Download biojava-1.6.jar
biojava/biojava-1.6.jar.zip( 3,448 k)
The download jar file contains the following class files or Java source files.
META-INF/MANIFEST.MF
org.biojava.bibliography.BibRef.class
org.biojava.bibliography.BibRefException.class
org.biojava.bibliography.BibRefQuery.class
org.biojava.bibliography.BibRefSupport.class
org.biojava.bibliography.BiblioArticle.class
org.biojava.bibliography.BiblioBook.class
org.biojava.bibliography.BiblioBookArticle.class
org.biojava.bibliography.BiblioCriterion.class
org.biojava.bibliography.BiblioDescription.class
org.biojava.bibliography.BiblioEntryStatus.class
org.biojava.bibliography.BiblioJournal.class
org.biojava.bibliography.BiblioJournalArticle.class
org.biojava.bibliography.BiblioOrganisation.class
org.biojava.bibliography.BiblioPatent.class
org.biojava.bibliography.BiblioPerson.class
org.biojava.bibliography.BiblioProceeding.class
org.biojava.bibliography.BiblioProvider.class
org.biojava.bibliography.BiblioScope.class
org.biojava.bibliography.BiblioService.class
org.biojava.bibliography.BiblioSubject.class
org.biojava.bibliography.BiblioTechReport.class
org.biojava.bibliography.BiblioThesis.class
org.biojava.bibliography.BiblioWebResource.class
org.biojava.bio.AbstractAnnotation.class
org.biojava.bio.Annotatable.class
org.biojava.bio.Annotation.class
org.biojava.bio.AnnotationChanger.class
org.biojava.bio.AnnotationRenamer.class
org.biojava.bio.AnnotationTools.class
org.biojava.bio.AnnotationType.class
org.biojava.bio.AnyPropertyConstraint.class
org.biojava.bio.BeanAsAnnotation.class
org.biojava.bio.BioError.class
org.biojava.bio.BioException.class
org.biojava.bio.BioRuntimeException.class
org.biojava.bio.CardinalityConstraint.class
org.biojava.bio.CollectionConstraint.class
org.biojava.bio.EcNumber.class
org.biojava.bio.EmptyAnnotation.class
org.biojava.bio.MergeAnnotation.class
org.biojava.bio.NoneCollectionConstraint.class
org.biojava.bio.NonePropertyConstraint.class
org.biojava.bio.OverlayAnnotation.class
org.biojava.bio.PropertyConstraint.class
org.biojava.bio.SimpleAnnotation.class
org.biojava.bio.SmallAnnotation.class
org.biojava.bio.alignment.ARAlignment.class
org.biojava.bio.alignment.AbstractULAlignment.class
org.biojava.bio.alignment.AlignmentElement.class
org.biojava.bio.alignment.EditableAlignment.class
org.biojava.bio.alignment.FlexibleAlignment.class
org.biojava.bio.alignment.IllegalAlignmentEditException.class
org.biojava.bio.alignment.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.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.HetatomImpl.class
org.biojava.bio.structure.Mutator.class
org.biojava.bio.structure.NucleotideImpl.class
org.biojava.bio.structure.PDBHeader.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.BiojavaJmol.class
org.biojava.bio.structure.gui.JMatrixPanel.class
org.biojava.bio.structure.gui.RasmolCommandListener.class
org.biojava.bio.structure.gui.ScaleableMatrixPanel.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.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.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.PDBFilter.class
org.biojava.bio.structure.server.PDBInstallation.class
org.biojava.bio.structure.server.PrepareIndexFile.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.Term.class
org.biojava.ontology.Triple.class
