org.biojava.bio.dp.twohead
Class PairwiseDP

java.lang.Object
  extended byorg.biojava.bio.dp.DP
      extended byorg.biojava.bio.dp.twohead.PairwiseDP
All Implemented Interfaces:
java.io.Serializable

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

Nested Class Summary
 
Nested classes inherited from class org.biojava.bio.dp.DP
DP.ReverseIterator
 
Constructor Summary
PairwiseDP(MarkovModel mm, CellCalculatorFactoryMaker ccfm)
           
 
Method Summary
 double backward(SymbolList[] seqs, ScoreType scoreType)
           
 DPMatrix backwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType)
           
 DPMatrix backwardMatrix(SymbolList[] seqs, ScoreType scoreType)
           
 double forward(SymbolList[] seqs, ScoreType scoreType)
           
 DPMatrix forwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType)
           
 DPMatrix forwardMatrix(SymbolList[] seqs, ScoreType scoreType)
           
 void update()
           
 StatePath viterbi(SymbolList[] seqs, ScoreType scoreType)
           
 
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,
                  CellCalculatorFactoryMaker ccfm)
           throws IllegalSymbolException,
                  IllegalTransitionException,
                  BioException
Method Detail

update

public void update()
Overrides:
update in class DP

backward

public double backward(SymbolList[] seqs,
                       ScoreType scoreType)
                throws IllegalSymbolException,
                       IllegalAlphabetException,
                       IllegalTransitionException
Specified by:
backward in class DP
Throws:
IllegalSymbolException
IllegalAlphabetException
IllegalTransitionException

backwardMatrix

public DPMatrix backwardMatrix(SymbolList[] seqs,
                               ScoreType scoreType)
                        throws IllegalSymbolException,
                               IllegalAlphabetException,
                               IllegalTransitionException
Specified by:
backwardMatrix in class DP
Throws:
IllegalSymbolException
IllegalAlphabetException
IllegalTransitionException

backwardMatrix

public DPMatrix backwardMatrix(SymbolList[] seqs,
                               DPMatrix d,
                               ScoreType scoreType)
                        throws IllegalSymbolException,
                               IllegalAlphabetException,
                               IllegalTransitionException
Specified by:
backwardMatrix in class DP
Throws:
IllegalSymbolException
IllegalAlphabetException
IllegalTransitionException

forward

public double forward(SymbolList[] seqs,
                      ScoreType scoreType)
               throws IllegalSymbolException,
                      IllegalAlphabetException,
                      IllegalTransitionException
Specified by:
forward in class DP
Throws:
IllegalSymbolException
IllegalAlphabetException
IllegalTransitionException

forwardMatrix

public DPMatrix forwardMatrix(SymbolList[] seqs,
                              ScoreType scoreType)
                       throws IllegalSymbolException,
                              IllegalAlphabetException,
                              IllegalTransitionException
Specified by:
forwardMatrix in class DP
Throws:
IllegalSymbolException
IllegalAlphabetException
IllegalTransitionException

forwardMatrix

public DPMatrix forwardMatrix(SymbolList[] seqs,
                              DPMatrix d,
                              ScoreType scoreType)
                       throws IllegalSymbolException,
                              IllegalAlphabetException,
                              IllegalTransitionException
Specified by:
forwardMatrix in class DP
Throws:
IllegalSymbolException
IllegalAlphabetException
IllegalTransitionException

viterbi

public StatePath viterbi(SymbolList[] seqs,
                         ScoreType scoreType)
                  throws IllegalSymbolException,
                         IllegalAlphabetException,
                         IllegalTransitionException
Specified by:
viterbi in class DP
Throws:
IllegalSymbolException
IllegalAlphabetException
IllegalTransitionException