net.maizegenetics.taxa.tree

Class NewickUtils

net.maizegenetics.taxa.tree.NewickUtils

public class NewickUtils

Method Detail

read

@NotNull
public static Tree read(@NotNull
                                 java.lang.String filename)

Creates a Tree from the given newick formatted file

write

public static void write(@NotNull
                         java.lang.String filename,
                         @NotNull
                         Tree tree,
                         boolean includeBranchLengths)

Writes give tree to Newick formatted file. http://evolution.genetics.washington.edu/phylip/newicktree.html

mergeTrees

@NotNull
public static Tree mergeTrees(@NotNull
                                       java.util.List<? extends net.maizegenetics.taxa.tree.Tree> trees)

This merges two or more trees into one tree. Nodes are merged when the names are the same.

Example: (AA:2,BB:2,CC:2); merged with (XX:2,YY:2,ZZ:2)AA; produces (('XX':2.0000000,'YY':2.0000000,'ZZ':2.0000000)'AA':2.0000000,'BB':2.0000000,'CC':2.0000000);

nodes

@NotNull
public static java.util.List<net.maizegenetics.taxa.tree.Node> nodes(@NotNull
                                                                              Tree $receiver)

Extension function that returns all nodes of the tree

subsetTree

@NotNull
public static Tree subsetTree(@NotNull
                                       Tree tree,
                                       @NotNull
                                       TaxaList taxaList)

Returns a tree that is a subset of the original containing only the taxa specified.

subsetTree

@NotNull
public static Tree subsetTree(@NotNull
                                       Tree tree,
                                       @NotNull
                                       java.util.List<java.lang.String> namesToKeep)

Returns a tree that is a subset of the original containing only the names specified.

removeBranchLengths

@NotNull
public static Tree removeBranchLengths(@NotNull
                                                Tree tree)

This removes the branch lengths from the given tree

convertNames

@NotNull
public static Tree convertNames(@NotNull
                                         Tree tree,
                                         @NotNull
                                         java.lang.String filename)

This converts tree node names based on the conversion file specified.