Class SplitUtils


  • public class SplitUtils
    extends java.lang.Object
    utilities for split systems
    Version:
    $Id: SplitUtils.java 849 2007-12-06 00:10:14Z twobeers $
    Author:
    Korbinian Strimmer
    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static void getSplit​(java.util.List<Taxon> taxa, Tree tree, Edge edge, boolean[] split)
      get split for branch associated with internal node
      static SplitSystem getSplits​(java.util.List<Taxon> taxa, Tree tree)
      creates a split system from a tree (using a pre-specified order of sequences)
      static SplitSystem getSplits​(Tree tree)
      creates a split system from a tree (using tree-induced order of sequences)
      static boolean isSame​(boolean[] s1, boolean[] s2)
      Checks two splits for identity.
      • Methods inherited from class java.lang.Object

        equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Method Detail

      • getSplits

        public static SplitSystem getSplits​(Tree tree)
        creates a split system from a tree (using tree-induced order of sequences)
        Parameters:
        tree -
      • getSplits

        public static SplitSystem getSplits​(java.util.List<Taxon> taxa,
                                            Tree tree)
        creates a split system from a tree (using a pre-specified order of sequences)
        Parameters:
        taxa - the list of taxa (order is important)
        tree -
      • getSplit

        public static void getSplit​(java.util.List<Taxon> taxa,
                                    Tree tree,
                                    Edge edge,
                                    boolean[] split)
        get split for branch associated with internal node
        Parameters:
        taxa - order of labels
        tree - Tree
        edge - Edge
        split -
      • isSame

        public static boolean isSame​(boolean[] s1,
                                     boolean[] s2)
        Checks two splits for identity. This method assumes that the two splits are of the same length and use the same leaf order/
        Parameters:
        s1 - split 1
        s2 - split 2
        Returns:
        true if the two splits are identical
        Throws:
        java.lang.IllegalArgumentException - if splits don't have the same length