- AbstractLatentVariableModel - Class in de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables
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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
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Constructor
- AbstractLatentVariableModel(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.latentVariables.AbstractLatentVariableModel
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Constructor from an XML representation
- AbstractParsimoniousModel - Class in de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious
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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
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- AbstractParsimoniousModel(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.AbstractParsimoniousModel
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- AbstractVariableStructureModel - Class in de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure
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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
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Standard constructor.
- AbstractVariableStructureModel(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.AbstractVariableStructureModel
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The standard constructor for the interface Storable
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- add(SymbolSet) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.Partition
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- add(String) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.SymbolSet
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- add(String[]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.SymbolSet
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- addSequenceToMarkovCounts(Sequence) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.variableStructure.parsimonious.dataStructures.ParsimoniousElement
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Computes Markov counts (e.g. conditional nucleotide frequencies) from data