private RelatedGenesEngineResponseDto runQuery(RelatedGenesEngineRequestDto request)
throws DataStoreException {
try {
request.setProgressReporter(NullProgressReporter.instance());
RelatedGenesEngineResponseDto result;
result = mania.findRelated(request);
request.setCombiningMethod(result.getCombiningMethodApplied());
networkUtils.normalizeNetworkWeights(result);
return result;
} catch (ApplicationException e) {
Logger logger = Logger.getLogger(getClass());
logger.error("Unexpected error", e); // $NON-NLS-1$
return null;
}
}
private RelatedGenesEngineRequestDto createRequest() throws ApplicationException {
RelatedGenesEngineRequestDto request = new RelatedGenesEngineRequestDto();
request.setNamespace(GeneMania.DEFAULT_NAMESPACE);
request.setOrganismId(human.getId());
request.setInteractionNetworks(collapseNetworks(networks));
Set<Long> nodes = new HashSet<Long>();
for (String geneName : genes) {
nodes.add(data.getCompletionProvider(human).getNodeId(geneName));
}
request.setPositiveNodes(nodes);
request.setLimitResults(geneLimit);
request.setCombiningMethod(combiningMethod);
request.setScoringMethod(org.genemania.type.ScoringMethod.DISCRIMINANT);
return request;
}
