X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAlignViewportTest.java;h=b2286e006b51b06aa99a8aeb5debafe895fda7e9;hb=1810df9d010000e434975a8a4e68dcbda238f7f1;hp=d76ac33f0bc923ab1507f06d55e66bced676b346;hpb=faa3d71f9d120d665870e72b7217ae6b8bd6062d;p=jalview.git

diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index d76ac33..b2286e0 100644
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -46,6 +46,7 @@ import jalview.schemes.ColourSchemeI;
 import jalview.schemes.PIDColourScheme;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MapList;
+import jalview.viewmodel.ViewportRanges;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -160,7 +161,7 @@ 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 +218,11 @@ 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 +281,12 @@ 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);
@@ -328,6 +329,8 @@ 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(
@@ -387,7 +390,8 @@ 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()
@@ -397,13 +401,21 @@ 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
@@ -439,6 +451,65 @@ 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());
+  }
+
+  @Test(groups = { "Functional" })
+  public void testHideRevealSequences()
+  {
+    ViewportRanges ranges = testee.getRanges();
+    assertEquals(3, al.getHeight());
+    assertEquals(0, ranges.getStartSeq());
+    assertEquals(2, ranges.getEndSeq());
 
+    /*
+     * hide first sequence
+     */
+    testee.hideSequence(new SequenceI[] { al.getSequenceAt(0) });
+    assertEquals(2, al.getHeight());
+    assertEquals(0, ranges.getStartSeq());
+    assertEquals(1, ranges.getEndSeq());
+
+    /*
+     * reveal hidden sequences above the first
+     */
+    testee.showSequence(0);
+    assertEquals(3, al.getHeight());
+    assertEquals(0, ranges.getStartSeq());
+    assertEquals(2, ranges.getEndSeq());
+
+    /*
+     * hide first and third sequences
+     */
+    testee.hideSequence(new SequenceI[] { al.getSequenceAt(0),
+        al.getSequenceAt(2) });
+    assertEquals(1, al.getHeight());
+    assertEquals(0, ranges.getStartSeq());
+    assertEquals(0, ranges.getEndSeq());
+
+    /*
+     * reveal all hidden sequences
+     */
+    testee.showAllHiddenSeqs();
+    assertEquals(3, al.getHeight());
+    assertEquals(0, ranges.getStartSeq());
+    assertEquals(2, ranges.getEndSeq());
   }
 }