/*
* This file is part of the OWL API.
*
* The contents of this file are subject to the LGPL License, Version 3.0.
*
* Copyright (C) 2011, The University of Manchester
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU 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 General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see http://www.gnu.org/licenses/.
*
*
* Alternatively, the contents of this file may be used under the terms of the Apache License, Version 2.0
* in which case, the provisions of the Apache License Version 2.0 are applicable instead of those above.
*
* Copyright 2011, University of Manchester
*
* 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 org.coode.owlapi.obo.parser;
import java.util.HashSet;
import java.util.Set;
import java.util.StringTokenizer;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.semanticweb.owlapi.model.AddAxiom;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLAnnotation;
import org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom;
import org.semanticweb.owlapi.model.OWLAnnotationProperty;
import org.semanticweb.owlapi.model.OWLDataFactory;
import org.semanticweb.owlapi.model.OWLEntity;
import org.semanticweb.owlapi.model.OWLLiteral;
/**
* Author: Matthew Horridge<br>
* The University of Manchester<br>
* Bio-Health Informatics Group<br>
* Date: 03/02/2011
*/
public class SynonymTagValueHandler extends AbstractTagValueHandler {
private static final String TAG_NAME = OBOVocabulary.SYNONYM.toString();
private static final Pattern valuePattern = Pattern.compile("\"([^\"]*)\"\\s*([^\\s]*)\\s*\\[([^\\]]*)\\]");
private static final int VALUE_GROUP = 1;
private static final int TYPE_GROUP = 2;
private static final int XREF_GROUP = 3;
public static final IRI SYNONYM_TYPE_IRI = OBOVocabulary.SYNONYM_TYPE.getIRI();
public static final IRI XREF_IRI = OBOVocabulary.XREF.getIRI();
public SynonymTagValueHandler(OBOConsumer consumer) {
super(TAG_NAME, consumer);
}
public void handle(String id, String value, String comment) {
Matcher matcher = valuePattern.matcher(value);
if(matcher.matches()) {
IRI synonymIRI = getTagIRI(TAG_NAME);
OWLDataFactory df = getDataFactory();
OWLAnnotationProperty property = df.getOWLAnnotationProperty(synonymIRI);
Set<OWLAnnotation> annotations = new HashSet<OWLAnnotation>();
OWLAnnotation typeAnnotation = getSynonymTypeAnnotation(matcher);
annotations.add(typeAnnotation);
annotations.addAll(getXRefAnnotations(matcher, df));
OWLEntity subject = getConsumer().getCurrentEntity();
String synonym = matcher.group(VALUE_GROUP);
OWLLiteral synonymLiteral = df.getOWLLiteral(synonym, "");
OWLAnnotationAssertionAxiom annoAssertion = df.getOWLAnnotationAssertionAxiom(property, subject.getIRI(), synonymLiteral, annotations);
applyChange(new AddAxiom(getOntology(), annoAssertion));
}
}
private Set<OWLAnnotation> getXRefAnnotations(Matcher matcher, OWLDataFactory df) {
Set<OWLAnnotation> annotations = new HashSet<OWLAnnotation>();
String xrefs = matcher.group(XREF_GROUP);
if (xrefs != null) {
StringTokenizer tokenizer = new StringTokenizer(xrefs, ",");
while(tokenizer.hasMoreTokens()) {
String xref = tokenizer.nextToken();
IRI xrefIRI = getTagIRI(xref);
OWLAnnotationProperty xrefProperty = df.getOWLAnnotationProperty(XREF_IRI);
OWLAnnotation xrefAnnotation = df.getOWLAnnotation(xrefProperty, xrefIRI);
annotations.add(xrefAnnotation);
}
}
return annotations;
}
private OWLAnnotation getSynonymTypeAnnotation(Matcher matcher) {
OWLDataFactory df = getDataFactory();
String synonymType = matcher.group(TYPE_GROUP);
return df.getOWLAnnotation(df.getOWLAnnotationProperty(SYNONYM_TYPE_IRI), df.getOWLLiteral(synonymType));
}
}