/*
* 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.ui;
import junit.framework.Assert;
import org.broad.igv.Globals;
import org.broad.igv.feature.genome.GenomeListItem;
import org.broad.igv.feature.genome.GenomeManager;
import org.broad.igv.track.Track;
import org.broad.igv.ui.panel.FrameManager;
import org.broad.igv.ui.panel.ReferenceFrame;
import org.broad.igv.util.ResourceLocator;
import org.broad.igv.util.TestUtils;
import org.fest.swing.fixture.FrameFixture;
import org.fest.swing.fixture.JButtonFixture;
import org.fest.swing.fixture.JComboBoxFixture;
import org.fest.swing.fixture.JPanelFixture;
import org.junit.Ignore;
import org.junit.Test;
import java.util.Collection;
import java.util.List;
import static org.junit.Assert.*;
/**
* User: jacob
* Date: 2012/02/08
*/
public class IGVTestHeaded extends AbstractHeadedTest {
@Test
public void testLoadSessionBatch() throws Exception {
try {
Globals.setBatch(true);
tstLoadSession();
} finally {
Globals.setBatch(false);
}
}
@Test
public void testLoadSessionNoBatch() throws Exception {
Globals.setBatch(false);
tstLoadSession();
}
public void tstLoadSession() throws Exception {
//Pretty basic, but at some point loading this view
//gave a class cast exception
String sessionPath = TestUtils.DATA_DIR + "sessions/CCLE_testSession_chr2.xml";
IGV igv = IGV.getInstance();
TestUtils.loadSession(igv, sessionPath);
Assert.assertEquals("chr2", FrameManager.getDefaultFrame().getChrName());
Assert.assertEquals(1, FrameManager.getDefaultFrame().getCurrentRange().getStart());
int rangeDiff = Math.abs(FrameManager.getDefaultFrame().getChromosomeLength() - FrameManager.getDefaultFrame().getCurrentRange().getEnd());
assertTrue(rangeDiff < 3);
Assert.assertEquals(1461, igv.getAllTracks().size());
}
/**
* Test loading a UCSC session, with some files that don't exist and some that do
*
* @throws Exception
*/
@Test
public void testLoadUCSCSessionBadFiles() throws Exception {
String sessionPath = TestUtils.DATA_DIR + "sessions/nonexistent_files.session";
IGV igv = IGV.getInstance();
TestUtils.loadSession(igv, sessionPath);
Assert.assertEquals(4, igv.getVisibleTrackCount());
int testBedTracks = 0;
for (Track track : igv.getAllTracks()) {
testBedTracks += track.getName().contains("Test Bed") ? 1 : 0;
}
Assert.assertEquals(2, testBedTracks);
}
@Ignore //Never seems to work on our testrunner for reasons unrelated to the code
@Test
public void testHome() throws Exception {
IGV igv = IGV.getInstance();
ReferenceFrame frame = FrameManager.getDefaultFrame();
String chr = "chr1";
int start = 5;
int end = 5000;
int limit = 2;
frame.jumpTo(chr, start, end);
Assert.assertEquals(chr, frame.getChrName());
assertTrue(Math.abs(frame.getCurrentRange().getStart() - start) < limit);
assertTrue(Math.abs(frame.getCurrentRange().getEnd() - end) < limit);
FrameFixture frameFixture = new FrameFixture(IGV.getMainFrame());
//Make sure frame has focus, or else homeButton won't work
JButtonFixture homeButton = frameFixture.button("homeButton");
homeButton.focus();
homeButton.click();
homeButton.focus();
homeButton.click();
igv.waitForNotify(500);
Assert.assertEquals(Globals.CHR_ALL, frame.getChrName());
//In all genome view these should be the same
assertEquals(frame.getChromosomeLength(), frame.getCurrentRange().getEnd());
Assert.assertEquals(0.0, frame.getOrigin());
}
@Test
public void testLoadNewGenomeByPath() throws Exception {
String sessionPath = TestUtils.DATA_DIR + "sessions/canFam2_local.xml";
String genomeId = "canFam2.unittest";
TestUtils.loadSession(IGV.getInstance(), sessionPath);
assertEquals(genomeId, GenomeManager.getInstance().getGenomeId());
}
/**
* Test loading a genome the user hasn't loaded before,
* by id (available from server)
*
* @throws Exception
*/
@Test
public void testLoadNewGenomeById() throws Exception {
Collection<GenomeListItem> currentGenomes = GenomeManager.getInstance().getGenomes();
String genomeId = "canFam2";
for (GenomeListItem genomeListItem : currentGenomes) {
assertNotSame(genomeId, genomeListItem.getId());
}
String sessionPath = TestUtils.DATA_DIR + "sessions/canFam2_server.xml";
TestUtils.loadSession(IGV.getInstance(), sessionPath);
assertEquals(genomeId, GenomeManager.getInstance().getGenomeId());
//CpG islands, RefSeq genes, ReferenceSequence (has height 0)
assertEquals(3, IGV.getInstance().getVisibleTrackCount());
}
/**
* Basic test showing usage of FEST and checking combo box
*
* @throws Exception
*/
//@Test
public void scratchTestFEST() throws Exception {
FrameFixture frame = new FrameFixture(IGV.getMainFrame());
JPanelFixture contentFixture = frame.panel("contentPane");
JPanelFixture commandBar = frame.panel("igvCommandBar");
JComboBoxFixture chromoBox = frame.comboBox("chromosomeComboBox");
String[] chromos = commandBar.comboBox("chromosomeComboBox").contents();
Assert.assertEquals(26, chromos.length);
}
public void testExomeView() throws Exception {
String file = "http://www.broadinstitute.org/igvdata/1KG/pilot2Bams/NA12891.SLX.bam";
List<Track> tracks = IGV.getInstance().load(new ResourceLocator(file));
Thread.sleep(10000);
//TestUtils.loadSession(igv, TestUtils.DATA_DIR + "sessions/slx_ceu_father.xml");
Assert.assertEquals(2, tracks.size());
FrameManager.setExomeMode(true, true);
IGV.getInstance().resetFrames();
String locus = "chr7:55,208,260-55,240,460";
igv.goToLocus(locus);
//File out = new File(TestUtils.DATA_DIR, "testsnap.png");
//SnapshotUtilities.doComponentSnapshot(IGV.getMainFrame(), out, SnapshotFileChooser.SnapshotFileType.PNG);
}
}