/*
* The MIT License
*
* Copyright (c) 2012 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.StringUtil;
import picard.PicardException;
import java.io.File;
import java.util.ArrayList;
import java.util.List;
import java.util.NoSuchElementException;
/** Abstract base class for Parsers that open a single tile file at a time and iterate through them. */
public abstract class PerTileParser<ILLUMINA_DATA extends IlluminaData> implements IlluminaParser<ILLUMINA_DATA> {
private final IlluminaFileMap tileToFiles;
private CloseableIterator<ILLUMINA_DATA> currentIterator;
private Integer nextTile;
private Integer currentTile;
/** Factory method for the iterator of each tile */
protected abstract CloseableIterator<ILLUMINA_DATA> makeTileIterator(final File nextTileFile);
public PerTileParser(final IlluminaFileMap tilesToFiles) {
this.tileToFiles = tilesToFiles;
this.nextTile = tilesToFiles.firstKey();
this.currentTile = null;
}
public PerTileParser(final IlluminaFileMap tilesToFiles, final int nextTile) {
this.tileToFiles = tilesToFiles;
this.currentTile = null;
this.nextTile = nextTile;
if(!tilesToFiles.containsKey(nextTile)) {
throw new IllegalArgumentException("NextTile (" + nextTile + ") is not contained by tilesToFiles (" + StringUtil.join(",", new ArrayList<Integer>(tilesToFiles.keySet())));
}
}
/**
* Return the tile of the NEXT ILLUMINA_DATA object to be returned by the method next. This might force us to advance to the
* next file (as it will contains the data for the next) tile/ILLUMINA_DATA object.
* @return tile number for the next ILLUMINA_DATA object to be returned
*/
public int getTileOfNextCluster() {
maybeAdvance();
return currentTile;
}
private void advanceTile() {
if(nextTile == null){
throw new NoSuchElementException("No more tiles to advance!");
}
if(currentIterator != null) {
currentIterator.close();
}
currentIterator = makeTileIterator(tileToFiles.get(nextTile));
currentTile = nextTile;
nextTile = tileToFiles.higherKey(nextTile);
}
public void seekToTile(int oneBasedTileNumber) {
nextTile = oneBasedTileNumber;
if(!tileToFiles.containsKey(oneBasedTileNumber)) {
throw new PicardException("PerTileParser does not contain key(" + oneBasedTileNumber +") keys available (" + StringUtil.join(",", new ArrayList<Integer>(tileToFiles.keySet())) + ")");
}
if(currentIterator != null) {
currentIterator.close();
}
currentIterator = null;
}
public void maybeAdvance() {
if(!hasNext()) {
throw new NoSuchElementException();
}
if(currentIterator == null || !currentIterator.hasNext()) {
advanceTile();
}
}
public ILLUMINA_DATA next() {
maybeAdvance();
return currentIterator.next();
}
public void remove() {
throw new UnsupportedOperationException();
}
public boolean hasNext() {
// Skip over empty tiles
while ((currentIterator == null || !currentIterator.hasNext()) && nextTile != null) {
advanceTile();
}
return currentIterator != null && currentIterator.hasNext();
}
public void close() {
if(currentIterator != null) {
currentIterator.close();
}
}
public void verifyData(List<Integer> tiles, final int [] cycles) {
final List<Integer> mapTiles = new ArrayList<Integer>(this.tileToFiles.keySet());
if(!mapTiles.containsAll(tiles)) {
throw new PicardException("Missing tiles in PerTileParser expected(" + StringUtil.join(",", tiles) + ") but found (" + StringUtil.join(",", mapTiles) + ")");
}
if(!tiles.containsAll(mapTiles)) {
throw new PicardException("Extra tiles where found in PerTileParser expected(" + StringUtil.join(",", tiles) + ") but found (" + StringUtil.join(",", mapTiles) + ")");
}
}
}