jebl.evolution.trees
Class NeighborJoiningTreeBuilder

java.lang.Object
  jebl.evolution.trees.ClusteringTreeBuilder<Tree>
      jebl.evolution.trees.NeighborJoiningTreeBuilder

All Implemented Interfaces:

TreeBuilder<Tree>

public class NeighborJoiningTreeBuilder
extends ClusteringTreeBuilder<Tree>

Constructs an unrooted tree by neighbor-joining using pairwise distances. Adapted from BEAST code.

Author:

Andrew Rambaut, Alexei Drummond, Joseph Heled

Field Summary

Fields inherited from class jebl.evolution.trees.ClusteringTreeBuilder

alias, besti, bestj, clusters, distance, distanceMatrix, minimumTaxa, newCluster, numClusters, tipCount

Constructor Summary

NeighborJoiningTreeBuilder(DistanceMatrix distanceMatrix)
construct NJ tree

Method Summary

protected Node	createExternalNode(Taxon taxon)
protected Node	createInternalNode(Node[] nodes, double[] distances) Creates a new internal node that will have the specified nodes as its children
protected void	findNextPair() Find next two clusters to join.
protected void	finish()
protected Tree	getTree()
protected double[]	joinClusters() Inform derived class that clusters besti,bestj are being joinded into a new cluster.
protected double	updatedDistance(int k) compute updated distance between the new cluster (besti,bestj) to any other cluster k.

Methods inherited from class jebl.evolution.trees.ClusteringTreeBuilder

addProgressListener, build, fireSetProgress, getBuilder, getDist, init, newCluster, removeProgressListener

Methods inherited from class java.lang.Object

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

Constructor Detail

NeighborJoiningTreeBuilder

public NeighborJoiningTreeBuilder(DistanceMatrix distanceMatrix)

construct NJ tree

Parameters:

distanceMatrix - distance matrix

Method Detail

findNextPair

protected void findNextPair()

Description copied from class: ClusteringTreeBuilder

Find next two clusters to join. set shared best{i,j}.

Overrides:

findNextPair in class ClusteringTreeBuilder<Tree>

getTree

protected Tree getTree()

Specified by:

getTree in class ClusteringTreeBuilder<Tree>

createExternalNode

protected Node createExternalNode(Taxon taxon)

Specified by:

createExternalNode in class ClusteringTreeBuilder<Tree>

createInternalNode

protected Node createInternalNode(Node[] nodes,
                                  double[] distances)

Creates a new internal node that will have the specified nodes as its children

Specified by:

createInternalNode in class ClusteringTreeBuilder<Tree>

Parameters:

nodes - Nodes whose parent is about to be created

distances - Distances of those nodes to the parent. distances.length == nodes.length must hold.

Returns:

the new node

finish

protected void finish()

Overrides:

finish in class ClusteringTreeBuilder<Tree>

joinClusters

protected double[] joinClusters()

Description copied from class: ClusteringTreeBuilder

Inform derived class that clusters besti,bestj are being joinded into a new cluster. New cluster will be (the smaller) besti while clusters greater than bestj are shifted one space back.

Specified by:

joinClusters in class ClusteringTreeBuilder<Tree>

Returns:

branch distances to new internal node [besti - dist , bestj dist]

updatedDistance

protected double updatedDistance(int k)

Description copied from class: ClusteringTreeBuilder

compute updated distance between the new cluster (besti,bestj) to any other cluster k. (i,j,k) are cluster indices in [0..numClusters-1]

Specified by:

updatedDistance in class ClusteringTreeBuilder<Tree>