/*
* Concept profile generation tool suite
* Copyright (C) 2015 Biosemantics Group, Erasmus University Medical Center,
* Rotterdam, The Netherlands
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
* by the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>
*/
package org.erasmusmc.dataimport.genes;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import org.erasmusmc.ids.DatabaseID;
import org.erasmusmc.ontology.Concept;
import org.erasmusmc.ontology.OntologyPSFLoader;
public class GeneID2CID extends HashMap<String, Integer>{
public void loadFromOntology(String filename, String idPrefix){
OntologyPSFLoader loader = new OntologyPSFLoader();
loader.loadFromPSF(filename);
Iterator<Concept> iterator = loader.ontology.getConceptIterator();
while (iterator.hasNext()){
Concept concept = iterator.next();
List<DatabaseID> databaseIDs = loader.ontology.getDatabaseIDsForConcept(concept.getID());
if (databaseIDs != null)
for (DatabaseID databaseID : databaseIDs)
if (databaseID.database.equals(idPrefix))
put(databaseID.ID, concept.getID());
}
}
private static final long serialVersionUID = 1L;
}