//  $Id: Stats.java,v 1.8 2004/04/08 23:55:07 moreland Exp $
//
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//  Molecular Biology Toolkit (MBT)
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//  History:
//  $Log: Stats.java,v $
//  Revision 1.8  2004/04/08 23:55:07  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  2003/12/09 21:14:40  moreland
//  Fixed print format typo.
//
//  Revision 1.5  2003/04/25 14:52:20  moreland
//  Now gets StructureMap from the Structure objects (instead of new).
//
//  Revision 1.4  2003/04/25 01:01:11  moreland
//  Added code to print out fragment ranges and types.
//
//  Revision 1.3  2003/04/24 18:01:55  moreland
//  Updated to use new fragment mechanism in the Chain class.
//
//  Revision 1.2  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 1.1  2003/01/27 22:32:51  moreland
//  Added statistics generation example.
//
//  Revision 1.0  2003/01/27 20:45:18  moreland
//  First revision.
//


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

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


/**
 *  An example program which gathers statistics about a structure.
 *  <P>
 *  @author	John L. Moreland
 */
public class Stats
{
	/**
	 *  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() );
		}

		//
		// Generate statistics about the raw data.
		//

		int atomCount = structure.getStructureComponentCount( StructureComponentRegistry.TYPE_ATOM );
		System.err.println( "Stats: atomCount = " + atomCount );

		int helixCount = structure.getStructureComponentCount( StructureComponentRegistry.TYPE_HELIX );
		System.err.println( "Stats: helixCount = " + helixCount );
		int turnCount = structure.getStructureComponentCount( StructureComponentRegistry.TYPE_TURN );
		System.err.println( "Stats: turnCount = " + turnCount );
		int strandCount = structure.getStructureComponentCount( StructureComponentRegistry.TYPE_STRAND );
		System.err.println( "Stats: strandCount = " + strandCount );

		double maxX=0.0, minX=0.0, maxY=0.0, minY=0.0, maxZ=0.0, minZ=0.0;
		for ( int i=0; i<atomCount; i++ )
		{
			Atom atom = (Atom) structure.getStructureComponentByIndex(
				StructureComponentRegistry.TYPE_ATOM, i );
			if ( i == 0 )
			{
				maxX = atom.coordinate[0];
				minX = atom.coordinate[0];
				maxY = atom.coordinate[1];
				minY = atom.coordinate[1];
				maxZ = atom.coordinate[2];
				minZ = atom.coordinate[2];
			}
			if ( atom.coordinate[0] >= maxX ) maxX = atom.coordinate[0];
			if ( atom.coordinate[0] <= minX ) minX = atom.coordinate[0];
			if ( atom.coordinate[1] >= maxY ) maxY = atom.coordinate[1];
			if ( atom.coordinate[1] <= minY ) minY = atom.coordinate[1];
			if ( atom.coordinate[2] >= maxZ ) maxZ = atom.coordinate[2];
			if ( atom.coordinate[2] <= minZ ) minZ = atom.coordinate[2];
		}
		System.err.println( "Stats: coordinate range = ( " +
			minX + ", " + minY + ", " + minZ + " ) - ( " +
			maxX + ", " + maxY + ", " + maxZ + " )"
		);

		//
		// Generate statistics about the StructureMap.
		//

		StructureMap structureMap = structure.getStructureMap( );

		int chainCount = structureMap.getChainCount( );
		System.err.println( "Stats: chainCount = " + chainCount );
		System.err.println( "Stats: residueCount = "
			+ structureMap.getResidueCount( ) );

		for ( int c=0; c<chainCount; c++ )
		{
			Chain chain = structureMap.getChain( c );
			int fragmentCount = chain.getFragmentCount( );
			System.err.println( "Stats: chain[" + c + "] has " + fragmentCount + " fragments." );
			for ( int f=0; f<fragmentCount; f++ )
			{
				String type = chain.getFragmentType( f );
				int start = chain.getFragmentStartResidue( f );
				int end = chain.getFragmentEndResidue( f );
				System.err.println( "Stats:    fragment[" + f + "] = { type=" + type + ", start=" + start + ", end=" + end + " }" );
			}
		}

	}
}