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;
}
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;
}