Package pal.alignment

Class SitePattern

  • All Implemented Interfaces:
    java.io.Serializable, Alignment, IdGroup, Report

    public class SitePattern
    extends AbstractAlignment
    takes an Alignment and determines its site patterns
    Version:
    $Id: SitePattern.java,v 1.11 2002/10/14 06:54:24 matt Exp $
    Author:
    Korbinian Strimmer, Alexei Drummond
    See Also:
    Serialized Form
    • Field Detail

      • numPatterns

        public int numPatterns
        number of site patterns
      • alias

        public int[] alias
        site -> site pattern
      • weight

        public int[] weight
        weights of each site pattern
      • pattern

        public byte[][] pattern
        site patterns [sequence][site pattern]
    • Constructor Detail

      • SitePattern

        public SitePattern​(Alignment a)
        infer site patterns for a given alignment
        Parameters:
        a - alignment
      • SitePattern

        public SitePattern​(DataType dataType,
                           int numSites,
                           int numSeqs,
                           IdGroup idGroup,
                           int numPatterns,
                           int[] alias,
                           int[] weight,
                           byte[][] pattern)
        construct SitePattern from scratch
        Parameters:
        dataType - data type
        numSites - number of sites
        numSeqs - number of sequences
        idGroup - sequence identifiers
        numPatterns - number of site patterns
        alias - link site -> site pattern
        weight - frequency of a site pattern
        pattern - site patterns
    • Method Detail

      • getPatternData

        public final char getPatternData​(int seq,
                                         int patternSite)
      • getPatternState

        public final int getPatternState​(int seq,
                                         int patternSite)
      • getSiteWeights

        public int[] getSiteWeights()
        Accessor method for weight
      • getNumberOfPatterns

        public int getNumberOfPatterns()
        Accessor method for numPatterns
      • getSitePattern

        public static final SitePattern getSitePattern​(Alignment a)
        Parameters:
        a - An alignment
        Returns:
        alignment as a site pattern if it isn't already one (other wise just returns alighnment)