/* TreeMerger actor merges a set of trees into one tree.
 *
 * Copyright (c) 2004 The Regents of the University of California.
 * All rights reserved.
 *
 * Permission is hereby granted, without written agreement and without
 * license or royalty fees, to use, copy, modify, and distribute this
 * software and its documentation for any purpose, provided that the
 * above copyright notice and the following two paragraphs appear in
 * all copies of this software.
 *
 * IN NO EVENT SHALL THE UNIVERSITY OF CALIFORNIA BE LIABLE TO ANY PARTY
 * FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES
 * ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN
 * IF THE UNIVERSITY OF CALIFORNIA HAS BEEN ADVISED OF THE POSSIBILITY
 * OF SUCH DAMAGE.
 *
 * THE UNIVERSITY OF CALIFORNIA SPECIFICALLY DISCLAIMS ANY WARRANTIES,
 * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
 * MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE
 * PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND THE UNIVERSITY
 * OF CALIFORNIA HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT,
 * UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
 *
 *                                       PT_COPYRIGHT_VERSION_2
 *                                       COPYRIGHTENDKEY
 */ 

package org.cipres.kepler;

// Ptolemy package
import ptolemy.actor.TypedAtomicActor;
import ptolemy.kernel.CompositeEntity;
import ptolemy.kernel.util.*;
import ptolemy.actor.TypedIOPort;
import ptolemy.data.BooleanToken;
import ptolemy.data.ObjectToken;
import ptolemy.data.expr.Parameter;
import ptolemy.data.type.BaseType;

// Cipres package
import org.cipres.CipresIDL.api1.TreeMerge;
import org.cipres.CipresIDL.api1.Tree;
import org.cipres.CipresIDL.api1.TreeScore;
import org.cipres.helpers.RegistryEntryWrapper;
import org.cipres.kepler.registry.Globals;

//////////////////////////////////////////////////////////////////////////
//// TreeMerger
/**
 * The TreeMerger actor merges a set of trees got from the input port and 
 *  sends the whole tree to the output port.This actor uses the "tree merge"
 *  services provided by the CIPRes CORBA registry.
 * 
 * @author Zhijie Guan  
 * @version $Id: TreeMerger.java,v 1.2 2006/04/26 00:43:04 guan Exp $
*/

public class TreeMerger extends TypedAtomicActor {

	// TODO: assign a proper hash value to this
	static final long serialVersionUID = 1L;

	/** Construct a TreeMerger actor with the given container and name.
	 *  @param container The container.
     *  @param name The name of this actor.
     *  @exception IllegalActionException If the entity cannot be contained
     *   by the proposed container.
     *  @exception NameDuplicationException If the container already has an
     *   actor with this name.
     */
	
    public TreeMerger(CompositeEntity container, String name)
            throws NameDuplicationException, IllegalActionException  {
        super(container, name);
        
        // construct the input port inputTrees
		inputTrees = new TypedIOPort(this, "inputTrees", true, false);
		//inputTrees.setDisplayName("Trees");
		inputTrees.setTypeEquals(BaseType.GENERAL);
		
		// construct the output port outputTree
        outputTree = new TypedIOPort(this, "outputTree", false, true);
        //outputTree.setDisplayName("Merged Tree");
        // Set the type constraint.
        outputTree.setTypeEquals(BaseType.GENERAL);

        // set inputTrees and outputTree names display
        new Parameter(inputTrees, "_showName", BooleanToken.TRUE);
        new Parameter(outputTree, "_showName", BooleanToken.TRUE);

        _attachText("_iconDescription", "<svg>\n" +
                "<rect x=\"0\" y=\"0\" "
                + "width=\"60\" height=\"20\" "
                + "style=\"fill:white\"/>\n" +
                "</svg>\n");
		
    }

    ///////////////////////////////////////////////////////////////////
    ////                     ports and parameters                  ////
    /** 
     * A set of trees in CIPRes tree data structure is passed to 
     *  the TreeMerger actor through this input port.
     * This port is an input port of type GENERAL.
     */
	public TypedIOPort inputTrees = null;
	
    /** 
     * The merged whole tree is sent through this output port. 
     * This port is an output port of type GENERAL.
     */
    public TypedIOPort outputTree = null;
	
	///////////////////////////////////////////////////////////////////
	////                    functional variables                   ////
	private org.cipres.CipresIDL.api1.Tree _finalTree = null;

    ///////////////////////////////////////////////////////////////////
    ////                         public methods                    ////

    /** Merge a set of trees and send the whole tree to the output port.
     *  @exception IllegalActionException If it is thrown by the
     *   send() method sending out the token.
     */
    public void fire() throws IllegalActionException {
        super.fire();
		if (inputTrees.hasToken(0)) {		
			
			RegistryEntryWrapper treeMergerWrapper = null;
			try {
				// get the TreeMerge CORBA service from CIPRes registry
				treeMergerWrapper = Globals.getInstance().getRegistry().getCipresService(TreeMerge.class);
				TreeMerge service = (TreeMerge)treeMergerWrapper.getService();
				
				// merge trees using TreeMerge service
				_finalTree = service.mergeTrees( (Tree[])( ( (ObjectToken)inputTrees.get(0) ).getValue() ) );
				
				// fix _finalTree. This section should be replaced once the fix_tree is open to public access
				_finalTree.m_newick = _finalTree.m_newick.trim();
				if (_finalTree.m_newick.lastIndexOf(';') == -1)
				{
					_finalTree.m_newick += ";";
				}
				if (_finalTree.m_score == null)
				{
					_finalTree.m_score = new TreeScore();
					_finalTree.m_score.noScore(0);
				}
				
				// This is the code to fix the whole tree with the fix_tree service.
				// Unfortunately this fix_tree service is not available for public access yet.
				// finalTree = RecIDcm3Impl.fix_tree( service.mergeTrees( (Tree[])((ObjectToken)inputTrees.get(0)).getValue() ) );
				
			} catch (Exception e) {
				e.printStackTrace();
			}
			finally {
				if (treeMergerWrapper != null) {
					// release the TreeMerge service
					treeMergerWrapper.releaseService();
				}
			}
			
			// send out the whole tree to the ouput tree port
			outputTree.send(0, new ObjectToken( _finalTree ));
		}				
    }
}