Package org.biojava.nbio.alignment.template

Interface GuideTreeNode<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,​C extends org.biojava.nbio.core.sequence.template.Compound>

  • Type Parameters:
    S - each Sequence in the tree is of type S
    C - each element of a Sequence is a Compound of type C
    All Superinterfaces:
    TreeNode
    All Known Implementing Classes:
    GuideTree.Node
    public interface GuideTreeNode<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,​C extends org.biojava.nbio.core.sequence.template.Compound>
extends TreeNode
    Defines a data structure for the node in a guide tree used during progressive multiple sequence alignment.
    Author:
    Mark Chapman

    • Method Detail

      • getChild1

        GuideTreeNode<S,​C> getChild1()
        Returns the first child node of this node. For leaf nodes (sequences), this will be null.
        Returns:
        the first child node of this node

      • getChild2

        GuideTreeNode<S,​C> getChild2()
        Returns the second child node of this node. For leaf nodes (sequences), this will be null.
        Returns:
        the second child node of this node

      • getDistanceToParent

        double getDistanceToParent()
        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.
        Returns:
        the difference in height of this node to it's parent node

      • getName

        String getName()
        Returns the name of this node. For leaf nodes (sequences), this will likely be the accession ID.
        Returns:
        the name of this node

      • getProfile

        org.biojava.nbio.core.alignment.template.Profile<S,​C> getProfile()
        Returns the profile stored at this node. If the node is a leaf, the profile is that of a single sequence. If not, this returns null until setProfile(Profile) has been called.
        Returns:
        the profile stored at this node

      • getProfileFuture

        Future<org.biojava.nbio.core.alignment.template.ProfilePair<S,​C>> getProfileFuture()
        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.
        Returns:
        the profile future stored at this node

      • setProfile

        void setProfile​(org.biojava.nbio.core.alignment.template.Profile<S,​C> profile)
        Stores the given profile.
        Parameters:
        profile - new profile stored at this node

      • setProfileFuture

        void setProfileFuture​(Future<org.biojava.nbio.core.alignment.template.ProfilePair<S,​C>> profileFuture)
        Stores the given profile future. This allows concurrent execution of alignment tasks.
        Parameters:
        profileFuture - new profile to be calculated and then stored at this node