jebl.evolution.align
Class Align

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

Direct Known Subclasses:

MaximalSegmentPair, NeedlemanWunsch, NeedlemanWunschAffine, NeedlemanWunschLinearSpace, NeedlemanWunschLinearSpaceAffine, NonOverlapMultipleLocalAffine, OldNeedlemanWunschAffine, OverlapAlign, SmithWaterman, SmithWatermanLinearSpace, SmithWatermanLinearSpaceAffine

public abstract class Align
extends Object

Constructor Summary

Align(Scores sub, float d)

Method Summary

abstract void	doAlignment(String sq1, String sq2) Performs the alignment, abstract.
void	doMatch(Output out, String msg) Print the score and the alignment
void	doMatch(Output out, String msg, boolean outputFMatrix) Print the score, the F matrix, and the alignment
String	formatScore(float val)
String[]	getMatch()
abstract float	getScore()
Traceback	next(Traceback tb) Get the next state in the traceback
abstract void	prepareAlignment(String seq1, String seq2) Initialises the matrices for the alignment.
abstract void	printf(Output out) Print the matrix (matrices) used to compute the alignment
void	setGapOpen(float d)
void	setScores(Scores sub)
void	traceback(TracebackPlotter plotter)

Methods inherited from class java.lang.Object

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

Constructor Detail

Align

public Align(Scores sub,
             float d)

Method Detail

doAlignment

public abstract void doAlignment(String sq1,
                                 String sq2)

Performs the alignment, abstract.

Parameters:

sq1 -

sq2 -

prepareAlignment

public abstract void prepareAlignment(String seq1,
                                      String seq2)

Initialises the matrices for the alignment.

Parameters:

seq1 -

seq2 -

setGapOpen

public void setGapOpen(float d)

setScores

public void setScores(Scores sub)

getMatch

public String[] getMatch()

Returns:

two-element array containing an alignment with maximal score

formatScore

public String formatScore(float val)

Parameters:

val -

Returns:

float value of string val

doMatch

public void doMatch(Output out,
                    String msg,
                    boolean outputFMatrix)

Print the score, the F matrix, and the alignment

Parameters:

out - output to print to

msg - message printed at start

outputFMatrix - print the score matrix

traceback

public void traceback(TracebackPlotter plotter)

doMatch

public void doMatch(Output out,
                    String msg)

Print the score and the alignment

Parameters:

out - output to print to

msg - msg printed at the start

next

public Traceback next(Traceback tb)

Get the next state in the traceback

Parameters:

tb - current Traceback

Returns:

next Traceback

getScore

public abstract float getScore()

Returns:

the score of the best alignment

printf

public abstract void printf(Output out)

Print the matrix (matrices) used to compute the alignment

Parameters:

out - output to print to