Uses of Class
de.jstacs.sequenceScores.statisticalModels.trainable.phylo.PhyloTree

Packages that use PhyloTree

de.jstacs.sequenceScores.statisticalModels.trainable.hmm	The package provides all interfaces and classes for a hidden Markov model (HMM).
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete
de.jstacs.sequenceScores.statisticalModels.trainable.phylo
de.jstacs.sequenceScores.statisticalModels.trainable.phylo.parser

Uses of PhyloTree in de.jstacs.sequenceScores.statisticalModels.trainable.hmm

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm with parameters of type PhyloTree

static AbstractHMM

HMMFactory.createSunflowerHMM(HMMTrainingParameterSet pars, AlphabetContainer con, double ess, int expectedSequenceLength, boolean startCentral, PhyloTree[] t, double[] motifProb, int[] motifLength) This method creates a first order sunflower HMM allowing phylogenetic emissions.

Uses of PhyloTree in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete

Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete with parameters of type PhyloTree

PhyloDiscreteEmission(AlphabetContainer con, double[] hyperParams, PhyloTree t)
This is a simple constructor for a DiscreteEmission defining the individual hyper parameters.

PhyloDiscreteEmission(AlphabetContainer con, double ess, PhyloTree t)
This is a simple constructor for a PhyloDiscreteEmission based on the equivalent sample size.

Uses of PhyloTree in de.jstacs.sequenceScores.statisticalModels.trainable.phylo

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.phylo that return PhyloTree

PhyloTree

PhyloTree.clone()

Uses of PhyloTree in de.jstacs.sequenceScores.statisticalModels.trainable.phylo.parser

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.phylo.parser that return PhyloTree

PhyloTree

NewickParser.tokenize() This method construct a PhyloTree from the given input stream