Class ReRootedTree

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

    public final class ReRootedTree
    extends AbstractRootedTree
    A rooted tree concrete class that wraps another tree and provides a differently rooted view of that tree.
    Author:
    Andrew Rambaut
    • Constructor Detail

      • ReRootedTree

        public ReRootedTree​(RootedTree source,
                            Node ingroupNode,
                            Node outgroupNode,
                            double ingroupBranchLength)
                     throws Graph.NoEdgeException
        Make a copy of the given unrooted tree
        Parameters:
        source - an unrooted source 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

      • getSourceNode

        public Node getSourceNode​(Node node)
      • 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
      • isHeightsKnown

        public boolean isHeightsKnown()
        Returns:
        Whether the node heights are known or need to be recalculated from the lengths
      • 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
      • 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.
      • 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.
      • 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 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 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.
      • 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​(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
      • rootTreeAtCenter

        public static RootedTree rootTreeAtCenter​(RootedTree tree)
        Root any tree by locating the "center" of tree and adding a new root node at that point

        for any point on the tree x let D(x) = Max{distance between x and t : for all tips t} The "center" c is the point with the smallest distance, i.e. D(c) = min{ D(x) : x in tree }

        Parameters:
        tree - to root
        Returns:
        rooted tree