private EnrichmentEngineResponseDto computeEnrichment(EnrichmentEngineRequestDto request)
throws ApplicationException, NoRelatedGenesInfoException {
if (request == null) {
return null;
}
if (request.getNodes().size() == 0) {
throw new NoRelatedGenesInfoException();
}
return mania.computeEnrichment(request);
}
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;
}