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getAlphabet() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.Partition
 
getAlphabet() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.PartitionSet
 
getAlphabet() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.SymbolSet
 
getCurrentParameterSet() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.inhomogeneous.InhomogeneousPMM
 
getElements() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.SymbolSet
 
getESS() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.inhomogeneous.InhomogeneousPMM
 
getFlankingModel() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables.ZOOPSModel
 
getGlobalIndexOfMotifInComponent(int, int) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables.ZOOPSModel
 
getGraphViz() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.AbstractParsimoniousModel
 
getGraphviz() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.ParsimoniousElement
returns the graphViz representation of this context tree
getIndexOfMaximalComponentFor(Sequence) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables.ZOOPSModel
 
getInstanceComment() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.inhomogeneous.InhPMMParameterSet
 
getInstanceName() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables.ZOOPSModel
 
getInstanceName() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.inhomogeneous.InhomogeneousPMM
 
getInstanceName() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.inhomogeneous.InhPMMParameterSet
 
getLearningMethod() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.AbstractParsimoniousModel
 
getLogPriorTerm() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables.ZOOPSModel
 
getLogPriorTerm() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.inhomogeneous.InhomogeneousPMM
 
getLogProbFor(Sequence, int, int) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables.ZOOPSModel
 
getLogProbFor(DataSet) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables.ZOOPSModel
 
getLogProbFor(Sequence, int) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.ParsimoniousElement
 
getLogProbFor(Sequence, int, int) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.inhomogeneous.InhomogeneousPMM
 
getLogProbForCurrentMarkovCounts() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.ParsimoniousElement
Computes the probability of data (represented by Markov counts) given the context tree
getLogScoreOfCurrentStructure() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.AbstractVariableStructureModel
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
 
getMaximalDepth() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.ParsimoniousElement
 
getMotifLength(int) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables.ZOOPSModel
 
getMotifModel() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables.ZOOPSModel
 
getNumberOfComponents() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables.ZOOPSModel
 
getNumberOfElements() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.SymbolSet
 
getNumberOfLeaves() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.ParsimoniousElement
 
getNumberOfLeaves() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.inhomogeneous.InhomogeneousPMM
 
getNumberOfMotifs() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables.ZOOPSModel
 
getNumberOfMotifsInComponent(int) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables.ZOOPSModel
 
getNumberOfSymbols() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.Partition
 
getNumericalCharacteristics() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables.ZOOPSModel
 
getNumericalCharacteristics() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.inhomogeneous.InhomogeneousPMM
 
getOrder() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.inhomogeneous.InhomogeneousPMM
 
getPartition() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.PartitionSet
 
getProfileOfScoresFor(int, int, Sequence, int, MotifDiscoverer.KindOfProfile) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables.ZOOPSModel
 
getSampleStorageDirectory() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables.AbstractLatentVariableModel
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
 
getScore() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.Partition
 
getScore() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.SymbolSet
 
getSetDifferenceAsString(SymbolSet) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.SymbolSet
 
getSparseParameterRepresentation() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.AbstractVariableStructureModel
 
getSparseParameterRepresentation() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.AbstractParsimoniousModel
 
getSparseParameterRepresentation() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.ParsimoniousElement
 
getStrandProbabilitiesFor(int, int, Sequence, int) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables.ZOOPSModel
 
getSymbolSet() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.PartitionSet
 
getTreeStructure() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.ParsimoniousElement
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
 
getXMLTag() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.inhomogeneous.InhomogeneousPMM
 
getXMLTAG() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.inhomogeneous.InhPMMParameterSet
 
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