+
+ /**
+ * Test for JAL-1306 - conservation thread should run even when only Quality
+ * (and not Conservation) is enabled in Preferences
+ */
+ @Test(groups = { "Functional" })
+ public void testUpdateConservation_qualityOnly()
+ {
+ Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
+ Boolean.TRUE.toString());
+ Cache.applicationProperties.setProperty("SHOW_QUALITY",
+ Boolean.TRUE.toString());
+ Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+ Boolean.FALSE.toString());
+ Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+ Boolean.FALSE.toString());
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/uniref50.fa", FormatAdapter.FILE);
+ AlignmentAnnotation[] anns = af.viewport.getAlignment()
+ .getAlignmentAnnotation();
+ assertNotNull("No annotations found", anns);
+ assertEquals("More than one annotation found", 1, anns.length);
+ assertTrue("Annotation is not Quality",
+ anns[0].description.startsWith("Alignment Quality"));
+ Annotation[] annotations = anns[0].annotations;
+ assertNotNull("Quality annotations are null", annotations);
+ assertNotNull("Quality in column 1 is null", annotations[0]);
+ assertTrue("No quality value in column 1", annotations[0].value > 10f);
+ }
+
+ @Test(groups = { "Functional" })
+ public void testSetGlobalColourScheme()
+ {
+ /*
+ * test for JAL-2283 don't inadvertently turn on colour by conservation
+ */
+ Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
+ Boolean.TRUE.toString());
+ Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+ Boolean.FALSE.toString());
+ Cache.applicationProperties.setProperty("DEFAULT_COLOUR_PROT", "NONE");
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/uniref50.fa", FormatAdapter.FILE);
+ ColourSchemeI cs = new PIDColourScheme();
+ af.getViewport().setGlobalColourScheme(cs);
+ assertFalse(cs.conservationApplied());
+ }