Class SimpleTree

java.lang.Object
jebl.evolution.trees.SimpleTree
All Implemented Interfaces:
Graph, Tree, Attributable

public final class SimpleTree extends 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 Details

    • SimpleTree

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

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

    • 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(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 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 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.
    • getEdge

      public Edge getEdge(Node node1, Node node2) throws Graph.NoEdgeException
      Returns the Edge that connects these two nodes
      Specified by:
      getEdge in interface Graph
      Parameters:
      node1 -
      node2 -
      Returns:
      the edge object.
      Throws:
      Graph.NoEdgeException - if the nodes are not directly connected by an edge.
    • getExternalNodes

      public 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 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 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.
    • renameTaxa

      public void renameTaxa(Taxon from, Taxon to)
      Specified by:
      renameTaxa in interface 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 Set<Node> getNodes()
      Specified by:
      getNodes in interface Graph
      Returns:
      the set of all nodes in this graph.
    • getEdges

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

      public 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 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 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(String name, 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 Object getAttribute(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(String name)
      Specified by:
      removeAttribute in interface Attributable
      Parameters:
      name - name of attribute to remove
    • getAttributeNames

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

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