org.biojava.ontology.Variable.class
org.biojava.ontology.io.GOParser.class
org.biojava.ontology.io.TabDelimParser.class
org.biojava.stats.svm.AbstractSVMClassifierModel.class
org.biojava.stats.svm.AbstractSVMTarget.class
org.biojava.stats.svm.CachingKernel.class
org.biojava.stats.svm.DiagonalAddKernel.class
org.biojava.stats.svm.DiagonalCachingKernel.class
org.biojava.stats.svm.ItemValue.class
org.biojava.stats.svm.LinearKernel.class
org.biojava.stats.svm.ListSumKernel.class
org.biojava.stats.svm.NestedKernel.class
org.biojava.stats.svm.NormalizingKernel.class
org.biojava.stats.svm.PolynomialKernel.class
org.biojava.stats.svm.RadialBaseKernel.class
org.biojava.stats.svm.SMORegressionTrainer.class
org.biojava.stats.svm.SMOTrainer.class
org.biojava.stats.svm.SVMClassifierModel.class
org.biojava.stats.svm.SVMKernel.class
org.biojava.stats.svm.SVMRegressionModel.class
org.biojava.stats.svm.SVMTarget.class
org.biojava.stats.svm.SigmoidKernel.class
org.biojava.stats.svm.SimpleItemValue.class
org.biojava.stats.svm.SimpleSVMClassifierModel.class
org.biojava.stats.svm.SimpleSVMTarget.class
org.biojava.stats.svm.SparseVector.class
org.biojava.stats.svm.TrainingContext.class
org.biojava.stats.svm.TrainingEvent.class
org.biojava.stats.svm.TrainingListener.class
org.biojava.stats.svm.tools.ClassifierExample.class
org.biojava.stats.svm.tools.Classify.class
org.biojava.stats.svm.tools.SVM_Light.class
org.biojava.stats.svm.tools.SuffixTreeKernel.class
org.biojava.stats.svm.tools.Train.class
org.biojava.stats.svm.tools.TrainRegression.class
org.biojava.utils.AbstractChangeable.class
org.biojava.utils.ActivityListener.class
org.biojava.utils.AssertionFailure.class
org.biojava.utils.BeanAsMap.class
org.biojava.utils.ChangeAdapter.class
org.biojava.utils.ChangeEvent.class
org.biojava.utils.ChangeForwarder.class
org.biojava.utils.ChangeHub.class
org.biojava.utils.ChangeListener.class
org.biojava.utils.ChangeSupport.class
org.biojava.utils.ChangeType.class
org.biojava.utils.ChangeVetoException.class
org.biojava.utils.Changeable.class
org.biojava.utils.ClassTools.class
org.biojava.utils.CommitFailure.class
org.biojava.utils.Commitable.class
org.biojava.utils.Constants.class
org.biojava.utils.ExecRunner.class
org.biojava.utils.FileAsList.class
org.biojava.utils.IndexedChangeHub.class
org.biojava.utils.JDBCConnectionPool.class
org.biojava.utils.JDBCPooledDataSource.class
org.biojava.utils.ListTools.class
org.biojava.utils.MergingIterator.class
org.biojava.utils.MergingSet.class
org.biojava.utils.ObjectUtil.class
org.biojava.utils.OverlayMap.class
org.biojava.utils.ParseErrorEvent.class
org.biojava.utils.ParseErrorListener.class
org.biojava.utils.ParseErrorSource.class
org.biojava.utils.ParserException.class
org.biojava.utils.ProcessTimeoutException.class
org.biojava.utils.ProcessTools.class
org.biojava.utils.RepeatedCharSequence.class
org.biojava.utils.Services.class
org.biojava.utils.SimpleThreadPool.class
org.biojava.utils.SingletonList.class
org.biojava.utils.SmallMap.class
org.biojava.utils.SmallSet.class
org.biojava.utils.StaticMemberPlaceHolder.class
org.biojava.utils.StreamGobbler.class
org.biojava.utils.ThreadPool.class
org.biojava.utils.TriState.class
org.biojava.utils.TypedProperties.class
org.biojava.utils.Unchangeable.class
