jebl.evolution.align
Class SequenceShuffler

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

public class SequenceShuffler
extends java.lang.Object

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

Version:
$Id: SequenceShuffler.java 185 2006-01-23 23:03:18Z rambaut $
Author:
Richard Moir, Alexei Drummond

Constructor Summary
SequenceShuffler()
           
 
Method Summary
 float getMax()
           
 float getMean()
           
 float getMin()
           
 double getStdev()
           
 void setProgressMonitor(javax.swing.ProgressMonitor monitor)
           
 void shuffle(Align algorithm, java.lang.String sq1, java.lang.String sq2, int numShuffles)
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

SequenceShuffler

public SequenceShuffler()
Method Detail

shuffle

public void shuffle(Align algorithm,
                    java.lang.String sq1,
                    java.lang.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(javax.swing.ProgressMonitor monitor)


http://code.google.com/p/jebl2/