// You need to add the groovy directory to the class path from the script window // or add the groovy directory to the java classpath when running Jalview jvtst = new JvLoadTester().newJvLoadTest('D:\\fooTest.jar'); try { jvtst.TestForAll('D:\\e6-workspace\\Jalview RNA\\examples\\rna\\rfamSml') } catch (OutOfMemoryError e) { // inspect jvtst to find out what file + file index it was on } // Terminate Jalview - useful if running from command line if (Jalview.isInBatchMode()) { Jalview.quit() }