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Jar File Download » b » biojava   Download biojava-1.4.jar  Files contained in biojava-1.4.jar:  META-INF/MANIFEST.MF org.biojava.bibliography.BibRef.class org.biojava.bibliography.BibRefException.class org.biojava.bibliography.BibRefQuery.class org.biojava.bibliography.BibRefSupport.class org.biojava.bibliography.BiblioArticle.class org.biojava.bibliography.BiblioBook.class org.biojava.bibliography.BiblioBookArticle.class org.biojava.bibliography.BiblioCriterion.class org.biojava.bibliography.BiblioDescription.class org.biojava.bibliography.BiblioEntryStatus.class org.biojava.bibliography.BiblioJournal.class org.biojava.bibliography.BiblioJournalArticle.class org.biojava.bibliography.BiblioOrganisation.class org.biojava.bibliography.BiblioPatent.class org.biojava.bibliography.BiblioPerson.class org.biojava.bibliography.BiblioProceeding.class org.biojava.bibliography.BiblioProvider.class org.biojava.bibliography.BiblioScope.class org.biojava.bibliography.BiblioService.class org.biojava.bibliography.BiblioSubject.class org.biojava.bibliography.BiblioTechReport.class org.biojava.bibliography.BiblioThesis.class org.biojava.bibliography.BiblioWebResource.class org.biojava.bio.AbstractAnnotation.class org.biojava.bio.Annotatable.class org.biojava.bio.Annotation.class org.biojava.bio.AnnotationChanger.class org.biojava.bio.AnnotationRenamer.class org.biojava.bio.AnnotationTools.class org.biojava.bio.AnnotationType.class org.biojava.bio.AnyPropertyConstraint.class org.biojava.bio.BeanAsAnnotation.class org.biojava.bio.BioError.class org.biojava.bio.BioException.class org.biojava.bio.BioRuntimeException.class org.biojava.bio.CardinalityConstraint.class org.biojava.bio.CollectionConstraint.class org.biojava.bio.EcNumber.class org.biojava.bio.EmptyAnnotation.class org.biojava.bio.MergeAnnotation.class org.biojava.bio.NoneCollectionConstraint.class org.biojava.bio.NonePropertyConstraint.class org.biojava.bio.OverlayAnnotation.class org.biojava.bio.PropertyConstraint.class org.biojava.bio.SimpleAnnotation.class org.biojava.bio.SmallAnnotation.class org.biojava.bio.alignment.ARAlignment.class org.biojava.bio.alignment.AbstractULAlignment.class org.biojava.bio.alignment.AlignmentElement.class org.biojava.bio.alignment.EditableAlignment.class org.biojava.bio.alignment.FlexibleAlignment.class org.biojava.bio.alignment.IllegalAlignmentEditException.class org.biojava.bio.alignment.QualitativeAlignment.class org.biojava.bio.alignment.SimpleAlignmentElement.class org.biojava.bio.alignment.UnequalLengthAlignment.class org.biojava.bio.annodb.AnnotationDB.class org.biojava.bio.annodb.EmptyAnnotationDB.class org.biojava.bio.annodb.IndexedAnnotationDB.class org.biojava.bio.annodb.LazyFilteredAnnotationDB.class org.biojava.bio.annodb.LazySearchedAnnotationDB.class org.biojava.bio.annodb.MergingAnnotationDB.class org.biojava.bio.annodb.SimpleAnnotationDB.class org.biojava.bio.chromatogram.AbstractChromatogram.class org.biojava.bio.chromatogram.Chromatogram.class org.biojava.bio.chromatogram.ChromatogramFactory.class org.biojava.bio.chromatogram.ChromatogramTools.class org.biojava.bio.chromatogram.SimpleChromatogram.class org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException.class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.class org.biojava.bio.chromatogram.graphic.ChromatogramNonlinearScaler.class org.biojava.bio.chromatogram.graphic.FixedBaseWidthScaler.class org.biojava.bio.dist.AbstractDistribution.class org.biojava.bio.dist.AbstractOrderNDistribution.class org.biojava.bio.dist.Count.class org.biojava.bio.dist.Distribution.class org.biojava.bio.dist.DistributionFactory.class org.biojava.bio.dist.DistributionTools.class org.biojava.bio.dist.DistributionTrainer.class org.biojava.bio.dist.DistributionTrainerContext.class org.biojava.bio.dist.GapDistribution.class org.biojava.bio.dist.GeneralNthOrderDistribution.class org.biojava.bio.dist.IgnoreCountsTrainer.class org.biojava.bio.dist.IndexedCount.class org.biojava.bio.dist.IndexedNthOrderDistribution.class org.biojava.bio.dist.OrderNDistribution.class org.biojava.bio.dist.OrderNDistributionFactory.class org.biojava.bio.dist.PairDistribution.class org.biojava.bio.dist.SimpleDistribution.class org.biojava.bio.dist.SimpleDistributionTrainer.class org.biojava.bio.dist.SimpleDistributionTrainerContext.class org.biojava.bio.dist.TranslatedDistribution.class org.biojava.bio.dist.UniformDistribution.class org.biojava.bio.dist.UntrainableDistribution.class org.biojava.bio.dist.XMLDistributionReader.class org.biojava.bio.dist.XMLDistributionWriter.class org.biojava.bio.dp.AbstractTrainer.class org.biojava.bio.dp.BackPointer.class org.biojava.bio.dp.BaumWelchSampler.class org.biojava.bio.dp.BaumWelchTrainer.class org.biojava.bio.dp.DP.class org.biojava.bio.dp.DPFactory.class org.biojava.bio.dp.DPMatrix.class org.biojava.bio.dp.DotState.class org.biojava.bio.dp.EmissionState.class org.biojava.bio.dp.FlatModel.class org.biojava.bio.dp.HMMTrainer.class org.biojava.bio.dp.IllegalTransitionException.class org.biojava.bio.dp.MagicalState.class org.biojava.bio.dp.MarkovModel.class org.biojava.bio.dp.ModelInState.class org.biojava.bio.dp.ModelTrainer.class org.biojava.bio.dp.ProfileHMM.class org.biojava.bio.dp.ScoreType.class org.biojava.bio.dp.SimpleDotState.class org.biojava.bio.dp.SimpleEmissionState.class org.biojava.bio.dp.SimpleHMMTrainer.class org.biojava.bio.dp.SimpleMarkovModel.class org.biojava.bio.dp.SimpleModelInState.class org.biojava.bio.dp.SimpleModelTrainer.class org.biojava.bio.dp.SimpleStatePath.class org.biojava.bio.dp.SimpleWeightMatrix.class org.biojava.bio.dp.State.class org.biojava.bio.dp.StatePath.class org.biojava.bio.dp.StoppingCriteria.class org.biojava.bio.dp.Trainable.class org.biojava.bio.dp.TrainerTransition.class org.biojava.bio.dp.TrainingAlgorithm.class org.biojava.bio.dp.Transition.class org.biojava.bio.dp.TransitionTrainer.class org.biojava.bio.dp.WMAsMM.class org.biojava.bio.dp.WeightMatrix.class org.biojava.bio.dp.WeightMatrixAnnotator.class org.biojava.bio.dp.XmlMarkovModel.class org.biojava.bio.dp.onehead.AbstractCursor.class org.biojava.bio.dp.onehead.DPCursor.class org.biojava.bio.dp.onehead.MatrixCursor.class org.biojava.bio.dp.onehead.SingleDP.class org.biojava.bio.dp.onehead.SingleDPMatrix.class org.biojava.bio.dp.onehead.SmallCursor.class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor.class org.biojava.bio.dp.twohead.BackMatrixPairDPCursor.class org.biojava.bio.dp.twohead.Cell.class org.biojava.bio.dp.twohead.CellCalculator.class org.biojava.bio.dp.twohead.CellCalculatorFactory.class org.biojava.bio.dp.twohead.CellCalculatorFactoryMaker.class org.biojava.bio.dp.twohead.DPCompiler.class org.biojava.bio.dp.twohead.DPInterpreter.class org.biojava.bio.dp.twohead.EmissionCache.class org.biojava.bio.dp.twohead.LightPairDPCursor.class org.biojava.bio.dp.twohead.MatrixPairDPCursor.class org.biojava.bio.dp.twohead.PairDPCursor.class org.biojava.bio.dp.twohead.PairDPMatrix.class org.biojava.bio.dp.twohead.PairwiseDP.class org.biojava.bio.gui.BarLogoPainter.class org.biojava.bio.gui.BlockPainter.class org.biojava.bio.gui.DNAStyle.class org.biojava.bio.gui.DistributionLogo.class org.biojava.bio.gui.FeatureTree.class