All Classes

Abort AbortRetry AbstractBatchClusteringMethod AbstractCentroidCluster AbstractCluster AbstractClusteringMethod AbstractDoubleHierarchicalTypedProperties AbstractGenericFactoryAware AbstractHierarchicalTypedPropertyNode AbstractHierarchyNode AbstractLabelChooserSet AbstractOnlineClusteringMethod AbstractRootedPhylogeny AbstractRootedPhylogeny.MutualExclusionResolutionMode AbstractSequenceFragmentIterator AbstractSupervisedOnlineClusteringMethod AbstractSvmProblem AbstractTaxonomyLabelChooser AbstractUnsupervisedOnlineClusteringMethod AdditiveCentroidCluster AdditiveClusterable AggregateSequenceFragment AlphaGradientPaintScale AlphaModel AnnotatedBinaryTree ArrayInterpolatingFunctionCache ArrayOperator ArrayParsers ArrayRank AssignabilityAlgorithm AsymmetricUnweightedUniFrac AsymmetricWeightedUniFrac BackoffCorrectedEntropy Base64 Base64.InputStream Base64.OutputStream BasicCentroidCluster BasicHierarchicalStringObjectMap BasicHierarchicalTypedPropertyNode BasicIncrementable BasicInterval BasicKernelQMatrix BasicLongRationalInterval BasicPhylogenyNode BasicRootedPhylogeny BatchAdditiveCentroidCluster BatchCluster BatchClusteringMethod BatchClusteringMethodAdapter BatchClusterLabelInverter BatchResultCollector BatchResultWriter BatchTreeClusteringMethod BatchTreeClusteringMethodAdapter BatchTreeLabelClusteringEvaluator BayesianClustering BayesianClusteringAdapter BinaryClassificationProblem BinaryClassificationProblemImpl BinaryClassificationSVM BinaryCrossValidationResults BinaryModel BinarySolver BinarySolverNu BinaryTree BinnedXYSeries BooleanArrayMapper BooleanClassificationProblemImpl BooleanInvertingKernelQMatrix BooleanMapper BooleanParameterValue BooleanParameterValueEditor BooleanParameterValueMapper BooleanParameterValueRenderer BooleanSetParameterRange BooleanSetParameterRangeRenderer BruteForceSearchStrategy ByteArraySequenceReader ByteLabelInverter C_SVC C_SVCTest CachedFile CachedFileDao CachedFileDaoImpl CachedResourceReleaser CacheManager CachingSFI Cancel CellIdXYZSeriesAdapter CentroidCluster CentroidClusteringMethod CentroidClusteringUtils ChainedError ChainedException ChainedRuntimeException ChainList CharacterDistributionOnTree ChartEncodeTask ChartUtils ChartUtils.AxisNumberFormat ChartUtils.ErrorBarType ChartUtils.PlotType ChartUtilsRuntimeException CiccarelliDistanceFromEColi CiccarelliPhylogeneticDistance CiccarelliTaxonomyService CircularBitField ClassMapper ClasspathFromFileClassLoader ClasspathFromFileWeavingClassLoader Client ClientBatchResultCollector ClientController Cluster Clusterable ClusterableDoubleArray ClusterableIterator ClusterableIteratorFactory ClusterException ClusteringMethod ClusteringMethodAdapter ClusteringTestResults ClusterList ClusterMove ClusterRuntimeException CoarseGridSearchStrategy CollectionClusterableIterator CollectionIteratorFactory CollectionRuntimeException ColorIcon ComboBoxWithNoneModel Command Community CommunityClustering CommunityDistanceVsDistance CommunityDiversityVsDiversity CommunityFactory CommunityKtrieMeasureEvaluator CommunityPairComplexBetaDiversity CommunityPhylogenyDistance CommunityPhylogenyDiversity CommunitySamplingSFI CommunitySequenceDistance CommunitySequenceDiversity CommunitySetPairComplexBetaDiversity CommunityUPGMAClusteringAdapter ComplexDissimilarityMeasure CompositeGaussianRBFKernel ComputedProperty ConfigurableContinuousDistribution1D ContextNotUniqueException ContinuousDistribution ContinuousDistribution1D