Merge remote-tracking branch 'origin/merge/Jalview-JS/develop_feature/JAL-3690_callba...

[jalview.git] / test / jalview / gui / AlignViewportTest.java

diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index d6c875b..9c1a412 100644 (file)
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -57,6 +57,7 @@ import jalview.structure.StructureSelectionManager;
 import jalview.util.MapList;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.ViewportRanges;
+import jalview.workers.AlignCalcManager;
 
 public class AlignViewportTest
 {
@@ -75,14 +76,16 @@ public class AlignViewportTest
   @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
-    Jalview.main(new String[] { "-nonews", "-props",
+    Jalview.main(new String[] {
+        //"-jabaws", "none", 
+        "-nonews", "-props",
         "test/jalview/testProps.jvprops" });
 
     /*
      * remove any sequence mappings left lying around by other tests
      */
     StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(Desktop.instance);
+            .getStructureSelectionManager(Desktop.getInstance());
     ssm.resetAll();
   }
 
@@ -130,7 +133,7 @@ public class AlignViewportTest
      * mappings
      */
     StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(Desktop.instance);
+            .getStructureSelectionManager(Desktop.getInstance());
     List<AlignedCodonFrame> sequenceMappings = ssm.getSequenceMappings();
     assertEquals(2, sequenceMappings.size());
     assertTrue(sequenceMappings.contains(acf1));
@@ -152,10 +155,10 @@ 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);
+            .getStructureSelectionManager(Desktop.getInstance());
     ssm.resetAll();
 
     AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
@@ -215,10 +218,10 @@ 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);
+            .getStructureSelectionManager(Desktop.getInstance());
     ssm.resetAll();
 
     AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
@@ -282,15 +285,15 @@ public class AlignViewportTest
   @Test(groups = { "Functional" }, 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("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);
@@ -321,15 +324,19 @@ public class AlignViewportTest
   {
     synchronized (this)
     {
-      while (viewport.getCalcManager().isWorking())
+      System.out.print("waiting...");
+      int n = 3;
+      while (--n >= 0 || viewport.getCalcManager().isWorking())
       {
         try
         {
+          System.out.print(((AlignCalcManager) viewport.getCalcManager()).getQueueLength());
           wait(50);
         } catch (InterruptedException e)
         {
         }
       }
+           System.out.println("...done");
     }
   }
 
@@ -339,8 +346,8 @@ 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);
@@ -482,7 +489,10 @@ public class AlignViewportTest
     AlignViewport testme = af.getViewport();
     waitForCalculations(testme);
     SequenceI cons = testme.getConsensusSeq();
-    assertEquals("A-C", cons.getSequenceAsString());
+    String s = cons.getSequenceAsString();
+    System.out.println("s is " + s);
+    
+    assertEquals("A-C", s);
   }
 
   @Test(groups = { "Functional" })