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Download biojava-1.7.jar : biojava « b « Jar File Download
Download biojava-1.7.jar
biojava/biojava-1.7.jar.zip( 3,237 k)
The download jar file contains the following class files or Java source files.
META-INF/MANIFEST.MF META-INF/services/org.biojava.bio.program.formats.Format META-INF/services/org.biojava.directory.SequenceDBProvider obda/naming/core.xml 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.NeedlemanWunsch.class org.biojava.bio.alignment.QualitativeAlignment.class org.biojava.bio.alignment.SequenceAlignment.class org.biojava.bio.alignment.SimpleAlignmentElement.class org.biojava.bio.alignment.SmithWaterman.class org.biojava.bio.alignment.SubstitutionMatrix.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.glyph.ArrowGlyph.class org.biojava.bio.gui.glyph.Glyph.class org.biojava.bio.gui.glyph.GlyphUtils.class org.biojava.bio.gui.glyph.HelixGlyph.class org.biojava.bio.gui.glyph.RectangleGlyph.class org.biojava.bio.gui.glyph.TurnGlyph.class org.biojava.bio.gui.glyph.TwoHeadedArrowGlyph.class org.biojava.bio.gui.sequence.AbiTraceRenderer.class org.biojava.bio.gui.sequence.AbstractBeadRenderer.class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer.class org.biojava.bio.gui.sequence.AlignmentRenderer.class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer.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.FeatureSource.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.GlyphFeatureRenderer.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.OffsetRulerRenderer.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.PeptideDigestRenderer.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.SecondaryStructureFeatureRenderer.class org.biojava.bio.gui.sequence.SequencePanel.class org.biojava.bio.gui.sequence.SequencePanelWrapper.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.gui.sequence.tracklayout.SimpleTrackLayout.class org.biojava.bio.gui.sequence.tracklayout.TrackLayout.class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout.class org.biojava.bio.molbio.Composition.class org.biojava.bio.molbio.DNAComposition.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.proteomics.aaindex.AAindex.class org.biojava.bio.proteomics.aaindex.AAindexStreamReader.class org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.class org.biojava.bio.proteomics.aaindex.SymbolPropertyTableDB.class org.biojava.bio.proteomics.aaindex.SymbolPropertyTableIterator.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.ByLocationMinMaxComparator.class org.biojava.bio.seq.ByLocationMinMaxFeatureComparator.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.AlternateTokenization.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.SubIntegerTokenization.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.Author.class org.biojava.bio.structure.Calc.class org.biojava.bio.structure.Chain.class org.biojava.bio.structure.ChainImpl.class org.biojava.bio.structure.Compound.class org.biojava.bio.structure.DBRef.class org.biojava.bio.structure.Group.class org.biojava.bio.structure.GroupIterator.class org.biojava.bio.structure.GroupType.class org.biojava.bio.structure.HetatomImpl.class org.biojava.bio.structure.JournalArticle.class org.biojava.bio.structure.Mutator.class org.biojava.bio.structure.NucleotideImpl.class org.biojava.bio.structure.PDBHeader.class org.biojava.bio.structure.PDBRecord.class org.biojava.bio.structure.SSBond.class org.biojava.bio.structure.SVDSuperimposer.class org.biojava.bio.structure.StandardAminoAcid.class org.biojava.bio.structure.Structure.class org.biojava.bio.structure.StructureException.class org.biojava.bio.structure.StructureImpl.class org.biojava.bio.structure.StructureTools.class org.biojava.bio.structure.align.ClusterAltAligs.class org.biojava.bio.structure.align.StrucAligParameters.class