private void initialize() {
try {
dataSetManager = new DataSetManager();
dataSetManager.addDataSetFactory(
new LuceneDataSetFactory<Object, Object, Object>(
dataSetManager,
null,
new FileUtils(),
new NullCytoscapeUtils<Object, Object, Object>(),
null),
Collections.emptyMap());
data = dataSetManager.open(DirectorySettings.getGeneManiaDirectory());
human = getHumanOrganism(data);
networkUtils = new NetworkUtils();
cache =
new DataCache(
new SynchronizedObjectCache(
new MemObjectCache(data.getObjectCache(NullProgressReporter.instance(), false))));
mania = new Mania2(cache);
setGeneLimit(DEFAULT_GENE_LIMIT);
setCombiningMethod(DEFAULT_COMBINING_METHOD);
setNetworks(new HashSet<String>(Arrays.asList(DEFAULT_NETWORKS)));
} catch (Exception e) {
LOG.error(e);
}
}
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 Organism getHumanOrganism(DataSet data) throws DataStoreException {
String human = "H. Sapiens";
human = human.toLowerCase();
List<Organism> organisms = data.getMediatorProvider().getOrganismMediator().getAllOrganisms();
for (Organism organism : organisms) {
String organismName = organism.getName();
String organismAlias = organism.getAlias();
if (organismName.toLowerCase().equals(human) || organismAlias.toLowerCase().equals(human)) {
return organism;
}
}
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;
}