Merge branch 'task/JAL-3992_update_docs' into bug/JAL-3365_extendedDSSP_via_stockholm

[jalview.git] / test / jalview / renderer / OverviewResColourFinderTest.java

diff --git a/test/jalview/renderer/OverviewResColourFinderTest.java b/test/jalview/renderer/OverviewResColourFinderTest.java
index 3d4ca6f..3931dbf 100644 (file)
--- 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;
@@ -62,11 +61,9 @@ public class OverviewResColourFinderTest
 
     // 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));
+            av.getResidueShading(), null, seq, 0, null));
+    assertEquals(Color.lightGray, rcf.getResidueColour(true,
+            av.getResidueShading(), null, seq, 2, null));
 
     // unaffected by showBoxes setting
     assertEquals(Color.white, rcf.getResidueColour(false,
@@ -86,23 +83,18 @@ public class OverviewResColourFinderTest
     av.setGlobalColourScheme(new ZappoColourScheme());
 
     // @see ResidueProperties.zappo
-    assertEquals(Color.pink,
-            rcf.getResidueColour(true, av.getResidueShading(),
-            null, seq, 0, null)); // M
-    assertEquals(Color.green,
-            rcf.getResidueColour(true, av.getResidueShading(),
-            null, seq, 2, null)); // T
-    assertEquals(Color.magenta,
-            rcf.getResidueColour(true, av.getResidueShading(),
-            null, seq, 5, null)); // G
-    assertEquals(Color.orange,
-            rcf.getResidueColour(true, av.getResidueShading(),
-            null, seq, 12, null)); // F
+    assertEquals(Color.pink, rcf.getResidueColour(true,
+            av.getResidueShading(), null, seq, 0, null)); // M
+    assertEquals(Color.green, rcf.getResidueColour(true,
+            av.getResidueShading(), null, seq, 2, null)); // T
+    assertEquals(Color.magenta, rcf.getResidueColour(true,
+            av.getResidueShading(), null, seq, 5, null)); // G
+    assertEquals(Color.orange, rcf.getResidueColour(true,
+            av.getResidueShading(), null, seq, 12, null)); // F
 
     // gap colour not specified so gaps are lightGray
-    assertEquals(Color.lightGray, rcf
-            .getResidueColour(true, av.getResidueShading(), null, seq, 3,
-                    null));
+    assertEquals(Color.lightGray, rcf.getResidueColour(true,
+            av.getResidueShading(), null, seq, 3, null));
 
     // unaffected by showBoxes setting
     assertEquals(Color.pink, rcf.getResidueColour(false,
@@ -115,9 +107,8 @@ public class OverviewResColourFinderTest
             av.getResidueShading(), null, seq, 12, null)); // F
 
     // gap colour not specified so gaps are lightGray
-    assertEquals(Color.lightGray, rcf
-            .getResidueColour(false, av.getResidueShading(), null, seq, 3,
-                    null));
+    assertEquals(Color.lightGray, rcf.getResidueColour(false,
+            av.getResidueShading(), null, seq, 3, null));
 
   }
 
@@ -139,17 +130,15 @@ public class OverviewResColourFinderTest
     av.setGlobalColourScheme(new UserColourScheme(newColours));
 
     // gap colour not specified so gaps are lightGray
-    assertEquals(Color.lightGray, rcf
-            .getResidueColour(true, av.getResidueShading(), null, seq, 3,
-                    null));
+    assertEquals(Color.lightGray, rcf.getResidueColour(true,
+            av.getResidueShading(), null, seq, 3, null));
 
     newColours[23] = Color.pink;
     av.setGlobalColourScheme(new UserColourScheme(newColours));
 
     // gap colour specified as pink
     assertEquals(Color.pink, rcf.getResidueColour(true,
-            av.getResidueShading(),
-            null, seq, 3, null));
+            av.getResidueShading(), null, seq, 3, null));
 
     // unaffected by showBoxes setting
     // gap colour not specified so gaps are lightGray
@@ -170,7 +159,7 @@ public class OverviewResColourFinderTest
   {
     SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF");
     AlignmentI al = new Alignment(new SequenceI[] { seq });
-    
+
     ColourSchemeI cs = new ZappoColourScheme();
     ArrayList<SequenceI> seqlist = new ArrayList<>();
     seqlist.add(seq);
@@ -179,10 +168,10 @@ public class OverviewResColourFinderTest
     al.addGroup(sg);
     SequenceGroup[] groups = new SequenceGroup[1];
     groups[0] = sg;
-    
+
     final AlignViewport av = new AlignViewport(al);
     ResidueColourFinder rcf = new OverviewResColourFinder();
-    
+
     // G in group specified as magenta in Zappo
     assertEquals(Color.magenta, rcf.getResidueColour(false,
             av.getResidueShading(), groups, seq, 7, null));
@@ -195,8 +184,9 @@ 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
     assertEquals(Color.magenta, rcf.getResidueColour(false,
             av.getResidueShading(), groups, seq, 7, null));
@@ -208,6 +198,21 @@ 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
@@ -228,7 +233,9 @@ 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 +259,9 @@ 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);