update spikes/mungo from JAL-3076 patch branch

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

diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index 6ab2622..5ed0cac 100644 (file)
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -26,7 +26,6 @@ import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
-import jalview.api.AlignViewportI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
 import jalview.datamodel.AlignedCodonFrame;
@@ -34,6 +33,8 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
@@ -45,7 +46,6 @@ 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 java.util.ArrayList;
@@ -68,7 +68,7 @@ public class AlignViewportTest
 
   AlignmentI al;
 
-  AlignmentViewport testee;
+  AlignViewport testee;
 
   @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
@@ -355,7 +355,7 @@ public class AlignViewportTest
   {
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
-    AlignViewportI av = af.getViewport();
+    AlignViewport av = af.getViewport();
     SequenceGroup sg1 = new SequenceGroup();
     SequenceGroup sg2 = new SequenceGroup();
     SequenceGroup sg3 = new SequenceGroup();
@@ -384,8 +384,8 @@ public class AlignViewportTest
     jalview.bin.Cache.setProperty("SHOW_OCCUPANCY", Boolean.FALSE.toString());
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
-    AlignViewportI av = af.getViewport();
-    Assert.assertNull(av.getOccupancyAnnotation(), "Preference did not disable occupancy row.");
+    AlignViewport 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"))
@@ -399,10 +399,10 @@ public class AlignViewportTest
     af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
     av = af.getViewport();
-    Assert.assertNotNull(av.getOccupancyAnnotation(), "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.getOccupancyAnnotation().label))
+            null, av.getAlignmentGapAnnotation().label))
     {
       c++;
     }
@@ -423,7 +423,7 @@ 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();
     SequenceI cons = testme.getConsensusSeq();
     assertEquals("A-C", cons.getSequenceAsString());
   }