Package jebl.evolution.trees
Class TreeBuilderFactory
java.lang.Object
jebl.evolution.trees.TreeBuilderFactory
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 ClassesModifier and TypeClassDescriptionstatic enum
Supported consensus methods.static enum
Supported pairwise distance methodsstatic enum
Supported methods for tree building -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic 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
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Constructor Details
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TreeBuilderFactory
public TreeBuilderFactory()
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Method Details
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isRootedMethod
- 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) -
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 rootedsupportThreshold
- minimum required consensus support (in [01])method
- which consensus method to use- Returns:
- consensus tree builder
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