ContinuousModel Copy CountOrderedMultiset CrossValidationResults CustomClassloaderObjectInputStream CuturiVertMIKernel DatabaseSelectionSplashScreen DataCollector DataSetUpdatedEvent DataSetUpdatedEvent.Listener Debug DefaultMultiListModel DefaultMultiProgressBarModel DefaultTypedTableCellEditor DegreeAlgorithm Delete DeleteChildren DeleteTask DepthFirstThreadPoolExecutor DepthFirstTreeIterator DepthFirstTreeIteratorImpl DetachedParameterSetModel DetachedParameterSetModelFactory DetachedParameterSetSetImpl DiffusableLabelClusteringMethod DisableableAnnotationBeanConfigurerAspect DisableBeanConfigurerPostProcessor DiscreteDistribution1D DiscreteModel DissimilarityMeasure DistanceBasedMultiClassCrossValidationResults DistanceMeasureRuntimeException DistanceMetric Distribution DistributionException DistributionProcessor DistributionProcessorException DistributionXYSeries DnaDist DoubleArrayBlob DoubleArrayContainer DoubleArrayDissimilarityMeasure DoubleArrayLinearScaler DoubleArrayMapper DoubleArrayNormalizer DoubleArrayParameterValue DoubleArrayParameterValueRenderer DoubleArraySquareNormalizer DoubleArrayZscoreScaler DoubleHierarchicalTypedProperties DoubleIntervalParameterRange DoubleIntervalParameterRangeRenderer DoubleKcount DoubleListParameterValue DoubleListParameterValueMapper DoubleListParameterValueRenderer DoubleMapper DoubleParameterValue DoubleParameterValueEditor DoubleParameterValueMapper DoubleParameterValueRenderer DoublePrimitiveArrayMapper DoublePseudocountAdder DoubleSetParameterRange DoubleSetParameterRangeRenderer DoubleSetRangeStringMapper DoubleSteppedParameterRange DoubleSteppedParameterRangeRenderer DoubleTimecourse DSArrayUtils DSClassUtils DSCollectionUtils DSDurationFormatUtils DSStringUtils DualAlphaGradientPaintScale EmpiricalZscore EnergyMove Enqueue EnumParameterValue EnumParameterValueEditor EnumParameterValueMapper EnumParameterValueRenderer EnumSetParameterRange EnumSetParameterRangeRenderer EnvironmentParser EnvironmentUtils EpsilonSVR EqualWeightHistogram1D EqualWeightHistogram2D EuclideanDistance EuclideanDistance EventMediator EventMediatorException EventObject EventSource ExactCommunityFactory ExactCommunitySetFactory ExactKcountScanner ExactSequenceBasedCommunityFactory ExceptionUtils ExplicitHybridRootedPhylogeny ExplicitLabelChooser ExplicitSvmProblem ExplicitSvmProblemImpl ExtendedHierarchicalTypedPropertyNode ExtendedHierarchicalTypedPropertyNodeImpl FaithPD FakeFuture FareyFractionUtils FastaFileSet FastaFilesetSFIMapper FastaLengthHistogram FastaParser FastaParserSet FileListParameterValue FileParameterValue FileSetParameterRange FileUtils FilterActionHandler FilterException FilteringSectionList FilteringSequenceReader FilterWindow FilterWindowController FilterWindowControllerImpl FirstWordProvider FixedWidthHistogram1D FloatMapper FragmentLabeller GammaKernel GapFrequency GaussianDemo GaussianDistribution GaussianFunction1D GaussianRBFKernel GenerateSimulatedFasta GenericDao GenericDaoImpl GenericFactory GenericFactoryAware GenericFactoryException GreenGenesFragmentDistanceCorrelationGrid GreenGenesFragmentDistances GreenGenesMutationsPerColumn GrowableKmeansClustering GUI GuiUtils HashMap2D HashWeightedSet HasReleaseableResources HeatmapDataset HeatmapPlotThemePanel HeatMapPlotType HeatmapSeries HeatmapSeries.HeatmapPoint HeatmapSeriesManager HierarchicalCentroidCluster HierarchicalClusteringMethod HierarchicalPropertyNodeException HierarchicalSpectrum