Class Utils

Method Details

• toNewick

  public static String toNewick(RootedTree tree)

  Parameters:

  tree -

  Returns:

  the rooted tree as a newick format string

• toUniqueNewick

  public static String toUniqueNewick(RootedTree tree)

  Constructs a unique newick representation of a tree

  Parameters:

  tree -

• toUniqueNewickByAttribute

  public static String toUniqueNewickByAttribute(RootedTree tree, String attribute)

  Constructs a unique newick representation of a tree print only an attribute

  Parameters:

  tree -

• safeNodeHeight

  public static double safeNodeHeight(RootedTree tree, Node node)

• maxLevels

  public static int maxLevels(RootedTree tree)

• asText

  public static String asText(Tree tree)

• asText

  public static String[] asText(Tree tree, int widthGuide)

• rootTheTree

  public static RootedTree rootTheTree(Tree tree)

  Return a rooted tree from any tree.

  If tree already rooted, return it. Otherwise if there is a "natuarl root" (i.e. a node of degree 2) use it as root. Otherwise use an internal node close to the center of the tree as a root.

  Parameters:

  tree - to root

  Returns:

  rooted representation

• rootTreeAtCenter

  public static RootedTree rootTreeAtCenter(Tree tree)

  Root any tree by locating the "center" of tree and adding a new root node at that point

  for any point on the tree x let D(x) = Max{distance between x and t : for all tips t} The "center" c is the point with the smallest distance, i.e. D(c) = min{ D(x) : x in tree }

  Parameters:

  tree - to root

  Returns:

  rooted tree

• getPathLength

  public static double getPathLength(Tree tree, Node node1, Node node2)

  Parameters:

  tree - the tree

  node1 -

  node2 -

  Returns:

  the path length between the two nodes

• isBinary

  public static boolean isBinary(RootedTree rootedTree)

  Parameters:

  rootedTree - the rooted tree

  Returns:

  true if all internal nodes in the given tree are of degree 3, except the root which must have a degree of 2.

• isUltrametric

  public static boolean isUltrametric(RootedTree rootedTree)

  Parameters:

  rootedTree - the rooted tree

  Returns:

  true if all the external nodes in the tree have a height of 0.0

• getLength

  public static double getLength(Tree tree)

  Parameters:

  tree - the tree

  Returns:

  the sum of all the branch lengths

• getLength

  public static double getLength(RootedTree tree)

  Parameters:

  tree - the tree

  Returns:

  the sum of all the branch lengths

• getExternalNodeCount

  public static int getExternalNodeCount(RootedTree tree, Node node)

  Return the number of external nodes under this node.

  Parameters:

  tree -

  node -

  Returns:

  the number of external nodes under this node.

• getNodes

  public static List<Node> getNodes(RootedTree tree, Node node)

  All nodes in subtree - parents before children (pre - order).

  Parameters:

  tree -

  node -

  Returns:

  nodes in pre-order

• rightNb

  public static Node rightNb(RootedTree tree, Node tipNode)

  Right Neighbour of a tip (taxon).

  When tree is laid with children in given order, this would be the taxon to the right.

  Parameters:

  tree -

  tipNode -

  Returns:

  Right Neighbour. null if node is the rightmost in tree or not a tip.

• leftNb

  public static Node leftNb(RootedTree tree, Node node)

  Left Neighbour of a tip (taxon).

  When tree is laid with children in given order, this would be the taxon to the left.

  Parameters:

  tree -

  node -

  Returns:

  Left Neighbour. null if node is the leftmost in tree or not a tip.

• getMinNodeHeight

  public static double getMinNodeHeight(RootedTree tree, Node node)

  Parameters:

  tree -

  node -

  Returns:

  the minimum node height

• createNodeDensityComparator

  public static Comparator<Node> createNodeDensityComparator(RootedTree tree)

• createNodeDensityMinNodeHeightComparator

  public static Comparator<Node> createNodeDensityMinNodeHeightComparator(RootedTree tree)

• assertAllTreesHaveTheSameTaxa

  public static void assertAllTreesHaveTheSameTaxa(List<? extends Tree> trees) throws IllegalArgumentException

  Checks whether all of the trees passed in have the same taxa sets (ignoring order of taxa), and throws an IllegalArgumentException if this is not the case. If no tree or only one tree is passed in, immediately returns without throwing an exception.

  Parameters:

  trees - Zero or more trees

  Throws:

  IllegalArgumentException - if not all of the trees have the same taxa

  NullPointerException - if trees is null

• DEBUGsubTreeRep

  public static String DEBUGsubTreeRep(RootedTree tree, Node node)

• copyTree

  public static RootedTree copyTree(RootedTree treeToCopy)

  This method creates an unattached copy of the given rooted tree such that changes to the copied tree do not affect the original tree.

  Parameters:

  treeToCopy - the tree to copy

  Returns:

  an equivalent tree to treeToCopy (NB this may not be of the same RootedTree subclass as treeToCopy)