/**
* 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 org.openbel.bel.xbel.model.XBELAnnotation;
import org.openbel.framework.common.enums.AnnotationType;
import org.openbel.framework.common.model.Annotation;
import org.openbel.framework.common.model.AnnotationDefinition;
import org.openbel.framework.common.model.CommonModelFactory;
/**
* Converter class for converting between {@link XBELAnnotation} and
* {@link Annotation}.
* <p>
* The XBEL schema defines a referential {@code refID} property of annotations
* that refers to a specific annotation definition instance. This instance is
* not available to the converter and will need to be resolved prior to use as a
* common {@link Annotation} object.
* </p>
*/
public final class AnnotationConverter extends
JAXBConverter<XBELAnnotation, Annotation> {
/**
* Constant used in annotation definition types. Only annotation definition
* references are available to this converter. This field will be used as a
* placeholder in annotation definition types.
*/
public static final AnnotationType UNRESOLVED_ANNOTATION_DEFINITION_TYPE =
AnnotationType.REGULAR_EXPRESSION;
/**
* Constant used in annotation definition values. Only annotation definition
* references are available to this converter. This field will be used as a
* placeholder in annotation definition values.
*/
public static final String UNRESOLVED_ANNOTATION_DEFINITION_VALUE =
"<unresolved_annotation>";
/**
* Constant used in annotation definition values. Only annotation definition
* references are available to this converter. This field will be used as a
* placeholder in annotation definition description.
*/
public static final String UNRESOLVED_ANNOTATION_DEFINITION_DESCRIPTION =
"<unresolved_annotation>";
/**
* Constant used in annotation definition values. Only annotation definition
* references are available to this converter. This field will be used as a
* placeholder in annotation definition usage.
*/
public static final String UNRESOLVED_ANNOTATION_DEFINITION_USAGE =
"<unresolved_annotation>";
/**
* {@inheritDoc}
*/
@Override
public Annotation convert(XBELAnnotation source) {
if (source == null) return null;
String refID = source.getRefID();
String value = source.getValue();
final AnnotationDefinition ad = CommonModelFactory.getInstance()
.createAnnotationDefinition(refID,
UNRESOLVED_ANNOTATION_DEFINITION_TYPE,
UNRESOLVED_ANNOTATION_DEFINITION_DESCRIPTION,
UNRESOLVED_ANNOTATION_DEFINITION_USAGE,
UNRESOLVED_ANNOTATION_DEFINITION_VALUE);
// Destination type
final Annotation dest = CommonModelFactory.getInstance()
.createAnnotation(value, ad);
return dest;
}
/**
* {@inheritDoc}
*/
@Override
public XBELAnnotation convert(Annotation source) {
if (source == null) return null;
AnnotationDefinition definition = source.getDefinition();
String refID = definition.getId();
String value = source.getValue();
XBELAnnotation xa = new XBELAnnotation();
xa.setRefID(refID);
xa.setValue(value);
return xa;
}
}