//  $Id: PrintDynamic.java,v 1.6 2004/04/08 23:55:06 moreland Exp $
//
//  Copyright 2000-2004 The Regents of the University of California.
//  All Rights Reserved.
//
//  Permission to use, copy, modify and distribute any part of this
//  Molecular Biology Toolkit (MBT)
//  for educational, research and non-profit purposes, without fee, and without
//  a written agreement is hereby granted, provided that the above copyright
//  notice, this paragraph and the following three paragraphs appear in all
//  copies.
//
//  Those desiring to incorporate this MBT into commercial products
//  or use for commercial purposes should contact the Technology Transfer &
//  Intellectual Property Services, University of California, San Diego, 9500
//  Gilman Drive, Mail Code 0910, La Jolla, CA 92093-0910, Ph: (858) 534-5815,
//  FAX: (858) 534-7345, E-MAIL:invent@ucsd.edu.
//
//  IN NO EVENT SHALL THE UNIVERSITY OF CALIFORNIA BE LIABLE TO ANY PARTY FOR
//  DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING
//  LOST PROFITS, ARISING OUT OF THE USE OF THIS MBT, EVEN IF THE
//  UNIVERSITY OF CALIFORNIA HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
//  THE MBT PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE
//  UNIVERSITY OF CALIFORNIA HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT,
//  UPDATES, ENHANCEMENTS, OR MODIFICATIONS. THE UNIVERSITY OF CALIFORNIA MAKES
//  NO REPRESENTATIONS AND EXTENDS NO WARRANTIES OF ANY KIND, EITHER IMPLIED OR
//  EXPRESS, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
//  MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, OR THAT THE USE OF THE
//  MBT WILL NOT INFRINGE ANY PATENT, TRADEMARK OR OTHER RIGHTS.
//
//  For further information, please see:  http://mbt.sdsc.edu
//
//  History:
//  $Log: PrintDynamic.java,v $
//  Revision 1.6  2004/04/08 23:55:06  moreland
//  Updated copyright to new UCSD wording.
//
//  Revision 1.5  2004/01/30 02:07:36  moreland
//  Updated copyright and class block comments.
//
//  Revision 1.4  2003/04/24 00:31:52  moreland
//  Updated to use the object-based hierarchical StructureMap and StructureComponent objects.
//
//  Revision 1.3  2003/02/21 23:03:09  moreland
//  Changed example URL load -u command line option to point to beta repository:
//  ftp://beta.rcsb.org/pub/pdb/uniformity/data/mmCIF.gz/all/5ebx.cif.gz
//
//  Revision 1.2  2003/01/27 20:45:18  moreland
//  Added code to example programs in order to support standardized command
//  line arguments for data-set loading from files, URLs or PDB-ID codes.
//
//  Revision 1.1  2002/10/24 17:24:22  moreland
//  Added new example programs which adhear to the improved Structure API.
//
//  Revision 1.1.1.1  2002/07/16 18:00:15  moreland
//  Imported sources
//
//  Revision 1.0  2002/06/10 23:38:39  moreland
//


// Core
import java.util.*;
import java.io.*;
import java.net.*;

// MBT
import edu.sdsc.mbt.*;
import edu.sdsc.mbt.io.*;
import edu.sdsc.mbt.util.*;


/**
 *  An example program which demonstrates how to load any structure using
 *  the StructureFactory class and then dynamically process all data types
 *  available in that structure using the StructureComponentRegistry class.
 *  <P>
 *  @author	John L. Moreland
 */
public class PrintDynamic
{
	/**
	 *  This the main application entry point for the example program.
	 */
	public static void main( String args[] )
	{
		//
		// Load a sample data set.
		//

		Structure structure = null;
		for ( int i=0; i<args.length; i++ )
		{
			if ( args[i].equals( "-f" ) )
			{
				structure = StructureFactory.load( new File( args[++i] ) );
			}
			else if ( args[i].equals( "-u" ) )
			{
				try
				{
					structure = StructureFactory.load( new URL( args[++i] ) );
				}
				catch ( MalformedURLException e )
				{
					System.err.println( e );
				}
			}
			else if ( args[i].equals( "-p" ) )
			{
				structure = StructureFactory.load( args[++i] );
			}
			else
			{
				System.err.println( "You must specify a structure data set:" );
				System.err.println( "   -f ../data/5ebx.cif" );
				System.err.println( "   -u ftp://beta.rcsb.org/pub/pdb/uniformity/data/mmCIF.gz/all/5ebx.cif.gz" );
				System.err.println( "   -p 5ebx" );
			}
		}

		if ( structure == null )
		{
			System.err.println( "Sorry, the Structure load failed." );
			System.exit( 1 );
		}
		else
		{
			System.err.println( "dataset = " + structure.getUrlString() );
		}

		//
		// Print all of the data
		//

		// Ask the StructureComponentRegistry for the set of currently
		// registered StructureComponent types.
		Enumeration scNames = StructureComponentRegistry.getTypeNames();

		// Iterate through all registered StructureComponent types
		String scName = null;
		while ( scNames.hasMoreElements() )
		{
			System.err.println( "------------------------------" );
			scName = (String) scNames.nextElement();
			System.err.println( "scName = " + scName );

			// See if the structure has any objects of this type
			int scCount = structure.getStructureComponentCount( scName );
			System.err.println( "scCount = " + scCount );

			// Dynamically create an appropriate StructureComponent object.
			StructureComponent structureComponent = null;
			try {
				structureComponent = (StructureComponent)
					Class.forName(scName).newInstance();
			} catch ( Exception e ) { continue; }

			// Iterate through all the StructureComponents
			for ( int i=0; i<scCount; i++ )
			{
				structureComponent = structure.getStructureComponentByIndex(
					scName, i );
				System.err.println( "structureComponent = " + structureComponent );
			}
		}
	}
}