Example usage for com.mongodb BasicDBList BasicDBList

List of usage examples for com.mongodb BasicDBList BasicDBList

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BasicDBList

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From source file:org.opencb.cellbase.lib.impl.ProteinMongoDBAdaptor.java

License:Apache License

@Override
public QueryResult<ProteinVariantAnnotation> getVariantAnnotation(String ensemblTranscriptId, int position,
        String aaReference, String aaAlternate, QueryOptions options) {
    QueryResult<ProteinVariantAnnotation> queryResult = new QueryResult<>();
    queryResult.setId(ensemblTranscriptId + "/" + position + "/" + aaAlternate);
    long dbTimeStart = System.currentTimeMillis();

    ProteinVariantAnnotation proteinVariantAnnotation = new ProteinVariantAnnotation();
    proteinVariantAnnotation.setPosition(position);
    proteinVariantAnnotation.setReference(aaReference);
    proteinVariantAnnotation.setAlternate(aaAlternate);
    //        proteinVariantAnnotation.setSubstitutionScores(getProteinSubstitutionScores(ensemblTranscriptId, position, aaAlternate));
    Query query = new Query("transcript", ensemblTranscriptId).append("position", position).append("aa",
            aaAlternate);/*from   w w w.  j  a  va2 s.  c  o  m*/
    //        try {
    //            if (ensemblTranscriptId.equals("ENST00000383037") || ensemblTranscriptId.equals("ENST00000428666")) {
    //                int a = 1;
    //            }
    // Stop_gain/lost variants do not have SIFT/POLYPHEN scores
    if (!aaAlternate.equals("STOP") && !aaReference.equals("STOP")) {
        proteinVariantAnnotation.setSubstitutionScores(getSubstitutionScores(query, null).getResult());
    }
    //        } catch (Exception e) {
    //            int a = 1;
    //        }

    QueryResult proteinVariantData = null;
    String shortAlternativeAa = aaShortNameMap.get(aaAlternate);
    if (shortAlternativeAa != null) {
        List<Bson> pipeline = new ArrayList<>();

        //            BasicDBList andDBList1 = new BasicDBList();
        //            andDBList1.add(new Document("dbReference.id", ensemblTranscriptId));
        //            andDBList1.add(new Document("feature.location.position.position", position));
        //            andDBList1.add(new Document("feature.variation", shortAlternativeAa));
        //            pipeline.add(new Document("$match", new Document("$and", andDBList1)));

        pipeline.add(new Document("$match", new Document("dbReference.id", ensemblTranscriptId)));

        Document projection = new Document();
        projection.put("accession", 1);
        projection.put("keyword", 1);
        projection.put("feature", 1);
        pipeline.add(new Document("$project", projection));

        pipeline.add(new Document("$unwind", "$feature"));

        BasicDBList andDBList2 = new BasicDBList();
        andDBList2.add(new Document("feature.location.position.position", position));
        andDBList2.add(new Document("feature.variation", shortAlternativeAa));
        Document firstOr = new Document("$and", andDBList2);
        BasicDBList andDBList3 = new BasicDBList();
        andDBList3.add(new Document("feature.location.end.position", new Document("$gte", position)));
        andDBList3.add(new Document("feature.location.begin.position", new Document("$lte", position)));
        Document secondOr = new Document();
        secondOr.put("$and", andDBList3);
        BasicDBList orList = new BasicDBList();
        orList.add(firstOr);
        orList.add(secondOr);
        pipeline.add(new Document("$match", new Document("$or", orList)));
        //            pipeline.add(new Document("$match", firstOr));
        //
        Document groupFields = new Document();
        groupFields.put("_id", "$accession");
        groupFields.put("keyword", new Document("$addToSet", "$keyword"));
        groupFields.put("feature", new Document("$addToSet", "$feature"));
        pipeline.add(new Document("$group", groupFields));

