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/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
* Created on June 7, 2010
* Author: Mark Chapman
*/
package org.biojava.nbio.alignment.template;
import org.biojava.nbio.core.alignment.template.ProfilePair;
import org.biojava.nbio.core.alignment.template.Profile;
import org.biojava.nbio.core.sequence.template.Compound;
import org.biojava.nbio.core.sequence.template.Sequence;
import javax.swing.tree.TreeNode;
import java.util.concurrent.Future;
/**
* Defines a data structure for the node in a guide tree used during progressive multiple sequence alignment.
*
* @author Mark Chapman
* @param each {@link Sequence} in the tree is of type S
* @param each element of a {@link Sequence} is a {@link Compound} of type C
*/
public interface GuideTreeNode, C extends Compound> extends TreeNode {
/**
* Returns the first child node of this node. For leaf nodes (sequences), this will be null.
*
* @return the first child node of this node
*/
GuideTreeNode getChild1();
/**
* Returns the second child node of this node. For leaf nodes (sequences), this will be null.
*
* @return the second child node of this node
*/
GuideTreeNode getChild2();
/**
* 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.
*
* @return the difference in height of this node to it's parent node
*/
double getDistanceToParent();
/**
* Returns the name of this node. For leaf nodes (sequences), this will likely be the accession ID.
*
* @return the name of this node
*/
String getName();
/**
* 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 {@link #setProfile(Profile)} has been called.
*
* @return the profile stored at this node
*/
Profile getProfile();
/**
* 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.
*
* @return the profile future stored at this node
*/
Future> getProfileFuture();
/**
* Stores the given profile.
*
* @param profile new profile stored at this node
*/
void setProfile(Profile profile);
/**
* Stores the given profile future. This allows concurrent execution of alignment tasks.
*
* @param profileFuture new profile to be calculated and then stored at this node
*/
void setProfileFuture(Future> profileFuture);
}