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/*
 * Copyright 2015-2020 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.lib.managers;

import org.opencb.biodata.models.core.Gene;
import org.opencb.biodata.models.core.GenomeSequenceFeature;
import org.opencb.biodata.models.core.Region;
import org.opencb.biodata.models.core.TranscriptTfbs;
import org.opencb.cellbase.core.api.GeneQuery;
import org.opencb.cellbase.core.api.query.ProjectionQueryOptions;
import org.opencb.cellbase.core.config.CellBaseConfiguration;
import org.opencb.cellbase.core.exception.CellBaseException;
import org.opencb.cellbase.core.result.CellBaseDataResult;
import org.opencb.cellbase.lib.impl.core.CellBaseCoreDBAdaptor;
import org.opencb.cellbase.lib.impl.core.GeneMongoDBAdaptor;
import org.opencb.cellbase.lib.impl.core.GenomeMongoDBAdaptor;
import org.opencb.commons.datastore.core.QueryOptions;

import java.util.ArrayList;
import java.util.List;

public class GeneManager extends AbstractManager implements AggregationApi {

    private GeneMongoDBAdaptor geneDBAdaptor;
    private GenomeMongoDBAdaptor genomeDBAdaptor;

    public GeneManager(String species, CellBaseConfiguration configuration) throws CellBaseException {
        this(species, null, configuration);
    }

    public GeneManager(String species, String assembly, CellBaseConfiguration configuration) throws CellBaseException {
        super(species, assembly, configuration);

        this.init();
    }

    private void init() {
        geneDBAdaptor = dbAdaptorFactory.getGeneDBAdaptor();
        genomeDBAdaptor = dbAdaptorFactory.getGenomeDBAdaptor();
    }

    @Override
    public CellBaseCoreDBAdaptor getDBAdaptor() {
        return geneDBAdaptor;
    }

    public List> info(List ids, ProjectionQueryOptions query, String source, int dataRelease,
                                               String apiKey) throws CellBaseException {
        return geneDBAdaptor.info(ids, query, source, dataRelease, apiKey);
    }

    public CellBaseDataResult getSequence(GeneQuery query) throws CellBaseException {
        // get the coordinates for the gene
        CellBaseDataResult geneCellBaseDataResult = geneDBAdaptor.query(query);
        // get the sequences for those coordinates
        if (geneCellBaseDataResult.getNumResults() > 0) {
            List results = geneCellBaseDataResult.getResults();
            Gene gene = results.get(0);
            Region region = new Region(gene.getChromosome(), gene.getStart(), gene.getEnd());
            return genomeDBAdaptor.getSequence(region, query.toQueryOptions(), query.getDataRelease());
        }
        return null;
    }

    public List> getSequence(List queries) throws CellBaseException {
        List> sequences = new ArrayList<>();
        for (GeneQuery query : queries) {
            sequences.add(getSequence(query));
        }
        return sequences;
    }

    public List> getTfbs(GeneQuery query) throws CellBaseException {
        List> geneQueryResults = new ArrayList<>();
        for (String gene : query.getIds()) {
            CellBaseDataResult geneQueryResult = geneDBAdaptor.getTfbs(gene, query.toQueryOptions(),
                    query.getDataRelease());
            geneQueryResult.setId(gene);
            geneQueryResults.add(geneQueryResult);
        }
        return geneQueryResults;
    }

    public CellBaseDataResult startsWith(String query, QueryOptions queryOptions, int dataRelease) throws CellBaseException {
        return geneDBAdaptor.startsWith(query, queryOptions, dataRelease);
    }

}