Class 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
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      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)