Class SimpleRootedTree

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

public final class SimpleRootedTree extends Object implements RootedTree
A simple, and initially immutable rooted tree implementation. All returned collections are defensively copied. The implementation of Node is private. A number of methods are provided that can be used to construct a tree (createExternalNode & createInternalNode).
Version:
$Id: SimpleRootedTree.java 1045 2010-01-13 03:09:14Z stevensh $
Author:
Andrew Rambaut, Alexei Drummond
  • Constructor Details

    • SimpleRootedTree

      public SimpleRootedTree()
    • SimpleRootedTree

      public SimpleRootedTree(RootedTree tree)
      Make a copy of the given rooted tree
      Parameters:
      tree - a rooted tree
    • SimpleRootedTree

      public SimpleRootedTree(RootedTree tree, Map<Node,Node> nodeMapping)
      Make a copy of the given rooted tree
      Parameters:
      tree - a rooted tree
      nodeMapping - store {source tree node -> new tree node} mapping in here if non-null
    • SimpleRootedTree

      public SimpleRootedTree(Tree tree, Node ingroupNode, Node outgroupNode, double ingroupBranchLength) throws Graph.NoEdgeException
      Make a copy of the given unrooted tree
      Parameters:
      tree - an unrooted tree
      ingroupNode - the node on one side of the root
      outgroupNode - the node on the other side of the root
      ingroupBranchLength - the branch length from the root to the ingroup node
      Throws:
      Graph.NoEdgeException
  • Method Details

    • createNodes

      public Node createNodes(RootedTree tree, Node node)
      Clones the entire tree structure from the given RootedTree.
      Parameters:
      tree -
      node -
      Returns:
      created node
    • createNodes

      public Node createNodes(Tree tree, Node parent, Node child) throws Graph.NoEdgeException
      Clones the entire tree structure from the given (unrooted) Tree.
      Parameters:
      tree - the unrooted tree
      parent - the parent node
      child - the child node
      Throws:
      Graph.NoEdgeException
    • 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.SimpleRootedTree.SimpleRootedNode createInternalNode(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
    • deleteInternalNode

      public void deleteInternalNode(Node node)
      Removes an internal node in this tree. It must not be a child of any other node.
      Parameters:
      node - the node to remove.
    • addNode

      public Node addNode(Node node)
      Adds a new node at the midpoint of the edge connecting the given node to its parent.
      Parameters:
      node - must be a node in the tree, which has a parent
      Returns:
      the newly created node
    • addNode

      public Node addNode(Edge edge)
      Adds a new node at the midpoint of the given edge
      Parameters:
      edge -
      Returns:
      the newly created node
    • swapNodes

      public void swapNodes(Node n, int i0, int i1)
    • 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)
      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.
    • 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.
    • 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)
      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.
    • 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.
    • 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.
    • 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.
    • 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
    • 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.
    • 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