org.biojava.utils.automata.ArrayStateMachineToolkit.class
org.biojava.utils.automata.AutomatonException.class
org.biojava.utils.automata.DfaBuilder.class
org.biojava.utils.automata.FiniteAutomaton.class
org.biojava.utils.automata.Nfa.class
org.biojava.utils.automata.NfaBuilder.class
org.biojava.utils.automata.NfaSubModel.class
org.biojava.utils.automata.PatternBlitz.class
org.biojava.utils.automata.PatternListener.class
org.biojava.utils.automata.PatternMaker.class
org.biojava.utils.automata.StateMachineFactory.class
org.biojava.utils.automata.StateMachineInstance.class
org.biojava.utils.automata.StateMachineToolkit.class
org.biojava.utils.cache.Cache.class
org.biojava.utils.cache.CacheMap.class
org.biojava.utils.cache.CacheReference.class
org.biojava.utils.cache.ChangeableCache.class
org.biojava.utils.cache.FixedSizeCache.class
org.biojava.utils.cache.FixedSizeMap.class
org.biojava.utils.cache.KeyedWeakReference.class
org.biojava.utils.cache.SoftReferenceCache.class
org.biojava.utils.cache.WeakCacheMap.class
org.biojava.utils.cache.WeakValueHashMap.class
org.biojava.utils.candy.CandyEntry.class
org.biojava.utils.candy.CandyException.class
org.biojava.utils.candy.CandyFinder.class
org.biojava.utils.candy.CandyVocabulary.class
org.biojava.utils.io.CachingInputStream.class
org.biojava.utils.io.CountedBufferedReader.class
org.biojava.utils.io.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.INSDseqFormat.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
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org/biojava/bibliography/doc-files/BibRefQuery_simple.jpg
org/biojava/bibliography/doc-files/BibRefQuery_soap.jpg
org/biojava/bibliography/doc-files/bibobjects_java.jpg
org/biojava/bibliography/package.html
org/biojava/bio/alignment/package.html
org/biojava/bio/annodb/package.html
org/biojava/bio/chromatogram/graphic/package.html
org/biojava/bio/chromatogram/package.html
org/biojava/bio/dist/package.html
org/biojava/bio/dist/package.inf
org/biojava/bio/dp/onehead/package.inf
org/biojava/bio/dp/package.html
org/biojava/bio/dp/package.inf
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org/biojava/bio/gui/glyph/package.html
org/biojava/bio/gui/package.html
org/biojava/bio/gui/package.inf
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/gui/sequence/package.html
org/biojava/bio/gui/sequence/package.inf
org/biojava/bio/gui/sequence/tracklayout/package.html
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org/biojava/bio/molbio/package.html
org/biojava/bio/molbio/rebase_common.dat
org/biojava/bio/package.html
org/biojava/bio/package.inf
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org/biojava/bio/program/blast2html/package.html
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org/biojava/bio/program/gff/package.inf
org/biojava/bio/program/gff3/package.html
org/biojava/bio/program/hmmer/package.html
org/biojava/bio/program/homologene/package.html
org/biojava/bio/program/indexdb/package.html
org/biojava/bio/program/package.html
org/biojava/bio/program/package.inf
org/biojava/bio/program/phred/package.html
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/sax/blastxml/package.html
org/biojava/bio/program/sax/package.html
org/biojava/bio/program/sax/package.inf
org/biojava/bio/program/scf/package.html
