/**
* 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.bel.converters;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import org.openbel.bel.model.BELAnnotation;
import org.openbel.framework.common.model.Annotation;
import org.openbel.framework.common.model.AnnotationDefinition;
import org.openbel.framework.common.model.CommonModelFactory;
public class BELAnnotationConverter extends
BELConverter<BELAnnotation, List<Annotation>> {
private final BELAnnotationDefinitionConverter badc =
new BELAnnotationDefinitionConverter();
private final Map<String, AnnotationDefinition> adefs;
public BELAnnotationConverter(Map<String, AnnotationDefinition> adefs) {
this.adefs = adefs;
}
/**
* {@inheritDoc}
*/
@Override
public List<Annotation> convert(BELAnnotation ba) {
if (ba == null) {
return null;
}
List<Annotation> annotations = new ArrayList<Annotation>();
AnnotationDefinition ad =
adefs.get(ba.getAnnotationDefinition().getName());
for (String value : ba.getValues()) {
annotations.add(CommonModelFactory.getInstance().createAnnotation(
value, ad));
}
return annotations;
}
/**
* {@inheritDoc}
*/
@Override
public BELAnnotation convert(List<Annotation> a) {
if (a == null) {
return null;
}
List<String> values = new ArrayList<String>();
AnnotationDefinition ad = null;
for (int i = 0; i < a.size(); i++) {
Annotation ann = a.get(i);
if (i == 0) {
ad = ann.getDefinition();
} else if (ad != null && !ad.equals(ann.getDefinition())) {
throw new IllegalStateException(
"annotations must have equal definitions.");
}
values.add(ann.getValue());
}
return new BELAnnotation(badc.convert(ad), values);
}
}