+ Assert.assertTrue(lookForSequenceName(sequence),
+ "Sequence '" + sequence
+ + "' was not found in opened alignment files: "
+ + cmdLine);
+ }
+
+ System.out.println("##### GOT TO END");
+ }
+
+ public static boolean lookForSequenceName(String sequenceName)
+ {
+ AlignFrame[] afs = Desktop.getAlignFrames();
+ for (AlignFrame af : afs)
+ {
+ for (String name : af.getViewport().getAlignment().getSequenceNames())