/*
* #%L
* gitools-kegg
* %%
* Copyright (C) 2013 Universitat Pompeu Fabra - Biomedical Genomics group
* %%
* 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/gpl-3.0.html>.
* #L%
*/
package org.gitools.datasources.kegg.idmapper;
import org.gitools.api.analysis.IProgressMonitor;
import org.gitools.datasources.idmapper.MappingContext;
import org.gitools.datasources.idmapper.MappingData;
import org.gitools.datasources.idmapper.MappingException;
import org.gitools.datasources.idmapper.MappingNode;
import org.gitools.datasources.kegg.service.KeggService;
import org.gitools.datasources.kegg.service.domain.KeggPathway;
import java.util.*;
public class KeggPathwaysMapper extends AbstractKeggMapper implements AllIds {
public KeggPathwaysMapper(KeggService service, String organismId) {
super("KeggPathways", false, true, service, organismId);
}
@Override
public MappingData map(MappingContext context, MappingData data, MappingNode src, MappingNode dst, IProgressMonitor monitor) throws MappingException {
if (!KEGG_PATHWAYS.equals(src.getId())) {
throw new MappingException("Unsupported mapping from " + src + " to " + dst);
}
if (data.isEmpty()) {
monitor.begin("Getting KEGG pathways ...", 1);
try {
List<KeggPathway> pathwaysDefs = service.getPathways(organismId);
for (KeggPathway d : pathwaysDefs)
data.put(d.getId(), d.getId());
} catch (Exception ex) {
throw new MappingException(ex);
}
}
if (monitor.isCancelled()) {
return null;
}
Map<String, Set<String>> map = new HashMap<>();
Set<String> dstIds = data.getDstIds();
monitor.begin("Getting KEGG genes ...", dstIds.size());
try {
//int count = 0;
for (String dstId : dstIds) {
monitor.info(dstId);
if (monitor.isCancelled()) {
return null;
}
//if (count++ > 10) //FIXME
// break;
List<String> genes = service.getGenesByPathway(dstId);
map.put(dstId, new HashSet<>(genes));
monitor.worked(1);
}
} catch (Exception ex) {
throw new MappingException(ex);
}
monitor.begin("Mapping KEGG pathways to KEGG genes ...", dstIds.size());
data.map(map);
return data;
}
}