/*
 *                  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/
 * 
 * 
 * 
 */

import java.util.List;

import org.biojava.bio.structure.PDBHeader;
import org.biojava.bio.structure.Structure;
import org.biojava.bio.structure.hibernate.HibernateSession;

import org.biojava.bio.structure.hibernate.StructureFile;
import org.hibernate.Session;
import org.hibernate.Query;



/** An example that loads all PDB files from the database and prints them to stdout.
 * 
 * @author Andreas Prlic
 *
 */
public class DemoLoadAllStructures {

	public static void main(String[] args){

		// since the data is lazy-loaded we keep the session open
		Object ownership = HibernateSession.createSession();
		Session session = HibernateSession.getSession();

		// init the example class
		DemoLoadAllStructures demo = new DemoLoadAllStructures();
		
		// and get a listing of all availabel PDB files
		System.out.println("load all structures");
		List<PDBHeader> structures = demo.loadAll();
		System.out.println("got " + structures.size() + " structures");

		
		// now let's iterate over the structures in the database and print the header info
		int pos = 0;
		for (PDBHeader header: structures){

			pos++;
			System.out.println(pos + " " + header);
			System.out.println(demo.getStructureFile(header.getIdCode()).getPath());
			Structure s = demo.getStructure(header.getIdCode());
			System.out.println(s);
			
			// prevent the session cache from getting too big and cause a MemoryException
			session.flush();


		}

		
		// at this point we can close the Hibernate session		
		HibernateSession.closeSession(ownership);
	}

	public DemoLoadAllStructures(){		
	}
	
	public Structure getStructure(String pdbCode){
		// taking control over session, in order to ensure thread -safety
		Object ownership = HibernateSession.createSession();
		Session session = HibernateSession.getSession();

		Query q = session.getNamedQuery("structure.byPDBCode");
		q.setParameter("pdbCode",pdbCode.toUpperCase());

		List<Structure> lst =  q.list();

		HibernateSession.closeSession(ownership);

		if ( lst.size() != 1){
			return null;
		}

		return lst.get(0);



	}

	public StructureFile getStructureFile(String pdbCode){
		Object ownership = HibernateSession.createSession();
		Session session = HibernateSession.getSession();

		Query q = session.getNamedQuery("structureFile.byPDBCode");
		q.setParameter("pdbCode", pdbCode.toUpperCase());

		List<StructureFile> lst = q.list();

		HibernateSession.closeSession(ownership);

		if ( lst.size() != 1)
			return null;
		return lst.get(0);

	}

	public List<PDBHeader>  loadAll(){

		Object ownership = HibernateSession.createSession();		
		Session session = HibernateSession.getSession();

		Query q = session.getNamedQuery("header.getAll");

		List<PDBHeader> lst =  q.list();
		HibernateSession.closeSession(ownership);

		return lst;
	}
}