org.biojava.bio.gui.LogoContext.class org.biojava.bio.gui.LogoPainter.class org.biojava.bio.gui.PlainBlock.class org.biojava.bio.gui.PlainStyle.class org.biojava.bio.gui.SimpleSymbolStyle.class org.biojava.bio.gui.StackedLogoPainter.class org.biojava.bio.gui.SymbolStyle.class org.biojava.bio.gui.TextBlock.class org.biojava.bio.gui.TextLogoPainter.class org.biojava.bio.gui.sequence.AbiTraceRenderer.class org.biojava.bio.gui.sequence.AbstractBeadRenderer.class org.biojava.bio.gui.sequence.AlignmentRenderer.class org.biojava.bio.gui.sequence.BasicFeatureRenderer.class org.biojava.bio.gui.sequence.BasicImapRenderer.class org.biojava.bio.gui.sequence.BeadFeatureRenderer.class org.biojava.bio.gui.sequence.BumpedRenderer.class org.biojava.bio.gui.sequence.CircularFeatureFilteringRenderer.class org.biojava.bio.gui.sequence.CircularFeatureRenderer.class org.biojava.bio.gui.sequence.CircularFeaturesRenderer.class org.biojava.bio.gui.sequence.CircularMLR.class org.biojava.bio.gui.sequence.CircularPaddedRenderer.class org.biojava.bio.gui.sequence.CircularRenderer.class org.biojava.bio.gui.sequence.CircularRendererContext.class org.biojava.bio.gui.sequence.CircularRendererPanel.class org.biojava.bio.gui.sequence.CrosshairRenderer.class org.biojava.bio.gui.sequence.EllipticalBeadRenderer.class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer.class org.biojava.bio.gui.sequence.FeatureLabelRenderer.class org.biojava.bio.gui.sequence.FeatureRenderer.class org.biojava.bio.gui.sequence.FilteringRenderer.class org.biojava.bio.gui.sequence.GUITools.class org.biojava.bio.gui.sequence.GappedRenderer.class org.biojava.bio.gui.sequence.HeadlessRenderContext.class org.biojava.bio.gui.sequence.ImageMap.class org.biojava.bio.gui.sequence.ImageMapRenderer.class org.biojava.bio.gui.sequence.LabelRenderer.class org.biojava.bio.gui.sequence.LabelledSequenceRenderer.class org.biojava.bio.gui.sequence.LayeredRenderer.class org.biojava.bio.gui.sequence.LineInfo.class org.biojava.bio.gui.sequence.MultiLineRenderer.class org.biojava.bio.gui.sequence.OverlayMarker.class org.biojava.bio.gui.sequence.OverlayRendererWrapper.class org.biojava.bio.gui.sequence.PaddingRenderer.class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer.class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer.class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer.class org.biojava.bio.gui.sequence.PairwiseRenderContext.class org.biojava.bio.gui.sequence.PairwiseSequencePanel.class org.biojava.bio.gui.sequence.PairwiseSequenceRenderer.class org.biojava.bio.gui.sequence.RectangularBeadRenderer.class org.biojava.bio.gui.sequence.RectangularImapRenderer.class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer.class org.biojava.bio.gui.sequence.RulerRenderer.class org.biojava.bio.gui.sequence.SequencePanel.class org.biojava.bio.gui.sequence.SequencePoster.class org.biojava.bio.gui.sequence.SequenceRenderContext.class org.biojava.bio.gui.sequence.SequenceRenderer.class org.biojava.bio.gui.sequence.SequenceRendererWrapper.class org.biojava.bio.gui.sequence.SequenceViewerEvent.class org.biojava.bio.gui.sequence.SequenceViewerListener.class org.biojava.bio.gui.sequence.SequenceViewerMotionListener.class org.biojava.bio.gui.sequence.SequenceViewerMotionSupport.class org.biojava.bio.gui.sequence.SequenceViewerSupport.class org.biojava.bio.gui.sequence.SimpleLabelRenderer.class org.biojava.bio.gui.sequence.SixFrameRenderer.class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer.class org.biojava.bio.gui.sequence.StackedFeatureRenderer.class org.biojava.bio.gui.sequence.StopRenderer.class org.biojava.bio.gui.sequence.SubCircularRendererContext.class org.biojava.bio.gui.sequence.SubPairwiseRenderContext.class org.biojava.bio.gui.sequence.SubSequenceRenderContext.class org.biojava.bio.gui.sequence.SymbolSequenceRenderer.class org.biojava.bio.gui.sequence.TickFeatureRenderer.class org.biojava.bio.gui.sequence.TranslatedSequencePanel.class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer.class org.biojava.bio.gui.sequence.ZiggyImapRenderer.class org.biojava.bio.molbio.RestrictionEnzyme.class org.biojava.bio.molbio.RestrictionEnzymeManager.class org.biojava.bio.molbio.RestrictionMapper.class org.biojava.bio.molbio.RestrictionSite.class org.biojava.bio.molbio.RestrictionSiteFinder.class org.biojava.bio.program.BlastLikeToXMLConverter.class org.biojava.bio.program.Meme.class org.biojava.bio.program.PdbToXMLConverter.class org.biojava.bio.program.abi.ABIFChromatogram.class org.biojava.bio.program.abi.ABIFParser.class org.biojava.bio.program.abi.ABITools.class org.biojava.bio.program.abi.ABITrace.class org.biojava.bio.program.blast2html.AbstractAlignmentStyler.class org.biojava.bio.program.blast2html.AlignmentMarker.class org.biojava.bio.program.blast2html.AlignmentStyler.class org.biojava.bio.program.blast2html.Blast2HTMLHandler.class org.biojava.bio.program.blast2html.BlastLikeAlignment.class org.biojava.bio.program.blast2html.BlastMatrixAlignmentStyler.class org.biojava.bio.program.blast2html.ColourCommand.class org.biojava.bio.program.blast2html.DatabaseURLGenerator.class org.biojava.bio.program.blast2html.DefaultURLGeneratorFactory.class org.biojava.bio.program.blast2html.DetailHit.class org.biojava.bio.program.blast2html.EbiDatabaseURLGenerator.class org.biojava.bio.program.blast2html.HSP.class org.biojava.bio.program.blast2html.HSPSummary.class org.biojava.bio.program.blast2html.HTMLRenderer.class org.biojava.bio.program.blast2html.HitDescription.class org.biojava.bio.program.blast2html.HitId.class org.biojava.bio.program.blast2html.HitSummary.class org.biojava.bio.program.blast2html.NcbiDatabaseURLGenerator.class org.biojava.bio.program.blast2html.Sequence.class org.biojava.bio.program.blast2html.SimpleAlignmentStyler.class org.biojava.bio.program.blast2html.URLGeneratorFactory.class org.biojava.bio.program.das.ComponentFeatureHandler.class org.biojava.bio.program.das.DAS.class org.biojava.bio.program.das.DASAnnotationDistDataSource.class org.biojava.bio.program.das.DASCapabilities.class org.biojava.bio.program.das.DASComponentFeature.class org.biojava.bio.program.das.DASDistDataSource.class org.biojava.bio.program.das.DASFeatureSet.class org.biojava.bio.program.das.DASGFFFeatureHandler.class org.biojava.bio.program.das.DASLink.class org.biojava.bio.program.das.DASLinkHandler.class org.biojava.bio.program.das.DASRawSymbolList.class org.biojava.bio.program.das.DASSequence.class org.biojava.bio.program.das.DASSequenceDB.class org.biojava.bio.program.das.DASSequenceDBProvider.class org.biojava.bio.program.das.DASSequenceI.class org.biojava.bio.program.das.DataSource.class org.biojava.bio.program.das.FeatureFetcher.class org.biojava.bio.program.das.FeatureRequestManager.class org.biojava.bio.program.das.Fetcher.class org.biojava.bio.program.das.RawAnnotationSequence.class org.biojava.bio.program.das.ReferenceServer.class org.biojava.bio.program.das.Segment.class org.biojava.bio.program.das.TypesFetcher.class org.biojava.bio.program.das.TypesListener.class org.biojava.bio.program.das.dasalignment.Alignment.class org.biojava.bio.program.das.dasalignment.DASAlignmentCall.class org.biojava.bio.program.das.dasalignment.DASAlignmentClient.class org.biojava.bio.program.das.dasalignment.DASAlignmentXMLResponseParser.class