HierarchicalStringObjectMap HierarchicalTypedPropertyNode HierarchicalTypedPropertyNode.PropertyConsumerFlags HierarchyNode HillClimbingSearchStrategy Histogram1D HugenholtzTaxonomyService HybridRootedPhylogeny ImmutableHierarchyNode ImmutableSortedSetHierarchyNode ImmutableSvmParameter ImmutableSvmParameter.Builder ImmutableSvmParameterGrid ImmutableSvmParameterGrid.Builder ImmutableSvmParameterPoint ImmutableSvmParameterPoint.Builder Incrementable IndelFilter IndependentDimensionScaler IndependentDimensionZscores InferredMixturePST Information Initializer InjectableValueMapper IntArrayContainer IntArrayReader IntDoubleMapReader IntegerArrayBlob IntegerArrayMapper IntegerArrayParameterValue IntegerArrayParameterValueRenderer IntegerIterator IntegerLabelMapper IntegerLabelSetMapper IntegerListParameterValue IntegerListParameterValueMapper IntegerListParameterValueRenderer IntegerMapper IntegerNodeNamer IntegerParameterValue IntegerParameterValueEditor IntegerParameterValueMapper IntegerParameterValueRenderer IntegerSetParameterRange IntegerSetParameterRangeRenderer IntegerSetRangeStringMapper IntegerSteppedParameterRange IntegerSteppedParameterRangeRenderer InterpolatingFunctionCache Interval IntKcount IntPrimitiveArrayMapper IntPseudocountAdder IntSetIntMapReader IteratorVsIteratorDistanceGraphs IteratorVsIteratorDistanceGraphs2 IteratorVsIteratorDistanceGraphTask IteratorVsKcountDistanceGraphs IteratorVsKcountDistanceGraphTask JandyClientService JandyClientServlet JandyCommand JandyCommands JandyCommandsServlet JandyDbContextFactory JandyDbRuntimeException JandyException JandyGuiException JandyRuntimeException JandyServer JandyServicesContextFactory JandyServicesException JDivergence JDivergence JDivergenceHierarchical JDivergenceKtrieUniform JDivergenceTreeIncremental JMultiList JMultiProgressBar JMultiProgressBarFrame Job JobDao JobDaoImpl JobModel JobStatsUpdater JsapResultToMapAdapter JsapUtility JukesCantorFilter K80Filter Kcount KcountScanner KernelFunction KernelQMatrix KLDivergence KLDivergenceHierarchical KLDivergenceTreeIncremental KmeansClustering KmerComparisonUtils KmerDistanceVsAllDistances KmerDistanceVsBestDistance KmerDistanceVsDistance KmerIdUtils KneserNeyPSASmoother KNNClustering KNNClusteringAdapter KohonenMapMaker KohonenSOM KohonenSOM2D KohonenSOM2DSearchStrategy KohonenSOMAdapter KohonenSOMCell KohonenSOMnD KohonenSOMPlotType KullbackLeibler LabelBalancingSFI LabelChooser LabelChooserSet LabelConstrainedSFIMapper LabelDecomposingBayesianClustering LabelDiffuser LabelFilteringSFI LabelInverter LabellerException LabellingSFI LabelParser LabelProhibitionModel LabelProvidingSFI LabelSelectableSFI LairdSaulPST LengthWeightHierarchyNode LevelMixedDistance LimitedSFI LinearFunction1D LinearKernel LinearRegression LinearScalingModelLearner ListHierarchyNode ListWithNoneModel LiveParameterSetSetImpl LiveResultCollector LogNormalDistribution LogNormalDistribution LogOddsSubstitutionMatrix LogProbabilityDissimilarity LogProbabilityDissimilarity.MinAvgMax LogTransitionMatrix LongRational MainWindow MainWindowController MainWindowControllerImpl ManhattanDistance Map2D Map2D.Entry MappingIterator MappingNextOnlyIterator MapToHierarchicalTypedPropertyNodeAdapter MarkovTreeNode MasterController MatepairIteratorVsSelfDistanceGraphs MathSupport MathUtils MathUtilsException MaxOperator MemoryManager MergedFastaFilesets MergingLabelChooser MersenneTwisterFast MetropolisCoupledMonteCarlo