/* PAUPConsensusTrees actor calls PAUP for finding consensus trees.
 *
 * 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;

import ptolemy.kernel.CompositeEntity;
import ptolemy.kernel.util.*;
import ptolemy.data.IntToken;
import ptolemy.data.BooleanToken;
import ptolemy.data.StringToken;
import ptolemy.data.expr.Parameter;

import org.cipres.helpers.GUIRun;
import org.cipres.kepler.registry.ActorInfo;
import org.cipres.kepler.registry.CipresKeplerRegistry;
import org.cipres.kepler.registry.Globals;
import org.cipres.util.CipresFile;
//////////////////////////////////////////////////////////////////////////
////PAUPConsensusTrees
/**
 * This actor calls PAUP to find consensus trees for a group of trees.
 * 
 * @author Zhijie Guan, Alex Borchers
 * @version $Id: $
*/

public class PAUPConsensusTrees extends GUIRunCIPRes {

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

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

		// get program information
		CipresKeplerRegistry registry = Globals.getInstance().getRegistry();
		_paupActor = registry.getActor("ConsensusTree_Paup");

		// set program related information
		command.setToken( new StringToken(_paupActor.getAppPath()) );
		uiXMLFile.setToken( new StringToken(_paupActor.getGuiXmlFile()) );
		outputFile.setToken( new StringToken(registry.getDefaultStdOutDir() + "PAUPConsensusOut.log") );
		errorFile.setToken( new StringToken(registry.getDefaultStdOutDir() + "PAUPConsensusError.log") );
		workingDirectory.setToken( new StringToken(_paupActor.getWorkingDir()) );
		parameterForOutput.setToken( new StringToken("outfile") );

		paupCmdFile = new Parameter(this, "paupCmdFile", new StringToken(""));
		paupCmdFile.setToken(new StringToken(registry.getDefaultStdOutDir() + "paup_consensus_cmds.nex"));
		paupCmdFile.setDisplayName("PAUP Command File Name");
		paupCmdFile.setVisibility(Settable.EXPERT);

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

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

    /** The parameter for PAUP command file.  This parameter will be set to String.
     */
	public Parameter paupCmdFile;
	
	///////////////////////////////////////////////////////////////////
	////                    functional variables                   ////
	
    ///////////////////////////////////////////////////////////////////
    ////                         public methods                    ////

    /** Run PAUP for finding consensus trees.
     *  @exception IllegalActionException If it is thrown by the
     *   send() method sending out the token.
     */
    public void fire() throws IllegalActionException {

		if ( inputParameterValue.hasToken(0) && inputParameterName.hasToken(0) ) {
			try {				
				GUIRun grun = new GUIRun("PAUP Consensus Trees");
				
				grun.setUseShell(true);
				
				//		if (command.hasToken(0)) {
				grun.setExecutable( ((StringToken)command.getToken()).stringValue() );
				//		}
				
				//		if (uiXMLFile.hasToken(0)) {
				grun.setUIXMLFile( ((StringToken)uiXMLFile.getToken()).stringValue() );
				//		}
				
				//		if (outputFile.hasToken(0)) {
				grun.setOutputFilename( ((StringToken)outputFile.getToken()).stringValue() );
				//		} 
				
				//		if (errorFile.hasToken(0)) {
				grun.setErrorFilename( ((StringToken)errorFile.getToken()).stringValue() );
				//		}
				
				//		if (workingDirectory.hasToken(0)) {
				grun.setWorkingDirPath( ((StringToken)workingDirectory.getToken()).stringValue() );
				//		}
				
				
				grun.setArgumentValue( ((StringToken)inputParameterName.get(0)).stringValue(), ((StringToken)inputParameterValue.get(0)).stringValue() );
				
				grun.setArgumentsWithGUIGen();
				
				// outfile is the file that user assigned for PAUP output
				// infile is the file that user assigned for PAUP input
				File outfile =  new File(grun.getArgumentValue("outfile"));
				File infile = new File(grun.getArgumentValue("infile"));
				
				//this command has paup:
				//1. import input and write to output
				//2. execute contree and append trees to output
				final StringBuilder commands = new StringBuilder();

				commands.append("EXECUTE ");
				commands.append(infile.getAbsolutePath());
				commands.append("; EXPORT File=");
				commands.append(outfile.getAbsolutePath());
				commands.append(" FORMAT = NEXUS TREES=NO REPLACE=YES; CLEARTREES NOWARN=YES; SET WARNRESET=NO; ");

				final String[] grunArgs = grun.getArguments();

				for (int i = 0 ; i < grunArgs.length ; i++) {
					commands.append(" ");
					commands.append(grunArgs[i]);
				}

				commands.append(" TreeFile =");
				commands.append(outfile.getAbsolutePath());
				commands.append(" APPEND=YES;");

				String[] paupCmdFileName = { ((StringToken)paupCmdFile.getToken()).stringValue() };
				CipresFile cmdFile = new CipresFile(paupCmdFileName[0]);
				cmdFile.fillFromString("#NEXUS\nBEGIN PAUP;\n" + commands.toString() + " QUIT;\nEND;");	
				
				grun.setArguments(paupCmdFileName);
				
				grun.setWaitForExecution(true);
				
				grun.execute();
				
				exitCode.send(0, new IntToken(grun.getExitCode()));
				
				standardOutput.send(0, new StringToken(grun.getStandardOutput()));
				standardError.send(0, new StringToken(grun.getStandardError()));
				
				outputParameterValue.send(0, new StringToken( grun.getArgumentValue( ((StringToken)parameterForOutput.getToken()).stringValue() ) ) );
			} catch (Exception e) {
				e.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
	 *  _paupActor records program information for PAUP.
	 */
	private ActorInfo _paupActor;

}