JAL-3690 Remove references to old AlignCalcManager.

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

diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index bd36a08..f675f68 100644 (file)
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -75,14 +75,16 @@ 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 +132,7 @@ 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 +154,10 @@ 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 +217,10 @@ 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 +284,15 @@ 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);
@@ -299,9 +301,31 @@ 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.getCalcManager().isWorking())
+      System.out.print("waiting...");
+      int n = 3;
+      while (--n >= 0 || viewport.getCalcManager().isWorking())
       {
         try
         {
@@ -310,17 +334,8 @@ public class AlignViewportTest
         {
         }
       }
+           System.out.println("...done");
     }
-    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" })
@@ -329,8 +344,8 @@ 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);
@@ -469,9 +484,13 @@ 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);
-    AlignmentViewport testme = af.getViewport();
+    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" })