Constructor Detail

• NodeUtils

  public NodeUtils()

Method Detail

• getExternalNodes

  public static void getExternalNodes​(Node root,
                                      java.util.Vector store)

  Appends all external nodes from tree defined by root to Vector store

  Parameters:

  root - The root node defining tree

  store - Where leaf nodes are stored (original contents is not touched)

• getExternalNodes

  public static Node[] getExternalNodes​(Node root)

  Obtains all external nodes from tree defined by root and returns as an array

  Parameters:

  root - The root node defining tree

  Returns:

  an array of nodes where each node is a leaf node, and is a member of the tree defined by root

• getInternalNodes

  public static void getInternalNodes​(Node root,
                                      java.util.Vector store)

  Appends all internal nodes from tree defined by root to Vector store

  Parameters:

  root - The root node defining tree

  store - Where internal nodes are stored (original contents is not touched)

• getInternalNodes

  public static Node[] getInternalNodes​(Node root,
                                        boolean includeRoot)

  Obtains all internal nodes from tree defined by root and returns as an array

  Parameters:

  root - The root node defining tree

  Returns:

  an array of nodes where each node is a internal node, and is a member of the tree defined by root

• getMaxNodeDepth

  public static int getMaxNodeDepth​(Node root)

  Returns:

  the maxium distance in nodes from root to a leaf

• getPathLengthInfo

  public static final double[] getPathLengthInfo​(Node root)

  Calculates max/min lengths of paths from root to leaf, taking into account branch lengths

  Returns:

  a double array where

  • The first element is the minimum length path from root to leaf.
  • The second element is the second most minimum length path from root to leaf.
  • The third element is the second most maximum length path from root to leaf.
  • The forth element is the maximum length path from root to leaf.

  See Also:

  getMaxNodeDepth()

• getMaximumPathLengthLengthToLeaf

  public static final double getMaximumPathLengthLengthToLeaf​(Node root)

  Returns:

  the maximum length of a path from root to a leaf

• getMinimumPathLengthLengthToLeaf

  public static final double getMinimumPathLengthLengthToLeaf​(Node root)

  Returns:

  the minimum length of a path from root to a leaf

• lengths2Heights

  public static void lengths2Heights​(Node root)

  Converts lengths to heights, *without* assuming contemporaneous tips.

• getInternalNodeCount

  public static int getInternalNodeCount​(Node root)

  Returns:

  the number of internal nodes from a root node

• lengths2HeightsKeepTips

  public static void lengths2HeightsKeepTips​(Node node,
                                             boolean useMax)

  Converts lengths to heights, but maintains tip heights.

• exchangeInfo

  public static void exchangeInfo​(Node node1,
                                  Node node2)

  Exchange field info between two nodes. Specifically identifiers, branch lengths, node heights and branch length SEs.

• heights2Lengths

  public static void heights2Lengths​(Node node)

  determines branch lengths of this and all descendent nodes from heights

• heights2Lengths

  public static void heights2Lengths​(Node node,
                                     boolean respectMinimum)

  determines branch lengths of this and all descendent nodes from heights

• localHeights2Lengths

  public static void localHeights2Lengths​(Node node,
                                          boolean respectMinimum)

  determines branch lengths of this node and its immediate descendent nodes from heights.

• findLargestChild

  public static double findLargestChild​(Node node)

  Finds the largest child (in terms of node height).

• removeChild

  public static void removeChild​(Node parent,
                                 Node child)

  remove child

  Parameters:

  node - child node to be removed

• removeBranch

  public static void removeBranch​(Node node)

  remove internal branch (collapse node with its parent)

  Parameters:

  node - node associated with internal branch

• restoreBranch

  public static void restoreBranch​(Node node)

  restore internal branch

  Parameters:

  node - node associated with internal branch

• joinChilds

  public static void joinChilds​(Node node,
                                int n1,
                                int n2)

  join two childs, introducing a new node/branch in the tree that replaces the first child

  Parameters:

  n1 - number of first child

  n2 - number of second child

• preorderSuccessor

  public static Node preorderSuccessor​(Node node)

  determine preorder successor of this node

  Returns:

  next node

• postorderSuccessor

  public static Node postorderSuccessor​(Node node)

  determine postorder successor of a node

  Returns:

  next node

• printNH

  public static void printNH​(java.io.PrintWriter out,
                             Node node,
                             boolean printLengths,
                             boolean printInternalLabels)

  prints node in New Hamshire format.

• printNH

  public static int printNH​(java.io.PrintWriter out,
                            Node node,
                            boolean printLengths,
                            boolean printInternalLabels,
                            int column,
                            boolean breakLines)

• findByIdentifier

  public static final Node[] findByIdentifier​(Node node,
                                              java.lang.String[] identifierNames)

  Returns the first nodes in this tree that has the required identifiers.

  Returns:

  null if none of the identifiers names match nodes in tree, else return array which may have null "blanks" for corresponding identifiers that do not match any node in the tree

• findByIdentifier

  public static final Node[] findByIdentifier​(Node node,
                                              Identifier[] identifiers)

  Returns the first nodes in this tree that has the required identifiers.

• findByIdentifier

  public static final Node findByIdentifier​(Node node,
                                            Identifier identifier)

  Returns the first node in this tree that has the required identifier.

• findByIdentifier

  public static final Node findByIdentifier​(Node node,
                                            java.lang.String identifierName)

  Returns the first node in this tree that has the required identifier.

• getDistanceToRoot

  public static double getDistanceToRoot​(Node node)

  determine distance to root

  Returns:

  distance to root

• getLeafCount

  public static int getLeafCount​(Node node)

  Return the number of terminal leaves below this node or 1 if this is a terminal leaf.

• isAncestor

  public static boolean isAncestor​(Node possibleAncestor,
                                   Node node)

  For two nodes in the tree true if the first node is the ancestor of the second

  Parameters:

  possibleAncestor - the node that may be the ancestor of the other node

  node - the node that may have the other node as it's ancestor

• getFirstCommonAncestor

  public static Node getFirstCommonAncestor​(Node[] nodes)

  For a set of nodes in the tree returns the common ancestor closest to all nodes (most recent common ancestor)

  Parameters:

  nodes - the nodes to check, is okay if array elements are null!

• getFirstCommonAncestor

  public static Node getFirstCommonAncestor​(Node nodeOne,
                                            Node nodeTwo)

  For two nodes in the tree returns the common ancestor closest to both nodes (most recent common ancestor)

  Parameters:

  nodeOne -

  nodeTwo -

• getUnrootedBranchCount

  public static final int getUnrootedBranchCount​(Node center)

  returns number of branches centered around an internal node in an unrooted tree

• convertNegativeBranchLengthsToZeroLength

  public static final void convertNegativeBranchLengthsToZeroLength​(Node node)

  If the given node or the sub tree defined by that node have negative branch lengths, they'll have zeron branch lengths after a call to this function!