MetropolisCoupledSwapMove MixedSpectrumKernel MixtureOfDistributions MonitoredSwingWorker MonteCarlo MonteCarloState Move MoveNotPossibleException MoveTypeSet MsensrDoubleKcount MsensrError MsensrException MsensrRun MsensrRuntimeException MultiClassCrossValidationResults MultiClassificationSVM MultiClassificationSVMAdapter MultiClassModel MultiClassModel.AllVsAllMode MultiClassModel.OneVsAllMode MultiClassProblem MultiClassProblemImpl MulticlassSVMAdapter MultiIntervalIntersection MultiIntervalUnion MultiListModel MultiNeighborClustering MultiNeighborClustering.BestLabelPair Multinomial MultinomialDistribution MultiPassScanner MultiProgressBarModel MultivariateGaussian MutableBasicInterval MutableBinaryClassificationProblemImpl MutableDistribution MutableMultiClassProblemImpl MutableOneClassProblemImpl MutableRegressionProblemImpl MutableSvmProblem NASTCommunityFactory NASTDistanceMapper NcbiCiccarelliHybridClient NcbiCiccarelliHybridService NcbiCiccarelliHybridServiceImpl NcbiCiccarelliHybridServlet NcbiNameRankLabelChooser NcbiNameRankLabelChooserSet NcbiTaxidLabelMapper NcbiTaxidRankLabelChooser NcbiTaxidRankLabelChooserSet NcbiTaxonomyClient NcbiTaxonomyDbContextFactory NcbiTaxonomyException NcbiTaxonomyName NcbiTaxonomyNameDao NcbiTaxonomyNameDaoImpl NcbiTaxonomyNode NcbiTaxonomyNodeDao NcbiTaxonomyNodeDaoImpl NcbiTaxonomyPhylogeny NcbiTaxonomyRuntimeException NcbiTaxonomyServer NcbiTaxonomyService NcbiTaxonomyServiceEngine NcbiTaxonomyServiceEngineImpl NcbiTaxonomyServicesContextFactory NcbiTaxonomyServlet NcbiTaxonomyWithUnitBranchLengthsClient NcbiTaxonomyWithUnitBranchLengthsPhylogeny NcbiTaxonomyWithUnitBranchLengthsService NcbiTaxonomyWithUnitBranchLengthsServlet NearCurrentPositionSearchStrategy NearestNeighborClustering NearestTaxonDistanceDistribution NeighborhoodCollectingLabelDiffuser NewickParser NewickTaxonomyService NextOnlyIterator NextOnlyIteratorAsNormalIterator NodeNamer NoGoodClusterException NonoverlappingFullyCachingTTSFI NonoverlappingTestOnlyCachingTTSFI NonPersistentEventSource NoopScalingModel NoopScalingModelLearner NormalDistribution NormalDistribution NormalizedWeightedUniFrac NoSuchNodeException NotDrawableException NotEnoughSequenceException NotRunnableException Nu_SVC Nu_SVR NucleotideKcount NucleotideKcountMutationDrifter NucleotideKcountSpectrumDrifter NucleotideKcountTree NucleotideKtrie NucleotideKtrieLevelWeightedMixer OneClassModel OneClassProblem OneClassProblemImpl OneClassSolver OneClassSVC OnlineClusteringMethod OrderedPair OrderedPairIterator PACAgent PaintScaleFactory Parallel ParameterKey ParameterKeyDao ParameterKeyDaoImpl ParameterKeyStringMapper ParameterSet ParameterSetCellRenderer ParameterSetCreatedEvent ParameterSetCreatedEvent.Listener ParameterSetDao ParameterSetDaoImpl ParameterSetDeletedEvent ParameterSetDeletedEvent.Listener ParameterSetDetailActionHandler ParameterSetDetailModelUpdatedEvent ParameterSetDetailModelUpdatedEvent.Listener ParameterSetDetailPanel ParameterSetDetailPanelController ParameterSetDetailPanelControllerImpl ParameterSetDetailPanelModelImpl ParameterSetFilter ParameterSetModel ParameterSetRangeForKey ParameterSetRangeForKeyDao ParameterSetRangeForKeyDaoImpl ParameterSetRangeStringMapper ParameterSetSelectedEvent ParameterSetSelectedEvent.Listener ParameterSetSelectionStatusChangedEvent ParameterSetSelectionStatusChangedEvent.Listener ParameterSetSet ParameterSetSetImpl ParameterSetSummaryActionHandler ParameterSetSummaryPanel