@Override public List<QueryResult> getAllByRegionList(List<Region> regionList, QueryOptions options) { // db.regulatory_region.find({"chunkIds": {$in:["1_200", "1_300"]}, "start": 601156}) QueryBuilder builder = new QueryBuilder(); List<Object> featureType = options.getList("featureType", null); List<Object> featureClass = options.getList("featureClass", null); // options = addExcludeReturnFields("chunkIds", options); List<DBObject> queries = new ArrayList<>(); for (Region region : regionList) { int firstChunkId = getChunkId(region.getStart(), regulatoryRegionChunkSize); int lastChunkId = getChunkId(region.getEnd(), regulatoryRegionChunkSize); BasicDBList chunksId = new BasicDBList(); for (int j = firstChunkId; j <= lastChunkId; j++) { String chunkId = region.getChromosome() + "_" + j + "_" + regulatoryRegionChunkSize / 1000 + "k"; chunksId.add(chunkId); } // logger.info(chunksId.toString()); builder = builder .start("_chunkIds") .in(chunksId) .and("start") .lessThanEquals(region.getEnd()) .and("end") .greaterThanEquals(region.getStart()); if (featureType != null && featureType.size() > 0) { BasicDBList featureTypeDBList = new BasicDBList(); featureTypeDBList.addAll(featureType); builder = builder.and("featureType").in(featureTypeDBList); } if (featureClass != null && featureClass.size() > 0) { BasicDBList featureClassDBList = new BasicDBList(); featureClassDBList.addAll(featureClass); builder = builder.and("featureClass").in(featureClassDBList); } queries.add(builder.get()); } // System.out.println(">>"+regionList); // System.out.println(">>"+builder.get().toString()); return executeQueryList2(regionList, queries, options); }