/*
* EuroCarbDB, a framework for carbohydrate bioinformatics
*
* Copyright (c) 2006-2009, Eurocarb project, or third-party contributors as
* indicated by the @author tags or express copyright attribution
* statements applied by the authors.
*
* This copyrighted material is made available to anyone wishing to use, modify,
* copy, or redistribute it subject to the terms and conditions of the GNU
* Lesser General Public License, as published by the Free Software Foundation.
* A copy of this license accompanies this distribution in the file LICENSE.txt.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
* or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
* for more details.
*
* Last commit: $Rev: 1924 $ by $Author: khaleefah $ on $Date:: 2010-06-21 #$
*/
package org.eurocarbdb.action.ms;
import java.util.*;
import org.hibernate.Criteria;
import org.hibernate.criterion.Restrictions;
import org.eurocarbdb.action.*;
import org.eurocarbdb.dataaccess.*;
import org.eurocarbdb.dataaccess.ms.*;
import static org.eurocarbdb.dataaccess.Eurocarb.getEntityManager;
/**
*
* @author aceroni
* @version $Rev: 1924 $
*/
public class InitIons extends EurocarbAction
{
static String[] ions = new String[4];
public int added_ions = 0;
static {
ions[0] = "H";
ions[1] = "Na";
ions[2] = "Li";
ions[3] = "K";
}
public int getAddedIons() {
return added_ions;
}
public Collection<Ion> getIons() {
Criteria crit = getEntityManager().createQuery(Ion.class);
return crit.list();
}
public String execute() throws Exception {
added_ions = 0;
for( int i=0; i<ions.length; i++ ) {
// check if the ion is existing
Ion ion = findIon(ions[i]);
if( ion==null ) {
// create a new ion
// ion = new Ion(ions[i]);
// store
Eurocarb.getEntityManager().store(ion);
added_ions++;
}
}
return SUCCESS;
}
public Ion findIon(String type) {
Criteria crit = getEntityManager().createQuery(Ion.class).add(Restrictions.eq("ionType", type));
Collection<Ion> list = crit.list();
if( list==null || list.size()==0 )
return null;
return list.iterator().next();
}
}