jebl.evolution.align
Class MaximalSegmentPair

java.lang.Object
  extended by jebl.evolution.align.Align
      extended by jebl.evolution.align.MaximalSegmentPair

public class MaximalSegmentPair
extends Align

Author:
Alexei Drummond

Constructor Summary
MaximalSegmentPair(Scores sub)
           
 
Method Summary
 void doAlignment(String sq1, String sq2)
          Performs the alignment.
 float getScore()
           
 Traceback next(Traceback tb)
          Get the next state in the traceback
 void prepareAlignment(String sq1, String sq2)
          Initialises the matrices for the alignment.
 void printf(Output out)
          Print matrix used to calculate this alignment.
 
Methods inherited from class jebl.evolution.align.Align
doMatch, doMatch, formatScore, getMatch, setGapOpen, setScores, traceback
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

MaximalSegmentPair

public MaximalSegmentPair(Scores sub)
Method Detail

doAlignment

public final void doAlignment(String sq1,
                              String sq2)
Performs the alignment. Abstract.

Parameters:
sq1 -
sq2 -

next

public final Traceback next(Traceback tb)
Get the next state in the traceback

Parameters:
tb - current Traceback
Returns:
next Traceback

prepareAlignment

public void prepareAlignment(String sq1,
                             String sq2)
Description copied from class: Align
Initialises the matrices for the alignment.

Specified by:
prepareAlignment in class Align

getScore

public float getScore()
Specified by:
getScore in class Align
Returns:
the score of the best alignment

printf

public void printf(Output out)
Print matrix used to calculate this alignment.

Specified by:
printf in class Align
Parameters:
out - Output to print to.