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);
}
}
public List<Gene> getRelatedGenesByScore()
throws ApplicationException, DataStoreException, NoRelatedGenesInfoException {
options = runGeneManiaAlgorithm();
final Map<Gene, Double> scores = options.getScores();
ArrayList<Gene> relatedGenes = new ArrayList<Gene>(scores.keySet());
Collections.sort(
relatedGenes,
new Comparator<Gene>() {
public int compare(Gene gene1, Gene gene2) {
return -Double.compare(scores.get(gene1), scores.get(gene2));
}
});
return relatedGenes;
}