public class RootedTreeUtils
extends java.lang.Object
Constructor | Description |
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RootedTreeUtils() |
Modifier and Type | Method | Description |
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static int |
cladeCount(Node subtree,
java.util.Vector trees) |
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static void |
collectProportions(Tree tree,
java.util.Vector trees) |
|
static int |
collectTaxa(Node root,
java.util.Hashtable table) |
Collects all of the names of the taxa in the tree into a hashtable.
|
static boolean |
containsClade(Node root,
Node clade) |
|
static boolean |
containsNovelTaxa(Node root,
java.util.Hashtable taxa) |
|
static boolean |
containsSubtree(Node root,
Node node) |
|
static boolean |
equal(Node node1,
Node node2) |
|
static Node |
getClade(Node root,
Node clade) |
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static double |
getMeanCladeHeight(Node clade,
java.util.Vector trees) |
|
static double |
getMeanSubtreeHeight(Node subtree,
java.util.Vector trees) |
|
static Node |
getSubtree(Node root,
Node node) |
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static boolean |
sameTaxa(Node node1,
Node node2) |
|
static int |
subtreeCount(Node subtree,
java.util.Vector trees) |
public static boolean containsSubtree(Node root, Node node)
root
- the root of the tree in which search for a subtreenode
- the subtree to search for.public static boolean containsClade(Node root, Node clade)
root
- the root of the tree in which search for a subtreetaxa
- the hashtable of taxa.public static Node getSubtree(Node root, Node node)
public static Node getClade(Node root, Node clade)
public static boolean equal(Node node1, Node node2)
public static boolean sameTaxa(Node node1, Node node2)
public static int collectTaxa(Node root, java.util.Hashtable table)
root
- the root node of the tree.taxa
- a hashtable to hold the taxa names, may already hold some taxa names.public static boolean containsNovelTaxa(Node root, java.util.Hashtable taxa)
root
- the root node of the tree.taxa
- a hashtable holding taxa names.public static int subtreeCount(Node subtree, java.util.Vector trees)
subtree
- the subtree being searched for.trees
- a vector of trees to search for the subtree in.public static double getMeanSubtreeHeight(Node subtree, java.util.Vector trees)
subtree
- the subtree being searched for.trees
- a vector of trees to search for the subtree in.public static double getMeanCladeHeight(Node clade, java.util.Vector trees)
clade
- a node containing the clade being searched for.trees
- a vector of trees to search for the clade in.public static int cladeCount(Node subtree, java.util.Vector trees)
subtree
- a subtree containing the taxaset being searched for.trees
- a vector of trees to search for the clade in.public static void collectProportions(Tree tree, java.util.Vector trees)