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; }