JAL-3383 minor code tidying and commenting

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

diff --git a/test/jalview/renderer/OverviewResColourFinderTest.java b/test/jalview/renderer/OverviewResColourFinderTest.java
index 2016087..bf1237d 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;
@@ -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" })
@@ -137,6 +137,7 @@ public class OverviewResColourFinderTest
     }
 
     av.setGlobalColourScheme(new UserColourScheme(newColours));
+    seq.resetColors();
 
     // gap colour not specified so gaps are lightGray
     assertEquals(Color.lightGray, rcf
@@ -145,6 +146,7 @@ public class OverviewResColourFinderTest
 
     newColours[23] = Color.pink;
     av.setGlobalColourScheme(new UserColourScheme(newColours));
+    seq.resetColors();
 
     // gap colour specified as pink
     assertEquals(Color.pink, rcf.getResidueColour(true,
@@ -154,18 +156,21 @@ public class OverviewResColourFinderTest
     // unaffected by showBoxes setting
     // gap colour not specified so gaps are lightGray
     newColours[23] = null;
+    seq.resetColors();
+
     assertEquals(Color.lightGray, rcf.getResidueColour(false,
             av.getResidueShading(), null, seq, 3, null));
 
     newColours[23] = Color.pink;
     av.setGlobalColourScheme(new UserColourScheme(newColours));
+    seq.resetColors();
 
     // gap colour specified as pink
     assertEquals(Color.pink, rcf.getResidueColour(false,
             av.getResidueShading(), null, seq, 3, null));
   }
 
-  @Test
+  @Test(groups = "Functional")
   public void testGetResidueBoxColour_group()
   {
     SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF");
@@ -197,6 +202,8 @@ public class OverviewResColourFinderTest
 
     // use legacy colouring
     rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
+
+    seq.resetColors();
   
     // G in group specified as magenta in Zappo
     assertEquals(Color.magenta, rcf.getResidueColour(false,
@@ -213,6 +220,8 @@ public class OverviewResColourFinderTest
     // use new colouring
     rcf = new OverviewResColourFinder(false, Color.blue, Color.red);
 
+    seq.resetColors();
+
     // G in group specified as magenta in Zappo
     assertEquals(Color.magenta, rcf.getResidueColour(false,
             av.getResidueShading(), groups, seq, 7, null));
@@ -226,7 +235,7 @@ public class OverviewResColourFinderTest
             av.getResidueShading(), groups, seq, 2, null));
   }
 
-  @Test
+  @Test(groups = "Functional")
   public void testGetBoxColour()
   {
     SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
@@ -238,18 +247,24 @@ public class OverviewResColourFinderTest
     ResidueColourFinder rcf = new OverviewResColourFinder();
     ResidueShaderI shader = new ResidueShader();
 
+    seq.resetColors();
+
     // residues white
     Color c = rcf.getBoxColour(shader, seq, 0);
     assertEquals(Color.white, c);
 
     // 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);
     shader = new ResidueShader();
 
+    seq.resetColors();
+
     // residues light gray
     c = rcf.getBoxColour(shader, seq, 0);
     assertEquals(Color.lightGray, c);
@@ -262,18 +277,24 @@ public class OverviewResColourFinderTest
     rcf = new OverviewResColourFinder();
     shader = new ResidueShader();
 
+    seq.resetColors();
+
     // residues white
     c = rcf.getBoxColour(shader, seq, 0);
     assertEquals(Color.white, c);
 
     // 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);
     shader = new ResidueShader(new ZappoColourScheme());
 
+    seq.resetColors();
+
     // M residue pink
     c = rcf.getBoxColour(shader, seq, 0);
     assertEquals(Color.pink, c);
@@ -285,6 +306,8 @@ public class OverviewResColourFinderTest
     // legacy colouring with colour scheme
     rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
 
+    seq.resetColors();
+
     // M residue pink
     c = rcf.getBoxColour(shader, seq, 0);
     assertEquals(Color.pink, c);