Package jebl.evolution.parsimony
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
-
-