phylosort
Class TreeNodeUtil

java.lang.Object
  phylosort.TreeNodeUtil

public final class TreeNodeUtil
extends java.lang.Object

Utility methods for general TreeNode processing.

Version:

$Revision: 1.11 $

Author:

Ahmed Moustafa

Constructor Summary

TreeNodeUtil()

Method Summary

static boolean	belongs(TreeNode node, java.util.Set<java.lang.String> taxa) Checks whether the set of all OTUs is a subset of taxa
static boolean	contains(TreeNode node, java.util.Set<java.lang.String> taxa) Checks whether each group of taxa is represented at least by one OTU
static TreeNode	copy(TreeNode root, TreeNode exclude) Returns a copy of a TreeNode
static TreeNode	findOutgroup(TreeNode node, java.util.List<java.util.Set<java.lang.String>> taxa) Finds a leaf node with a taxon not included within a list of taxa
static TreeNode	findOutgroup(TreeNode node, java.util.Set<java.lang.String> taxa) Finds a leaf node with a taxon not included within a list of taxa
static java.util.Collection<TreeNode>	getAllMonophyleticNodes(TreeNode tree, java.util.List<java.util.List<java.lang.String>> taxa) Checks whether a tree has a common branch holding groups of taxa
static java.util.Collection<TreeNode>	getAllMonophyleticNodes(TreeNode tree, java.util.List<java.util.List<java.lang.String>> taxa, boolean exclusive) Checks whether a tree has a common branch holding groups of taxa
static float	getAverageNumberOfCopies(TreeNode root) Returns the average number of copies per species
static TreeNode	getMonophyleticNode(TreeNode tree, java.util.List<java.util.List<java.lang.String>> taxa) Checks whether a tree has a common branch holding groups of taxa
static TreeNode	getMonophyleticNode(TreeNode tree, java.util.List<java.util.List<java.lang.String>> taxa, boolean exclusive) Checks whether a tree has a common branch holding groups of taxa
static java.util.Collection<TreeNode>	getNodesByTaxa(TreeNode tree, java.util.Set<java.lang.String> taxa) Returns all OTU nodes with labels matching the set of taxa
static java.util.Collection<TreeNode>	getNodesByTaxa(TreeNode node, java.util.Set<java.lang.String> taxa, boolean equal) Returns all OTU nodes with labels matching the set of taxa
static java.util.Set<java.lang.String>	getTaxa(java.io.File file) Returns a Set of String of all taxa in a file
static java.util.Set<java.lang.String>	getTaxa(TreeNode node) Returns a Set of String of taxa in a TreeNode
static int	hasMonophyly(TreeNode node, java.util.Set<java.lang.String> extended, java.util.List<java.util.Set<java.lang.String>> sets, java.util.Set<java.lang.Integer> excluded) Returns node id if the node is valid, otherwise returns -1
static int	lca(java.lang.Iterable<TreeNode> nodes) Returns the lowest common ancestor (LCA) for a list of nodes
static TreeNode	load(java.io.File file) Loads a tree from a text file
static TreeNode	reroot(TreeNode outgroup) Reroots a tree based on an outgroup node.

Methods inherited from class java.lang.Object

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

Constructor Detail

TreeNodeUtil

public TreeNodeUtil()

Method Detail

belongs

public static boolean belongs(TreeNode node,
                              java.util.Set<java.lang.String> taxa)

Checks whether the set of all OTUs is a subset of taxa

Parameters:

node - Tree to check it OTUs

taxa - Set of taxa to check aganist

Returns:

True if the set of all OTUs is a subset of taxa, otherwise false

contains

public static boolean contains(TreeNode node,
                               java.util.Set<java.lang.String> taxa)

Checks whether each group of taxa is represented at least by one OTU

Parameters:

node - Tree to check it OTUs

taxa - Sets of taxa to check

Returns:

True if each group of taxa is represented in the tree, otherwise false

getMonophyleticNode

public static TreeNode getMonophyleticNode(TreeNode tree,
                                           java.util.List<java.util.List<java.lang.String>> taxa)

Checks whether a tree has a common branch holding groups of taxa

Parameters:

tree - Tree to search in for a common branch

taxa - Groups of taxa (labels) to search for a common branch

Returns:

Node id of the internal node rooting the taxa

getMonophyleticNode

public static TreeNode getMonophyleticNode(TreeNode tree,
                                           java.util.List<java.util.List<java.lang.String>> taxa,
                                           boolean exclusive)

Checks whether a tree has a common branch holding groups of taxa

Parameters:

tree - Tree to search in for a common branch

taxa - Groups of taxa (labels) to search for a common branch

exclusive - Validation type indicator

Returns:

