Class SimpleTree

  • All Implemented Interfaces:
    Graph, Tree, Attributable

    public final class SimpleTree
    extends java.lang.Object
    implements Tree
    A basic implementation on an unrooted tree.
    Version:
    $Id: SimpleTree.java 956 2008-11-30 01:18:20Z rambaut $
    Author:
    Joseph Heled
    • Constructor Detail

      • SimpleTree

        public SimpleTree()
        Tree (to be constructed by subsequent calls).
      • SimpleTree

        public SimpleTree​(Tree tree)
        Duplicate a tree.
        Parameters:
        tree -
    • Method Detail

      • createExternalNode

        public Node createExternalNode​(Taxon taxon)
        Creates a new external node with the given taxon. See createInternalNode for a description of how to use these methods.
        Parameters:
        taxon - the taxon associated with this node
        Returns:
        the created node reference
      • createInternalNode

        public Node createInternalNode​(java.util.List<Node> adjacencies)
        Once a SimpleTree has been created, the node stucture can be created by calling createExternalNode and createInternalNode. First of all createExternalNode is called giving Taxon objects for the external nodes. Then these are put into sets and passed to createInternalNode to create new internal nodes. It is the caller responsibility to insure no cycles are created.
        Parameters:
        adjacencies - the child nodes of this node
        Returns:
        the created node.
      • setEdgeLength

        public void setEdgeLength​(Node node1,
                                  Node node2,
                                  double length)
        Set edge distance between two adjacent nodes.
        Parameters:
        node1 -
        node2 -
        length -
      • setEdgeLength

        public void setEdgeLength​(Edge edge,
                                  double length)
        Change length of an existing edge.
        Parameters:
        edge -
        length -
      • addEdge

        public void addEdge​(Node node1,
                            Node node2,
                            double length)
        Add a new edge between two existing (non adjacent yet) nodes.
        Parameters:
        node1 -
        node2 -
        length -
      • getEdges

        public java.util.List<Edge> getEdges​(Node node)
        Returns a list of edges connected to this node
        Specified by:
        getEdges in interface Graph
        Parameters:
        node -
        Returns:
        the set of nodes that are attached by edges to the given node.
      • getAdjacencies

        public java.util.List<Node> getAdjacencies​(Node node)
        Description copied from interface: Graph
        Returns a list of nodes connected to this node by an edge
        Specified by:
        getAdjacencies in interface Graph
        Parameters:
        node -
        Returns:
        the set of nodes that are attached by edges to the given node.
      • getExternalNodes

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

        public java.util.Set<Node> getInternalNodes()
        Specified by:
        getInternalNodes in interface Tree
        Returns:
        a set of all nodes that have degree 2 or more. These nodes are often refered to as internal nodes.
      • getTaxa

        public java.util.Set<Taxon> getTaxa()
        Specified by:
        getTaxa in interface Tree
        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

        public Taxon getTaxon​(Node node)
        Specified by:
        getTaxon in interface Tree
        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

        public boolean isExternal​(Node node)
        Specified by:
        isExternal in interface Tree
        Parameters:
        node - the node
        Returns:
        true if the node is of degree 1.
      • isExternal

        public boolean isExternal​(Edge edge)
        Parameters:
        edge - the edge
        Returns:
        true if the edge has a node of degree 1.
      • getNode

        public Node getNode​(Taxon taxon)
        Specified by:
        getNode in interface Tree
        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.
      • getEdgeLength

        public double getEdgeLength​(Node node1,
                                    Node node2)
                             throws Graph.NoEdgeException
        Description copied from interface: Graph
        Returns the length of the edge that connects these two nodes
        Specified by:
        getEdgeLength in interface Graph
        Parameters:
        node1 -
        node2 -
        Returns:
        the length of the edge connecting node1 and node2.
        Throws:
        Graph.NoEdgeException - if the nodes are not directly connected by an edge.
      • getNodes

        public Node[] getNodes​(Edge edge)
        Returns an array of 2 nodes which are the nodes at either end of the edge.
        Specified by:
        getNodes in interface Graph
        Parameters:
        edge -
        Returns:
        an array of 2 edges
      • getNodes

        public java.util.Set<Node> getNodes()
        Specified by:
        getNodes in interface Graph
        Returns:
        the set of all nodes in this graph.
      • getEdges

        public java.util.Set<Edge> getEdges()
        Specified by:
        getEdges in interface Graph
        Returns:
        the set of all edges in this graph.
      • getNodes

        public java.util.Set<Node> getNodes​(int degree)
        Specified by:
        getNodes in interface Graph
        Parameters:
        degree - the number of edges connected to a node
        Returns:
        a set containing all nodes in this graph of the given degree.
      • getExternalEdges

        public java.util.Set<Edge> getExternalEdges()
        The set of external edges. This is a pretty inefficient implementation because a new set is constructed each time this is called.
        Specified by:
        getExternalEdges in interface Tree
        Returns:
        the set of external edges.
      • getInternalEdges

        public java.util.Set<Edge> getInternalEdges()
        The set of internal edges. This is a pretty inefficient implementation because a new set is constructed each time this is called.
        Specified by:
        getInternalEdges in interface Tree
        Returns:
        the set of internal edges.
      • setAttribute

        public void setAttribute​(java.lang.String name,
                                 java.lang.Object value)
        Description copied from interface: Attributable
        Sets an named attribute for this object.
        Specified by:
        setAttribute in interface Attributable
        Parameters:
        name - the name of the attribute.
        value - the new value of the attribute.
      • getAttribute

        public java.lang.Object getAttribute​(java.lang.String name)
        Specified by:
        getAttribute in interface Attributable
        Parameters:
        name - the name of the attribute of interest, or null if the attribute doesn't exist.
        Returns:
        an object representing the named attributed for this object.
      • removeAttribute

        public void removeAttribute​(java.lang.String name)
        Specified by:
        removeAttribute in interface Attributable
        Parameters:
        name - name of attribute to remove
      • getAttributeNames

        public java.util.Set<java.lang.String> getAttributeNames()
        Specified by:
        getAttributeNames in interface Attributable
        Returns:
        an array of the attributeNames that this object has.
      • getAttributeMap

        public java.util.Map<java.lang.String,​java.lang.Object> getAttributeMap()
        Description copied from interface: Attributable
        Gets the entire attribute map.
        Specified by:
        getAttributeMap in interface Attributable
        Returns:
        an unmodifiable map