BioJava contains 1557 classes/interfaces, of which 182 (11.7%) exist in BioSharp.
Of the classes that have been ported, not all are complete, as shown in the following table.
| BioJava | BioSharp | Status |
| org.biojava.bibliography | BioSharp.Core.Bibliography | |
| | BiblioArticle | | BiblioArticle | NotPorted |
| | BiblioBook | | BiblioBook | NotPorted |
| | BiblioBookArticle | | BiblioBookArticle | NotPorted |
| | BiblioCriterion | | BiblioCriterion | NotPorted |
| | BiblioDescription | | BiblioDescription | NotPorted |
| | BiblioEntryStatus | | BiblioEntryStatus | NotPorted |
| | BiblioJournal | | BiblioJournal | NotPorted |
| | BiblioJournalArticle | | BiblioJournalArticle | NotPorted |
| | BiblioOrganisation | | BiblioOrganisation | NotPorted |
| | BiblioPatent | | BiblioPatent | NotPorted |
| | BiblioPerson | | BiblioPerson | NotPorted |
| | BiblioProceeding | | BiblioProceeding | NotPorted |
| | BiblioProvider | | BiblioProvider | NotPorted |
| | BiblioScope | | BiblioScope | NotPorted |
| | BiblioService | | BiblioService | NotPorted |
| | BiblioSubject | | BiblioSubject | NotPorted |
| | BiblioTechReport | | BiblioTechReport | NotPorted |
| | BiblioThesis | | BiblioThesis | NotPorted |
| | BiblioWebResource | | BiblioWebResource | NotPorted |
| | BibRef | | BibRef | NotPorted |
| | BibRefException | | BibRefException | NotPorted |
| | BibRefQuery | | IBibRefQuery | NotPorted |
| | BibRefSupport | | IBibRefSupport | NotPorted |
| org.biojava.bio | BioSharp.Core.Bio | |
| | AbstractAnnotation | | AbstractAnnotation | Complete |
| | Annotatable | | IAnnotatable | Complete |
| | Annotatable.AnnotationForwarder | | Annotatable.AnnotationForwarder | Complete |
| | Annotation | | IAnnotation | Complete |
| | AnnotationChanger | | AnnotationChanger | NotPorted |
| | AnnotationRenamer | | AnnotationRenamer | NotPorted |
| | AnnotationTools | | AnnotationTools | NotPorted |
| | AnnotationType | | IAnnotationType | NotPorted |
| | AnnotationType.Abstract | | AnnotationType.Abstract | NotPorted |
| | AnnotationType.Impl | | AnnotationType.Impl | NotPorted |
| | BeanAsAnnotation | | BeanAsAnnotation | NotPorted |
| | BioError | | BioError | Partial |
| | BioException | | BioException | Complete |
| | BioRuntimeException | | BioRuntimeException | Partial |
| | CardinalityConstraint | | CardinalityConstraint | NotPorted |
| | CollectionConstraint | | ICollectionConstraint | NotPorted |
| | CollectionConstraint.AllValuesIn | | CollectionConstraint.AllValuesIn | NotPorted |
| | CollectionConstraint.And | | CollectionConstraint.And | NotPorted |
| | CollectionConstraint.Contains | | CollectionConstraint.Contains | NotPorted |
| | CollectionConstraint.Or | | CollectionConstraint.Or | NotPorted |
| | EcNumber | | IEcNumber | NotPorted |
| | EcNumber.Impl | | EcNumber.Impl | NotPorted |
| | MergeAnnotation | | MergeAnnotation | NotPorted |
| | OverlayAnnotation | | OverlayAnnotation | Stub |
| | PropertyConstraint | | IPropertyConstraint | NotPorted |
| | PropertyConstraint.And | | PropertyConstraint.And | NotPorted |
| | PropertyConstraint.ByAnnotationType | | PropertyConstraint.ByAnnotationType | NotPorted |
| | PropertyConstraint.ByClass | | PropertyConstraint.ByClass | NotPorted |
| | PropertyConstraint.Enumeration | | PropertyConstraint.Enumeration | NotPorted |
| | PropertyConstraint.ExactValue | | PropertyConstraint.ExactValue | NotPorted |
| | PropertyConstraint.Or | | PropertyConstraint.Or | NotPorted |
| | SimpleAnnotation | | SimpleAnnotation | Partial |
| | SmallAnnotation | | SmallAnnotation | Partial |
| org.biojava.bio.alignment | BioSharp.Core.Bio.Alignment | |
| | AbstractULAlignment | | AbstractULAlignment | NotPorted |
| | AlignmentElement | | IAlignmentElement | NotPorted |
| | ARAlignment | | IARAlignment | NotPorted |
| | EditableAlignment | | IEditableAlignment | NotPorted |
| | FlexibleAlignment | | FlexibleAlignment | NotPorted |
| | IllegalAlignmentEditException | | IllegalAlignmentEditException | NotPorted |
| | NeedlemanWunsch | | NeedlemanWunsch | Partial |
| | QualitativeAlignment | | IQualitativeAlignment | NotPorted |
| | SequenceAlignment | | SequenceAlignment | Stub |
| | SimpleAlignmentElement | | SimpleAlignmentElement | NotPorted |
| | SmithWaterman | | SmithWaterman | NotPorted |
| | SubstitutionMatrix | | SubstitutionMatrix | Partial |
| | UnequalLengthAlignment | | IUnequalLengthAlignment | NotPorted |
| org.biojava.bio.annodb | BioSharp.Core.Bio.Annodb | |
| | AnnotationDB | | IAnnotationDB | NotPorted |
| | IndexedAnnotationDB | | IndexedAnnotationDB | NotPorted |
| | IndexedAnnotationDB.ParserListenerFactory | | IndexedAnnotationDB.IParserListenerFactory | NotPorted |
| | IndexedAnnotationDB.StaticMethodRPFactory | | IndexedAnnotationDB.StaticMethodRPFactory | NotPorted |
| | LazyFilteredAnnotationDB | | LazyFilteredAnnotationDB | NotPorted |
| | LazySearchedAnnotationDB | | LazySearchedAnnotationDB | NotPorted |
| | MergingAnnotationDB | | MergingAnnotationDB | NotPorted |
| | SimpleAnnotationDB | | SimpleAnnotationDB | NotPorted |
| org.biojava.bio.chromatogram | BioSharp.Core.Bio.Chromatogram | |
| | AbstractChromatogram | | AbstractChromatogram | NotPorted |
| | Chromatogram | | IChromatogram | NotPorted |
| | ChromatogramFactory | | ChromatogramFactory | NotPorted |
| | ChromatogramTools | | ChromatogramTools | NotPorted |
| | SimpleChromatogram | | SimpleChromatogram | NotPorted |
| | UnsupportedChromatogramFormatException | | UnsupportedChromatogramFormatException | NotPorted |
| org.biojava.bio.chromatogram.graphic | BioSharp.Core.Bio.Chromatogram.Graphic | |
| | ChromatogramGraphic | | ChromatogramGraphic | NotPorted |
| | ChromatogramGraphic.Option | | ChromatogramGraphic.Option | NotPorted |
| | ChromatogramNonlinearScaler | | IChromatogramNonlinearScaler | NotPorted |
| | ChromatogramNonlinearScaler.Identity | | ChromatogramNonlinearScaler.Identity | NotPorted |
| | FixedBaseWidthScaler | | FixedBaseWidthScaler | NotPorted |
| org.biojava.bio.dist | BioSharp.Core.Bio.Dist | |
| | AbstractDistribution | | AbstractDistribution | NotPorted |
| | AbstractOrderNDistribution | | AbstractOrderNDistribution | NotPorted |
| | Count | | ICount | NotPorted |
| | Distribution | | IDistribution | NotPorted |
| | Distribution.NullModelForwarder | | Distribution.NullModelForwarder | NotPorted |
| | DistributionFactory | | IDistributionFactory | NotPorted |
| | DistributionFactory.DefaultDistributionFactory | | DistributionFactory.DefaultDistributionFactory | NotPorted |
| | DistributionTools | | DistributionTools | NotPorted |
| | DistributionTrainer | | IDistributionTrainer | NotPorted |
| | DistributionTrainerContext | | IDistributionTrainerContext | NotPorted |
| | GapDistribution | | GapDistribution | NotPorted |
| | IgnoreCountsTrainer | | IgnoreCountsTrainer | NotPorted |
| | IndexedCount | | IndexedCount | NotPorted |
| | OrderNDistribution | | IOrderNDistribution | NotPorted |
| | OrderNDistributionFactory | | OrderNDistributionFactory | NotPorted |
| | PairDistribution | | PairDistribution | NotPorted |
| | SimpleDistribution | | SimpleDistribution | NotPorted |
| | SimpleDistributionTrainer | | SimpleDistributionTrainer | NotPorted |
| | SimpleDistributionTrainerContext | | SimpleDistributionTrainerContext | NotPorted |
| | TranslatedDistribution | | TranslatedDistribution | NotPorted |
| | UniformDistribution | | UniformDistribution | NotPorted |
| | UntrainableDistribution | | UntrainableDistribution | NotPorted |
| | XMLDistributionReader | | XMLDistributionReader | NotPorted |
| | XMLDistributionWriter | | XMLDistributionWriter | NotPorted |
| org.biojava.bio.dp | BioSharp.Core.Bio.Dp | |
| | AbstractTrainer | | AbstractTrainer | NotPorted |
| | BackPointer | | BackPointer | NotPorted |
| | BaumWelchSampler | | BaumWelchSampler | NotPorted |
| | BaumWelchTrainer | | BaumWelchTrainer | NotPorted |
| | DotState | | IDotState | NotPorted |
| | DP | | DP | NotPorted |
| | DP.ReverseIterator | | DP.ReverseIterator | NotPorted |
| | DPFactory | | IDPFactory | NotPorted |
| | DPFactory.DefaultFactory | | DPFactory.DefaultFactory | NotPorted |
| | DPMatrix | | IDPMatrix | NotPorted |
| | EmissionState | | IEmissionState | NotPorted |
| | HMMTrainer | | IHMMTrainer | NotPorted |
| | IllegalTransitionException | | IllegalTransitionException | NotPorted |
| | MagicalState | | MagicalState | NotPorted |
| | MarkovModel | | IMarkovModel | NotPorted |
| | ModelInState | | IModelInState | NotPorted |
| | ModelTrainer | | IModelTrainer | NotPorted |
| | ProfileHMM | | ProfileHMM | NotPorted |
| | ScoreType | | IScoreType | NotPorted |
| | ScoreType.NullModel | | ScoreType.NullModel | NotPorted |
| | ScoreType.Odds | | ScoreType.Odds | NotPorted |
| | ScoreType.Probability | | ScoreType.Probability | NotPorted |
| | SimpleDotState | | SimpleDotState | NotPorted |
| | SimpleEmissionState | | SimpleEmissionState | NotPorted |
| | SimpleHMMTrainer | | SimpleHMMTrainer | NotPorted |
| | SimpleMarkovModel | | SimpleMarkovModel | NotPorted |
| | SimpleModelInState | | SimpleModelInState | NotPorted |
| | SimpleModelTrainer | | SimpleModelTrainer | NotPorted |
| | SimpleStatePath | | SimpleStatePath | NotPorted |
| | SimpleWeightMatrix | | SimpleWeightMatrix | NotPorted |
| | State | | IState | NotPorted |
| | StatePath | | IStatePath | NotPorted |
| | StoppingCriteria | | IStoppingCriteria | NotPorted |
| | Trainable | | ITrainable | NotPorted |
| | TrainerTransition | | TrainerTransition | NotPorted |
| | TrainingAlgorithm | | ITrainingAlgorithm | NotPorted |
| | Transition | | Transition | NotPorted |
| | TransitionTrainer | | ITransitionTrainer | NotPorted |
| | WeightMatrix | | IWeightMatrix | NotPorted |
| | WeightMatrixAnnotator | | WeightMatrixAnnotator | NotPorted |
| | WMAsMM | | WMAsMM | NotPorted |
| | XmlMarkovModel | | XmlMarkovModel | NotPorted |
| org.biojava.bio.dp.onehead | BioSharp.Core.Bio.Dp.Onehead | |
| | DPCursor | | IDPCursor | NotPorted |
| | SingleDP | | SingleDP | NotPorted |
| | SingleDPMatrix | | SingleDPMatrix | NotPorted |
| | SmallCursor | | SmallCursor | NotPorted |
| org.biojava.bio.dp.twohead | BioSharp.Core.Bio.Dp.Twohead | |
| | AbstractMatrixPairDPCursor | | AbstractMatrixPairDPCursor | NotPorted |
| | BackMatrixPairDPCursor | | BackMatrixPairDPCursor | NotPorted |
| | Cell | | Cell | NotPorted |
| | CellCalculator | | ICellCalculator | NotPorted |
| | CellCalculatorFactory | | ICellCalculatorFactory | NotPorted |
| | CellCalculatorFactoryMaker | | ICellCalculatorFactoryMaker | NotPorted |
| | DPCompiler | | DPCompiler | NotPorted |
| | DPInterpreter | | DPInterpreter | NotPorted |
| | DPInterpreter.Maker | | DPInterpreter.Maker | NotPorted |
| | EmissionCache | | EmissionCache | NotPorted |
| | LightPairDPCursor | | LightPairDPCursor | NotPorted |
| | MatrixPairDPCursor | | MatrixPairDPCursor | NotPorted |
| | PairDPCursor | | IPairDPCursor | NotPorted |
| | PairDPMatrix | | PairDPMatrix | NotPorted |
| | PairwiseDP | | PairwiseDP | NotPorted |
| org.biojava.bio.gui | BioSharp.Gui | |
| | BarLogoPainter | | BarLogoPainter | NotPorted |
| | BlockPainter | | IBlockPainter | NotPorted |
| | DistributionLogo | | DistributionLogo | NotPorted |
| | DNAStyle | | DNAStyle | NotPorted |
| | FeatureTree | | FeatureTree | NotPorted |
| | LogoContext | | ILogoContext | NotPorted |
| | LogoPainter | | ILogoPainter | NotPorted |
| | PlainBlock | | PlainBlock | NotPorted |
| | PlainStyle | | PlainStyle | NotPorted |
| | SimpleSymbolStyle | | SimpleSymbolStyle | NotPorted |
| | StackedLogoPainter | | StackedLogoPainter | NotPorted |
| | SymbolStyle | | ISymbolStyle | NotPorted |
| | TextBlock | | TextBlock | NotPorted |
| | TextLogoPainter | | TextLogoPainter | NotPorted |
| org.biojava.bio.gui.glyph | BioSharp.Gui.Glyph | |
| | ArrowGlyph | | ArrowGlyph | NotPorted |
| | Glyph | | IGlyph | NotPorted |
| | GlyphUtils | | GlyphUtils | NotPorted |
| | HelixGlyph | | HelixGlyph | NotPorted |
| | RectangleGlyph | | RectangleGlyph | NotPorted |
| | TurnGlyph | | TurnGlyph | NotPorted |
| | TwoHeadedArrowGlyph | | TwoHeadedArrowGlyph | NotPorted |
| org.biojava.bio.gui.sequence | BioSharp.Gui.Sequence | |
| | AbiTraceRenderer | | AbiTraceRenderer | NotPorted |
| | AbstractBeadRenderer | | AbstractBeadRenderer | NotPorted |
| | AbstractPeptideDigestRenderer | | AbstractPeptideDigestRenderer | NotPorted |
| | AlignmentRenderer | | AlignmentRenderer | NotPorted |
| | ArrowedFeatureRenderer | | ArrowedFeatureRenderer | NotPorted |
| | BasicFeatureRenderer | | BasicFeatureRenderer | NotPorted |
| | BasicImapRenderer | | BasicImapRenderer | NotPorted |
| | BeadFeatureRenderer | | IBeadFeatureRenderer | NotPorted |
