public static void getHitsFromCDD(String queryString, Map<String, CyIdentifiable> reverseMap, 
	                                  Map<CyIdentifiable, List<CDDHit>> hitMap) throws Exception {
		BufferedReader in = queryCDD("hits", queryString);
		List<String> inputLines = new ArrayList<String>();
		String line;
		while ((line  = in.readLine()) != null) {
			// System.out.println("Hit line from CDD: "+line);
			line = line.trim();
			// Skip over the header lines
			if (line.startsWith("#") || line.startsWith("Query") || line.length()==0) continue;
			CDDHit hit = new CDDHit(line);
			if (reverseMap.containsKey(hit.getProteinId())) {
				CyIdentifiable cyId = reverseMap.get(hit.getProteinId());
				if (!hitMap.containsKey(cyId)) {
					// System.out.println("Assigning hit to "+cyId);
					hitMap.put(cyId, new ArrayList<CDDHit>());
				}
				hitMap.get(cyId).add(hit);
			}
		}
		return;
	}