/*
* Copyright (c) 2007-2012 The Broad Institute, Inc.
* SOFTWARE COPYRIGHT NOTICE
* This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
*
* This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
*
* This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
* Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
*/
package org.broad.igv.feature.tribble;
import com.google.common.base.Function;
import com.google.common.base.Supplier;
import org.apache.commons.lang.StringUtils;
import org.broad.igv.AbstractHeadlessTest;
import org.broad.igv.Globals;
import org.broad.igv.feature.BasicFeature;
import org.broad.igv.track.Track;
import org.broad.igv.track.TrackLoader;
import org.broad.igv.util.ResourceLocator;
import org.broad.igv.util.TestUtils;
import org.junit.Ignore;
import org.junit.Test;
import java.util.List;
import static org.junit.Assert.assertTrue;
/**
* User: jacob
* Date: 2012-Dec-11
*/
@Ignore("No Runnable Tests")
public class IGVBEDCodecTest extends AbstractHeadlessTest {
@Ignore("We always ignore this test anyway, performance not consistent")
@Test
public void decodeSpeedTest() throws Exception {
long benchTime = TestUtils.getBenchmarkTime();
int nTrials = 5000000;
BEDStringSupplier supplier = new BEDStringSupplier(nTrials);
final IGVBEDCodec codec = new IGVBEDCodec();
Function<String, Void> decodeFunc = new Function<String, Void>(){
@Override
public Void apply(String input) {
BasicFeature feat = codec.decode(input);
return null;
}
};
supplier.reset();
String jVersion = System.getProperty(Globals.JAVA_VERSION_STRING);
System.out.println("\nIGVBEDCodec.decode. java version " + jVersion);
long[] times = TestUtils.timeMethod(supplier, decodeFunc, nTrials);
//Calculate average (in nanoseconds)
double average = TestUtils.average(times);
long median = times[times.length / 2];
//we are somewhat forgiving, for the sake of portability. Less than 2 uSec okay, even if it
//breaks benchmark
int maxMultiplier = 200000;
int maxMedian = 3000;
if (jVersion.contains("1.7")) {
maxMultiplier = 10000;
maxMedian = 2000;
}
assertTrue("Decoding median speed too slow", median < benchTime / maxMultiplier || median < maxMedian);
}
public void timeLoadBigFile() throws Exception {
//File not in repo
final String path = "GSM288345_Nanog.bed";
Supplier<String> supplier = new Supplier<String>() {
@Override
public String get() {
return path;
}
};
final TrackLoader loader = new TrackLoader();
Function<String, Void> loadFileFunc = new Function<String, Void>() {
@Override
public Void apply(String input) {
try {
List<Track> newTrack = loader.load(new ResourceLocator(path), genome);
} catch (Exception e) {
e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
}
return null;
}
};
TestUtils.timeMethod(supplier, loadFileFunc, 1);
}
private class BEDStringSupplier implements Supplier<String> {
//final String[] testStrings;
private int counter = 0;
private final String chr = "chr1";
private final int maxLength = 500;
BEDStringSupplier(int nTrials) {
// testStrings = new String[nTrials];
// for(int ft=0; ft < nTrials; ft++){
// testStrings[ft] = gen(ft);
// }
}
private String gen(int start) {
String end = "" + (start + (int) Math.random() * maxLength);
String[] dat = {chr, "" + start, end, "0", "0", "+"};
return StringUtils.join(dat, '\t');
}
@Override
public String get() {
return gen(counter++);
//return testStrings[counter++];
}
public void reset() {
counter = 0;
}
}
}