/*
* The MIT License
*
* Copyright (c) 2011 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.CloserUtil;
import picard.PicardException;
import picard.util.BasicInputParser;
import java.io.File;
import java.util.Iterator;
import java.util.List;
import java.util.NoSuchElementException;
/**
* Abstract class for parsing text-based whitespace-delimited Illumina output files, organized
* by tile. Concrete implementations must call setFiles() in order to provide the list of files
* to be iterated over.
*
* @author jburke@broadinstitute.org
*/
class IlluminaTextIterator implements Iterator<String[]> {
// Location of illumina output files to be parsed
private final int lane;
private int currentTile = 0;
// List of files of the given type, sorted by tile #
private IlluminaFileMap files;
private boolean treatGroupedDelimitersAsOne = true;
private BasicInputParser parser;
public IlluminaTextIterator(final int lane, final IlluminaFileMap files) {
this.lane = lane;
this.files = files;
currentTile = files.firstKey();
}
public IlluminaTextIterator(final int lane, final IlluminaFileMap files,
final boolean treatGroupedDelimitersAsOne) {
this(lane, files);
this.treatGroupedDelimitersAsOne = treatGroupedDelimitersAsOne;
currentTile = files.firstKey();
}
/**
* Jump so that the next record returned will be the first one from the specified tile.
*/
public void seekToTile(final int oneBasedTileNumber) {
CloserUtil.close(parser);
currentTile = oneBasedTileNumber;
initializeParser();
}
/**
* Prepare to iterate.
*/
private void initializeParser() {
final List<File> fileSubset = files.getFilesStartingAt(currentTile);
parser = new BasicInputParser(treatGroupedDelimitersAsOne, fileSubset.toArray(new File[fileSubset.size()]));
}
/**
* Read the next record from the list of input files, and load into data argument.
*/
@Override
public String [] next() {
if (!hasNext()) {
throw new NoSuchElementException();
}
return parser.next();
}
@Override
public void remove() {
throw new UnsupportedOperationException("Remove is not supported by IlluminaTextIterator");
}
public boolean hasNext() {
if(parser == null) initializeParser();
return parser.hasNext();
}
protected int getLane() {
return lane;
}
public String getCurrentFilename() {
if(parser == null) initializeParser();
return parser.getFileName();
}
protected void validateLane(final int lane) {
if (lane != getLane()) {
throw new PicardException("Lane number mismatch: " + lane + " != " + getLane());
}
}
}