org.biojava.bio.program.das.dasalignment.DASException.class org.biojava.bio.program.das.dasstructure.DASStructureCall.class org.biojava.bio.program.das.dasstructure.DASStructureXMLResponseParser.class org.biojava.bio.program.formats.Embl.class org.biojava.bio.program.formats.Enzyme.class org.biojava.bio.program.formats.Format.class org.biojava.bio.program.formats.FormatTools.class org.biojava.bio.program.formats.Ligand.class org.biojava.bio.program.formats.Swissprot.class org.biojava.bio.program.gff.GFFComparator.class org.biojava.bio.program.gff.GFFDocumentHandler.class org.biojava.bio.program.gff.GFFEntrySet.class org.biojava.bio.program.gff.GFFErrorHandler.class org.biojava.bio.program.gff.GFFFilterer.class org.biojava.bio.program.gff.GFFParser.class org.biojava.bio.program.gff.GFFRecord.class org.biojava.bio.program.gff.GFFRecordFilter.class org.biojava.bio.program.gff.GFFTools.class org.biojava.bio.program.gff.GFFWriter.class org.biojava.bio.program.gff.IgnoreRecordException.class org.biojava.bio.program.gff.SequencesAsGFF.class org.biojava.bio.program.gff.SimpleGFFRecord.class org.biojava.bio.program.gff3.GFF3DocumentHandler.class org.biojava.bio.program.gff3.GFF3Parser.class org.biojava.bio.program.gff3.GFF3Record.class org.biojava.bio.program.hmmer.FullHmmerProfileHMM.class org.biojava.bio.program.hmmer.HmmerProfileHMM.class org.biojava.bio.program.hmmer.HmmerProfileParser.class org.biojava.bio.program.hmmer.ProfileEmissionState.class org.biojava.bio.program.homologene.AbstractOrthoPairCollection.class org.biojava.bio.program.homologene.AbstractOrthoPairSet.class org.biojava.bio.program.homologene.AbstractOrthologueSet.class org.biojava.bio.program.homologene.DuplicateTaxonException.class org.biojava.bio.program.homologene.HomologeneBuilder.class org.biojava.bio.program.homologene.HomologeneDB.class org.biojava.bio.program.homologene.HomologeneTools.class org.biojava.bio.program.homologene.OrthoPair.class org.biojava.bio.program.homologene.OrthoPairCollection.class org.biojava.bio.program.homologene.OrthoPairFilter.class org.biojava.bio.program.homologene.OrthoPairSet.class org.biojava.bio.program.homologene.OrthoPairSetFilter.class org.biojava.bio.program.homologene.Orthologue.class org.biojava.bio.program.homologene.OrthologueFilter.class org.biojava.bio.program.homologene.OrthologueSet.class org.biojava.bio.program.homologene.SimilarityType.class org.biojava.bio.program.homologene.SimpleHomologeneBuilder.class org.biojava.bio.program.homologene.SimpleHomologeneDB.class org.biojava.bio.program.homologene.SimpleOrthoPair.class org.biojava.bio.program.homologene.SimpleOrthoPairCollection.class org.biojava.bio.program.homologene.SimpleOrthoPairSet.class org.biojava.bio.program.homologene.SimpleOrthologue.class org.biojava.bio.program.homologene.SimpleOrthologueSet.class org.biojava.bio.program.homologene.Taxon.class org.biojava.bio.program.indexdb.BioStore.class org.biojava.bio.program.indexdb.BioStoreFactory.class org.biojava.bio.program.indexdb.CacheList.class org.biojava.bio.program.indexdb.ConfigFile.class org.biojava.bio.program.indexdb.IndexStore.class org.biojava.bio.program.indexdb.IndexTools.class org.biojava.bio.program.indexdb.KeyPair.class org.biojava.bio.program.indexdb.PrimaryIDList.class org.biojava.bio.program.indexdb.PropertiesAnnotation.class org.biojava.bio.program.indexdb.Record.class org.biojava.bio.program.indexdb.SearchableFileAsList.class org.biojava.bio.program.indexdb.SearchableList.class org.biojava.bio.program.indexdb.SecondaryFileAsList.class org.biojava.bio.program.phred.PhredFormat.class org.biojava.bio.program.phred.PhredSequence.class org.biojava.bio.program.phred.PhredTools.class org.biojava.bio.program.phred.Qualitative.class org.biojava.bio.program.sax.AbstractNativeAppSAXParser.class org.biojava.bio.program.sax.BaseXMLWriterTestHelper.class org.biojava.bio.program.sax.BlastLikeAlignmentSAXParser.class org.biojava.bio.program.sax.BlastLikeSAXParser.class org.biojava.bio.program.sax.BlastLikeVersionSupport.class org.biojava.bio.program.sax.BlastSAXParser.class org.biojava.bio.program.sax.ClustalWAlignmentSAXParser.class org.biojava.bio.program.sax.DomainSectionSAXParser.class org.biojava.bio.program.sax.FastaSearchParser.class org.biojava.bio.program.sax.FastaSearchSAXParser.class org.biojava.bio.program.sax.FastaSequenceSAXParser.class org.biojava.bio.program.sax.GCGBlastSummaryLineHelper.class org.biojava.bio.program.sax.GenericSAXParserTest.class org.biojava.bio.program.sax.HSPSummaryHelper.class org.biojava.bio.program.sax.HitSectionSAXParser.class org.biojava.bio.program.sax.HmmerAlignmentSAXParser.class org.biojava.bio.program.sax.HmmerSummaryLineHelper.class org.biojava.bio.program.sax.NamespaceConfigurationIF.class org.biojava.bio.program.sax.NcbiBlastSummaryLineHelper.class org.biojava.bio.program.sax.NeedleAlignmentSAXParser.class org.biojava.bio.program.sax.PdbSAXParser.class org.biojava.bio.program.sax.QName.class org.biojava.bio.program.sax.SequenceAlignmentSAXParser.class org.biojava.bio.program.sax.SimpleXMLEmitterTestHelper.class org.biojava.bio.program.sax.SummaryLineHelperIF.class org.biojava.bio.program.sax.WuBlastSummaryLineHelper.class org.biojava.bio.program.sax.blastxml.BlastAggregator.class org.biojava.bio.program.sax.blastxml.BlastOutputHandler.class org.biojava.bio.program.sax.blastxml.BlastOutputIterationsHandler.class org.biojava.bio.program.sax.blastxml.BlastXMLParser.class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade.class org.biojava.bio.program.sax.blastxml.HitHandler.class org.biojava.bio.program.sax.blastxml.HitHspsHandler.class org.biojava.bio.program.sax.blastxml.HspHandler.class org.biojava.bio.program.sax.blastxml.IterationHandler.class org.biojava.bio.program.sax.blastxml.IterationHitsHandler.class org.biojava.bio.program.sax.blastxml.StAXFeatureHandler.class org.biojava.bio.program.sax.blastxml.StAXFeatureHandlerMod.class org.biojava.bio.program.sax.blastxml.StAXHandlerFactory.class org.biojava.bio.program.scf.SCF.class org.biojava.bio.program.ssaha.CompactedDataStore.class org.biojava.bio.program.ssaha.CompactedDataStoreFactory.class org.biojava.bio.program.ssaha.DataStore.class org.biojava.bio.program.ssaha.DataStoreFactory.class org.biojava.bio.program.ssaha.HitMerger.class org.biojava.bio.program.ssaha.MappedDataStore.class org.biojava.bio.program.ssaha.MappedDataStoreFactory.class org.biojava.bio.program.ssaha.NIODataStore.class org.biojava.bio.program.ssaha.NIODataStoreFactory.class org.biojava.bio.program.ssaha.SearchException.class org.biojava.bio.program.ssaha.SearchListener.class org.biojava.bio.program.ssaha.SequenceStreamer.class org.biojava.bio.program.ssbind.AlignmentStAXHandler.class org.biojava.bio.program.ssbind.AlphabetResolver.class org.biojava.bio.program.ssbind.AnnotationFactory.class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder.class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder.class org.biojava.bio.program.ssbind.HSPStAXHandler.class org.biojava.bio.program.ssbind.HSPSummaryStAXHandler.class org.biojava.bio.program.ssbind.HeaderStAXHandler.class org.biojava.bio.program.ssbind.HitStAXHandler.class org.biojava.bio.program.ssbind.SeqSimilarityAdapter.class