/*
* 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.tdf;
import org.broad.igv.track.TrackType;
import org.broad.igv.track.WindowFunction;
import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Test;
import java.io.File;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;
import static org.junit.Assert.assertEquals;
/**
* File file, TrackType trackType, String trackLine, String[] trackNames
*
* @author jrobinso
*/
public class TDFReadWriteTest {
static String[] trackNames = {"sample 1", "sample 2", "sample 3"};
static TrackType type = TrackType.COPY_NUMBER;
static String trackLine = "track line";
static List<WindowFunction> wfs = Arrays.asList();
public TDFReadWriteTest() {
}
@BeforeClass
public static void setUpClass() throws Exception {
}
@AfterClass
public static void tearDownClass() throws Exception {
}
/**
* Test of createGroup method, of class IBFWriter.
*/
@Test
public void testCreateGroup() {
File testFile = new File("test1.tdf");
testFile.deleteOnExit();
String groupName = "/chr1";
TDFWriter writer = new TDFWriter(testFile, "hg18", type, trackLine, trackNames, wfs, false);
TDFGroup group = writer.createGroup(groupName);
group.setAttribute("attKey", "attValue");
group.setAttribute("attKey2", "attValue2");
writer.closeFile();
TDFReader reader = TDFReader.getReader(testFile.getAbsolutePath());
group = reader.getGroup(groupName);
assertEquals(groupName, group.getName());
assertEquals(2, group.attributes.size());
assertEquals("attValue", group.attributes.get("attKey"));
assertEquals("attValue2", group.attributes.get("attKey2"));
reader.close();
}
/**
* Test of createDataset method, of class IBFWriter.
*/
@Test
public void testCreateFile() {
File testFile = new File("test2.tdf");
testFile.deleteOnExit();
TDFWriter writer = new TDFWriter(testFile, "hg18", type, trackLine, trackNames, wfs, false);
writer.closeFile();
TDFReader reader = TDFReader.getReader(testFile.getAbsolutePath());
String[] tn = reader.getTrackNames();
assertEquals(trackNames.length, tn.length);
for (int i = 0; i < tn.length; i++) {
assertEquals(trackNames[i], tn[i]);
}
assertEquals(type, reader.getTrackType());
assertEquals(trackLine, reader.getTrackLine());
reader.close();
}
/**
* Test of writeTile method, of class IBFWriter.
*/
@Test
public void testWriteTile() throws IOException {
writeTile("test3.tdf", false);
}
/**
* Test of writeTile method, of class IBFWriter.
*/
@Test
public void testWriteCompressedTile() throws IOException {
writeTile("test4.tdf", true);
}
public void writeTile(String file, boolean gzipped) throws IOException {
File testFile = new File(file);
testFile.deleteOnExit();
String dsName = "/chr1/zoom1/medians";
int tileNumber = 0;
int start = 10;
float span = 1;
float[][] data = new float[trackNames.length][100000];
for (int i = 0; i < trackNames.length; i++) {
for (int j = 0; j < 10; j++) {
data[i][j] = (float) Math.random();
}
}
//System.out.println("----------------");
TDFWriter writer = new TDFWriter(testFile, "hg18", type, trackLine, trackNames, wfs, gzipped);
TDFDataset dataset = writer.createDataset(dsName, TDFDataset.DataType.FLOAT, 1000, 1);
dataset.setAttribute("attr1", "value1");
dataset.setAttribute("attr2", "value2");
TDFFixedTile tile = new TDFFixedTile(start, start, span, data);
writer.writeTile(dsName, tileNumber, tile);
writer.closeFile();
TDFReader reader = TDFReader.getReader(testFile.getAbsolutePath());
TDFDataset ds = reader.getDataset(dsName);
assertEquals("value1", ds.getAttribute("attr1"));
assertEquals("value2", ds.getAttribute("attr2"));
TDFTile dsTile = reader.readTile(ds, 0);
for (int i = 0; i < trackNames.length; i++) {
assertEquals(start + i * span, dsTile.getStartPosition(i), 1.0e-6);
for (int j = 0; j < 10; j++) {
assertEquals(data[i][j], dsTile.getValue(i, j), 1.0e-6);
}
}
reader.close();
}
public static void main(String[] args) {
org.junit.runner.JUnitCore.runClasses(TDFReadWriteTest.class);
}
}