Package jebl.evolution.trees
Class TreeBuilderFactory
- java.lang.Object
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- jebl.evolution.trees.TreeBuilderFactory
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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
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
TreeBuilderFactory.ConsensusMethod
Supported consensus methods.static class
TreeBuilderFactory.DistanceModel
Supported pairwise distance methodsstatic class
TreeBuilderFactory.Method
Supported methods for tree building
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Constructor Summary
Constructors Constructor Description TreeBuilderFactory()
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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)
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Method Detail
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isRootedMethod
public static boolean isRootedMethod(TreeBuilderFactory.Method method)
- Parameters:
method
- to check- Returns:
- Wheather method generates a rooted or unrooted tree.
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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
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buildUnRooted
public static ConsensusTreeBuilder buildUnRooted(Tree[] trees, Taxon outGroup, double supportThreshold, TreeBuilderFactory.ConsensusMethod method)
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buildRooted
public static ConsensusTreeBuilder buildRooted(RootedTree[] trees, double supportThreshold, TreeBuilderFactory.ConsensusMethod method)
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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 rootedsupportThreshold
- minimum required consensus support (in [01])method
- which consensus method to use- Returns:
- consensus tree builder
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