Node id of the internal node rooting the taxa

getAllMonophyleticNodes

public static java.util.Collection<TreeNode> getAllMonophyleticNodes(TreeNode tree,
                                                                     java.util.List<java.util.List<java.lang.String>> taxa)

Checks whether a tree has a common branch holding groups of taxa

Parameters:

tree - Tree to search in for a common branch

taxa - Groups of taxa (labels) to search for a common branch

Returns:

Node id of the internal node rooting the taxa

getAllMonophyleticNodes

public static java.util.Collection<TreeNode> getAllMonophyleticNodes(TreeNode tree,
                                                                     java.util.List<java.util.List<java.lang.String>> taxa,
                                                                     boolean exclusive)

Checks whether a tree has a common branch holding groups of taxa

Parameters:

tree - Tree to search in for a common branch

taxa - Groups of taxa (labels) to search for a common branch

exclusive - Validation type indicator

Returns:

Node id of the internal node rooting the taxa

hasMonophyly

public static int hasMonophyly(TreeNode node,
                               java.util.Set<java.lang.String> extended,
                               java.util.List<java.util.Set<java.lang.String>> sets,
                               java.util.Set<java.lang.Integer> excluded)

Returns node id if the node is valid, otherwise returns -1

Parameters:

node - Node to validate

extended - Extended list of taxa

sets - Taxa in groups

excluded - List of ids of exlcuded nodes (already visited)

Returns:

If valid node, returns node id; otherwise, returns -1

getTaxa

public static java.util.Set<java.lang.String> getTaxa(TreeNode node)

Returns a Set of String of taxa in a TreeNode

Parameters:

node - TreeNode

Returns:

A Set of String of taxa in a TreeNode

getTaxa

public static java.util.Set<java.lang.String> getTaxa(java.io.File file)
                                               throws java.lang.Exception

Returns a Set of String of all taxa in a file

Parameters:

file - Input file

Returns:

A Set of String of all taxa in a file

Throws:

java.lang.Exception

getNodesByTaxa

public static java.util.Collection<TreeNode> getNodesByTaxa(TreeNode tree,
                                                            java.util.Set<java.lang.String> taxa)

Returns all OTU nodes with labels matching the set of taxa

Parameters:

tree - Tree to search in

taxa - Taxa to search for

Returns:

Collection of the OTU TreeNode

getNodesByTaxa

public static java.util.Collection<TreeNode> getNodesByTaxa(TreeNode node,
                                                            java.util.Set<java.lang.String> taxa,
                                                            boolean equal)

Returns all OTU nodes with labels matching the set of taxa

Parameters:

node - Tree to search in

taxa - Taxa to search for

equal - Flag to search of equality or non-equality

Returns:

Collection of the OTU TreeNode

load

public static TreeNode load(java.io.File file)
                     throws java.lang.Exception

Loads a tree from a text file

Parameters:

file - Tree text file

Returns:

TreeNode root of the tree (midpoint?)

Throws:

java.lang.Exception

lca

public static int lca(java.lang.Iterable<TreeNode> nodes)

Returns the lowest common ancestor (LCA) for a list of nodes

Parameters:

nodes - The list of tree nodes

Returns:

The id (int) of the LCA

See Also:

TreeNode

reroot

public static TreeNode reroot(TreeNode outgroup)

Reroots a tree based on an outgroup node.

Parameters:

outgroup - TreeNode outgroup node

Returns:

Rerooted TreeNode

copy

public static TreeNode copy(TreeNode root,
                            TreeNode exclude)

Returns a copy of a TreeNode

Parameters:

root - TreeNode to start coping from

exclude - TreeNode to exclude while coping

Returns:

TreeNode copy of the root node

findOutgroup

public static TreeNode findOutgroup(TreeNode node,
                                    java.util.List<java.util.Set<java.lang.String>> taxa)

Finds a leaf node with a taxon not included within a list of taxa

Parameters:

node - TreeNode root of a tree to search for an outgroup

taxa - List of taxa (ingroup)

Returns:

TreeNode outgroup leaf node or null if no outgroup is found

findOutgroup

public static TreeNode findOutgroup(TreeNode node,
                                    java.util.Set<java.lang.String> taxa)

Finds a leaf node with a taxon not included within a list of taxa

Parameters:

node - TreeNode root of a tree to search for an outgroup

taxa - List of taxa (ingroup)

Returns:

TreeNode outgroup leaf node or null if no outgroup is found

getAverageNumberOfCopies

public static float getAverageNumberOfCopies(TreeNode root)

Returns the average number of copies per species

Parameters:

root - TreeNode root of a tree

Returns:

The average number of copies per species (decimal number)