private static boolean validGene(String geneName) throws SAXException, DataStoreException, ApplicationException { Gene gene = data.getCompletionProvider(human).getGene(geneName); if (gene == null) { return false; } return true; }
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; }