Package pal.alignment

Class SitePattern

java.lang.Object
pal.alignment.AbstractAlignment
pal.alignment.SitePattern
All Implemented Interfaces:
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:

  • Field Details

    • 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 Details

    • 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 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

    • 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)