/*
 *                    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/
 *
 *
 * Author: Andreas Prlic
 *
 */
package org.biojava.nbio.structure.domain;

import org.biojava.nbio.structure.*;
import org.biojava.nbio.structure.domain.pdp.*;

import java.util.List;


/** Protein Domain Parser is a an algorithm that attempts at assigning domains for 3D protein structures.
 * Since domains in proteins are difficult to define, results detected by automated algorithms have to be taken with a grain of salt.
 *
 *   see<pre>
J Mol Biol. 2004 Jun 4;339(3):647-78.

Toward consistent assignment of structural domains in proteins.

Veretnik S, Bourne PE, Alexandrov NN, Shindyalov IN.
</pre>

 * This implementation is based on a Java port of the PDP algorithm, as described in:
 *
 *
 * @author Andreas Prlic
 * @since 3.0.2
 */
public class LocalProteinDomainParser {


	/** make sure this class can only get accessed via the static method calls
	 *
	 */
	private LocalProteinDomainParser(){

	}

	/** Suggest domains for a protein structure
	 *
	 * @param s the protein structure
	 * @return a list of possible domains
	 * @throws StructureException
	 */
	public static List<Domain> suggestDomains(Structure s) throws StructureException{

		Atom[] ca = StructureTools.getRepresentativeAtomArray(s);

		return suggestDomains(ca);
	}


	/** Suggest domains for a set of Calpha atoms
	 *
	 * @param ca an array of Calpha atoms
	 * @return a list of possible domains
	 * @throws StructureException
	 */
	public static List<Domain> suggestDomains(Atom[] ca) throws StructureException{

		GetDistanceMatrix distMaxCalculator = new GetDistanceMatrix();

		PDPDistanceMatrix pdpMatrix = distMaxCalculator.getDistanceMatrix(ca);



		Domain dom = new Domain();
		Chain c = ca[0].getGroup().getChain();
		dom.setId("D"+c.getStructure().getPDBCode()+c.getId()+"1");
		dom.setSize(ca.length);
		dom.setNseg(1);
		dom.getSegmentAtPos(0).setFrom(0);
		dom.getSegmentAtPos(0).setTo(ca.length-1);

		CutSites cutSites = new CutSites();

		// Do the initial splitting
		CutDomain cutDomain = new CutDomain(ca,pdpMatrix);
		cutDomain.cutDomain(dom, cutSites, pdpMatrix);
		List<Domain> domains =  cutDomain.getDomains();


		//
		domains = ClusterDomains.cluster(domains, pdpMatrix);

		ShortSegmentRemover.cleanup(domains);


		return domains;

	}



}