JAL-2602 unit test added

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

diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index e6c16b7..346d74d 100644 (file)
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -160,7 +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);
@@ -217,11 +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);
@@ -280,12 +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);
@@ -389,7 +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()
@@ -399,13 +400,21 @@ 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
@@ -441,6 +450,23 @@ public class AlignViewportTest
     }
     ;
     Assert.assertEquals(c, 1, "Expected to find one occupancy row.");
+  }
 
+  @Test(groups = { "Functional" })
+  public void testGetConsensusSeq()
+  {
+    /*
+     * A-C
+     * A-C
+     * A-D
+     * --D
+     * consensus expected to be A-C
+     */
+    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);
+    AlignViewport testme = af.getViewport();
+    SequenceI cons = testme.getConsensusSeq();
+    assertEquals("A-C", cons.getSequenceAsString());
   }
 }