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 double[] computeEdgeWeightExtrema(RelatedGenesEngineResponseDto response) {
double[] extrema = new double[] {1, 0};
for (NetworkDto network : response.getNetworks()) {
for (InteractionDto interaction : network.getInteractions()) {
double weight = interaction.getWeight() * network.getWeight();
if (extrema[0] > weight) {
extrema[0] = weight;
}
if (extrema[1] < weight) {
extrema[1] = weight;
}
}
}
return extrema;
}
private EnrichmentEngineRequestDto createEnrichmentRequest(
RelatedGenesEngineResponseDto response) {
if (human.getOntology() == null) {
return null;
}
EnrichmentEngineRequestDto request = new EnrichmentEngineRequestDto();
request.setProgressReporter(NullProgressReporter.instance());
request.setMinCategories(MIN_CATEGORIES);
request.setqValueThreshold(Q_VALUE_THRESHOLD);
request.setOrganismId(human.getId());
request.setOntologyId(human.getOntology().getId());
Set<Long> nodes = new HashSet<Long>();
for (NetworkDto network : response.getNetworks()) {
for (InteractionDto interaction : network.getInteractions()) {
nodes.add(interaction.getNodeVO1().getId());
nodes.add(interaction.getNodeVO2().getId());
}
}
request.setNodes(nodes);
return request;
}