Package jebl.evolution.alignments

Class ResampledAlignment

  • All Implemented Interfaces:
    Alignment, Patterns, Sequences
    Direct Known Subclasses:
    BootstrappedAlignment, JackknifedAlignment
    public class ResampledAlignment
extends java.lang.Object
implements Alignment
    Date: 17/01/2006 Time: 08:08:44
    Version:
    $Id: ResampledAlignment.java 482 2006-10-25 06:30:57Z twobeers $ Provide a re-sampled alignment. This means an alignment constructed by choosing a set of sites from the source alignment and concataneting them. The set may be of any length and may contain duplications (sampling with replacment). Due to Java restrictions on constructors, class is implemented using delegation.
    Author:
    Joseph Heled

    • Constructor Detail

      • ResampledAlignment

        public ResampledAlignment()

    • Method Detail

      • init

        public void init​(Alignment srcAlignment,
                 int[] siteIndices)
        Setup resampled alignment.
        Parameters:
        srcAlignment - sample sites from this alignment
        siteIndices - Use this set to construct the resampled alignment

      • getPatterns

        public java.util.List<Pattern> getPatterns()
        Description copied from interface: Patterns
        Get a list of all the patterns
        Specified by:
        getPatterns in interface Patterns
        Returns:
        the list

      • getTaxa

        public java.util.List<Taxon> getTaxa()
        Specified by:
        getTaxa in interface Patterns
        Returns:
        the list of taxa that the state values correspond to.