jebl.evolution.align
Class NonOverlapMultipleLocalAffine

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

public class NonOverlapMultipleLocalAffine
extends Align

Performs recursive local alignments. each time splitting the longer of the two sequences into two subsequences either side of the local alignment and aligning those. Uses SmithWatermanLinearSpaceAffine. Stores all of the local alignments and their scores. Threshold T is the minimum score that an alignment must be for inclusion.

Author:

Richard Moir

Constructor Summary

NonOverlapMultipleLocalAffine(Scores sub, float d, float e, int T)

Method Summary

void	doAlignment(String sq1, String sq2) Performs the alignment.
String[][]	getAlignments() The indices for these correspond to those for the getScoreMatrix() matrix.
String[]	getMatch()
String	getMatchScores(int width)
float	getScore()
float[]	getScores() The indices for these correspond to those for the getAlignments() matrix.
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	recurseAlignment(String sq1, int leftIndex)
void	setGapExtend(float e)
void	setThreshold(int T)

Methods inherited from class jebl.evolution.align.Align

doMatch, doMatch, formatScore, setGapOpen, setScores, traceback

Methods inherited from class java.lang.Object

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

Constructor Detail

NonOverlapMultipleLocalAffine

public NonOverlapMultipleLocalAffine(Scores sub,
                                     float d,
                                     float e,
                                     int T)

Method Detail

doAlignment

public void doAlignment(String sq1,
                        String sq2)

Performs the alignment. Abstract.

Parameters:

sq1 -

sq2 -

recurseAlignment

public void recurseAlignment(String sq1,
                             int leftIndex)

getMatch

public String[] getMatch()

Overrides:

getMatch in class Align

Returns:

two-element array containing all of the local alignments separated by " - ";

getMatchScores

public String getMatchScores(int width)

Parameters:

width - length to trim lines to. -1 = infinite width.

Returns:

String containing all local alignments with the score next to them.

getScore

public float getScore()

Returns:

the score of the best alignment

getScores

public float[] getScores()

The indices for these correspond to those for the getAlignments() matrix.

Returns:

a matrix of scores for all the alignments.

getAlignments

public String[][] getAlignments()

The indices for these correspond to those for the getScoreMatrix() matrix.

Returns:

a 2d matrix of alignments. first index is the alignment number. second is the sequence number (0 or 1)

printf

public void printf(Output out)

Print matrix used to calculate this alignment.

Parameters:

out - Output to print to.

prepareAlignment

public void prepareAlignment(String sq1,
                             String sq2)

Description copied from class: Align

Initialises the matrices for the alignment.

setGapExtend

public void setGapExtend(float e)

next

public Traceback next(Traceback tb)

Get the next state in the traceback

Parameters:

tb - current Traceback

Returns:

next Traceback

setThreshold

public void setThreshold(int T)