Method Detail

• getTipCount

  public static final int getTipCount​(RootedTree tree,
                                      Node node)

  Return the number of leaves under this node.

  Parameters:

  tree -

  node -

  Returns:

  the number of leaves under this node.

• getMinTipHeight

  public static double getMinTipHeight​(RootedTree tree,
                                       Node node)

• getMaxTipHeight

  public static double getMaxTipHeight​(RootedTree tree,
                                       Node node)

• isUltrametric

  public static boolean isUltrametric​(RootedTree tree,
                                      double tolerance)

  Returns:

  true only if all tips have height 0.0

• isBinary

  public static boolean isBinary​(RootedTree tree)

  Returns:

  true only if internal nodes have 2 children

• getTipsForTaxa

  public static java.util.Set<Node> getTipsForTaxa​(RootedTree tree,
                                                   java.util.Collection<Taxon> taxa)
                                            throws MissingTaxonException

  Gets a set of external nodes that correspond to the given taxa.

  Throws:

  MissingTaxonException

• getDescendantTips

  public static java.util.Set<Node> getDescendantTips​(RootedTree tree,
                                                      Node node)

  Gets a set of tip nodes descended from the given node.

• getCommonAncestorNode

  public static Node getCommonAncestorNode​(RootedTree tree,
                                           java.util.Set<Node> tipNodes)

  Gets the most recent common ancestor (MRCA) node of a set of tip nodes.

  Parameters:

  tree - the Tree

  tipNodes - a set of tip nodes

  Returns:

  the Node of the MRCA

• isMonophyletic

  public static boolean isMonophyletic​(RootedTree tree,
                                       java.util.Set<Node> tipNodes)

  Performs the a monophyly test on a set of tip nodes. The nodes are monophyletic if there is a node in the tree which subtends all the tips in the set (and only those tips).

  Parameters:

  tree - a tree object to perform test on

  tipNodes - a set containing the tip node.

  Returns:

  boolean is monophyletic?

• uniqueNewick

  public static java.lang.String uniqueNewick​(RootedTree tree,
                                              Node node)

  Recursive function for constructing a newick tree representation in the given buffer.

• equal

  public static boolean equal​(RootedTree tree1,
                              RootedTree tree2)

  Compares 2 trees and returns true if they have the same topology.