X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAlignViewportTest.java;h=780125016791750cb8ab79830377d517c86f1c37;hb=43699f9bc6ba2f390d3652f69b6db8975ff727c0;hp=5ed0cacca927f8c850da8f3c8ac609ae7992af24;hpb=e87f3076c7826c6bb2bc54583406f7e719df77ed;p=jalview.git

diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index 5ed0cac..7801250 100644
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -277,7 +277,7 @@ public class AlignViewportTest
    * Test for JAL-1306 - conservation thread should run even when only Quality
    * (and not Conservation) is enabled in Preferences
    */
-  @Test(groups = { "Functional" })
+  @Test(groups = { "Functional" }, timeOut=2000)
   public void testUpdateConservation_qualityOnly()
   {
     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
@@ -292,7 +292,24 @@ public class AlignViewportTest
             Boolean.FALSE.toString());
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
-    AlignmentAnnotation[] anns = af.viewport.getAlignment()
+
+    /*
+     * wait for Conservation thread to complete
+     */
+    AlignViewport viewport = af.getViewport();
+    synchronized (this)
+    {
+      while (viewport.getAlignmentConservationAnnotation() != null)
+      {
+        try
+        {
+          wait(50);
+        } catch (InterruptedException e)
+        {
+        }
+      }
+    }
+    AlignmentAnnotation[] anns = viewport.getAlignment()
             .getAlignmentAnnotation();
     assertNotNull("No annotations found", anns);
     assertEquals("More than one annotation found", 1, anns.length);