jebl.evolution.parsimony
public class FitchParsimony extends java.lang.Object implements ParsimonyCriterion
Constructor and Description |
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FitchParsimony(java.util.List<Pattern> patterns,
boolean gapsAreStates) |
FitchParsimony(Patterns patterns,
boolean gapsAreStates) |
Modifier and Type | Method and Description |
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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.
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State[] |
getStates(Tree tree,
Node node)
Returns the reconstructed character states for a given node in the tree.
|
public FitchParsimony(java.util.List<Pattern> patterns, boolean gapsAreStates)
public FitchParsimony(Patterns patterns, boolean gapsAreStates)
public double[] getSiteScores(Tree tree)
getSiteScores
in interface ParsimonyCriterion
tree
- a tree object to reconstruct the characters onpublic double getScore(Tree tree)
ParsimonyCriterion
getScore
in interface ParsimonyCriterion
tree
- a tree object to reconstruct the characters onpublic State[] getStates(Tree tree, Node node)
getStates
in interface ParsimonyCriterion
tree
- a tree object to reconstruct the characters onnode
- the node of the treehttp://code.google.com/p/jebl2/