Package pal.tree

Class SimulatedAlignment

All Implemented Interfaces:
Serializable, Alignment, IdGroup, Report

public class SimulatedAlignment extends AbstractAlignment
generates an artificial data set
Version:
$Id: SimulatedAlignment.java,v 1.19 2003/03/23 00:21:33 matt Exp $
Author:
Korbinian Strimmer, Alexei Drummond
See Also:
  • Constructor Details

    • SimulatedAlignment

      public SimulatedAlignment(int sites, Tree t, SubstitutionModel m)
      Inititalisation
      Parameters:
      sites - number of sites
      t - tree relating the sequences
      m - model of evolution
  • Method Details

    • getData

      public char getData(int seq, int site)
      sequence alignment at (sequence, site)
      Specified by:
      getData in interface Alignment
      Specified by:
      getData in class AbstractAlignment
    • simulate

      public void simulate()
      generate new artificial data set (random root sequence)
    • simulate

      public void simulate(String givenRootSequence)
      generate new artificial data set (random root sequence)
    • simulate

      public void simulate(byte[] rootSeq)
      generate new artificial data set (specified root sequence)