X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAlignViewportTest.java;h=00267b31d4ee5b3cda04325dde87c5493f4cf633;hb=01e36c0ce9358948c93009c93b54d6a8ec69138b;hp=959abb086155807e590011b6265180df5a9a7e90;hpb=0356abc2cb7040672bc8fde68cafb77a2d623b5d;p=jalview.git

diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index 959abb0..00267b3 100644
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -27,6 +27,14 @@ import static org.testng.AssertJUnit.assertNotSame;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
+import java.util.ArrayList;
+import java.util.List;
+
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
 import jalview.datamodel.AlignedCodonFrame;
@@ -48,14 +56,6 @@ import jalview.structure.StructureSelectionManager;
 import jalview.util.MapList;
 import jalview.viewmodel.ViewportRanges;
 
-import java.util.ArrayList;
-import java.util.List;
-
-import org.testng.Assert;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
 public class AlignViewportTest
 {
 
@@ -297,9 +297,29 @@ public class AlignViewportTest
      * wait for Conservation thread to complete
      */
     AlignViewport viewport = af.getViewport();
+    waitForCalculations(viewport);
+    AlignmentAnnotation[] anns = 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);
+  }
+
+  /**
+   * Wait for consensus etc calculation threads to complete
+   * 
+   * @param viewport
+   */
+  protected void waitForCalculations(AlignViewport viewport)
+  {
     synchronized (this)
     {
-      while (viewport.getAlignmentConservationAnnotation() != null)
+      while (viewport.getCalcManager().isWorking())
       {
         try
         {
@@ -309,16 +329,6 @@ public class AlignViewportTest
         }
       }
     }
-    AlignmentAnnotation[] anns = 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" })
@@ -466,6 +476,7 @@ public class AlignViewportTest
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(fasta,
             DataSourceType.PASTE);
     AlignViewport testme = af.getViewport();
+    waitForCalculations(testme);
     SequenceI cons = testme.getConsensusSeq();
     assertEquals("A-C", cons.getSequenceAsString());
   }