//  $Id: Relations.java,v 1.7 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.
//
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//  or use for commercial purposes should contact the Technology Transfer &
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//  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.
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//  UNIVERSITY OF CALIFORNIA HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT,
//  UPDATES, ENHANCEMENTS, OR MODIFICATIONS. THE UNIVERSITY OF CALIFORNIA MAKES
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//
//  History:
//  $Log: Relations.java,v $
//  Revision 1.7  2004/04/08 23:55:07  moreland
//  Updated copyright to new UCSD wording.
//
//  Revision 1.6  2004/01/30 02:07:36  moreland
//  Updated copyright and class block comments.
//
//  Revision 1.5  2003/04/24 00:41:27  moreland
//  Updated to use the return-value version of structure.getStructureComponentByIndex.
//
//  Revision 1.4  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 1.3  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 1.2  2002/12/16 06:14:01  moreland
//  Changed code to support differentiation of Conformation into Coil, Helix,
//  Strand, and Turn sub-class types (at Eliot Clingman's suggestion).
//
//  Revision 1.1  2002/10/24 17:24:22  moreland
//  Added new example programs which adhear to the improved Structure API.
//
//


// Core
import java.io.File;
import java.net.*;
import java.lang.Integer;
import java.util.Hashtable;

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


/**
 *  An example program which demonstrates how to access
 *  related structure components. In this example, we walk through
 *  all of the Conformation objects and print each of their
 *  related Atom objects.
 *  <P>
 *  @author	John L. Moreland
 */
public class Relations
{
	/**
	 *  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() );
		}

		//
		// Walk the secondary structure conformation data (do just Helix),
		// and subsequently walk the corresponding Atom data.
		//

		// How many helix records are in this structure?
		int helixCount = structure.getStructureComponentCount(
			StructureComponentRegistry.TYPE_HELIX );

		// Allocate an Atom object as a container for our walk
		Atom atom = new Atom( );

		// Loop through the helix records
		for ( int conIndex=0; conIndex<helixCount; conIndex++ )
		{
			// Get the next Helix record
			Helix helix = (Helix) structure.getStructureComponentByIndex(
				StructureComponentRegistry.TYPE_HELIX, conIndex );

			System.err.println( "Helix chain = " + helix.start_chain + ", residue range = " + helix.start_residue + " - " + helix.end_residue );

			// Get an iterator to walk this Helix record's related
			// Atom set. The RELATION_CONFORMATION_ATOMS relation describes
			// atoms that fall within a Helix record's start and end
			// residue numbers.
			StructureComponentIterator relations =
				structure.getStructureComponentRelations(
					StructureComponentRegistry.RELATION_CONFORMATION_ATOMS,
					helix );

			// Are there more related Atom records?
			while ( relations.hasMore() )
			{
				int index = relations.nextIndex();
				relations.next( atom );
				if ( atom.name.equalsIgnoreCase( "CA" ) )
				{
					System.err.println( "atom" +
						", index = " + index +
						", name = " + atom.name +
						", chain_id = " + atom.chain_id +
						", residue_id = " + atom.residue_id +
						", coord = " + atom.coordinate[0] + " " +
						atom.coordinate[1] + " " + atom.coordinate[2] );
				}
			}
		}
	}
}