Package pal.tree

Class CladeSystem


  • public class CladeSystem
    extends java.lang.Object
    data structure for a set of splits
    Version:
    $Id: CladeSystem.java,v 1.1 2002/06/03 09:17:52 alexi Exp $
    Author:
    Alexei Drummond
    • Constructor Detail

      • CladeSystem

        public CladeSystem​(IdGroup idGroup,
                           int size)
        Parameters:
        idGroup - sequence labels
        size - number of clades
    • Method Detail

      • getCladeCount

        public int getCladeCount()
        get number of clades
      • getLabelCount

        public int getLabelCount()
        get number of labels
      • getCladeArray

        public boolean[][] getCladeArray()
        get clade array
      • getClade

        public boolean[] getClade​(int i)
        get clade
      • getIdGroup

        public IdGroup getIdGroup()
        get idGroup
      • hasClade

        public boolean hasClade​(boolean[] clade)
        + test whether a clade is contained in this clade system (assuming the same leaf order)
        Parameters:
        clade - clade
      • toString

        public java.lang.String toString()
        print clade system
        Overrides:
        toString in class java.lang.Object
      • getCladeSystems

        public static CladeSystem[] getCladeSystems​(Tree[] trees)
        Returns:
        all clade systems for a group of trees.
      • calculateCladeProbabilities

        public static void calculateCladeProbabilities​(Tree tree,
                                                       CladeSystem[] cladeSystems)
      • getClades

        public static CladeSystem getClades​(IdGroup idGroup,
                                            Tree tree)
        creates a clade system from a tree (using a pre-specified order of sequences)
        Parameters:
        idGroup - sequence order for the matrix
        tree -
      • getClades

        public static CladeSystem getClades​(Tree tree)
        creates a clade system from a tree (using tree-induced order of sequences)
        Parameters:
        tree -
      • getClade

        public static void getClade​(IdGroup idGroup,
                                    Node internalNode,
                                    boolean[] clade)
        get clade for internal node
        Parameters:
        idGroup - order of labels
        internalNode - Node
        boolean - [] clade
      • isSame

        public static boolean isSame​(boolean[] s1,
                                     boolean[] s2)
        checks whether two clades are identical (assuming they are of the same length and use the same leaf order)
        Parameters:
        s1 - clade 1
        s2 - clade 2