//  $Id: StructureMapping.java,v 1.14 2004/04/08 23:55:07 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: StructureMapping.java,v $
//  Revision 1.14  2004/04/08 23:55:07  moreland
//  Updated copyright to new UCSD wording.
//
//  Revision 1.13  2004/01/30 02:07:37  moreland
//  Updated copyright and class block comments.
//
//  Revision 1.12  2003/12/08 21:48:48  moreland
//  Commented out old debug/print statement.
//
//  Revision 1.11  2003/04/24 00:38:30  moreland
//  Now uses the new object-based hierarchical StructureMap class and StructureComponents.
//
//  Revision 1.10  2003/03/10 22:56:17  moreland
//  Changed calls to reflect StructureMap get*AlphaIndex method name changes.
//  Added examples for coordinate bounds and coordinate average calculations.
//  Added examples for basic ligand traversal.
//
//  Revision 1.9  2003/02/21 23:03:10  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 1.8  2003/02/21 21:59:20  moreland
//  Added command line argument to set Status output level.
//
//  Revision 1.7  2003/02/03 21:56:10  moreland
//  Added support for MBT Status class to output run-time messages.
//
//  Revision 1.6  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 1.5  2003/01/18 00:25:51  agramada
//  Just added a print statement for debug purposes
//
//  Revision 1.4  2003/01/17 22:17:30  moreland
//  Added code to help debug problems in getTrailingAlphaAtomIndex and
//  getLeadingAlphaAtomIndex method index calculations.
//
//  Revision 1.3  2003/01/07 19:33:09  moreland
//  Added "Atom" to the StructureMap leading and trailing C-Alpha Atom index methods.
//
//  Revision 1.2  2002/12/21 00:27:11  moreland
//  Test to compare output of 3ebx.
//
//  Revision 1.1  2002/12/16 06:18:59  moreland
//  Added example to demonstrate the StructureMap class.
//
//  Revision 1.0  2002/10/24 17:24:22  moreland
//  First revision.
//


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

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


/**
 *  An example program which demonstrates the use of the StructureMap class.
 *  <P>
 *  @author	John L. Moreland
 */
public class StructureMapping
{
	/**
	 *  This the main application entry point for the example program.
	 */
	public static void main( String args[] )
	{
		//
		// Load a sample data set.
		//

		long millis; // Do some timing tests.
		millis = System.currentTimeMillis();

		Structure structure = null;
		for ( int i=0; i<args.length; i++ )
		{
			if ( args[i].equals( "-s" ) )
			{
				// Set the status level
				Status.setOutputLevel( args[++i] );
			}
			else 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 )
				{
					Status.output( Status.LEVEL_ERROR, e.toString() );
				}
			}
			else if ( args[i].equals( "-p" ) )
			{
				structure = StructureFactory.load( args[++i] );
			}
			else
			{
				Status.output( Status.LEVEL_ERROR, "Arguments:" );
				Status.output( Status.LEVEL_ERROR, "   -f ../data/5ebx.cif" );
				Status.output( Status.LEVEL_ERROR, "   -u ftp://beta.rcsb.org/pub/pdb/uniformity/data/mmCIF.gz/all/5ebx.cif.gz" );
				Status.output( Status.LEVEL_ERROR, "   -p 5ebx" );
				Status.output( Status.LEVEL_ERROR, "   -s STATUS_LEVEL_NAME" );
			}
		}

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

		millis = System.currentTimeMillis() - millis;
		Status.output( Status.LEVEL_DEBUG, "StructureMapping: load millis = " + millis );

		//
		// Create a StructureMap.
		//

		millis = System.currentTimeMillis();

		StructureMap structureMap = structure.getStructureMap( );

		millis = System.currentTimeMillis() - millis;
		Status.output( Status.LEVEL_DEBUG, "StructureMapping: map millis = " + millis );

		//
		// Print some StructureMap statistics.
		//

		double coordBounds[][] = structureMap.getAtomCoordinateBounds( );
		System.err.println( "StructureMapping: coordBounds = {" + coordBounds[0][0] + "," + coordBounds[0][1] + "," + coordBounds[0][2] + "} - {" + coordBounds[1][0] + "," + coordBounds[1][1] + "," + coordBounds[1][2] + "}" );

		double coordAverage[] = structureMap.getAtomCoordinateAverage( );
		System.err.println( "StructureMapping: coordAverage = {" + coordAverage[0] + "," + coordAverage[1] + "," + coordAverage[2] + "}" );

		int ligandCount = structureMap.getLigandCount( );
		System.err.println( "StructureMapping: ligandCount = " + ligandCount );

		//
		// Print the StructureMap internal tables.
		//

		// structureMap.print( );

		//
		// Print the StructureMap as a hierarchy.
		//

		int chainCount = structureMap.getChainCount( );
		System.err.println( "StructureMapping: chainCount=" + chainCount );
		for ( int c=0; c<chainCount; c++ )
		{
			Chain chain = structureMap.getChain( c );
			System.err.println( "StructureMapping: chain[" + c + "] = " + chain.getChainId() );
			int residueCount = chain.getResidueCount( );
			System.err.println( "StructureMapping:   residueCount = " + residueCount );
			for ( int r=0; r<residueCount; r++ )
			{
				Residue residue = chain.getResidue( r );
				System.err.println( "StructureMapping:    residue[" + r + "]" );
				Atom caAtom = residue.getAlphaAtom( );
				if ( caAtom != null )
				{
					System.err.println( "StructureMapping:         caAtom=" +    caAtom.coordinate[0] + "," + caAtom.coordinate[0] + "," + caAtom.coordinate[0] );
				}
				// else, its a residue with a Het Atom (no C-Alpha)
			}
		}
		System.err.println( "StructureMapping: end" );
	}
}