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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.client.rest;

import org.opencb.biodata.models.core.*;
import org.opencb.biodata.models.variant.Variant;
import org.opencb.biodata.models.variant.avro.Repeat;
import org.opencb.cellbase.client.config.ClientConfiguration;
import org.opencb.cellbase.core.result.CellBaseDataResponse;
import org.opencb.commons.datastore.core.QueryOptions;


import java.io.IOException;
import java.util.List;

/**
 * Created by imedina on 26/05/16.
 */
public class GenomicRegionClient extends ParentRestClient {

    GenomicRegionClient(String species, String assembly, String dataRelease, String apiKey, ClientConfiguration clientConfiguration) {
        super(species, assembly, dataRelease, apiKey, clientConfiguration);

        this.clazz = GenomeSequenceFeature.class;

        this.category = "genomic";
        this.subcategory = "region";
    }


    public CellBaseDataResponse getGene(List id, QueryOptions options) throws IOException {
        return execute(id, "gene", options, Gene.class);
    }

    public CellBaseDataResponse getTranscript(List id, QueryOptions options) throws IOException {
        return execute(id, "transcript", options, Transcript.class);
    }

    public CellBaseDataResponse getRepeat(List id, QueryOptions options) throws IOException {
        return execute(id, "repeat", options, Repeat.class);
    }

    public CellBaseDataResponse getVariant(List id, QueryOptions options) throws IOException {
        return execute(id, "variant", options, Variant.class);
    }

    public CellBaseDataResponse getSequence(List id, QueryOptions options) throws IOException {
        return execute(id, "sequence", options, GenomeSequenceFeature.class);
    }

    public CellBaseDataResponse getRegulatory(List id, QueryOptions options) throws IOException {
        return execute(id, "regulatory", options, RegulatoryFeature.class);
    }

    public CellBaseDataResponse getTfbs(List id, QueryOptions options) throws IOException {
        return execute(id, "tfbs", options, RegulatoryFeature.class);
    }

    public CellBaseDataResponse getConservation(List id, QueryOptions options) throws IOException {
        return execute(id, "conservation", options, GenomicScoreRegion.class);
    }

//    public CellBaseDataResponse<> getClinical(String id, QueryOptions options) throws IOException {
//        return execute(id, "clinical", options, .class);
//    }
}