/**
* 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 static org.openbel.framework.common.BELUtilities.sizedArrayList;
import java.util.ArrayList;
import java.util.List;
import org.openbel.bel.xbel.model.XBELAnnotationDefinitionGroup;
import org.openbel.bel.xbel.model.XBELDocument;
import org.openbel.bel.xbel.model.XBELExternalAnnotationDefinition;
import org.openbel.bel.xbel.model.XBELHeader;
import org.openbel.bel.xbel.model.XBELInternalAnnotationDefinition;
import org.openbel.bel.xbel.model.XBELNamespaceGroup;
import org.openbel.bel.xbel.model.XBELStatementGroup;
import org.openbel.framework.common.model.AnnotationDefinition;
import org.openbel.framework.common.model.Document;
import org.openbel.framework.common.model.Header;
import org.openbel.framework.common.model.NamespaceGroup;
import org.openbel.framework.common.model.StatementGroup;
/**
* Converter class for converting between {@link XBELDocument} and
* {@link Document}.
*/
public final class DocumentConverter extends
JAXBConverter<XBELDocument, Document> {
/**
* {@inheritDoc}
*/
@Override
public Document convert(XBELDocument source) {
if (source == null) return null;
List<XBELStatementGroup> xstmtGroups = source.getStatementGroup();
List<StatementGroup> stmtGroups =
new ArrayList<StatementGroup>(xstmtGroups.size());
StatementGroupConverter sgConverter = new StatementGroupConverter();
for (final XBELStatementGroup xsg : xstmtGroups) {
// Defer to StatementGroupConverter
stmtGroups.add(sgConverter.convert(xsg));
}
XBELHeader header = source.getHeader();
HeaderConverter hConverter = new HeaderConverter();
// Defer to HeaderConverter
Document dest = new Document(hConverter.convert(header), stmtGroups);
if (source.isSetAnnotationDefinitionGroup()) {
XBELAnnotationDefinitionGroup adGroup =
source.getAnnotationDefinitionGroup();
List<XBELInternalAnnotationDefinition> internals =
adGroup.getInternalAnnotationDefinition();
List<XBELExternalAnnotationDefinition> externals =
adGroup.getExternalAnnotationDefinition();
int size = internals.size() + externals.size();
List<AnnotationDefinition> l2 = sizedArrayList(size);
// Defer to converters
InternalAnnotationDefinitionConverter iConverter =
new InternalAnnotationDefinitionConverter();
for (final XBELInternalAnnotationDefinition iad : internals) {
l2.add(iConverter.convert(iad));
}
ExternalAnnotationDefinitionConverter eConverter =
new ExternalAnnotationDefinitionConverter();
for (final XBELExternalAnnotationDefinition ead : externals) {
l2.add(eConverter.convert(ead));
}
dest.setDefinitions(l2);
}
if (source.isSetNamespaceGroup()) {
XBELNamespaceGroup namespaceGroup = source.getNamespaceGroup();
NamespaceGroupConverter ngConverter = new NamespaceGroupConverter();
// Defer to DocumentHeaderConverter
dest.setNamespaceGroup(ngConverter.convert(namespaceGroup));
}
// Resolve any property references to instances
dest.resolveReferences();
return dest;
}
/**
* {@inheritDoc}
*/
@Override
public XBELDocument convert(Document source) {
if (source == null) return null;
XBELDocument xd = new XBELDocument();
List<StatementGroup> stmtGroups = source.getStatementGroups();
List<XBELStatementGroup> xstmtGroups = xd.getStatementGroup();
StatementGroupConverter sgConverter = new StatementGroupConverter();
for (final StatementGroup sg : stmtGroups) {
// Defer to StatementGroupConverter
xstmtGroups.add(sgConverter.convert(sg));
}
List<AnnotationDefinition> definitions = source.getDefinitions();
if (hasItems(definitions)) {
XBELAnnotationDefinitionGroup xadGroup =
new XBELAnnotationDefinitionGroup();
List<XBELInternalAnnotationDefinition> internals =
xadGroup.getInternalAnnotationDefinition();
List<XBELExternalAnnotationDefinition> externals =
xadGroup.getExternalAnnotationDefinition();
InternalAnnotationDefinitionConverter iConverter =
new InternalAnnotationDefinitionConverter();
ExternalAnnotationDefinitionConverter eConverter =
new ExternalAnnotationDefinitionConverter();
for (final AnnotationDefinition ad : definitions) {
XBELInternalAnnotationDefinition iad = iConverter.convert(ad);
if (iad != null) {
internals.add(iad);
continue;
}
XBELExternalAnnotationDefinition ead = eConverter.convert(ad);
if (ead != null) {
externals.add(ead);
}
}
xd.setAnnotationDefinitionGroup(xadGroup);
}
Header header = source.getHeader();
HeaderConverter hConverter = new HeaderConverter();
// Defer to HeaderConverter
xd.setHeader(hConverter.convert(header));
NamespaceGroup nsGroup = source.getNamespaceGroup();
if (nsGroup != null) {
NamespaceGroupConverter ngConverter = new NamespaceGroupConverter();
// Defer to NamespaceGroupConverter
xd.setNamespaceGroup(ngConverter.convert(nsGroup));
}
return xd;
}
}