/**
* 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;
}