ParameterSetSummaryPanelController ParameterSetSummaryPanelControllerImpl ParameterSetToHierarchicalTypedPropertyNodeAdapter ParameterSetToWHTPNTranslator ParameterSetToWHTPNTranslatorImpl ParameterSetTreeRenderer ParameterSetTreeTableModelImpl ParameterSetTreeTableNodeImpl ParameterSetUpdatedEvent ParameterSetUpdatedEvent.Listener ParameterSetValueForKey ParameterSetValueForKeyDao ParameterSetValueForKeyDaoImpl ParameterSetValueOrRange ParameterSetValueOrRangeFactory ParameterSetValueStringMapper ParameterTreeRenderer ParameterTreeTableModelImpl ParameterTreeTableNode ParameterValueOrRangeCellEditor ParameterValueOrRangeCellRenderer PearsonCorrelation PearsonCorrelationDistance PermutingClusterableIteratorFactory PermutingCollectionIteratorFactory PhylogeneticDistance PhylogeneticDistanceAlternateTaxonomy PhylogeneticDistanceI PhylogeneticDistanceS PhylogeneticJDivergence PhylogeneticKullbackLeibler PhylogeneticShannon PhylogenyNode PhylogenyTypeConverter PhyloUtilsException PhyloUtilsRuntimeException PlotPersonalityPanel PlotPersonalityPanelSocket Plottable PlotType PluginDemo PluginException PluginManager PluginMap PluginMapParameterValue PluginMapParameterValueMapper PluginMapParameterValueRenderer PluginMapStringMapper PluginParameterValue PluginParameterValueEditor PluginParameterValueMapper PluginParameterValueRenderer PluginSetParameterRange PluginSetParameterRangeRenderer PointClusterFilter PointDistribution PolynomialKernel Pool PostEntityManagerInitializer PowerFunction1D PrecomputedKernel PrefersLiveResultCollector PrintPSAs ProbabilisticDissimilarityMeasure ProbabilityMove ProductOperator ProgressMonitorSwingWorker ProgressReportingThreadPoolExecutor ProhibitionModel PropertiesToMapAdapter PropertiesUtils Property PropertyConsumer PropertyConsumerClassParser PropertyConsumerFactory PropertyConsumerNodeException PropertyConsumerRuntimeException PropsException PropsRuntimeException PrototypeBasedCentroidClusteringMethod PSADivergence QMatrix QueueableTask RandomCiccarelliCommunityFactory RandomCommunityFactory RandomDissimilarity RandomPositionSFI RandomSectionList RandomSectionSFI RandomSequenceBasedCommunityFactory RandomSequentialMatePairSFI RandomSubstitutionFilter RandomTaxonDistanceDistribution RandomTaxonomyLeavesCommunityFactory Range RBFSpectrumKernel RefreshTask RegressionCrossValidationResults RegressionModel RegressionProblem RegressionProblemImpl RegressionSolver RegressionSolverNu RegressionSVM RepeatingAggregateSFI RequireExistingNodeNamer RequiresPreparationDistanceMetric RequiresPreparationTaxonomyService ResultCollector ResultsCollectingProgramRun ResultStoringPlotType Retry REUtils RonPSA RonPSAAdapter RonPSANode RonPSASmoother RonPST RonPSTNode RonPSTSmoother RootedPhylogeny RootNameAncestorPathLabeller RootNameLabeller RuntimeExecutionException RunUnsuccessfulException SafeIntegerArithmetic SafeIntegerArithmetic.IllegalArithArgsException SafeIntegerArithmetic.OperationKindTy SafeIntegerArithmetic.PrimTypeIndTy SampleInitializedOnlineClusteringMethod ScalingModel ScalingModelLearner ScanningSFI ScatterPlotSeriesManager ScatterPlotType SchbathExpecter SchbathExpecter.SchbathExpectation SchbathRatio SchbathZScores SectionDecomposingSFI SectionList SectionListBasedSequenceFragmentIterator SectionSFI SelectionChangePermitter SemisupervisedClassificationEvaluator SemisupervisedClusteringMethod SemisupervisedClusteringMethodAdapter SeparateTrainingTestSFI SequenceArrayException