/* AlignmentEditor_Seaview actor displays the alignment and facilitates
 * the user to manipulate the alignment with a GUI.
 *
 * 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;

import org.cipres.kepler.registry.*;

//Ptolemy packages
import ptolemy.kernel.CompositeEntity;
import ptolemy.kernel.util.*;
import ptolemy.actor.TypedIOPort;
import ptolemy.data.BooleanToken;
import ptolemy.data.StringToken;
import ptolemy.data.expr.Parameter;
import ptolemy.data.type.BaseType;

//////////////////////////////////////////////////////////////////////////
////AlignmentEditor_Seaview
/**
* Given an alignment, the AlignmentEditor_Seaview actor displays the alignment 
* in the seaview window and facititates the user to edit the alignment.
* Note1: since Seaview is an application running as another process with GUI, 
* the actor cannot monitor the execution of Seaview. Thus the actor cannot know 
* when the user finishes the work and closes the Seaview window.
* Note2: Here we assume the user will save the output file with the same name 
* as the input file. We will change it to let the user input the output file 
* name in the future.
* 
* @author Zhijie Guan, Alex Borchers
* @version $Id:  $
*/

public class AlignmentEditor_Seaview  extends JRunCIPRes {

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

	/** Construct a AlignmentEditor_Seaview 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 AlignmentEditor_Seaview(CompositeEntity container, String name) 
			throws NameDuplicationException, IllegalActionException {
		super(container, name);

		// get the information of Seaview application
		CipresKeplerRegistry registry = Globals.getInstance().getRegistry();
		_seaviewActor = registry.getActor("AlignmentEditor_Seaview");

		// SeaView has different invocation methods in different OSs
		// In Mac, SeaView runs by "open -a Seaview.app input_file_name"
		// In all the other OS, SeaView runs by "Seaview input_file_name"
		if(System.getProperty("os.name").startsWith("Mac")){
			command.setToken( new StringToken("open -a " + _seaviewActor.getAppPath()) );
		}
		else {
			command.setToken( new StringToken(_seaviewActor.getAppPath()));
		}

		// set the standard output file
		outputFile.setToken( new StringToken(registry.getDefaultStdOutDir() + "SeaviewOut.log") );

		// set the standard error file
		errorFile.setToken( new StringToken(registry.getDefaultStdOutDir() + "SeaviewError.log") );

		// set the working directory 
		workingDirectory.setToken( new StringToken(_seaviewActor.getWorkingDir()) );

		// initialize the port for getting in the input file name
		inputFileName = new TypedIOPort(this, "inputFileName", true, false);
		//inputFileName.setDisplayName("Input File Name");
		inputFileName.setTypeEquals(BaseType.STRING);
		inputFileName.setRequired(true);
		new Parameter(inputFileName, "_showName", BooleanToken.TRUE);

		// initialize the port for sending out the output file name
		outputFileName = new TypedIOPort(this, "outputFileName", false, true);
		//outputFileName.setDisplayName("Output File Name");
		outputFileName.setTypeEquals(BaseType.STRING);
		outputFileName.setUseful(true);
		new Parameter(outputFileName, "_showName", BooleanToken.TRUE);

		// inputTrigger name display
		new Parameter(inputTrigger, "_showName", BooleanToken.TRUE);
	}

    ///////////////////////////////////////////////////////////////////
    ////                     ports and parameters                  ////

    /**
     * The input file name is transferred into the actor through this port.
     * The input file contains the alignment for reviewing and editing.
     */
	public TypedIOPort inputFileName;
	
	/**
	 * The output file name is sent out throught this port.
	 * The output file contains the edited alignment.
	 */
	public TypedIOPort outputFileName;
	
	///////////////////////////////////////////////////////////////////
	////                    functional variables                   ////
	
    ///////////////////////////////////////////////////////////////////
    ////                         public methods                    ////

    /** Run seaview for alignment reviw and manipulation.
     *  @exception IllegalActionException If it is thrown by the
     *   send() method sending out the token.
     */
    public void fire() throws IllegalActionException {

    	// get the input file name and send it to JRun object as the command argument
    	StringToken inputFileNameToken = (StringToken)inputFileName.get(0);
    	arguments.setToken(inputFileNameToken);

    	super.fire();

    	// the output file name must be the same as the input file name
    	// currently we don't support the function that an user can save the result to another file
    	outputFileName.send(0, inputFileNameToken);
    }
	
	/** Post fire the actor. Return false to indicated that the
	 *  process has finished. If it returns true, the process will
	 *  continue indefinitely.
	 */
    // Note here we want to let this actor be able to run multiple times to view and edit
    // multiple different alignments.
/*	public boolean postfire() {
		return false;
	}	
*/
    
	/** private variables
	 *  This is the ActorInfo object which comes from the Cipres-kepler registry
	 *  and records all the appliation information for Seaview.
	 */
	private ActorInfo _seaviewActor;

}