Updated with latest from mchmmer branch

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

diff --git a/test/jalview/gui/AlignFrameTest.java b/test/jalview/gui/AlignFrameTest.java
index 1ee25c7..0f15ce4 100644 (file)
--- a/test/jalview/gui/AlignFrameTest.java
+++ b/test/jalview/gui/AlignFrameTest.java
@@ -26,11 +26,13 @@ import static org.testng.Assert.assertNotSame;
 import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 
+import jalview.api.AlignViewportI;
 import jalview.api.FeatureColourI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
@@ -46,9 +48,10 @@ import jalview.schemes.JalviewColourScheme;
 import jalview.schemes.StrandColourScheme;
 import jalview.schemes.TurnColourScheme;
 import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.Color;
-import java.util.List;
+import java.util.Iterator;
 
 import org.testng.annotations.AfterMethod;
 import org.testng.annotations.BeforeClass;
@@ -92,21 +95,25 @@ public class AlignFrameTest
      */
     assertFalse(alignFrame.hideFeatureColumns("exon", true));
     assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
-    assertTrue(alignFrame.getViewport().getAlignment().getHiddenColumns()
-            .getHiddenColumnsCopy().isEmpty());
+
+    assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
+            .getNumberOfRegions(), 0);
+
     assertFalse(alignFrame.hideFeatureColumns("exon", false));
     assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
-    assertTrue(alignFrame.getViewport().getAlignment().getHiddenColumns()
-            .getHiddenColumnsCopy().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().getAlignment()
-            .getHiddenColumns().getHiddenColumnsCopy();
-    assertTrue(hidden.isEmpty());
+
+    assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
+            .getNumberOfRegions(), 0);
+
 
     /*
      * threshold Metal to hide features where score < 5
@@ -118,11 +125,12 @@ public class AlignFrameTest
     fc.setThreshold(5f);
     alignFrame.getFeatureRenderer().setColour("Metal", fc);
     assertTrue(alignFrame.hideFeatureColumns("Metal", true));
-    hidden = alignFrame.getViewport().getAlignment().getHiddenColumns()
-            .getHiddenColumnsCopy();
-    assertEquals(hidden.size(), 1);
-    assertEquals(hidden.get(0)[0], 5);
-    assertEquals(hidden.get(0)[1], 9);
+    HiddenColumns hidden = alignFrame.getViewport().getAlignment().getHiddenColumns();
+    assertEquals(hidden.getNumberOfRegions(), 1);
+    Iterator<int[]> regions = hidden.iterator();
+    int[] next = regions.next();
+    assertEquals(next[0], 5);
+    assertEquals(next[1], 9);
 
     /*
      * hide a feature present in some columns
@@ -131,13 +139,16 @@ public class AlignFrameTest
      */
     alignFrame.getViewport().showAllHiddenColumns();
     assertTrue(alignFrame.hideFeatureColumns("Turn", true));
-    hidden = alignFrame.getViewport().getAlignment().getHiddenColumns()
-            .getHiddenColumnsCopy();
-    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);
+    regions = alignFrame.getViewport().getAlignment()
+            .getHiddenColumns().iterator();
+    assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
+            .getNumberOfRegions(), 2);
+    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)
@@ -199,7 +210,7 @@ public class AlignFrameTest
   @Test(groups = "Functional")
   public void testChangeColour_background_groupsAndThresholds()
   {
-    AlignViewport av = af.getViewport();
+    AlignViewportI av = af.getViewport();
     AlignmentI al = av.getAlignment();
 
     /*
@@ -330,7 +341,7 @@ public class AlignFrameTest
   @Test(groups = "Functional")
   public void testColourThresholdActions()
   {
-    AlignViewport av = af.getViewport();
+    AlignViewportI av = af.getViewport();
     AlignmentI al = av.getAlignment();
 
     /*
@@ -499,7 +510,7 @@ public class AlignFrameTest
   @Test(groups = "Functional")
   public void testNewView_colourThresholds()
   {
-    AlignViewport av = af.getViewport();
+    AlignViewportI av = af.getViewport();
     AlignmentI al = av.getAlignment();
 
     /*
@@ -563,7 +574,7 @@ public class AlignFrameTest
      */
     af.newView_actionPerformed(null);
     assertEquals(af.alignPanel.getViewName(), "View 1");
-    AlignViewport av2 = af.getViewport();
+    AlignmentViewport av2 = af.getViewport();
     assertNotSame(av, av2);
     assertSame(av2, af.alignPanel.av);
     rs = av2.getResidueShading();