/*
* #%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.IdConversion;
import java.util.*;
public class KeggGenesMapper extends AbstractKeggMapper implements AllIds {
public static final String NCBI_DB = "ncbi-geneid";
public static final String UNIPROT_DB = "uniprot";
public static final String PDB_DB = "pdb";
public static final String ENSEMBL_DB = "ensembl";
private static final Map<String, String> fileKey = new HashMap<>();
static {
fileKey.put(NCBI_GENES, NCBI_DB);
fileKey.put(UNIPROT, UNIPROT_DB);
fileKey.put(PDB, PDB_DB);
fileKey.put(ENSEMBL_GENES, ENSEMBL_DB);
}
public KeggGenesMapper(KeggService service, String organismId) {
super("KeggGenes", false, true, service, organismId);
}
@Override
public MappingData map(MappingContext context, MappingData data, MappingNode src, MappingNode dst, IProgressMonitor monitor) throws MappingException {
Map<String, Set<String>> map = new HashMap<>();
monitor.begin("Getting mapping information from KEGG ...", 1);
// TODO Filter out items not in data if data is not empty
// Get map from the API
try {
String prefix = fileKey.get(dst.getId());
if (!KEGG_GENES.equals(src.getId()) || prefix == null) {
throw new MappingException("Unsupported mapping from " + src + " to " + dst);
}
if (prefix.equals(ENSEMBL_DB)) {
prefix = prefix + "-" + organismId;
}
List<IdConversion> relations = service.getConvert(organismId, prefix);
int plen = prefix.length() + 1;
for (IdConversion rel : relations) {
String srcId = rel.getSourceId();
String dstId = rel.getTargetId();
Set<String> b = map.get(srcId);
if (b == null) {
b = new HashSet<>();
map.put(srcId, b);
}
b.add(dstId.substring(plen));
}
} catch (Exception ex) {
throw new MappingException(ex);
}
monitor.begin("Mapping KEGG genes ...", 1);
if (data.isEmpty()) {
data.identity(map.keySet());
}
data.map(map);
return data;
}
}