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 76021ce..f675f68 100644 (file)
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -27,6 +27,7 @@ import static org.testng.AssertJUnit.assertNotSame;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.api.AlignViewportI;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -54,6 +55,7 @@ import jalview.schemes.ColourSchemeI;
 import jalview.schemes.PIDColourScheme;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MapList;
+import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.ViewportRanges;
 
 public class AlignViewportTest
@@ -68,19 +70,21 @@ public class AlignViewportTest
 
   AlignmentI al;
 
-  AlignViewport testee;
+  AlignmentViewport testee;
 
   @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();
   }
 
@@ -128,7 +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));
@@ -150,10 +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(
@@ -213,10 +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(
@@ -319,7 +323,9 @@ public class AlignViewportTest
   {
     synchronized (this)
     {
-      while (viewport.getCalcManager().isWorking())
+      System.out.print("waiting...");
+      int n = 3;
+      while (--n >= 0 || viewport.getCalcManager().isWorking())
       {
         try
         {
@@ -328,6 +334,7 @@ public class AlignViewportTest
         {
         }
       }
+           System.out.println("...done");
     }
   }
 
@@ -407,7 +414,7 @@ public class AlignViewportTest
   {
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
-    AlignViewport av = af.getViewport();
+    AlignViewportI av = af.getViewport();
     SequenceGroup sg1 = new SequenceGroup();
     SequenceGroup sg2 = new SequenceGroup();
     SequenceGroup sg3 = new SequenceGroup();
@@ -436,8 +443,9 @@ public class AlignViewportTest
     jalview.bin.Cache.setProperty("SHOW_OCCUPANCY", Boolean.FALSE.toString());
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
-    AlignViewport av = af.getViewport();
-    Assert.assertNull(av.getAlignmentGapAnnotation(), "Preference did not disable occupancy row.");
+    AlignViewportI av = af.getViewport();
+    Assert.assertNull(av.getAlignmentGapAnnotation(),
+            "Preference did not disable occupancy row.");
     int c = 0;
     for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null,
             null, "Occupancy"))
@@ -451,7 +459,8 @@ public class AlignViewportTest
     af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
     av = af.getViewport();
-    Assert.assertNotNull(av.getAlignmentGapAnnotation(), "Preference did not enable occupancy row.");
+    Assert.assertNotNull(av.getAlignmentGapAnnotation(),
+            "Preference did not enable occupancy row.");
     c = 0;
     for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null,
             null, av.getAlignmentGapAnnotation().label))
@@ -478,7 +487,10 @@ 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" })