/* ClustalWSeqAlign actor calls ClustalW for Sequence Alignement.
 *
 * 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 java.io.File;

// ptolemy package
import ptolemy.kernel.CompositeEntity;
import ptolemy.kernel.util.IllegalActionException;
import ptolemy.kernel.util.NameDuplicationException;
import ptolemy.data.BooleanToken;
import ptolemy.data.StringToken;
import ptolemy.data.expr.Parameter;

import org.cipres.kepler.registry.ActorInfo;
import org.cipres.kepler.registry.CipresKeplerRegistry;
import org.cipres.kepler.registry.Globals;
import org.cipres.util.CipresFile;

//////////////////////////////////////////////////////////////////////////
////ClustalWSeqAlign
/**
* This actor calls ClustalW for Sequence Alignment. The Cipres-Kepler registry
* is used to provide the application information for ClustalW. After setting 
* all the application related information, such as command name, GUIGen XML 
* file, and standard output/error files, this actor invokes ClustalW and 
* retrieves back the alignment result after the execution.
* 
* This actor inherits GUIRunCIPRes actor since basically it is a customized 
* GUIRunCIPRes actor to call external Cipres programs.
* 
* @author Zhijie Guan, Alex Borchers
* @version $Id:  $
*/

public class ClustalWSeqAlign extends GUIRunCIPRes {

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

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

		// get the application information from the Cipers-Kepler registry
		CipresKeplerRegistry registry = Globals.getInstance().getRegistry();
		_clustalWActor = registry.getActor("SequenceAlign_Clustal");

		// set the application information into the parameters
		command.setToken(new StringToken(_clustalWActor.getAppPath()));
		uiXMLFile.setToken(new StringToken(_clustalWActor.getGuiXmlFile()));
		outputFile.setToken(new StringToken(registry.getDefaultStdOutDir() + "ClustalWOut.log"));
		errorFile.setToken(new StringToken(registry.getDefaultStdOutDir() + "ClustalWError.log"));
		workingDirectory.setToken(new StringToken(_clustalWActor.getWorkingDir()));
		parameterForOutput.setToken(new StringToken("outfile"));

		// set port "importance"
		inputParameterName.setRequired(true);
		inputParameterValue.setRequired(true);
		outputParameterValue.setUseful(true);

		// inputParameterName, inputParameterValue and outputParameterValue names display
		new Parameter(inputParameterName, "_showName", BooleanToken.TRUE);
		new Parameter(inputParameterValue, "_showName", BooleanToken.TRUE);
		new Parameter(outputParameterValue, "_showName", BooleanToken.TRUE);
	}
	
   ///////////////////////////////////////////////////////////////////
   ////                     ports and parameters                  ////
	
	///////////////////////////////////////////////////////////////////
	////                    functional variables                   ////
	
   ///////////////////////////////////////////////////////////////////
   ////                         public methods                    ////

   /** Run ClustalW for Sequence Alignment.
    *  @exception IllegalActionException If it is thrown by the
    *   send() method sending out the token.
    */
   public void fire() throws IllegalActionException {
		super.fire();
   }
   
   /**
    * After the sequence alignment with ClustalW, the output file usually does not 
    * comply with the standard Nexus file format. Thus, a post execution process 
    * is need to fix the file format of the ClustalW output. This function reads in 
    * the ClustalW output file, finds the symbol lists that does not comply with 
    * the Nexus format, and removes the symbol list from the output file.
    */
   public void postExecutionProcess(String outputFileName) {
	   // Fix the ClustalW output
		File inFile = new File( outputFileName );
		try {
			CipresFile cfIn = new CipresFile(inFile.getAbsolutePath());
			// put the fixed output in a temp file
			CipresFile cfOut = new CipresFile(Globals.getInstance().getTempDir() + "ClustalWTempOutput.tmp");
			String content = cfIn.getContent();
			//find beginnning of symbols statement
			int pos1 = content.toLowerCase().indexOf("symbols");
			//find end of symbols statement (will be the 2nd quotation mark after "symbols")
			int pos2 = content.indexOf("\"", pos1);
			pos2 = content.indexOf("\"", pos2+1);
			if ( (pos1 != -1) && (pos2 != -1)) {		// need to fix
				String symbolsString  = content.substring(pos1, pos2);
				cfOut.fillFromString(content.substring(0,pos1) + 
					content.substring(pos1 + symbolsString.length() + 1, content.length()));
				// rename the fixed output file to the original ClustalW output file
				cfOut.copy(cfIn, false);
			}
		} catch (Exception ex) {
			System.out.println("Exception on fixing ClustalW's output Nexus file: ");
			ex.printStackTrace();
		}
   }
   
	/** Post fire the actor. Return false to indicated that the
	 *  process has finished. If it returns true, the process will
	 *  continue indefinitely.
	 */
	public boolean postfire() {
		return false;
	}	
	
	/** private variables
	 * _clustalWActor is an application information record that stores all the ClustalW-related information.
	 */
	private ActorInfo _clustalWActor;

}