/*
* 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 java.io.File;
import java.util.ArrayList;
import java.util.List;
import java.util.TreeMap;
/**
* For "non-cycle" files (files that have multiple cycles per file). Maps a Tile -> File
* @author jburke@broadinstitute.org
*/
class IlluminaFileMap extends TreeMap<Integer, File> {
/** Return a file map that includes only the tiles listed */
public IlluminaFileMap keep(final List<Integer> tilesToKeep) {
final IlluminaFileMap fileMap = new IlluminaFileMap();
for(final Integer tile : tilesToKeep) {
final File file = this.get(tile);
if(file != null) {
fileMap.put(tile, file);
}
}
return fileMap;
}
/**
* Return the List of Files in order starting at the given tile and containing all files with tile numbers greater than startingTile that
* are within this map
* @param startingTile The first File in the returned list will correspond to this tile
* @return A List of files for all tiles >= startingTile that are contained in this FileMap
*/
public List<File> getFilesStartingAt(final int startingTile) {
return new ArrayList<File>(this.tailMap(startingTile).values());
}
}