org.biojava.bio.dp.onehead
Class SingleDP

java.lang.Object
  org.biojava.bio.dp.DP
      org.biojava.bio.dp.onehead.SingleDP

All Implemented Interfaces:

Serializable

public class SingleDP
extends DP
implements Serializable

An implementation of DP that aligns a single sequence against a single model.

Author:

Matthew Pocock, Thomas Down, Samiul Hasan, Lukas Kall

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class org.biojava.bio.dp.DP

DP.ReverseIterator

Field Summary

protected HashMap	emissionsNull
protected HashMap	emissionsOdds
protected HashMap	emissionsProb

Constructor Summary

SingleDP(MarkovModel model)

Method Summary

protected void	backward_initialize(DPCursor dpCursor, ScoreType scoreType)
protected void	backward_recurse(DPCursor dpCursor, ScoreType scoreType)
protected double	backward_termination(DPCursor dpCursor, ScoreType scoreType)
protected double	backward(DPCursor dpCursor, ScoreType scoreType)
double	backward(SymbolList[] seq, ScoreType scoreType)
DPMatrix	backwardMatrix(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType)
DPMatrix	backwardMatrix(SymbolList[] seq, ScoreType scoreType)
protected void	forward_initialize(DPCursor dpCursor, ScoreType scoreType)
protected double	forward(DPCursor dpCursor, ScoreType scoreType)
double	forward(SymbolList[] seq, ScoreType scoreType)
DPMatrix	forwardMatrix(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType)
DPMatrix	forwardMatrix(SymbolList[] seq, ScoreType scoreType)
double[]	getEmission(Symbol sym, ScoreType scoreType) This method is public for the benefit of training algorithms, and in the future we should look at a better way of exposing the emissions cache.
void	update()
StatePath	viterbi(SymbolList[] symList, 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

Field Detail

emissionsProb

protected final HashMap emissionsProb

emissionsOdds

protected final HashMap emissionsOdds

emissionsNull

protected final HashMap emissionsNull

Constructor Detail

SingleDP

public SingleDP(MarkovModel model)
         throws IllegalSymbolException,
                IllegalTransitionException,
                BioException

Throws:

IllegalSymbolException

IllegalTransitionException

BioException

Method Detail

update

public void update()

Overrides:

update in class DP

getEmission

public double[] getEmission(Symbol sym,
                            ScoreType scoreType)
                     throws IllegalSymbolException

This method is public for the benefit of training algorithms, and in the future we should look at a better way of exposing the emissions cache.

Throws:

IllegalSymbolException

forward

public double forward(SymbolList[] seq,
                      ScoreType scoreType)
               throws IllegalSymbolException,
                      IllegalAlphabetException,
                      IllegalSymbolException

Specified by:

forward in class DP

Throws:

IllegalSymbolException

IllegalAlphabetException

backward

public double backward(SymbolList[] seq,
                       ScoreType scoreType)
                throws IllegalSymbolException,
                       IllegalAlphabetException,
                       IllegalSymbolException

Specified by:

backward in class DP

Throws:

IllegalSymbolException

IllegalAlphabetException

forwardMatrix

public DPMatrix forwardMatrix(SymbolList[] seq,
                              ScoreType scoreType)
                       throws IllegalSymbolException,
                              IllegalAlphabetException,
                              IllegalSymbolException

Specified by:

forwardMatrix in class DP

Throws:

IllegalSymbolException

IllegalAlphabetException

backwardMatrix

public DPMatrix backwardMatrix(SymbolList[] seq,
                               ScoreType scoreType)
                        throws IllegalSymbolException,
                               IllegalAlphabetException,
                               IllegalSymbolException

Specified by:

backwardMatrix in class DP

Throws:

IllegalSymbolException

IllegalAlphabetException

forwardMatrix

public DPMatrix forwardMatrix(SymbolList[] seq,
                              DPMatrix matrix,
                              ScoreType scoreType)
                       throws IllegalArgumentException,
                              IllegalSymbolException,
                              IllegalAlphabetException,
                              IllegalSymbolException

Specified by:

forwardMatrix in class DP

Throws:

IllegalArgumentException

IllegalSymbolException

IllegalAlphabetException

backwardMatrix

public DPMatrix backwardMatrix(SymbolList[] seq,
                               DPMatrix matrix,
                               ScoreType scoreType)
                        throws IllegalArgumentException,
                               IllegalSymbolException,
                               IllegalAlphabetException,
                               IllegalSymbolException

Specified by:

backwardMatrix in class DP

Throws:

IllegalArgumentException

IllegalSymbolException

IllegalAlphabetException

forward

protected double forward(DPCursor dpCursor,
                         ScoreType scoreType)
                  throws IllegalSymbolException

Throws:

IllegalSymbolException

backward

protected double backward(DPCursor dpCursor,
                          ScoreType scoreType)
                   throws IllegalSymbolException

Throws:

IllegalSymbolException

forward_initialize

protected void forward_initialize(DPCursor dpCursor,
                                  ScoreType scoreType)
                           throws IllegalSymbolException

Throws:

IllegalSymbolException

backward_initialize

protected void backward_initialize(DPCursor dpCursor,
                                   ScoreType scoreType)
                            throws IllegalSymbolException

Throws:

IllegalSymbolException

backward_recurse

protected void backward_recurse(DPCursor dpCursor,
                                ScoreType scoreType)
                         throws IllegalSymbolException

Throws:

IllegalSymbolException

backward_termination

protected double backward_termination(DPCursor dpCursor,
                                      ScoreType scoreType)
                               throws IllegalSymbolException

Throws:

IllegalSymbolException

viterbi

public StatePath viterbi(SymbolList[] symList,
                         ScoreType scoreType)
                  throws IllegalSymbolException

Specified by:

viterbi in class DP

Throws:

IllegalSymbolException