Interface Tree

    • Method Detail

      • getExternalNodes

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

        java.util.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

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

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

        java.util.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)