| | BumpedRenderer | | BumpedRenderer | NotPorted |
| | CircularFeatureFilteringRenderer | | CircularFeatureFilteringRenderer | NotPorted |
| | CircularFeatureRenderer | | ICircularFeatureRenderer | NotPorted |
| | CircularFeaturesRenderer | | CircularFeaturesRenderer | NotPorted |
| | CircularMLR | | CircularMLR | NotPorted |
| | CircularPaddedRenderer | | CircularPaddedRenderer | NotPorted |
| | CircularRenderer | | ICircularRenderer | NotPorted |
| | CircularRendererContext | | ICircularRendererContext | NotPorted |
| | CircularRendererPanel | | CircularRendererPanel | NotPorted |
| | CrosshairRenderer | | CrosshairRenderer | NotPorted |
| | EllipticalBeadRenderer | | EllipticalBeadRenderer | NotPorted |
| | FeatureBlockSequenceRenderer | | FeatureBlockSequenceRenderer | NotPorted |
| | FeatureLabelRenderer | | FeatureLabelRenderer | NotPorted |
| | FeatureLabelRenderer.AnnotationLabelMaker | | FeatureLabelRenderer.AnnotationLabelMaker | NotPorted |
| | FeatureLabelRenderer.LabelMaker | | FeatureLabelRenderer.ILabelMaker | NotPorted |
| | FeatureLabelRenderer.SourceLabelMaker | | FeatureLabelRenderer.SourceLabelMaker | NotPorted |
| | FeatureLabelRenderer.TypeLabelMaker | | FeatureLabelRenderer.TypeLabelMaker | NotPorted |
| | FeatureRenderer | | IFeatureRenderer | NotPorted |
| | FeatureSource | | IFeatureSource | NotPorted |
| | FilteringRenderer | | FilteringRenderer | NotPorted |
| | GappedRenderer | | GappedRenderer | NotPorted |
| | GlyphFeatureRenderer | | GlyphFeatureRenderer | NotPorted |
| | GUITools | | GUITools | NotPorted |
| | HeadlessRenderContext | | HeadlessRenderContext | NotPorted |
| | ImageMap | | IImageMap | NotPorted |
| | ImageMap.ClientSide | | ImageMap.ClientSide | NotPorted |
| | ImageMap.HotSpot | | ImageMap.HotSpot | NotPorted |
| | ImageMap.ServerSide | | ImageMap.ServerSide | NotPorted |
| | ImageMapRenderer | | IImageMapRenderer | NotPorted |
| | LabelledSequenceRenderer | | LabelledSequenceRenderer | NotPorted |
| | LabelRenderer | | ILabelRenderer | NotPorted |
| | LabelRenderer.RenderNothing | | LabelRenderer.RenderNothing | NotPorted |
| | LayeredRenderer | | LayeredRenderer | NotPorted |
| | LineInfo | | LineInfo | NotPorted |
| | MultiLineRenderer | | MultiLineRenderer | NotPorted |
| | OffsetRulerRenderer | | OffsetRulerRenderer | NotPorted |
| | OverlayMarker | | IOverlayMarker | NotPorted |
| | OverlayRendererWrapper | | OverlayRendererWrapper | NotPorted |
| | PaddingRenderer | | PaddingRenderer | NotPorted |
| | PairwiseDiagonalRenderer | | PairwiseDiagonalRenderer | NotPorted |
| | PairwiseFilteringRenderer | | PairwiseFilteringRenderer | NotPorted |
| | PairwiseOverlayRenderer | | PairwiseOverlayRenderer | NotPorted |
| | PairwiseRenderContext | | IPairwiseRenderContext | NotPorted |
| | PairwiseSequencePanel | | PairwiseSequencePanel | NotPorted |
| | PairwiseSequenceRenderer | | IPairwiseSequenceRenderer | NotPorted |
| | PairwiseSequenceRenderer.PairwiseRendererForwarder | | PairwiseSequenceRenderer.PairwiseRendererForwarder | NotPorted |
| | PeptideDigestRenderer | | PeptideDigestRenderer | NotPorted |
| | RectangularBeadRenderer | | RectangularBeadRenderer | NotPorted |
| | RectangularImapRenderer | | RectangularImapRenderer | NotPorted |
| | RoundRectangularBeadRenderer | | RoundRectangularBeadRenderer | NotPorted |
| | RulerRenderer | | RulerRenderer | NotPorted |
| | SecondaryStructureFeatureRenderer | | SecondaryStructureFeatureRenderer | NotPorted |
| | SequencePanel | | SequencePanel | NotPorted |
| | SequencePanelWrapper | | SequencePanelWrapper | NotPorted |
| | SequencePoster | | SequencePoster | NotPorted |
| | SequenceRenderContext | | ISequenceRenderContext | NotPorted |
| | SequenceRenderContext.Border | | SequenceRenderContext.Border | NotPorted |
| | SequenceRenderer | | ISequenceRenderer | NotPorted |
| | SequenceRenderer.RendererForwarder | | SequenceRenderer.RendererForwarder | NotPorted |
| | SequenceRendererWrapper | | SequenceRendererWrapper | NotPorted |
| | SequenceViewerEvent | | SequenceViewerEvent | NotPorted |
| | SequenceViewerListener | | ISequenceViewerListener | NotPorted |
| | SequenceViewerMotionListener | | ISequenceViewerMotionListener | NotPorted |
| | SequenceViewerMotionSupport | | SequenceViewerMotionSupport | NotPorted |
| | SequenceViewerSupport | | SequenceViewerSupport | NotPorted |
| | SimpleLabelRenderer | | SimpleLabelRenderer | NotPorted |
| | SixFrameRenderer | | SixFrameRenderer | NotPorted |
| | SixFrameZiggyRenderer | | SixFrameZiggyRenderer | NotPorted |
| | StackedFeatureRenderer | | StackedFeatureRenderer | NotPorted |
| | StopRenderer | | StopRenderer | NotPorted |
| | SubCircularRendererContext | | SubCircularRendererContext | NotPorted |
| | SubPairwiseRenderContext | | SubPairwiseRenderContext | NotPorted |
| | SubSequenceRenderContext | | SubSequenceRenderContext | NotPorted |
| | SymbolSequenceRenderer | | SymbolSequenceRenderer | NotPorted |
| | TickFeatureRenderer | | TickFeatureRenderer | NotPorted |
| | TranslatedSequencePanel | | TranslatedSequencePanel | NotPorted |
| | ZiggyFeatureRenderer | | ZiggyFeatureRenderer | NotPorted |
| | ZiggyImapRenderer | | ZiggyImapRenderer | NotPorted |
| org.biojava.bio.gui.sequence.tracklayout | BioSharp.Gui.Sequence.Tracklayout | |
| | SimpleTrackLayout | | SimpleTrackLayout | NotPorted |
| | TrackLayout | | ITrackLayout | NotPorted |
| | UserDefinedTrackLayout | | UserDefinedTrackLayout | NotPorted |
| org.biojava.bio.molbio | BioSharp.Core.Bio.Molbio | |
| | Composition | | Composition | NotPorted |
| | DNAComposition | | DNAComposition | NotPorted |
| | RestrictionEnzyme | | RestrictionEnzyme | Complete |
| | RestrictionEnzymeManager | | RestrictionEnzymeManager | Partial |
| | RestrictionMapper | | RestrictionMapper | Complete |
| | RestrictionSite | | IRestrictionSite | Complete |
| | RestrictionSite.Template | | RestrictionSite.Template | Complete |
| org.biojava.bio.program | BioSharp.Core.Bio.Program | |
| | BlastLikeToXMLConverter | | BlastLikeToXMLConverter | NotPorted |
| | Meme | | Meme | NotPorted |
| | PdbToXMLConverter | | PdbToXMLConverter | NotPorted |
| org.biojava.bio.program.abi | BioSharp.Core.Bio.Program.Abi | |
| | ABIFChromatogram | | ABIFChromatogram | NotPorted |
| | ABIFParser | | ABIFParser | NotPorted |
| | ABIFParser.DataAccess | | ABIFParser.IDataAccess | NotPorted |
| | ABIFParser.TaggedDataRecord | | ABIFParser.TaggedDataRecord | NotPorted |
| | ABITools | | ABITools | NotPorted |
| | ABITrace | | ABITrace | NotPorted |
| org.biojava.bio.program.blast2html | BioSharp.Core.Bio.Program.Blast2html | |
| | AbstractAlignmentStyler | | AbstractAlignmentStyler | NotPorted |
| | AlignmentMarker | | AlignmentMarker | NotPorted |
| | Blast2HTMLHandler | | Blast2HTMLHandler | NotPorted |
| | ColourCommand | | IColourCommand | NotPorted |
| | DatabaseURLGenerator | | IDatabaseURLGenerator | NotPorted |
| | DefaultURLGeneratorFactory | | DefaultURLGeneratorFactory | NotPorted |
| | EbiDatabaseURLGenerator | | EbiDatabaseURLGenerator | NotPorted |
| | HTMLRenderer | | HTMLRenderer | NotPorted |
| | NcbiDatabaseURLGenerator | | NcbiDatabaseURLGenerator | NotPorted |
| | SimpleAlignmentStyler | | SimpleAlignmentStyler | NotPorted |
| | URLGeneratorFactory | | IURLGeneratorFactory | NotPorted |
| org.biojava.bio.program.das | BioSharp.Core.Bio.Program.Das | |
| | DAS | | DAS | NotPorted |
| | DASLink | | DASLink | NotPorted |
| | DASSequence | | DASSequence | NotPorted |
| | DASSequenceDB | | DASSequenceDB | NotPorted |
| | DASSequenceDBProvider | | DASSequenceDBProvider | NotPorted |
| | DataSource | | DataSource | NotPorted |
| | ReferenceServer | | ReferenceServer | NotPorted |
| org.biojava.bio.program.das.dasalignment | BioSharp.Core.Bio.Program.Das.Dasalignment | |
| | Alignment | | Alignment | NotPorted |
| | DASAlignmentCall | | DASAlignmentCall | NotPorted |
| | DASAlignmentClient | | DASAlignmentClient | NotPorted |
| | DASAlignmentXMLResponseParser | | DASAlignmentXMLResponseParser | NotPorted |
| | DASException | | DASException | NotPorted |
| org.biojava.bio.program.das.dasstructure | BioSharp.Core.Bio.Program.Das.Dasstructure | |
| | DASStructureCall | | DASStructureCall | NotPorted |
| | DASStructureXMLResponseParser | | DASStructureXMLResponseParser | NotPorted |
| org.biojava.bio.program.formats | BioSharp.Core.Bio.Program.Formats | |
| | Embl | | Embl | NotPorted |
| | Enzyme | | Enzyme | NotPorted |
| | Format | | IFormat | NotPorted |
| | FormatTools | | FormatTools | NotPorted |
| | Ligand | | Ligand | NotPorted |
| | Ligand.Compound | | Ligand.Compound | NotPorted |
| | Ligand.Enzyme | | Ligand.Enzyme | NotPorted |
| | Ligand.Reaction | | Ligand.Reaction | NotPorted |
| | Swissprot | | Swissprot | NotPorted |
| org.biojava.bio.program.gff | BioSharp.Core.Bio.Program.Gff | |
| | GFFDocumentHandler | | IGFFDocumentHandler | NotPorted |
| | GFFEntrySet | | GFFEntrySet | NotPorted |
| | GFFErrorHandler | | IGFFErrorHandler | NotPorted |
| | GFFErrorHandler.AbortErrorHandler | | GFFErrorHandler.AbortErrorHandler | NotPorted |
| | GFFErrorHandler.SkipRecordErrorHandler | | GFFErrorHandler.SkipRecordErrorHandler | NotPorted |
| | GFFFilterer | | GFFFilterer | NotPorted |
| | GFFParser | | GFFParser | NotPorted |
| | GFFRecord | | IGFFRecord | NotPorted |
| | GFFRecordFilter | | IGFFRecordFilter | NotPorted |
| | GFFRecordFilter.AcceptAll | | GFFRecordFilter.AcceptAll | NotPorted |
| | GFFRecordFilter.FeatureFilter | | GFFRecordFilter.FeatureFilter | NotPorted |
| | GFFRecordFilter.FrameFilter | | GFFRecordFilter.FrameFilter | NotPorted |
| | GFFRecordFilter.NotFilter | | GFFRecordFilter.NotFilter | NotPorted |
| | GFFRecordFilter.SequenceFilter | | GFFRecordFilter.SequenceFilter | NotPorted |
| | GFFRecordFilter.SourceFilter | | GFFRecordFilter.SourceFilter | NotPorted |
| | GFFRecordFilter.StrandFilter | | GFFRecordFilter.StrandFilter | NotPorted |
| | GFFTools | | GFFTools | NotPorted |
| | GFFWriter | | GFFWriter | NotPorted |
| | IgnoreRecordException | | IgnoreRecordException | NotPorted |
| | SequencesAsGFF | | SequencesAsGFF | NotPorted |
| | SimpleGFFRecord | | SimpleGFFRecord | NotPorted |
| org.biojava.bio.program.gff3 | BioSharp.Core.Bio.Program.Gff3 | |
| | GFF3DocumentHandler | | IGFF3DocumentHandler | NotPorted |
| | GFF3Parser | | GFF3Parser | NotPorted |
| | GFF3Record | | IGFF3Record | NotPorted |
| | GFF3Record.Impl | | GFF3Record.Impl | NotPorted |
| org.biojava.bio.program.hmmer | BioSharp.Core.Bio.Program.Hmmer | |
| | FullHmmerProfileHMM | | FullHmmerProfileHMM | NotPorted |
| | HmmerProfileHMM | | HmmerProfileHMM | NotPorted |
| | HmmerProfileParser | | HmmerProfileParser | NotPorted |
| | ProfileEmissionState | | ProfileEmissionState | NotPorted |
| org.biojava.bio.program.homologene | BioSharp.Core.Bio.Program.Homologene | |
| | AbstractOrthologueSet | | AbstractOrthologueSet | NotPorted |
| | AbstractOrthoPairCollection | | AbstractOrthoPairCollection | NotPorted |
| | AbstractOrthoPairSet | | AbstractOrthoPairSet | NotPorted |
| | DuplicateTaxonException | | DuplicateTaxonException | NotPorted |
| | HomologeneBuilder | | IHomologeneBuilder | NotPorted |
| | HomologeneDB | | IHomologeneDB | NotPorted |
| | HomologeneTools | | HomologeneTools | NotPorted |
| | Orthologue | | IOrthologue | NotPorted |
| | OrthologueFilter | | IOrthologueFilter | NotPorted |
| | OrthologueFilter.AcceptAll | | OrthologueFilter.AcceptAll | NotPorted |
| | OrthologueFilter.And | | OrthologueFilter.And | NotPorted |
| | OrthologueFilter.ByAccession | | OrthologueFilter.ByAccession | NotPorted |
| | OrthologueFilter.ByHomologeneID | | OrthologueFilter.ByHomologeneID | NotPorted |
| | OrthologueFilter.ByLocusID | | OrthologueFilter.ByLocusID | NotPorted |
| | OrthologueFilter.ByTaxon | | OrthologueFilter.ByTaxon | NotPorted |
| | OrthologueFilter.ByTaxonID | | OrthologueFilter.ByTaxonID | NotPorted |
| | OrthologueFilter.ByTitle | | OrthologueFilter.ByTitle | NotPorted |
| | OrthologueFilter.Not | | OrthologueFilter.Not | NotPorted |
| | OrthologueFilter.Or | | OrthologueFilter.Or | NotPorted |
| | OrthologueFilter.Xor | | OrthologueFilter.Xor | NotPorted |
| | OrthologueSet | | IOrthologueSet | NotPorted |
| | OrthologueSet.Iterator | | OrthologueSet.IIterator | NotPorted |
| | OrthoPair | | IOrthoPair | NotPorted |
| | OrthoPairCollection | | IOrthoPairCollection | NotPorted |
| | OrthoPairCollection.Iterator | | OrthoPairCollection.IIterator | NotPorted |
| | OrthoPairFilter | | IOrthoPairFilter | NotPorted |
| | OrthoPairFilter.AcceptAll | | OrthoPairFilter.AcceptAll | NotPorted |