        //TODO:terminar el pipeline de agregacion
        //            QueryBuilder builder = QueryBuilder.start("dbReference.id").is(ensemblTranscriptId)
        //                    .and("feature.location.position.position").is(position)
        //                    .and("feature.variation").is(shortAlternativeAa);
        //
        //            Document firstOr = new Document();
        //            firstOr.put("location.position.position", position);
        //            firstOr.put("variation", shortAlternativeAa);
        //
        //            BasicDBList andList = new BasicDBList();
        //            andList.add(new Document("location.end.position", new Document("$gte", position)));
        //            andList.add(new Document("location.begin.position", new Document("$lte", position)));
        //            Document secondOr = new Document();
        //            secondOr.put("$and", andList);
        //
        //            BasicDBList orList = new BasicDBList();
        //            orList.add(firstOr);
        //            orList.add(secondOr);
        //
        //            Document elemMatch = new Document();
        //            elemMatch.put("$elemMatch", new Document("$or", orList));
        //
        //            Document projection = new Document();
        //            projection.put("feature", elemMatch);
        //
        //            QueryOptions localQueryOptions = new QueryOptions();
        //            localQueryOptions.put("elemMatch",projection);
        //            localQueryOptions.put("include","accession,keyword,feature");
        //            proteinVariantData = executeQuery(ensemblTranscriptId + "_" + String.valueOf(position) + "_"
        //                            + aaAlternate, new Document(builder.get().toMap()), localQueryOptions);
        proteinVariantData = executeAggregation2(
                ensemblTranscriptId + "_" + String.valueOf(position) + "_" + aaAlternate, pipeline,
                new QueryOptions());
        if (proteinVariantData.getNumResults() > 0) {
            proteinVariantAnnotation = processProteinVariantData(proteinVariantAnnotation, shortAlternativeAa,
                    (Document) proteinVariantData.getResult().get(0));
        }
    }

    long dbTimeEnd = System.currentTimeMillis();
    queryResult.setDbTime(Long.valueOf(dbTimeEnd - dbTimeStart).intValue());

    //        if (proteinVariantAnnotation.getSubstitutionScores() != null || proteinVariantAnnotation.getUniprotAccession() != null) {
    queryResult.setNumResults(1);
    queryResult.setResult(Collections.singletonList(proteinVariantAnnotation));
    //        }
    return queryResult;
}

From source file:org.opencb.cellbase.mongodb.db.ClinicalMongoDBAdaptor.java

License:Apache License

private DBObject getClinvarRegionFilterDBObject(List<Region> regionList) {
    BasicDBList orDBList = new BasicDBList();
    for (Region region : regionList) {
        BasicDBList andDBList = new BasicDBList();
        andDBList.add(new BasicDBObject("chromosome", region.getChromosome()));
        andDBList.add(new BasicDBObject("end", new BasicDBObject("$gte", region.getStart())));
        andDBList.add(new BasicDBObject("start", new BasicDBObject("$lte", region.getEnd())));
        orDBList.add(new BasicDBObject("$and", andDBList));
    }/*from  w  w  w .jav  a 2s.c o m*/

    return new BasicDBObject("$match", new BasicDBObject("$or", orDBList));
}

From source file:org.opencb.cellbase.mongodb.db.ClinicalMongoDBAdaptor.java

License:Apache License

private QueryBuilder addClinvarRegionFilter(QueryBuilder builder, QueryOptions options) {
    List<Object> regions = options.getList("region", null);
    BasicDBList regionList = new BasicDBList();
    if (regions != null) {
        Region region = (Region) regions.get(0);
        QueryBuilder regionQueryBuilder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("end")
                .greaterThanEquals(region.getStart()).and("start").lessThanEquals(region.getEnd());
        for (int i = 1; i < regions.size(); i++) {
            region = (Region) regions.get(i);
            regionQueryBuilder = regionQueryBuilder.or(QueryBuilder.start("chromosome")
                    .is(region.getChromosome()).and("end").greaterThanEquals(region.getStart()).and("start")
                    .lessThanEquals(region.getEnd()).get());
        }//from   ww  w  .ja  v  a  2s. c  om
        builder = builder.and(regionQueryBuilder.get());
    }
    return builder;
}

From source file:org.opencb.cellbase.mongodb.db.ClinicalMongoDBAdaptor.java

License:Apache License

private QueryBuilder addClinvarGeneFilter(QueryBuilder builder, QueryOptions options) {
    List<Object> genes = options.getList("gene", null);
    BasicDBList geneSymbols = new BasicDBList();
    if (genes != null && genes.size() > 0) {
        geneSymbols.addAll(genes);//from   w ww  .j av  a2s.  c o m
        builder = builder.and(
                "clinvarList.clinvarSet.referenceClinVarAssertion.measureSet.measure.measureRelationship.symbol.elementValue.value")
                .in(geneSymbols);
    }
    return builder;
}

