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

      All Methods Instance Methods Abstract Methods 
      Modifier and Type Method Description
      double getScore​(Tree tree)
      Calculates the minimum number of steps for the parsimony reconstruction for the given tree.
      double[] getSiteScores​(Tree tree)
      Calculates the minimum number of steps for the parsimony reconstruction for the given tree.
      State[] getStates​(Tree tree, Node node)
      Returns the reconstructed character states for a given node in the tree.
    • Method Detail

      • 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