jebl.evolution.trees
Class TreeBuilderFactory

java.lang.Object
  jebl.evolution.trees.TreeBuilderFactory

public class TreeBuilderFactory
extends Object

A meeting point for tree building from sequence data. A very initial form which will develope to encompass more methods and distances. Currently only pairwise distance methods are implemented.

Author:

Joseph Heled

Nested Class Summary

static class	TreeBuilderFactory.ConsensusMethod Supported consensus methods.
static class	TreeBuilderFactory.DistanceModel Supported pairwise distance methods
static class	TreeBuilderFactory.Method Supported methods for tree building

Constructor Summary

TreeBuilderFactory()

Method Summary

static ConsensusTreeBuilder	buildRooted(RootedTree[] trees, double supportThreshold, TreeBuilderFactory.ConsensusMethod method)
static ConsensusTreeBuilder	buildRooted(Tree[] trees, double supportThreshold, TreeBuilderFactory.ConsensusMethod method) convenience method.
static ConsensusTreeBuilder	buildUnRooted(Tree[] trees, Taxon outGroup, double supportThreshold, TreeBuilderFactory.ConsensusMethod method)
static ClusteringTreeBuilder	getBuilder(TreeBuilderFactory.Method method, DistanceMatrix distances)
static boolean	isRootedMethod(TreeBuilderFactory.Method method)

Methods inherited from class java.lang.Object

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

Constructor Detail

TreeBuilderFactory

public TreeBuilderFactory()

Method Detail

isRootedMethod

public static boolean isRootedMethod(TreeBuilderFactory.Method method)

Parameters:

method -

Returns:

Wheather method generates a rooted or unrooted tree.

getBuilder

public static ClusteringTreeBuilder getBuilder(TreeBuilderFactory.Method method,
                                               DistanceMatrix distances)

Parameters:

method - build method to use.

distances - Pre computed pairwise distances.

Returns:

A tree builder using method and distance matrix

buildUnRooted

public static ConsensusTreeBuilder buildUnRooted(Tree[] trees,
                                                 Taxon outGroup,
                                                 double supportThreshold,
                                                 TreeBuilderFactory.ConsensusMethod method)

buildRooted

public static ConsensusTreeBuilder buildRooted(RootedTree[] trees,
                                               double supportThreshold,
                                               TreeBuilderFactory.ConsensusMethod method)

buildRooted

public static ConsensusTreeBuilder buildRooted(Tree[] trees,
                                               double supportThreshold,
                                               TreeBuilderFactory.ConsensusMethod method)

convenience method. Convert arrays of trees, guaranteed to be rooted to the array of the appropriate type.

Parameters:

trees - trees - all must be rooted

supportThreshold - minimum required consensus support

method - which consensus method to use

Returns:

consensus tree builder