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;
}
