+
+ @Test(groups="Functional")
+ public void testAnnotateAlignmentView()
+ {
+ long t1 = System.currentTimeMillis();
+ /*
+ * JAL-3779 test multiple groups of the same name get annotated
+ */
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ ">Seq1\nQRSIL\n>Seq2\nFTHND\n>Seq3\nRPVSL\n",
+ DataSourceType.PASTE);
+ long t2 = System.currentTimeMillis();
+ System.err.println("t0: " + (t2 - t1));
+ // seq1 and seq3 are in distinct groups both named Group1
+ String annotationFile = "JALVIEW_ANNOTATION\nSEQUENCE_GROUP\tGroup1\t*\t*\t1\n"
+ + "SEQUENCE_GROUP\tGroup2\t*\t*\t2\n"
+ + "SEQUENCE_GROUP\tGroup1\t*\t*\t3\n"
+ + "PROPERTIES\tGroup1\toutlineColour=blue\tidColour=red\n";
+ new AnnotationFile().annotateAlignmentView(af.getViewport(), annotationFile, DataSourceType.PASTE);
+
+ AlignmentI al = af.getViewport().getAlignment();
+ List<SequenceGroup> groups = al.getGroups();
+ assertEquals(3, groups.size());
+ SequenceGroup sg = groups.get(0);
+ assertEquals("Group1", sg.getName());
+ assertTrue(sg.contains(al.getSequenceAt(0)));
+ assertEquals(Color.BLUE, sg.getOutlineColour());
+ assertEquals(Color.RED, sg.getIdColour());
+ sg = groups.get(1);
+ assertEquals("Group2", sg.getName());
+ assertTrue(sg.contains(al.getSequenceAt(1)));
+
+ /*
+ * the bug fix: a second group of the same name is also given properties
+ */
+ sg = groups.get(2);
+ assertEquals("Group1", sg.getName());
+ assertTrue(sg.contains(al.getSequenceAt(2)));
+ assertEquals(Color.BLUE, sg.getOutlineColour());
+ assertEquals(Color.RED, sg.getIdColour());
+ }