| | OrthoPairFilter.And | | OrthoPairFilter.And | NotPorted |
| | OrthoPairFilter.ByMaxIdentity | | OrthoPairFilter.ByMaxIdentity | NotPorted |
| | OrthoPairFilter.ByMinIdentity | | OrthoPairFilter.ByMinIdentity | NotPorted |
| | OrthoPairFilter.ByRef | | OrthoPairFilter.ByRef | NotPorted |
| | OrthoPairFilter.BySimilarityType | | OrthoPairFilter.BySimilarityType | NotPorted |
| | OrthoPairFilter.Not | | OrthoPairFilter.Not | NotPorted |
| | OrthoPairFilter.Or | | OrthoPairFilter.Or | NotPorted |
| | OrthoPairFilter.Xor | | OrthoPairFilter.Xor | NotPorted |
| | OrthoPairSet | | IOrthoPairSet | NotPorted |
| | OrthoPairSet.Iterator | | OrthoPairSet.IIterator | NotPorted |
| | OrthoPairSetFilter | | IOrthoPairSetFilter | NotPorted |
| | OrthoPairSetFilter.AcceptAll | | OrthoPairSetFilter.AcceptAll | NotPorted |
| | OrthoPairSetFilter.AllPairsInCollection | | OrthoPairSetFilter.AllPairsInCollection | NotPorted |
| | OrthoPairSetFilter.And | | OrthoPairSetFilter.And | NotPorted |
| | OrthoPairSetFilter.ByMinIdentity | | OrthoPairSetFilter.ByMinIdentity | NotPorted |
| | OrthoPairSetFilter.ByTaxon | | OrthoPairSetFilter.ByTaxon | NotPorted |
| | OrthoPairSetFilter.Not | | OrthoPairSetFilter.Not | NotPorted |
| | OrthoPairSetFilter.Or | | OrthoPairSetFilter.Or | NotPorted |
| | OrthoPairSetFilter.SomePairsInCollection | | OrthoPairSetFilter.SomePairsInCollection | NotPorted |
| | OrthoPairSetFilter.Xor | | OrthoPairSetFilter.Xor | NotPorted |
| | SimilarityType | | ISimilarityType | NotPorted |
| | SimilarityType.PlaceHolder | | SimilarityType.PlaceHolder | NotPorted |
| | SimpleHomologeneBuilder | | SimpleHomologeneBuilder | NotPorted |
| | SimpleHomologeneDB | | SimpleHomologeneDB | NotPorted |
| | SimpleOrthologue | | SimpleOrthologue | NotPorted |
| | SimpleOrthologueSet | | SimpleOrthologueSet | NotPorted |
| | SimpleOrthoPair | | SimpleOrthoPair | NotPorted |
| | SimpleOrthoPairCollection | | SimpleOrthoPairCollection | NotPorted |
| | SimpleOrthoPairSet | | SimpleOrthoPairSet | NotPorted |
| | Taxon | | ITaxon | NotPorted |
| | Taxon.TaxonStub | | Taxon.TaxonStub | NotPorted |
| org.biojava.bio.program.indexdb | BioSharp.Core.Bio.Program.Indexdb | |
| | BioStore | | BioStore | NotPorted |
| | BioStoreFactory | | BioStoreFactory | NotPorted |
| | IndexStore | | IIndexStore | NotPorted |
| | IndexTools | | IndexTools | NotPorted |
| | Record | | IRecord | NotPorted |
| | Record.Impl | | Record.Impl | NotPorted |
| org.biojava.bio.program.phred | BioSharp.Core.Bio.Program.Phred | |
| | PhredFormat | | PhredFormat | NotPorted |
| | PhredSequence | | PhredSequence | NotPorted |
| | PhredTools | | PhredTools | NotPorted |
| | Qualitative | | IQualitative | NotPorted |
| org.biojava.bio.program.sax | BioSharp.Core.Bio.Program.Sax | |
| | BlastLikeSAXParser | | BlastLikeSAXParser | NotPorted |
| | ClustalWAlignmentSAXParser | | ClustalWAlignmentSAXParser | NotPorted |
| | FastaSearchSAXParser | | FastaSearchSAXParser | NotPorted |
| | FastaSequenceSAXParser | | FastaSequenceSAXParser | NotPorted |
| | PdbSAXParser | | PdbSAXParser | NotPorted |
| | SequenceAlignmentSAXParser | | SequenceAlignmentSAXParser | NotPorted |
| org.biojava.bio.program.sax.blastxml | BioSharp.Core.Bio.Program.Sax.Blastxml | |
| | BlastXMLParser | | BlastXMLParser | NotPorted |
| | BlastXMLParserFacade | | BlastXMLParserFacade | NotPorted |
| org.biojava.bio.program.scf | BioSharp.Core.Bio.Program.Scf | |
| | SCF | | SCF | NotPorted |
| org.biojava.bio.program.ssaha | BioSharp.Core.Bio.Program.Ssaha | |
| | CompactedDataStore | | CompactedDataStore | NotPorted |
| | CompactedDataStoreFactory | | CompactedDataStoreFactory | NotPorted |
| | DataStore | | IDataStore | NotPorted |
| | DataStoreFactory | | IDataStoreFactory | NotPorted |
| | HitMerger | | HitMerger | NotPorted |
| | MappedDataStoreFactory | | MappedDataStoreFactory | NotPorted |
| | NIODataStoreFactory | | NIODataStoreFactory | NotPorted |
| | SearchException | | SearchException | NotPorted |
| | SearchListener | | ISearchListener | NotPorted |
| | SearchListener.Echo | | SearchListener.Echo | NotPorted |
| | SearchListener.FilterByLength | | SearchListener.FilterByLength | NotPorted |
| | SearchListener.Tee | | SearchListener.Tee | NotPorted |
| | SearchListener.Wrapper | | SearchListener.Wrapper | NotPorted |
| | SequenceStreamer | | ISequenceStreamer | NotPorted |
| | SequenceStreamer.FileStreamer | | SequenceStreamer.FileStreamer | NotPorted |
| | SequenceStreamer.SequenceDBStreamer | | SequenceStreamer.SequenceDBStreamer | NotPorted |
| org.biojava.bio.program.ssbind | BioSharp.Core.Bio.Program.Ssbind | |
| | AlignmentStAXHandler | | AlignmentStAXHandler | NotPorted |
| | AlphabetResolver | | AlphabetResolver | NotPorted |
| | AnnotationFactory | | AnnotationFactory | NotPorted |
| | BlastLikeHomologyBuilder | | BlastLikeHomologyBuilder | NotPorted |
| | BlastLikeSearchBuilder | | BlastLikeSearchBuilder | NotPorted |
| | HeaderStAXHandler | | HeaderStAXHandler | NotPorted |
| | HitStAXHandler | | HitStAXHandler | NotPorted |
| | HSPStAXHandler | | HSPStAXHandler | NotPorted |
| | HSPSummaryStAXHandler | | HSPSummaryStAXHandler | NotPorted |
| | SeqSimilarityAdapter | | SeqSimilarityAdapter | NotPorted |
| | SeqSimilarityStAXAdapter | | SeqSimilarityStAXAdapter | NotPorted |
| | SeqSimilarityStAXHandler | | SeqSimilarityStAXHandler | NotPorted |
| | SimilarityPairBuilder | | SimilarityPairBuilder | NotPorted |
| | StAXHandlerBinding | | StAXHandlerBinding | NotPorted |
| | StAXHandlerFactory | | IStAXHandlerFactory | NotPorted |
| | ViewSequenceFactory | | ViewSequenceFactory | NotPorted |
| org.biojava.bio.program.tagvalue | BioSharp.Core.Bio.Program.Tagvalue | |
| | AbstractWrapper | | AbstractWrapper | NotPorted |
| | Aggregator | | Aggregator | NotPorted |
| | AnnotationBuilder | | AnnotationBuilder | NotPorted |
| | BoundaryFinder | | IBoundaryFinder | NotPorted |
| | ChangeTable | | ChangeTable | Partial |
| | ChangeTable.ChainedChanger | | ChangeTable.ChainedChanger | NotPorted |
| | ChangeTable.Changer | | ChangeTable.IChanger | Complete |
| | ChangeTable.Splitter | | ChangeTable.ISplitter | Complete |
| | Echo | | Echo | NotPorted |
| | Formats | | Formats | NotPorted |
| | Index2Model | | Index2Model | NotPorted |
| | Indexer | | Indexer | NotPorted |
| | Indexer2 | | Indexer2 | NotPorted |
| | LineSplitParser | | LineSplitParser | Complete |
| | MultiTagger | | MultiTagger | NotPorted |
| | Parser | | Parser | Complete |
| | ParserListener | | ParserListener | NotPorted |
| | PropertyChanger | | IPropertyChanger | NotPorted |
| | RegexChanger | | RegexChanger | NotPorted |
| | RegexFieldFinder | | RegexFieldFinder | NotPorted |
| | RegexParser | | RegexParser | NotPorted |
| | RegexSplitter | | RegexSplitter | Complete |
| | SimpleTagValueWrapper | | SimpleTagValueWrapper | Complete |
| | StateMachine | | StateMachine | NotPorted |
| | StateMachine.ExitNotification | | StateMachine.IExitNotification | NotPorted |
| | StateMachine.State | | StateMachine.IState | NotPorted |
| | TagDelegator | | TagDelegator | NotPorted |
| | TagDropper | | TagDropper | Complete |
| | TagMapper | | TagMapper | NotPorted |
| | TagRenamer | | TagRenamer | NotPorted |
| | TagValue | | TagValue | Complete |
| | TagValueContext | | ITagValueContext | Complete |
| | TagValueListener | | ITagValueListener | Complete |
| | TagValueParser | | ITagValueParser | Complete |
| | TagValueWrapper | | ITagValueWrapper | Complete |
| | ValueChanger | | ValueChanger | Complete |
| org.biojava.bio.program.unigene | BioSharp.Core.Bio.Program.Unigene | |
| | FlatFileUnigeneFactory | | FlatFileUnigeneFactory | NotPorted |
| | SQLUnigeneFactory | | SQLUnigeneFactory | NotPorted |
| | UnigeneCluster | | IUnigeneCluster | NotPorted |
| | UnigeneDB | | IUnigeneDB | NotPorted |
| | UnigeneFactory | | IUnigeneFactory | NotPorted |
| | UnigeneTools | | UnigeneTools | NotPorted |
| org.biojava.bio.program.xff | BioSharp.Core.Bio.Program.Xff | |
| | BasicXFFHelper | | BasicXFFHelper | NotPorted |
| | ElementRecognizer | | IElementRecognizer | NotPorted |
| | ElementRecognizer.AllElementRecognizer | | ElementRecognizer.AllElementRecognizer | NotPorted |
| | ElementRecognizer.ByLocalName | | ElementRecognizer.ByLocalName | NotPorted |
| | ElementRecognizer.ByNSName | | ElementRecognizer.ByNSName | NotPorted |
| | ElementRecognizer.HasAttribute | | ElementRecognizer.HasAttribute | NotPorted |
| | FeatureHandler | | FeatureHandler | NotPorted |
| | LocationHandlerBase | | LocationHandlerBase | NotPorted |
| | PropDetailHandler | | PropDetailHandler | NotPorted |
| | PropertyWriter | | PropertyWriter | NotPorted |
| | StrandedFeatureHandler | | StrandedFeatureHandler | NotPorted |
| | XFFFeatureSetHandler | | XFFFeatureSetHandler | NotPorted |
| | XFFHelper | | IXFFHelper | NotPorted |
| | XFFPartHandlerFactory | | IXFFPartHandlerFactory | NotPorted |
| | XFFTools | | XFFTools | NotPorted |
| | XFFWriter | | XFFWriter | NotPorted |
| org.biojava.bio.program.xml | BioSharp.Core.Bio.Program.Xml | |
| | BaseXMLWriter | | BaseXMLWriter | NotPorted |
| | SimpleXMLEmitter | | SimpleXMLEmitter | NotPorted |
| org.biojava.bio.proteomics | BioSharp.Core.Bio.Proteomics | |
| | Digest | | Digest | NotPorted |
| | IsoelectricPointCalc | | IsoelectricPointCalc | NotPorted |
| | MassCalc | | MassCalc | NotPorted |
| | Protease | | Protease | NotPorted |
| | ProteaseManager | | ProteaseManager | NotPorted |
| | StructureTools | | StructureTools | NotPorted |
| org.biojava.bio.proteomics.aaindex | BioSharp.Core.Bio.Proteomics.Aaindex | |
| | AAindex | | AAindex | NotPorted |
| | AAindexStreamReader | | AAindexStreamReader | NotPorted |
| | SimpleSymbolPropertyTableDB | | SimpleSymbolPropertyTableDB | NotPorted |
| | SymbolPropertyTableDB | | ISymbolPropertyTableDB | NotPorted |
| | SymbolPropertyTableIterator | | ISymbolPropertyTableIterator | NotPorted |
| org.biojava.bio.search | BioSharp.Core.Bio.Search | |
| | BioMatcher | | IBioMatcher | NotPorted |
| | BioPattern | | IBioPattern | NotPorted |
| | BlastLikeSearchFilter | | IBlastLikeSearchFilter | NotPorted |
| | BlastLikeSearchFilter.AbstractBlastLikeSearchFilter | | BlastLikeSearchFilter.AbstractBlastLikeSearchFilter | NotPorted |
| | BlastLikeSearchFilter.And | | BlastLikeSearchFilter.And | NotPorted |
| | BlastLikeSearchFilter.ByHitProperty | | BlastLikeSearchFilter.ByHitProperty | NotPorted |
| | BlastLikeSearchFilter.BySearchProperty | | BlastLikeSearchFilter.BySearchProperty | NotPorted |
| | BlastLikeSearchFilter.BySubHitProperty | | BlastLikeSearchFilter.BySubHitProperty | NotPorted |
| | BlastLikeSearchFilter.Node | | BlastLikeSearchFilter.INode | NotPorted |
| | BlastLikeSearchFilter.Not | | BlastLikeSearchFilter.Not | NotPorted |
| | BlastLikeSearchFilter.Or | | BlastLikeSearchFilter.Or | NotPorted |
| | FilteringContentHandler | | FilteringContentHandler | NotPorted |
| | FilterTest | | IFilterTest | NotPorted |
| | FilterTest.Equals | | FilterTest.Equals | NotPorted |
| | FilterTest.FindRegex | | FilterTest.FindRegex | NotPorted |
| | FilterTest.GreaterThan | | FilterTest.GreaterThan | NotPorted |
| | FilterTest.LessThan | | FilterTest.LessThan | NotPorted |
| | FilterTest.MatchRegex | | FilterTest.MatchRegex | NotPorted |
| | KnuthMorrisPrattSearch | | KnuthMorrisPrattSearch | Complete |
| | MaxMismatchMatcher | | MaxMismatchMatcher | NotPorted |
| | MaxMismatchPattern | | MaxMismatchPattern | NotPorted |
| | SearchBuilder | | ISearchBuilder | NotPorted |
| | SearchContentAdapter | | SearchContentAdapter | NotPorted |
| | SearchContentFilter | | SearchContentFilter | NotPorted |
| | SearchContentHandler | | ISearchContentHandler | NotPorted |
| | SearchContentHandlerDebugger | | SearchContentHandlerDebugger | NotPorted |
| | SeqContentPattern | | SeqContentPattern | NotPorted |
| | SeqSimilaritySearcher | | ISeqSimilaritySearcher | NotPorted |
| | SeqSimilaritySearchHit | | ISeqSimilaritySearchHit | NotPorted |
| | SeqSimilaritySearchHit.ByScoreComparator | | SeqSimilaritySearchHit.ByScoreComparator | NotPorted |
| | SeqSimilaritySearchHit.BySubHitCountComparator | | SeqSimilaritySearchHit.BySubHitCountComparator | NotPorted |
| | SeqSimilaritySearchResult | | ISeqSimilaritySearchResult | NotPorted |
| | SeqSimilaritySearchSubHit | | ISeqSimilaritySearchSubHit | NotPorted |
| | SeqSimilaritySearchSubHit.ByScoreComparator | | SeqSimilaritySearchSubHit.ByScoreComparator | NotPorted |
| | SeqSimilaritySearchSubHit.BySubjectStartComparator | | SeqSimilaritySearchSubHit.BySubjectStartComparator | NotPorted |
| | SequenceDBSearchHit | | SequenceDBSearchHit | NotPorted |
