All Classes

AbsoluteValueCondition AbsoluteValueCondition.AbsoluteValueConditionParameterSet AbstractBurnInTest AbstractBurnInTestParameterSet AbstractClassifier AbstractConditionalDiscreteEmission AbstractDifferentiableSequenceScore AbstractDifferentiableStatisticalModel AbstractHMM AbstractMixtureDiffSM AbstractMixtureTrainSM AbstractMixtureTrainSM.Algorithm AbstractMixtureTrainSM.Parameterization AbstractMultiThreadedOptimizableFunction AbstractNumericalTwoClassPerformanceMeasure AbstractOptimizableFunction AbstractPerformanceMeasure AbstractPerformanceMeasureParameterSet AbstractScoreBasedClassifier AbstractScoreBasedClassifier.DoubleTableResult AbstractSelectionParameter AbstractStringExtractor AbstractTerminationCondition AbstractTerminationCondition.AbstractTerminationConditionParameterSet AbstractTrainableStatisticalModel AbstractTwoClassPerformanceMeasure AbstractVariableLengthDiffSM AffineCosts Alignment Alignment.AlignmentType Alphabet Alphabet.AlphabetParameterSet AlphabetContainer AlphabetContainer.AbstractAlphabetContainerParameterSet AlphabetContainer.AlphabetContainerType AlphabetContainerParameterSet AlphabetContainerParameterSet.AlphabetArrayParameterSet AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet AnnotatedEntity AnnotatedEntityList ArbitraryFloatSequence ArbitrarySequence ArrayHandler ArrayParameterSet AsymmetricTensor AucPR AucROC BasicHigherOrderTransition BasicHigherOrderTransition.AbstractTransitionElement BasicPluginTransitionElement BasicTransitionElement BaumWelchParameterSet BayesianNetworkDiffSM BayesianNetworkDiffSMParameterSet BayesianNetworkTrainSM BayesianNetworkTrainSMParameterSet BioJavaAdapter BNDiffSMParameter BNDiffSMParameterTree BTExplainingAwayResidual BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet BTMutualInformation BTMutualInformation.BTMutualInformationParameterSet BTMutualInformation.DataSource BurnInTest ByteSequence CappedHistory CategoricalResult CDFOfNormal Chu_Liu_Edmonds CisRegulatoryModuleAnnotation ClassDimensionException ClassificationRate ClassificationVisualizer ClassifierAssessment ClassifierAssessmentAssessParameterSet ClassifierFactory CombinationIterator CombinedCondition CombinedCondition.CombinedConditionParameterSet CombinedFileFilter ComparableElement ComplementableDiscreteAlphabet CompositeLogPrior CompositeTrainSM ConfusionMatrix ConstantStartDistance Constraint Constraint ConstraintManager ConstraintManager.Decomposition ConstraintParameterSet ConstraintValidator ContinuousAlphabet ContinuousAlphabet.ContinuousAlphabetParameterSet Costs CyclicMarkovModelDiffSM DAG DAGTrainSM DataSet DataSet.ElementEnumerator DataSet.PartitionMethod DataSet.WeightedDataSetFactory DataSet.WeightedDataSetFactory.SortOperation DataSetKMerEnumerator DataSetResult DataType DateFileFilter DefaultProgressUpdater DGTrainSMParameterSet DifferentiableEmission DifferentiableFunction DifferentiableHigherOrderHMM DifferentiableSequenceScore DifferentiableState DifferentiableStatisticalModel DifferentiableStatisticalModelFactory DifferentiableStatisticalModelWrapperTrainSM DifferentiableTransition DiffSSBasedOptimizableFunction DimensionException DiMRGParams DinucleotideProperty DinucleotideProperty.HowCreated DinucleotideProperty.MeanSmoothing DinucleotideProperty.MedianSmoothing DinucleotideProperty.NoSmoothing DinucleotideProperty.Smoothing DinucleotideProperty.Type DirichletMRG DirichletMRGParams DiscreteAlphabet DiscreteAlphabet.DiscreteAlphabetParameterSet DiscreteAlphabetMapping DiscreteEmission DiscreteGraphicalTrainSM DiscreteInhomogenousDataSetEmitter DiscreteSequenceEnumerator DistanceBasedScaledTransitionElement DNAAlphabet DNAAlphabet.DNAAlphabetParameterSet DNAAlphabetContainer DNAAlphabetContainer.DNAAlphabetContainerParameterSet DNADataSet DoesNothingLogPrior DoubleArrayComparator DoubleList DoubleSymbolException DurationDiffSM Edge Emission EmptyDataSetException EnumParameter EqualParts ErlangMRG ErlangMRGParams EvaluationException ExpandableParameterSet ExtendedZOOPSDiffSM FalsePositiveRateForFixedSensitivity