All Classes

AbstractFeatureManager AbstractTestCase AlignmentTree AllIntergenicHiddenStateReader Assert BasicStats BasicStatsTest BeanModel BeanModel.Edge BeanModel.Node BinaryTreeNode BlastInterval13 BooleanInput CacheProcessor CacheProcessor.FeatureEvaluation CacheProcessor.LengthFeatureEvaluation CacheProcessor.SolverSetup CacheProcessor.StatePotentials CacheProcessorBasic CacheProcessorDeluxe CacheProcessorTest CacheProcessorTestRealShort CacheStrategySpec CacheStrategySpec.CacheStrategy CacheStrategySpec.DenseBoundaryCachingDetails CacheStrategySpec.DenseBoundaryEntry CacheStrategySpec.DenseCachingDetails CacheTest CheckException CleanLocalScoreSemiMarkovGradient CleanMaximumLikelihoodSemiMarkovGradient CodingStopFeature ColtUtil ColumnConditionalLogProbability CompositeFeatureManager CompositeInput CompositeInput.InputComponent CompositeInput.LegacyInputHandler ConfigException Conrad ConstrainedFeatureManager ConstraintTest ConstraintTest.FixedEdges CRFInference CRFInference.InferenceResult CRFIOTest CRFObjectiveFunctionGradient CRFTest CRFTraining DataException DenseBooleanMatrix2D DenseIntMatrix2D EmissionMarkovFeature EmissionMarkovFeature.MarkovHistory EndFeatures ErrorException ESTEdge ESTExon ESTInterval13 ESTInterval29 ESTIntron EvolutionaryModel ExampleTrees ExtensionMapper FastaAlignmentInput FastaInput FastaIterator FastaIterator.ReaderSequence FastaSequence FastaWriter FeatureList FeatureManager FeatureManagerEdge FeatureManagerEdgeExplicitLength FeatureManagerNode FeatureManagerNodeBoundaries FeatureManagerNodeExplicitLength FeatureTest FelsensteinFeatures FileDiff FileInputHandlerTest FilenameMapper FileUtil FilterIterator FixedWeightOptimizer FootprintsInterval13 FootprintsInterval29 FunctionEvalTest GammaDistribution GammaDistributionsTest GapConjunctionFeatures GapConjunctionFeaturesTest GapFeaturesInterval13 GapFeaturesInterval29 GeneConstraints GeneConstraintsInterval13 GeneConstraintsInterval13Test GeneConstraintsInterval29 GeneConstraintsToy GTFInputInterval13 GTFInputInterval29 GTFWriterTest HKY85Model IndicatorEdges InputComponentIO InputHandler InputHandlerBase InputHandlerDirectory InputHandlerFile InputHandlerInterleaved InputSequence InputSequenceBoolean InputSequenceCharacter InputSequenceComposite InputSequenceInt InputSequenceObject InterleavedInputComponent InterleavedInputComponentBase Interval13BaselineTest Interval13FeatureTest Interval13Model Interval13Tools Interval21HiddenSequenceTranslator Interval29BaselineTest Interval29FeatureTest Interval29Model Interval29Tools IntervalInput IntervalInputSequence IntervalInputSequence.IntervalRangeMapValue IntervalPresenceFeatures IntInput IntInputInterval29 IntronLengthFeature IteratorAdapterInputComponent IteratorAdapterTrainingSequenceInput Kimura80Model KmerFeatures KmerFeatures.Cardinality KmerHasher KmerHasher.CharacterHash KmerHasherTest LBFGSTest LocalPathSimilarityScore LogFiles LogProbLookup LogprobLookupTest LookbackBuffer MarkovPredictorLogprob MatrixOperationsTest MaxentMotifFeatures MaxentMotifModel MaxentMotifModelTest MaximumExpectedAccuracySemiMarkovGradient MaximumExpectedAccuracyTest MaximumLikelihoodGradient MaximumLikelihoodSemiMarkovGradient MixtureOfGammas ModelManager MultipleAlignmentInput MultipleAlignmentInputSequence MultipleSequenceTest NameInput NameInputSequence NewickTreeManipulationTest NoCachingCacheProcessor NonGradientTest NucleotideSubstitutionModel NucleotideSubstitutionModelTest OutputHandler OutputHandlerComposite OutputHandlerGeneCallPredict OutputHandlerGeneCallPredict.Results OutputHandlerGeneCallStats OutputHandlerGeneCallStats.Results OutputHandlerGeneCallStatsInterval29 OutputHandlerWriter PfamGenic PfamPhase PhylogeneticLogprobInterval13 PhylogeneticTreeFelsensteinOrder PositionWeightMatrixFeatures PositionWeightMatrixFeatures.Geometry PredictedActualBinaryContingencyTable PredictedActualBinaryContingencyTableTest PrimeUtil PWM_evolution PWMInterval13 PWMInterval29 PWMLookup QualityIterator RangeMap RangeMap.Interval RangeMapExamples RealIOTest RecyclingBuffer RecyclingBufferTest ReferenceBasePredictorInterval13 ReferenceBasePredictorInterval13Base ReferenceBasePredictorInterval29 ReferenceBasePredictorInterval29Base ReferenceBasePredictorNodeOnlyInterval13 ReferenceBasePredictorNodeOnlyInterval29 ReferenceBasePredictorTest ReferenceBasePredictorZeroPadInterval13 ReferenceBasePredictorZeroPadInterval29 RepeatedSubsequence RepeatedSubsequenceTest ResourceLoader ResourceLoader.ResourceFinder RootedBinaryPhylogeneticTree SeededOptimizer SemiMarkovSetup SemiMarkovTest SemiMarkovViterbi SemiMarkovViterbiNoCache SequenceConverter SequenceConverterTest SimpleFastaSequence SimplerFormatter SimplexOptimizer SimScoreMaxStateAgreement SimScoreMinCodingMiscallsSV13 SimScoreMinExonBoundaryMiscallsSV13 SimScoreStateAndExonBoundariesInt13 SlowTestMaxentMotifModel StandardOptimizer StartFeatures StateLengthLogprobInterval13 StateLengthLogprobInterval29 StateTransitionsInterval13 StateTransitionsInterval29 StringInput TestFeatures TestFeatures.EmissionFeature TestFeatures.ExplicitHalfExponentialLengthFeature TestFeatures.ExponentialLengthFeature TestFeatures.GaussianLengthFeature TestFeatures.HalfExponentialLengthFeature TestFeatures.TestFeature TrainingSequence TrainingSequenceIO TwoPassOptimizer TypedProperties Util ValidPathsTest Viterbi ViterbiTableModel ViterbiViewerApp WeightedEdges WeightedStateChanges XmlDiff XmlUtil ZeroOrderManager ZeroOrderModel