jebl.evolution.align
Class NeedlemanWunschAffine

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

public class NeedlemanWunschAffine
extends Align

Constructor Summary

NeedlemanWunschAffine(Scores sub, float d, float e)

Method Summary

void	allocateMatrices(int n, int m)
void	appendMatch(jebl.evolution.align.AlignmentResult result1, jebl.evolution.align.AlignmentResult result2)
void	doAlignment(jebl.evolution.align.Profile sequence1, jebl.evolution.align.Profile sequence2, int offset1, int offset2, int n, int m, int startType, int endType)
void	doAlignment(jebl.evolution.align.Profile sequence1, jebl.evolution.align.Profile sequence2, int offset1, int offset2, int n, int m, int startType, int endType, boolean freeStartGap, boolean freeEndGap)
void	doAlignment(String sq1, String sq2) Performs the alignment.
void	doAlignment(String sequence1, String sequence2, int startType, int endType)
String[]	getMatch()
String[]	getMatch(char[] sq1, char[] sq2)
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	setGapExtend(float e)

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

NeedlemanWunschAffine

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

Method Detail

doAlignment

public void doAlignment(String sq1,
                        String sq2)

Performs the alignment. Abstract.

Parameters:

sq1 -

sq2 -

allocateMatrices

public void allocateMatrices(int n,
                             int m)

prepareAlignment

public void prepareAlignment(String sq1,
                             String sq2)

Description copied from class: Align

Initialises the matrices for the alignment.

doAlignment

public void doAlignment(String sequence1,
                        String sequence2,
                        int startType,
                        int endType)

doAlignment

public void doAlignment(jebl.evolution.align.Profile sequence1,
                        jebl.evolution.align.Profile sequence2,
                        int offset1,
                        int offset2,
                        int n,
                        int m,
                        int startType,
                        int endType)

doAlignment

public void doAlignment(jebl.evolution.align.Profile sequence1,
                        jebl.evolution.align.Profile sequence2,
                        int offset1,
                        int offset2,
                        int n,
                        int m,
                        int startType,
                        int endType,
                        boolean freeStartGap,
                        boolean freeEndGap)

appendMatch

public void appendMatch(jebl.evolution.align.AlignmentResult result1,
                        jebl.evolution.align.AlignmentResult result2)

getMatch

public String[] getMatch()

Overrides:

getMatch in class Align

Returns:

two-element array containing an alignment with maximal score

getMatch

public String[] getMatch(char[] sq1,
                         char[] sq2)

getScore

public float getScore()

Returns:

score for this alignment

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

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.