From source file:org.opencb.cellbase.mongodb.db.ClinicalMongoDBAdaptor.java

License:Apache License

private List<QueryResult> prepareClinvarQueryResultList(List<QueryResult> clinicalQueryResultList) {
    List<QueryResult> queryResultList = new ArrayList<>();
    for (QueryResult clinicalQueryResult : clinicalQueryResultList) {
        QueryResult queryResult = new QueryResult();
        queryResult.setId(clinicalQueryResult.getId());
        queryResult.setDbTime(clinicalQueryResult.getDbTime());
        BasicDBList basicDBList = new BasicDBList();
        int numResults = 0;
        for (BasicDBObject clinicalRecord : (List<BasicDBObject>) clinicalQueryResult.getResult()) {
            if (clinicalRecord.containsKey("clinvarList")) {
                basicDBList.add(clinicalRecord);
                numResults += 1;//w w w .  j a v  a2s  .  c  om
            }
        }
        queryResult.setResult(basicDBList);
        queryResult.setNumResults(numResults);
        queryResultList.add(queryResult);
    }
    return queryResultList;
}

From source file:org.opencb.cellbase.mongodb.db.ConservationMongoDBAdaptor.java

License:Apache License

@Deprecated
@Override//ww w. j a v  a2 s  .  c o m
public List<QueryResult> getAllByRegionList(List<Region> regions, QueryOptions options) {
    //TODO not finished yet
    List<DBObject> queries = new ArrayList<>();
    List<String> ids = new ArrayList<>(regions.size());
    List<String> integerChunkIds;
    for (Region region : regions) {
        integerChunkIds = new ArrayList<>();
        // positions below 1 are not allowed
        if (region.getStart() < 1) {
            region.setStart(1);
        }
        if (region.getEnd() < 1) {
            region.setEnd(1);
        }

        /****/
        QueryBuilder builder;
        int regionChunkStart = getChunkId(region.getStart(), this.chunkSize);
        int regionChunkEnd = getChunkId(region.getEnd(), this.chunkSize);
        if (regionChunkStart == regionChunkEnd) {
            builder = QueryBuilder.start("_chunkIds")
                    .is(getChunkIdPrefix(region.getChromosome(), region.getStart(), this.chunkSize));
        } else {
            //                for (int chunkId = regionChunkStart; chunkId <= regionChunkEnd; chunkId++) {
            ////                    integerChunkIds.add(chunkId);
            //                    integerChunkIds.add(region.getChromosome() + "_" + chunkId + "_" + this.chunkSize/1000 + "k");
            //                }
            //                builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("chunkId").in(integerChunkIds);
            builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("end")
                    .greaterThanEquals(region.getStart()).and("start").lessThanEquals(region.getEnd());
        }
        //            QueryBuilder builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("chunkId").in(hunkIds);
        /****/

        queries.add(builder.get());
        ids.add(region.toString());

        logger.info(builder.get().toString());
    }

    List<QueryResult> queryResults = executeQueryList(ids, queries, options);

    for (int i = 0; i < regions.size(); i++) {
        Region region = regions.get(i);
        QueryResult queryResult = queryResults.get(i);
        BasicDBList list = (BasicDBList) queryResult.getResult();

        Map<String, List<Float>> typeMap = new HashMap();

        //            int start = region.getStart();

        for (int j = 0; j < list.size(); j++) {
            BasicDBObject chunk = (BasicDBObject) list.get(j);
            String type = chunk.getString("type");
            List<Float> valuesList;
            if (!typeMap.containsKey(type)) {
                valuesList = new ArrayList<>(region.getEnd() - region.getStart() + 1);
                for (int val = 0; val < region.getEnd() - region.getStart() + 1; val++) {
                    valuesList.add(null);
                }
                typeMap.put(type, valuesList);
            } else {
                valuesList = typeMap.get(type);
            }

