Class CompactRootedTree

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

public class CompactRootedTree extends Object implements RootedTree
A memory efficient rooted tree. - Uses a compact representation for the tree structure based primarily on indices instead of pointers and objects - Minimize penalty for unused features. Trees not using attributes or edges do not require additional per node/edge memory. Limitations: - Maximun of 2^16 nodes and 2^15 external nodes. This should not be a problem with the current sizes of phlogenetic trees we currently handle. - Some of the accessors are slower, typically the ones getting all nodes, all edges, all internal nodes etc. Traversing the tree and handling attributes speed should be fine (compared to SimpkeRootedTree)
Version:
$Id: CompactRootedTree.java 935 2008-07-22 16:52:04Z rambaut $
Author:
Joseph Heled
  • Constructor Details

    • CompactRootedTree

      public CompactRootedTree(RootedTree t)
      Do all the hard work.
      Parameters:
      t -
  • Method Details

    • 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 set may be empty for a terminal node (a tip).
    • getExternalNodeCount

      public int getExternalNodeCount(Node node)
      Specified by:
      getExternalNodeCount in interface RootedTree
    • getExternalNodes

      public List<Node> getExternalNodes(Node node)
      Specified by:
      getExternalNodes in interface RootedTree
      Parameters:
      node - the node whose external nodes are being requested.
      Returns:
      the list of external nodes descendent of the given node. The set 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).
    • isHeightsKnown

      public boolean isHeightsKnown()
      Specified by:
      isHeightsKnown in interface RootedTree
      Returns:
      Whether the node heights are known or need to be recalculated from the lengths
    • isLengthsKnown

      public boolean isLengthsKnown()
      Specified by:
      isLengthsKnown in interface RootedTree
      Returns:
      Whether the branch lengths are known or need to be recalculated from the heights
    • 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()
      Description copied from interface: RootedTree
      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.
    • 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
    • setConceptuallyUnrooted

      public void setConceptuallyUnrooted(boolean conceptuallyUnrooted)
    • 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 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.
    • getExternalEdges

      public Set<Edge> getExternalEdges()
      Specified by:
      getExternalEdges in interface Tree
      Returns:
      a set of all edges that have a degree 1 node.
    • getInternalEdges

      public Set<Edge> getInternalEdges()
      Specified by:
      getInternalEdges in interface Tree
      Returns:
      a set of all edges for which both nodes have degree 2 or more.
    • 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)
      Description copied from interface: Graph
      Returns a list of edges connected to this node
      Specified by:
      getEdges in interface Graph
      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
      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
      Description copied from interface: Graph
      Returns the Edge that connects these two nodes
      Specified by:
      getEdge in interface Graph
      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
      Returns:
      the edge length.
      Throws:
      Graph.NoEdgeException - if the nodes are not directly connected by an edge.
    • getNodes

      public Node[] getNodes(Edge edge)
      Description copied from interface: Graph
      Returns an array of 2 nodes which are the nodes at either end of the edge.
      Specified by:
      getNodes in interface Graph
      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.
    • 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.
    • 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