code: private void mapIds() {
  		if (queryReferences != null) {
  			queryReferencesMap = new HashMap<String,Sequence>(queryReferences.size());
  			for (int counter=0; counter < queryReferences.size() ; counter ++){
  				String id = "Query_"+(counter+1);
  				queryReferencesMap.put(id, queryReferences.get(counter));
  			}
  		}
  
  		if (databaseReferences != null) {
  			databaseReferencesMap = new HashMap<String,Sequence>(databaseReferences.size());
  			for (int counter=0; counter < databaseReferences.size() ; counter ++){
  				// this is strange: while Query_id are 1 based, Hit (database) id are 0 based
  				String id = "gnl|BL_ORD_ID|"+(counter);
  				databaseReferencesMap.put(id, databaseReferences.get(counter));
  			}
  		}
  	}
docs: fill the map association between sequences an a unique id