X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAlignViewportTest.java;h=3ba93bc4f7ac37c463488fb70117f50e71f98ca8;hb=447c5c1b22bd12a78730640321264fb38c39ec7b;hp=959abb086155807e590011b6265180df5a9a7e90;hpb=0356abc2cb7040672bc8fde68cafb77a2d623b5d;p=jalview.git

diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index 959abb0..3ba93bc 100644
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -79,9 +79,7 @@ public class AlignViewportTest
     /*
      * remove any sequence mappings left lying around by other tests
      */
-    StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(Desktop.instance);
-    ssm.resetAll();
+    Desktop.getStructureSelectionManager().resetAll();
   }
 
   @BeforeMethod(alwaysRun = true)
@@ -127,9 +125,8 @@ public class AlignViewportTest
      * Verify that creating the alignment for the new View has registered the
      * mappings
      */
-    StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(Desktop.instance);
-    List<AlignedCodonFrame> sequenceMappings = ssm.getSequenceMappings();
+    List<AlignedCodonFrame> sequenceMappings = Desktop.getInstance()
+            .getStructureSelectionManager().getSequenceMappings();
     assertEquals(2, sequenceMappings.size());
     assertTrue(sequenceMappings.contains(acf1));
     assertTrue(sequenceMappings.contains(acf2));
@@ -150,10 +147,10 @@ public class AlignViewportTest
   @Test(groups = { "Functional" })
   public void testDeregisterMapping_withNoReference()
   {
-    Desktop d = Desktop.instance;
+    Desktop d = Desktop.getInstance();
     assertNotNull(d);
-    StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(Desktop.instance);
+    StructureSelectionManager ssm = Desktop.getInstance()
+            .getStructureSelectionManager();
     ssm.resetAll();
 
     AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
@@ -213,10 +210,10 @@ public class AlignViewportTest
   @Test(groups = { "Functional" })
   public void testDeregisterMapping_withReference()
   {
-    Desktop d = Desktop.instance;
+    Desktop d = Desktop.getInstance();
     assertNotNull(d);
-    StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(Desktop.instance);
+    StructureSelectionManager ssm = Desktop.getInstance()
+            .getStructureSelectionManager();
     ssm.resetAll();
 
     AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
@@ -277,18 +274,18 @@ 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" }, timeOut=2000)
+  @Test(groups = { "Functional" }, timeOut = 2000) // BH removed timeOut=2000
   public void testUpdateConservation_qualityOnly()
   {
-    Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
+    Cache.setPropertyNoSave("SHOW_ANNOTATIONS",
             Boolean.TRUE.toString());
-    Cache.applicationProperties.setProperty("SHOW_QUALITY",
+    Cache.setPropertyNoSave(Preferences.SHOW_QUALITY,
             Boolean.TRUE.toString());
-    Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+    Cache.setPropertyNoSave("SHOW_CONSERVATION",
             Boolean.FALSE.toString());
-    Cache.applicationProperties.setProperty("SHOW_OCCUPANCY",
+    Cache.setPropertyNoSave("SHOW_OCCUPANCY",
             Boolean.FALSE.toString());
-    Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+    Cache.setPropertyNoSave("SHOW_IDENTITY",
             Boolean.FALSE.toString());
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
@@ -299,16 +296,29 @@ public class AlignViewportTest
     AlignViewport viewport = af.getViewport();
     synchronized (this)
     {
+      System.out.println("AVT consv: "
+              + viewport.getAlignmentConservationAnnotation());
+      try
+      {
+        wait(250); // BH increased from 50 -- was getting Quality in column 1
+                   // is null
+      } catch (InterruptedException e)
+      {
+      }
+      System.out.println("AVT consv: "
+              + viewport.getAlignmentConservationAnnotation());
       while (viewport.getAlignmentConservationAnnotation() != null)
       {
         try
         {
-          wait(50);
+          wait(250); // BH increased from 50 -- was getting Quality in column 1
+                     // is null
         } catch (InterruptedException e)
         {
         }
       }
     }
+    af.paintImmediately(af.getBounds());
     AlignmentAnnotation[] anns = viewport.getAlignment()
             .getAlignmentAnnotation();
     assertNotNull("No annotations found", anns);
@@ -327,8 +337,8 @@ public class AlignViewportTest
     /*
      * test for JAL-2283: don't inadvertently turn on colour by conservation
      */
-    Cache.applicationProperties.setProperty("DEFAULT_COLOUR_PROT", "None");
-    Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+    Cache.setPropertyNoSave("DEFAULT_COLOUR_PROT", "None");
+    Cache.setPropertyNoSave("SHOW_CONSERVATION",
             Boolean.TRUE.toString());
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
@@ -448,7 +458,6 @@ public class AlignViewportTest
     {
       c++;
     }
-    ;
     Assert.assertEquals(c, 1, "Expected to find one occupancy row.");
   }
 
@@ -465,8 +474,21 @@ public class AlignViewportTest
     String fasta = ">s1\nA-C\n>s2\nA-C\n>s3\nA-D\n>s4\n--D\n";
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(fasta,
             DataSourceType.PASTE);
+    synchronized (this)
+    {
+    try
+    {
+        wait(50);
+    } catch (InterruptedException e)
+    {
+      // TODO Auto-generated catch block
+      e.printStackTrace();
+    }
+    }
+    // af.paintImmediately(af.getBounds());
     AlignViewport testme = af.getViewport();
     SequenceI cons = testme.getConsensusSeq();
+    System.out.println("AVT " + cons.getSequenceAsString());
     assertEquals("A-C", cons.getSequenceAsString());
   }