org/biojava/bio/program/ssaha/package.html
org/biojava/bio/program/ssbind/package.html
org/biojava/bio/program/tagvalue/package.html
org/biojava/bio/program/unigene/createUnigene.sql
org/biojava/bio/program/unigene/package.html
org/biojava/bio/program/xff/package.html
org/biojava/bio/program/xff/package.inf
org/biojava/bio/program/xml/package.html
org/biojava/bio/program/xml/package.inf
org/biojava/bio/proteomics/ProteaseManager.xml
org/biojava/bio/proteomics/aaindex/package.html
org/biojava/bio/proteomics/package.html
org/biojava/bio/proteomics/package.inf
org/biojava/bio/search/package.html
org/biojava/bio/search/package.inf
org/biojava/bio/seq/TranslationTables.xml
org/biojava/bio/seq/db/biofetch/package.html
org/biojava/bio/seq/db/biosql/package.html
org/biojava/bio/seq/db/emblcd/package.html
org/biojava/bio/seq/db/flat/package.html
org/biojava/bio/seq/db/package.html
org/biojava/bio/seq/db/package.inf
org/biojava/bio/seq/distributed/package.html
org/biojava/bio/seq/homol/package.html
org/biojava/bio/seq/impl/package.html
org/biojava/bio/seq/impl/package.inf
org/biojava/bio/seq/io/FeatureQualifier.xml
org/biojava/bio/seq/io/agave/package.html
org/biojava/bio/seq/io/filterxml/package.html
org/biojava/bio/seq/io/game/StAXAdditions.note
org/biojava/bio/seq/io/game/package.html
org/biojava/bio/seq/io/game12/package.html
org/biojava/bio/seq/io/package.html
org/biojava/bio/seq/io/package.inf
org/biojava/bio/seq/package.html
org/biojava/bio/seq/package.inf
org/biojava/bio/seq/projection/package.html
org/biojava/bio/structure/align/helper/package.html
org/biojava/bio/structure/align/package.html
org/biojava/bio/structure/align/pairwise/package.html
org/biojava/bio/structure/blosum62.mat
org/biojava/bio/structure/gui/package.html
org/biojava/bio/structure/io/package.html
org/biojava/bio/structure/jama/README.txt
org/biojava/bio/structure/jama/package.html
org/biojava/bio/structure/package.html
org/biojava/bio/structure/server/package.html
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/bio/symbol/package.html
org/biojava/bio/symbol/package.inf
org/biojava/bio/taxa/package.html
org/biojava/directory/package.html
org/biojava/directory/seqdatabase.ini
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/io/package.html
org/biojava/ontology/ontology.pred
org/biojava/ontology/package.html
org/biojava/stats/package.html
org/biojava/stats/svm/package.html
org/biojava/stats/svm/package.inf
org/biojava/stats/svm/tools/package.html
org/biojava/stats/svm/tools/package.inf
org/biojava/utils/cache/package.html
org/biojava/utils/cache/package.inf
org/biojava/utils/candy/package.html
org/biojava/utils/io/package.html
org/biojava/utils/lsid/package.html
org/biojava/utils/math/package.html
org/biojava/utils/net/package.html
org/biojava/utils/package.html
org/biojava/utils/package.inf
org/biojava/utils/process/package.html
org/biojava/utils/regex/package.html
org/biojava/utils/stax/package.html
org/biojava/utils/stax/package.inf
org/biojava/utils/xml/package.html
org/biojava/utils/xml/package.inf
org/biojavax/bio/db/biosql/hsqldb/BioEntry.hbm.xml
org/biojavax/bio/db/biosql/hsqldb/BioEntryRelationship.hbm.xml
org/biojavax/bio/db/biosql/hsqldb/Comment.hbm.xml
org/biojavax/bio/db/biosql/hsqldb/CrossRef.hbm.xml
org/biojavax/bio/db/biosql/hsqldb/DocRef.hbm.xml
