Package picard.illumina.parser

Source Code of picard.illumina.parser.BarcodeParser$BarcodeDataIterator

/*
* The MIT License
*
* Copyright (c) 2009 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package picard.illumina.parser;

import htsjdk.samtools.util.CloseableIterator;
import htsjdk.samtools.util.CollectionUtil;
import picard.illumina.parser.readers.BarcodeFileReader;

import java.io.File;
import java.util.Collections;
import java.util.Set;

/**
* @author jburke@broadinstitute.org
*/
class BarcodeParser extends PerTileParser<BarcodeData> {

    private static final Set<IlluminaDataType> SUPPORTED_TYPES = Collections.unmodifiableSet(CollectionUtil.makeSet(IlluminaDataType.Barcodes));

    public BarcodeParser(final IlluminaFileMap tilesToFiles) {
        super(tilesToFiles);
    }

    public BarcodeParser(final IlluminaFileMap tilesToFiles, final int nextTile) {
        super(tilesToFiles, nextTile);
    }

    @Override
    protected CloseableIterator<BarcodeData> makeTileIterator(File nextTileFile) {
        return new BarcodeDataIterator(nextTileFile);
    }

    public Set<IlluminaDataType> supportedTypes() {
        return SUPPORTED_TYPES;
    }

    private static class BarcodeDataIterator implements CloseableIterator<BarcodeData>{
        private BarcodeFileReader bfr;
        public BarcodeDataIterator(final File file) {
            bfr = new BarcodeFileReader(file);
        }

        public void close() {
            bfr.close();
        }

        public boolean hasNext() {
            return bfr.hasNext();
        }

        public BarcodeData next() {
            return new BarcodeData() {
                public String getBarcode() {
                    return bfr.next();
                }
            };
        }

        public void remove() {
            throw new UnsupportedOperationException();
        }
    }
}
TOP

Related Classes of picard.illumina.parser.BarcodeParser$BarcodeDataIterator

TOP
Copyright © 2018 www.massapi.com. All rights reserved.
All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.