org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter.class org.biojava.bio.program.ssbind.SeqSimilarityStAXHandler.class org.biojava.bio.program.ssbind.SimilarityPairBuilder.class org.biojava.bio.program.ssbind.StAXHandlerBinding.class org.biojava.bio.program.ssbind.StAXHandlerFactory.class org.biojava.bio.program.ssbind.ViewSequenceFactory.class org.biojava.bio.program.tagvalue.AbstractWrapper.class org.biojava.bio.program.tagvalue.Aggregator.class org.biojava.bio.program.tagvalue.AnnotationBuilder.class org.biojava.bio.program.tagvalue.BoundaryFinder.class org.biojava.bio.program.tagvalue.ChangeTable.class org.biojava.bio.program.tagvalue.Echo.class org.biojava.bio.program.tagvalue.Formats.class org.biojava.bio.program.tagvalue.Index2Model.class org.biojava.bio.program.tagvalue.Indexer.class org.biojava.bio.program.tagvalue.Indexer2.class org.biojava.bio.program.tagvalue.LineSplitParser.class org.biojava.bio.program.tagvalue.MultiTagger.class org.biojava.bio.program.tagvalue.Parser.class org.biojava.bio.program.tagvalue.ParserListener.class org.biojava.bio.program.tagvalue.PropertyChanger.class org.biojava.bio.program.tagvalue.RegexChanger.class org.biojava.bio.program.tagvalue.RegexFieldFinder.class org.biojava.bio.program.tagvalue.RegexParser.class org.biojava.bio.program.tagvalue.RegexSplitter.class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper.class org.biojava.bio.program.tagvalue.StateMachine.class org.biojava.bio.program.tagvalue.TagDelegator.class org.biojava.bio.program.tagvalue.TagDropper.class org.biojava.bio.program.tagvalue.TagMapper.class org.biojava.bio.program.tagvalue.TagRenamer.class org.biojava.bio.program.tagvalue.TagValue.class org.biojava.bio.program.tagvalue.TagValueContext.class org.biojava.bio.program.tagvalue.TagValueListener.class org.biojava.bio.program.tagvalue.TagValueParser.class org.biojava.bio.program.tagvalue.TagValueWrapper.class org.biojava.bio.program.tagvalue.ValueChanger.class org.biojava.bio.program.unigene.FlatFileUnigeneDB.class org.biojava.bio.program.unigene.FlatFileUnigeneFactory.class org.biojava.bio.program.unigene.SQLUnigeneDB.class org.biojava.bio.program.unigene.SQLUnigeneFactory.class org.biojava.bio.program.unigene.UnigeneCluster.class org.biojava.bio.program.unigene.UnigeneDB.class org.biojava.bio.program.unigene.UnigeneFactory.class org.biojava.bio.program.unigene.UnigeneTools.class org.biojava.bio.program.xff.BasicXFFHelper.class org.biojava.bio.program.xff.ElementRecognizer.class org.biojava.bio.program.xff.FeatureHandler.class org.biojava.bio.program.xff.LocationHandlerBase.class org.biojava.bio.program.xff.PropDetailHandler.class org.biojava.bio.program.xff.PropertyWriter.class org.biojava.bio.program.xff.StrandedFeatureHandler.class org.biojava.bio.program.xff.XFFFeatureSetHandler.class org.biojava.bio.program.xff.XFFHelper.class org.biojava.bio.program.xff.XFFPartHandlerFactory.class org.biojava.bio.program.xff.XFFTools.class org.biojava.bio.program.xff.XFFWriter.class org.biojava.bio.program.xml.BaseXMLWriter.class org.biojava.bio.program.xml.SimpleXMLEmitter.class org.biojava.bio.proteomics.Digest.class org.biojava.bio.proteomics.IsoelectricPointCalc.class org.biojava.bio.proteomics.MassCalc.class org.biojava.bio.proteomics.Protease.class org.biojava.bio.proteomics.ProteaseManager.class org.biojava.bio.proteomics.StructureTools.class org.biojava.bio.search.BioMatcher.class org.biojava.bio.search.BioPattern.class org.biojava.bio.search.BlastLikeSearchFilter.class org.biojava.bio.search.FilterTest.class org.biojava.bio.search.FilteringContentHandler.class org.biojava.bio.search.KnuthMorrisPrattSearch.class org.biojava.bio.search.MaxMismatchMatcher.class org.biojava.bio.search.MaxMismatchPattern.class org.biojava.bio.search.SearchBuilder.class org.biojava.bio.search.SearchContentAdapter.class org.biojava.bio.search.SearchContentFilter.class org.biojava.bio.search.SearchContentHandler.class org.biojava.bio.search.SearchContentHandlerDebugger.class org.biojava.bio.search.SeqContentMatcher.class org.biojava.bio.search.SeqContentPattern.class org.biojava.bio.search.SeqSimilaritySearchHit.class org.biojava.bio.search.SeqSimilaritySearchResult.class org.biojava.bio.search.SeqSimilaritySearchSubHit.class org.biojava.bio.search.SeqSimilaritySearcher.class org.biojava.bio.search.SequenceDBSearchHit.class org.biojava.bio.search.SequenceDBSearchResult.class org.biojava.bio.search.SequenceDBSearchSubHit.class org.biojava.bio.search.SimpleSeqSimilaritySearchHit.class org.biojava.bio.search.SimpleSeqSimilaritySearchResult.class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit.class org.biojava.bio.seq.AbstractFeatureHolder.class org.biojava.bio.seq.AcceptAllFilter.class org.biojava.bio.seq.AcceptNoneFilter.class org.biojava.bio.seq.ByHierarchy.class org.biojava.bio.seq.CircularView.class org.biojava.bio.seq.ComponentFeature.class org.biojava.bio.seq.DNATools.class org.biojava.bio.seq.Down.class org.biojava.bio.seq.Feature.class org.biojava.bio.seq.FeatureFilter.class org.biojava.bio.seq.FeatureHolder.class org.biojava.bio.seq.FeatureHolderUtils.class org.biojava.bio.seq.FeatureRealizer.class org.biojava.bio.seq.FeatureTypes.class org.biojava.bio.seq.FilterUtils.class org.biojava.bio.seq.Frame.class org.biojava.bio.seq.FramedFeature.class org.biojava.bio.seq.GappedSequence.class org.biojava.bio.seq.GeneticCodes.class org.biojava.bio.seq.IsLeaf.class org.biojava.bio.seq.IsTopLevel.class org.biojava.bio.seq.LazyFeatureHolder.class org.biojava.bio.seq.MergeFeatureHolder.class org.biojava.bio.seq.NewSimpleAssembly.class org.biojava.bio.seq.NucleotideTools.class org.biojava.bio.seq.OptimizableFilter.class org.biojava.bio.seq.ProteinTools.class org.biojava.bio.seq.RNATools.class org.biojava.bio.seq.RealizingFeatureHolder.class org.biojava.bio.seq.RemoteFeature.class org.biojava.bio.seq.Sequence.class org.biojava.bio.seq.SequenceAnnotator.class org.biojava.bio.seq.SequenceFactory.class org.biojava.bio.seq.SequenceIterator.class org.biojava.bio.seq.SequenceTools.class org.biojava.bio.seq.SimpleAssembly.class org.biojava.bio.seq.SimpleComponentFeature.class org.biojava.bio.seq.SimpleFeatureHolder.class org.biojava.bio.seq.SimpleFeatureRealizer.class org.biojava.bio.seq.StrandParser.class org.biojava.bio.seq.StrandedFeature.class org.biojava.bio.seq.Up.class org.biojava.bio.seq.db.AbstractSequenceDB.class org.biojava.bio.seq.db.AnnotatedSequenceDB.class org.biojava.bio.seq.db.BioIndex.class org.biojava.bio.seq.db.CachingSequenceDB.class org.biojava.bio.seq.db.DummySequenceDB.class org.biojava.bio.seq.db.DummySequenceDBInstallation.class org.biojava.bio.seq.db.EmblCDROMIndexStore.class org.biojava.bio.seq.db.FetchURL.class org.biojava.bio.seq.db.GenbankSequenceDB.class org.biojava.bio.seq.db.GenpeptSequenceDB.class org.biojava.bio.seq.db.HashSequenceDB.class org.biojava.bio.seq.db.IDMaker.class org.biojava.bio.seq.db.IllegalIDException.class org.biojava.bio.seq.db.Index.class org.biojava.bio.seq.db.IndexStore.class org.biojava.bio.seq.db.IndexedSequenceDB.class org.biojava.bio.seq.db.NCBISequenceDB.class org.biojava.bio.seq.db.SequenceDB.class org.biojava.bio.seq.db.SequenceDBInstallation.class org.biojava.bio.seq.db.SequenceDBLite.class org.biojava.bio.seq.db.SequenceDBWrapper.class