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

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

All Implemented Interfaces:

java.io.Serializable

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

See Also:

Serialized Form

Constructor Summary

ColumnConditionalLogProbability(java.util.List<int[]> clusters, int eModelNum)

Method Summary

double	condLogProb(InputSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn> seq, int pos, int state)
int	numClusters()
int	state2cluster(int state)
void	train(ModelManager modelInfo, java.util.List<? extends TrainingSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn>> data)

Methods inherited from class java.lang.Object

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

Constructor Detail

ColumnConditionalLogProbability

public ColumnConditionalLogProbability(java.util.List<int[]> clusters,
                                       int eModelNum)

Method Detail

numClusters

public int numClusters()

state2cluster

public int state2cluster(int state)

condLogProb

public double condLogProb(InputSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn> seq,
                          int pos,
                          int state)

train

public void train(ModelManager modelInfo,
                  java.util.List<? extends TrainingSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn>> data)