/**
 * Copyright © 2011-2013 EMBL - European Bioinformatics Institute
 * 
 * Licensed under the Apache License, Version 2.0 (the "License"); 
 * you may not use this file except in compliance with the License.  
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package uk.ac.ebi.phenotype.dao;

/**
 * 
 * Allele manager implementation.
 * 
 * @author Gautier Koscielny (EMBL-EBI) <koscieln@ebi.ac.uk>
 * @since February 2012
 */

import java.util.List;

import org.hibernate.SessionFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;

import uk.ac.ebi.phenotype.pojo.Allele;

@Service
public class AlleleDAOImpl extends HibernateDAOImpl implements AlleleDAO {

	@Autowired
	SessionFactory sessionFactory;
	
	@Transactional(readOnly = true)
	@SuppressWarnings("unchecked")
	public List<Allele> getAllAlleles() {
		return getCurrentSession().createQuery("from Allele").list();
	}

	@Transactional(readOnly = true)
	public Allele getAlleleByAccession(String accession) {
		return (Allele) getCurrentSession().createQuery("from Allele as a where a.id.accession = ?").setString(0, accession).uniqueResult();
		
	}

	@Transactional(readOnly = true)
	public Allele getAlleleBySymbol(String symbol) {
		return (Allele) getCurrentSession().createQuery("from Allele as a where a.symbol = ?").setString(0, symbol).uniqueResult();
		
	}

	@Transactional(readOnly = true)
	@SuppressWarnings("unchecked")
	public List<Allele> getAlleleByGeneSymbol(String geneSymbol) {
		return getCurrentSession().createQuery("from Allele as a where a.gene.symbol = ?").setString(0, geneSymbol).list();
	}

	@Transactional(readOnly = true)
	@SuppressWarnings("unchecked")
	public List<Allele> getAlleleByGeneAccession(String geneAccession) {
		return getCurrentSession().createQuery("from Allele as a where a.gene.id.accession = ?").setString(0, geneAccession).list();
	}

}

@@ -891,21 +891,19 @@
 ork.
-be
+tr
 ans
-.f
 act
-ory
+ion
 .ann
@@ -914,131 +914,63 @@
 ion.
-Autowired;%0Aimport org.springframework.stereotype.Service;%0Aimport org.springframework.transaction.annotation.Transactional;%0A
+Transactional;%0A%0Aimport uk.ac.ebi.phenotype.pojo.Allele;
 %0Aimp
@@ -1002,25 +1002,24 @@
 ojo.
-Allele;%0A%0A@Service
+GenomicFeature;%0A
 %0Apub
@@ -1096,52 +1096,229 @@
 %7B%0A%0A%09
-@Autowired%0A%09SessionFactory sessionFactory;%0A%09
+/**%0A%09 * Creates a new Hibernate project data access manager.%0A%09 * @param sessionFactory the Hibernate session factory%0A%09 */%0A%09public AlleleDAOImpl(SessionFactory sessionFactory) %7B%0A%09%09this.sessionFactory = sessionFactory;%0A%09%7D%09%0A
 %0A%09@T
@@ -1709,32 +1709,360 @@
 esult();%0A%09%09%0A%09%7D%0A%0A
+%0A%09@Transactional(readOnly = true)%0A%09public Allele getAlleleBySymbolAndGene(String symbol, GenomicFeature gene) %7B%0A%09%09return (Allele) getCurrentSession().createQuery(%22from Allele as a where a.symbol = ? and a.gene.id.accession=?%22)%0A%09%09%09%09.setString(0, symbol)%0A%09%09%09%09.setString(1, gene.getId().getAccession())%0A%09%09%09%09.uniqueResult();%0A%09%09%0A%09%7D%0A%0A
 %09@Transactional(

add get allele by symbol and gene method to disambiguate alleles of the same symbol that are associated to multiple genes