X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Frenderer%2FOverviewResColourFinderTest.java;h=76beab80e27d0c58c1ed6c532815f035c9dddb6c;hb=447c5c1b22bd12a78730640321264fb38c39ec7b;hp=3d4ca6f68b295bda4d243b5621559580cf1e58a1;hpb=dbd4cbab0473d8ecac0432cc9ce74a552c7409d1;p=jalview.git

diff --git a/test/jalview/renderer/OverviewResColourFinderTest.java b/test/jalview/renderer/OverviewResColourFinderTest.java
index 3d4ca6f..76beab8 100644
--- a/test/jalview/renderer/OverviewResColourFinderTest.java
+++ b/test/jalview/renderer/OverviewResColourFinderTest.java
@@ -30,7 +30,6 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignViewport;
 import jalview.gui.JvOptionPane;
-import jalview.gui.Preferences;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.UserColourScheme;
 import jalview.schemes.ZappoColourScheme;
@@ -60,19 +59,20 @@ public class OverviewResColourFinderTest
     final AlignViewport av = new AlignViewport(al);
     ResidueColourFinder rcf = new OverviewResColourFinder();
 
+    ResidueShaderI sh = av.getResidueShading();
+
     // gaps are grey, residues white
-    assertEquals(Color.white, rcf.getResidueColour(true,
-            av.getResidueShading(),
-            null, seq, 0, null));
-    assertEquals(Color.lightGray, rcf
-            .getResidueColour(true, av.getResidueShading(), null, seq, 2,
-                    null));
+    assertEquals(Color.white,
+            rcf.getResidueColour(true, sh, null, seq, 0, null));
+    System.out.println(rcf.getResidueColour(true, sh, null, seq, 2, null));
+    assertEquals(Color.lightGray, rcf.getResidueColour(true,
+            sh, null, seq, 2, null));
 
     // unaffected by showBoxes setting
     assertEquals(Color.white, rcf.getResidueColour(false,
-            av.getResidueShading(), null, seq, 0, null));
+            sh, null, seq, 0, null));
     assertEquals(Color.lightGray, rcf.getResidueColour(false,
-            av.getResidueShading(), null, seq, 2, null));
+            sh, null, seq, 2, null));
   }
 
   @Test(groups = { "Functional" })
@@ -154,6 +154,7 @@ public class OverviewResColourFinderTest
     // unaffected by showBoxes setting
     // gap colour not specified so gaps are lightGray
     newColours[23] = null;
+
     assertEquals(Color.lightGray, rcf.getResidueColour(false,
             av.getResidueShading(), null, seq, 3, null));
 
@@ -165,7 +166,7 @@ public class OverviewResColourFinderTest
             av.getResidueShading(), null, seq, 3, null));
   }
 
-  @Test
+  @Test(groups = "Functional")
   public void testGetResidueBoxColour_group()
   {
     SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF");
@@ -195,6 +196,7 @@ public class OverviewResColourFinderTest
     assertEquals(Color.lightGray, rcf.getResidueColour(false,
             av.getResidueShading(), groups, seq, 2, null));
 
+    // use legacy colouring
     rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
   
     // G in group specified as magenta in Zappo
@@ -208,9 +210,24 @@ public class OverviewResColourFinderTest
     // Gap outside group coloured white
     assertEquals(Color.white, rcf.getResidueColour(false,
             av.getResidueShading(), groups, seq, 2, null));
+
+    // use new colouring
+    rcf = new OverviewResColourFinder(false, Color.blue, Color.red);
+
+    // G in group specified as magenta in Zappo
+    assertEquals(Color.magenta, rcf.getResidueColour(false,
+            av.getResidueShading(), groups, seq, 7, null));
+
+    // Residue outside group coloured white
+    assertEquals(Color.white, rcf.getResidueColour(false,
+            av.getResidueShading(), groups, seq, 0, null));
+
+    // Gap outside group coloured blue
+    assertEquals(Color.blue, rcf.getResidueColour(false,
+            av.getResidueShading(), groups, seq, 2, null));
   }
 
-  @Test
+  @Test(groups = "Functional")
   public void testGetBoxColour()
   {
     SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
@@ -228,7 +245,9 @@ public class OverviewResColourFinderTest
 
     // gaps gap colour
     c = rcf.getBoxColour(shader, seq, 3);
-    assertEquals(Preferences.OVERVIEW_DEFAULT_GAP, c);
+    assertEquals(
+            jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP,
+            c);
 
     // legacy colouring set explicitly via constructor
     rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
@@ -252,7 +271,9 @@ public class OverviewResColourFinderTest
 
     // gaps gap colour
     c = rcf.getBoxColour(shader, seq, 3);
-    assertEquals(Preferences.OVERVIEW_DEFAULT_GAP, c);
+    assertEquals(
+            jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP,
+            c);
 
     // non legacy colouring with colour scheme
     rcf = new OverviewResColourFinder(false, Color.blue, Color.red);