jebl.evolution.align
Class NeedlemanWunsch

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

public class NeedlemanWunsch
extends Align


Constructor Summary
NeedlemanWunsch(Scores sub, float d)
           
 
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

NeedlemanWunsch

public NeedlemanWunsch(Scores sub,
                       float d)
Method Detail

doAlignment

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

Parameters:
sq1 -
sq2 -

getScore

public float getScore()
Returns:
the score of the best alignment

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

next

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

Overrides:
next in class Align
Parameters:
tb - current Traceback
Returns:
next Traceback

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.