JAL-1933 test for SHOW_OCCUPANCY .jalview_properties setting

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

diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index 213f769..d76ac33 100644 (file)
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -38,6 +38,7 @@ import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
@@ -49,6 +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;
@@ -70,7 +72,8 @@ public class AlignViewportTest
   @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
-    Jalview.main(new String[] { "-props", "test/jalview/testProps.jvprops" });
+    Jalview.main(new String[] { "-nonews", "-props",
+        "test/jalview/testProps.jvprops" });
   }
 
   @BeforeMethod(alwaysRun = true)
@@ -354,7 +357,8 @@ public class AlignViewportTest
             "examples/uniref50.fa", DataSourceType.FILE);
     ColourSchemeI cs = new PIDColourScheme();
     af.getViewport().setGlobalColourScheme(cs);
-    assertFalse(cs.conservationApplied());
+    assertFalse(af.getViewport().getResidueShading()
+            .conservationApplied());
   }
 
   @Test(groups = { "Functional" })
@@ -380,4 +384,61 @@ public class AlignViewportTest
     af.getViewport().setSearchResults(null);
     assertFalse(af.getViewport().hasSearchResults());
   }
+
+  /**
+   * Verify that setting the selection group has the side-effect of setting the
+   * context on the group, unless it already has one
+   */
+  @Test(groups = { "Functional" })
+  public void testSetSelectionGroup()
+  {
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/uniref50.fa", DataSourceType.FILE);
+    AlignViewport av = af.getViewport();
+    SequenceGroup sg1 = new SequenceGroup();
+    SequenceGroup sg2 = new SequenceGroup();
+
+    av.setSelectionGroup(sg1);
+    assertSame(sg1.getContext(), av.getAlignment()); // context set
+
+    sg2.setContext(sg1);
+    av.setSelectionGroup(sg2);
+    assertSame(sg2.getContext(), sg1); // 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.");
+
+  }
 }