jebl.evolution.align

Class MaximalSegmentPair

java.lang.Object

jebl.evolution.align.Align

jebl.evolution.align.MaximalSegmentPair

public class MaximalSegmentPair
extends Align

Version:

$Id: MaximalSegmentPair.java 185 2006-01-23 23:03:18Z rambaut $

Author:

Alexei Drummond

Constructor Summary

Constructors

Constructor and Description
MaximalSegmentPair(Scores sub)

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.

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

MaximalSegmentPair

public MaximalSegmentPair(Scores sub)

Method Detail

doAlignment

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

Performs the alignment. Abstract.

Parameters:

sq1 -

sq2 -

next

public final Traceback next(Traceback tb)

Get the next state in the traceback

Parameters:

tb - current Traceback

Returns:

next Traceback

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

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.