Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into alpha/merge_212_JalviewJS_2112

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

diff --git a/test/jalview/renderer/OverviewResColourFinderTest.java b/test/jalview/renderer/OverviewResColourFinderTest.java
index 3d4ca6f..e44dbe0 100644 (file)
--- a/test/jalview/renderer/OverviewResColourFinderTest.java
+++ b/test/jalview/renderer/OverviewResColourFinderTest.java
@@ -22,6 +22,7 @@ package jalview.renderer;
 
 import static org.testng.AssertJUnit.assertEquals;
 
+import jalview.api.AlignViewportI;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
@@ -30,11 +31,9 @@ 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;
-
 import java.awt.Color;
 import java.util.ArrayList;
 
@@ -57,7 +56,7 @@ public class OverviewResColourFinderTest
   {
     SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF");
     AlignmentI al = new Alignment(new SequenceI[] { seq });
-    final AlignViewport av = new AlignViewport(al);
+    final AlignViewportI av = new AlignViewport(al);
     ResidueColourFinder rcf = new OverviewResColourFinder();
 
     // gaps are grey, residues white
@@ -81,7 +80,7 @@ public class OverviewResColourFinderTest
     SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
                                                             // gap
     AlignmentI al = new Alignment(new SequenceI[] { seq });
-    final AlignViewport av = new AlignViewport(al);
+    final AlignViewportI av = new AlignViewport(al);
     ResidueColourFinder rcf = new OverviewResColourFinder();
     av.setGlobalColourScheme(new ZappoColourScheme());
 
@@ -127,7 +126,7 @@ public class OverviewResColourFinderTest
     SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
                                                             // gap
     AlignmentI al = new Alignment(new SequenceI[] { seq });
-    final AlignViewport av = new AlignViewport(al);
+    final AlignViewportI av = new AlignViewport(al);
     ResidueColourFinder rcf = new OverviewResColourFinder();
 
     Color[] newColours = new Color[24];
@@ -180,7 +179,7 @@ public class OverviewResColourFinderTest
     SequenceGroup[] groups = new SequenceGroup[1];
     groups[0] = sg;
     
-    final AlignViewport av = new AlignViewport(al);
+    final AlignViewportI av = new AlignViewport(al);
     ResidueColourFinder rcf = new OverviewResColourFinder();
     
     // G in group specified as magenta in Zappo
@@ -195,6 +194,7 @@ 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
@@ -208,6 +208,21 @@ 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
@@ -215,8 +230,6 @@ public class OverviewResColourFinderTest
   {
     SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
                                                             // gap
-    AlignmentI al = new Alignment(new SequenceI[] { seq });
-    final AlignViewport av = new AlignViewport(al);
 
     // non-legacy colouring
     ResidueColourFinder rcf = new OverviewResColourFinder();
@@ -228,7 +241,9 @@ 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 +267,7 @@ public class OverviewResColourFinderTest
 
     // gaps gap colour
     c = rcf.getBoxColour(shader, seq, 3);
-    assertEquals(Preferences.OVERVIEW_DEFAULT_GAP, c);
+    assertEquals(OverviewResColourFinder.OVERVIEW_DEFAULT_GAP, c);
 
     // non legacy colouring with colour scheme
     rcf = new OverviewResColourFinder(false, Color.blue, Color.red);