| | SequenceDBSearchResult | | SequenceDBSearchResult | NotPorted |
| | SequenceDBSearchSubHit | | SequenceDBSearchSubHit | NotPorted |
| | SimpleSeqSimilaritySearchHit | | SimpleSeqSimilaritySearchHit | NotPorted |
| | SimpleSeqSimilaritySearchResult | | SimpleSeqSimilaritySearchResult | NotPorted |
| | SimpleSeqSimilaritySearchSubHit | | SimpleSeqSimilaritySearchSubHit | NotPorted |
| org.biojava.bio.seq | BioSharp.Core.Bio.Seq | |
| | AbstractFeatureHolder | | AbstractFeatureHolder | Partial |
| | ByLocationMinMaxComparator | | ByLocationMinMaxComparator | NotPorted |
| | ByLocationMinMaxFeatureComparator | | ByLocationMinMaxFeatureComparator | NotPorted |
| | CircularView | | CircularView | Stub |
| | ComponentFeature | | IComponentFeature | NotPorted |
| | ComponentFeature.Template | | ComponentFeature.Template | NotPorted |
| | DNATools | | DNATools | Partial |
| | Feature | | IFeature | Complete |
| | Feature.ByLocationComparator | | Feature.ByLocationComparator | NotPorted |
| | Feature.Template | | Feature.Template | Partial |
| | FeatureFilter | | IFeatureFilter | Complete |
| | FeatureFilter.And | | FeatureFilter.And | NotPorted |
| | FeatureFilter.AnnotationContains | | FeatureFilter.AnnotationContains | NotPorted |
| | FeatureFilter.ByAncestor | | FeatureFilter.ByAncestor | Stub |
| | FeatureFilter.ByAnnotation | | FeatureFilter.ByAnnotation | NotPorted |
| | FeatureFilter.ByAnnotationType | | FeatureFilter.ByAnnotationType | NotPorted |
| | FeatureFilter.ByChild | | FeatureFilter.ByChild | NotPorted |
| | FeatureFilter.ByClass | | FeatureFilter.ByClass | NotPorted |
| | FeatureFilter.ByComponentName | | FeatureFilter.ByComponentName | NotPorted |
| | FeatureFilter.ByDescendant | | FeatureFilter.ByDescendant | NotPorted |
| | FeatureFilter.ByFeature | | FeatureFilter.ByFeature | NotPorted |
| | FeatureFilter.ByPairwiseScore | | FeatureFilter.ByPairwiseScore | NotPorted |
| | FeatureFilter.ByParent | | FeatureFilter.ByParent | Stub |
| | FeatureFilter.BySequenceName | | FeatureFilter.BySequenceName | NotPorted |
| | FeatureFilter.BySource | | FeatureFilter.BySource | NotPorted |
| | FeatureFilter.ByType | | FeatureFilter.ByType | NotPorted |
| | FeatureFilter.ContainedByLocation | | FeatureFilter.ContainedByLocation | NotPorted |
| | FeatureFilter.FrameFilter | | FeatureFilter.FrameFilter | NotPorted |
| | FeatureFilter.HasAnnotation | | FeatureFilter.HasAnnotation | NotPorted |
| | FeatureFilter.Not | | FeatureFilter.Not | NotPorted |
| | FeatureFilter.OnlyChildren | | FeatureFilter.OnlyChildren | NotPorted |
| | FeatureFilter.OnlyDescendants | | FeatureFilter.OnlyDescendants | NotPorted |
| | FeatureFilter.Or | | FeatureFilter.Or | NotPorted |
| | FeatureFilter.OverlapsLocation | | FeatureFilter.OverlapsLocation | NotPorted |
| | FeatureFilter.ShadowContainedByLocation | | FeatureFilter.ShadowContainedByLocation | NotPorted |
| | FeatureFilter.ShadowOverlapsLocation | | FeatureFilter.ShadowOverlapsLocation | NotPorted |
| | FeatureFilter.StrandFilter | | FeatureFilter.StrandFilter | NotPorted |
| | FeatureHolder | | IFeatureHolder | Complete |
| | FeatureHolder.EmptyFeatureHolder | | FeatureHolder.EmptyFeatureHolder | NotPorted |
| | FeatureHolderUtils | | FeatureHolderUtils | NotPorted |
| | FeatureRealizer | | IFeatureRealizer | Complete |
| | FeatureTypes | | FeatureTypes | NotPorted |
| | FeatureTypes.Repository | | FeatureTypes.IRepository | NotPorted |
| | FeatureTypes.RepositoryImpl | | FeatureTypes.RepositoryImpl | NotPorted |
| | FeatureTypes.Type | | FeatureTypes.IType | NotPorted |
| | FilterUtils | | FilterUtils | NotPorted |
| | FilterUtils.FilterTransformer | | FilterUtils.IFilterTransformer | NotPorted |
| | Frame | | IFrame | Stub |
| | FramedFeature | | IFramedFeature | Stub |
| | FramedFeature.ReadingFrame | | FramedFeature.ReadingFrame | NotPorted |
| | FramedFeature.Template | | FramedFeature.Template | Stub |
| | GappedSequence | | IGappedSequence | NotPorted |
| | GeneticCodes | | GeneticCodes | NotPorted |
| | LazyFeatureHolder | | LazyFeatureHolder | NotPorted |
| | MergeFeatureHolder | | MergeFeatureHolder | Partial |
| | NewSimpleAssembly | | NewSimpleAssembly | NotPorted |
| | NucleotideTools | | NucleotideTools | NotPorted |
| | OptimizableFilter | | IOptimizableFilter | Complete |
| | ProteinTools | | ProteinTools | Partial |
| | RealizingFeatureHolder | | IRealizingFeatureHolder | Complete |
| | RemoteFeature | | IRemoteFeature | Stub |
| | RemoteFeature.Region | | RemoteFeature.Region | Complete |
| | RemoteFeature.Resolver | | RemoteFeature.IResolver | NotPorted |
| | RemoteFeature.Template | | RemoteFeature.Template | Complete |
| | RNATools | | RNATools | Partial |
| | Sequence | | ISequence | Complete |
| | SequenceAnnotator | | ISequenceAnnotator | Complete |
| | SequenceFactory | | ISequenceFactory | Complete |
| | SequenceIterator | | ISequenceIterator | Complete |
| | SequenceTools | | SequenceTools | Partial |
| | SimpleAssembly | | SimpleAssembly | NotPorted |
| | SimpleFeatureHolder | | SimpleFeatureHolder | Complete |
| | SimpleFeatureRealizer | | SimpleFeatureRealizer | Complete |
| | StrandedFeature | | IStrandedFeature | Complete |
| | StrandedFeature.Strand | | StrandedFeature.Strand | Complete |
| | StrandedFeature.Template | | StrandedFeature.Template | Complete |
| | StrandParser | | StrandParser | NotPorted |
| org.biojava.bio.seq.db | BioSharp.Core.Bio.Seq.Db | |
| | AbstractSequenceDB | | AbstractSequenceDB | NotPorted |
| | AnnotatedSequenceDB | | AnnotatedSequenceDB | NotPorted |
| | BioIndex | | BioIndex | NotPorted |
| | CachingSequenceDB | | CachingSequenceDB | NotPorted |
| | DummySequenceDB | | DummySequenceDB | NotPorted |
| | DummySequenceDBInstallation | | DummySequenceDBInstallation | NotPorted |
| | EmblCDROMIndexStore | | EmblCDROMIndexStore | NotPorted |
| | FetchURL | | FetchURL | NotPorted |
| | GenbankSequenceDB | | GenbankSequenceDB | NotPorted |
| | GenpeptSequenceDB | | GenpeptSequenceDB | NotPorted |
| | HashSequenceDB | | HashSequenceDB | NotPorted |
| | IDMaker | | IIDMaker | NotPorted |
| | IDMaker.ByName | | IDMaker.ByName | NotPorted |
| | IDMaker.ByURN | | IDMaker.ByURN | NotPorted |
| | IllegalIDException | | IllegalIDException | NotPorted |
| | Index | | IIndex | NotPorted |
| | IndexedSequenceDB | | IndexedSequenceDB | NotPorted |
| | IndexStore | | IIndexStore | NotPorted |
| | NCBISequenceDB | | NCBISequenceDB | NotPorted |
| | SequenceDB | | ISequenceDB | NotPorted |
| | SequenceDBInstallation | | ISequenceDBInstallation | NotPorted |
| | SequenceDBLite | | ISequenceDBLite | NotPorted |
| | SequenceDBWrapper | | SequenceDBWrapper | NotPorted |
| | SimpleIndex | | SimpleIndex | NotPorted |
| | SimpleSequenceDBInstallation | | SimpleSequenceDBInstallation | NotPorted |
| | SubSequenceDB | | SubSequenceDB | NotPorted |
| | SwissprotSequenceDB | | SwissprotSequenceDB | NotPorted |
| | TabIndexStore | | TabIndexStore | NotPorted |
| | ViewingSequenceDB | | ViewingSequenceDB | NotPorted |
| | WebSequenceDB | | WebSequenceDB | NotPorted |
| org.biojava.bio.seq.db.biofetch | BioSharp.Core.Bio.Seq.Db.Biofetch | |
| | BioFetchSequenceDB | | BioFetchSequenceDB | NotPorted |
| | BioFetchSequenceDBProvider | | BioFetchSequenceDBProvider | NotPorted |
| org.biojava.bio.seq.db.biosql | BioSharp.Core.Bio.Seq.Db.Biosql | |
| | BioSQLSequenceDB | | BioSQLSequenceDB | NotPorted |
| | BioSQLSequenceDBProvider | | BioSQLSequenceDBProvider | NotPorted |
| | DBHelper | | DBHelper | NotPorted |
| | DBHelper.BioSequenceStyle | | DBHelper.BioSequenceStyle | NotPorted |
| | DBHelper.DeleteStyle | | DBHelper.DeleteStyle | NotPorted |
| | DBHelper.JoinStyle | | DBHelper.JoinStyle | NotPorted |
| | HypersonicDBHelper | | HypersonicDBHelper | NotPorted |
| | MySQLDBHelper | | MySQLDBHelper | NotPorted |
| | OracleDBHelper | | OracleDBHelper | NotPorted |
| | PostgreSQLDBHelper | | PostgreSQLDBHelper | NotPorted |
| | TaxonSQL | | TaxonSQL | NotPorted |
| | UnknownDBHelper | | UnknownDBHelper | NotPorted |
| org.biojava.bio.seq.db.emblcd | BioSharp.Core.Bio.Seq.Db.Emblcd | |
| | AcnumHitReader | | AcnumHitReader | NotPorted |
| | AcnumTrgReader | | AcnumTrgReader | NotPorted |
| | DivisionLkpReader | | DivisionLkpReader | NotPorted |
| | EmblCDROMIndexReader | | EmblCDROMIndexReader | NotPorted |
| | EmblCDROMRandomAccess | | EmblCDROMRandomAccess | NotPorted |
| | EntryNamIdxReader | | EntryNamIdxReader | NotPorted |
| | EntryNamRandomAccess | | EntryNamRandomAccess | NotPorted |
| org.biojava.bio.seq.db.flat | BioSharp.Core.Bio.Seq.Db.Flat | |
| | FlatSequenceDB | | FlatSequenceDB | NotPorted |
| | FlatSequenceDBProvider | | FlatSequenceDBProvider | NotPorted |
| org.biojava.bio.seq.distributed | BioSharp.Core.Bio.Seq.Distributed | |
| | DistDataSource | | IDistDataSource | NotPorted |
| | DistributedSequenceDB | | DistributedSequenceDB | NotPorted |
| | GFFDataSource | | GFFDataSource | NotPorted |
| | SequenceDBDataSource | | SequenceDBDataSource | NotPorted |
| org.biojava.bio.seq.filter | BioSharp.Core.Bio.Seq.Filter | |
| | FilterTransformer | | FilterTransformer | NotPorted |
| org.biojava.bio.seq.homol | BioSharp.Core.Bio.Seq.Homol | |
| | Homology | | IHomology | NotPorted |
| | HomologyDB | | IHomologyDB | NotPorted |
| | HomologyFeature | | IHomologyFeature | Stub |
| | HomologyFeature.Template | | HomologyFeature.Template | Stub |
| | SimilarityPairFeature | | ISimilarityPairFeature | Stub |
| | SimilarityPairFeature.EmptyPairwiseAlignment | | SimilarityPairFeature.EmptyPairwiseAlignment | NotPorted |
| | SimilarityPairFeature.Template | | SimilarityPairFeature.Template | Stub |
| | SimpleHomology | | SimpleHomology | NotPorted |
| org.biojava.bio.seq.impl | BioSharp.Core.Bio.Seq.Impl | |
| | AssembledSymbolList | | AssembledSymbolList | NotPorted |
| | DummySequence | | DummySequence | NotPorted |
| | FeatureImpl | | FeatureImpl | Partial |
| | LazyFilterFeatureHolder | | LazyFilterFeatureHolder | NotPorted |
| | NewAssembledSymbolList | | NewAssembledSymbolList | NotPorted |
| | RevCompSequence | | RevCompSequence | NotPorted |
| | SimpleFeature | | SimpleFeature | Partial |
| | SimpleFramedFeature | | SimpleFramedFeature | Stub |
| | SimpleGappedSequence | | SimpleGappedSequence | NotPorted |
| | SimpleHomologyFeature | | SimpleHomologyFeature | Stub |
| | SimpleRemoteFeature | | SimpleRemoteFeature | Stub |
| | SimpleRemoteFeature.DBResolver | | SimpleRemoteFeature.DBResolver | NotPorted |
| | SimpleRestrictionSite | | SimpleRestrictionSite | Complete |
| | SimpleSequence | | SimpleSequence | Partial |
| | SimpleSequenceFactory | | SimpleSequenceFactory | Complete |
| | SimpleSimilarityPairFeature | | SimpleSimilarityPairFeature | Stub |
| | SimpleStrandedFeature | | SimpleStrandedFeature | Complete |
| | SubSequence | | SubSequence | NotPorted |
| | SubSequence.SubProjectedFeatureContext | | SubSequence.SubProjectedFeatureContext | NotPorted |
| | TemplateUtils | | TemplateUtils | NotPorted |
| | ViewSequence | | ViewSequence | Partial |
| org.biojava.bio.seq.io | BioSharp.Core.Bio.Seq.IO | |
| | AlignIOConstants | | AlignIOConstants | NotPorted |
| | AlignmentFormat | | IAlignmentFormat | NotPorted |
| | AlternateTokenization | | AlternateTokenization | Partial |
| | CharacterTokenization | | CharacterTokenization | Complete |
| | ChunkedSymbolListFactory | | ChunkedSymbolListFactory | Complete |
| | CrossProductTokenization | | CrossProductTokenization | NotPorted |
| | DoubleTokenization | | DoubleTokenization | NotPorted |
| | EmblFileFormer | | EmblFileFormer | NotPorted |
| | EmblLikeFormat | | EmblLikeFormat | NotPorted |
| | EmblLikeLocationParser | | EmblLikeLocationParser | Complete |
| | EmblProcessor | | EmblProcessor | NotPorted |
| | EmblProcessor.Factory | | EmblProcessor.Factory | NotPorted |
| | EmblReferenceComparator | | EmblReferenceComparator | NotPorted |
| | FastaAlignmentFormat | | FastaAlignmentFormat | NotPorted |
| | FastaDescriptionLineParser | | FastaDescriptionLineParser | NotPorted |
| | FastaDescriptionLineParser.Factory | | FastaDescriptionLineParser.Factory | NotPorted |
| | FastaFormat | | FastaFormat | NotPorted |
| | FeatureTableParser | | FeatureTableParser | Complete |
| | GAMEFormat | | GAMEFormat | NotPorted |
| | GenbankFileFormer | | GenbankFileFormer | NotPorted |
| | GenbankFormat | | GenbankFormat | Partial |
| | GenbankProcessor | | GenbankProcessor | Complete |
| | GenbankProcessor.Factory | | GenbankProcessor.Factory | Complete |
| | GenbankXmlFormat | | GenbankXmlFormat | NotPorted |
| | GenEmblFeatureComparator | | GenEmblFeatureComparator | NotPorted |
| | GenEmblPropertyComparator | | GenEmblPropertyComparator | NotPorted |
