/**
* Copyright (C) 2012-2013 Selventa, Inc.
*
* This file is part of the OpenBEL Framework.
*
* This program is free software; you can redistribute it and/or modify it
* under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* The OpenBEL Framework 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.
*
* You should have received a copy of the GNU Lesser General Public License
* along with the OpenBEL Framework. If not, see <http://www.gnu.org/licenses/>.
*
* Additional Terms under LGPL v3:
*
* This license does not authorize you and you are prohibited from using the
* name, trademarks, service marks, logos or similar indicia of Selventa, Inc.,
* or, in the discretion of other licensors or authors of the program, the
* name, trademarks, service marks, logos or similar indicia of such authors or
* licensors, in any marketing or advertising materials relating to your
* distribution of the program or any covered product. This restriction does
* not waive or limit your obligation to keep intact all copyright notices set
* forth in the program as delivered to you.
*
* If you distribute the program in whole or in part, or any modified version
* of the program, and you assume contractual liability to the recipient with
* respect to the program or modified version, then you will indemnify the
* authors and licensors of the program for any liabilities that these
* contractual assumptions directly impose on those licensors and authors.
*/
package org.openbel.framework.common.xbel.converters;
import static org.openbel.framework.common.BELUtilities.hasItems;
import java.util.ArrayList;
import java.util.List;
import org.openbel.bel.xbel.model.XBELAnnotation;
import org.openbel.bel.xbel.model.XBELAnnotationGroup;
import org.openbel.bel.xbel.model.XBELCitation;
import org.openbel.framework.common.model.Annotation;
import org.openbel.framework.common.model.AnnotationGroup;
import org.openbel.framework.common.model.Citation;
import org.openbel.framework.common.model.CommonModelFactory;
import org.openbel.framework.common.model.Evidence;
/**
* Converter class for converting between {@link XBELAnnotationGroup} and
* {@link AnnotationGroup}.
*/
public final class AnnotationGroupConverter extends
JAXBConverter<XBELAnnotationGroup, AnnotationGroup> {
/**
* {@inheritDoc}
*/
@Override
public AnnotationGroup convert(XBELAnnotationGroup source) {
if (source == null) return null;
List<Object> list = source.getAnnotationOrEvidenceOrCitation();
// Destination type
AnnotationGroup dest = new AnnotationGroup();
// Capture XBELCitation elements of list as a new list
List<XBELCitation> l1 = listCapture(list, XBELCitation.class);
List<Citation> l2 = new ArrayList<Citation>();
CitationConverter cConverter = new CitationConverter();
for (final XBELCitation xc : l1) {
// Defer to CitationConverter
l2.add(cConverter.convert(xc));
}
if (!l2.isEmpty()) {
dest.setCitation(l2.get(0));
}
// Capture XBELAnnotation elements of list as a new list
List<XBELAnnotation> l3 = listCapture(list, XBELAnnotation.class);
List<Annotation> l4 = new ArrayList<Annotation>();
AnnotationConverter aConverter = new AnnotationConverter();
for (final XBELAnnotation xa : l3) {
// Defer to AnnotationConverter
l4.add(aConverter.convert(xa));
}
dest.setAnnotations(l4);
// Capture evidence strings of list as a new list
List<String> l5 = listCapture(list, String.class);
List<Evidence> l6 = new ArrayList<Evidence>();
for (final String str : l5) {
l6.add(CommonModelFactory.getInstance().createEvidence(str));
}
if (!l6.isEmpty()) {
dest.setEvidence(l6.get(0));
}
return dest;
}
/**
* {@inheritDoc}
*/
@Override
public XBELAnnotationGroup convert(AnnotationGroup source) {
if (source == null) return null;
List<Annotation> annotations = source.getAnnotations();
Citation citation = source.getCitation();
Evidence evidence = source.getEvidence();
XBELAnnotationGroup xag = new XBELAnnotationGroup();
List<Object> list = xag.getAnnotationOrEvidenceOrCitation();
if (hasItems(annotations)) {
// Defer to AnnotationConverter
AnnotationConverter aConverter = new AnnotationConverter();
for (final Annotation a : annotations) {
XBELAnnotation xa = aConverter.convert(a);
list.add(xa);
}
}
if (citation != null) {
// Defer to CitationConverter
CitationConverter cConverter = new CitationConverter();
XBELCitation xc = cConverter.convert(citation);
list.add(xc);
}
if (evidence != null) {
list.add(evidence.getValue());
}
return xag;
}
}