X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAlignFrameTest.java;h=dd1a4dedc667f59b426e47804f4dbf7004655f86;hb=a946e51c2626014b3d4b0bc2790770e847f08bf4;hp=2ea94a4d567d21dabd458e9b7751b6869aeb2af4;hpb=4f094851cd2247ea2d982e7829a6f5b663042573;p=jalview.git

diff --git a/test/jalview/gui/AlignFrameTest.java b/test/jalview/gui/AlignFrameTest.java
index 2ea94a4..dd1a4de 100644
--- a/test/jalview/gui/AlignFrameTest.java
+++ b/test/jalview/gui/AlignFrameTest.java
@@ -46,7 +46,7 @@ import jalview.schemes.TurnColourScheme;
 import jalview.util.MessageManager;
 
 import java.awt.Color;
-import java.util.List;
+import java.util.Iterator;
 
 import org.testng.annotations.AfterMethod;
 import org.testng.annotations.BeforeClass;
@@ -85,21 +85,20 @@ public class AlignFrameTest
      */
     assertFalse(alignFrame.hideFeatureColumns("exon", true));
     assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
-    assertTrue(alignFrame.getViewport().getColumnSelection().getHiddenColumns()
-            .isEmpty());
+    assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
+            .getNumberOfRegions(), 0);
     assertFalse(alignFrame.hideFeatureColumns("exon", false));
     assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
-    assertTrue(alignFrame.getViewport().getColumnSelection().getHiddenColumns()
-            .isEmpty());
+    assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
+            .getNumberOfRegions(), 0);
 
     /*
      * hiding a feature in all columns does nothing
      */
     assertFalse(alignFrame.hideFeatureColumns("Metal", true));
     assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
-    List<int[]> hidden = alignFrame.getViewport().getColumnSelection()
-            .getHiddenColumns();
-    assertTrue(hidden.isEmpty());
+    assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
+            .getNumberOfRegions(), 0);
 
     /*
      * hide a feature present in some columns
@@ -107,12 +106,16 @@ public class AlignFrameTest
      * [1-3], [6-8] base zero
      */
     assertTrue(alignFrame.hideFeatureColumns("Turn", true));
-    hidden = alignFrame.getViewport().getColumnSelection().getHiddenColumns();
-    assertEquals(hidden.size(), 2);
-    assertEquals(hidden.get(0)[0], 1);
-    assertEquals(hidden.get(0)[1], 3);
-    assertEquals(hidden.get(1)[0], 6);
-    assertEquals(hidden.get(1)[1], 8);
+    Iterator<int[]> regions = alignFrame.getViewport().getAlignment()
+            .getHiddenColumns().iterator();
+    assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
+            .getNumberOfRegions(), 2);
+    int[] next = regions.next();
+    assertEquals(next[0], 1);
+    assertEquals(next[1], 3);
+    next = regions.next();
+    assertEquals(next[0], 6);
+    assertEquals(next[1], 8);
   }
 
   @BeforeClass(alwaysRun = true)
@@ -540,10 +543,11 @@ public class AlignFrameTest
     assertEquals(af.alignPanel.getViewName(), "View 1");
     AlignViewport av2 = af.getViewport();
     assertNotSame(av, av2);
+    assertSame(av2, af.alignPanel.av);
     rs = av2.getResidueShading();
     assertNotSame(av.getResidueShading(), rs);
     assertEquals(rs.getThreshold(), 10);
-    assertTrue(rs.conservationApplied());
+    assertTrue(rs.conservationApplied(), rs.toString());
     assertEquals(rs.getConservationInc(), 20);
     assertEquals(av2.getAlignment().getGroups().size(), 1);
     sg = av2.getAlignment().getGroups().get(0);