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

Fields

Modifier and Type

Field

Description

protected final HashMap

emissionsNull

protected final HashMap

emissionsOdds

protected final HashMap

emissionsProb
Constructor Summary

Constructors

Constructor

Description

SingleDP(MarkovModel model)
Method Summary

Modifier and Type

Method

Description

protected double

backward(DPCursor dpCursor, ScoreType scoreType)

double

backward(SymbolList[] seq, ScoreType scoreType)

protected void

backward_initialize(DPCursor dpCursor, ScoreType scoreType)

protected void

backward_recurse(DPCursor dpCursor, ScoreType scoreType)

protected double

backward_termination(DPCursor dpCursor, ScoreType scoreType)

DPMatrix

backwardMatrix(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType)

DPMatrix

backwardMatrix(SymbolList[] seq, ScoreType scoreType)

protected double

forward(DPCursor dpCursor, ScoreType scoreType)

double

forward(SymbolList[] seq, ScoreType scoreType)

protected void

forward_initialize(DPCursor dpCursor, 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 Details
- emissionsProb
  
  protected final HashMap emissionsProb
- emissionsOdds
  
  protected final HashMap emissionsOdds
- emissionsNull
  
  protected final HashMap emissionsNull
Constructor Details
- SingleDP
  
  public SingleDP(MarkovModel model) throws IllegalSymbolException, IllegalTransitionException, BioException
  
  Throws:
  
  IllegalSymbolException
  
  IllegalTransitionException
  
  BioException
Method Details
- 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
  
  IllegalSymbolException
- backward
  
  public double backward(SymbolList[] seq, ScoreType scoreType) throws IllegalSymbolException, IllegalAlphabetException, IllegalSymbolException
  
  Specified by:
  
  backward in class DP
  
  Throws:
  
  IllegalSymbolException
  
  IllegalAlphabetException
  
  IllegalSymbolException
- forwardMatrix
  
  public DPMatrix forwardMatrix(SymbolList[] seq, ScoreType scoreType) throws IllegalSymbolException, IllegalAlphabetException, IllegalSymbolException
  
  Specified by:
  
  forwardMatrix in class DP
  
  Throws:
  
  IllegalSymbolException
  
  IllegalAlphabetException
  
  IllegalSymbolException
- backwardMatrix
  
  public DPMatrix backwardMatrix(SymbolList[] seq, ScoreType scoreType) throws IllegalSymbolException, IllegalAlphabetException, IllegalSymbolException
  
  Specified by:
  
  backwardMatrix in class DP
  
  Throws:
  
  IllegalSymbolException
  
  IllegalAlphabetException
  
  IllegalSymbolException
- 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
  
  IllegalSymbolException
- 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
  
  IllegalSymbolException
- 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

Class SingleDP

Nested Class Summary

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

Field Summary

Constructor Summary

Method Summary

Methods inherited from class org.biojava.bio.dp.DP

Methods inherited from class java.lang.Object

Field Details

emissionsProb

emissionsOdds

emissionsNull

Constructor Details

SingleDP

Method Details

update

getEmission

forward

backward

forwardMatrix

backwardMatrix

forwardMatrix

backwardMatrix

forward

backward

forward_initialize

backward_initialize

backward_recurse

backward_termination

viterbi