calhoun.analysis.crf.features.supporting.phylogenetic
Class EvolutionaryModel

java.lang.Object
  calhoun.analysis.crf.features.supporting.phylogenetic.EvolutionaryModel

All Implemented Interfaces:

java.io.Serializable

public class EvolutionaryModel
extends java.lang.Object
implements java.io.Serializable

See Also:

Serialized Form

Constructor Summary

EvolutionaryModel(PhylogeneticTreeFelsensteinOrder T, double[] pi, NucleotideSubstitutionModel R)

Method Summary

double	logprob(MultipleAlignmentInputSequence.MultipleAlignmentColumn col, boolean conditionref)
double	logprobRC(MultipleAlignmentInputSequence.MultipleAlignmentColumn col, boolean conditionref)
void	summarize()

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

EvolutionaryModel

public EvolutionaryModel(PhylogeneticTreeFelsensteinOrder T,
                         double[] pi,
                         NucleotideSubstitutionModel R)

Method Detail

logprobRC

public double logprobRC(MultipleAlignmentInputSequence.MultipleAlignmentColumn col,
                        boolean conditionref)

logprob

public double logprob(MultipleAlignmentInputSequence.MultipleAlignmentColumn col,
                      boolean conditionref)

summarize

public void summarize()