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Packages that use PhyloTree | |
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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 |
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Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm with parameters of type PhyloTree | |
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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 |
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Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete with parameters of type PhyloTree | |
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PhyloDiscreteEmission(AlphabetContainer con,
double[] hyperParams,
PhyloTree t)
This is a simple constructor for a DiscreteEmission defining the individual hyper parameters. |
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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 |
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Methods in de.jstacs.sequenceScores.statisticalModels.trainable.phylo that return PhyloTree | |
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PhyloTree |
PhyloTree.clone()
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Uses of PhyloTree in de.jstacs.sequenceScores.statisticalModels.trainable.phylo.parser |
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Methods in de.jstacs.sequenceScores.statisticalModels.trainable.phylo.parser that return PhyloTree | |
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PhyloTree |
NewickParser.tokenize()
This method construct a PhyloTree from the given input stream |
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