jebl.evolution.parsimony
Class FitchParsimony

java.lang.Object
  jebl.evolution.parsimony.FitchParsimony

All Implemented Interfaces:

ParsimonyCriterion

public class FitchParsimony
extends Object
implements ParsimonyCriterion

Class for reconstructing characters using Fitch parsimony. This is intended to be much faster than the static methods in the utility "Parsimony" class.

Author:

Andrew Rambaut, Alexei Drummond

Constructor Summary

FitchParsimony(List<Pattern> patterns, boolean gapsAreStates)

FitchParsimony(Patterns patterns, boolean gapsAreStates)

Method Summary

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 siteScores for the parsimony reconstruction of a a set of character patterns on a tree.
State[]	getStates(Tree tree, Node node) Returns the reconstructed character states for a given node in the tree.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

FitchParsimony

public FitchParsimony(List<Pattern> patterns,
                      boolean gapsAreStates)

FitchParsimony

public FitchParsimony(Patterns patterns,
                      boolean gapsAreStates)

Method Detail

getSiteScores

public double[] getSiteScores(Tree tree)

Calculates the minimum number of siteScores for the parsimony reconstruction of a a set of character patterns on a tree. This only does the first pass of the Fitch algorithm so it does not store ancestral state reconstructions.

Specified by:

getSiteScores in interface ParsimonyCriterion

Parameters:

tree - a tree object to reconstruct the characters on

Returns:

number of parsimony siteScores

getScore

public double getScore(Tree tree)

Description copied from interface: ParsimonyCriterion

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.

Specified by:

getScore in interface ParsimonyCriterion

Parameters:

tree - a tree object to reconstruct the characters on

Returns:

the total score

getStates

public State[] getStates(Tree tree,
                         Node node)

Returns the reconstructed character states for a given node in the tree. If this method is repeatedly called with the same tree and patterns then only the first call will reconstruct the states and each subsequent call will return the stored states.

Specified by:

getStates in interface ParsimonyCriterion

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