/*
* 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 picard.PicardException;
import java.util.List;
import java.util.Set;
import java.util.TreeMap;
/**
* For per cycle files. Maps a Cycle -> Tile -> List<File>
*
* @author jburke@broadinstitute.org
*/
class CycleIlluminaFileMap extends TreeMap<Integer, IlluminaFileMap> {
/**
* Return a CycleIlluminaFileMap with only the tiles listed and all of the cycles provided.
* Important NOTE: this DOES NOT eliminate cycles from the cycles parameter passed in that are missing in the cyclesFileIterator of any given lane in the CycleIlluminaFileMap
*/
public CycleIlluminaFileMap keep(final List<Integer> tilesToKeep, final Set<Integer> cycles) {
final CycleIlluminaFileMap ciMap = new CycleIlluminaFileMap();
if (cycles != null) {
for (final int cycle : cycles) {
final IlluminaFileMap template = this.get(cycle);
if (template != null) {
ciMap.put(cycle, template.keep(tilesToKeep));
}
}
}
return ciMap;
}
/**
* Assert that this map has an iterator for all of the expectedTiles and each iterator has expectedCycles number
* of files. Also, assert that each cycle file for a given tile is the same size
*
* @param expectedTiles A list of tiles that should be in this map
* @param expectedCycles The total number of files(cycles) that should be in each CycledFilesIterator
*/
public void assertValid(final List<Integer> expectedTiles, final int[] expectedCycles) {
if (size() != expectedCycles.length) {
throw new PicardException("Expected CycledIlluminaFileMap to contain " + expectedCycles.length + " cycles but only " + size() + " were found!");
}
if (this.firstEntry().getValue().size() != expectedTiles.size()) {
throw new PicardException("Expected CycledIlluminaFileMap to contain " + expectedTiles.size()
+ " tiles but only " + this.firstEntry().getValue().size() + " were found!");
}
}
}