FastDirichletMRGParams FileManager FileParameter FileParameter.FileRepresentation FSDAGModelForGibbsSampling FSDAGModelForGibbsSamplingParameterSet FSDAGTrainSM FSDAGTrainSMParameterSet FSMEManager FSMEMParameterSet Function GalaxyAdaptor GalaxyAdaptor.FileResult GalaxyAdaptor.LinkedImageResult GalaxyAdaptor.Protocol GalaxyConvertible GaussianEmission GaussianLikePositionPrior GenDisMixClassifier GenDisMixClassifierParameterSet GenericComplementableDiscreteAlphabet GenericComplementableDiscreteAlphabet.GenericComplementableDiscreteAlphabetParameterSet GibbsSamplingModel GUIProgressUpdater HiddenMotifMixture HigherOrderHMM HigherOrderHMM.Type HigherOrderTransition History HMMFactory HMMFactory.HMMType HMMFactory.PseudoTransitionElement HMMTrainingParameterSet HomMMParameterSet HomogeneousDiffSM HomogeneousMM HomogeneousMM0DiffSM HomogeneousMMDiffSM HomogeneousTrainSM HomogeneousTrainSMParameterSet IDGTrainSMParameterSet ImageResult IndependentProductDiffSM IndependentProductDiffSS InfixStringExtractor InhCondProb InhConstraint InhomogeneousDGTrainSM InhomogeneousMarkov InhomogeneousMarkov.InhomogeneousMarkovParameterSet InstanceParameterSet InstantiableFromParameterSet IntList IntronAnnotation IntSequence IterationCondition IterationCondition.IterationConditionParameterSet KFoldCrossValidation KFoldCrossValidationAssessParameterSet KMereStatistic LearningPrinciple LimitedMedianStartDistance LimitedStringExtractor ListResult LocatedSequenceAnnotation LocatedSequenceAnnotationWithLength LogGenDisMixFunction LogisticConstraint LogisticDiffSS LogPrior MappedDiscreteSequence MappingClassifier MappingDiffSM MarkovModelDiffSM MarkovRandomFieldDiffSM MatrixCosts MaxHMMTrainingParameterSet MaximumCorrelationCoefficient MaximumFMeasure MaximumNumericalTwoClassMeasure MeanResultSet MeanResultSet.AdditionImpossibleException MeanResultSet.InconsistentResultNumberException Measure Measure.MeasureParameterSet MEM MEManager MEManagerParameterSet MEMConstraint MEMTools MEMTools.DualFunction MixtureDiffSM MixtureDurationDiffSM MixtureEmission MixtureTrainSM MotifAnnotation MotifAnnotationParser MotifDiscoverer MotifDiscoverer.KindOfProfile MotifDiscovererToolBox MotifDiscoveryAssessment MRGParams MSPClassifier MST MultiDimensionalArbitrarySequence MultiDimensionalDiscreteSequence MultiDimensionalSequence MultiDimensionalSequenceWrapperDiffSS MultilineSimpleParameter MultipleIterationsCondition MultipleIterationsCondition.MultipleIterationsConditionParameterSet MultiSelectionParameter MultiThreadedTrainingParameterSet MultivariateGaussianEmission MultivariateRandomGenerator Mutable MutableMotifDiscoverer MutableMotifDiscovererToolbox MutableMotifDiscovererToolbox.InitMethodForDiffSM NegativeDifferentiableFunction NegativeFunction NegativeOneDimensionalFunction NewickParser NonParsableException NoRevertHistory Normalisation NormalizedDiffSM NotTrainedException NullProgressUpdater NullSequenceAnnotationParser NumberValidator NumericalDifferentiableFunction NumericalHMMTrainingParameterSet NumericalPerformanceMeasure NumericalPerformanceMeasureParameterSet NumericalResult NumericalResultSet OneDataSetLogGenDisMixFunction OneDimensionalFunction OneDimensionalSubFunction OptimizableFunction OptimizableFunction.KindOfParameter Optimizer Pair PairwiseStringAlignment Parameter ParameterException ParameterSet ParameterSetContainer ParameterSetParser ParameterSetParser.NotInstantiableException ParameterSetParser.WrongParameterTypeException ParameterSetTagger ParameterSetTagger.KeyEntryComparator ParameterValidator PerformanceMeasure PerformanceMeasureParameterSet PermutedSequence PFMComparator PFMComparator.NormalizedEuclideanDistance PFMComparator.OneMinusPearsonCorrelationCoefficient PFMComparator.PFMDistance PFMComparator.SymmetricKullbackLeiblerDivergence PhyloDiscreteEmission PhyloNode PhyloTree PluginGaussianEmission PMMExplainingAwayResidual PMMExplainingAwayResidual.PMMExplainingAwayResidualParameterSet PMMMutualInformation PMMMutualInformation.PMMMutualInformationParameterSet PositionDiffSM PositionPrior