Interface Tree

All Superinterfaces:
Attributable, Graph
All Known Subinterfaces:
RootedTree
All Known Implementing Classes:
AbstractRootedTree, CompactRootedTree, FilteredRootedTree, MutableRootedTree, ReRootedTree, RootedFromUnrooted, RootedSubtree, SimpleRootedTree, SimpleTree, SortedRootedTree, TransformedRootedTree
public interface Tree extends Graph
A rooted or unrooted tree. This interface is the common base class for all trees, and contains only operations for unrooted trees. The subinterface RootedTree contains additional methods that make sense only on rooted trees. Both interfaces contain no mutator methods. As of 2006-12-08, the only way to mutate a tree after it has been built is to use its concrete class instead of the Tree or RootedTree interface.
Version:
$Id: Tree.java 627 2007-01-15 03:50:40Z pepster $
Author:
rambaut, Alexei Drummond

  • Method Details

    • getExternalNodes

      Set<Node> getExternalNodes()
      Returns:
      a set of all nodes that have degree 1. These nodes are often refered to as 'tips'.

    • getInternalNodes

      Set<Node> getInternalNodes()
      Returns:
      a set of all nodes that have degree 2 or more. These nodes are often refered to as internal nodes.

    • getExternalEdges

      Set<Edge> getExternalEdges()
      Returns:
      a set of all edges that have a degree 1 node.

    • getInternalEdges

      Set<Edge> getInternalEdges()
      Returns:
      a set of all edges for which both nodes have degree 2 or more.

    • getTaxa

      Set<Taxon> getTaxa()
      Returns:
      the set of taxa associated with the external nodes of this tree. The size of this set should be the same as the size of the external nodes set.

    • getTaxon

      Taxon getTaxon(Node node)
      Parameters:
      node - the node whose associated taxon is being requested.
      Returns:
      the taxon object associated with the given node, or null if the node is an internal node.

    • isExternal

      boolean isExternal(Node node)
      Parameters:
      node - the node
      Returns:
      true if the node is of degree 1.

    • getNode

      Node getNode(Taxon taxon)
      Parameters:
      taxon - the taxon
      Returns:
      the external node associated with the given taxon, or null if the taxon is not a member of the taxa set associated with this tree.

    • renameTaxa

      void renameTaxa(Taxon from, Taxon to)