| | GenpeptFormat | | GenpeptFormat | NotPorted |
| | IntegerTokenization | | IntegerTokenization | NotPorted |
| | MSFAlignmentFormat | | MSFAlignmentFormat | NotPorted |
| | NameTokenization | | NameTokenization | Partial |
| | OrganismParser | | OrganismParser | NotPorted |
| | OrganismParser.Factory | | OrganismParser.Factory | NotPorted |
| | ParseException | | ParseException | Complete |
| | ProteinRefSeqFileFormer | | ProteinRefSeqFileFormer | NotPorted |
| | ProteinRefSeqProcessor | | ProteinRefSeqProcessor | NotPorted |
| | ProteinRefSeqProcessor.Factory | | ProteinRefSeqProcessor.Factory | NotPorted |
| | ReferenceAnnotation | | ReferenceAnnotation | NotPorted |
| | SeqFileFormer | | ISeqFileFormer | NotPorted |
| | SeqIOAdapter | | SeqIOAdapter | NotPorted |
| | SeqIOConstants | | SeqIOConstants | NotPorted |
| | SeqIOEventEmitter | | SeqIOEventEmitter | NotPorted |
| | SeqIOFilter | | SeqIOFilter | NotPorted |
| | SeqIOListener | | ISeqIOListener | Complete |
| | SeqIOTools | | SeqIOTools | Partial |
| | SequenceBuilder | | ISequenceBuilder | Complete |
| | SequenceBuilderBase | | SequenceBuilderBase | Complete |
| | SequenceBuilderFactory | | ISequenceBuilderFactory | Complete |
| | SequenceBuilderFilter | | SequenceBuilderFilter | Complete |
| | SequenceDBSequenceBuilder | | SequenceDBSequenceBuilder | NotPorted |
| | SequenceFormat | | ISequenceFormat | Complete |
| | SimpleAssemblyBuilder | | SimpleAssemblyBuilder | NotPorted |
| | SimpleSequenceBuilder | | SimpleSequenceBuilder | NotPorted |
| | SmartSequenceBuilder | | SmartSequenceBuilder | Complete |
| | StreamParser | | IStreamParser | Complete |
| | StreamReader | | StreamReader | Complete |
| | StreamWriter | | StreamWriter | NotPorted |
| | SubIntegerTokenization | | SubIntegerTokenization | NotPorted |
| | SwissprotFileFormer | | SwissprotFileFormer | NotPorted |
| | SwissprotProcessor | | SwissprotProcessor | NotPorted |
| | SwissprotProcessor.Factory | | SwissprotProcessor.Factory | NotPorted |
| | SymbolListCharSequence | | SymbolListCharSequence | NotPorted |
| | SymbolReader | | ISymbolReader | NotPorted |
| | SymbolTokenization | | ISymbolTokenization | Complete |
| | SymbolTokenization.TokenType | | SymbolTokenization.TokenType | Complete |
| | WordTokenization | | WordTokenization | Complete |
| org.biojava.bio.seq.io.agave | BioSharp.Core.Bio.Seq.IO.Agave | |
| | Agave2AgaveAnnotFilter | | Agave2AgaveAnnotFilter | NotPorted |
| | AGAVEAltIdsPropHandler | | AGAVEAltIdsPropHandler | NotPorted |
| | AGAVEAnnotationsHandler | | AGAVEAnnotationsHandler | NotPorted |
| | AGAVEAnnotFilter | | IAGAVEAnnotFilter | NotPorted |
| | AGAVEAnnotFilterFactory | | IAGAVEAnnotFilterFactory | NotPorted |
| | AGAVEAssemblyHandler | | AGAVEAssemblyHandler | NotPorted |
| | AGAVEBioSeqCallbackItf | | IAGAVEBioSeqCallbackItf | NotPorted |
| | AGAVEBioSeqHandler | | AGAVEBioSeqHandler | NotPorted |
| | AGAVEBioSequenceHandler | | AGAVEBioSequenceHandler | NotPorted |
| | AGAVECallbackItf | | IAGAVECallbackItf | NotPorted |
| | AGAVECdsHandler | | AGAVECdsHandler | NotPorted |
| | AGAVEChromosomeCallbackItf | | IAGAVEChromosomeCallbackItf | NotPorted |
| | AGAVEChromosomeHandler | | AGAVEChromosomeHandler | NotPorted |
| | AGAVEClassificationHandler | | AGAVEClassificationHandler | NotPorted |
| | AGAVECompResultHandler | | AGAVECompResultHandler | NotPorted |
| | AGAVEComputationHandler | | AGAVEComputationHandler | NotPorted |
| | AGAVEContigCallbackItf | | IAGAVEContigCallbackItf | NotPorted |
| | AGAVEContigHandler | | AGAVEContigHandler | NotPorted |
| | AGAVEDbId | | AGAVEDbId | NotPorted |
| | AGAVEDbIdCallbackItf | | IAGAVEDbIdCallbackItf | NotPorted |
| | AGAVEDbIdPropCallbackItf | | IAGAVEDbIdPropCallbackItf | NotPorted |
| | AGAVEDbIdPropHandler | | AGAVEDbIdPropHandler | NotPorted |
| | AGAVEDescPropHandler | | AGAVEDescPropHandler | NotPorted |
| | AGAVEElementIdPropHandler | | AGAVEElementIdPropHandler | NotPorted |
| | AGAVEEvidenceCallbackItf | | IAGAVEEvidenceCallbackItf | NotPorted |
| | AGAVEEvidenceHandler | | AGAVEEvidenceHandler | NotPorted |
| | AGAVEExonsPropHandler | | AGAVEExonsPropHandler | NotPorted |
| | AGAVEFeatureCallbackItf | | IAGAVEFeatureCallbackItf | NotPorted |
| | AGAVEFragmentOrderHandler | | AGAVEFragmentOrderHandler | NotPorted |
| | AGAVEFragmentOrientationHandler | | AGAVEFragmentOrientationHandler | NotPorted |
| | AGAVEGeneHandler | | AGAVEGeneHandler | NotPorted |
| | AGAVEHandler | | AGAVEHandler | NotPorted |
| | AGAVEIdAlias | | AGAVEIdAlias | NotPorted |
| | AGAVEIdAliasCallbackItf | | IAGAVEIdAliasCallbackItf | NotPorted |
| | AGAVEIdAliasPropHandler | | AGAVEIdAliasPropHandler | NotPorted |
| | AGAVEKeywordPropHandler | | AGAVEKeywordPropHandler | NotPorted |
| | AGAVEMapLocation | | AGAVEMapLocation | NotPorted |
| | AGAVEMapLocationPropHandler | | AGAVEMapLocationPropHandler | NotPorted |
| | AGAVEMapPosition | | AGAVEMapPosition | NotPorted |
| | AGAVEMapPositionPropHandler | | AGAVEMapPositionPropHandler | NotPorted |
| | AGAVEMatchAlignPropHandler | | AGAVEMatchAlignPropHandler | NotPorted |
| | AGAVEMatchDescPropHandler | | AGAVEMatchDescPropHandler | NotPorted |
| | AGAVEMatchRegion | | AGAVEMatchRegion | NotPorted |
| | AGAVEMatchRegionPropHandler | | AGAVEMatchRegionPropHandler | NotPorted |
| | AGAVEMrnaHandler | | AGAVEMrnaHandler | NotPorted |
| | AGAVENotePropHandler | | AGAVENotePropHandler | NotPorted |
| | AGAVEPredictedProteinHandler | | AGAVEPredictedProteinHandler | NotPorted |
| | AGAVEProperty | | AGAVEProperty | NotPorted |
| | AGAVEQualifierPropHandler | | AGAVEQualifierPropHandler | NotPorted |
| | AGAVEQueryRegion | | AGAVEQueryRegion | NotPorted |
| | AGAVEQueryRegionPropHandler | | AGAVEQueryRegionPropHandler | NotPorted |
| | AGAVERelatedAnnot | | AGAVERelatedAnnot | NotPorted |
| | AGAVERelatedAnnotPropHandler | | AGAVERelatedAnnotPropHandler | NotPorted |
| | AGAVEResultGroupHandler | | AGAVEResultGroupHandler | NotPorted |
| | AGAVEResultPropertyPropHandler | | AGAVEResultPropertyPropHandler | NotPorted |
| | AGAVESciPropertyPropHandler | | AGAVESciPropertyPropHandler | NotPorted |
| | AGAVESeqFeatureHandler | | AGAVESeqFeatureHandler | NotPorted |
| | AGAVESeqLocationPropHandler | | AGAVESeqLocationPropHandler | NotPorted |
| | AGAVESeqMapHandler | | AGAVESeqMapHandler | NotPorted |
| | AGAVESeqPropHandler | | AGAVESeqPropHandler | NotPorted |
| | AGAVETranscriptHandler | | AGAVETranscriptHandler | NotPorted |
| | AGAVEUnorderedFragmentsHandler | | AGAVEUnorderedFragmentsHandler | NotPorted |
| | AGAVEViewPropHandler | | AGAVEViewPropHandler | NotPorted |
| | AgaveWriter | | AgaveWriter | NotPorted |
| | AGAVEXref | | AGAVEXref | NotPorted |
| | AGAVEXrefCallbackItf | | IAGAVEXrefCallbackItf | NotPorted |
| | AGAVEXrefPropHandler | | AGAVEXrefPropHandler | NotPorted |
| | AGAVEXrefPropPropHandler | | AGAVEXrefPropPropHandler | NotPorted |
| | AGAVEXrefs | | AGAVEXrefs | NotPorted |
| | AGAVEXrefsPropHandler | | AGAVEXrefsPropHandler | NotPorted |
| | DelegationManager | | IDelegationManager | NotPorted |
| | ElementRecognizer | | IElementRecognizer | NotPorted |
| | ElementRecognizer.AllElementRecognizer | | ElementRecognizer.AllElementRecognizer | NotPorted |
| | ElementRecognizer.ByLocalName | | ElementRecognizer.ByLocalName | NotPorted |
| | ElementRecognizer.ByNSName | | ElementRecognizer.ByNSName | NotPorted |
| | ElementRecognizer.HasAttribute | | ElementRecognizer.HasAttribute | NotPorted |
| | Embl2AgaveAnnotFilter | | Embl2AgaveAnnotFilter | NotPorted |
| | SAX2StAXAdaptor | | SAX2StAXAdaptor | NotPorted |
| | SequenceHandler | | ISequenceHandler | NotPorted |
| | SimpleAnnotFilter | | SimpleAnnotFilter | NotPorted |
| | StAXContentHandler | | IStAXContentHandler | NotPorted |
| | StAXContentHandlerBase | | StAXContentHandlerBase | NotPorted |
| | StAXFeatureHandler | | StAXFeatureHandler | NotPorted |
| | StAXHandlerFactory | | IStAXHandlerFactory | NotPorted |
| | StAXPropertyHandler | | StAXPropertyHandler | NotPorted |
| | UtilHelper | | UtilHelper | NotPorted |
| org.biojava.bio.seq.io.filterxml | BioSharp.Core.Bio.Seq.IO.Filterxml | |
| | XMLAnnotationTypeHandler | | XMLAnnotationTypeHandler | NotPorted |
| | XMLAnnotationTypeHandler.CollectionConstraintHandler | | XMLAnnotationTypeHandler.ICollectionConstraintHandler | NotPorted |
| | XMLAnnotationTypeHandler.CollectionConstraintHandlerFactory | | XMLAnnotationTypeHandler.ICollectionConstraintHandlerFactory | NotPorted |
| | XMLAnnotationTypeHandler.PropertyConstraintHandler | | XMLAnnotationTypeHandler.IPropertyConstraintHandler | NotPorted |
| | XMLAnnotationTypeHandler.PropertyConstraintHandlerFactory | | XMLAnnotationTypeHandler.IPropertyConstraintHandlerFactory | NotPorted |
| | XMLAnnotationTypeWriter | | XMLAnnotationTypeWriter | NotPorted |
| | XMLAnnotationTypeWriter.XMLCollectionConstraintWriter | | XMLAnnotationTypeWriter.IXMLCollectionConstraintWriter | NotPorted |
| | XMLAnnotationTypeWriter.XMLPropertyConstraintWriter | | XMLAnnotationTypeWriter.IXMLPropertyConstraintWriter | NotPorted |
| | XMLFilterHandler | | XMLFilterHandler | NotPorted |
| | XMLFilterHandler.FilterHandler | | XMLFilterHandler.IFilterHandler | NotPorted |
| | XMLFilterHandler.FilterHandlerFactory | | XMLFilterHandler.IFilterHandlerFactory | NotPorted |
| | XMLFilterWriter | | XMLFilterWriter | NotPorted |
| | XMLFilterWriter.FilterWriter | | XMLFilterWriter.IFilterWriter | NotPorted |
| org.biojava.bio.seq.io.game | BioSharp.Core.Bio.Seq.IO.Game | |
| | ElementRecognizer | | IElementRecognizer | NotPorted |
| | ElementRecognizer.AllElementRecognizer | | ElementRecognizer.AllElementRecognizer | NotPorted |
| | ElementRecognizer.ByLocalName | | ElementRecognizer.ByLocalName | NotPorted |
| | ElementRecognizer.ByNSName | | ElementRecognizer.ByNSName | NotPorted |
| | ElementRecognizer.HasAttribute | | ElementRecognizer.HasAttribute | NotPorted |
| | GAMEAnnotationHandler | | GAMEAnnotationHandler | NotPorted |
| | GAMEAspectPropHandler | | GAMEAspectPropHandler | NotPorted |
| | GAMEDbxrefPropHandler | | GAMEDbxrefPropHandler | NotPorted |
| | GAMEDescriptionPropHandler | | GAMEDescriptionPropHandler | NotPorted |
| | GAMEFeatureCallbackItf | | IGAMEFeatureCallbackItf | NotPorted |
| | GAMEFeatureSetHandler | | GAMEFeatureSetHandler | NotPorted |
| | GAMEFeatureSetPropHandler | | GAMEFeatureSetPropHandler | NotPorted |
| | GAMEFeatureSpanHandler | | GAMEFeatureSpanHandler | NotPorted |
| | GAMEGenePropHandler | | GAMEGenePropHandler | NotPorted |
| | GAMEHandler | | GAMEHandler | NotPorted |
| | GAMEMapPosPropHandler | | GAMEMapPosPropHandler | NotPorted |
| | GAMENameCallbackItf | | IGAMENameCallbackItf | NotPorted |
| | GAMENamePropHandler | | GAMENamePropHandler | NotPorted |
| | GAMEResiduesPropHandler | | GAMEResiduesPropHandler | NotPorted |
| | GAMESeqPropHandler | | GAMESeqPropHandler | NotPorted |
| | GAMESeqRelPropHandler | | GAMESeqRelPropHandler | NotPorted |
| | GAMESpanPropHandler | | GAMESpanPropHandler | NotPorted |
| | GAMETranscriptCallbackItf | | IGAMETranscriptCallbackItf | NotPorted |
| | GAMETypePropHandler | | GAMETypePropHandler | NotPorted |
| | SequenceContentHandlerBase | | SequenceContentHandlerBase | NotPorted |
| | StAXFeatureHandler | | StAXFeatureHandler | NotPorted |
| | StAXHandlerFactory | | IStAXHandlerFactory | NotPorted |
| | StAXPropertyHandler | | StAXPropertyHandler | NotPorted |
| org.biojava.bio.seq.io.game12 | BioSharp.Core.Bio.Seq.IO.Game12 | |
| | GAMEAnnotationHandler | | GAMEAnnotationHandler | NotPorted |
| | GAMEAspectHandler | | GAMEAspectHandler | NotPorted |
| | GAMEDbxrefHandler | | GAMEDbxrefHandler | NotPorted |
| | GAMEFeatureSetHandler | | GAMEFeatureSetHandler | NotPorted |
| | GAMEFeatureSpanHandler | | GAMEFeatureSpanHandler | NotPorted |
| | GAMEGeneHandler | | GAMEGeneHandler | NotPorted |
| | GAMEHandler | | GAMEHandler | NotPorted |
| | GAMEPropertyHandler | | GAMEPropertyHandler | NotPorted |
| | GAMESeqHandler | | GAMESeqHandler | NotPorted |
| | GAMESeqRelHandler | | GAMESeqRelHandler | NotPorted |
| | GAMESpanHandler | | GAMESpanHandler | NotPorted |
| | StAXFeatureHandler | | StAXFeatureHandler | NotPorted |
| | StAXHandlerFactory | | IStAXHandlerFactory | NotPorted |
| org.biojava.bio.seq.projection | BioSharp.Core.Bio.Seq.Projection | |
| | ProjectedFeature | | ProjectedFeature | Partial |
| | ProjectedFeatureHolder | | ProjectedFeatureHolder | Complete |
| | Projection | | IProjection | Complete |
| | ProjectionContext | | IProjectionContext | Complete |
| | ProjectionEngine | | ProjectionEngine | Partial |
