Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

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

diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index c2983ec..db41f3e 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;
 
@@ -35,7 +36,6 @@ import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
-import jalview.api.AlignCalcWorkerI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
 import jalview.datamodel.AlignedCodonFrame;
@@ -55,8 +55,8 @@ import jalview.schemes.ColourSchemeI;
 import jalview.schemes.PIDColourScheme;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MapList;
+import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.ViewportRanges;
-import jalview.workers.AlignCalcManager;
 
 public class AlignViewportTest
 {
@@ -70,15 +70,14 @@ public class AlignViewportTest
 
   AlignmentI al;
 
-  AlignViewport testee;
+  AlignmentViewport testee;
 
   @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
-    Jalview.main(new String[] {
-        //"-jabaws", "none", 
-        "-nonews", "-props",
-        "test/jalview/testProps.jvprops" });
+    Jalview.main(
+            new String[]
+            { "-nonews", "-props", "test/jalview/testProps.jvprops" });
 
     /*
      * remove any sequence mappings left lying around by other tests
@@ -329,7 +328,6 @@ public class AlignViewportTest
       {
         try
         {
-          System.out.print(((AlignCalcManager) viewport.getCalcManager()).getQueueLength());
           wait(50);
         } catch (InterruptedException e)
         {
@@ -415,7 +413,7 @@ 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();
@@ -444,8 +442,9 @@ 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"))
@@ -459,7 +458,8 @@ 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))
@@ -486,10 +486,7 @@ public class AlignViewportTest
     AlignViewport testme = af.getViewport();
     waitForCalculations(testme);
     SequenceI cons = testme.getConsensusSeq();
-    String s = cons.getSequenceAsString();
-    System.out.println("s is " + s);
-    
-    assertEquals("A-C", s);
+    assertEquals("A-C", cons.getSequenceAsString());
   }
 
   @Test(groups = { "Functional" })
@@ -519,8 +516,9 @@ public class AlignViewportTest
     /*
      * hide first and third sequences
      */
-    testee.hideSequence(new SequenceI[] { al.getSequenceAt(0),
-        al.getSequenceAt(2) });
+    testee.hideSequence(
+            new SequenceI[]
+            { al.getSequenceAt(0), al.getSequenceAt(2) });
     assertEquals(1, al.getHeight());
     assertEquals(0, ranges.getStartSeq());
     assertEquals(0, ranges.getEndSeq());