X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAlignViewportTest.java;h=4660842760352cbf6ee510820f6b72a263899436;hb=d9a5e7ac4957e98089c082e629d6e79dd5d30199;hp=06df70ab6c7aa972572f6b1f214d1e24e69bd478;hpb=a25f31a9140c9764baf76ec1c2ede98c1e3e52f9;p=jalview.git

diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index 06df70a..4660842 100644
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -50,6 +50,7 @@ import jalview.util.MapList;
 import java.util.ArrayList;
 import java.util.List;
 
+import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
@@ -159,7 +160,7 @@ public class AlignViewportTest
     acf2.addMap(s1, s1, new MapList(new int[] { 1, 4 }, new int[] { 4, 1 },
             1, 1));
 
-    List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
+    List<AlignedCodonFrame> mappings = new ArrayList<>();
     mappings.add(acf1);
     mappings.add(acf2);
     af1.getViewport().getAlignment().setCodonFrames(mappings);
@@ -216,11 +217,11 @@ public class AlignViewportTest
     acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1,
         12 }, 1, 1));
 
-    List<AlignedCodonFrame> mappings1 = new ArrayList<AlignedCodonFrame>();
+    List<AlignedCodonFrame> mappings1 = new ArrayList<>();
     mappings1.add(acf1);
     af1.getViewport().getAlignment().setCodonFrames(mappings1);
 
-    List<AlignedCodonFrame> mappings2 = new ArrayList<AlignedCodonFrame>();
+    List<AlignedCodonFrame> mappings2 = new ArrayList<>();
     mappings2.add(acf2);
     mappings2.add(acf3);
     af2.getViewport().getAlignment().setCodonFrames(mappings2);
@@ -279,12 +280,12 @@ public class AlignViewportTest
     acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1,
         12 }, 1, 1));
 
-    List<AlignedCodonFrame> mappings1 = new ArrayList<AlignedCodonFrame>();
+    List<AlignedCodonFrame> mappings1 = new ArrayList<>();
     mappings1.add(acf1);
     mappings1.add(acf2);
     af1.getViewport().getAlignment().setCodonFrames(mappings1);
 
-    List<AlignedCodonFrame> mappings2 = new ArrayList<AlignedCodonFrame>();
+    List<AlignedCodonFrame> mappings2 = new ArrayList<>();
     mappings2.add(acf2);
     mappings2.add(acf3);
     af2.getViewport().getAlignment().setCodonFrames(mappings2);
@@ -327,6 +328,8 @@ public class AlignViewportTest
             Boolean.TRUE.toString());
     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
             Boolean.FALSE.toString());
+    Cache.applicationProperties.setProperty("SHOW_OCCUPANCY",
+            Boolean.FALSE.toString());
     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
             Boolean.FALSE.toString());
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
@@ -386,7 +389,8 @@ public class AlignViewportTest
 
   /**
    * Verify that setting the selection group has the side-effect of setting the
-   * context on the group, unless it already has one
+   * context on the group, unless it already has one, but does not change
+   * whether the group is defined or not.
    */
   @Test(groups = { "Functional" })
   public void testSetSelectionGroup()
@@ -396,12 +400,56 @@ public class AlignViewportTest
     AlignViewport av = af.getViewport();
     SequenceGroup sg1 = new SequenceGroup();
     SequenceGroup sg2 = new SequenceGroup();
+    SequenceGroup sg3 = new SequenceGroup();
 
     av.setSelectionGroup(sg1);
     assertSame(sg1.getContext(), av.getAlignment()); // context set
+    assertFalse(sg1.isDefined()); // group not defined
 
-    sg2.setContext(sg1);
+    sg2.setContext(sg1, false);
     av.setSelectionGroup(sg2);
+    assertFalse(sg2.isDefined()); // unchanged
     assertSame(sg2.getContext(), sg1); // unchanged
+
+    // create a defined group
+    sg3.setContext(av.getAlignment(), true);
+    av.setSelectionGroup(sg3);
+    assertTrue(sg3.isDefined()); // unchanged
+  }
+  /**
+   * Verify that setting/clearing SHOW_OCCUPANCY preference adds or omits occupancy row from viewport
+   */
+  @Test(groups = { "Functional" })
+  public void testShowOrDontShowOccupancy()
+  {
+    // disable occupancy
+    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.");
+    int c = 0;
+    for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null,
+            null, "Occupancy"))
+    {
+      c++;
+    }
+    Assert.assertEquals(c, 0, "Expected zero occupancy rows.");
+    
+    // enable occupancy
+    jalview.bin.Cache.setProperty("SHOW_OCCUPANCY", Boolean.TRUE.toString());
+    af = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/uniref50.fa", DataSourceType.FILE);
+    av = af.getViewport();
+    Assert.assertNotNull(av.getAlignmentGapAnnotation(), "Preference did not enable occupancy row.");
+    c = 0;
+    for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null,
+            null, av.getAlignmentGapAnnotation().label))
+    {
+      c++;
+    }
+    ;
+    Assert.assertEquals(c, 1, "Expected to find one occupancy row.");
+
   }
 }