Class SimpleRootedTree

  • All Implemented Interfaces:
    Graph, RootedTree, Tree, Attributable

    public final class SimpleRootedTree
    extends java.lang.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 Detail

      • 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,
                                java.util.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 Detail

      • 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​(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
      • 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 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.
      • 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.
      • 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.
      • 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.
      • 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
      • 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​(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