//  $Id: Conformation.java,v 1.1 2006/05/20 17:02:06 Sasha Buzko Exp $
//
//  Copyright (c) 2000-2002  San Diego Supercomputer Center (SDSC),
//  a facility operated jointly by the University of California,
//  San Diego (UCSD) and General Atomics, San Diego, California, USA.
//
//  Users and possessors of this source code are hereby granted a
//  nonexclusive, royalty-free copyright and design patent license to
//  use this code in individual software.  License is not granted for
//  commercial resale, in whole or in part, without prior written
//  permission from SDSC.  This source is provided "AS IS" without express
//  or implied warranty of any kind.
//
//  For further information, please see:  http://mbt.sdsc.edu
//
//  History:
//  $Log: Conformation.java,v $
//  Revision 1.1  2006/05/20 17:02:06  Sasha Buzko
//  Updated version
//
//  Revision 1.1  2006/04/30 20:14:05  Sasha Buzko
//  New version of the app
//
//  Revision 1.1  2006/04/15 19:42:28  Sasha Buzko
//  Initial commit
//
//  Revision 1.1  2005/11/13 04:35:27  Administrator
//  *** empty log message ***
//
//  Revision 1.5  2003/04/25 00:57:02  moreland
//  Changed TYPE_UNDEFINED string value so it is more intuitive.
//
//  Revision 1.4  2003/04/24 17:12:55  moreland
//  Added an "undefined" conformation type string in order to support
//  secondary structure conformation fragment assignments in the Chain class.
//
//  Revision 1.3  2003/04/23 17:22:06  moreland
//  Removed unused constructor.
//
//  Revision 1.2  2002/12/16 06:24:41  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 17:54:01  moreland
//  Provides implementation for the improved Structure API/implementation.
//
//  Revision 1.1.1.1  2002/07/16 18:00:18  moreland
//  Imported sources
//
//  Revision 1.0  2002/06/10 23:38:39  moreland
//


package edu.sdsc.mbt;


/**
 *  Implements a an abstract StructureComponent container for conformation
 *  (secondary structure) data.
 *  <P>
 *  See the "PROGRAMMING NOTE" section of the StructureComponent class.
 *  <P>
 *  @see edu.sdsc.mbt.Atom
 *  @see edu.sdsc.mbt.Structure
 *  @see edu.sdsc.mbt.StructureComponent
 *  @see edu.sdsc.mbt.StructureComponentIterator
 *  @see edu.sdsc.mbt.util.AminoAcidInfo
 *  <P>
 *  @author John L. Moreland
 */
public abstract class Conformation
	extends StructureComponent
	implements java.lang.Cloneable, java.io.Serializable
{
	/**
	 *  If a residue conformation / chain fragment type is not defined, use this value.
	 *  That is, assign this value when secondary structure has not been assigned.
	 */
	public static final String TYPE_UNDEFINED = "UNDEFINED_CONFORMATION";

	//
	// StructureComponent methods
	//

	/**
	 *  Copy all of the field values from the parameter object into "this".
	 */
	public void copy( StructureComponent structureComponent )
	{
		Conformation conformation = (Conformation) structureComponent;
		name           = conformation.name;
		start_compound = conformation.start_compound;
		start_chain    = conformation.start_chain;
		start_residue  = conformation.start_residue;
		end_compound   = conformation.end_compound;
		end_chain      = conformation.end_chain;
		end_residue    = conformation.end_residue;
	}

	/**
	 *  Clone this object.
	 */
	public Object clone( )
		throws CloneNotSupportedException
	{
		return super.clone( );
	}

	/**
	 *  This method returns the fully qualified name of this class.
	 *  <P>
	 *  This name is used by the StructureComponentRegistry class to enable
	 *  dynamic registration and discovery of new StructureComponent
	 *  sub-classes/types. The name is also used to create a unique integer
	 *  indentifier for each type in order to make run-time type comparisons
	 *  fast.
	 */
	private static String className = null;
	public static String getClassName()
	{
		if ( className == null )
		className = ((new Throwable()).getStackTrace())[0].getClassName();
		return className;
	}

	//
	// Conformation fields
	//

	/**
	 *  For example, "helix_BA", "turn_1A"
	 */
	public String name = null;

	/**
	 *  For example, "ALA", "GLU", "LYS", etc.
	 */
	public String start_compound = null;

	/**
	 *  This value corresponds to the start Atom.chain_id value.
	 *  For example, "A", "B", "D", etc.
	 */
	public String start_chain = null;

	/**
	 *  This value corresponds to the Atom.residue_id value.
	 *  For example, 22, 27, etc.
	 */
	public int start_residue = -1;

	/**
	 *  For example, "ALA", "GLU", "LYS", etc.
	 */
	public String end_compound = null;

	/**
	 *  This value corresponds to the end Atom.chain_id value.
	 *  For example, "A", "B", "D", etc.
	 */
	public String end_chain = null;

	/**
	 *  This value corresponds to the end Atom.residue_id value.
	 *  For example, 27, 137, etc.
	 */
	public int end_residue = -1;
	
	
	private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException {
		out.defaultWriteObject();               
	}
	private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, ClassNotFoundException {
		in.defaultReadObject();
	} 

}