org.biojava.nbio.phylo

Class CheckTreeAccuracy

java.lang.Object

org.biojava.nbio.phylo.CheckTreeAccuracy

public class CheckTreeAccuracy
extends Object

Author:

Scooter

Constructor Summary

Constructors

Constructor and Description
CheckTreeAccuracy()

Method Summary

Methods

Modifier and Type	Method and Description
static org.forester.evoinference.matrix.distance.DistanceMatrix	copyMatrix(org.forester.evoinference.matrix.distance.DistanceMatrix matrix)
org.forester.phylogeny.PhylogenyNode	findCommonParent(org.forester.phylogeny.PhylogenyNode node, Set<org.forester.phylogeny.PhylogenyNode> path)
double	getNodeDistance(org.forester.phylogeny.PhylogenyNode parentNode, org.forester.phylogeny.PhylogenyNode childNode)
void	markPathToRoot(org.forester.phylogeny.PhylogenyNode node, Set<org.forester.phylogeny.PhylogenyNode> path)
void	process(org.forester.phylogeny.Phylogeny tree, org.forester.evoinference.matrix.distance.DistanceMatrix matrix)

Methods inherited from class java.lang.Object

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

Constructor Detail

CheckTreeAccuracy

public CheckTreeAccuracy()

Method Detail

copyMatrix

public static org.forester.evoinference.matrix.distance.DistanceMatrix copyMatrix(org.forester.evoinference.matrix.distance.DistanceMatrix matrix)

process

public void process(org.forester.phylogeny.Phylogeny tree,
           org.forester.evoinference.matrix.distance.DistanceMatrix matrix)

getNodeDistance

public double getNodeDistance(org.forester.phylogeny.PhylogenyNode parentNode,
                     org.forester.phylogeny.PhylogenyNode childNode)

findCommonParent

public org.forester.phylogeny.PhylogenyNode findCommonParent(org.forester.phylogeny.PhylogenyNode node,
                                                    Set<org.forester.phylogeny.PhylogenyNode> path)

markPathToRoot

public void markPathToRoot(org.forester.phylogeny.PhylogenyNode node,
                  Set<org.forester.phylogeny.PhylogenyNode> path)