org.biojava.bio.structure.align.StructurePairAligner.class org.biojava.bio.structure.align.helper.AligMatEl.class org.biojava.bio.structure.align.helper.AlignTools.class org.biojava.bio.structure.align.helper.GapArray.class org.biojava.bio.structure.align.helper.IndexPair.class org.biojava.bio.structure.align.helper.JointFragments.class org.biojava.bio.structure.align.pairwise.AligNPE.class org.biojava.bio.structure.align.pairwise.Alignable.class org.biojava.bio.structure.align.pairwise.AltAligComparator.class org.biojava.bio.structure.align.pairwise.AlternativeAlignment.class org.biojava.bio.structure.align.pairwise.FragmentJoiner.class org.biojava.bio.structure.align.pairwise.FragmentPair.class org.biojava.bio.structure.align.pairwise.Gotoh.class org.biojava.bio.structure.align.pairwise.JointFragmentsComparator.class org.biojava.bio.structure.align.pairwise.StrCompAlignment.class org.biojava.bio.structure.gui.AlignmentGui.class org.biojava.bio.structure.gui.BiojavaJmol.class org.biojava.bio.structure.gui.JMatrixPanel.class org.biojava.bio.structure.gui.ProgressThreadDrawer.class org.biojava.bio.structure.gui.RasmolCommandListener.class org.biojava.bio.structure.gui.ScaleableMatrixPanel.class org.biojava.bio.structure.gui.SequenceDisplay.class org.biojava.bio.structure.gui.events.AlignmentPositionListener.class org.biojava.bio.structure.gui.events.JmolAlignedPositionListener.class org.biojava.bio.structure.gui.util.AlignedPosition.class org.biojava.bio.structure.gui.util.AlignmentCalc.class org.biojava.bio.structure.gui.util.AlternativeAlignmentFrame.class org.biojava.bio.structure.gui.util.ChooseAction.class org.biojava.bio.structure.gui.util.ChooseDirAction.class org.biojava.bio.structure.gui.util.CoordManager.class org.biojava.bio.structure.gui.util.JButtonTableCellRenderer.class org.biojava.bio.structure.gui.util.JTableDataButtonModel.class org.biojava.bio.structure.gui.util.JTableMouseButtonListener.class org.biojava.bio.structure.gui.util.MatrixMouseListener.class org.biojava.bio.structure.gui.util.MenuCreator.class org.biojava.bio.structure.gui.util.MyButtonMouseListener.class org.biojava.bio.structure.gui.util.PDBDirPanel.class org.biojava.bio.structure.gui.util.PDBServerPanel.class org.biojava.bio.structure.gui.util.PDBUploadPanel.class org.biojava.bio.structure.gui.util.SequenceMouseListener.class org.biojava.bio.structure.gui.util.SequenceScalePanel.class org.biojava.bio.structure.gui.util.StructurePairSelector.class org.biojava.bio.structure.io.CAConverter.class org.biojava.bio.structure.io.DASStructureClient.class org.biojava.bio.structure.io.FileConvert.class org.biojava.bio.structure.io.MMCIFFileReader.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.SeqRes2AtomAligner.class org.biojava.bio.structure.io.StructureIO.class org.biojava.bio.structure.io.StructureIOFile.class org.biojava.bio.structure.io.mmcif.ChemCompConsumer.class org.biojava.bio.structure.io.mmcif.ChemicalComponentDictionary.class org.biojava.bio.structure.io.mmcif.MMcifConsumer.class org.biojava.bio.structure.io.mmcif.MMcifParser.class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer.class org.biojava.bio.structure.io.mmcif.SimpleMMcifParser.class org.biojava.bio.structure.io.mmcif.chem.ChemCompTools.class org.biojava.bio.structure.io.mmcif.chem.PolymerType.class org.biojava.bio.structure.io.mmcif.chem.ResidueType.class org.biojava.bio.structure.io.mmcif.model.AbstractBean.class org.biojava.bio.structure.io.mmcif.model.AtomSite.class org.biojava.bio.structure.io.mmcif.model.ChemComp.class org.biojava.bio.structure.io.mmcif.model.DatabasePDBremark.class org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev.class org.biojava.bio.structure.io.mmcif.model.Entity.class org.biojava.bio.structure.io.mmcif.model.EntityPolySeq.class org.biojava.bio.structure.io.mmcif.model.Exptl.class