jebl.evolution.align
Class SequenceShuffler

java.lang.Object
  jebl.evolution.align.SequenceShuffler

public class SequenceShuffler
extends Object

Shuffles a sequence and aligns it again multiple times to give mean and variance of alignments on random sequences.

Author:

Richard Moir, Alexei Drummond

Constructor Summary

SequenceShuffler()

Method Summary

float	getMax()
float	getMean()
float	getMin()
double	getStdev()
void	setProgressMonitor(ProgressMonitor monitor)
void	shuffle(Align algorithm, String sq1, String sq2, int numShuffles)

Methods inherited from class java.lang.Object

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

Constructor Detail

SequenceShuffler

public SequenceShuffler()

Method Detail

shuffle

public void shuffle(Align algorithm,
                    String sq1,
                    String sq2,
                    int numShuffles)

getMean

public float getMean()

Returns:

the mean score of the shuffled alignments.

getMax

public float getMax()

getMin

public float getMin()

getStdev

public double getStdev()

Returns:

the standard deviation of scores for the shuffled alignments.

setProgressMonitor

public void setProgressMonitor(ProgressMonitor monitor)