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.

• 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 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.

• 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 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