Package org.biojava.nbio.alignment.template

Interface GuideTreeNode<S extends Sequence<C>,C extends 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 Sequence<C>,C extends Compound> extends TreeNode
Defines a data structure for the node in a guide tree used during progressive multiple sequence alignment.
Author:
Mark Chapman

  • Method Details

    • 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

      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<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(Profile<S,C> profile)
      Stores the given profile.
      Parameters:
      profile - new profile stored at this node

    • setProfileFuture

      void setProfileFuture(Future<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