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/* 
 *  Copyright or © or Copr. Ecole des Mines d'Alès (2012-2014) 
 *  
 *  This software is a computer program whose purpose is to provide 
 *  several functionalities for the processing of semantic data 
 *  sources such as ontologies or text corpora.
 *  
 *  This software is governed by the CeCILL  license under French law and
 *  abiding by the rules of distribution of free software.  You can  use, 
 *  modify and/ or redistribute the software under the terms of the CeCILL
 *  license as circulated by CEA, CNRS and INRIA at the following URL
 *  "http://www.cecill.info". 
 * 
 *  As a counterpart to the access to the source code and  rights to copy,
 *  modify and redistribute granted by the license, users are provided only
 *  with a limited warranty  and the software's author,  the holder of the
 *  economic rights,  and the successive licensors  have only  limited
 *  liability. 

 *  In this respect, the user's attention is drawn to the risks associated
 *  with loading,  using,  modifying and/or developing or reproducing the
 *  software by the user in light of its specific status of free software,
 *  that may mean  that it is complicated to manipulate,  and  that  also
 *  therefore means  that it is reserved for developers  and  experienced
 *  professionals having in-depth computer knowledge. Users are therefore
 *  encouraged to load and test the software's suitability as regards their
 *  requirements in conditions enabling the security of their systems and/or 
 *  data to be ensured and,  more generally, to use and operate it in the 
 *  same conditions as regards security. 
 * 
 *  The fact that you are presently reading this means that you have had
 *  knowledge of the CeCILL license and that you accept its terms.
 */
package slib.examples.sml.go;

import java.util.Set;
import org.openrdf.model.URI;
import org.openrdf.model.vocabulary.OWL;
import slib.graph.algo.accessor.GraphAccessor;
import slib.graph.algo.utils.GAction;
import slib.graph.algo.utils.GActionType;
import slib.graph.io.conf.GDataConf;
import slib.graph.io.conf.GraphConf;
import slib.graph.io.loader.GraphLoaderGeneric;
import slib.graph.io.util.GFormat;
import slib.graph.model.graph.G;
import slib.graph.model.impl.repo.URIFactoryMemory;
import slib.graph.model.repo.URIFactory;
import slib.sml.sm.core.utils.SMConstants;
import slib.sml.sm.core.engine.SM_Engine;
import slib.sml.sm.core.metrics.ic.utils.IC_Conf_Corpus;
import slib.sml.sm.core.metrics.ic.utils.ICconf;
import slib.utils.ex.SLIB_Exception;

/**
 *
 * Example which shows how to use the Semantic Measures Library to compute 
 * the Information Content (IC) of Gene Ontology terms using an Extrinsic IC 
 * (e.g. using Resnik IC). 
 * 
 * In this snippet we compute the IC of the GO terms defined in the 
 * Gene Ontology using Resnik IC formulation
 *
 * More information at http://www.semantic-measures-library.org/
 *
 * 
 * @author Sébastien Harispe 
 */
public class SMComputationGO_extrinsic_IC {

    public static void main(String[] params) throws SLIB_Exception {

        // The input files.
        // - The Gene Ontology (OBO format) 
        // - Annotations (GAF2)
        String goOBO = "/data/go/gene_ontology_ext.obo";
        String annot = "/data/go/gene_association.goa_human";

        
        URIFactory factory = URIFactoryMemory.getSingleton();
        URI graph_uri = factory.getURI("http://go/");

        // We define a prefix in order to build valid uris from ids such as GO:XXXXX, 
        // considering the configuration specified below the URI associated 
        // to GO:XXXXX will be http://go/XXXXX
        factory.loadNamespacePrefix("GO", graph_uri.toString());

        // We configure the graph
        GraphConf graphConf = new GraphConf(graph_uri);
        graphConf.addGDataConf(new GDataConf(GFormat.OBO, goOBO));
        graphConf.addGDataConf(new GDataConf(GFormat.GAF2, annot));

        GAction rooting = new GAction(GActionType.REROOTING);
        rooting.addParameter("root_uri", OWL.THING.stringValue());

        graphConf.addGAction(rooting);

        G graph = GraphLoaderGeneric.load(graphConf);

        // General information about the graph
        System.out.println(graph.toString());

        // We retrieve only the classes, i.e. GO terms
        // Note that the graph also contains the genes
        Set goTerms = GraphAccessor.getClasses(graph);
        System.out.println("GO terms : " + goTerms.size());

        // We configure the IC
        ICconf icConfRes = new IC_Conf_Corpus(SMConstants.FLAG_IC_ANNOT_RESNIK_1995);
        
        SM_Engine engine = new SM_Engine(graph);

        for (URI goTerm : goTerms) {

            System.out.println(goTerm + "\t" + engine.getIC(icConfRes,goTerm));
        }
    }
}