/* SubsetChooserActor actor reads the phylodataset from the input file,
 * lists each entities in a dialog box, facilitates the user to choose
 * a subset of the entities for the next step analysis, and outputs the
 * selected entities into another phylodataset as output files.
 *
 * 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 ptolemy.actor.TypedAtomicActor;
import ptolemy.kernel.CompositeEntity;
import ptolemy.kernel.util.*;
import ptolemy.actor.TypedIOPort;
import ptolemy.data.BooleanToken;
import ptolemy.data.StringToken;
import ptolemy.data.type.BaseType;
import ptolemy.data.expr.FileParameter;
import ptolemy.data.expr.Parameter;
import ptolemy.data.expr.StringParameter;

import org.cipres.CipresIDL.api1.DataMatrix;
import org.cipres.CipresIDL.api1.Tree;
import org.cipres.datatypes.PhyloDataset;
import org.cipres.kepler.DisplayObject;
import org.cipres.kepler.SubsetChooser;
import org.cipres.kepler.registry.CipresKeplerRegistry;
import org.cipres.kepler.registry.Globals;


import java.io.File;

import javax.swing.JOptionPane;


//////////////////////////////////////////////////////////////////////////
////SubsetChooserActor
/**
* This actor reads the input file, generates the entities list, facilitates 
* the user to choose a subset of entities, and stores the selected entities
* into an output file.
* 
* @author Alex Borchers, Zhijie Guan  
* @version $Id: $
*/

public class SubsetChooserActor extends TypedAtomicActor {

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

   /** Construct SubsetChooserActor 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 SubsetChooserActor(CompositeEntity container, String name)
           throws NameDuplicationException, IllegalActionException  {
	   super(container, name);
       
	   inputFileName = new TypedIOPort(this, "Subset Chooser Input File", true, false);
	   inputFileName.setTypeEquals(BaseType.STRING);
		
	   outputFileName = new TypedIOPort(this, "Selected entities file", false, true);
       // Set the type constraint.
       outputFileName.setTypeEquals(BaseType.STRING);

       outputFileDefaultName = new FileParameter(this, "Output File Path and Name");

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

       // set the type parameter of the subset chooser
       type = new StringParameter(this, "type");
       for (int i=0; i< typeOptions.length; i++) {
    	   		type.addChoice(typeOptions[i]);
       }
       type.setExpression(typeOptions[0]);

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

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

   /** The input file name is received from this port.
    */
	public TypedIOPort inputFileName = null;

	/** The output file name is sent out through this port.
	 */
	public TypedIOPort outputFileName = null;
	
	/** The file name parameter, which defines the default output file name.
	 */
    public FileParameter outputFileDefaultName = null;
	
    /** The type of the subset chooser, which defines the type of the entities 
     * that the user can choose from.
     * Currently the type is either the tree or the taxa.
     */
    public StringParameter type=null;
    
	///////////////////////////////////////////////////////////////////
	////                    functional variables                   ////
	
   ///////////////////////////////////////////////////////////////////
   ////                         public methods                    ////

   /** Choose a subset from the displayed objects.
    *  @exception IllegalActionException If it is thrown by the
    *   send() method sending out the token.
    */
   public void fire() throws IllegalActionException {
		super.fire();

		if (inputFileName.hasToken(0)) {
			try {
				String typeChosed = type.getExpression();
				
				// check if the user set a valid value for the type
				int typeIndex = 0;
				while ( (typeIndex<typeOptions.length) && (!typeChosed.equalsIgnoreCase(typeOptions[typeIndex])) )  
						typeIndex++;
				if (typeIndex==typeOptions.length)		// no match in typeOptions, the user sets an invalid value
					typeChosed = typeOptions[0];			// reset the value to the default choice type, which is the first type
				
				if (typeChosed.equalsIgnoreCase("taxa")) {			// choose from trees
	
					PhyloDataset pdIn = new PhyloDataset();
//					System.out.println(inputFileName.hasToken(0));
					StringToken inFileName = (StringToken)inputFileName.get(0);
					File inputNexusFile = new File(inFileName.stringValue());
					pdIn.initialize(inputNexusFile);
	
					if (pdIn.getTaxaInfo() == null) {
						JOptionPane.showMessageDialog(null,
								"There are no taxa to subset");
					}
	
					DisplayObject[] displayObjects = new DisplayObject[pdIn
							.getTaxaInfo().length];
					for (int i = 0; i < pdIn.getTaxaInfo().length; i++) {
						displayObjects[i] = new DisplayObject(new Integer(i), pdIn
								.getTaxaInfo()[i]);
					}
	
