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* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
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* 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
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package org.broad.igv.tools.sort;
import com.google.common.base.Function;
import com.google.common.base.Supplier;
import org.broad.igv.AbstractHeadlessTest;
import org.broad.igv.feature.genome.ChromosomeNameComparator;
import org.broad.igv.util.TestUtils;
import org.junit.Test;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.util.Comparator;
import java.util.HashSet;
import java.util.Set;
import static org.junit.Assert.*;
/**
* Created by IntelliJ IDEA.
* User: jrobinso
* Date: Sep 18, 2009
* Time: 6:19:28 PM
*/
public class SorterTest extends AbstractHeadlessTest {
@Test
public void testSortBed() throws Exception {
testSort(TestUtils.DATA_DIR + "bed/Unigene.unsorted.bed", 0, 1, 10, 71, 0);
}
@Test
public void testSortBed1() throws Exception {
testSort(TestUtils.DATA_DIR + "bed/Unigene.unsorted1.bed", 0, 1, 10, 71, 0);
}
@Test
public void testSortBed2() throws Exception {
testSort(TestUtils.DATA_DIR + "bed/GSM1004654_10k.bed", 0, 1, 50, 10000, 0);
}
@Test
public void testSortVCF() throws Exception {
testSort(TestUtils.DATA_DIR + "vcf/SRP32_v4.0.vcf", 0, 1);
}
@Test
public void testSortGFF() throws Exception {
testSort(TestUtils.DATA_DIR + "gff/aliased.unsorted.gff", 0, 3);
}
@Test
public void testSortCN() throws Exception{
String path = TestUtils.DATA_DIR + "cn/1klines.cn";
testSort(path, 1, 2, 10, 1000, 1);
}
@Test
public void testSortGWAS() throws Exception{
String path = TestUtils.DATA_DIR + "gwas/random.gwas";
testSort(path, 0, 1, 10, 100, 1);
}
public void testSort(String infile, int chrCol, int startCol) throws IOException {
testSort(infile, chrCol, startCol, 10, null, 0);
}
public void testSort(String infile, int chrCol, int startCol, int maxRecords, Integer expectedLines, int skipTopLines) throws IOException {
File ifile = new File(infile);
File ofile = new File(infile + ".sorted");
ofile.deleteOnExit();
Sorter sorter = SorterFactory.getSorter(ifile, ofile);
sorter.setMaxRecords(maxRecords);
sorter.run();
int outLines = checkFileSorted(ofile, chrCol, startCol, skipTopLines);
if(expectedLines != null){
assertEquals((int) expectedLines, outLines);
}
}
public static int checkFileSorted(File ofile, int chrCol, int startCol, int skipTopLines) {
BufferedReader reader = null;
int numlines = 0;
String nextLine = "";
try {
reader = new BufferedReader(new FileReader(ofile));
String lastChr = "";
int lastStart = 0;
Set<String> chromosomes = new HashSet();
for(int ii=0; ii < skipTopLines; ii++){
reader.readLine();
}
while ((nextLine = reader.readLine()) != null) {
if (nextLine.startsWith("track") || nextLine.startsWith(("#"))) {
continue;
}
String[] tokens = nextLine.split("\t");
String chr = tokens[chrCol];
int start = Integer.parseInt(tokens[startCol]);
if (chr.equals(lastChr)) {
assertTrue(start >= lastStart);
} else {
String msg = String.format("Chromosome %s out of order in line: %s", chr, nextLine);
assertFalse(msg, chromosomes.contains(chr));
chromosomes.add(chr);
}
numlines++;
lastChr = chr;
lastStart = start;
}
} catch (Exception e) {
e.printStackTrace();
String msg = "Exception during checking on line: " + nextLine;
throw new AssertionError(msg);
} finally {
try {
reader.close();
} catch (Exception e) {
}
}
return numlines;
}
//@Test
public void testCurrentCompSpeed() throws IOException {
tstComparatorSpeed(AsciiSorter.getDefaultComparator());
}
//@Test
// public void testTestCompSpeed() throws IOException{
// tstComparatorSpeed(getTestComparator());
// }
public void tstComparatorSpeed(final Comparator<SortableRecord> testComp) throws IOException {
final File inputFile = new File(TestUtils.DATA_DIR + "bed", "GSM1004654_10k.bed");
final File outputFile = new File(TestUtils.TMP_OUTPUT_DIR, "GSM1004654_10k.sorted.bed");
int nTrials = 100;
Supplier<Sorter> supplier = new Supplier<Sorter>() {
@Override
public Sorter get() {
ChromosomeNameComparator.get().resetCache();
AsciiSorter sorter = new BedSorter(inputFile, outputFile);
sorter.setComparator(testComp);
return sorter;
}
};
Function<Sorter, Void> func = new Function<Sorter, Void>() {
@Override
public Void apply(Sorter input) {
try {
input.run();
} catch (IOException e) {
e.printStackTrace();
}
return null;
}
};
long[] times = TestUtils.timeMethod(supplier, func, nTrials);
}
}