jebl.evolution.align
Class SmithWatermanLinearSpace

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

public class SmithWatermanLinearSpace
extends Align

Constructor Summary

SmithWatermanLinearSpace(Scores sub, float d)

Method Summary

void	doAlignment(String sq1, String sq2) Performs the alignment.
String[]	getMatch()
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.
void	traceback(TracebackPlotter plotter)

Methods inherited from class jebl.evolution.align.Align

doMatch, doMatch, formatScore, setGapOpen, setScores

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SmithWatermanLinearSpace

public SmithWatermanLinearSpace(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

getMatch

public String[] getMatch()

Overrides:

getMatch in class Align

Returns:

two-element array containing an alignment with maximal score

traceback

public void traceback(TracebackPlotter plotter)

Overrides:

traceback in class Align

prepareAlignment

public void prepareAlignment(String sq1,
                             String sq2)

Description copied from class: Align

Initialises the matrices for the alignment.

printf

public void printf(Output out)

Print matrix used to calculate this alignment.

Parameters:

out - Output to print to.

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