org.biojava.bio.structure.io.mmcif.model.PdbxEntityNonPoly.class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme.class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme.class org.biojava.bio.structure.io.mmcif.model.Refine.class org.biojava.bio.structure.io.mmcif.model.Struct.class org.biojava.bio.structure.io.mmcif.model.StructAsym.class org.biojava.bio.structure.io.mmcif.model.StructKeywords.class org.biojava.bio.structure.io.mmcif.model.StructRef.class org.biojava.bio.structure.io.mmcif.model.StructRefSeq.class org.biojava.bio.structure.jama.CholeskyDecomposition.class org.biojava.bio.structure.jama.EigenvalueDecomposition.class org.biojava.bio.structure.jama.LUDecomposition.class org.biojava.bio.structure.jama.Maths.class org.biojava.bio.structure.jama.Matrix.class org.biojava.bio.structure.jama.QRDecomposition.class org.biojava.bio.structure.jama.SingularValueDecomposition.class org.biojava.bio.structure.server.DemoStructureServer.class org.biojava.bio.structure.server.FlatFileInstallation.class org.biojava.bio.structure.server.MMCIFFileInstallation.class org.biojava.bio.structure.server.PDBFilter.class org.biojava.bio.structure.server.PDBInstallation.class org.biojava.bio.structure.server.PrepareIndexFile.class org.biojava.bio.structure.server.PrepareMMcifIndexFile.class org.biojava.bio.structure.server.SimpleStructureServer.class org.biojava.bio.structure.server.StructureEvent.class org.biojava.bio.structure.server.StructureEventImpl.class org.biojava.bio.structure.server.StructureFetcherRunnable.class org.biojava.bio.structure.server.StructureListener.class org.biojava.bio.structure.server.StructureServer.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.SimpleGeneticCodeTable.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.Synonym.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.OboParser.class org.biojava.ontology.io.TabDelimParser.class org.biojava.ontology.obo.NestedValue.class org.biojava.ontology.obo.OboFileEventListener.class org.biojava.ontology.obo.OboFileHandler.class org.biojava.ontology.obo.OboFileParser.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.InputStreamProvider.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.io.UncompressInputStream.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.process.ExternalProcess.class org.biojava.utils.process.InputHandler.class org.biojava.utils.process.OutputHandler.class org.biojava.utils.process.ReaderInputHandler.class org.biojava.utils.process.ReaderWriterPipe.class org.biojava.utils.process.SimpleInputHandler.class org.biojava.utils.process.SimpleOutputHandler.class org.biojava.utils.process.StreamPipe.class org.biojava.utils.process.WriterOutputHandler.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 org.biojavax.Comment.class org.biojavax.CrossRef.class org.biojavax.CrossReferenceResolutionException.class org.biojavax.CrossReferenceResolver.class org.biojavax.DocRef.class org.biojavax.DocRefAuthor.class org.biojavax.DummyCrossReferenceResolver.class org.biojavax.EmptyRichAnnotation.class org.biojavax.Namespace.class org.biojavax.Note.class org.biojavax.RankedCrossRef.class org.biojavax.RankedCrossRefable.class org.biojavax.RankedDocRef.class org.biojavax.RichAnnotatable.class org.biojavax.RichAnnotation.class org.biojavax.RichObjectBuilder.class org.biojavax.RichObjectFactory.class org.biojavax.SimpleComment.class org.biojavax.SimpleCrossRef.class org.biojavax.SimpleDocRef.class org.biojavax.SimpleDocRefAuthor.class org.biojavax.SimpleNamespace.class org.biojavax.SimpleNote.class org.biojavax.SimpleRankedCrossRef.class org.biojavax.SimpleRankedDocRef.class org.biojavax.SimpleRichAnnotation.class org.biojavax.SimpleRichObjectBuilder.class org.biojavax.bio.BioEntry.class org.biojavax.bio.BioEntryIterator.class org.biojavax.bio.BioEntryRelationship.class org.biojavax.bio.SimpleBioEntry.class org.biojavax.bio.SimpleBioEntryRelationship.class org.biojavax.bio.db.AbstractBioEntryDB.class