X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fgui%2FAlignFrameTest.java;h=af9c045f993e8e20c45e18f4e1cdb814a8dbaf8b;hb=6157950da0bf97e1fafa6b60ed95df21d9c609de;hp=8ba165ec849279d4198c7873e2d462ae8e583b36;hpb=424f6f03e8fb5e40cceca09fc8ffd72b41e3a9e4;p=jalview.git

diff --git a/test/jalview/gui/AlignFrameTest.java b/test/jalview/gui/AlignFrameTest.java
index 8ba165e..af9c045 100644
--- a/test/jalview/gui/AlignFrameTest.java
+++ b/test/jalview/gui/AlignFrameTest.java
@@ -85,11 +85,13 @@ public class AlignFrameTest
      */
     assertFalse(alignFrame.hideFeatureColumns("exon", true));
     assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
-    assertTrue(alignFrame.getViewport().getColumnSelection().getHiddenColumns()
+    assertTrue(alignFrame.getViewport().getAlignment().getHiddenColumns()
+            .getHiddenColumnsCopy()
             .isEmpty());
     assertFalse(alignFrame.hideFeatureColumns("exon", false));
     assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
-    assertTrue(alignFrame.getViewport().getColumnSelection().getHiddenColumns()
+    assertTrue(alignFrame.getViewport().getAlignment().getHiddenColumns()
+            .getHiddenColumnsCopy()
             .isEmpty());
 
     /*
@@ -97,8 +99,9 @@ public class AlignFrameTest
      */
     assertFalse(alignFrame.hideFeatureColumns("Metal", true));
     assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
-    List<int[]> hidden = alignFrame.getViewport().getColumnSelection()
-            .getHiddenColumns();
+    List<int[]> hidden = alignFrame.getViewport().getAlignment()
+            .getHiddenColumns()
+            .getHiddenColumnsCopy();
     assertTrue(hidden.isEmpty());
 
     /*
@@ -107,7 +110,8 @@ public class AlignFrameTest
      * [1-3], [6-8] base zero
      */
     assertTrue(alignFrame.hideFeatureColumns("Turn", true));
-    hidden = alignFrame.getViewport().getColumnSelection().getHiddenColumns();
+    hidden = alignFrame.getViewport().getAlignment().getHiddenColumns()
+            .getHiddenColumnsCopy();
     assertEquals(hidden.size(), 2);
     assertEquals(hidden.get(0)[0], 1);
     assertEquals(hidden.get(0)[1], 3);
@@ -183,8 +187,8 @@ 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 +200,8 @@ 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 +213,9 @@ 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 +267,9 @@ 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 +282,9 @@ 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 +318,8 @@ 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 +327,7 @@ 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 +343,7 @@ 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 +494,7 @@ 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 +544,11 @@ 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 +567,6 @@ public class AlignFrameTest
             "label.conservation_colour_increment",
             new String[] { "View 1" }));
     sp.valueChanged(22);
-    assertEquals(av2.getViewportColourScheme().getConservationInc(), 22);
+    assertEquals(av2.getResidueShading().getConservationInc(), 22);
   }
 }