net.maizegenetics.taxa.tree

Class RootedTreeUtils

net.maizegenetics.taxa.tree.RootedTreeUtils

public class RootedTreeUtils

This class contains utility methods. These include:
1. gathering information about subtrees from a set of trees
2. comparing subtrees and clades.
All these methods assume rooted trees!

Method Detail

containsSubtree

public static boolean containsSubtree(Node root,
                                      Node node)

Parameters:

root - the root of the tree in which search for a subtree

node - the subtree to search for.

Returns:

org.jetbrains.dokka.NodeRenderContent@661613fb: true if the first node contains a subtree identical to the second node or is identical to the second node.

containsClade

public static boolean containsClade(Node root,
                                    Node clade)

Parameters:

root - the root of the tree in which search for a subtree

clade - the hashtable of taxa.

Returns:

org.jetbrains.dokka.NodeRenderContent@2433b628: true if the given tree contains a clade holding all the taxa in the given subtree.

getSubtree

public static Node getSubtree(Node root,
                              Node node)

Returns:

org.jetbrains.dokka.NodeRenderContent@53678eef: a subtree within the first node with the same labelled topology as the second node or null if it doesn't exist.

getClade

public static Node getClade(Node root,
                            Node clade)

Returns:

org.jetbrains.dokka.NodeRenderContent@6d4d18c6: a subtree within the first node with the same labels as the second node or null if it doesn't exist.

equal

public static boolean equal(Node node1,
                            Node node2)

Returns:

org.jetbrains.dokka.NodeRenderContent@3b12575f: true if the trees have the same tip-labelled structure. Child order is not important.

sameTaxa

public static boolean sameTaxa(Node node1,
                               Node node2)

Returns:

org.jetbrains.dokka.NodeRenderContent@22934e3: true if the trees have the same tip labels. topology unimportant.

collectTaxa

public static int collectTaxa(Node root,
                              java.util.Map<java.lang.String,java.lang.String> table)

Collects all of the names of the taxa in the tree into a hashtable.

Parameters:

root - the root node of the tree.

table - a hashtable to hold the taxa names, may already hold some taxa names.

Returns:

org.jetbrains.dokka.NodeRenderContent@6dd6d2bf: the number of new taxa added to the hashtable from this tree.

containsNovelTaxa

public static boolean containsNovelTaxa(Node root,
                                        java.util.Map<java.lang.String,java.lang.String> taxa)

Parameters:

root - the root node of the tree.

taxa - a hashtable holding taxa names.

Returns:

org.jetbrains.dokka.NodeRenderContent@68586ceb: true if the given tree contains taxa not already in the given hashtable.

subtreeCount

public static int subtreeCount(Node subtree,
                               java.util.Vector<net.maizegenetics.taxa.tree.Tree> trees)

Parameters:

subtree - the subtree being searched for.

trees - a vector of trees to search for the subtree in.

Returns:

org.jetbrains.dokka.NodeRenderContent@41d97610: the number of times the subtree was found in the given list of trees. If a subtree occurs more than once in a tree (for some bizarre reason) it is counted only once.

getMeanSubtreeHeight

public static double getMeanSubtreeHeight(Node subtree,
                                          java.util.Vector<net.maizegenetics.taxa.tree.Tree> trees)

Parameters:

subtree - the subtree being searched for.

trees - a vector of trees to search for the subtree in.

Returns:

org.jetbrains.dokka.NodeRenderContent@a1ccce4: the mean height of the given subtree in the given list of trees. If a subtree occurs more than once in a tree (for some bizarre reason) results are undefined.

getMeanCladeHeight

public static double getMeanCladeHeight(Node clade,
                                        java.util.Vector<net.maizegenetics.taxa.tree.Tree> trees)

Parameters:

clade - a node containing the clade being searched for.

trees - a vector of trees to search for the clade in.

Returns:

org.jetbrains.dokka.NodeRenderContent@5104b432: the mean height of the given clade in the given list of trees. If a clade occurs more than once in a tree (for some bizarre reason) results are undefined.

cladeCount

public static int cladeCount(Node subtree,
                             java.util.Vector<net.maizegenetics.taxa.tree.Tree> trees)

Parameters:

subtree - a subtree containing the taxaset being searched for.

trees - a vector of trees to search for the clade in.

Returns:

org.jetbrains.dokka.NodeRenderContent@7a10a5cd: the number of times the clade was found in the given list of trees. If a clade occurs more than once in a tree (for some bizarre reason) it is counted only once.

collectProportions

public static void collectProportions(Tree tree,
                                      java.util.Vector<net.maizegenetics.taxa.tree.Tree> trees)