org.biojava.bio.seq.db.SimpleIndex.class org.biojava.bio.seq.db.SimpleSequenceDBInstallation.class org.biojava.bio.seq.db.SubSequenceDB.class org.biojava.bio.seq.db.SwissprotSequenceDB.class org.biojava.bio.seq.db.TabIndexStore.class org.biojava.bio.seq.db.ViewingSequenceDB.class org.biojava.bio.seq.db.WebSequenceDB.class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDB.class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDBProvider.class org.biojava.bio.seq.db.biosql.BioSQLAllFeatures.class org.biojava.bio.seq.db.biosql.BioSQLAssembly.class org.biojava.bio.seq.db.biosql.BioSQLComponentFeature.class org.biojava.bio.seq.db.biosql.BioSQLEntryAnnotationChangeHub.class org.biojava.bio.seq.db.biosql.BioSQLEntryChangeHub.class org.biojava.bio.seq.db.biosql.BioSQLFeature.class org.biojava.bio.seq.db.biosql.BioSQLFeatureAnnotation.class org.biojava.bio.seq.db.biosql.BioSQLFeatureAnnotationChangeHub.class org.biojava.bio.seq.db.biosql.BioSQLFeatureChangeHub.class org.biojava.bio.seq.db.biosql.BioSQLFeatureReceiver.class org.biojava.bio.seq.db.biosql.BioSQLSequence.class org.biojava.bio.seq.db.biosql.BioSQLSequenceAnnotation.class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.class org.biojava.bio.seq.db.biosql.BioSQLSequenceDBProvider.class org.biojava.bio.seq.db.biosql.BioSQLSequenceI.class org.biojava.bio.seq.db.biosql.BioSQLStrandedFeature.class org.biojava.bio.seq.db.biosql.BioSQLTiledFeatures.class org.biojava.bio.seq.db.biosql.DBHelper.class org.biojava.bio.seq.db.biosql.FeaturesSQL.class org.biojava.bio.seq.db.biosql.HypersonicDBHelper.class org.biojava.bio.seq.db.biosql.MySQLDBHelper.class org.biojava.bio.seq.db.biosql.OntologySQL.class org.biojava.bio.seq.db.biosql.OracleDBHelper.class org.biojava.bio.seq.db.biosql.PostgreSQLDBHelper.class org.biojava.bio.seq.db.biosql.TaxonSQL.class org.biojava.bio.seq.db.biosql.UnknownDBHelper.class org.biojava.bio.seq.db.emblcd.AcnumHitReader.class org.biojava.bio.seq.db.emblcd.AcnumTrgReader.class org.biojava.bio.seq.db.emblcd.DivisionLkpReader.class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader.class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess.class org.biojava.bio.seq.db.emblcd.EntryNamIdxReader.class org.biojava.bio.seq.db.emblcd.EntryNamRandomAccess.class org.biojava.bio.seq.db.emblcd.RecordParser.class org.biojava.bio.seq.db.flat.FlatSequenceDB.class org.biojava.bio.seq.db.flat.FlatSequenceDBProvider.class org.biojava.bio.seq.distributed.DistComponentFeature.class org.biojava.bio.seq.distributed.DistDataSource.class org.biojava.bio.seq.distributed.DistProjectionContext.class org.biojava.bio.seq.distributed.DistributedSequence.class org.biojava.bio.seq.distributed.DistributedSequenceDB.class org.biojava.bio.seq.distributed.GFFDataSource.class org.biojava.bio.seq.distributed.SequenceDBDataSource.class org.biojava.bio.seq.filter.FilterTransformer.class org.biojava.bio.seq.homol.Homology.class org.biojava.bio.seq.homol.HomologyDB.class org.biojava.bio.seq.homol.HomologyFeature.class org.biojava.bio.seq.homol.SimilarityPairFeature.class org.biojava.bio.seq.homol.SimpleHomology.class org.biojava.bio.seq.impl.AssembledSymbolList.class org.biojava.bio.seq.impl.DummySequence.class org.biojava.bio.seq.impl.FeatureImpl.class org.biojava.bio.seq.impl.LazyFilterFeatureHolder.class org.biojava.bio.seq.impl.NewAssembledSymbolList.class org.biojava.bio.seq.impl.RevCompSequence.class org.biojava.bio.seq.impl.SimpleFeature.class org.biojava.bio.seq.impl.SimpleFramedFeature.class org.biojava.bio.seq.impl.SimpleGappedSequence.class org.biojava.bio.seq.impl.SimpleHomologyFeature.class org.biojava.bio.seq.impl.SimpleRemoteFeature.class org.biojava.bio.seq.impl.SimpleRestrictionSite.class org.biojava.bio.seq.impl.SimpleSequence.class org.biojava.bio.seq.impl.SimpleSequenceFactory.class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature.class org.biojava.bio.seq.impl.SimpleStrandedFeature.class org.biojava.bio.seq.impl.SubSequence.class org.biojava.bio.seq.impl.TemplateUtils.class org.biojava.bio.seq.impl.ViewSequence.class org.biojava.bio.seq.io.AbstractGenEmblFileFormer.class org.biojava.bio.seq.io.AlignIOConstants.class org.biojava.bio.seq.io.AlignmentFormat.class org.biojava.bio.seq.io.CharacterTokenization.class org.biojava.bio.seq.io.ChunkedSymbolListFactory.class org.biojava.bio.seq.io.CrossProductTokenization.class org.biojava.bio.seq.io.DoubleTokenization.class org.biojava.bio.seq.io.EmblFileFormer.class org.biojava.bio.seq.io.EmblLikeFormat.class org.biojava.bio.seq.io.EmblLikeLocationParser.class org.biojava.bio.seq.io.EmblProcessor.class org.biojava.bio.seq.io.EmblReferenceComparator.class org.biojava.bio.seq.io.FastaAlignmentFormat.class org.biojava.bio.seq.io.FastaDescriptionLineParser.class org.biojava.bio.seq.io.FastaFormat.class org.biojava.bio.seq.io.FeatureTableParser.class org.biojava.bio.seq.io.GAMEFormat.class org.biojava.bio.seq.io.GenEmblFeatureComparator.class org.biojava.bio.seq.io.GenEmblPropertyComparator.class org.biojava.bio.seq.io.GenbankContext.class org.biojava.bio.seq.io.GenbankFileFormer.class org.biojava.bio.seq.io.GenbankFormat.class org.biojava.bio.seq.io.GenbankProcessor.class org.biojava.bio.seq.io.GenbankXmlFormat.class org.biojava.bio.seq.io.GenpeptFileFormer.class org.biojava.bio.seq.io.GenpeptFormat.class org.biojava.bio.seq.io.IntegerTokenization.class org.biojava.bio.seq.io.MSFAlignmentFormat.class org.biojava.bio.seq.io.NameTokenization.class org.biojava.bio.seq.io.OrganismParser.class org.biojava.bio.seq.io.ParseException.class org.biojava.bio.seq.io.ProteinRefSeqFileFormer.class org.biojava.bio.seq.io.ProteinRefSeqProcessor.class org.biojava.bio.seq.io.ReferenceAnnotation.class org.biojava.bio.seq.io.SeqFileFormer.class org.biojava.bio.seq.io.SeqIOAdapter.class org.biojava.bio.seq.io.SeqIOConstants.class org.biojava.bio.seq.io.SeqIOEventEmitter.class org.biojava.bio.seq.io.SeqIOFilter.class org.biojava.bio.seq.io.SeqIOListener.class org.biojava.bio.seq.io.SeqIOTools.class org.biojava.bio.seq.io.SequenceBuilder.class org.biojava.bio.seq.io.SequenceBuilderBase.class org.biojava.bio.seq.io.SequenceBuilderFactory.class org.biojava.bio.seq.io.SequenceBuilderFilter.class org.biojava.bio.seq.io.SequenceDBSequenceBuilder.class org.biojava.bio.seq.io.SequenceFormat.class org.biojava.bio.seq.io.SimpleAssemblyBuilder.class org.biojava.bio.seq.io.SimpleSequenceBuilder.class org.biojava.bio.seq.io.SmartSequenceBuilder.class org.biojava.bio.seq.io.StreamParser.class org.biojava.bio.seq.io.StreamReader.class org.biojava.bio.seq.io.StreamWriter.class org.biojava.bio.seq.io.SwissprotFeatureTableParser.class org.biojava.bio.seq.io.SwissprotFileFormer.class org.biojava.bio.seq.io.SwissprotProcessor.class org.biojava.bio.seq.io.SymbolListCharSequence.class org.biojava.bio.seq.io.SymbolReader.class org.biojava.bio.seq.io.SymbolTokenization.class org.biojava.bio.seq.io.WordTokenization.class org.biojava.bio.seq.io.agave.AGAVEAltIdsPropHandler.class org.biojava.bio.seq.io.agave.AGAVEAnnotFilter.class org.biojava.bio.seq.io.agave.AGAVEAnnotFilterFactory.class org.biojava.bio.seq.io.agave.AGAVEAnnotationsHandler.class org.biojava.bio.seq.io.agave.AGAVEAssemblyHandler.class org.biojava.bio.seq.io.agave.AGAVEBioSeqCallbackItf.class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler.class