            BasicDBList valuesChunk = (BasicDBList) chunk.get("values");

            int pos = 0;
            if (region.getStart() > chunk.getInt("start")) {
                pos = region.getStart() - chunk.getInt("start");
            }

            for (; pos < valuesChunk.size() && (pos + chunk.getInt("start") <= region.getEnd()); pos++) {
                //                    System.out.println("valuesList SIZE = " + valuesList.size());
                //                    System.out.println("pos = " + pos);
                //                    System.out.println("DIV " + (chunk.getInt("start") - region.getStart()));
                //                    System.out.println("valuesChunk = " + valuesChunk.get(pos));
                //                    System.out.println("indexFinal = " + (pos + chunk.getInt("start") - region.getStart()));
                valuesList.set(pos + chunk.getInt("start") - region.getStart(),
                        new Float((Double) valuesChunk.get(pos)));
            }
        }
        //
        BasicDBList resultList = new BasicDBList();
        ConservedRegionFeature conservedRegionChunk;
        for (Map.Entry<String, List<Float>> elem : typeMap.entrySet()) {
            conservedRegionChunk = new ConservedRegionFeature(region.getChromosome(), region.getStart(),
                    region.getEnd(), elem.getKey(), elem.getValue());
            resultList.add(conservedRegionChunk);
        }
        queryResult.setResult(resultList);
    }

    return queryResults;
}

From source file:org.opencb.cellbase.mongodb.db.ConservationMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getAllScoresByRegionList(List<Region> regions, QueryOptions options) {
    //TODO not finished yet
    List<DBObject> queries = new ArrayList<>();
    List<String> ids = new ArrayList<>(regions.size());
    List<Integer> integerChunkIds;
    for (Region region : regions) {
        integerChunkIds = new ArrayList<>();
        // positions below 1 are not allowed
        if (region.getStart() < 1) {
            region.setStart(1);/*w w  w  .  j a  v a  2 s  .  c o m*/
        }
        if (region.getEnd() < 1) {
            region.setEnd(1);
        }

        /****/
        QueryBuilder builder;
        int regionChunkStart = getChunkId(region.getStart(), this.chunkSize);
        int regionChunkEnd = getChunkId(region.getEnd(), this.chunkSize);
        if (regionChunkStart == regionChunkEnd) {
            builder = QueryBuilder.start("_chunkIds")
                    .is(getChunkIdPrefix(region.getChromosome(), region.getStart(), chunkSize));
        } else {
            //                for (int chunkId = regionChunkStart; chunkId <= regionChunkEnd; chunkId++) {
            //                    integerChunkIds.add(chunkId);
            //                }
            //    //            QueryBuilder builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("chunkId").in(hunkIds);
            //                builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("chunkId").in(integerChunkIds);
            builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("end")
                    .greaterThanEquals(region.getStart()).and("start").lessThanEquals(region.getEnd());
        }
        /****/

        queries.add(builder.get());
        ids.add(region.toString());

        logger.info(builder.get().toString());

    }
    List<QueryResult> queryResults = executeQueryList2(ids, queries, options);
    //        List<QueryResult> queryResults = executeQueryList(ids, queries, options);

    for (int i = 0; i < regions.size(); i++) {
        Region region = regions.get(i);
        QueryResult queryResult = queryResults.get(i);
        List<BasicDBObject> list = (List<BasicDBObject>) queryResult.getResult();

        Map<String, List<Float>> typeMap = new HashMap();

        //            int start = region.getStart();

        for (int j = 0; j < list.size(); j++) {
            BasicDBObject chunk = (BasicDBObject) list.get(j);
            String type = chunk.getString("type");
            List<Float> valuesList;
            if (!typeMap.containsKey(type)) {
                valuesList = new ArrayList<>(region.getEnd() - region.getStart() + 1);
                for (int val = 0; val < region.getEnd() - region.getStart() + 1; val++) {
                    valuesList.add(null);
                }
                typeMap.put(type, valuesList);
            } else {
                valuesList = typeMap.get(type);
            }

            BasicDBList valuesChunk = (BasicDBList) chunk.get("values");

            int pos = 0;
            if (region.getStart() > chunk.getInt("start")) {
                pos = region.getStart() - chunk.getInt("start");
            }

            for (; pos < valuesChunk.size() && (pos + chunk.getInt("start") <= region.getEnd()); pos++) {
                valuesList.set(pos + chunk.getInt("start") - region.getStart(),
                        new Float((Double) valuesChunk.get(pos)));
            }
        }

        BasicDBList resultList = new BasicDBList();
        for (Map.Entry<String, List<Float>> elem : typeMap.entrySet()) {
            for (Float value : elem.getValue()) {
                resultList.add(value != null ? (new Score(new Double(value), elem.getKey())) : null);
            }
        }
        queryResult.setResult(resultList);
    }

    return queryResults;
}

From source file:org.opencb.cellbase.mongodb.db.core.ConservationMongoDBAdaptor.java

