Class CompactRootedTree

Method Details

• getChildren

  public List<Node> getChildren(Node node)

  Specified by:

  getChildren in interface RootedTree

  Parameters:

  node - the node whose children are being requested.

  Returns:

  the list of nodes that are the children of the given node. The set may be empty for a terminal node (a tip).

• getExternalNodeCount

  public int getExternalNodeCount(Node node)

  Specified by:

  getExternalNodeCount in interface RootedTree

• getExternalNodes

  public List<Node> getExternalNodes(Node node)

  Specified by:

  getExternalNodes in interface RootedTree

  Parameters:

  node - the node whose external nodes are being requested.

  Returns:

  the list of external nodes descendent of the given node. The set may be empty for a terminal node (a tip).

• hasHeights

  public boolean hasHeights()

  Specified by:

  hasHeights in interface RootedTree

  Returns:

  Whether this tree has node heights available

• getHeight

  public double getHeight(Node node)

  Specified by:

  getHeight in interface RootedTree

  Parameters:

  node - the node whose height is being requested.

  Returns:

  the height of the given node. The height will be less than the parent's height and greater than it children's heights.

• hasLengths

  public boolean hasLengths()

  Specified by:

  hasLengths in interface RootedTree

  Returns:

  Whether this tree has branch lengths available

• getLength

  public double getLength(Node node)

  Specified by:

  getLength in interface RootedTree

  Parameters:

  node - the node whose branch length (to its parent) is being requested.

  Returns:

  the length of the branch to the parent node (0.0 if the node is the root).

• isHeightsKnown

  public boolean isHeightsKnown()

  Specified by:

  isHeightsKnown in interface RootedTree

  Returns:

  Whether the node heights are known or need to be recalculated from the lengths

• isLengthsKnown

  public boolean isLengthsKnown()

  Specified by:

  isLengthsKnown in interface RootedTree

  Returns:

  Whether the branch lengths are known or need to be recalculated from the heights

• getParent

  public Node getParent(Node node)

  Specified by:

  getParent in interface RootedTree

  Parameters:

  node - the node whose parent is requested

  Returns:

  the parent node of the given node, or null if the node is the root node.

• getParentEdge

  public Edge getParentEdge(Node node)

• getRootNode

  public Node getRootNode()

  Description copied from interface: RootedTree

  The root of the tree has the largest node height of all nodes in the tree.

  Specified by:

  getRootNode in interface RootedTree

  Returns:

  the root of the tree.

• conceptuallyUnrooted

  public boolean conceptuallyUnrooted()

  Description copied from interface: RootedTree

  Due to current implementation limitations, trees store "branch" information in nodes. So, internally rooted trees are genetrated when un-rooted would be more natural. This should be removed. If this is a rooted tree then it is rooted. This can really only confuse things. Trees are unrooted, RootedTrees are rooted. This is not an implementation limitation. It may be that a RootedTree has an arbitrary root but it is still rooted. With a rooted tree, it is convenient to store branch information at the node (i.e., for the branch above the node) because there is no "branch" object. Andrew. This function will probably become deprecated once the "development" tree viewer becomes in sync with the main tree viewer branch and some method of handling this concept has been introduced. Until then, this method remains.

  Specified by:

  conceptuallyUnrooted in interface RootedTree

  Returns:

  true if tree(s) are to be viewed as unrooted

• setConceptuallyUnrooted

  public void setConceptuallyUnrooted(boolean conceptuallyUnrooted)

• isRoot

  public boolean isRoot(Node node)

  Specified by:

  isRoot in interface RootedTree

  Parameters:

  node - the node

  Returns:

  true if the node is the root of this tree.

• 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.

• getExternalEdges

  public Set<Edge> getExternalEdges()

  Specified by:

  getExternalEdges in interface Tree

  Returns:

  a set of all edges that have a degree 1 node.

• getInternalEdges

  public Set<Edge> getInternalEdges()

  Specified by:

  getInternalEdges in interface Tree

  Returns:

  a set of all edges for which both nodes have degree 2 or more.

• 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.

• 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

• getEdges

  public List<Edge> getEdges(Node node)

  Description copied from interface: Graph

  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

  Description copied from interface: Graph

  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.

• 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 edge length.

  Throws:

  Graph.NoEdgeException - if the nodes are not directly connected by an edge.

• getNodes

  public Node[] getNodes(Edge edge)

  Description copied from interface: Graph

  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.

• 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