Class RootedSubtree

Method Details

• setHeight

  public void setHeight(Node node, double height)

  Parameters:

  node - the node whose height is being set

  height - the height

• setLength

  public void setLength(Node node, double length)

  Parameters:

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

  length - the length

• getChildren

  public List<Node> getChildren(Node node)

  Parameters:

  node - the node whose children are being requested.

  Returns:

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

• hasHeights

  public boolean hasHeights()

  Returns:

  Whether this tree has node heights available

• getHeight

  public double getHeight(Node node)

  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()

  Returns:

  Whether this tree has branch lengths available

• getLength

  public double getLength(Node node)

  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()

  Returns:

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

• isLengthsKnown

  public boolean isLengthsKnown()

  Returns:

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

• getParent

  public Node getParent(Node node)

  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()

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

  Returns:

  the root of the tree.

• getExternalNodes

  public Set<Node> getExternalNodes()

  Returns:

  a set of all nodes that have degree 1. These nodes are often refered to as 'tips'.

• getInternalNodes

  public Set<Node> getInternalNodes()

  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()

  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)

  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)

  Parameters:

  node - the node

  Returns:

  true if the node is of degree 1.

• getNode

  public 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

  public void renameTaxa(Taxon from, Taxon to)

• getEdges

  public List<Edge> getEdges(Node node)

  Returns a list of edges connected to this node

  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

  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

  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

  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.

  Parameters:

  edge -

  Returns:

  an array of 2 edges

• getNodes

  public Set<Node> getNodes()

  Returns:

  the set of all nodes in this graph.

• getEdges

  public Set<Edge> getEdges()

  Returns:

  the set of all edges in this graph.

• 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.

  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.

  Returns:

  the set of internal edges.

• getNodes

  public Set<Node> getNodes(int degree)

  Parameters:

  degree - the number of edges connected to a node

  Returns:

  a set containing all nodes in this graph of the given degree.

• setConceptuallyUnrooted

  public void setConceptuallyUnrooted(boolean intent)

• 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.

  Returns:

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

• isRoot

  public boolean isRoot(Node node)

  Parameters:

  node - the node

  Returns:

  true if the node is the root of this tree.

• setAttribute

  public void setAttribute(String name, Object value)

  Description copied from interface: Attributable

  Sets an named attribute for this object.

  Parameters:

  name - the name of the attribute.

  value - the new value of the attribute.

• getAttribute

  public Object getAttribute(String name)

  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)

  Parameters:

  name - name of attribute to remove

• getAttributeNames

  public Set<String> getAttributeNames()

  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.

  Returns:

  an unmodifiable map