Class GuideTree.Node

  • All Implemented Interfaces:
    javax.swing.tree.TreeNode, GuideTreeNode<S,​C>
    Enclosing class:
    GuideTree<S extends Sequence<C>,​C extends Compound>

    public class GuideTree.Node
    extends java.lang.Object
    implements GuideTreeNode<S,​C>
    Implements a data structure for the node in a guide tree used during progressive multiple sequence alignment.
    • Method Detail

      • getDistanceToParent

        public double getDistanceToParent()
        Description copied from interface: GuideTreeNode
        Returns the difference in height of this node and it's parent node. A likely meaning of this distance is half the percent difference between this node and it's sibling node.
        Specified by:
        getDistanceToParent in interface GuideTreeNode<S extends Sequence<C>,​C extends Compound>
        Returns:
        the difference in height of this node to it's parent node
      • getName

        public java.lang.String getName()
        Description copied from interface: GuideTreeNode
        Returns the name of this node. For leaf nodes (sequences), this will likely be the accession ID.
        Specified by:
        getName in interface GuideTreeNode<S extends Sequence<C>,​C extends Compound>
        Returns:
        the name of this node
      • getProfileFuture

        public java.util.concurrent.Future<ProfilePair<S,​C>> getProfileFuture()
        Description copied from interface: GuideTreeNode
        Returns the profile future stored at this node, but does not force the calculation, yet. This allows alignment tasks for the entire tree to be queued in a post-order traversal before concurrent execution.
        Specified by:
        getProfileFuture in interface GuideTreeNode<S extends Sequence<C>,​C extends Compound>
        Returns:
        the profile future stored at this node
      • setProfileFuture

        public void setProfileFuture​(java.util.concurrent.Future<ProfilePair<S,​C>> profileFuture)
        Description copied from interface: GuideTreeNode
        Stores the given profile future. This allows concurrent execution of alignment tasks.
        Specified by:
        setProfileFuture in interface GuideTreeNode<S extends Sequence<C>,​C extends Compound>
        Parameters:
        profileFuture - new profile to be calculated and then stored at this node
      • children

        public java.util.Enumeration<GuideTreeNode<S,​C>> children()
        Specified by:
        children in interface javax.swing.tree.TreeNode
      • getAllowsChildren

        public boolean getAllowsChildren()
        Specified by:
        getAllowsChildren in interface javax.swing.tree.TreeNode
      • getChildAt

        public GuideTreeNode<S,​C> getChildAt​(int childIndex)
        Specified by:
        getChildAt in interface javax.swing.tree.TreeNode
      • getChildCount

        public int getChildCount()
        Specified by:
        getChildCount in interface javax.swing.tree.TreeNode
      • getIndex

        public int getIndex​(javax.swing.tree.TreeNode child)
        Specified by:
        getIndex in interface javax.swing.tree.TreeNode
      • getParent

        public GuideTreeNode<S,​C> getParent()
        Specified by:
        getParent in interface javax.swing.tree.TreeNode
      • isLeaf

        public boolean isLeaf()
        Specified by:
        isLeaf in interface javax.swing.tree.TreeNode