Interface ParsimonyCriterion

All Known Implementing Classes:
FitchParsimony

public interface ParsimonyCriterion
Version:
$Id: ParsimonyCriterion.java 185 2006-01-23 23:03:18Z rambaut $
Author:
rambaut, Alexei Drummond Date: Jun 20, 2005 Time: 4:56:34 PM
  • Method Summary

    Modifier and Type
    Method
    Description
    double
    getScore(Tree tree)
    Calculates the minimum number of steps for the parsimony reconstruction for the given tree.
    double[]
    Calculates the minimum number of steps for the parsimony reconstruction for the given tree.
    getStates(Tree tree, Node node)
    Returns the reconstructed character states for a given node in the tree.
  • Method Details

    • getSiteScores

      double[] getSiteScores(Tree tree)
      Calculates the minimum number of steps for the parsimony reconstruction for the given tree. It is expected that the implementation's constructor will be set up with the characters so that repeated calls can be made to this function to evaluate different trees.
      Parameters:
      tree - a tree object to reconstruct the characters on
      Returns:
      an array containing the parsimony score for each site
    • getScore

      double getScore(Tree tree)
      Calculates the minimum number of steps for the parsimony reconstruction for the given tree. It is expected that the implementation's constructor will be set up with the characters so that repeated calls can be made to this function to evaluate different trees.
      Parameters:
      tree - a tree object to reconstruct the characters on
      Returns:
      the total score
    • getStates

      State[] getStates(Tree tree, Node node)
      Returns the reconstructed character states for a given node in the tree.
      Parameters:
      tree - a tree object to reconstruct the characters on
      node - the node of the tree
      Returns:
      an array containing the reconstructed states for this node