X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAlignViewportTest.java;fp=test%2Fjalview%2Fgui%2FAlignViewportTest.java;h=bbad963736616e0b381e4161769186d61a0ec997;hb=b5c03446e1c939f40b560fa672e1dc503d7f2ff8;hp=eff3fdca05e1e690cc0d7211094ea8b7b7905a5e;hpb=83160def81ce83c64408212f3bc04298fa063ade;p=jalview.git

diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index eff3fdc..bbad963 100644
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -26,9 +26,13 @@ import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.Sequence;
@@ -55,8 +59,7 @@ public class AlignViewportTest
   @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
-    jalview.bin.Jalview.main(new String[] { "-props",
-        "test/jalview/testProps.jvprops" });
+    Jalview.main(new String[] { "-props", "test/jalview/testProps.jvprops" });
   }
 
   @BeforeMethod(alwaysRun = true)
@@ -297,4 +300,32 @@ public class AlignViewportTest
     assertTrue(ssmMappings.contains(acf2));
     assertFalse(ssmMappings.contains(acf3));
   }
+  
+  /**
+   * 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);
+  }
 }