JAL-2674 Removing most calls to getHiddenColumnsCopy

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

diff --git a/test/jalview/gui/AlignFrameTest.java b/test/jalview/gui/AlignFrameTest.java
index 8ba165e..dd1a4de 100644 (file)
--- 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)
@@ -183,8 +186,8 @@ public class AlignFrameTest
     af.applyToAllGroups_actionPerformed(false);
     af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
     assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
-    assertFalse(av.getViewportColourScheme().conservationApplied());
-    assertEquals(av.getViewportColourScheme().getThreshold(), 0);
+    assertFalse(av.getResidueShading().conservationApplied());
+    assertEquals(av.getResidueShading().getThreshold(), 0);
 
     /*
      * Apply Conservation 20%
@@ -196,8 +199,8 @@ public class AlignFrameTest
             new String[] { "Background" }));
     assertTrue(sp.isForConservation());
     sp.valueChanged(20);
-    assertTrue(av.getViewportColourScheme().conservationApplied());
-    assertEquals(av.getViewportColourScheme().getConservationInc(), 20);
+    assertTrue(av.getResidueShading().conservationApplied());
+    assertEquals(av.getResidueShading().getConservationInc(), 20);
 
     /*
      * Apply PID threshold 10% (conservation still applies as well)
@@ -209,9 +212,9 @@ public class AlignFrameTest
             "label.percentage_identity_threshold",
             new String[] { "Background" }));
     sp.valueChanged(10);
-    assertEquals(av.getViewportColourScheme().getThreshold(), 10);
-    assertTrue(av.getViewportColourScheme().conservationApplied());
-    assertEquals(av.getViewportColourScheme().getConservationInc(), 20);
+    assertEquals(av.getResidueShading().getThreshold(), 10);
+    assertTrue(av.getResidueShading().conservationApplied());
+    assertEquals(av.getResidueShading().getConservationInc(), 20);
 
     /*
      * create a group with Strand colouring, 30% Conservation
@@ -263,9 +266,9 @@ public class AlignFrameTest
      */
     af.changeColour_actionPerformed(JalviewColourScheme.Turn.toString());
     assertTrue(av.getGlobalColourScheme() instanceof TurnColourScheme);
-    assertTrue(av.getViewportColourScheme().conservationApplied());
-    assertEquals(av.getViewportColourScheme().getConservationInc(), 20);
-    assertEquals(av.getViewportColourScheme().getThreshold(), 10);
+    assertTrue(av.getResidueShading().conservationApplied());
+    assertEquals(av.getResidueShading().getConservationInc(), 20);
+    assertEquals(av.getResidueShading().getThreshold(), 10);
     assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
     assertTrue(sg.getGroupColourScheme().conservationApplied());
     assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
@@ -278,9 +281,9 @@ public class AlignFrameTest
     af.applyToAllGroups_actionPerformed(true);
     af.changeColour_actionPerformed(JalviewColourScheme.Helix.toString());
     assertTrue(av.getGlobalColourScheme() instanceof HelixColourScheme);
-    assertTrue(av.getViewportColourScheme().conservationApplied());
-    assertEquals(av.getViewportColourScheme().getConservationInc(), 20);
-    assertEquals(av.getViewportColourScheme().getThreshold(), 10);
+    assertTrue(av.getResidueShading().conservationApplied());
+    assertEquals(av.getResidueShading().getConservationInc(), 20);
+    assertEquals(av.getResidueShading().getThreshold(), 10);
     assertTrue(sg.getColourScheme() instanceof HelixColourScheme);
     assertTrue(sg.getGroupColourScheme().conservationApplied());
     assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
@@ -314,8 +317,8 @@ public class AlignFrameTest
     af.applyToAllGroups_actionPerformed(false);
     af.changeColour_actionPerformed(JalviewColourScheme.Helix.toString());
     assertTrue(av.getGlobalColourScheme() instanceof HelixColourScheme);
-    assertFalse(av.getViewportColourScheme().conservationApplied());
-    assertEquals(av.getViewportColourScheme().getThreshold(), 0);
+    assertFalse(av.getResidueShading().conservationApplied());
+    assertEquals(av.getResidueShading().getThreshold(), 0);
 
     /*
      * inspect the colour of 
@@ -323,7 +326,7 @@ public class AlignFrameTest
      * FER_CAPAN.10(SER), column 16 (15 base 0)
      */
     SequenceI ferCapan = al.findName("FER_CAPAN");
-    ResidueShaderI rs = av.getViewportColourScheme();
+    ResidueShaderI rs = av.getResidueShading();
     Color c = rs.findColour('I', 14, ferCapan);
     Color i_original = new Color(138, 117, 138);
     assertEquals(c, i_original);
@@ -339,7 +342,7 @@ public class AlignFrameTest
     assertTrue(sp.isForConservation());
     assertEquals(sp.getValue(), 30); // initial slider setting
     sp.valueChanged(10);
-    assertSame(rs, av.getViewportColourScheme());
+    assertSame(rs, av.getResidueShading());
     c = rs.findColour('I', 14, ferCapan);
     Color i_faded = new Color(196, 186, 196);
     assertEquals(c, i_faded);
@@ -490,7 +493,7 @@ public class AlignFrameTest
     sp = SliderPanel.getSliderPanel();
     assertTrue(sp.isForConservation());
     sp.valueChanged(20);
-    ResidueShaderI rs = av.getViewportColourScheme();
+    ResidueShaderI rs = av.getResidueShading();
     assertEquals(rs.getThreshold(), 10);
     assertTrue(rs.conservationApplied());
     assertEquals(rs.getConservationInc(), 20);
@@ -540,10 +543,11 @@ public class AlignFrameTest
     assertEquals(af.alignPanel.getViewName(), "View 1");
     AlignViewport av2 = af.getViewport();
     assertNotSame(av, av2);
-    rs = av2.getViewportColourScheme();
-    assertNotSame(av.getViewportColourScheme(), rs);
+    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);
@@ -562,6 +566,6 @@ public class AlignFrameTest
             "label.conservation_colour_increment",
             new String[] { "View 1" }));
     sp.valueChanged(22);
-    assertEquals(av2.getViewportColourScheme().getConservationInc(), 22);
+    assertEquals(av2.getResidueShading().getConservationInc(), 22);
   }
 }