org.biojava.bio.dp.onehead

Class SingleDPMatrix

java.lang.Object

org.biojava.bio.dp.onehead.SingleDPMatrix

All Implemented Interfaces:

Serializable, DPMatrix

public class SingleDPMatrix
extends Object
implements DPMatrix, Serializable

The dynamic programming matrix for a single sequence.

Author:

Matthew Pocock, Lukas Kall

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected MarkovModel	model
protected double	score
double[][]	scores
protected State[]	states
protected SymbolList[]	symList

Constructor Summary

Constructors

Constructor and Description
SingleDPMatrix(DP dp, SymbolList symList)

Method Summary

Methods

Modifier and Type	Method and Description
double	getCell(int[] index)
double	getScore()
MarkovModel	model()
void	setScore(double score)
State[]	states()
SymbolList[]	symList()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

states

protected final State[] states

model

protected final MarkovModel model

symList

protected final SymbolList[] symList

scores

public final double[][] scores

score

protected double score

Constructor Detail

SingleDPMatrix

public SingleDPMatrix(DP dp,
              SymbolList symList)

Method Detail

states

public State[] states()

Specified by:

states in interface DPMatrix

model

public MarkovModel model()

Specified by:

model in interface DPMatrix

symList

public SymbolList[] symList()

Specified by:

symList in interface DPMatrix

getScore

public double getScore()

Specified by:

getScore in interface DPMatrix

setScore

public void setScore(double score)

getCell

public double getCell(int[] index)
               throws IndexOutOfBoundsException

Specified by:

getCell in interface DPMatrix

Throws:

IndexOutOfBoundsException