| Package | Description |
|---|---|
| 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 |
| Modifier and Type | Method and Description |
|---|---|
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.
|
| Constructor and Description |
|---|
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. |
| Modifier and Type | Method and Description |
|---|---|
PhyloTree |
PhyloTree.clone() |
| Modifier and Type | Method and Description |
|---|---|
PhyloTree |
NewickParser.tokenize()
This method construct a
PhyloTree from the given input stream |