org.biojava.bio.dp.twohead
Class EmissionCache

java.lang.Object
  |
  +--org.biojava.bio.dp.twohead.EmissionCache

public class EmissionCache

extends java.lang.Object

Cache for columns of emission probabilities in pair-wise alignment algorithms.

Author:

Matthew Pocock

Constructor Summary

EmissionCache(Alphabet alpha, State[] states, int dsi, ScoreType scoreType)

Method Summary

void	clear()
double[]	getEmissions(java.util.List symList)

Methods inherited from class java.lang.Object

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

Constructor Detail

EmissionCache

public EmissionCache(Alphabet alpha,
                     State[] states,
                     int dsi,
                     ScoreType scoreType)

Method Detail

getEmissions

public final double[] getEmissions(java.util.List symList)
                            throws IllegalSymbolException

IllegalSymbolException

clear

public void clear()