/*
* 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.peaks;
import org.broad.igv.Globals;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.feature.tribble.UCSCCodec;
/**
* Created by IntelliJ IDEA.
* User: jrobinso
* Date: Dec 20, 2009
* Time: 10:15:49 PM
* To change this template use File | Settings | File Templates.
*/
public class PeakCodec extends UCSCCodec<Peak> {
Genome genome;
public PeakCodec(Genome genome) {
super(Peak.class);
this.genome = genome;
}
// Declare a static array once, to be reused.
public Peak decode(String nextLine) {
if (nextLine.trim().length() == 0 || nextLine.startsWith("#") || nextLine.startsWith("track") ||
nextLine.startsWith("browser")) {
return null;
}
String [] tokens = Globals.singleTabMultiSpacePattern.split(nextLine);
int tokenCount = tokens.length;
String chrToken = tokens[0];
String chr = genome == null ? chrToken : genome.getCanonicalChrName(chrToken);
int start = Integer.parseInt(tokens[1]);
int end = Integer.parseInt(tokens[2]);
String name = tokens[3];
float combinedScore = Float.parseFloat(tokens[4]);
int nTimePoints = tokenCount - 5;
float[] timePointScores = new float[nTimePoints];
for (int i = 0; i < nTimePoints; i++) {
timePointScores[i] = Float.parseFloat(tokens[5 + i]);
}
return new Peak(chr, start, end, name, combinedScore, timePointScores);
}
/**
* This function returns true iff the File potentialInput can be parsed by this
* codec.
* <p/>
* There is an assumption that there's never a situation where two different Codecs
* return true for the same file. If this occurs, the recommendation would be to error out.
* <p/>
* Note this function must never throw an error. All errors should be trapped
* and false returned.
*
* @param path the file to test for parsability with this codec
* @return true if potentialInput can be parsed, false otherwise
*/
public boolean canDecode(String path) {
return false; //To change body of implemented methods use File | Settings | File Templates.
}
}