org.biojava.bio.dp.twohead
Class EmissionCache

java.lang.Object
  extended byorg.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
Throws:
IllegalSymbolException

clear

public void clear()