism.java
          • Population.java
          • util
            • GATools.java
            • WeightedSet.java
        • Namespace.java
        • Note.java
        • ontology
          • ComparableOntology.java
          • ComparableTerm.java
          • ComparableTriple.java
          • SimpleComparableOntology.java
          • SimpleComparableTerm.java
          • SimpleComparableTriple.java
        • RankedCrossRef.java
        • RankedCrossRefable.java
        • RankedDocRef.java
        • RichAnnotatable.java
        • RichAnnotation.java
        • RichObjectBuilder.java
        • RichObjectFactory.java
        • SimpleComment.java
        • SimpleCrossRef.java
        • SimpleDocRef.java
        • SimpleDocRefAuthor.java
        • SimpleNamespace.java
        • SimpleNote.java
        • SimpleRankedCrossRef.java
        • SimpleRankedDocRef.java
        • SimpleRichAnnotation.java
        • SimpleRichObjectBuilder.java
        • utils
          • CRC64Checksum.java
          • StringTools.java
          • XMLTools.java