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 dfe0e68..d76ac33 100644 (file)
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -38,9 +38,10 @@ 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;
-import jalview.io.FormatAdapter;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.PIDColourScheme;
 import jalview.structure.StructureSelectionManager;
@@ -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;
@@ -56,6 +58,13 @@ import org.testng.annotations.Test;
 public class AlignViewportTest
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   AlignmentI al;
 
   AlignViewport testee;
@@ -63,7 +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)
@@ -140,7 +150,7 @@ public class AlignViewportTest
      * alignment with reference to mappings
      */
     AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
-            ">Seq1\nCAGT\n", FormatAdapter.PASTE);
+            ">Seq1\nCAGT\n", DataSourceType.PASTE);
 
     SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
     AlignedCodonFrame acf1 = new AlignedCodonFrame();
@@ -189,9 +199,9 @@ public class AlignViewportTest
     ssm.resetAll();
 
     AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
-            ">Seq1\nRSVQ\n", FormatAdapter.PASTE);
+            ">Seq1\nRSVQ\n", DataSourceType.PASTE);
     AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
-            ">Seq2\nDGEL\n", FormatAdapter.PASTE);
+            ">Seq2\nDGEL\n", DataSourceType.PASTE);
     SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA");
     SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA");
     SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
@@ -252,9 +262,9 @@ public class AlignViewportTest
     ssm.resetAll();
 
     AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
-            ">Seq1\nRSVQ\n", FormatAdapter.PASTE);
+            ">Seq1\nRSVQ\n", DataSourceType.PASTE);
     AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
-            ">Seq2\nDGEL\n", FormatAdapter.PASTE);
+            ">Seq2\nDGEL\n", DataSourceType.PASTE);
     SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA");
     SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA");
     SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
@@ -321,7 +331,7 @@ public class AlignViewportTest
     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
             Boolean.FALSE.toString());
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
-            "examples/uniref50.fa", FormatAdapter.FILE);
+            "examples/uniref50.fa", DataSourceType.FILE);
     AlignmentAnnotation[] anns = af.viewport.getAlignment()
             .getAlignmentAnnotation();
     assertNotNull("No annotations found", anns);
@@ -338,23 +348,24 @@ public class AlignViewportTest
   public void testSetGlobalColourScheme()
   {
     /*
-     * test for JAL-2283 don't inadvertently turn on colour by conservation
+     * test for JAL-2283: don't inadvertently turn on colour by conservation
      */
-    Cache.applicationProperties.setProperty("DEFAULT_COLOUR_PROT", "NONE");
+    Cache.applicationProperties.setProperty("DEFAULT_COLOUR_PROT", "None");
     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
             Boolean.TRUE.toString());
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
-            "examples/uniref50.fa", FormatAdapter.FILE);
+            "examples/uniref50.fa", DataSourceType.FILE);
     ColourSchemeI cs = new PIDColourScheme();
     af.getViewport().setGlobalColourScheme(cs);
-    assertFalse(cs.conservationApplied());
+    assertFalse(af.getViewport().getResidueShading()
+            .conservationApplied());
   }
 
   @Test(groups = { "Functional" })
   public void testSetGetHasSearchResults()
   {
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
-            "examples/uniref50.fa", FormatAdapter.FILE);
+            "examples/uniref50.fa", DataSourceType.FILE);
     SearchResultsI sr = new SearchResults();
     SequenceI s1 = af.getViewport().getAlignment().getSequenceAt(0);
 
@@ -373,4 +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.");
+
+  }
 }