org.biojava.bio.dp
Class PairDPMatrix

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

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()
           
 SymbolList[] resList()
           
 State[] states()
           
 
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

resList

public SymbolList[] resList()
Specified by:
resList 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