Constructor Detail

• MutableRootedTree

  public MutableRootedTree​(Tree tree,
                           Node outGroup)

  Construct a rooted tree from unrooted.

  Parameters:

  tree - Unrooted tree to root

  outGroup - Node in tree assumed to be the outgroup

• MutableRootedTree

  public MutableRootedTree​(RootedTree tree)

  Construct a rooted tree from an immutable rooted tree.

  Parameters:

  tree - Rooted tree to copy

Method Detail

• removeInternalNode

  public void removeInternalNode​(Node node)

  Remove internal node. Move all children to their grandparent.

  Parameters:

  node - to be removed

• addChild

  public void addChild​(Node child,
                       Node parent)

  Insert a child node.

  Parameters:

  child - to be added

  parent - into which it should be added

• removeChild

  public void removeChild​(Node child,
                          Node parent)

  Remove a child node.

  Parameters:

  child - to be removed

  parent - from which it should be removed

• setRoot

  public void setRoot​(Node root)

  Set the root node.

  Parameters:

  root - the new root node

• refineNode

  public void refineNode​(Node node,
                         int[] leftSet)

  Parameters:

  node - Node to refine

  leftSet - indices of children in the left new subtree.

• reRootWithOutgroup

  public void reRootWithOutgroup​(Node outGroup,
                                 java.util.Set<java.lang.String> attributeNames)

  Re-root tree using an outgroup.

  Parameters:

  outGroup -

  attributeNames - Move those attributes (if they exist in node) to their previous parent. The idea is to preserve "branch" attributes which we now store in the child since only "node" properties are supported.

• detachChildren

  public Node detachChildren​(Node node,
                             java.util.List<java.lang.Integer> split)

• 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 jebl.evolution.trees.MutableRootedTree.MutableRootedNode createInternalNode​(java.util.List<? extends Node> children)

  Once a SimpleRootedTree 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 a parent of these nodes. The last node created using createInternalNode is automatically the root so when all the nodes are created, the tree is complete.

  Parameters:

  children - the child nodes of this nodes

  Returns:

  the created node reference

• 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 java.util.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 list 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).

• 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()

  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.

• 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 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.

• 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 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.

• 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

• 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.

• 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 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.

• 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.

• 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.

• 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.

  Specified by:

  conceptuallyUnrooted in interface RootedTree

  Returns:

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

• 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