SequenceArrayUtils SequenceBasedCommunity SequenceBasedCommunityFactory SequenceBasedCommunitySFI SequenceBasedCommunityTrainingTestSFI SequenceException SequenceFragment SequenceFragmentFactory SequenceFragmentIterator SequenceFragmentMetadata SequenceReader SequenceSpectrum SequenceSpectrumException SequenceSpectrumRuntimeException SequenceSpectrumScanner SequentialMatePairSFI SerializableHierarchicalTypedPropertyNodeImpl SerializableOrderedPair SerializablePhylogenyNode SerializableRootedPhylogeny SeriesManager SeriesPlotType SeriesXYBlockRenderer SetHierarchyNode Shannon ShapeSizingDrawingSupplier Shell ShellController Show ShowErrors SigmoidKernel SigmoidProbabilityModel SimpleFunction SimpleStringMapper SimplexVectorTargetAndProportion SimpleXYSeries SimpleXYSeries.XYPoint SimpleXYZSeries SimpleXYZSeries.XYZPoint SingleIndelFilter SingletonRegistry SmtpUtils SolutionModel SolutionVector SolutionVector.Status Solver Solver_NU SortedListModel SparseVector SpectrumKernel SpectrumMutationFilter SpringJpaObject StackedBox Statistic StatsException StatsRuntimeException Status StatusDao StatusDaoImpl StrainDirectoryLabelChooser StrainDirectoryLabelChooserSet StrainResolvedCiccarelliPhylogeneticDistance StrainResolvedCiccarelliPhylogeneticDistanceS StreamUtils StringArrayMapper StringDoubleMapReader StringIntegerNodeNamer StringIntMapReader StringLabelInverter StringListDoubleMapReader StringListParameterValue StringListParameterValueMapper StringListParameterValueRenderer StringMapper StringMapperException StringNodeNamer StringParameterValue StringParameterValueEditor StringParameterValueMapper StringParameterValueRenderer StringSetIntMapReader StringSetParameterRange StringSetParameterRangeRenderer StringSetRangeStringMapper SubclassFinder SubstitutionFilter SubtractionMap SumOperator SupervisedClassificationEvaluator SupervisedClusteringMethod SupervisedClusteringMethodAdapter SVM svm_predict svm_scale svm_toy svm_train SvmBinaryCrossValidationResults SvmContext SvmException SvmMultiClassCrossValidationResults SvmProblem Symmetric2dBiMap TacoaClustering TacoaClusteringAdapter TacoaDistanceWeighted TaskListener TaskQueue TaskQueueProcessorThread TaxonDistanceVsDistance TaxonIdMapper TaxonMerger TaxonMergingPhylogeny TaxonomyService TaxonomySynonymService TaxonOverlapReport TaxonStringIdMapper TestSetupHelper TextFileDataCollector TextPlotType ThreadingException ThreadPoolPerformanceStats ToSubIteratorBestDistance TraditionalTaxonMerger TrainingTestSFI TransitionMatrix TranslatingSequenceReader TranslationException TreeException TreeException TreeExecutorService TreeFactory TreePrinter TreeRuntimeException TropashkoFareyNestedSetNode TypedProperties TypedTableCellEditor TypedTableCellRenderer TypedValueStringMapper TypeUtils UniformDistribution UniformDistribution UniformDistribution UnorderedPair UnorderedPairIterator UnsupervisedClusteringMethod UnweightedUniFrac UPGMA UpgmaAdapter UrlContentCache UrlContentCacheException UrlContentCacheImpl VariableHierarchy VariableWidthHistogram1D VotingResult WeakHashSet WeightedMixtureDivergenceHierarchical WeightedSet WeightedUniFrac WholeGenomeTTSFI WindowedSFI WithinCurrentRadiusSearchStrategy WorstCasePhylogeneticDistance WorstCasePhylogeneticDistanceS WrapLayout WrappedHierarchicalTypedPropertyNode WrappedHierarchicalTypedPropertyNodeImpl XYPlotSpec XYPlotThemePanel XYSeriesAdapter XYZSeriesManager ZeroMarkovRatio ZeroMarkovRatioTacoa ZscoreScalingModelLearner