/*
* 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.
*/
/*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.broad.igv.tools.sort;
import htsjdk.tribble.readers.AsciiLineReader;
import java.io.File;
import java.io.IOException;
import java.io.PrintWriter;
/**
* @author jrobinso
*/
public class GenericSorter extends AsciiSorter {
private int chrCol;
private int startCol;
public GenericSorter(File inputFile, File outputFile, int chrCol, int startCol) {
super(inputFile, outputFile);
this.chrCol = chrCol;
this.startCol = startCol;
}
@Override
Parser getParser() {
return new Parser(chrCol, startCol);
}
@Override
String writeHeader(AsciiLineReader reader, PrintWriter writer) throws IOException {
String nextLine = reader.readLine();
if (nextLine.startsWith("psLayout")) {
do {
writer.println(nextLine);
nextLine = reader.readLine();
} while (!nextLine.startsWith("-"));
nextLine = reader.readLine();
}
// TODO -- check "browser" line syntax, is it a multi-line directive?
while (nextLine.startsWith("#") ||
nextLine.startsWith("browser") ||
nextLine.startsWith("track") ||
nextLine.trim().length() == 0) {
writer.println(nextLine);
nextLine = reader.readLine();
}
return nextLine;
}
}