org.biojava.bio.seq.io.agave.AGAVEBioSequenceHandler.class org.biojava.bio.seq.io.agave.AGAVECallbackItf.class org.biojava.bio.seq.io.agave.AGAVECdsHandler.class org.biojava.bio.seq.io.agave.AGAVEChromosomeCallbackItf.class org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler.class org.biojava.bio.seq.io.agave.AGAVEClassificationHandler.class org.biojava.bio.seq.io.agave.AGAVECompResultHandler.class org.biojava.bio.seq.io.agave.AGAVEComputationHandler.class org.biojava.bio.seq.io.agave.AGAVEContigCallbackItf.class org.biojava.bio.seq.io.agave.AGAVEContigHandler.class org.biojava.bio.seq.io.agave.AGAVEDbId.class org.biojava.bio.seq.io.agave.AGAVEDbIdCallbackItf.class org.biojava.bio.seq.io.agave.AGAVEDbIdPropCallbackItf.class org.biojava.bio.seq.io.agave.AGAVEDbIdPropHandler.class org.biojava.bio.seq.io.agave.AGAVEDescPropHandler.class org.biojava.bio.seq.io.agave.AGAVEElementIdPropHandler.class org.biojava.bio.seq.io.agave.AGAVEEvidenceCallbackItf.class org.biojava.bio.seq.io.agave.AGAVEEvidenceHandler.class org.biojava.bio.seq.io.agave.AGAVEExonsPropHandler.class org.biojava.bio.seq.io.agave.AGAVEFeatureCallbackItf.class org.biojava.bio.seq.io.agave.AGAVEFragmentOrderHandler.class org.biojava.bio.seq.io.agave.AGAVEFragmentOrientationHandler.class org.biojava.bio.seq.io.agave.AGAVEGeneHandler.class org.biojava.bio.seq.io.agave.AGAVEHandler.class org.biojava.bio.seq.io.agave.AGAVEIdAlias.class org.biojava.bio.seq.io.agave.AGAVEIdAliasCallbackItf.class org.biojava.bio.seq.io.agave.AGAVEIdAliasPropHandler.class org.biojava.bio.seq.io.agave.AGAVEKeywordPropHandler.class org.biojava.bio.seq.io.agave.AGAVEMapLocation.class org.biojava.bio.seq.io.agave.AGAVEMapLocationPropHandler.class org.biojava.bio.seq.io.agave.AGAVEMapPosition.class org.biojava.bio.seq.io.agave.AGAVEMapPositionPropHandler.class org.biojava.bio.seq.io.agave.AGAVEMatchAlignPropHandler.class org.biojava.bio.seq.io.agave.AGAVEMatchDescPropHandler.class org.biojava.bio.seq.io.agave.AGAVEMatchRegion.class org.biojava.bio.seq.io.agave.AGAVEMatchRegionPropHandler.class org.biojava.bio.seq.io.agave.AGAVEMrnaHandler.class org.biojava.bio.seq.io.agave.AGAVENotePropHandler.class org.biojava.bio.seq.io.agave.AGAVEPredictedProteinHandler.class org.biojava.bio.seq.io.agave.AGAVEProperty.class org.biojava.bio.seq.io.agave.AGAVEQualifierPropHandler.class org.biojava.bio.seq.io.agave.AGAVEQueryRegion.class org.biojava.bio.seq.io.agave.AGAVEQueryRegionPropHandler.class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot.class org.biojava.bio.seq.io.agave.AGAVERelatedAnnotPropHandler.class org.biojava.bio.seq.io.agave.AGAVEResultGroupHandler.class org.biojava.bio.seq.io.agave.AGAVEResultPropertyPropHandler.class org.biojava.bio.seq.io.agave.AGAVESciPropertyPropHandler.class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler.class org.biojava.bio.seq.io.agave.AGAVESeqLocationPropHandler.class org.biojava.bio.seq.io.agave.AGAVESeqMapHandler.class org.biojava.bio.seq.io.agave.AGAVESeqPropHandler.class org.biojava.bio.seq.io.agave.AGAVETranscriptHandler.class org.biojava.bio.seq.io.agave.AGAVEUnorderedFragmentsHandler.class org.biojava.bio.seq.io.agave.AGAVEViewPropHandler.class org.biojava.bio.seq.io.agave.AGAVEXref.class org.biojava.bio.seq.io.agave.AGAVEXrefCallbackItf.class org.biojava.bio.seq.io.agave.AGAVEXrefPropHandler.class org.biojava.bio.seq.io.agave.AGAVEXrefPropPropHandler.class org.biojava.bio.seq.io.agave.AGAVEXrefs.class org.biojava.bio.seq.io.agave.AGAVEXrefsPropHandler.class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter.class org.biojava.bio.seq.io.agave.AgaveWriter.class org.biojava.bio.seq.io.agave.DelegationManager.class org.biojava.bio.seq.io.agave.ElementRecognizer.class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter.class org.biojava.bio.seq.io.agave.PCDATAFilterWriter.class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor.class org.biojava.bio.seq.io.agave.SequenceHandler.class org.biojava.bio.seq.io.agave.SimpleAnnotFilter.class org.biojava.bio.seq.io.agave.StAXContentHandler.class org.biojava.bio.seq.io.agave.StAXContentHandlerBase.class org.biojava.bio.seq.io.agave.StAXFeatureHandler.class org.biojava.bio.seq.io.agave.StAXHandlerFactory.class org.biojava.bio.seq.io.agave.StAXPropertyHandler.class org.biojava.bio.seq.io.agave.UtilHelper.class org.biojava.bio.seq.io.filterxml.QName.class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter.class org.biojava.bio.seq.io.filterxml.XMLFilterHandler.class org.biojava.bio.seq.io.filterxml.XMLFilterWriter.class org.biojava.bio.seq.io.game.ElementRecognizer.class org.biojava.bio.seq.io.game.GAMEAnnotationHandler.class org.biojava.bio.seq.io.game.GAMEAspectPropHandler.class org.biojava.bio.seq.io.game.GAMEDbxrefPropHandler.class org.biojava.bio.seq.io.game.GAMEDescriptionPropHandler.class org.biojava.bio.seq.io.game.GAMEFeatureCallbackItf.class org.biojava.bio.seq.io.game.GAMEFeatureSetHandler.class org.biojava.bio.seq.io.game.GAMEFeatureSetPropHandler.class org.biojava.bio.seq.io.game.GAMEFeatureSpanHandler.class org.biojava.bio.seq.io.game.GAMEGenePropHandler.class org.biojava.bio.seq.io.game.GAMEHandler.class org.biojava.bio.seq.io.game.GAMEMapPosPropHandler.class org.biojava.bio.seq.io.game.GAMENameCallbackItf.class org.biojava.bio.seq.io.game.GAMENamePropHandler.class org.biojava.bio.seq.io.game.GAMEResiduesPropHandler.class org.biojava.bio.seq.io.game.GAMESeqPropHandler.class org.biojava.bio.seq.io.game.GAMESeqRelPropHandler.class org.biojava.bio.seq.io.game.GAMESpanPropHandler.class org.biojava.bio.seq.io.game.GAMETranscriptCallbackItf.class org.biojava.bio.seq.io.game.GAMETypePropHandler.class org.biojava.bio.seq.io.game.SequenceContentHandlerBase.class org.biojava.bio.seq.io.game.StAXFeatureHandler.class org.biojava.bio.seq.io.game.StAXHandlerFactory.class org.biojava.bio.seq.io.game.StAXPropertyHandler.class org.biojava.bio.seq.io.game12.GAMEAnnotationHandler.class org.biojava.bio.seq.io.game12.GAMEAspectHandler.class org.biojava.bio.seq.io.game12.GAMEDbxrefHandler.class org.biojava.bio.seq.io.game12.GAMEFeatureSetHandler.class org.biojava.bio.seq.io.game12.GAMEFeatureSpanHandler.class org.biojava.bio.seq.io.game12.GAMEGeneHandler.class org.biojava.bio.seq.io.game12.GAMEHandler.class org.biojava.bio.seq.io.game12.GAMEPropertyHandler.class org.biojava.bio.seq.io.game12.GAMESeqHandler.class org.biojava.bio.seq.io.game12.GAMESeqRelHandler.class org.biojava.bio.seq.io.game12.GAMESpanHandler.class org.biojava.bio.seq.io.game12.StAXFeatureHandler.class org.biojava.bio.seq.io.game12.StAXHandlerFactory.class org.biojava.bio.seq.projection.ProjectedFeature.class org.biojava.bio.seq.projection.ProjectedFeatureHolder.class org.biojava.bio.seq.projection.Projection.class org.biojava.bio.seq.projection.ProjectionContext.class org.biojava.bio.seq.projection.ProjectionEngine.class org.biojava.bio.seq.projection.ProjectionUtils.class org.biojava.bio.seq.projection.ReparentContext.class org.biojava.bio.seq.projection.TranslateFlipContext.class org.biojava.bio.structure.AlphaCTools.class org.biojava.bio.structure.AminoAcid.class org.biojava.bio.structure.AminoAcidImpl.class org.biojava.bio.structure.Atom.class org.biojava.bio.structure.AtomImpl.class