Package pal.tree

Class SimulatedAlignment

  • All Implemented Interfaces:
    java.io.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:
    Serialized Form
    • Constructor Detail

      • 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 Detail

      • simulate

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

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

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