@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);
}