					SubsetChooser sc = new SubsetChooser(displayObjects);
					DisplayObject[] displayObjectsSubset = sc
							.showSubsetChooserAsDialog();
	
					// create new PhyloDataset comprised of the subset and write it
					// to nexus file
					PhyloDataset pdOut;
					DataMatrix dmIn = pdIn.getDataMatrix();
					DataMatrix dmOut = new DataMatrix();
					String[] taxa = new String[displayObjectsSubset.length];
					short[][] matrix = new short[displayObjectsSubset.length][pdIn
							.getDataMatrix().m_numCharacters];
					Integer jInt;
					int j = 0;
					for (int i = 0; i < displayObjectsSubset.length; i++) {
						jInt = (Integer) displayObjectsSubset[i].getObject();
						j = jInt.intValue();
						taxa[i] = pdIn.getTaxaInfo()[j];
						for (int k = 0; k < dmIn.m_matrix[0].length; k++) {
							matrix[i][k] = dmIn.m_matrix[j][k];
						}
					}
	
					dmOut.m_matrix = matrix;
					dmOut.m_symbols = dmIn.m_symbols;
					dmOut.m_charStateLookup = dmIn.m_charStateLookup;
					dmOut.m_datatype = dmIn.m_datatype;
					dmOut.m_numCharacters = dmIn.m_numCharacters;
					dmOut.m_numStates = dmIn.m_numStates;
					dmOut.m_charStateLookup = dmIn.m_charStateLookup;
	
					pdOut = new PhyloDataset(dmOut, pdIn.getTrees(), taxa);
	
					String outFileName = ((StringToken) outputFileDefaultName
							.getToken()).stringValue();
					if (outFileName.length() == 0) {			// the user did not set the default output file name
						CipresKeplerRegistry registry = Globals.getInstance().getRegistry();
						outFileName = registry.getDefaultStdOutDir() + "SubsetChooser.out";
					}
					File outputNexusFile = new File(outFileName);
	
					pdOut.writeToNexus(outputNexusFile, null, null, PhyloDataset.WRITE_DEFAULT, true);
					outputFileName.send(0, new StringToken(outFileName));
				} else if (typeChosed.equalsIgnoreCase("trees")) {
					
					PhyloDataset pdIn = new PhyloDataset();
					StringToken inFileName = (StringToken)inputFileName.get(0);
					File inputNexusFile = new File(inFileName.stringValue());
					pdIn.initialize(inputNexusFile);
					
					if(pdIn.getTrees()==null){
						JOptionPane.showMessageDialog(null, "There are no trees to subset");
					}
					
					DisplayObject[] displayObjects = new DisplayObject[pdIn.getTrees().length];
					Tree tree = null;
					String treeName;
					int j;
					for (int i = 0; i < pdIn.getTrees().length; i++) {
						tree = pdIn.getTrees()[i];
						if(tree.m_name==null || tree.m_name.trim().length()==0){
							j = i + 1;
							treeName = "Tree" + j;
						}
						else {
							treeName = tree.m_name;
						}			
						displayObjects[i] = new DisplayObject(new Integer(i), treeName);
					}

					SubsetChooser sc = new SubsetChooser(displayObjects);
					DisplayObject[] displayObjectsSubset = sc.showSubsetChooserAsDialog();

					// create new PhyloDataset comprised of the subset and write it to nexus
					PhyloDataset pdOut;
					Integer jInt;
					Tree[] treesOut = new Tree[displayObjectsSubset.length];
					for (int i = 0; i < displayObjectsSubset.length; i++) {
						jInt = (Integer) displayObjectsSubset[i].getObject();
						j = jInt.intValue();
						treesOut[i] = pdIn.getTrees()[j];
					}


					pdOut = new PhyloDataset(pdIn.getDataMatrix(), treesOut, pdIn.getTaxaInfo());
					
					String outFileName = ((StringToken) outputFileDefaultName
							.getToken()).stringValue();
					if (outFileName.length() == 0) {			// the user did not set the default output file name
						CipresKeplerRegistry registry = Globals.getInstance().getRegistry();
						outFileName = registry.getDefaultStdOutDir() + "SubsetChooser.out";
					}
					File outputNexusFile = new File(outFileName);
	
					pdOut.writeToNexus(outputNexusFile, null, null, PhyloDataset.WRITE_DEFAULT, true);
					outputFileName.send(0, new StringToken(outFileName));
					
				}
			} catch (Exception e) {
				System.out.println("Exception on Subset Chooser: ");
				e.printStackTrace();
			}
		}
	}
   
   /** The options of the type. 
    * Currently this actor can only support choose from trees or taxa.
    */
   private String [] typeOptions = {"trees", "taxa"};
   
   public boolean postfire() {
		return false;
   }

}