License:Apache License

@Deprecated
@Override/*from   w  w  w  .j  a v  a 2  s .  c o  m*/
public List<QueryResult> getAllByRegionList(List<Region> regions, QueryOptions options) {
    //TODO not finished yet
    List<DBObject> queries = new ArrayList<>();
    List<String> ids = new ArrayList<>(regions.size());
    List<String> integerChunkIds;
    for (Region region : regions) {
        integerChunkIds = new ArrayList<>();
        // positions below 1 are not allowed
        if (region.getStart() < 1) {
            region.setStart(1);
        }
        if (region.getEnd() < 1) {
            region.setEnd(1);
        }

        // Max region size is 10000bp
        if (region.getEnd() - region.getStart() > 10000) {
            region.setEnd(region.getStart() + 10000);
        }

        QueryBuilder builder;
        int regionChunkStart = getChunkId(region.getStart(), this.chunkSize);
        int regionChunkEnd = getChunkId(region.getEnd(), this.chunkSize);
        if (regionChunkStart == regionChunkEnd) {
            builder = QueryBuilder.start("_chunkIds")
                    .is(getChunkIdPrefix(region.getChromosome(), region.getStart(), this.chunkSize));
        } else {
            //                for (int chunkId = regionChunkStart; chunkId <= regionChunkEnd; chunkId++) {
            ////                    integerChunkIds.add(chunkId);
            //                    integerChunkIds.add(region.getChromosome() + "_" + chunkId + "_" + this.chunkSize/1000 + "k");
            //                }
            //                builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("chunkId").in(integerChunkIds);
            builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("end")
                    .greaterThanEquals(region.getStart()).and("start").lessThanEquals(region.getEnd());
        }
        //            QueryBuilder builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("chunkId").in(hunkIds);
        /****/

        queries.add(builder.get());
        ids.add(region.toString());

        logger.debug(builder.get().toString());
    }

    List<QueryResult> queryResults = executeQueryList2(ids, queries, options);
    for (int i = 0; i < regions.size(); i++) {
        Region region = regions.get(i);
        QueryResult queryResult = queryResults.get(i);
        //            BasicDBList list = (BasicDBList) queryResult.getResult();
        List list = queryResult.getResult();

        Map<String, List<Float>> typeMap = new HashMap();

        //            int start = region.getStart();

        for (int j = 0; j < list.size(); j++) {
            BasicDBObject chunk = (BasicDBObject) list.get(j);
            String type = chunk.getString("type");
            List<Float> valuesList;
            if (!typeMap.containsKey(type)) {
                valuesList = new ArrayList<>(region.getEnd() - region.getStart() + 1);
                for (int val = 0; val < region.getEnd() - region.getStart() + 1; val++) {
                    valuesList.add(null);
                }
                typeMap.put(type, valuesList);
            } else {
                valuesList = typeMap.get(type);
            }

            BasicDBList valuesChunk = (BasicDBList) chunk.get("values");

            int pos = 0;
            if (region.getStart() > chunk.getInt("start")) {
                pos = region.getStart() - chunk.getInt("start");
            }

            for (; pos < valuesChunk.size() && (pos + chunk.getInt("start") <= region.getEnd()); pos++) {
                //                    System.out.println("valuesList SIZE = " + valuesList.size());
                //                    System.out.println("pos = " + pos);
                //                    System.out.println("DIV " + (chunk.getInt("start") - region.getStart()));
                //                    System.out.println("valuesChunk = " + valuesChunk.get(pos));
                //                    System.out.println("indexFinal = " + (pos + chunk.getInt("start") - region.getStart()));
                valuesList.set(pos + chunk.getInt("start") - region.getStart(),
                        new Float((Double) valuesChunk.get(pos)));
            }
        }
        //
        BasicDBList resultList = new BasicDBList();
        ConservedRegionFeature conservedRegionChunk;
        for (Map.Entry<String, List<Float>> elem : typeMap.entrySet()) {
            conservedRegionChunk = new ConservedRegionFeature(region.getChromosome(), region.getStart(),
                    region.getEnd(), elem.getKey(), elem.getValue());
            resultList.add(conservedRegionChunk);
        }
        queryResult.setResult(resultList);
    }

