jebl.evolution.align
Class SmithWaterman

java.lang.Object
  jebl.evolution.align.Align
      jebl.evolution.align.SmithWaterman

public class SmithWaterman
extends Align

Constructor Summary

SmithWaterman(Scores sub, float d)

Method Summary

void	doAlignment(String sq1, String sq2) Performs the alignment.
void	doAlignment(String sq1, String sq2, ProgressListener progress)
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

SmithWaterman

public SmithWaterman(Scores sub,
                     float d)

Method Detail

doAlignment

public void doAlignment(String sq1,
                        String sq2,
                        ProgressListener progress)

Parameters:

sq1 -

sq2 -

progress -

doAlignment

public void doAlignment(String sq1,
                        String sq2)

Performs the alignment. Abstract.

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

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.