jebl.evolution.align

Class SmithWatermanLinearSpaceAffine

java.lang.Object

jebl.evolution.align.Align

jebl.evolution.align.SmithWatermanLinearSpaceAffine

public class SmithWatermanLinearSpaceAffine
extends Align

Version:

$Id: SmithWatermanLinearSpaceAffine.java 384 2006-07-17 07:17:39Z pepster $

Author:

Alexei Drummond

Constructor Summary

Constructors

Constructor and Description
SmithWatermanLinearSpaceAffine(Scores sub, float d, float e)

Method Summary

Methods

Modifier and Type	Method and Description
void	doAlignment(java.lang.String sequence1, java.lang.String sequence2) Performs the alignment.
void	doAlignment(java.lang.String sq1, java.lang.String sq2, ProgressListener progress)
java.lang.String[]	getMatch()
float	getScore()
Traceback	next(Traceback tb) Get the next state in the traceback
void	prepareAlignment(java.lang.String sq1, java.lang.String sq2) Initialises the matrices for the alignment.
void	printf(Output out) Print matrix used to calculate this alignment.
void	setGapExtend(float e)
void	traceback(TracebackPlotter plotter)

Methods inherited from class jebl.evolution.align.Align

doMatch, doMatch, formatScore, setGapOpen, setScores

Methods inherited from class java.lang.Object

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

Constructor Detail

SmithWatermanLinearSpaceAffine

public SmithWatermanLinearSpaceAffine(Scores sub,
                              float d,
                              float e)

Method Detail

doAlignment

public void doAlignment(java.lang.String sq1,
               java.lang.String sq2,
               ProgressListener progress)

Parameters:

sq1 -

sq2 -

doAlignment

public void doAlignment(java.lang.String sequence1,
               java.lang.String sequence2)

Performs the alignment. Abstract.

getScore

public float getScore()

Returns:

the score of the best alignment

getMatch

public java.lang.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(java.lang.String sq1,
                    java.lang.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.

setGapExtend

public void setGapExtend(float e)

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