org.biojava.bio.dp.twohead

Class PairwiseDP

java.lang.Object

org.biojava.bio.dp.DP

org.biojava.bio.dp.twohead.PairwiseDP

All Implemented Interfaces:

Serializable

public class PairwiseDP
extends DP
implements 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/interfaces inherited from class org.biojava.bio.dp.DP

DP.ReverseIterator

Constructor Summary

Constructors

Constructor and Description
PairwiseDP(MarkovModel mm, CellCalculatorFactoryMaker ccfm)

Method Summary

Methods

Modifier and Type	Method and Description
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, scoreWeightMatrix, setModel, 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

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