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
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Method Summary
Modifier and TypeMethodDescriptiondouble
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[]
Returns the reconstructed character states for a given node in the tree.
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Method Details
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getSiteScores
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
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getScore
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
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getStates
Returns the reconstructed character states for a given node in the tree.- Parameters:
tree
- a tree object to reconstruct the characters onnode
- the node of the tree- Returns:
- an array containing the reconstructed states for this node
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