org.biojava.bio.dp.twohead
Class PairDPMatrix

java.lang.Object
  |
  +--org.biojava.bio.dp.twohead.PairDPMatrix

All Implemented Interfaces:

DPMatrix, java.io.Serializable

public class PairDPMatrix

extends java.lang.Object

implements DPMatrix, java.io.Serializable

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

Author:

Thomas Down

See Also:

Serialized Form

Constructor Summary

PairDPMatrix(DP dp, SymbolList seq0, SymbolList seq1)

Method Summary

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