org.opencb.cellbase.mongodb.db.ProteinFunctionPredictorMongoDBAdaptor.java Source code

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Here is the source code for org.opencb.cellbase.mongodb.db.ProteinFunctionPredictorMongoDBAdaptor.java

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/*
 * Copyright 2015 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */

package org.opencb.cellbase.mongodb.db;

import com.mongodb.*;
import org.opencb.cellbase.core.lib.api.core.ProteinFunctionPredictorDBAdaptor;
import org.opencb.datastore.core.QueryOptions;
import org.opencb.datastore.core.QueryResult;
import org.opencb.datastore.mongodb.MongoDataStore;

import java.util.*;

/**
 * Created by imedina on 10/12/13.
 */
public class ProteinFunctionPredictorMongoDBAdaptor extends MongoDBAdaptor
        implements ProteinFunctionPredictorDBAdaptor {

    private static Map<String, String> aaShortName = new HashMap();

    static {
        aaShortName.put("ALA", "A");
        aaShortName.put("ARG", "R");
        aaShortName.put("ASN", "N");
        aaShortName.put("ASP", "D");
        aaShortName.put("CYS", "C");
        aaShortName.put("GLN", "Q");
        aaShortName.put("GLU", "E");
        aaShortName.put("GLY", "G");
        aaShortName.put("HIS", "H");
        aaShortName.put("ILE", "I");
        aaShortName.put("LEU", "L");
        aaShortName.put("LYS", "K");
        aaShortName.put("MET", "M");
        aaShortName.put("PHE", "F");
        aaShortName.put("PRO", "P");
        aaShortName.put("SER", "S");
        aaShortName.put("THR", "T");
        aaShortName.put("TRP", "W");
        aaShortName.put("TYR", "Y");
        aaShortName.put("VAL", "V");
    }

    public ProteinFunctionPredictorMongoDBAdaptor(DB db) {
        super(db);
    }

    public ProteinFunctionPredictorMongoDBAdaptor(DB db, String species, String version) {
        super(db, species, version);
        mongoDBCollection = db.getCollection("protein_functional_prediction");

        logger.info("ProteinFunctionPredictorMongoDBAdaptor: in 'constructor'");
    }

    public ProteinFunctionPredictorMongoDBAdaptor(String species, String assembly, MongoDataStore mongoDataStore) {
        super(species, assembly, mongoDataStore);
        mongoDBCollection = db.getCollection("protein_functional_prediction");
        mongoDBCollection2 = mongoDataStore.getCollection("protein_functional_prediction");

        logger.info("ProteinFunctionPredictorMongoDBAdaptor: in 'constructor'");
    }

    @Override
    public QueryResult getAllByEnsemblTranscriptId(String transcriptId, QueryOptions options) {
        return getAllByEnsemblTranscriptIdList(Arrays.asList(transcriptId), options).get(0);
    }

    @Override
    public List<QueryResult> getAllByEnsemblTranscriptIdList(List<String> transcriptIdList, QueryOptions options) {
        List<DBObject> queries = new ArrayList<>(transcriptIdList.size());

        if (options.containsKey("aaPosition")) {
            if (options.containsKey("aaChange")) {
                addIncludeReturnFields(
                        "aaPositions." + options.getString("aaPosition") + "." + options.getString("aaChange"),
                        options);
            } else {
                addIncludeReturnFields("aaPositions." + options.getString("aaPosition"), options);
            }
        }

        for (String id : transcriptIdList) {
            QueryBuilder builder = QueryBuilder.start("transcriptId").is(id);
            queries.add(builder.get());
        }

        //        options = addExcludeReturnFields("transcripts", options);
        return executeQueryList(transcriptIdList, queries, options);
    }

    public QueryResult getByAaChange(String transcriptId, Integer aaPosition, String newAa,
            QueryOptions queryOptions) {

        QueryBuilder builder = QueryBuilder.start("transcriptId").is(transcriptId);
        QueryResult allChangesQueryResult = executeQuery(transcriptId, builder.get(), queryOptions);

        QueryResult proteinSubstitionScoresQueryResult = new QueryResult();
        proteinSubstitionScoresQueryResult.setDbTime(allChangesQueryResult.getDbTime());
        proteinSubstitionScoresQueryResult.setId(transcriptId + "-" + aaPosition + "-" + newAa);

        String currentAaShortName;
        Map aaPositions;
        if (allChangesQueryResult.getNumResults() > 0 && (currentAaShortName = aaShortName.get(newAa)) != null
                && (aaPositions = ((HashMap) ((BasicDBObject) allChangesQueryResult.getResult().get(0))
                        .get("aaPositions"))) != null) {
            proteinSubstitionScoresQueryResult.setNumResults(1);
            proteinSubstitionScoresQueryResult.setResult(Arrays.asList(
                    ((BasicDBObject) aaPositions.get(Integer.toString(aaPosition))).get(currentAaShortName)));
        } else {
            proteinSubstitionScoresQueryResult.setNumResults(0);
        }

        return proteinSubstitionScoresQueryResult;
    }

}