- AlignFrame frame = Desktop.getAlignFrames()[0];
- AlignmentI al = frame.getViewport().getAlignment();
- assertNotEquals(al, null);
- List<SequenceI> hmmSeqs = al.getHMMConsensusSequences(false);
- assertNotEquals(hmmSeqs, null);
-
+ /*
+ * now have the original align frame, and another for realigned sequences
+ */
+ assertEquals(alignFrames.length, 2);
+ AlignmentI original = alignFrames[0].getViewport().getAlignment();
+ assertNotNull(original);
+ AlignmentI realigned = alignFrames[1].getViewport().getAlignment();
+ assertNotNull(realigned);
+ assertFalse(original.getHmmSequences().isEmpty());
+ assertFalse(realigned.getHmmSequences().isEmpty());
+
+ SequenceI ferCapan = original.findName("FER_CAPAN");
+ assertTrue(ferCapan.getSequenceAsString().startsWith("MA------SVSAT"));
+
+ SequenceI ferCapanRealigned = realigned.findName("FER_CAPAN");
+ assertTrue(ferCapanRealigned.getSequenceAsString()
+ .startsWith("-------m-A----SVSAT"));