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AbstractLatentVariableModel - Class in de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables
Abstract class for all models that require latent variables, such as mixture models and promoter models.
AbstractLatentVariableModel(AlphabetContainer, int) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables.AbstractLatentVariableModel
Constructor
AbstractLatentVariableModel(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables.AbstractLatentVariableModel
Constructor from an XML representation
AbstractParsimoniousModel - Class in de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious
Abstract class for all trainable statistical models that include parsimonious context trees (PCTs).
AbstractParsimoniousModel(AlphabetContainer, int) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.AbstractParsimoniousModel
 
AbstractParsimoniousModel(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.AbstractParsimoniousModel
 
AbstractVariableStructureModel - Class in de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure
Abstract class for all trainable statistical models that include a model (structure) selection.
AbstractVariableStructureModel(AlphabetContainer, int) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.AbstractVariableStructureModel
Standard constructor.
AbstractVariableStructureModel(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.AbstractVariableStructureModel
The standard constructor for the interface Storable.
add(SymbolSet) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.Partition
 
add(String) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.SymbolSet
 
add(String[]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.SymbolSet
 
addSequenceToMarkovCounts(Sequence) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.ParsimoniousElement
Computes Markov counts (e.g. conditional nucleotide frequencies) from data
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