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

```
public class TreeBuilderFactory
extends java.lang.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.

Version:

$Id: TreeBuilderFactory.java 853 2007-12-07 07:32:42Z twobeers $

Author:

Joseph Heled

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description
`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

Constructors
Constructor Description

TreeBuilderFactory()

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method	Description
`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
equals, 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 - to check

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 (in [01])

method - which consensus method to use

Returns:

consensus tree builder

Class TreeBuilderFactory

Nested Class Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

TreeBuilderFactory

Method Detail

isRootedMethod

getBuilder

buildUnRooted

buildRooted

buildRooted