org.biojavax.bio.db.AbstractRichSequenceDB.class org.biojavax.bio.db.BioEntryDB.class org.biojavax.bio.db.BioEntryDBLite.class org.biojavax.bio.db.HashBioEntryDB.class org.biojavax.bio.db.HashRichSequenceDB.class org.biojavax.bio.db.RichSequenceDB.class org.biojavax.bio.db.RichSequenceDBLite.class org.biojavax.bio.db.biosql.BioSQLAcceptAllFilter.class org.biojavax.bio.db.biosql.BioSQLAcceptNoneFilter.class org.biojavax.bio.db.biosql.BioSQLBioEntryDB.class org.biojavax.bio.db.biosql.BioSQLCrossReferenceResolver.class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.class org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder.class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB.class org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler.class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB.class org.biojavax.bio.phylo.DistanceBasedTreeMethod.class org.biojavax.bio.phylo.MultipleHitCorrection.class org.biojavax.bio.phylo.ParsimonyTreeMethod.class org.biojavax.bio.phylo.io.nexus.CharactersBlock.class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder.class org.biojavax.bio.phylo.io.nexus.CharactersBlockListener.class org.biojavax.bio.phylo.io.nexus.CharactersBlockParser.class org.biojavax.bio.phylo.io.nexus.DataBlock.class org.biojavax.bio.phylo.io.nexus.DataBlockBuilder.class org.biojavax.bio.phylo.io.nexus.DataBlockListener.class org.biojavax.bio.phylo.io.nexus.DataBlockParser.class org.biojavax.bio.phylo.io.nexus.DistancesBlock.class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder.class org.biojavax.bio.phylo.io.nexus.DistancesBlockListener.class org.biojavax.bio.phylo.io.nexus.DistancesBlockParser.class org.biojavax.bio.phylo.io.nexus.NexusBlock.class org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder.class org.biojavax.bio.phylo.io.nexus.NexusBlockListener.class org.biojavax.bio.phylo.io.nexus.NexusBlockParser.class org.biojavax.bio.phylo.io.nexus.NexusComment.class org.biojavax.bio.phylo.io.nexus.NexusFile.class org.biojavax.bio.phylo.io.nexus.NexusFileBuilder.class org.biojavax.bio.phylo.io.nexus.NexusFileFormat.class org.biojavax.bio.phylo.io.nexus.NexusFileListener.class org.biojavax.bio.phylo.io.nexus.NexusObject.class org.biojavax.bio.phylo.io.nexus.TaxaBlock.class org.biojavax.bio.phylo.io.nexus.TaxaBlockBuilder.class org.biojavax.bio.phylo.io.nexus.TaxaBlockListener.class org.biojavax.bio.phylo.io.nexus.TaxaBlockParser.class org.biojavax.bio.phylo.io.nexus.TreesBlock.class org.biojavax.bio.phylo.io.nexus.TreesBlockBuilder.class org.biojavax.bio.phylo.io.nexus.TreesBlockListener.class org.biojavax.bio.phylo.io.nexus.TreesBlockParser.class org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder.class org.biojavax.bio.phylo.io.phylip.PHYLIPFileFormat.class org.biojavax.bio.phylo.io.phylip.PHYLIPFileListener.class org.biojavax.bio.seq.CompoundRichLocation.class org.biojavax.bio.seq.DummyRichSequenceHandler.class org.biojavax.bio.seq.EmptyRichLocation.class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList.class org.biojavax.bio.seq.MultiSourceCompoundRichLocation.class org.biojavax.bio.seq.Position.class org.biojavax.bio.seq.PositionResolver.class org.biojavax.bio.seq.RichFeature.class org.biojavax.bio.seq.RichFeatureRelationship.class org.biojavax.bio.seq.RichFeatureRelationshipHolder.class org.biojavax.bio.seq.RichLocation.class org.biojavax.bio.seq.RichSequence.class org.biojavax.bio.seq.RichSequenceHandler.class org.biojavax.bio.seq.RichSequenceIterator.class org.biojavax.bio.seq.SimplePosition.class org.biojavax.bio.seq.SimpleRichFeature.class org.biojavax.bio.seq.SimpleRichFeatureRelationship.class org.biojavax.bio.seq.SimpleRichLocation.class org.biojavax.bio.seq.SimpleRichSequence.class org.biojavax.bio.seq.ThinRichSequence.class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener.class org.biojavax.bio.seq.io.EMBLFormat.class