| | ProjectionEngine.Instantiator | | ProjectionEngine.IInstantiator | NotPorted |
| | ProjectionEngine.TemplateProjector | | ProjectionEngine.ITemplateProjector | NotPorted |
| | ProjectionUtils | | ProjectionUtils | NotPorted |
| | ReparentContext | | ReparentContext | Partial |
| | TranslateFlipContext | | TranslateFlipContext | NotPorted |
| org.biojava.bio.structure | BioSharp.Core.Bio.Structure | |
| | AlphaCTools | | AlphaCTools | NotPorted |
| | AminoAcid | | IAminoAcid | NotPorted |
| | AminoAcidImpl | | AminoAcidImpl | NotPorted |
| | Atom | | IAtom | NotPorted |
| | AtomImpl | | AtomImpl | NotPorted |
| | AtomIterator | | AtomIterator | NotPorted |
| | Calc | | Calc | NotPorted |
| | Chain | | IChain | NotPorted |
| | ChainImpl | | ChainImpl | NotPorted |
| | Compound | | Compound | NotPorted |
| | DBRef | | DBRef | NotPorted |
| | Group | | IGroup | NotPorted |
| | GroupIterator | | GroupIterator | NotPorted |
| | HetatomImpl | | HetatomImpl | NotPorted |
| | Mutator | | Mutator | NotPorted |
| | NucleotideImpl | | NucleotideImpl | NotPorted |
| | PDBHeader | | PDBHeader | NotPorted |
| | SSBond | | SSBond | NotPorted |
| | StandardAminoAcid | | StandardAminoAcid | NotPorted |
| | Structure | | IStructure | NotPorted |
| | StructureException | | StructureException | NotPorted |
| | StructureImpl | | StructureImpl | NotPorted |
| | StructureTools | | StructureTools | NotPorted |
| | SVDSuperimposer | | SVDSuperimposer | NotPorted |
| org.biojava.bio.structure.align | BioSharp.Core.Bio.Structure.Align | |
| | ClusterAltAligs | | ClusterAltAligs | NotPorted |
| | StrucAligParameters | | StrucAligParameters | NotPorted |
| | StructurePairAligner | | StructurePairAligner | NotPorted |
| org.biojava.bio.structure.align.helper | BioSharp.Core.Bio.Structure.Align.Helper | |
| | AligMatEl | | AligMatEl | NotPorted |
| | AlignTools | | AlignTools | NotPorted |
| | GapArray | | GapArray | NotPorted |
| | IndexPair | | IndexPair | NotPorted |
| | JointFragments | | JointFragments | NotPorted |
| org.biojava.bio.structure.align.pairwise | BioSharp.Core.Bio.Structure.Align.Pairwise | |
| | Alignable | | IAlignable | NotPorted |
| | AligNPE | | AligNPE | NotPorted |
| | AltAligComparator | | AltAligComparator | NotPorted |
| | AlternativeAlignment | | AlternativeAlignment | NotPorted |
| | FragmentJoiner | | FragmentJoiner | NotPorted |
| | FragmentPair | | FragmentPair | NotPorted |
| | Gotoh | | Gotoh | NotPorted |
| | StrCompAlignment | | StrCompAlignment | NotPorted |
| org.biojava.bio.structure.gui | BioSharp.Core.Bio.Structure.Gui | |
| | BiojavaJmol | | BiojavaJmol | NotPorted |
| | JMatrixPanel | | JMatrixPanel | NotPorted |
| | RasmolCommandListener | | RasmolCommandListener | NotPorted |
| | ScaleableMatrixPanel | | ScaleableMatrixPanel | NotPorted |
| org.biojava.bio.structure.io | BioSharp.Core.Bio.Structure.IO | |
| | CAConverter | | CAConverter | NotPorted |
| | DASStructureClient | | DASStructureClient | NotPorted |
| | FileConvert | | FileConvert | NotPorted |
| | PDBFileParser | | PDBFileParser | NotPorted |
| | PDBFileReader | | PDBFileReader | NotPorted |
| | PDBMSDReader | | PDBMSDReader | NotPorted |
| | PDBParseException | | PDBParseException | NotPorted |
| | PDBSRSReader | | PDBSRSReader | NotPorted |
| | SeqRes2AtomAligner | | SeqRes2AtomAligner | NotPorted |
| | StructureIO | | IStructureIO | NotPorted |
| | StructureIOFile | | IStructureIOFile | NotPorted |
| org.biojava.bio.structure.jama | BioSharp.Core.Bio.Structure.Jama | |
| | CholeskyDecomposition | | CholeskyDecomposition | NotPorted |
| | EigenvalueDecomposition | | EigenvalueDecomposition | NotPorted |
| | LUDecomposition | | LUDecomposition | NotPorted |
| | Maths | | Maths | NotPorted |
| | Matrix | | Matrix | NotPorted |
| | QRDecomposition | | QRDecomposition | NotPorted |
| | SingularValueDecomposition | | SingularValueDecomposition | NotPorted |
| org.biojava.bio.structure.server | BioSharp.Core.Bio.Structure.Server | |
| | DemoStructureServer | | DemoStructureServer | NotPorted |
| | FlatFileInstallation | | FlatFileInstallation | NotPorted |
| | PDBFilter | | IPDBFilter | NotPorted |
| | PDBInstallation | | IPDBInstallation | NotPorted |
| | PrepareIndexFile | | PrepareIndexFile | NotPorted |
| | SimpleStructureServer | | SimpleStructureServer | NotPorted |
| | StructureEvent | | IStructureEvent | NotPorted |
| | StructureEventImpl | | StructureEventImpl | NotPorted |
| | StructureFetcherRunnable | | StructureFetcherRunnable | NotPorted |
| | StructureListener | | IStructureListener | NotPorted |
| | StructureServer | | IStructureServer | NotPorted |
| org.biojava.bio.symbol | BioSharp.Core.Bio.Symbol | |
| | AbstractAlphabet | | AbstractAlphabet | Partial |
| | AbstractLocation | | AbstractLocation | Complete |
| | AbstractLocationDecorator | | AbstractLocationDecorator | Complete |
| | AbstractManyToOneTranslationTable | | AbstractManyToOneTranslationTable | Partial |
| | AbstractRangeLocation | | AbstractRangeLocation | Partial |
| | AbstractReversibleTranslationTable | | AbstractReversibleTranslationTable | Complete |
| | AbstractSymbol | | AbstractSymbol | Complete |
| | AbstractSymbolList | | AbstractSymbolList | Complete |
| | Alignment | | IAlignment | Stub |
| | Alignment.SymbolListIterator | | Alignment.SymbolListIterator | NotPorted |
| | Alphabet | | IAlphabet | Complete |
| | AlphabetIndex | | IAlphabetIndex | Complete |
| | AlphabetManager | | AlphabetManager | Partial |
| | AtomicSymbol | | IAtomicSymbol | Partial |
| | BasisSymbol | | IBasisSymbol | Partial |
| | BetweenLocation | | BetweenLocation | Complete |
| | ChunkedSymbolList | | ChunkedSymbolList | Complete |
| | CircularLocation | | CircularLocation | NotPorted |
| | CodonPref | | ICodonPref | NotPorted |
| | CodonPrefFilter | | ICodonPrefFilter | NotPorted |
| | CodonPrefFilter.AcceptAll | | CodonPrefFilter.AcceptAll | NotPorted |
| | CodonPrefFilter.ByName | | CodonPrefFilter.ByName | NotPorted |
| | CodonPrefFilter.EverythingToXML | | CodonPrefFilter.EverythingToXML | NotPorted |
| | CodonPrefTools | | CodonPrefTools | NotPorted |
| | DNAAmbPack | | DNAAmbPack | Complete |
| | DNANoAmbPack | | DNANoAmbPack | Complete |
| | DoubleAlphabet | | DoubleAlphabet | NotPorted |
| | DoubleAlphabet.DoubleRange | | DoubleAlphabet.DoubleRange | NotPorted |
| | DoubleAlphabet.DoubleSymbol | | DoubleAlphabet.DoubleSymbol | NotPorted |
| | DoubleAlphabet.SubDoubleAlphabet | | DoubleAlphabet.SubDoubleAlphabet | NotPorted |
| | DummySymbolList | | DummySymbolList | NotPorted |
| | Edit | | Edit | Complete |
| | FiniteAlphabet | | IFiniteAlphabet | Partial |
| | FundamentalAtomicSymbol | | FundamentalAtomicSymbol | Partial |
| | FuzzyLocation | | FuzzyLocation | Complete |
| | FuzzyLocation.RangeResolver | | FuzzyLocation.IRangeResolver | Complete |
| | FuzzyPointLocation | | FuzzyPointLocation | Complete |
| | FuzzyPointLocation.PointResolver | | FuzzyPointLocation.IPointResolver | Complete |
| | GappedSymbolList | | IGappedSymbolList | NotPorted |
| | IllegalAlphabetException | | IllegalAlphabetException | Complete |
| | IllegalSymbolException | | IllegalSymbolException | Complete |
| | IntegerAlphabet | | IntegerAlphabet | NotPorted |
| | IntegerAlphabet.IntegerSymbol | | IntegerAlphabet.IntegerSymbol | NotPorted |
| | IntegerAlphabet.SubIntegerAlphabet | | IntegerAlphabet.SubIntegerAlphabet | NotPorted |
| | Location | | ILocation | Partial |
| | LocationTools | | LocationTools | Partial |
| | ManyToOneTranslationTable | | IManyToOneTranslationTable | Complete |
| | MergeLocation | | MergeLocation | NotPorted |
| | MotifTools | | MotifTools | Partial |
| | PackedSymbolList | | PackedSymbolList | Partial |
| | PackedSymbolListFactory | | PackedSymbolListFactory | Complete |
| | Packing | | IPacking | Complete |
| | PackingFactory | | PackingFactory | Complete |
| | PointLocation | | PointLocation | Complete |
| | RangeLocation | | RangeLocation | Complete |
| | RelabeledAlignment | | RelabeledAlignment | NotPorted |
| | ReversibleTranslationTable | | IReversibleTranslationTable | Complete |
| | SimpleAlignment | | SimpleAlignment | NotPorted |
| | SimpleAlphabet | | SimpleAlphabet | Partial |
| | SimpleAtomicSymbol | | SimpleAtomicSymbol | Partial |
| | SimpleCodonPref | | SimpleCodonPref | NotPorted |
| | SimpleGappedSymbolList | | SimpleGappedSymbolList | NotPorted |
| | SimpleGappedSymbolList.Block | | SimpleGappedSymbolList.Block | NotPorted |
| | SimpleGeneticCodeTable | | SimpleGeneticCodeTable | Complete |
| | SimpleManyToOneTranslationTable | | SimpleManyToOneTranslationTable | Complete |
| | SimpleReversibleTranslationTable | | SimpleReversibleTranslationTable | Partial |
| | SimpleSymbolList | | SimpleSymbolList | Complete |
| | SimpleSymbolListFactory | | SimpleSymbolListFactory | Complete |
| | SimpleSymbolPropertyTable | | SimpleSymbolPropertyTable | NotPorted |
| | SimpleTranslationTable | | SimpleTranslationTable | NotPorted |
| | SingletonAlphabet | | SingletonAlphabet | Partial |
| | SoftMaskedAlphabet | | SoftMaskedAlphabet | NotPorted |
| | SoftMaskedAlphabet.MaskingDetector | | SoftMaskedAlphabet.IMaskingDetector | NotPorted |
| | SuffixTree | | SuffixTree | NotPorted |
| | SuffixTree.SuffixNode | | SuffixTree.SuffixNode | NotPorted |
| | Symbol | | ISymbol | Complete |
| | SymbolList | | ISymbolList | Complete |
| | SymbolListFactory | | ISymbolListFactory | Complete |
| | SymbolListViews | | SymbolListViews | Partial |
| | SymbolPropertyTable | | ISymbolPropertyTable | NotPorted |
| | TranslationTable | | ITranslationTable | Complete |
| | UkkonenSuffixTree | | UkkonenSuffixTree | NotPorted |
| | UkkonenSuffixTree.SuffixNode | | UkkonenSuffixTree.SuffixNode | NotPorted |
| | WobbleDistribution | | IWobbleDistribution | NotPorted |
| org.biojava.bio.symbol.SoftMaskedAlphabet | BioSharp.Core.Bio.Symbol.SoftMaskedAlphabet | |
| | MaskingDetector.DefaultMaskingDetector | | MaskingDetector.DefaultMaskingDetector | NotPorted |
| org.biojava.bio.taxa | BioSharp.Core.Bio.Taxa | |
| | AbstractTaxon | | AbstractTaxon | NotPorted |
| | CircularReferenceException | | CircularReferenceException | NotPorted |
| | EbiFormat | | EbiFormat | NotPorted |
| | SimpleTaxon | | SimpleTaxon | NotPorted |
| | SimpleTaxonFactory | | SimpleTaxonFactory | NotPorted |
| | Taxon | | ITaxon | NotPorted |
| | TaxonFactory | | ITaxonFactory | NotPorted |
| | TaxonParser | | ITaxonParser | NotPorted |
| | WeakTaxon | | WeakTaxon | NotPorted |
| | WeakTaxonFactory | | WeakTaxonFactory | NotPorted |
| org.biojava.directory | BioSharp.Core.Directory | |
| | OBDARegistryParser | | OBDARegistryParser | NotPorted |
| | ProviderNotFoundException | | ProviderNotFoundException | NotPorted |
| | Registry | | Registry | NotPorted |
| | RegistryConfiguration | | IRegistryConfiguration | NotPorted |
| | RegistryConfiguration.Composite | | RegistryConfiguration.Composite | NotPorted |
| | RegistryConfiguration.Impl | | RegistryConfiguration.Impl | NotPorted |
| | RegistryException | | RegistryException | NotPorted |
| | SequenceDBProvider | | ISequenceDBProvider | NotPorted |
| | SystemRegistry | | SystemRegistry | NotPorted |
| org.biojava.naming | BioSharp.Core.Naming | |
| | ObdaContext | | ObdaContext | NotPorted |
| | ObdaInitialContextFactory | | ObdaInitialContextFactory | NotPorted |
| | ObdaUriParser | | ObdaUriParser | NotPorted |
| org.biojava.ontology | BioSharp.Core.Ontology | |
| | AbstractTerm | | AbstractTerm | NotPorted |
| | AlreadyExistsException | | AlreadyExistsException | NotPorted |
| | DefaultOps | | DefaultOps | NotPorted |
| | IntegerOntology | | IntegerOntology | NotPorted |
| | InvalidTermException | | InvalidTermException | NotPorted |
| | Ontology | | IOntology | NotPorted |
| | Ontology.Impl | | Ontology.Impl | NotPorted |
| | OntologyException | | OntologyException | NotPorted |
| | OntologyFactory | | IOntologyFactory | NotPorted |
| | OntologyOps | | IOntologyOps | NotPorted |
| | OntologyTerm | | IOntologyTerm | NotPorted |
| | OntologyTerm.Impl | | OntologyTerm.Impl | NotPorted |
| | OntoTools | | OntoTools | Stub |
| | RemoteTerm | | IRemoteTerm | NotPorted |
| | RemoteTerm.Impl | | RemoteTerm.Impl | NotPorted |
| | Term | | ITerm | Stub |
| | Term.Impl | | Term.Impl | NotPorted |
| | Triple | | ITriple | NotPorted |
| | Triple.Impl | | Triple.Impl | NotPorted |
| | Variable | | IVariable | NotPorted |
| | Variable.Impl | | Variable.Impl | NotPorted |
| org.biojava.ontology.io | BioSharp.Core.Ontology.IO | |
| | GOParser | | GOParser | NotPorted |
| | TabDelimParser | | TabDelimParser | NotPorted |
| org.biojava.stats.svm | BioSharp.Core.Stats.Svm | |
