Package jebl.evolution.align

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)