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
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