    return queryResults;
}

From source file:org.opencb.cellbase.mongodb.db.core.ConservationMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getAllScoresByRegionList(List<Region> regions, QueryOptions options) {
    //TODO not finished yet
    List<DBObject> queries = new ArrayList<>();
    List<String> ids = new ArrayList<>(regions.size());
    List<Integer> integerChunkIds;
    for (Region region : regions) {
        integerChunkIds = new ArrayList<>();
        // positions below 1 are not allowed
        if (region.getStart() < 1) {
            region.setStart(1);/*from  ww  w  .  j a  v  a  2s .  co m*/
        }
        if (region.getEnd() < 1) {
            region.setEnd(1);
        }

        /****/
        QueryBuilder builder;
        int regionChunkStart = getChunkId(region.getStart(), this.chunkSize);
        int regionChunkEnd = getChunkId(region.getEnd(), this.chunkSize);
        if (regionChunkStart == regionChunkEnd) {
            builder = QueryBuilder.start("_chunkIds")
                    .is(getChunkIdPrefix(region.getChromosome(), region.getStart(), chunkSize));
        } else {
            //                for (int chunkId = regionChunkStart; chunkId <= regionChunkEnd; chunkId++) {
            //                    integerChunkIds.add(chunkId);
            //                }
            //    //            QueryBuilder builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("chunkId").in(hunkIds);
            //                builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("chunkId").in(integerChunkIds);
            builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("end")
                    .greaterThanEquals(region.getStart()).and("start").lessThanEquals(region.getEnd());
        }
        /****/

        queries.add(builder.get());
        ids.add(region.toString());

        logger.debug(builder.get().toString());

    }
    List<QueryResult> queryResults = executeQueryList2(ids, queries, options);
    //        List<QueryResult> queryResults = executeQueryList(ids, queries, options);

    for (int i = 0; i < regions.size(); i++) {
        Region region = regions.get(i);
        QueryResult queryResult = queryResults.get(i);
        List<BasicDBObject> list = (List<BasicDBObject>) queryResult.getResult();

        Map<String, List<Float>> typeMap = new HashMap();

        //            int start = region.getStart();

        for (int j = 0; j < list.size(); j++) {
            BasicDBObject chunk = (BasicDBObject) list.get(j);
            String type = chunk.getString("type");
            List<Float> valuesList;
            if (!typeMap.containsKey(type)) {
                valuesList = new ArrayList<>(region.getEnd() - region.getStart() + 1);
                for (int val = 0; val < region.getEnd() - region.getStart() + 1; val++) {
                    valuesList.add(null);
                }
                typeMap.put(type, valuesList);
            } else {
                valuesList = typeMap.get(type);
            }

            BasicDBList valuesChunk = (BasicDBList) chunk.get("values");

            int pos = 0;
            if (region.getStart() > chunk.getInt("start")) {
                pos = region.getStart() - chunk.getInt("start");
            }

            for (; pos < valuesChunk.size() && (pos + chunk.getInt("start") <= region.getEnd()); pos++) {
                valuesList.set(pos + chunk.getInt("start") - region.getStart(),
                        new Float((Double) valuesChunk.get(pos)));
            }
        }

        BasicDBList resultList = new BasicDBList();
        for (Map.Entry<String, List<Float>> elem : typeMap.entrySet()) {
            for (Float value : elem.getValue()) {
                if (value != null) {
                    resultList.add(new Score(new Double(value), elem.getKey()));
                }
            }
        }
        if (!resultList.isEmpty()) {
            queryResult.setResult(resultList);
        } else {
            queryResult.setResult(null);
        }
    }

    return queryResults;
}

From source file:org.opencb.cellbase.mongodb.db.core.GeneMongoDBAdaptor.java

License:Apache License

@Override
public QueryResult getAll(QueryOptions options) {
    QueryBuilder builder = new QueryBuilder();

    List<String> biotypes = options.getAsStringList("biotype");
    if (biotypes != null && biotypes.size() > 0) {
        BasicDBList biotypeIds = new BasicDBList();
        biotypeIds.addAll(biotypes);/*  w w  w. j av a  2s.c om*/
        builder = builder.and("biotype").in(biotypeIds);
    }

    return executeQuery("result", builder.get(), options);
}