Package pal.tree

Class CladeSystem

java.lang.Object
pal.tree.CladeSystem
public class CladeSystem extends 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 Details

    • CladeSystem

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

  • Method Details

    • 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 String toString()
      print clade system
      Overrides:
      toString in class 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