org.biojava.bio.structure.AtomIterator.class org.biojava.bio.structure.Calc.class org.biojava.bio.structure.Chain.class org.biojava.bio.structure.ChainImpl.class org.biojava.bio.structure.Group.class org.biojava.bio.structure.GroupIterator.class org.biojava.bio.structure.HetatomImpl.class org.biojava.bio.structure.NucleotideImpl.class org.biojava.bio.structure.Structure.class org.biojava.bio.structure.StructureException.class org.biojava.bio.structure.StructureImpl.class org.biojava.bio.structure.io.DASStructureClient.class org.biojava.bio.structure.io.FileConvert.class org.biojava.bio.structure.io.PDBFileParser.class org.biojava.bio.structure.io.PDBFileReader.class org.biojava.bio.structure.io.PDBMSDReader.class org.biojava.bio.structure.io.PDBParseException.class org.biojava.bio.structure.io.PDBSRSReader.class org.biojava.bio.structure.io.StructureIO.class org.biojava.bio.structure.io.StructureIOFile.class org.biojava.bio.symbol.AbstractAlphabet.class org.biojava.bio.symbol.AbstractLocation.class org.biojava.bio.symbol.AbstractLocationDecorator.class org.biojava.bio.symbol.AbstractManyToOneTranslationTable.class org.biojava.bio.symbol.AbstractRangeLocation.class org.biojava.bio.symbol.AbstractReversibleTranslationTable.class org.biojava.bio.symbol.AbstractSimpleBasisSymbol.class org.biojava.bio.symbol.AbstractSymbol.class org.biojava.bio.symbol.AbstractSymbolList.class org.biojava.bio.symbol.AbstractTranslationTable.class org.biojava.bio.symbol.Alignment.class org.biojava.bio.symbol.Alphabet.class org.biojava.bio.symbol.AlphabetIndex.class org.biojava.bio.symbol.AlphabetManager.class org.biojava.bio.symbol.AtomicSymbol.class org.biojava.bio.symbol.BasisSymbol.class org.biojava.bio.symbol.BetweenLocation.class org.biojava.bio.symbol.BetweenLocationTools.class org.biojava.bio.symbol.ChunkedSymbolList.class org.biojava.bio.symbol.CircularLocation.class org.biojava.bio.symbol.CircularLocationTools.class org.biojava.bio.symbol.CodonPref.class org.biojava.bio.symbol.CodonPrefFilter.class org.biojava.bio.symbol.CodonPrefTools.class org.biojava.bio.symbol.CompoundLocation.class org.biojava.bio.symbol.CrossProductAlphabetIndex.class org.biojava.bio.symbol.DNAAmbPack.class org.biojava.bio.symbol.DNANoAmbPack.class org.biojava.bio.symbol.DoubleAlphabet.class org.biojava.bio.symbol.DummySymbolList.class org.biojava.bio.symbol.Edit.class org.biojava.bio.symbol.EmptyAlphabet.class org.biojava.bio.symbol.EmptyLocation.class org.biojava.bio.symbol.EmptySymbolList.class org.biojava.bio.symbol.FiniteAlphabet.class org.biojava.bio.symbol.FullDnaAlphabetIndex.class org.biojava.bio.symbol.FundamentalAtomicSymbol.class org.biojava.bio.symbol.FuzzyLocation.class org.biojava.bio.symbol.FuzzyPointLocation.class org.biojava.bio.symbol.GappedSymbolList.class org.biojava.bio.symbol.HashedAlphabetIndex.class org.biojava.bio.symbol.IllegalAlphabetException.class org.biojava.bio.symbol.IllegalSymbolException.class org.biojava.bio.symbol.IndexedNoAmbPack.class org.biojava.bio.symbol.InfiniteCrossProductAlphabet.class org.biojava.bio.symbol.IntegerAlphabet.class org.biojava.bio.symbol.LinearAlphabetIndex.class org.biojava.bio.symbol.Location.class org.biojava.bio.symbol.LocationComparator.class org.biojava.bio.symbol.LocationTools.class org.biojava.bio.symbol.ManyToOneTranslationTable.class org.biojava.bio.symbol.MergeLocation.class org.biojava.bio.symbol.MotifTools.class org.biojava.bio.symbol.OrderNSymbolList.class org.biojava.bio.symbol.PackedSymbolList.class org.biojava.bio.symbol.PackedSymbolListFactory.class org.biojava.bio.symbol.Packing.class org.biojava.bio.symbol.PackingFactory.class org.biojava.bio.symbol.PointLocation.class org.biojava.bio.symbol.RangeLocation.class org.biojava.bio.symbol.RelabeledAlignment.class org.biojava.bio.symbol.ReverseSymbolList.class org.biojava.bio.symbol.ReversibleTranslationTable.class org.biojava.bio.symbol.SimpleAlignment.class org.biojava.bio.symbol.SimpleAlphabet.class org.biojava.bio.symbol.SimpleAtomicSymbol.class org.biojava.bio.symbol.SimpleBasisSymbol.class org.biojava.bio.symbol.SimpleCodonPref.class org.biojava.bio.symbol.SimpleCrossProductAlphabet.class org.biojava.bio.symbol.SimpleGappedSymbolList.class org.biojava.bio.symbol.SimpleManyToOneTranslationTable.class org.biojava.bio.symbol.SimpleReversibleTranslationTable.class org.biojava.bio.symbol.SimpleSymbol.class org.biojava.bio.symbol.SimpleSymbolList.class org.biojava.bio.symbol.SimpleSymbolListFactory.class org.biojava.bio.symbol.SimpleSymbolPropertyTable.class org.biojava.bio.symbol.SimpleTranslationTable.class org.biojava.bio.symbol.SimpleWobbleDistribution.class org.biojava.bio.symbol.SingletonAlphabet.class org.biojava.bio.symbol.SoftMaskedAlphabet.class org.biojava.bio.symbol.SparseCrossProductAlphabet.class org.biojava.bio.symbol.SubList.class org.biojava.bio.symbol.SuffixTree.class org.biojava.bio.symbol.Symbol.class org.biojava.bio.symbol.SymbolList.class org.biojava.bio.symbol.SymbolListFactory.class org.biojava.bio.symbol.SymbolListViews.class org.biojava.bio.symbol.SymbolPropertyTable.class org.biojava.bio.symbol.TranslatedSymbolList.class org.biojava.bio.symbol.TranslationTable.class org.biojava.bio.symbol.UkkonenSuffixTree.class org.biojava.bio.symbol.WindowedSymbolList.class org.biojava.bio.symbol.WobbleDistribution.class org.biojava.bio.taxa.AbstractTaxon.class org.biojava.bio.taxa.CircularReferenceException.class org.biojava.bio.taxa.EbiFormat.class org.biojava.bio.taxa.SimpleTaxon.class org.biojava.bio.taxa.SimpleTaxonFactory.class org.biojava.bio.taxa.Taxon.class org.biojava.bio.taxa.TaxonFactory.class org.biojava.bio.taxa.TaxonParser.class org.biojava.bio.taxa.WeakTaxon.class org.biojava.bio.taxa.WeakTaxonFactory.class org.biojava.directory.OBDARegistryParser.class org.biojava.directory.ProviderNotFoundException.class org.biojava.directory.Registry.class org.biojava.directory.RegistryConfiguration.class org.biojava.directory.RegistryException.class org.biojava.directory.SequenceDBProvider.class org.biojava.directory.SystemRegistry.class org.biojava.naming.ObdaContext.class org.biojava.naming.ObdaInitialContextFactory.class org.biojava.naming.ObdaUriParser.class org.biojava.ontology.AbstractTerm.class org.biojava.ontology.AlreadyExistsException.class org.biojava.ontology.DefaultOps.class org.biojava.ontology.IntegerOntology.class org.biojava.ontology.InvalidTermException.class org.biojava.ontology.OntoTools.class org.biojava.ontology.Ontology.class org.biojava.ontology.OntologyException.class org.biojava.ontology.OntologyFactory.class org.biojava.ontology.OntologyOps.class org.biojava.ontology.OntologyTerm.class org.biojava.ontology.RemoteTerm.class org.biojava.ontology.Term.class org.biojava.ontology.Triple.class org.biojava.ontology.Variable.class org.biojava.ontology.io.GOParser.class org.biojava.ontology.io.TabDelimParser.class org.biojava.stats.svm.AbstractSVMClassifierModel.class org.biojava.stats.svm.AbstractSVMTarget.class org.biojava.stats.svm.CachingKernel.class org.biojava.stats.svm.DiagonalAddKernel.class org.biojava.stats.svm.DiagonalCachingKernel.class org.biojava.stats.svm.ItemValue.class org.biojava.stats.svm.LinearKernel.class org.biojava.stats.svm.ListSumKernel.class org.biojava.stats.svm.NestedKernel.class org.biojava.stats.svm.NormalizingKernel.class