org.opencb.opencga.storage.mongodb.variant.VariantMongoDBIterator.java Source code

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Here is the source code for org.opencb.opencga.storage.mongodb.variant.VariantMongoDBIterator.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.opencga.storage.mongodb.variant;

import com.mongodb.DBCursor;
import com.mongodb.DBObject;
import org.opencb.biodata.models.variant.Variant;
import org.opencb.opencga.storage.core.variant.adaptors.VariantDBIterator;

/**
 * Created by jacobo on 9/01/15.
 */
public class VariantMongoDBIterator extends VariantDBIterator {

    private DBCursor dbCursor;
    private DBObjectToVariantConverter dbObjectToVariantConverter;

    VariantMongoDBIterator(DBCursor dbCursor, DBObjectToVariantConverter dbObjectToVariantConverter) { //Package protected
        this(dbCursor, dbObjectToVariantConverter, 100);
    }

    VariantMongoDBIterator(DBCursor dbCursor, DBObjectToVariantConverter dbObjectToVariantConverter,
            int batchSize) { //Package protected
        this.dbCursor = dbCursor;
        this.dbObjectToVariantConverter = dbObjectToVariantConverter;
        if (batchSize > 0) {
            dbCursor.batchSize(batchSize);
        }
    }

    @Override
    public boolean hasNext() {
        return dbCursor.hasNext();
    }

    @Override
    public Variant next() {
        long start = System.currentTimeMillis();
        DBObject dbObject;
        dbObject = dbCursor.next();
        timeFetching += System.currentTimeMillis() - start;
        start = System.currentTimeMillis();
        Variant variant = dbObjectToVariantConverter.convertToDataModelType(dbObject);
        timeConverting += System.currentTimeMillis() - start;

        return variant;
    }

    @Override
    public void remove() {
        throw new UnsupportedOperationException("can't remove from a cursor");
    }

}