org.biojava.bio.dp.twohead

Class PairDPMatrix

java.lang.Object

org.biojava.bio.dp.twohead.PairDPMatrix

All Implemented Interfaces:

Serializable, DPMatrix

public class PairDPMatrix
extends Object
implements DPMatrix, Serializable

Storage structure for intermediate values from a pairwise dynamic programming run.

Author:

Thomas Down

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
PairDPMatrix(DP dp, SymbolList seq0, SymbolList seq1)

Method Summary

Methods

Modifier and Type	Method and Description
double	getCell(int[] indxs)
double	getScore()
MarkovModel	model()
State[]	states()
SymbolList[]	symList()

Methods inherited from class java.lang.Object

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

Constructor Detail

PairDPMatrix

public PairDPMatrix(DP dp,
            SymbolList seq0,
            SymbolList seq1)

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

getCell

public double getCell(int[] indxs)

Specified by:

getCell in interface DPMatrix