/*
* 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();
}
}
}