/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 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 org.broad.igv.feature.genome;
import org.apache.log4j.Logger;
import org.broad.igv.Globals;
import org.broad.igv.feature.Chromosome;
import org.broad.igv.util.ParsingUtils;
import java.io.BufferedReader;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
/**
* @author jrobinso
* Date: 4/16/13
* Time: 2:25 PM
*/
public class ChromSizesParser {
private static Logger log = Logger.getLogger(ChromSizesParser.class);
public static List<Chromosome> parse(String path) throws IOException {
BufferedReader br = null;
try {
br = ParsingUtils.openBufferedReader(path);
List<Chromosome> chromosomes = new ArrayList<Chromosome>();
String nextLine;
int idx = 0;
while ((nextLine = br.readLine()) != null) {
String[] tokens = Globals.whitespacePattern.split(nextLine);
if (tokens.length >= 2) {
String chr = tokens[0];
int length = Integer.parseInt(tokens[1]);
chromosomes.add(new Chromosome(idx, chr, length));
idx++;
} else {
log.info("Unexpected # of tokens at line: " + nextLine);
}
}
return chromosomes;
} finally {
if (br != null) br.close();
}
}
}