| | AbstractSVMClassifierModel | | AbstractSVMClassifierModel | NotPorted |
| | AbstractSVMTarget | | AbstractSVMTarget | NotPorted |
| | CachingKernel | | CachingKernel | NotPorted |
| | DiagonalAddKernel | | DiagonalAddKernel | NotPorted |
| | DiagonalCachingKernel | | DiagonalCachingKernel | NotPorted |
| | ItemValue | | IItemValue | NotPorted |
| | LinearKernel | | LinearKernel | NotPorted |
| | ListSumKernel | | ListSumKernel | NotPorted |
| | NestedKernel | | NestedKernel | NotPorted |
| | NormalizingKernel | | NormalizingKernel | NotPorted |
| | PolynomialKernel | | PolynomialKernel | NotPorted |
| | RadialBaseKernel | | RadialBaseKernel | NotPorted |
| | SigmoidKernel | | SigmoidKernel | NotPorted |
| | SimpleItemValue | | SimpleItemValue | NotPorted |
| | SimpleSVMClassifierModel | | SimpleSVMClassifierModel | NotPorted |
| | SimpleSVMTarget | | SimpleSVMTarget | NotPorted |
| | SMORegressionTrainer | | SMORegressionTrainer | NotPorted |
| | SMOTrainer | | SMOTrainer | NotPorted |
| | SparseVector | | SparseVector | NotPorted |
| | SparseVector.NormalizingKernel | | SparseVector.NormalizingKernel | NotPorted |
| | SVMClassifierModel | | ISVMClassifierModel | NotPorted |
| | SVMKernel | | ISVMKernel | NotPorted |
| | SVMRegressionModel | | SVMRegressionModel | NotPorted |
| | SVMTarget | | ISVMTarget | NotPorted |
| | TrainingContext | | ITrainingContext | NotPorted |
| | TrainingEvent | | TrainingEvent | NotPorted |
| | TrainingListener | | ITrainingListener | NotPorted |
| org.biojava.stats.svm.tools | BioSharp.Core.Stats.Svm.Tools | |
| | ClassifierExample | | ClassifierExample | NotPorted |
| | ClassifierExample.PointClassifier | | ClassifierExample.PointClassifier | NotPorted |
| | Classify | | Classify | NotPorted |
| | SuffixTreeKernel | | SuffixTreeKernel | NotPorted |
| | SuffixTreeKernel.DepthScaler | | SuffixTreeKernel.IDepthScaler | NotPorted |
| | SuffixTreeKernel.MultipleScalar | | SuffixTreeKernel.MultipleScalar | NotPorted |
| | SuffixTreeKernel.NullModelScaler | | SuffixTreeKernel.NullModelScaler | NotPorted |
| | SuffixTreeKernel.SelectionScalar | | SuffixTreeKernel.SelectionScalar | NotPorted |
| | SuffixTreeKernel.UniformScaler | | SuffixTreeKernel.UniformScaler | NotPorted |
| | SVM_Light | | SVM_Light | NotPorted |
| | SVM_Light.LabelledVector | | SVM_Light.LabelledVector | NotPorted |
| | Train | | Train | NotPorted |
| | TrainRegression | | TrainRegression | NotPorted |
| org.biojava.utils | BioSharp.Core.Utils | |
| | AbstractChangeable | | AbstractChangeable | Complete |
| | ActivityListener | | IActivityListener | NotPorted |
| | AssertionFailure | | AssertionFailure | NotPorted |
| | BeanAsMap | | BeanAsMap | NotPorted |
| | Changeable | | IChangeable | Complete |
| | ChangeAdapter | | ChangeAdapter | Complete |
| | ChangeEvent | | ChangeEvent | Complete |
| | ChangeForwarder | | ChangeForwarder | Complete |
| | ChangeForwarder.Retyper | | ChangeForwarder.Retyper | Complete |
| | ChangeHub | | IChangeHub | NotPorted |
| | ChangeListener | | IChangeListener | Complete |
| | ChangeListener.AlwaysVetoListener | | ChangeListener.AlwaysVetoListener | NotPorted |
| | ChangeListener.ChangeEventRecorder | | ChangeListener.ChangeEventRecorder | Complete |
| | ChangeListener.LoggingListener | | ChangeListener.LoggingListener | Complete |
| | ChangeSupport | | ChangeSupport | Complete |
| | ChangeType | | ChangeType | Complete |
| | ChangeVetoException | | ChangeVetoException | Complete |
| | ClassTools | | ClassTools | NotPorted |
| | Commitable | | ICommitable | NotPorted |
| | CommitFailure | | CommitFailure | NotPorted |
| | Constants | | Constants | NotPorted |
| | ExecRunner | | ExecRunner | NotPorted |
| | FileAsList | | FileAsList | NotPorted |
| | IndexedChangeHub | | IndexedChangeHub | NotPorted |
| | JDBCConnectionPool | | JDBCConnectionPool | NotPorted |
| | JDBCPooledDataSource | | JDBCPooledDataSource | NotPorted |
| | ListTools | | ListTools<T> | Partial |
| | ListTools.Doublet | | ListTools.Doublet | NotPorted |
| | ListTools.Mapper | | ListTools.IMapper | NotPorted |
| | ListTools.SeriesList | | ListTools.SeriesList | NotPorted |
| | ListTools.Triplet | | ListTools.Triplet | NotPorted |
| | MergingIterator | | MergingIterator | NotPorted |
| | MergingSet | | MergingSet | NotPorted |
| | ObjectUtil | | ObjectUtil | NotPorted |
| | OverlayMap | | OverlayMap | NotPorted |
| | ParseErrorEvent | | ParseErrorEvent | Complete |
| | ParseErrorListener | | IParseErrorListener | Complete |
| | ParseErrorSource | | IParseErrorSource | Complete |
| | ParserException | | ParserException | Complete |
| | ProcessTimeoutException | | ProcessTimeoutException | NotPorted |
| | ProcessTools | | ProcessTools | NotPorted |
| | RepeatedCharSequence | | RepeatedCharSequence | NotPorted |
| | Services | | Services | NotPorted |
| | SimpleThreadPool | | SimpleThreadPool | NotPorted |
| | SingletonList | | SingletonList<T> | Complete |
| | SmallMap | | SmallMap | NotPorted |
| | SmallSet | | SmallSet | NotPorted |
| | StaticMemberPlaceHolder | | StaticMemberPlaceHolder | NotPorted |
| | ThreadPool | | IThreadPool | NotPorted |
| | TriState | | TriState | NotPorted |
| | TypedProperties | | TypedProperties | NotPorted |
| | Unchangeable | | Unchangeable | Partial |
| org.biojava.utils.automata | BioSharp.Core.Utils.Automata | |
| | ArrayStateMachineToolkit | | ArrayStateMachineToolkit | NotPorted |
| | AutomatonException | | AutomatonException | NotPorted |
| | DfaBuilder | | DfaBuilder | NotPorted |
| | FiniteAutomaton | | FiniteAutomaton | NotPorted |
| | Nfa | | Nfa | NotPorted |
| | NfaBuilder | | INfaBuilder | NotPorted |
| | NfaSubModel | | NfaSubModel | NotPorted |
| | PatternBlitz | | PatternBlitz | NotPorted |
| | PatternListener | | IPatternListener | NotPorted |
| | PatternMaker | | PatternMaker | NotPorted |
| | StateMachineFactory | | IStateMachineFactory | NotPorted |
| | StateMachineInstance | | IStateMachineInstance | NotPorted |
| org.biojava.utils.cache | BioSharp.Core.Utils.Cache | |
| | Cache | | ICache | NotPorted |
| | CacheMap | | ICacheMap | NotPorted |
| | CacheReference | | ICacheReference | NotPorted |
| | ChangeableCache | | ChangeableCache | NotPorted |
| | FixedSizeCache | | FixedSizeCache | NotPorted |
| | FixedSizeMap | | FixedSizeMap | NotPorted |
| | KeyedWeakReference | | KeyedWeakReference | NotPorted |
| | SoftReferenceCache | | SoftReferenceCache | NotPorted |
| | WeakCacheMap | | WeakCacheMap | NotPorted |
| | WeakValueHashMap | | WeakValueHashMap | NotPorted |
| org.biojava.utils.candy | BioSharp.Core.Utils.Candy | |
| | CandyEntry | | CandyEntry | NotPorted |
| | CandyException | | CandyException | NotPorted |
| | CandyFinder | | ICandyFinder | NotPorted |
| | CandyVocabulary | | ICandyVocabulary | NotPorted |
| org.biojava.utils.io | BioSharp.Core.Utils.IO | |
| | CachingInputStream | | CachingInputStream | NotPorted |
| | CountedBufferedReader | | CountedBufferedReader | NotPorted |
| | InputStreamProvider | | InputStreamProvider | NotPorted |
| | LargeBuffer | | LargeBuffer | NotPorted |
| | RAF | | RAF | NotPorted |
| | RandomAccessReader | | RandomAccessReader | NotPorted |
| | Seekable | | ISeekable | NotPorted |
| | UncompressInputStream | | UncompressInputStream | NotPorted |
| org.biojava.utils.lsid | BioSharp.Core.Utils.Lsid | |
| | Identifiable | | IIdentifiable | NotPorted |
| | LifeScienceIdentifier | | LifeScienceIdentifier | Partial |
| | LifeScienceIdentifierParseException | | LifeScienceIdentifierParseException | Partial |
| org.biojava.utils.math | BioSharp.Core.Utils.Math | |
| | BinarySearch | | BinarySearch | NotPorted |
| | ComputeObject | | IComputeObject | NotPorted |
| org.biojava.utils.net | BioSharp.Core.Utils.Net | |
| | URLFactory | | IURLFactory | NotPorted |
| org.biojava.utils.process | BioSharp.Core.Utils.Process | |
| | ExternalProcess | | ExternalProcess | NotPorted |
| | InputHandler | | IInputHandler | NotPorted |
| | OutputHandler | | IOutputHandler | NotPorted |
| | ReaderInputHandler | | ReaderInputHandler | NotPorted |
| | ReaderWriterPipe | | ReaderWriterPipe | NotPorted |
| | SimpleInputHandler | | SimpleInputHandler | NotPorted |
| | SimpleOutputHandler | | SimpleOutputHandler | NotPorted |
| | StreamPipe | | StreamPipe | NotPorted |
| | WriterOutputHandler | | WriterOutputHandler | NotPorted |
| org.biojava.utils.regex | BioSharp.Core.Utils.Regex | |
| | Matcher | | Matcher | NotPorted |
| | Pattern | | Pattern | NotPorted |
| | PatternFactory | | PatternFactory | NotPorted |
| | RegexException | | RegexException | NotPorted |
| | Search | | Search | NotPorted |
| | Search.Listener | | Search.IListener | NotPorted |
| org.biojava.utils.stax | BioSharp.Core.Utils.Stax | |
| | BooleanElementHandlerBase | | BooleanElementHandlerBase | NotPorted |
| | ByteElementHandlerBase | | ByteElementHandlerBase | NotPorted |
| | CharElementHandlerBase | | CharElementHandlerBase | NotPorted |
| | DelegationManager | | IDelegationManager | NotPorted |
| | DoubleElementHandlerBase | | DoubleElementHandlerBase | NotPorted |
| | FloatElementHandlerBase | | FloatElementHandlerBase | NotPorted |
| | IntElementHandlerBase | | IntElementHandlerBase | NotPorted |
| | LongElementHandlerBase | | LongElementHandlerBase | NotPorted |
| | SAX2StAXAdaptor | | SAX2StAXAdaptor | NotPorted |
| | StAXContentHandler | | IStAXContentHandler | NotPorted |
| | StAXContentHandlerBase | | StAXContentHandlerBase | NotPorted |
| | StringElementHandlerBase | | StringElementHandlerBase | NotPorted |
| org.biojava.utils.walker | BioSharp.Core.Utils.Walker | |
| | Visitor | | IVisitor | NotPorted |
| | Walker | | IWalker | NotPorted |
| | WalkerFactory | | WalkerFactory | NotPorted |
| org.biojava.utils.xml | BioSharp.Core.Utils.Xml | |
| | AppBeanRunner | | AppBeanRunner | NotPorted |
| | AppEntry | | IAppEntry | NotPorted |
| | AppException | | AppException | NotPorted |
| | FastXMLWriter | | FastXMLWriter | NotPorted |
| | Initializable | | IInitializable | NotPorted |
| | PrettyXMLWriter | | PrettyXMLWriter | NotPorted |
| | ResourceEntityResolver | | ResourceEntityResolver | NotPorted |
| | XMLBeans | | XMLBeans | NotPorted |
| | XMLWritable | | IXMLWritable | NotPorted |
| | XMLWriter | | IXMLWriter | NotPorted |
| org.biojavax | BioSharp.Extensions | |
| | Comment | | IComment | NotPorted |
| | CrossRef | | ICrossRef | NotPorted |
| | CrossReferenceResolutionException | | CrossReferenceResolutionException | NotPorted |
| | CrossReferenceResolver | | ICrossReferenceResolver | NotPorted |
| | DocRef | | IDocRef | NotPorted |
| | DocRefAuthor | | IDocRefAuthor | NotPorted |
| | DocRefAuthor.Tools | | DocRefAuthor.Tools | NotPorted |
| | DummyCrossReferenceResolver | | DummyCrossReferenceResolver | NotPorted |
| | EmptyRichAnnotation | | EmptyRichAnnotation | NotPorted |
| | Namespace | | INamespace | NotPorted |
| | Note | | INote | NotPorted |
| | RankedCrossRef | | IRankedCrossRef | NotPorted |
| | RankedCrossRefable | | IRankedCrossRefable | NotPorted |
| | RankedDocRef | | IRankedDocRef | NotPorted |
| | RichAnnotatable | | IRichAnnotatable | NotPorted |
| | RichAnnotation | | IRichAnnotation | NotPorted |
| | RichObjectBuilder | | IRichObjectBuilder | NotPorted |
| | RichObjectFactory | | RichObjectFactory | NotPorted |
| | SimpleComment | | SimpleComment | NotPorted |
| | SimpleCrossRef | | SimpleCrossRef | NotPorted |
| | SimpleDocRef | | SimpleDocRef | NotPorted |
| | SimpleDocRefAuthor | | SimpleDocRefAuthor | NotPorted |
| | SimpleNamespace | | SimpleNamespace | NotPorted |
| | SimpleNote | | SimpleNote | NotPorted |
| | SimpleRankedCrossRef | | SimpleRankedCrossRef | NotPorted |
| | SimpleRankedDocRef | | SimpleRankedDocRef | NotPorted |
| | SimpleRichAnnotation | | SimpleRichAnnotation | NotPorted |
| | SimpleRichObjectBuilder | | SimpleRichObjectBuilder | NotPorted |
| org.biojavax.bio | BioSharp.Extensions.Bio | |
| | BioEntry | | IBioEntry | NotPorted |
| | BioEntryIterator | | IBioEntryIterator | NotPorted |
| | BioEntryRelationship | | IBioEntryRelationship | NotPorted |
| | SimpleBioEntry | | SimpleBioEntry | NotPorted |
| | SimpleBioEntryRelationship | | SimpleBioEntryRelationship | NotPorted |
| org.biojavax.bio.db | BioSharp.Extensions.Bio.Db | |
| | AbstractBioEntryDB | | AbstractBioEntryDB | NotPorted |
| | AbstractRichSequenceDB | | AbstractRichSequenceDB | NotPorted |
| | BioEntryDB | | IBioEntryDB | NotPorted |
| | BioEntryDBLite | | IBioEntryDBLite | NotPorted |
| | HashBioEntryDB | | HashBioEntryDB | NotPorted |
| | HashRichSequenceDB | | HashRichSequenceDB | NotPorted |
| | RichSequenceDB | | IRichSequenceDB | NotPorted |
| | RichSequenceDBLite | | IRichSequenceDBLite | NotPorted |