org.biojavax.bio.seq.io.EMBLxmlFormat.class org.biojavax.bio.seq.io.FastaFormat.class org.biojavax.bio.seq.io.FastaHeader.class org.biojavax.bio.seq.io.GenbankFormat.class org.biojavax.bio.seq.io.GenbankLocationParser.class org.biojavax.bio.seq.io.HashedFastaIterator.class org.biojavax.bio.seq.io.INSDseqFormat.class org.biojavax.bio.seq.io.MyRichSeqIOListener.class org.biojavax.bio.seq.io.RichSeqIOAdapter.class org.biojavax.bio.seq.io.RichSeqIOListener.class org.biojavax.bio.seq.io.RichSequenceBuilder.class org.biojavax.bio.seq.io.RichSequenceBuilderFactory.class org.biojavax.bio.seq.io.RichSequenceFormat.class org.biojavax.bio.seq.io.RichStreamReader.class org.biojavax.bio.seq.io.RichStreamWriter.class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder.class org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory.class org.biojavax.bio.seq.io.UniProtCommentParser.class org.biojavax.bio.seq.io.UniProtFormat.class org.biojavax.bio.seq.io.UniProtLocationParser.class org.biojavax.bio.seq.io.UniProtXMLFormat.class org.biojavax.bio.taxa.NCBITaxon.class org.biojavax.bio.taxa.SimpleNCBITaxon.class org.biojavax.bio.taxa.SimpleNCBITaxonName.class org.biojavax.bio.taxa.io.NCBITaxonomyLoader.class org.biojavax.bio.taxa.io.SimpleNCBITaxonomyLoader.class org.biojavax.ga.GAStoppingCriteria.class org.biojavax.ga.GeneticAlgorithm.class org.biojavax.ga.Organism.class org.biojavax.ga.Population.class org.biojavax.ga.exception.IllegalOrganismException.class org.biojavax.ga.functions.AbstractCrossOverFunction.class org.biojavax.ga.functions.AbstractMutationFunction.class org.biojavax.ga.functions.CrossOverFunction.class org.biojavax.ga.functions.FitnessFunction.class org.biojavax.ga.functions.GACross.class org.biojavax.ga.functions.GACrossResult.class org.biojavax.ga.functions.MutationFunction.class org.biojavax.ga.functions.OrderCrossover.class org.biojavax.ga.functions.ProportionalSelection.class org.biojavax.ga.functions.SelectionFunction.class org.biojavax.ga.functions.SimpleCrossOverFunction.class org.biojavax.ga.functions.SimpleGACrossResult.class org.biojavax.ga.functions.SimpleMutationFunction.class org.biojavax.ga.functions.SwapMutationFunction.class org.biojavax.ga.functions.TournamentSelection.class org.biojavax.ga.impl.AbstractGeneticAlgorithm.class org.biojavax.ga.impl.AbstractOrganism.class org.biojavax.ga.impl.AbstractPopulation.class org.biojavax.ga.impl.SimpleGeneticAlgorithm.class org.biojavax.ga.impl.SimpleOrganism.class org.biojavax.ga.impl.SimplePopulation.class org.biojavax.ga.util.GATools.class org.biojavax.ga.util.WeightedSet.class org.biojavax.ontology.ComparableOntology.class org.biojavax.ontology.ComparableTerm.class org.biojavax.ontology.ComparableTriple.class org.biojavax.ontology.SimpleComparableOntology.class org.biojavax.ontology.SimpleComparableTerm.class org.biojavax.ontology.SimpleComparableTriple.class org.biojavax.utils.CRC64Checksum.class org.biojavax.utils.StringTools.class org.biojavax.utils.XMLTools.class org/biojava/bio/gui/sequence/NoDesc.html org/biojava/bio/gui/sequence/NoSample.txt org/biojava/bio/gui/sequence/aprDesc.html org/biojava/bio/gui/sequence/aprExamp.apr org/biojava/bio/gui/sequence/fastaDesc.html org/biojava/bio/gui/sequence/fastaExamp.fasta org/biojava/bio/gui/sequence/msfDesc.html org/biojava/bio/gui/sequence/msfExamp.msf org/biojava/bio/molbio/RestrictionEnzymeManager.properties org/biojava/bio/molbio/rebase_common.dat 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/structure/blosum62.mat org/biojava/bio/structure/standardaminos.pdb 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
Related examples in the same category
| 1. | Download biojava-1.4.jar | | |
| 2. | Download biojava-1.6-bin.jar | | |
| 3. | Download biojava-1.6.jar | | |
| 4. | Download biojava-1.7.1.jar | | |
| 5. | Download biojava-ensembl.jar | | |
| 6. | Download biojava-live.jar | |