/*
* 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.ontology.ontologyutilities.evaluationScripts;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import org.erasmusmc.ontology.Ontology;
import org.erasmusmc.ontology.OntologyPSFLoader;
import org.erasmusmc.ontology.ontologyutilities.FamilyNameFinder;
import org.erasmusmc.utilities.TextFileUtilities;
public class FamilyNameFinderScript {
public static void main(String[] args) {
FamilyNameFinder familyNameFinder = new FamilyNameFinder();
// OntologyManager ontologyManager = new OntologyManager();
// Ontology ontology = ontologyManager.fetchStoreFromDatabase("Homologene_curated_min3_291206");
OntologyPSFLoader loader = new OntologyPSFLoader();
loader.loadFromPSF("/home/schuemie/Leiden/ecoli/ecoli.psf");
Ontology ontology = loader.ontology;
Map<String, Integer> familyNames = familyNameFinder.findFamilyNames(ontology);
List<String> lines = new ArrayList<String>();
for (Entry<String, Integer> family: familyNames.entrySet()) {
lines.add(family.getKey()+ "\t" + family.getValue().toString());
}
TextFileUtilities.saveToFile(lines, "/home/temp/ECOliNames.txt");
}
}