@Before
public void setUp() throws Exception {
igv.newSession();
IGV.getMainFrame().requestFocus();
TestUtils.resetPrefsFile();
TestUtils.resetTestUserDefinedGenomes();
IGV.getInstance().getContentPane().getCommandBar().refreshGenomeListComboBox();
}
/** This closes the IGV window. */
public static void stopGUI() {
if (!IGV.hasInstance()) {
return;
}
IGV.getMainFrame().setVisible(false);
IGV.getMainFrame().dispose();
IGV.destroyInstance();
}
public void testTest() throws Exception {
java.util.List<Track> tracks = IGV.getInstance().getAllTracks();
System.out.println("# tracks: " + tracks.size());
for (Track track : tracks) {
System.out.println(track.getName());
}
java.util.List<Track> featureTracks =
IGV.getInstance().getTrackPanel(IGV.FEATURE_PANEL_NAME).getTracks();
System.out.println(featureTracks.size());
}
/**
* Load a gui with the specified genome file. No genome is loaded if null
*
* @param genomeFile
* @return
* @throws IOException
*/
protected static IGV startGUI(String genomeFile) throws IOException {
Globals.setHeadless(false);
IGV igv;
// If IGV is already open, we get the instance.
if (IGV.hasInstance()) {
igv = IGV.getInstance();
IGV.getMainFrame().setVisible(true);
System.out.println("Using old IGV");
} else {
JFrame frame = new JFrame();
frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
Main.open(frame);
System.out.println("Started new IGV");
igv = IGV.getInstance();
assertTrue(IGV.getInstance().waitForNotify(1000));
}
if (genomeFile != null) {
igv.loadGenome(genomeFile, null);
genome = igv.getGenomeManager().getCurrentGenome();
}
return igv;
}
protected static String rewriteRestoreSession(String sessionPath) throws Exception {
sessionPath = (TestUtils.replaceTestPaths(new File(sessionPath))).getAbsolutePath();
IGV.getInstance().doRestoreSession(sessionPath, null, false);
return sessionPath;
}