jebl.evolution.align

Class OldNeedlemanWunschAffine

java.lang.Object

jebl.evolution.align.Align

jebl.evolution.align.OldNeedlemanWunschAffine

public class OldNeedlemanWunschAffine
extends Align

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
void	doAlignment(java.lang.String sq1, java.lang.String sq2) Performs the alignment.
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)

Methods inherited from class jebl.evolution.align.Align

doMatch, doMatch, formatScore, getMatch, setGapOpen, setScores, traceback

Methods inherited from class java.lang.Object

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

Constructor Detail

OldNeedlemanWunschAffine

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

Method Detail

doAlignment

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

Performs the alignment. Abstract.

Parameters:

sq1 -

sq2 -

prepareAlignment

public void prepareAlignment(java.lang.String sq1,
                    java.lang.String sq2)

Description copied from class: Align

Initialises the matrices for the alignment.

Specified by:

prepareAlignment in class Align

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

getScore

public float getScore()

Specified by:

getScore in class Align

Returns:

score for this 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.