//  $Id: Fragments.java,v 1.9 2004/05/13 16:05:15 moreland Exp $
//
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//  Molecular Biology Toolkit (MBT)
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//  History:
//  $Log: Fragments.java,v $
//  Revision 1.9  2004/05/13 16:05:15  moreland
//  Now prints compound code for each residue line.
//
//  Revision 1.8  2004/04/08 23:55:06  moreland
//  Updated copyright to new UCSD wording.
//
//  Revision 1.7  2004/01/30 02:07:36  moreland
//  Updated copyright and class block comments.
//
//  Revision 1.6  2004/01/30 01:57:51  moreland
//  Corrected fetching/index bug.
//
//  Revision 1.5  2004/01/14 18:35:54  moreland
//  Added code to print the global residue indexes to show the difference
//  compared to chain-relative residue indexes.
//
//  Revision 1.4  2003/07/21 20:52:49  moreland
//  Now uses new Fragment StructureComponent object.
//
//  Revision 1.3  2003/04/25 17:06:24  moreland
//  Changed a break to a continue so UNDEFINED fragments are not skipped.
//
//  Revision 1.2  2003/04/25 16:41:45  moreland
//  Added code to check for Conformation.TYPE_UNDEFINED type fragments.
//
//  Revision 1.1  2003/04/25 15:12:43  moreland
//  First revision.
//
//  Revision 1.0  2003/01/27 20:45:18  moreland
//  First version.
//


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

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


/**
 *  An example program which walks chains-fragments-residues-atoms in order
 *  to simulate the procesing of the secondary structure map.
 *  <P>
 *  @author	John L. Moreland
 */
public class Fragments
{
	/**
	 *  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 chains-fragments-residues-atoms and print type+color.
		//

		StructureMap structureMap = structure.getStructureMap( );
		StructureStyles structureStyles = structureMap.getStructureStyles( );
		float color[] = new float[3];

		// Walk the chains
		int chainCount = structureMap.getChainCount( );
		System.err.println( "Fragments: structure has " + chainCount + " chains." );
		int residueCount = structureMap.getResidueCount( );
		System.err.println( "Fragments: structure has " + residueCount + " residues." );
		for ( int c=0; c<chainCount; c++ )
		{
			Chain chain = structureMap.getChain( c );
			int fragmentCount = chain.getFragmentCount( );
			System.err.println( "Fragments: chain[" + c + "] has " + fragmentCount + " fragments." );

			// Walk the secondary structure fragments of this chain
			for ( int f=0; f<fragmentCount; f++ )
			{
				Fragment fragment = chain.getFragment( f );
				String type = fragment.getConformationType( );
				int start = fragment.getStartResidueIndex( );
				int end = fragment.getEndResidueIndex( );

				// Look up the global residue indexes for the fragment
				Residue residueA = chain.getResidue( start );
				Residue residueB = chain.getResidue( end );
				int globalStart = structureMap.getResidueIndex( residueA );
				int globalEnd = structureMap.getResidueIndex( residueB );

				System.err.println( "Fragments:    fragment[" + f + "] = { " +
					"type=" + type +
					", chainResidues=" + start + "-" + end +
					", globalResidues=" + globalStart + "-" + globalEnd +
					" }"
				);

				// Skip fragments that are not defined (they should be gaps).
				if ( type == Conformation.TYPE_UNDEFINED )
					continue;

				// Walk the residues of this fragment.
				for ( int r=start; r<=end; r++ )
				{
					Residue residue = chain.getResidue( r );
					structureStyles.getResidueColor( residue, color );
					System.err.println( "Fragments:       residue[" + r +
						"] = { color=" +
						color[0] + "," + color[1] + "," + color[2] + " } : "
						+ residue.getCompoundCode()
					);

					// Get the alpha atom of this residue.
					Atom atom = residue.getAlphaAtom( );
					System.err.println( "Fragments:          alpha atom = { " +
						"coordinate=" + atom.coordinate[0] + "," +
						atom.coordinate[1] + "," + atom.coordinate[2] + " }"
					);
				}
			}
		}
	}
}