| org.biojavax.bio.db.biosql | BioSharp.Extensions.Bio.Db.Biosql | |
| | BioSQLAcceptAllFilter | | BioSQLAcceptAllFilter | NotPorted |
| | BioSQLAcceptNoneFilter | | BioSQLAcceptNoneFilter | NotPorted |
| | BioSQLBioEntryDB | | BioSQLBioEntryDB | NotPorted |
| | BioSQLCrossReferenceResolver | | BioSQLCrossReferenceResolver | NotPorted |
| | BioSQLFeatureFilter | | IBioSQLFeatureFilter | NotPorted |
| | BioSQLFeatureFilter.And | | BioSQLFeatureFilter.And | NotPorted |
| | BioSQLFeatureFilter.ByName | | BioSQLFeatureFilter.ByName | NotPorted |
| | BioSQLFeatureFilter.ByNote | | BioSQLFeatureFilter.ByNote | NotPorted |
| | BioSQLFeatureFilter.ByNoteTermOnly | | BioSQLFeatureFilter.ByNoteTermOnly | NotPorted |
| | BioSQLFeatureFilter.ByRank | | BioSQLFeatureFilter.ByRank | NotPorted |
| | BioSQLFeatureFilter.BySequenceName | | BioSQLFeatureFilter.BySequenceName | NotPorted |
| | BioSQLFeatureFilter.BySourceTerm | | BioSQLFeatureFilter.BySourceTerm | NotPorted |
| | BioSQLFeatureFilter.BySourceTermName | | BioSQLFeatureFilter.BySourceTermName | NotPorted |
| | BioSQLFeatureFilter.ByStrand | | BioSQLFeatureFilter.ByStrand | NotPorted |
| | BioSQLFeatureFilter.ByTypeTerm | | BioSQLFeatureFilter.ByTypeTerm | NotPorted |
| | BioSQLFeatureFilter.ByTypeTermName | | BioSQLFeatureFilter.ByTypeTermName | NotPorted |
| | BioSQLFeatureFilter.ContainedByRichLocation | | BioSQLFeatureFilter.ContainedByRichLocation | NotPorted |
| | BioSQLFeatureFilter.HibernateFeatureFilter | | BioSQLFeatureFilter.HibernateFeatureFilter | NotPorted |
| | BioSQLFeatureFilter.Not | | BioSQLFeatureFilter.Not | NotPorted |
| | BioSQLFeatureFilter.Or | | BioSQLFeatureFilter.Or | NotPorted |
| | BioSQLFeatureFilter.OverlapsRichLocation | | BioSQLFeatureFilter.OverlapsRichLocation | NotPorted |
| | BioSQLFeatureFilter.Tools | | BioSQLFeatureFilter.Tools | NotPorted |
| | BioSQLRichObjectBuilder | | BioSQLRichObjectBuilder | NotPorted |
| | BioSQLRichSequenceDB | | BioSQLRichSequenceDB | NotPorted |
| | BioSQLRichSequenceHandler | | BioSQLRichSequenceHandler | NotPorted |
| org.biojavax.bio.db.ncbi | BioSharp.Extensions.Bio.Db.Ncbi | |
| | GenbankRichSequenceDB | | GenbankRichSequenceDB | NotPorted |
| | GenpeptRichSequenceDB | | GenpeptRichSequenceDB | NotPorted |
| org.biojavax.bio.phylo | BioSharp.Extensions.Bio.Phylo | |
| | DistanceBasedTreeMethod | | DistanceBasedTreeMethod | NotPorted |
| | MultipleHitCorrection | | MultipleHitCorrection | NotPorted |
| | ParsimonyTreeMethod | | ParsimonyTreeMethod | NotPorted |
| org.biojavax.bio.phylo.io.nexus | BioSharp.Extensions.Bio.Phylo.IO.Nexus | |
| | CharactersBlock | | CharactersBlock | NotPorted |
| | CharactersBlockBuilder | | CharactersBlockBuilder | NotPorted |
| | CharactersBlockListener | | ICharactersBlockListener | NotPorted |
| | CharactersBlockParser | | CharactersBlockParser | NotPorted |
| | DataBlock | | DataBlock | NotPorted |
| | DataBlockBuilder | | DataBlockBuilder | NotPorted |
| | DataBlockListener | | IDataBlockListener | NotPorted |
| | DataBlockParser | | DataBlockParser | NotPorted |
| | DistancesBlock | | DistancesBlock | NotPorted |
| | DistancesBlockBuilder | | DistancesBlockBuilder | NotPorted |
| | DistancesBlockListener | | IDistancesBlockListener | NotPorted |
| | DistancesBlockParser | | DistancesBlockParser | NotPorted |
| | NexusBlock | | INexusBlock | NotPorted |
| | NexusBlock.Abstract | | NexusBlock.Abstract | NotPorted |
| | NexusBlockBuilder | | INexusBlockBuilder | NotPorted |
| | NexusBlockBuilder.Abstract | | NexusBlockBuilder.Abstract | NotPorted |
| | NexusBlockListener | | INexusBlockListener | NotPorted |
| | NexusBlockParser | | INexusBlockParser | NotPorted |
| | NexusBlockParser.Abstract | | NexusBlockParser.Abstract | NotPorted |
| | NexusComment | | NexusComment | NotPorted |
| | NexusFile | | NexusFile | NotPorted |
| | NexusFileBuilder | | NexusFileBuilder | NotPorted |
| | NexusFileFormat | | NexusFileFormat | NotPorted |
| | NexusFileListener | | INexusFileListener | NotPorted |
| | NexusFileListener.Abstract | | NexusFileListener.Abstract | NotPorted |
| | NexusObject | | INexusObject | NotPorted |
| | TaxaBlock | | TaxaBlock | NotPorted |
| | TaxaBlockBuilder | | TaxaBlockBuilder | NotPorted |
| | TaxaBlockListener | | ITaxaBlockListener | NotPorted |
| | TaxaBlockParser | | TaxaBlockParser | NotPorted |
| | TreesBlock | | TreesBlock | NotPorted |
| | TreesBlock.NewickTreeString | | TreesBlock.NewickTreeString | NotPorted |
| | TreesBlockBuilder | | TreesBlockBuilder | NotPorted |
| | TreesBlockListener | | ITreesBlockListener | NotPorted |
| | TreesBlockParser | | TreesBlockParser | NotPorted |
| org.biojavax.bio.phylo.io.phylip | BioSharp.Extensions.Bio.Phylo.IO.Phylip | |
| | PHYLIPFileBuilder | | PHYLIPFileBuilder | NotPorted |
| | PHYLIPFileFormat | | PHYLIPFileFormat | NotPorted |
| | PHYLIPFileListener | | IPHYLIPFileListener | NotPorted |
| org.biojavax.bio.seq | BioSharp.Extensions.Bio.Seq | |
| | CompoundRichLocation | | CompoundRichLocation | NotPorted |
| | DummyRichSequenceHandler | | DummyRichSequenceHandler | NotPorted |
| | EmptyRichLocation | | EmptyRichLocation | NotPorted |
| | InfinitelyAmbiguousSymbolList | | InfinitelyAmbiguousSymbolList | NotPorted |
| | MultiSourceCompoundRichLocation | | MultiSourceCompoundRichLocation | NotPorted |
| | Position | | IPosition | NotPorted |
| | PositionResolver | | IPositionResolver | NotPorted |
| | PositionResolver.AverageResolver | | PositionResolver.AverageResolver | NotPorted |
| | PositionResolver.MaximalResolver | | PositionResolver.MaximalResolver | NotPorted |
| | PositionResolver.MinimalResolver | | PositionResolver.MinimalResolver | NotPorted |
| | RichFeature | | IRichFeature | NotPorted |
| | RichFeature.Template | | RichFeature.Template | NotPorted |
| | RichFeature.Tools | | RichFeature.Tools | NotPorted |
| | RichFeatureRelationship | | IRichFeatureRelationship | NotPorted |
| | RichFeatureRelationshipHolder | | IRichFeatureRelationshipHolder | NotPorted |
| | RichLocation | | IRichLocation | NotPorted |
| | RichLocation.Strand | | RichLocation.Strand | NotPorted |
| | RichLocation.Tools | | RichLocation.Tools | NotPorted |
| | RichSequence | | IRichSequence | NotPorted |
| | RichSequence.IOTools | | RichSequence.IOTools | NotPorted |
| | RichSequence.Terms | | RichSequence.Terms | NotPorted |
| | RichSequence.Tools | | RichSequence.Tools | NotPorted |
| | RichSequenceHandler | | IRichSequenceHandler | NotPorted |
| | RichSequenceIterator | | IRichSequenceIterator | NotPorted |
| | SimplePosition | | SimplePosition | NotPorted |
| | SimpleRichFeature | | SimpleRichFeature | NotPorted |
| | SimpleRichFeatureRelationship | | SimpleRichFeatureRelationship | NotPorted |
| | SimpleRichLocation | | SimpleRichLocation | NotPorted |
| | SimpleRichSequence | | SimpleRichSequence | NotPorted |
| | ThinRichSequence | | ThinRichSequence | NotPorted |
| org.biojavax.bio.seq.io | BioSharp.Extensions.Bio.Seq.IO | |
| | DebuggingRichSeqIOListener | | DebuggingRichSeqIOListener | NotPorted |
| | EMBLFormat | | EMBLFormat | NotPorted |
| | EMBLFormat.Terms | | EMBLFormat.Terms | NotPorted |
| | EMBLxmlFormat | | EMBLxmlFormat | NotPorted |
| | EMBLxmlFormat.Terms | | EMBLxmlFormat.Terms | NotPorted |
| | FastaFormat | | FastaFormat | NotPorted |
| | FastaHeader | | FastaHeader | NotPorted |
| | GenbankFormat | | GenbankFormat | NotPorted |
| | GenbankFormat.Terms | | GenbankFormat.Terms | NotPorted |
| | GenbankLocationParser | | GenbankLocationParser | NotPorted |
| | INSDseqFormat | | INSDseqFormat | NotPorted |
| | INSDseqFormat.Terms | | INSDseqFormat.Terms | NotPorted |
| | RichSeqIOAdapter | | RichSeqIOAdapter | NotPorted |
| | RichSeqIOListener | | IRichSeqIOListener | NotPorted |
| | RichSequenceBuilder | | IRichSequenceBuilder | NotPorted |
| | RichSequenceBuilderFactory | | IRichSequenceBuilderFactory | NotPorted |
| | RichSequenceFormat | | IRichSequenceFormat | NotPorted |
| | RichSequenceFormat.BasicFormat | | RichSequenceFormat.BasicFormat | NotPorted |
| | RichSequenceFormat.HeaderlessFormat | | RichSequenceFormat.HeaderlessFormat | NotPorted |
| | RichStreamReader | | RichStreamReader | NotPorted |
| | RichStreamWriter | | RichStreamWriter | NotPorted |
| | SimpleRichSequenceBuilder | | SimpleRichSequenceBuilder | NotPorted |
| | SimpleRichSequenceBuilderFactory | | SimpleRichSequenceBuilderFactory | NotPorted |
| | UniProtCommentParser | | UniProtCommentParser | NotPorted |
| | UniProtCommentParser.Event | | UniProtCommentParser.Event | NotPorted |
| | UniProtCommentParser.Interaction | | UniProtCommentParser.Interaction | NotPorted |
| | UniProtCommentParser.Isoform | | UniProtCommentParser.Isoform | NotPorted |
| | UniProtCommentParser.SeqCaution | | UniProtCommentParser.SeqCaution | NotPorted |
| | UniProtFormat | | UniProtFormat | NotPorted |
| | UniProtFormat.Terms | | UniProtFormat.Terms | NotPorted |
| | UniProtLocationParser | | UniProtLocationParser | NotPorted |
| | UniProtXMLFormat | | UniProtXMLFormat | NotPorted |
| | UniProtXMLFormat.Terms | | UniProtXMLFormat.Terms | NotPorted |
| org.biojavax.bio.seq.RichSequence | BioSharp.Extensions.Bio.Seq.RichSequence | |
| | IOTools.SingleRichSeqIterator | | IOTools.SingleRichSeqIterator | NotPorted |
| org.biojavax.bio.taxa | BioSharp.Extensions.Bio.Taxa | |
| | NCBITaxon | | INCBITaxon | NotPorted |
| | SimpleNCBITaxon | | SimpleNCBITaxon | NotPorted |
| | SimpleNCBITaxonName | | SimpleNCBITaxonName | NotPorted |
| org.biojavax.bio.taxa.io | BioSharp.Extensions.Bio.Taxa.IO | |
| | NCBITaxonomyLoader | | INCBITaxonomyLoader | NotPorted |
| | SimpleNCBITaxonomyLoader | | SimpleNCBITaxonomyLoader | NotPorted |
| org.biojavax.ga | BioSharp.Extensions.Ga | |
| | GAStoppingCriteria | | IGAStoppingCriteria | NotPorted |
| | GAStoppingCriteria.MaximumGeneration | | GAStoppingCriteria.MaximumGeneration | NotPorted |
| | GeneticAlgorithm | | IGeneticAlgorithm | NotPorted |
| | Organism | | IOrganism | NotPorted |
| | Population | | IPopulation | NotPorted |
| org.biojavax.ga.exception | BioSharp.Extensions.Ga.Exception | |
| | IllegalOrganismException | | IllegalOrganismException | NotPorted |
| org.biojavax.ga.functions | BioSharp.Extensions.Ga.Functions | |
| | AbstractCrossOverFunction | | AbstractCrossOverFunction | NotPorted |
| | AbstractMutationFunction | | AbstractMutationFunction | NotPorted |
| | CrossOverFunction | | ICrossOverFunction | NotPorted |
| | CrossOverFunction.NoCross | | CrossOverFunction.NoCross | NotPorted |
| | FitnessFunction | | IFitnessFunction | NotPorted |
| | GACross | | IGACross | NotPorted |
| | GACrossResult | | IGACrossResult | NotPorted |
| | MutationFunction | | IMutationFunction | NotPorted |
| | MutationFunction.NoMutation | | MutationFunction.NoMutation | NotPorted |
| | OrderCrossover | | OrderCrossover | NotPorted |
| | ProportionalSelection | | ProportionalSelection | NotPorted |
| | SelectionFunction | | ISelectionFunction | NotPorted |
| | SelectionFunction.SelectAll | | SelectionFunction.SelectAll | NotPorted |
| | SelectionFunction.Threshold | | SelectionFunction.Threshold | NotPorted |
| | SimpleCrossOverFunction | | SimpleCrossOverFunction | NotPorted |
| | SimpleGACrossResult | | SimpleGACrossResult | NotPorted |
| | SimpleMutationFunction | | SimpleMutationFunction | NotPorted |
| | SwapMutationFunction | | SwapMutationFunction | NotPorted |
| | TournamentSelection | | TournamentSelection | NotPorted |
| org.biojavax.ga.impl | BioSharp.Extensions.Ga.Impl | |
| | AbstractGeneticAlgorithm | | AbstractGeneticAlgorithm | NotPorted |
| | AbstractOrganism | | AbstractOrganism | NotPorted |
| | AbstractPopulation | | AbstractPopulation | NotPorted |
| | SimpleGeneticAlgorithm | | SimpleGeneticAlgorithm | NotPorted |
| | SimpleOrganism | | SimpleOrganism | NotPorted |
| | SimplePopulation | | SimplePopulation | NotPorted |
| org.biojavax.ga.util | BioSharp.Extensions.Ga.Util | |
| | GATools | | GATools | NotPorted |
| | WeightedSet | | WeightedSet | NotPorted |
| org.biojavax.ontology | BioSharp.Extensions.Ontology | |
| | ComparableOntology | | IComparableOntology | NotPorted |
| | ComparableTerm | | IComparableTerm | NotPorted |
| | ComparableTriple | | IComparableTriple | NotPorted |
| | SimpleComparableOntology | | SimpleComparableOntology | NotPorted |
| | SimpleComparableTerm | | SimpleComparableTerm | NotPorted |
| | SimpleComparableTriple | | SimpleComparableTriple | NotPorted |
| org.biojavax.utils | BioSharp.Extensions.Utils | |
| | CRC64Checksum | | CRC64Checksum | NotPorted |
| | StringTools | | StringTools | NotPorted |
| | XMLTools | | XMLTools | NotPorted |