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

    • SequenceShuffler

      public SequenceShuffler()
  • Method Details

    • 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)