org/biojavax/bio/db/biosql/hsqldb/Feature.hbm.xml
org/biojavax/bio/db/biosql/hsqldb/FeatureRelationship.hbm.xml
org/biojavax/bio/db/biosql/hsqldb/Location.hbm.xml
org/biojavax/bio/db/biosql/hsqldb/Namespace.hbm.xml
org/biojavax/bio/db/biosql/hsqldb/Ontology.hbm.xml
org/biojavax/bio/db/biosql/hsqldb/Taxon.hbm.xml
org/biojavax/bio/db/biosql/hsqldb/Term.hbm.xml
org/biojavax/bio/db/biosql/hsqldb/Triple.hbm.xml
org/biojavax/bio/db/biosql/hsqldb/hibernate.cfg.xml
org/biojavax/bio/db/biosql/mysql/BioEntry.hbm.xml
org/biojavax/bio/db/biosql/mysql/BioEntryRelationship.hbm.xml
org/biojavax/bio/db/biosql/mysql/Comment.hbm.xml
org/biojavax/bio/db/biosql/mysql/CrossRef.hbm.xml
org/biojavax/bio/db/biosql/mysql/DocRef.hbm.xml
org/biojavax/bio/db/biosql/mysql/Feature.hbm.xml
org/biojavax/bio/db/biosql/mysql/FeatureRelationship.hbm.xml
org/biojavax/bio/db/biosql/mysql/Location.hbm.xml
org/biojavax/bio/db/biosql/mysql/Namespace.hbm.xml
org/biojavax/bio/db/biosql/mysql/Ontology.hbm.xml
org/biojavax/bio/db/biosql/mysql/Taxon.hbm.xml
org/biojavax/bio/db/biosql/mysql/Term.hbm.xml
org/biojavax/bio/db/biosql/mysql/Triple.hbm.xml
org/biojavax/bio/db/biosql/mysql/hibernate.cfg.xml
org/biojavax/bio/db/biosql/oracle/BioEntry.hbm.xml
org/biojavax/bio/db/biosql/oracle/BioEntryRelationship.hbm.xml
org/biojavax/bio/db/biosql/oracle/Comment.hbm.xml
org/biojavax/bio/db/biosql/oracle/CrossRef.hbm.xml
org/biojavax/bio/db/biosql/oracle/DocRef.hbm.xml
org/biojavax/bio/db/biosql/oracle/Feature.hbm.xml
org/biojavax/bio/db/biosql/oracle/FeatureRelationship.hbm.xml
org/biojavax/bio/db/biosql/oracle/Location.hbm.xml
org/biojavax/bio/db/biosql/oracle/Namespace.hbm.xml
org/biojavax/bio/db/biosql/oracle/Ontology.hbm.xml
org/biojavax/bio/db/biosql/oracle/Taxon.hbm.xml
org/biojavax/bio/db/biosql/oracle/Term.hbm.xml
org/biojavax/bio/db/biosql/oracle/Triple.hbm.xml
org/biojavax/bio/db/biosql/oracle/hibernate.cfg.xml
org/biojavax/bio/db/biosql/package.html
org/biojavax/bio/db/biosql/pg/BioEntry.hbm.xml
org/biojavax/bio/db/biosql/pg/BioEntryRelationship.hbm.xml
org/biojavax/bio/db/biosql/pg/Comment.hbm.xml
org/biojavax/bio/db/biosql/pg/CrossRef.hbm.xml
org/biojavax/bio/db/biosql/pg/DocRef.hbm.xml
org/biojavax/bio/db/biosql/pg/Feature.hbm.xml
org/biojavax/bio/db/biosql/pg/FeatureRelationship.hbm.xml
org/biojavax/bio/db/biosql/pg/Location.hbm.xml
org/biojavax/bio/db/biosql/pg/Namespace.hbm.xml
org/biojavax/bio/db/biosql/pg/Ontology.hbm.xml
org/biojavax/bio/db/biosql/pg/Taxon.hbm.xml
org/biojavax/bio/db/biosql/pg/Term.hbm.xml
org/biojavax/bio/db/biosql/pg/Triple.hbm.xml
org/biojavax/bio/db/biosql/pg/hibernate.cfg.xml
org/biojavax/bio/db/ncbi/package.html
org/biojavax/bio/db/package.html
org/biojavax/bio/package.html
org/biojavax/bio/phylo/io/nexus/package.html
org/biojavax/bio/phylo/io/package.html
org/biojavax/bio/phylo/io/phylip/package.html
org/biojavax/bio/phylo/package.html
org/biojavax/bio/seq/io/package.html
org/biojavax/bio/seq/package.html
org/biojavax/bio/taxa/package.html
org/biojavax/ga/exception/package.html
org/biojavax/ga/functions/package.html
org/biojavax/ga/impl/package.html
org/biojavax/ga/package.html
org/biojavax/ga/util/package.html
org/biojavax/ontology/package.html
org/biojavax/package.html
org/biojavax/utils/package.html
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