Class MutableRootedTree

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

    public class MutableRootedTree
    extends AbstractRootedTree
    A simple rooted tree providing some ability to manipulate the tree. - Root an unrooted tree using an outgroup. - Remove internal node: all children of node are adopted by it's parent. - Split/Refine node by creating two new children and distributing the children to new nodes. - Re-root a rooted tree given an outgroup.
    Version:
    $Id: MutableRootedTree.java 935 2008-07-22 16:52:04Z rambaut $
    Author:
    Joseph Heled
    • 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)
        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
      • 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
      • 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).
      • 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.
      • isRoot

        public boolean isRoot​(Node node)
        Parameters:
        node - the node
        Returns:
        true if the node is the root of this tree.
      • getExternalNodes

        public java.util.Set<Node> getExternalNodes()
        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()
        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()
        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 java.util.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.
      • 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
      • 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
        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 java.util.Set<Node> getNodes()
        Returns:
        the set of all nodes in this graph.
      • getEdges

        public java.util.Set<Edge> getEdges()
        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.
        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.
        Returns:
        the set of internal edges.
      • getNodes

        public java.util.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
      • setAttribute

        public void setAttribute​(java.lang.String name,
                                 java.lang.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 java.lang.Object getAttribute​(java.lang.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​(java.lang.String name)
        Parameters:
        name - name of attribute to remove
      • getAttributeNames

        public java.util.Set<java.lang.String> getAttributeNames()
        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.
        Returns:
        an unmodifiable map