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The protein structure modules of BioJava.
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/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 *
 */

package org.biojava.nbio.structure.io.mmcif;

import org.biojava.nbio.structure.io.mmcif.model.ChemComp;

import java.util.HashMap;
import java.util.Map;

/** A representation of the Chemical Component Dictionary.
 *
 * @author Andreas Prlic
 * @since 1.7
 * @see link into mmCIF dictionary
 *
 */
public class ChemicalComponentDictionary {

	private Map dictionary;
	private Map replaces;
	private Map isreplacedby;

	public ChemicalComponentDictionary(){
		dictionary = new HashMap();
		replaces   = new HashMap();
		isreplacedby = new HashMap();
	}

	public boolean isReplaced(ChemComp c){
		return isReplaced(c.getId());

	}
	public boolean isReplaced(String id){
		if ( isreplacedby.containsKey(id))
			return true;
		return false;
	}
	public boolean isReplacer(ChemComp c){
		return isReplacer(c.getId());
	}
	public boolean isReplacer(String id){
		if ( replaces.containsKey(id) )
			return true;
		return false;
	}

	/** if ChemComp is replaced by another one, get the newer version
	 * otherwise return the same ChemComp again.
	 * @param c
	 * @return get the component that replaced ChemComp.
	 */
	public ChemComp getReplacer(ChemComp c){
		return getReplacer(c.getId());
	}
	public ChemComp getReplacer(String id){
		if (isReplaced(id)){
			return dictionary.get(isreplacedby.get(id));
		}
		return dictionary.get(id);
	}

	/** if ChemComp is replacing another one, get the old version
	 * otherwise return the same ChemComp again.
	 * @param  c the ChemComp for which older versions should be looked up.
	 */

	public ChemComp getReplaced(ChemComp c){
		return getReplaced(c.getId());
	}
	public ChemComp getReplaced(String id){
		if (isReplacer(id)){
			return dictionary.get(replaces.get(id));
		}
		return dictionary.get(id);
	}

	/** Get the parent of a component. If component has no parent, return null
	 *
	 * @param c
	 * @return get the parent component or null if ChemComp has no parent.
	 */
	public ChemComp getParent(ChemComp c){

		if (c.hasParent()){
			return dictionary.get(c.getMon_nstd_parent_comp_id());
		}
		return null;
	}



	/** add a new component to the dictionary
	 *
	 * @param comp
	 */
	public void addChemComp(ChemComp comp){

		dictionary.put(comp.getId(),comp);
		String rep = comp.getPdbx_replaces();
		if ( (rep != null) && ( ! rep.equals("?"))){
			replaces.put(comp.getId(),rep);
		}

		String isrep = comp.getPdbx_replaced_by();
		if ( (isrep != null) && ( ! isrep.equals("?"))){
			isreplacedby.put(comp.getId(),isrep);
		}
	}

	public ChemComp getChemComp(String id){
		return dictionary.get(id);
	}
}