- getAlphabet() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.Partition
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- getAlphabet() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.PartitionSet
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- getAlphabet() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.SymbolSet
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- getCurrentParameterSet() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.inhomogeneous.InhomogeneousPMM
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- getElements() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.SymbolSet
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- getESS() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.inhomogeneous.InhomogeneousPMM
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- getFlankingModel() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables.ZOOPSModel
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- getGlobalIndexOfMotifInComponent(int, int) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables.ZOOPSModel
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- getGraphViz() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.AbstractParsimoniousModel
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- getGraphviz() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.ParsimoniousElement
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returns the graphViz representation of this context tree
- getIndexOfMaximalComponentFor(Sequence) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables.ZOOPSModel
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- getInstanceComment() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.inhomogeneous.InhPMMParameterSet
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- getInstanceName() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables.ZOOPSModel
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- getInstanceName() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.inhomogeneous.InhomogeneousPMM
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- getInstanceName() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.inhomogeneous.InhPMMParameterSet
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- getLearningMethod() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.AbstractParsimoniousModel
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- getLogPriorTerm() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables.ZOOPSModel
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- getLogPriorTerm() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.inhomogeneous.InhomogeneousPMM
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- getLogProbFor(Sequence, int, int) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables.ZOOPSModel
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- getLogProbFor(DataSet) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables.ZOOPSModel
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- getLogProbFor(Sequence, int) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.ParsimoniousElement
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- getLogProbFor(Sequence, int, int) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.inhomogeneous.InhomogeneousPMM
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- getLogProbForCurrentMarkovCounts() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.ParsimoniousElement
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Computes the probability of data (represented by Markov counts) given the context tree
- getLogScoreOfCurrentStructure() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.AbstractVariableStructureModel
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The function returns the score (AIC, BIC, NML, Bayes) of the currently selected structure.
- getLogScoreOfCurrentStructure() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.inhomogeneous.InhomogeneousPMM
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- getMaximalDepth() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.ParsimoniousElement
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- getMotifLength(int) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables.ZOOPSModel
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- getMotifModel() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables.ZOOPSModel
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- getNumberOfComponents() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables.ZOOPSModel
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- getNumberOfElements() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.SymbolSet
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- getNumberOfLeaves() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.ParsimoniousElement
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- getNumberOfLeaves() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.inhomogeneous.InhomogeneousPMM
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- getNumberOfMotifs() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables.ZOOPSModel
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- getNumberOfMotifsInComponent(int) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables.ZOOPSModel
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- getNumberOfSymbols() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.Partition
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- getNumericalCharacteristics() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables.ZOOPSModel
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- getNumericalCharacteristics() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.inhomogeneous.InhomogeneousPMM
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- getOrder() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.inhomogeneous.InhomogeneousPMM
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- getPartition() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.PartitionSet
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- getProfileOfScoresFor(int, int, Sequence, int, MotifDiscoverer.KindOfProfile) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables.ZOOPSModel
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- getSampleStorageDirectory() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables.AbstractLatentVariableModel
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Returns the directiory of samples parameter sets, i.e., for reading the Gibbs sampling output
- getScore() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.ParsimoniousElement
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- getScore() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.Partition
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- getScore() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.SymbolSet
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- getSetDifferenceAsString(SymbolSet) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.SymbolSet
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- getSparseParameterRepresentation() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.AbstractVariableStructureModel
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- getSparseParameterRepresentation() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.AbstractParsimoniousModel
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- getSparseParameterRepresentation() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.ParsimoniousElement
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- getStrandProbabilitiesFor(int, int, Sequence, int) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables.ZOOPSModel
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- getSymbolSet() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.PartitionSet
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- getTreeStructure() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.ParsimoniousElement
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A node is represented by its label, surrounded by [ ] brackets, followed by the representation of all children in ( ) brackets.
- getTreeStructures() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.AbstractParsimoniousModel
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- getXMLTag() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.inhomogeneous.InhomogeneousPMM
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- getXMLTAG() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.inhomogeneous.InhPMMParameterSet
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