org.biojava.stats.svm.PolynomialKernel.class org.biojava.stats.svm.RadialBaseKernel.class org.biojava.stats.svm.SMORegressionTrainer.class org.biojava.stats.svm.SMOTrainer.class org.biojava.stats.svm.SVMClassifierModel.class org.biojava.stats.svm.SVMKernel.class org.biojava.stats.svm.SVMRegressionModel.class org.biojava.stats.svm.SVMTarget.class org.biojava.stats.svm.SigmoidKernel.class org.biojava.stats.svm.SimpleItemValue.class org.biojava.stats.svm.SimpleSVMClassifierModel.class org.biojava.stats.svm.SimpleSVMTarget.class org.biojava.stats.svm.SparseVector.class org.biojava.stats.svm.TrainingContext.class org.biojava.stats.svm.TrainingEvent.class org.biojava.stats.svm.TrainingListener.class org.biojava.stats.svm.tools.ClassifierExample.class org.biojava.stats.svm.tools.Classify.class org.biojava.stats.svm.tools.SVM_Light.class org.biojava.stats.svm.tools.SuffixTreeKernel.class org.biojava.stats.svm.tools.Train.class org.biojava.stats.svm.tools.TrainRegression.class org.biojava.utils.AbstractChangeable.class org.biojava.utils.ActivityListener.class org.biojava.utils.AssertionFailure.class org.biojava.utils.BeanAsMap.class org.biojava.utils.ChangeAdapter.class org.biojava.utils.ChangeEvent.class org.biojava.utils.ChangeForwarder.class org.biojava.utils.ChangeHub.class org.biojava.utils.ChangeListener.class org.biojava.utils.ChangeSupport.class org.biojava.utils.ChangeType.class org.biojava.utils.ChangeVetoException.class org.biojava.utils.Changeable.class org.biojava.utils.ClassTools.class org.biojava.utils.CommitFailure.class org.biojava.utils.Commitable.class org.biojava.utils.Constants.class org.biojava.utils.ExecRunner.class org.biojava.utils.FileAsList.class org.biojava.utils.IndexedChangeHub.class org.biojava.utils.JDBCConnectionPool.class org.biojava.utils.JDBCPooledDataSource.class org.biojava.utils.ListTools.class org.biojava.utils.MergingIterator.class org.biojava.utils.MergingSet.class org.biojava.utils.ObjectUtil.class org.biojava.utils.OverlayMap.class org.biojava.utils.ParseErrorEvent.class org.biojava.utils.ParseErrorListener.class org.biojava.utils.ParseErrorSource.class org.biojava.utils.ParserException.class org.biojava.utils.ProcessTimeoutException.class org.biojava.utils.ProcessTools.class org.biojava.utils.RepeatedCharSequence.class org.biojava.utils.Services.class org.biojava.utils.SimpleThreadPool.class org.biojava.utils.SingletonList.class org.biojava.utils.SmallMap.class org.biojava.utils.SmallSet.class org.biojava.utils.StaticMemberPlaceHolder.class org.biojava.utils.StreamGobbler.class org.biojava.utils.ThreadPool.class org.biojava.utils.TriState.class org.biojava.utils.TypedProperties.class org.biojava.utils.Unchangeable.class org.biojava.utils.automata.ArrayStateMachineToolkit.class org.biojava.utils.automata.AutomatonException.class org.biojava.utils.automata.DfaBuilder.class org.biojava.utils.automata.FiniteAutomaton.class org.biojava.utils.automata.Nfa.class org.biojava.utils.automata.NfaBuilder.class org.biojava.utils.automata.NfaSubModel.class org.biojava.utils.automata.PatternBlitz.class org.biojava.utils.automata.PatternListener.class org.biojava.utils.automata.PatternMaker.class org.biojava.utils.automata.StateMachineFactory.class org.biojava.utils.automata.StateMachineInstance.class org.biojava.utils.automata.StateMachineToolkit.class org.biojava.utils.cache.Cache.class org.biojava.utils.cache.CacheMap.class org.biojava.utils.cache.CacheReference.class org.biojava.utils.cache.ChangeableCache.class org.biojava.utils.cache.FixedSizeCache.class org.biojava.utils.cache.FixedSizeMap.class org.biojava.utils.cache.KeyedWeakReference.class org.biojava.utils.cache.SoftReferenceCache.class org.biojava.utils.cache.WeakCacheMap.class org.biojava.utils.cache.WeakValueHashMap.class org.biojava.utils.candy.CandyEntry.class org.biojava.utils.candy.CandyException.class org.biojava.utils.candy.CandyFinder.class org.biojava.utils.candy.CandyVocabulary.class org.biojava.utils.io.CachingInputStream.class org.biojava.utils.io.CountedBufferedReader.class org.biojava.utils.io.LargeBuffer.class org.biojava.utils.io.RAF.class org.biojava.utils.io.RandomAccessReader.class org.biojava.utils.io.Seekable.class org.biojava.utils.lsid.Identifiable.class org.biojava.utils.lsid.LifeScienceIdentifier.class org.biojava.utils.lsid.LifeScienceIdentifierParseException.class org.biojava.utils.math.BinarySearch.class org.biojava.utils.math.ComputeObject.class org.biojava.utils.net.URLFactory.class org.biojava.utils.regex.Matcher.class org.biojava.utils.regex.Pattern.class org.biojava.utils.regex.PatternChecker.class org.biojava.utils.regex.PatternFactory.class org.biojava.utils.regex.RegexException.class org.biojava.utils.regex.Search.class org.biojava.utils.stax.BooleanElementHandlerBase.class org.biojava.utils.stax.ByteElementHandlerBase.class org.biojava.utils.stax.CharElementHandlerBase.class org.biojava.utils.stax.DelegationManager.class org.biojava.utils.stax.DoubleElementHandlerBase.class org.biojava.utils.stax.FloatElementHandlerBase.class org.biojava.utils.stax.IntElementHandlerBase.class org.biojava.utils.stax.LongElementHandlerBase.class org.biojava.utils.stax.SAX2StAXAdaptor.class org.biojava.utils.stax.StAXContentHandler.class org.biojava.utils.stax.StAXContentHandlerBase.class org.biojava.utils.stax.StringElementHandlerBase.class org.biojava.utils.walker.Visitor.class org.biojava.utils.walker.Walker.class org.biojava.utils.walker.WalkerFactory.class org.biojava.utils.xml.AppBeanRunner.class org.biojava.utils.xml.AppEntry.class org.biojava.utils.xml.AppException.class org.biojava.utils.xml.FastXMLWriter.class org.biojava.utils.xml.Initializable.class org.biojava.utils.xml.PrettyXMLWriter.class org.biojava.utils.xml.ResourceEntityResolver.class org.biojava.utils.xml.XMLBeans.class org.biojava.utils.xml.XMLWritable.class org.biojava.utils.xml.XMLWriter.class META-INF/services/org.biojava.bio.program.formats.Format META-INF/services/org.biojava.directory.SequenceDBProvider obda/naming/core.xml org/agavexml/agave.dtd org/biojava/bio/molbio/RestrictionEnzymeManager.properties org/biojava/bio/molbio/rebase_common.dat org/biojava/bio/ontology/core.onto org/biojava/bio/program/sax/blastxml/NCBI_BlastOutput.dtd org/biojava/bio/program/sax/blastxml/NCBI_BlastOutput.mod org/biojava/bio/program/sax/blastxml/NCBI_Entity.mod org/biojava/bio/program/unigene/createUnigene.sql org/biojava/bio/proteomics/ProteaseManager.xml org/biojava/bio/seq/TranslationTables.xml org/biojava/bio/seq/io/FeatureQualifier.xml org/biojava/bio/symbol/AlphabetManager.xml org/biojava/bio/symbol/CodonPrefTables.xml org/biojava/bio/symbol/ResidueProperties.xml org/biojava/ontology/colonel-west.pred org/biojava/ontology/core.agregate.pred org/biojava/ontology/core.list.pred org/biojava/ontology/core.onto org/biojava/ontology/core.pred org/biojava/ontology/core.set.pred org/biojava/ontology/ontology.pred org/biojava/utils/query/QueryBuilder.xml                          biojava/biojava-1.4.jar.zip( 2,492 k) Related examples in the same category 1. Download biojava-1.4cvs.jar 2. Download biojava-1.6-bin.jar 3. Download biojava-1.6.jar 4. Download biojava-1.7.1.jar 5. Download biojava-1.7.jar 6. Download biojava-ensembl.jar 7. Download biojava-live.jar