/*
* 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.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.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 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().getGenomeListItems();
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);
}
}