net.maizegenetics.taxa.tree

Class TreeUtils

net.maizegenetics.taxa.tree.TreeUtils

public class TreeUtils

various utility functions on trees.

Method Detail

getRobinsonFouldsDistance

public static double getRobinsonFouldsDistance(Tree t1,
                                               Tree t2)

computes Robinson-Foulds (1981) distance between two trees

Parameters:

t1 - tree 1

t2 - tree 2 Definition: Assuming that t1 is the reference tree, let fn be the false negatives, i.e. the number of edges in t1 missing in t2, and fp the number of false positives, i.e. the number of edges in t2 missing in t1. The RF distance is then (fn + fp)/2

getRobinsonFouldsDistance

public static double getRobinsonFouldsDistance(SplitSystem s1,
                                               Tree t2)

computes Robinson-Foulds (1981) distance between two trees

Parameters:

s1 - tree 1 (as represented by a SplitSystem)

t2 - tree 2

getRobinsonFouldsRescaledDistance

public static double getRobinsonFouldsRescaledDistance(Tree t1,
                                                       Tree t2)

computes Robinson-Foulds (1981) distance between two trees rescaled to a number between 0 and 1

Parameters:

t1 - tree 1

t2 - tree 2

getRobinsonFouldsRescaledDistance

public static double getRobinsonFouldsRescaledDistance(SplitSystem s1,
                                                       Tree t2)

computes Robinson-Foulds (1981) distance between two trees rescaled to a number between 0 and 1

Parameters:

s1 - tree 1 (as represented by a SplitSystem)

t2 - tree 2

getRandomNode

public static Node getRandomNode(Tree tree)

Returns a uniformly distributed random node from the tree, including both internal and external nodes.

getNodeByName

public static Node getNodeByName(Tree tree,
                                 java.lang.String name)

Parameters:

tree - The Tree supposidly containing such a named node

name - The name of the node to find.

Returns:

org.jetbrains.dokka.NodeRenderContent@24c1502c: The node with the name, or null if no such node exists

getNodeByName

public static Node getNodeByName(Node root,
                                 java.lang.String name)

Parameters:

root - The root node of a tree

name - The name of the node to find.

Returns:

org.jetbrains.dokka.NodeRenderContent@64e266b8: The node with the name, or null if no such node exists

rotateByLeafCount

public static void rotateByLeafCount(Tree tree)

Rotates branches by leaf count. WARNING: assumes binary tree!

getLeafIdGroup

public static TaxaList getLeafIdGroup(Tree tree)

get list of the identifiers of the external nodes

Returns:

org.jetbrains.dokka.NodeRenderContent@185d9cc0: leaf identifier group

printNH

public static void printNH(Tree tree,
                           java.io.PrintWriter out)

print a this tree in New Hampshire format (including distances and internal labels)

Parameters:

out - output stream

printNH

public static void printNH(Tree tree,
                           java.io.PrintWriter out,
                           boolean printLengths,
                           boolean printInternalLabels)

print this tree in New Hampshire format

Parameters:

out - output stream

printLengths - boolean variable determining whether branch lengths should be included in output

printInternalLabels - boolean variable determining whether internal labels should be included in output

reroot

public static void reroot(Tree tree,
                          Node node)

a tree that has been re-rooted at the given internal node. The original root of the tree must have had at least 3 children.

findMidpointNode

public static Node findMidpointNode(Tree tree)

Return node with the highest average minimum and maximum distance. Ed thinks this is roughly the midpoint - need to look this up

Parameters:

tree -

Returns:

org.jetbrains.dokka.NodeRenderContent@570ee7b6:

computeAllDistances

public static void computeAllDistances(Tree tree,
                                       int a,
                                       kotlin.Array[] dist,
                                       kotlin.Array[] idist,
                                       boolean countEdges,
                                       double epsilon)

computeDistance

public static double computeDistance(Tree tree,
                                     int a,
                                     int b)

compute distance between two external nodes

Parameters:

tree - tree

a - external node 1

b - external node 2

Returns:

org.jetbrains.dokka.NodeRenderContent@79609d4b: distance between node a and b

report

public static void report(Tree tree,
                          java.io.Writer out)