Package jebl.evolution.trees
Class RootedTreeUtils
java.lang.Object
jebl.evolution.trees.RootedTreeUtils
Static utility functions for rooted trees.
- Version:
- $Id: RootedTreeUtils.java 889 2008-02-27 01:13:21Z matt_kearse $
- Author:
- Andrew Rambaut, Alexei Drummond
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Method Summary
Modifier and TypeMethodDescriptionstatic boolean
equal
(RootedTree tree1, RootedTree tree2) Compares 2 trees and returns true if they have the same topology.static double
getAverageTipDistance
(RootedTree tree, Node node) returns the average distance from the given node to all the tips below itstatic Node
getCommonAncestorNode
(RootedTree tree, Set<Node> tipNodes) Gets the most recent common ancestor (MRCA) node of a set of tip nodes.getDescendantTips
(RootedTree tree, Node node) Gets a set of tip nodes descended from the given node.static double
getMaxTipHeight
(RootedTree tree, Node node) static double
getMinTipHeight
(RootedTree tree, Node node) static final int
getTipCount
(RootedTree tree, Node node) Return the number of leaves under this node.getTipsForTaxa
(RootedTree tree, Collection<Taxon> taxa) Gets a set of external nodes that correspond to the given taxa.static boolean
isBinary
(RootedTree tree) static boolean
isMonophyletic
(RootedTree tree, Set<Node> tipNodes) Performs the a monophyly test on a set of tip nodes.static boolean
isUltrametric
(RootedTree tree, double tolerance) static String
uniqueNewick
(RootedTree tree, Node node) Recursive function for constructing a newick tree representation in the given buffer.
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Method Details
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getTipCount
Return the number of leaves under this node.- Parameters:
tree
-node
-- Returns:
- the number of leaves under this node.
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getMinTipHeight
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getMaxTipHeight
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getAverageTipDistance
returns the average distance from the given node to all the tips below it- Parameters:
tree
-node
-- Returns:
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isUltrametric
- Returns:
- true only if all tips have height 0.0
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isBinary
- Returns:
- true only if internal nodes have 2 children
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getTipsForTaxa
public static Set<Node> getTipsForTaxa(RootedTree tree, Collection<Taxon> taxa) throws MissingTaxonException Gets a set of external nodes that correspond to the given taxa.- Throws:
MissingTaxonException
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getDescendantTips
Gets a set of tip nodes descended from the given node. -
getCommonAncestorNode
Gets the most recent common ancestor (MRCA) node of a set of tip nodes.- Parameters:
tree
- the TreetipNodes
- a set of tip nodes- Returns:
- the Node of the MRCA
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isMonophyletic
Performs the a monophyly test on a set of tip nodes. The nodes are monophyletic if there is a node in the tree which subtends all the tips in the set (and only those tips).- Parameters:
tree
- a tree object to perform test ontipNodes
- a set containing the tip node.- Returns:
- boolean is monophyletic?
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uniqueNewick
Recursive function for constructing a newick tree representation in the given buffer. -
equal
Compares 2 trees and returns true if they have the same topology.
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