> biojava-1.4.jar.zip
标签:biojava-1.4.jar.zip,biojava,1.4,jar.zip包下载,依赖包
META-INF
MANIFEST.MFservicesorg.biojava.bio.program.formats.Formatorg.biojava.directory.SequenceDBProviderobdanamingcore.xmlorgagavexmlagave.dtdbiojavabibliography
BiblioArticle.javaBiblioBook.javaBiblioBookArticle.javaBiblioCriterion.javaBiblioDescription.javaBiblioEntryStatus.javaBiblioJournal.javaBiblioJournalArticle.javaBiblioOrganisation.javaBiblioPatent.javaBiblioPerson.javaBiblioProceeding.javaBiblioProvider.javaBiblioScope.javaBiblioService.javaBiblioSubject.javaBiblioTechReport.javaBiblioThesis.javaBiblioWebResource.javaBibRef.javaBibRefException.javaBibRefQuery.javaBibRefSupport.javabioAbstractAnnotation.javaalignmentAbstractULAlignment.javaAlignmentElement.javaARAlignment.javaEditableAlignment.javaFlexibleAlignment.javaIllegalAlignmentEditException.javaQualitativeAlignment.javaSimpleAlignmentElement.javaUnequalLengthAlignment.javaannodbAnnotationDB.javaEmptyAnnotationDB.javaIndexedAnnotationDB.javaLazyFilteredAnnotationDB.javaLazySearchedAnnotationDB.javaMergingAnnotationDB.javaSimpleAnnotationDB.javaAnnotatable.javaAnnotation.javaAnnotationChanger.javaAnnotationRenamer.javaAnnotationTools.javaAnnotationType.javaAnyPropertyConstraint.javaBeanAsAnnotation.javaBioError.javaBioException.javaBioRuntimeException.javaCardinalityConstraint.javachromatogramAbstractChromatogram.javaChromatogram.javaChromatogramFactory.javaChromatogramTools.javagraphicChromatogramGraphic.javaChromatogramNonlinearScaler.javaFixedBaseWidthScaler.javaSimpleChromatogram.javaUnsupportedChromatogramFormatException.javaCollectionConstraint.javadistAbstractDistribution.javaAbstractOrderNDistribution.javaCount.javaDistribution.javaDistributionFactory.javaDistributionTools.javaDistributionTrainer.javaDistributionTrainerContext.javaGapDistribution.javaGeneralNthOrderDistribution.javaIgnoreCountsTrainer.javaIndexedCount.javaIndexedNthOrderDistribution.javaOrderNDistribution.javaOrderNDistributionFactory.javaPairDistribution.javaSimpleDistribution.javaSimpleDistributionTrainer.javaSimpleDistributionTrainerContext.javaTranslatedDistribution.javaUniformDistribution.javaUntrainableDistribution.javaXMLDistributionReader.javaXMLDistributionWriter.javadpAbstractTrainer.javaBackPointer.javaBaumWelchSampler.javaBaumWelchTrainer.javaDotState.javaDP.javaDPFactory.javaDPMatrix.javaEmissionState.javaFlatModel.javaHMMTrainer.javaIllegalTransitionException.javaMagicalState.javaMarkovModel.javaModelInState.javaModelTrainer.javaoneheadAbstractCursor.javaDPCursor.javaMatrixCursor.javaSingleDP.javaSingleDPMatrix.javaSmallCursor.javaProfileHMM.javaScoreType.javaSimpleDotState.javaSimpleEmissionState.javaSimpleHMMTrainer.javaSimpleMarkovModel.javaSimpleModelInState.javaSimpleModelTrainer.javaSimpleStatePath.javaSimpleWeightMatrix.javaState.javaStatePath.javaStoppingCriteria.javaTrainable.javaTrainerTransition.javaTrainingAlgorithm.javaTransition.javaTransitionTrainer.javatwoheadAbstractMatrixPairDPCursor.javaBackMatrixPairDPCursor.javaCell.javaCellCalculator.javaCellCalculatorFactory.javaCellCalculatorFactoryMaker.javaDPCompiler.javaDPInterpreter.javaEmissionCache.javaLightPairDPCursor.javaMatrixPairDPCursor.javaPairDPCursor.javaPairDPMatrix.javaPairwiseDP.javaWeightMatrix.javaWeightMatrixAnnotator.javaWMAsMM.javaXmlMarkovModel.javaEcNumber.javaEmptyAnnotation.javaguiBarLogoPainter.javaBlockPainter.javaDistributionLogo.javaDNAStyle.javaFeatureTree.javaLogoContext.javaLogoPainter.javaPlainBlock.javaPlainStyle.javasequenceAbiTraceRenderer.javaAbstractBeadRenderer.javaAlignmentRenderer.javaBasicFeatureRenderer.javaBasicImapRenderer.javaBeadFeatureRenderer.javaBumpedRenderer.javaCircularFeatureFilteringRenderer.javaCircularFeatureRenderer.javaCircularFeaturesRenderer.javaCircularMLR.javaCircularPaddedRenderer.javaCircularRenderer.javaCircularRendererContext.javaCircularRendererPanel.javaCrosshairRenderer.javaEllipticalBeadRenderer.javaFeatureBlockSequenceRenderer.javaFeatureLabelRenderer.javaFeatureRenderer.javaFilteringRenderer.javaGappedRenderer.javaGUITools.javaHeadlessRenderContext.javaImageMap.javaImageMapRenderer.javaLabelledSequenceRenderer.javaLabelRenderer.javaLayeredRenderer.javaLineInfo.javaMultiLineRenderer.javaOverlayMarker.javaOverlayRendererWrapper.javaPaddingRenderer.javaPairwiseDiagonalRenderer.javaPairwiseFilteringRenderer.javaPairwiseOverlayRenderer.javaPairwiseRenderContext.javaPairwiseSequencePanel.javaPairwiseSequenceRenderer.javaRectangularBeadRenderer.javaRectangularImapRenderer.javaRoundRectangularBeadRenderer.javaRulerRenderer.javaSequencePanel.javaSequencePoster.javaSequenceRenderContext.javaSequenceRenderer.javaSequenceRendererWrapper.javaSequenceViewerEvent.javaSequenceViewerListener.javaSequenceViewerMotionListener.javaSequenceViewerMotionSupport.javaSequenceViewerSupport.javaSimpleLabelRenderer.javaSixFrameRenderer.javaSixFrameZiggyRenderer.javaStackedFeatureRenderer.javaStopRenderer.javaSubCircularRendererContext.javaSubPairwiseRenderContext.javaSubSequenceRenderContext.javaSymbolSequenceRenderer.javaTickFeatureRenderer.javaTranslatedSequencePanel.javaZiggyFeatureRenderer.javaZiggyImapRenderer.javaSimpleSymbolStyle.javaStackedLogoPainter.javaSymbolStyle.javaTextBlock.javaTextLogoPainter.javaMergeAnnotation.javamolbiorebase_common.datRestrictionEnzyme.javaRestrictionEnzymeManager.javaRestrictionEnzymeManager.propertiesRestrictionMapper.javaRestrictionSite.javaRestrictionSiteFinder.javaNoneCollectionConstraint.javaNonePropertyConstraint.javaontologycore.ontoOverlayAnnotation.javaprogramabiABIFChromatogram.javaABIFParser.javaABITools.javaABITrace.javablast2htmlAbstractAlignmentStyler.javaAlignmentMarker.javaAlignmentStyler.javaBlast2HTMLHandler.javaBlastLikeAlignment.javaBlastMatrixAlignmentStyler.javaColourCommand.javaDatabaseURLGenerator.javaDefaultURLGeneratorFactory.javaDetailHit.javaEbiDatabaseURLGenerator.javaHitDescription.javaHitId.javaHitSummary.javaHSP.javaHSPSummary.javaHTMLRenderer.javaNcbiDatabaseURLGenerator.javaSequence.javaSimpleAlignmentStyler.javaURLGeneratorFactory.javaBlastLikeToXMLConverter.javadasComponentFeatureHandler.javaDAS.javadasalignmentAlignment.javaDASAlignmentCall.javaDASAlignmentClient.javaDASAlignmentXMLResponseParser.javaDASException.javaDASAnnotationDistDataSource.javaDASCapabilities.javaDASComponentFeature.javaDASDistDataSource.javaDASFeatureSet.javaDASGFFFeatureHandler.javaDASLink.javaDASLinkHandler.javaDASRawSymbolList.javaDASSequence.javaDASSequenceDB.javaDASSequenceDBProvider.javaDASSequenceI.javadasstructureDASStructureCall.javaDASStructureXMLResponseParser.javaDataSource.javaFeatureFetcher.javaFeatureRequestManager.javaFetcher.javaRawAnnotationSequence.javaReferenceServer.javaSegment.javaTypesFetcher.javaTypesListener.javaformatsEmbl.javaEnzyme.javaFormat.javaFormatTools.javaLigand.javaSwissprot.javagffGFFComparator.javaGFFDocumentHandler.javaGFFEntrySet.javaGFFErrorHandler.javaGFFFilterer.javaGFFParser.javaGFFRecord.javaGFFRecordFilter.javaGFFTools.javaGFFWriter.javaIgnoreRecordException.javaSequencesAsGFF.javaSimpleGFFRecord.javagff3GFF3DocumentHandler.javaGFF3Parser.javaGFF3Record.javahmmerFullHmmerProfileHMM.javaHmmerProfileHMM.javaHmmerProfileParser.javaProfileEmissionState.javahomologeneAbstractOrthologueSet.javaAbstractOrthoPairCollection.javaAbstractOrthoPairSet.javaDuplicateTaxonException.javaHomologeneBuilder.javaHomologeneDB.javaHomologeneTools.javaOrthologue.javaOrthologueFilter.javaOrthologueSet.javaOrthoPair.javaOrthoPairCollection.javaOrthoPairFilter.javaOrthoPairSet.javaOrthoPairSetFilter.javaSimilarityType.javaSimpleHomologeneBuilder.javaSimpleHomologeneDB.javaSimpleOrthologue.javaSimpleOrthologueSet.javaSimpleOrthoPair.javaSimpleOrthoPairCollection.javaSimpleOrthoPairSet.javaTaxon.javaindexdbBioStore.javaBioStoreFactory.javaCacheList.javaConfigFile.javaIndexStore.javaIndexTools.javaKeyPair.javaPrimaryIDList.javaPropertiesAnnotation.javaRecord.javaSearchableFileAsList.javaSearchableList.javaSecondaryFileAsList.javaMeme.javaPdbToXMLConverter.javaphredPhredFormat.javaPhredSequence.javaPhredTools.javaQualitative.javasaxAbstractNativeAppSAXParser.javaBaseXMLWriterTestHelper.javaBlastLikeAlignmentSAXParser.javaBlastLikeSAXParser.javaBlastLikeVersionSupport.javaBlastSAXParser.javablastxmlBlastAggregator.javaBlastOutputHandler.javaBlastOutputIterationsHandler.javaBlastXMLParser.javaBlastXMLParserFacade.javaHitHandler.javaHitHspsHandler.javaHspHandler.javaIterationHandler.javaIterationHitsHandler.javaNCBI_BlastOutput.dtdNCBI_BlastOutput.modNCBI_Entity.modStAXFeatureHandler.javaStAXFeatureHandlerMod.javaStAXHandlerFactory.javaClustalWAlignmentSAXParser.javaDomainSectionSAXParser.javaFastaSearchParser.javaFastaSearchSAXParser.javaFastaSequenceSAXParser.javaGCGBlastSummaryLineHelper.javaGenericSAXParserTest.javaHitSectionSAXParser.javaHmmerAlignmentSAXParser.javaHmmerSummaryLineHelper.javaHSPSummaryHelper.javaNamespaceConfigurationIF.javaNcbiBlastSummaryLineHelper.javaNeedleAlignmentSAXParser.javaPdbSAXParser.javaQName.javaSequenceAlignmentSAXParser.javaSimpleXMLEmitterTestHelper.javaSummaryLineHelperIF.javaWuBlastSummaryLineHelper.javascfSCF.javassahaCompactedDataStore.javaCompactedDataStoreFactory.javaDataStore.javaDataStoreFactory.javaHitMerger.javaMappedDataStore.javaMappedDataStoreFactory.javaNIODataStore.javaNIODataStoreFactory.javaSearchException.javaSearchListener.javaSequenceStreamer.javassbindAlignmentStAXHandler.javaAlphabetResolver.javaAnnotationFactory.javaBlastLikeHomologyBuilder.javaBlastLikeSearchBuilder.javaHeaderStAXHandler.javaHitStAXHandler.javaHSPStAXHandler.javaHSPSummaryStAXHandler.javaSeqSimilarityAdapter.javaSeqSimilarityStAXAdapter.javaSeqSimilarityStAXHandler.javaSimilarityPairBuilder.javaStAXHandlerBinding.javaStAXHandlerFactory.javaViewSequenceFactory.javatagvalueAbstractWrapper.javaAggregator.javaAnnotationBuilder.javaBoundaryFinder.javaChangeTable.javaEcho.javaFormats.javaIndex2Model.javaIndexer.javaIndexer2.javaLineSplitParser.javaMultiTagger.javaParser.javaParserListener.javaPropertyChanger.javaRegexChanger.javaRegexFieldFinder.javaRegexParser.javaRegexSplitter.javaSimpleTagValueWrapper.javaStateMachine.javaTagDelegator.javaTagDropper.javaTagMapper.javaTagRenamer.javaTagValue.javaTagValueContext.javaTagValueListener.javaTagValueParser.javaTagValueWrapper.javaValueChanger.javaunigenecreateUnigene.sqlFlatFileUnigeneDB.javaFlatFileUnigeneFactory.javaSQLUnigeneDB.javaSQLUnigeneFactory.javaUnigeneCluster.javaUnigeneDB.javaUnigeneFactory.javaUnigeneTools.javaxffBasicXFFHelper.javaElementRecognizer.javaFeatureHandler.javaLocationHandlerBase.javaPropDetailHandler.javaPropertyWriter.javaStrandedFeatureHandler.javaXFFFeatureSetHandler.javaXFFHelper.javaXFFPartHandlerFactory.javaXFFTools.javaXFFWriter.javaxmlBaseXMLWriter.javaSimpleXMLEmitter.javaPropertyConstraint.javaproteomicsDigest.javaIsoelectricPointCalc.javaMassCalc.javaProtease.javaProteaseManager.javaProteaseManager.xmlStructureTools.javasearchBioMatcher.javaBioPattern.javaBlastLikeSearchFilter.javaFilteringContentHandler.javaFilterTest.javaKnuthMorrisPrattSearch.javaMaxMismatchMatcher.javaMaxMismatchPattern.javaSearchBuilder.javaSearchContentAdapter.javaSearchContentFilter.javaSearchContentHandler.javaSearchContentHandlerDebugger.javaSeqContentMatcher.javaSeqContentPattern.javaSeqSimilaritySearcher.javaSeqSimilaritySearchHit.javaSeqSimilaritySearchResult.javaSeqSimilaritySearchSubHit.javaSequenceDBSearchHit.javaSequenceDBSearchResult.javaSequenceDBSearchSubHit.javaSimpleSeqSimilaritySearchHit.javaSimpleSeqSimilaritySearchResult.javaSimpleSeqSimilaritySearchSubHit.javaseqAbstractFeatureHolder.javaAcceptAllFilter.javaAcceptNoneFilter.javaByHierarchy.javaCircularView.javaComponentFeature.javadbAbstractSequenceDB.javaAnnotatedSequenceDB.javabiofetchBioFetchSequenceDB.javaBioFetchSequenceDBProvider.javaBioIndex.javabiosqlBioSQLAllFeatures.javaBioSQLAssembly.javaBioSQLComponentFeature.javaBioSQLEntryAnnotationChangeHub.javaBioSQLEntryChangeHub.javaBioSQLFeature.javaBioSQLFeatureAnnotation.javaBioSQLFeatureAnnotationChangeHub.javaBioSQLFeatureChangeHub.javaBioSQLFeatureReceiver.javaBioSQLSequence.javaBioSQLSequenceAnnotation.javaBioSQLSequenceDB.javaBioSQLSequenceDBProvider.javaBioSQLSequenceI.javaBioSQLStrandedFeature.javaBioSQLTiledFeatures.javaDBHelper.javaFeaturesSQL.javaHypersonicDBHelper.javaMySQLDBHelper.javaOntologySQL.javaOracleDBHelper.javaPostgreSQLDBHelper.javaTaxonSQL.javaUnknownDBHelper.javaCachingSequenceDB.javaDummySequenceDB.javaDummySequenceDBInstallation.javaemblcdAcnumHitReader.javaAcnumTrgReader.javaDivisionLkpReader.javaEmblCDROMIndexReader.javaEmblCDROMRandomAccess.javaEntryNamIdxReader.javaEntryNamRandomAccess.javaRecordParser.javaEmblCDROMIndexStore.javaFetchURL.javaflatFlatSequenceDB.javaFlatSequenceDBProvider.javaGenbankSequenceDB.javaGenpeptSequenceDB.javaHashSequenceDB.javaIDMaker.javaIllegalIDException.javaIndex.javaIndexedSequenceDB.javaIndexStore.javaNCBISequenceDB.javaSequenceDB.javaSequenceDBInstallation.javaSequenceDBLite.javaSequenceDBWrapper.javaSimpleIndex.javaSimpleSequenceDBInstallation.javaSubSequenceDB.javaSwissprotSequenceDB.javaTabIndexStore.javaViewingSequenceDB.javaWebSequenceDB.javadistributedDistComponentFeature.javaDistDataSource.javaDistProjectionContext.javaDistributedSequence.javaDistributedSequenceDB.javaGFFDataSource.javaSequenceDBDataSource.javaDNATools.javaDown.javaFeature.javaFeatureFilter.javaFeatureHolder.javaFeatureHolderUtils.javaFeatureRealizer.javaFeatureTypes.javafilterFilterTransformer.javaFilterUtils.javaFrame.javaFramedFeature.javaGappedSequence.javaGeneticCodes.javahomolHomology.javaHomologyDB.javaHomologyFeature.javaSimilarityPairFeature.javaSimpleHomology.javaimplAssembledSymbolList.javaDummySequence.javaFeatureImpl.javaLazyFilterFeatureHolder.javaNewAssembledSymbolList.javaRevCompSequence.javaSimpleFeature.javaSimpleFramedFeature.javaSimpleGappedSequence.javaSimpleHomologyFeature.javaSimpleRemoteFeature.javaSimpleRestrictionSite.javaSimpleSequence.javaSimpleSequenceFactory.javaSimpleSimilarityPairFeature.javaSimpleStrandedFeature.javaSubSequence.javaTemplateUtils.javaViewSequence.javaioAbstractGenEmblFileFormer.javaagaveAgave2AgaveAnnotFilter.javaAGAVEAltIdsPropHandler.javaAGAVEAnnotationsHandler.javaAGAVEAnnotFilter.javaAGAVEAnnotFilterFactory.javaAGAVEAssemblyHandler.javaAGAVEBioSeqCallbackItf.javaAGAVEBioSeqHandler.javaAGAVEBioSequenceHandler.javaAGAVECallbackItf.javaAGAVECdsHandler.javaAGAVEChromosomeCallbackItf.javaAGAVEChromosomeHandler.javaAGAVEClassificationHandler.javaAGAVECompResultHandler.javaAGAVEComputationHandler.javaAGAVEContigCallbackItf.javaAGAVEContigHandler.javaAGAVEDbId.javaAGAVEDbIdCallbackItf.javaAGAVEDbIdPropCallbackItf.javaAGAVEDbIdPropHandler.javaAGAVEDescPropHandler.javaAGAVEElementIdPropHandler.javaAGAVEEvidenceCallbackItf.javaAGAVEEvidenceHandler.javaAGAVEExonsPropHandler.javaAGAVEFeatureCallbackItf.javaAGAVEFragmentOrderHandler.javaAGAVEFragmentOrientationHandler.javaAGAVEGeneHandler.javaAGAVEHandler.javaAGAVEIdAlias.javaAGAVEIdAliasCallbackItf.javaAGAVEIdAliasPropHandler.javaAGAVEKeywordPropHandler.javaAGAVEMapLocation.javaAGAVEMapLocationPropHandler.javaAGAVEMapPosition.javaAGAVEMapPositionPropHandler.javaAGAVEMatchAlignPropHandler.javaAGAVEMatchDescPropHandler.javaAGAVEMatchRegion.javaAGAVEMatchRegionPropHandler.javaAGAVEMrnaHandler.javaAGAVENotePropHandler.javaAGAVEPredictedProteinHandler.javaAGAVEProperty.javaAGAVEQualifierPropHandler.javaAGAVEQueryRegion.javaAGAVEQueryRegionPropHandler.javaAGAVERelatedAnnot.javaAGAVERelatedAnnotPropHandler.javaAGAVEResultGroupHandler.javaAGAVEResultPropertyPropHandler.javaAGAVESciPropertyPropHandler.javaAGAVESeqFeatureHandler.javaAGAVESeqLocationPropHandler.javaAGAVESeqMapHandler.javaAGAVESeqPropHandler.javaAGAVETranscriptHandler.javaAGAVEUnorderedFragmentsHandler.javaAGAVEViewPropHandler.javaAgaveWriter.javaAGAVEXref.javaAGAVEXrefCallbackItf.javaAGAVEXrefPropHandler.javaAGAVEXrefPropPropHandler.javaAGAVEXrefs.javaAGAVEXrefsPropHandler.javaDelegationManager.javaElementRecognizer.javaEmbl2AgaveAnnotFilter.javaPCDATAFilterWriter.javaSAX2StAXAdaptor.javaSequenceHandler.javaSimpleAnnotFilter.javaStAXContentHandler.javaStAXContentHandlerBase.javaStAXFeatureHandler.javaStAXHandlerFactory.javaStAXPropertyHandler.javaUtilHelper.javaAlignIOConstants.javaAlignmentFormat.javaCharacterTokenization.javaChunkedSymbolListFactory.javaCrossProductTokenization.javaDoubleTokenization.javaEmblFileFormer.javaEmblLikeFormat.javaEmblLikeLocationParser.javaEmblProcessor.javaEmblReferenceComparator.javaFastaAlignmentFormat.javaFastaDescriptionLineParser.javaFastaFormat.javaFeatureQualifier.xmlFeatureTableParser.javafilterxmlQName.javaXMLAnnotationTypeHandler.javaXMLAnnotationTypeWriter.javaXMLFilterHandler.javaXMLFilterWriter.javagameElementRecognizer.javaGAMEAnnotationHandler.javaGAMEAspectPropHandler.javaGAMEDbxrefPropHandler.javaGAMEDescriptionPropHandler.javaGAMEFeatureCallbackItf.javaGAMEFeatureSetHandler.javaGAMEFeatureSetPropHandler.javaGAMEFeatureSpanHandler.javaGAMEGenePropHandler.javaGAMEHandler.javaGAMEMapPosPropHandler.javaGAMENameCallbackItf.javaGAMENamePropHandler.javaGAMEResiduesPropHandler.javaGAMESeqPropHandler.javaGAMESeqRelPropHandler.javaGAMESpanPropHandler.javaGAMETranscriptCallbackItf.javaGAMETypePropHandler.javaSequenceContentHandlerBase.javaStAXFeatureHandler.javaStAXHandlerFactory.javaStAXPropertyHandler.javagame12GAMEAnnotationHandler.javaGAMEAspectHandler.javaGAMEDbxrefHandler.javaGAMEFeatureSetHandler.javaGAMEFeatureSpanHandler.javaGAMEGeneHandler.javaGAMEHandler.javaGAMEPropertyHandler.javaGAMESeqHandler.javaGAMESeqRelHandler.javaGAMESpanHandler.javaStAXFeatureHandler.javaStAXHandlerFactory.javaGAMEFormat.javaGenbankContext.javaGenbankFileFormer.javaGenbankFormat.javaGenbankProcessor.javaGenbankXmlFormat.javaGenEmblFeatureComparator.javaGenEmblPropertyComparator.javaGenpeptFileFormer.javaGenpeptFormat.javaIntegerTokenization.javaMSFAlignmentFormat.javaNameTokenization.javaOrganismParser.javaParseException.javaProteinRefSeqFileFormer.javaProteinRefSeqProcessor.javaReferenceAnnotation.javaSeqFileFormer.javaSeqIOAdapter.javaSeqIOConstants.javaSeqIOEventEmitter.javaSeqIOFilter.javaSeqIOListener.javaSeqIOTools.javaSequenceBuilder.javaSequenceBuilderBase.javaSequenceBuilderFactory.javaSequenceBuilderFilter.javaSequenceDBSequenceBuilder.javaSequenceFormat.javaSimpleAssemblyBuilder.javaSimpleSequenceBuilder.javaSmartSequenceBuilder.javaStreamParser.javaStreamReader.javaStreamWriter.javaSwissprotFeatureTableParser.javaSwissprotFileFormer.javaSwissprotProcessor.javaSymbolListCharSequence.javaSymbolReader.javaSymbolTokenization.javaWordTokenization.javaIsLeaf.javaIsTopLevel.javaLazyFeatureHolder.javaMergeFeatureHolder.javaNewSimpleAssembly.javaNucleotideTools.javaOptimizableFilter.javaprojectionProjectedFeature.javaProjectedFeatureHolder.javaProjection.javaProjectionContext.javaProjectionEngine.javaProjectionUtils.javaReparentContext.javaTranslateFlipContext.javaProteinTools.javaRealizingFeatureHolder.javaRemoteFeature.javaRNATools.javaSequence.javaSequenceAnnotator.javaSequenceFactory.javaSequenceIterator.javaSequenceTools.javaSimpleAssembly.javaSimpleComponentFeature.javaSimpleFeatureHolder.javaSimpleFeatureRealizer.javaStrandedFeature.javaStrandParser.javaTranslationTables.xmlUp.javaSimpleAnnotation.javaSmallAnnotation.javastructureAlphaCTools.javaAminoAcid.javaAminoAcidImpl.javaAtom.javaAtomImpl.javaAtomIterator.javaCalc.javaChain.javaChainImpl.javaGroup.javaGroupIterator.javaHetatomImpl.javaioDASStructureClient.javaFileConvert.javaPDBFileParser.javaPDBFileReader.javaPDBMSDReader.javaPDBParseException.javaPDBSRSReader.javaStructureIO.javaStructureIOFile.javaNucleotideImpl.javaStructure.javaStructureException.javaStructureImpl.javasymbolAbstractAlphabet.javaAbstractLocation.javaAbstractLocationDecorator.javaAbstractManyToOneTranslationTable.javaAbstractRangeLocation.javaAbstractReversibleTranslationTable.javaAbstractSimpleBasisSymbol.javaAbstractSymbol.javaAbstractSymbolList.javaAbstractTranslationTable.javaAlignment.javaAlphabet.javaAlphabetIndex.javaAlphabetManager.javaAlphabetManager.xmlAtomicSymbol.javaBasisSymbol.javaBetweenLocation.javaBetweenLocationTools.javaChunkedSymbolList.javaCircularLocation.javaCircularLocationTools.javaCodonPref.javaCodonPrefFilter.javaCodonPrefTables.xmlCodonPrefTools.javaCompoundLocation.javaCrossProductAlphabetIndex.javaDNAAmbPack.javaDNANoAmbPack.javaDoubleAlphabet.javaDummySymbolList.javaEdit.javaEmptyAlphabet.javaEmptyLocation.javaEmptySymbolList.javaFiniteAlphabet.javaFullDnaAlphabetIndex.javaFundamentalAtomicSymbol.javaFuzzyLocation.javaFuzzyPointLocation.javaGappedSymbolList.javaHashedAlphabetIndex.javaIllegalAlphabetException.javaIllegalSymbolException.javaIndexedNoAmbPack.javaInfiniteCrossProductAlphabet.javaIntegerAlphabet.javaLinearAlphabetIndex.javaLocation.javaLocationComparator.javaLocationTools.javaManyToOneTranslationTable.javaMergeLocation.javaMotifTools.javaOrderNSymbolList.javaPackedSymbolList.javaPackedSymbolListFactory.javaPacking.javaPackingFactory.javaPointLocation.javaRangeLocation.javaRelabeledAlignment.javaResidueProperties.xmlReverseSymbolList.javaReversibleTranslationTable.javaSimpleAlignment.javaSimpleAlphabet.javaSimpleAtomicSymbol.javaSimpleBasisSymbol.javaSimpleCodonPref.javaSimpleCrossProductAlphabet.javaSimpleGappedSymbolList.javaSimpleManyToOneTranslationTable.javaSimpleReversibleTranslationTable.javaSimpleSymbol.javaSimpleSymbolList.javaSimpleSymbolListFactory.javaSimpleSymbolPropertyTable.javaSimpleTranslationTable.javaSimpleWobbleDistribution.javaSingletonAlphabet.javaSoftMaskedAlphabet.javaSparseCrossProductAlphabet.javaSubList.javaSuffixTree.javaSymbol.javaSymbolList.javaSymbolListFactory.javaSymbolListViews.javaSymbolPropertyTable.javaTranslatedSymbolList.javaTranslationTable.javaUkkonenSuffixTree.javaWindowedSymbolList.javaWobbleDistribution.javataxaAbstractTaxon.javaCircularReferenceException.javaEbiFormat.javaSimpleTaxon.javaSimpleTaxonFactory.javaTaxon.javaTaxonFactory.javaTaxonParser.javaWeakTaxon.javaWeakTaxonFactory.javadirectoryOBDARegistryParser.javaProviderNotFoundException.javaRegistry.javaRegistryConfiguration.javaRegistryException.javaSequenceDBProvider.javaSystemRegistry.javanamingObdaContext.javaObdaInitialContextFactory.javaObdaUriParser.javaontologyAbstractTerm.javaAlreadyExistsException.javacolonel-west.predcore.agregate.predcore.list.predcore.ontocore.predcore.set.predDefaultOps.javaIntegerOntology.javaInvalidTermException.javaioGOParser.javaTabDelimParser.javaOntology.javaontology.predOntologyException.javaOntologyFactory.javaOntologyOps.javaOntologyTerm.javaOntoTools.javaRemoteTerm.javaTerm.javaTriple.javaVariable.javastatssvmAbstractSVMClassifierModel.javaAbstractSVMTarget.javaCachingKernel.javaDiagonalAddKernel.javaDiagonalCachingKernel.javaItemValue.javaLinearKernel.javaListSumKernel.javaNestedKernel.javaNormalizingKernel.javaPolynomialKernel.javaRadialBaseKernel.javaSigmoidKernel.javaSimpleItemValue.javaSimpleSVMClassifierModel.javaSimpleSVMTarget.javaSMORegressionTrainer.javaSMOTrainer.javaSparseVector.javaSVMClassifierModel.javaSVMKernel.javaSVMRegressionModel.javaSVMTarget.javatoolsClassifierExample.javaClassify.javaSuffixTreeKernel.javaSVM_Light.javaTrain.javaTrainRegression.javaTrainingContext.javaTrainingEvent.javaTrainingListener.javautilsAbstractChangeable.javaActivityListener.javaAssertionFailure.javaautomataArrayStateMachineToolkit.javaAutomatonException.javaDfaBuilder.javaFiniteAutomaton.javaNfa.javaNfaBuilder.javaNfaSubModel.javaPatternBlitz.javaPatternListener.javaPatternMaker.javaStateMachineFactory.javaStateMachineInstance.javaStateMachineToolkit.javaBeanAsMap.javacacheCache.javaCacheMap.javaCacheReference.javaChangeableCache.javaFixedSizeCache.javaFixedSizeMap.javaKeyedWeakReference.javaSoftReferenceCache.javaWeakCacheMap.javaWeakValueHashMap.javacandyCandyEntry.javaCandyException.javaCandyFinder.javaCandyVocabulary.javaChangeable.javaChangeAdapter.javaChangeEvent.javaChangeForwarder.javaChangeHub.javaChangeListener.javaChangeSupport.javaChangeType.javaChangeVetoException.javaClassTools.javaCommitable.javaCommitFailure.javaConstants.javaExecRunner.javaFileAsList.javaIndexedChangeHub.javaioCachingInputStream.javaCountedBufferedReader.javaLargeBuffer.javaRAF.javaRandomAccessReader.javaSeekable.javaJDBCConnectionPool.javaJDBCPooledDataSource.javaListTools.javalsidIdentifiable.javaLifeScienceIdentifier.javaLifeScienceIdentifierParseException.javamathBinarySearch.javaComputeObject.javaMergingIterator.javaMergingSet.javanetURLFactory.javaObjectUtil.javaOverlayMap.javaParseErrorEvent.javaParseErrorListener.javaParseErrorSource.javaParserException.javaProcessTimeoutException.javaProcessTools.javaqueryQueryBuilder.xmlregexMatcher.javaPattern.javaPatternChecker.javaPatternFactory.javaRegexException.javaSearch.javaRepeatedCharSequence.javaServices.javaSimpleThreadPool.javaSingletonList.javaSmallMap.javaSmallSet.javaStaticMemberPlaceHolder.javastaxBooleanElementHandlerBase.javaByteElementHandlerBase.javaCharElementHandlerBase.javaDelegationManager.javaDoubleElementHandlerBase.javaFloatElementHandlerBase.javaIntElementHandlerBase.javaLongElementHandlerBase.javaSAX2StAXAdaptor.javaStAXContentHandler.javaStAXContentHandlerBase.javaStringElementHandlerBase.javaStreamGobbler.javaThreadPool.javaTriState.javaTypedProperties.javaUnchangeable.javawalkerVisitor.javaWalker.javaWalkerFactory.javaxmlAppBeanRunner.javaAppEntry.javaAppException.javaFastXMLWriter.javaInitializable.javaPrettyXMLWriter.javaResourceEntityResolver.javaXMLBeans.javaXMLWritable.javaXMLWriter.java