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);
}
}
static DataSetManager createDataSetManager() {
DataSetManager dataSetManager = new DataSetManager();
dataSetManager.addDataSetFactory(
new LuceneDataSetFactory<Object, Object, Object>(
dataSetManager,
null,
new FileUtils(),
new NullCytoscapeUtils<Object, Object, Object>(),
null),
Collections.emptyMap());
return dataSetManager;
}