org.biojava.bio.dp
Class PairwiseDP

java.lang.Object
  |
  +--org.biojava.bio.dp.DP
        |
        +--org.biojava.bio.dp.PairwiseDP

public class PairwiseDP
extends DP
implements java.io.Serializable

Algorithms for dynamic programming (alignments) between pairs of SymbolLists. Based on a single-head DP implementation by Matt Pocock.

Author:
Thomas Down, Matthew Pocock
See Also:
Serialized Form

Inner classes inherited from class org.biojava.bio.dp.DP
DP.ReverseIterator
 
Constructor Summary
PairwiseDP(MarkovModel mm)
           
 
Method Summary
 double backward(SymbolList[] seqs)
           
 DPMatrix backwardMatrix(SymbolList[] seqs)
           
 DPMatrix backwardMatrix(SymbolList[] seqs, DPMatrix d)
           
 double forward(SymbolList[] seqs)
           
 DPMatrix forwardMatrix(SymbolList[] seqs)
           
 DPMatrix forwardMatrix(SymbolList[] seqs, DPMatrix d)
           
protected  double[] getEmission(java.util.List symList, CrossProductAlphabet alpha)
           
 void updateTransitions()
           
 StatePath viterbi(SymbolList[] seqs)
           
 
Methods inherited from class org.biojava.bio.dp.DP
backwardTransitions, backwardTransitionScores, flatView, forwardsBackwards, forwardTransitions, forwardTransitionScores, generate, getBackwardTransitions, getBackwardTransitionScores, getDotStatesIndex, getForwardTransitions, getForwardTransitionScores, getModel, getStates, lockModel, scoreWeightMatrix, stateList, unlockModel
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

PairwiseDP

public PairwiseDP(MarkovModel mm)
           throws IllegalSymbolException,
                  IllegalTransitionException,
                  BioException
Method Detail

updateTransitions

public void updateTransitions()
Overrides:
updateTransitions in class DP

getEmission

protected double[] getEmission(java.util.List symList,
                               CrossProductAlphabet alpha)
                        throws IllegalSymbolException

backward

public double backward(SymbolList[] seqs)
                throws IllegalSymbolException,
                       IllegalAlphabetException,
                       IllegalTransitionException
Overrides:
backward in class DP

backwardMatrix

public DPMatrix backwardMatrix(SymbolList[] seqs)
                        throws IllegalSymbolException,
                               IllegalAlphabetException,
                               IllegalTransitionException
Overrides:
backwardMatrix in class DP

backwardMatrix

public DPMatrix backwardMatrix(SymbolList[] seqs,
                               DPMatrix d)
                        throws IllegalSymbolException,
                               IllegalAlphabetException,
                               IllegalTransitionException
Overrides:
backwardMatrix in class DP

forward

public double forward(SymbolList[] seqs)
               throws IllegalSymbolException,
                      IllegalAlphabetException,
                      IllegalTransitionException
Overrides:
forward in class DP

forwardMatrix

public DPMatrix forwardMatrix(SymbolList[] seqs)
                       throws IllegalSymbolException,
                              IllegalAlphabetException,
                              IllegalTransitionException
Overrides:
forwardMatrix in class DP

forwardMatrix

public DPMatrix forwardMatrix(SymbolList[] seqs,
                              DPMatrix d)
                       throws IllegalSymbolException,
                              IllegalAlphabetException,
                              IllegalTransitionException
Overrides:
forwardMatrix in class DP

viterbi

public StatePath viterbi(SymbolList[] seqs)
                  throws IllegalSymbolException,
                         IllegalAlphabetException,
                         IllegalTransitionException
Overrides:
viterbi in class DP