PositivePredictiveValueForFixedSensitivity PRCurve ProductConstraint ProgressUpdater ProteinAlphabet ProteinAlphabet.ProteinAlphabetParameterSet PValueComputation QuadraticFunction RandomNumberGenerator Rangeable RangeIterator RangeParameter RangeParameter.RangeType RangeParameter.Scale RealTime RecyclableSequenceEnumerator ReferenceBasedTransitionElement ReferenceSequenceAnnotation ReferenceSequenceAnnotationParser ReferenceSequenceDiscreteEmission RegExFilenameFilter RegExFilenameFilter.Directory RegExFilterOutputStream REnvironment RepeatedHoldOutAssessParameterSet RepeatedHoldOutExperiment RepeatedSubSamplingAssessParameterSet RepeatedSubSamplingExperiment RestrictedRepeatHistory Result ResultSet ROCCurve RUtils SafeOutputStream Sampled_RepeatedHoldOutAssessParameterSet Sampled_RepeatedHoldOutExperiment SamplingComponent SamplingDifferentiableStatisticalModel SamplingEmission SamplingFromStatistic SamplingGenDisMixClassifier SamplingGenDisMixClassifierParameterSet SamplingHigherOrderHMM SamplingHigherOrderHMM.ViterbiComputation SamplingHMMTrainingParameterSet SamplingPhyloHMM SamplingScoreBasedClassifier SamplingScoreBasedClassifier.SamplingScheme SamplingScoreBasedClassifierParameterSet SamplingState SamplingTransition ScaledTransitionElement ScoreClassifier ScoreClassifierParameterSet SelectionParameter SensitivityForFixedSpecificity SeparateGaussianLogPrior SeparateLaplaceLogPrior SeparateLogPrior SeqLogoPlotter Sequence Sequence.CompositeSequence Sequence.RecursiveSequence Sequence.SubSequence SequenceAnnotation SequenceAnnotationParser SequenceEnumeration SequenceIterator SequenceScore SequenceScoringParameterSet SharedStructureClassifier SharedStructureMixture ShortSequence SignificantMotifOccurrencesFinder SignificantMotifOccurrencesFinder.JoinMethod SignificantMotifOccurrencesFinder.RandomSeqType SignificantMotifOccurrencesFinder.SumOfProbabilities SilentEmission SimpleBurnInTest SimpleCosts SimpleDifferentiableState SimpleDiscreteSequence SimpleGaussianSumLogPrior SimpleHistory SimpleParameter SimpleParameter.DatatypeNotValidException SimpleParameter.IllegalValueException SimpleParameterSet SimpleResult SimpleSamplingState SimpleSequenceAnnotationParser SimpleSequenceIterator SimpleState SimpleStaticConstraint SimpleStringExtractor SinglePositionSequenceAnnotation SinglePositionSequenceAnnotation.Type Singleton Singleton.SingletonHandler SkewNormalLikeDurationDiffSM SmallDifferenceOfFunctionEvaluationsCondition SmallDifferenceOfFunctionEvaluationsCondition.SmallDifferenceOfFunctionEvaluationsConditionParameterSet SmallGradientConditon SmallGradientConditon.SmallGradientConditonParameterSet SmallStepCondition SmallStepCondition.SmallStepConditionParameterSet SoftOneOfN SparseSequence SparseStringExtractor SplitSequenceAnnotationParser StartDistanceForecaster State StationaryDistribution StatisticalModel StatisticalModelTester StatisticalTest Storable StorableResult StorableValidator StrandDiffSM StrandDiffSM.InitMethod StrandedLocatedSequenceAnnotationWithLength StrandedLocatedSequenceAnnotationWithLength.Strand StrandTrainSM StringAlignment StringExtractor StructureLearner StructureLearner.LearningType StructureLearner.ModelType SubclassFinder SubTensor SymbolExtractor SymmetricTensor Tensor TerminationCondition TerminationException Time TimeCondition TimeCondition.TimeConditionParameterSet TimeLimitedProgressUpdater ToolBox ToolBox.TiedRanks TopSort TrainableAndDifferentiableTransition TrainableState TrainableStatisticalModel TrainableStatisticalModelFactory TrainableTransition TrainSMBasedClassifier Transition TransitionElement TransitionWithSufficientStatistic TwoPointEvaluater UniformDiffSM UniformDiffSS UniformDurationDiffSM UniformEmission UniformHomogeneousDiffSM UniformPositionPrior UniformTrainSM UnionFind UserTime VariableLengthDiffSM VariableLengthMixtureDiffSM VariableLengthWrapperTrainSM VarianceRatioBurnInTest VarianceRatioBurnInTestParameterSet ViterbiParameterSet WrongAlphabetException WrongLengthException WrongSequenceTypeException XMLParser ZOOPSTrainSM