Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

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

diff --git a/test/jalview/renderer/OverviewResColourFinderTest.java b/test/jalview/renderer/OverviewResColourFinderTest.java
index 3931dbf..518fdef 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;
@@ -56,14 +57,16 @@ 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
     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,
@@ -78,23 +81,28 @@ 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());
 
     // @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,
@@ -107,8 +115,9 @@ 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));
 
   }
 
@@ -118,7 +127,7 @@ 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];
@@ -130,15 +139,17 @@ 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
@@ -159,7 +170,7 @@ 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);
@@ -168,10 +179,10 @@ public class OverviewResColourFinderTest
     al.addGroup(sg);
     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
     assertEquals(Color.magenta, rcf.getResidueColour(false,
             av.getResidueShading(), groups, seq, 7, null));
@@ -186,7 +197,7 @@ public class OverviewResColourFinderTest
 
     // 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));
@@ -220,8 +231,6 @@ 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();
@@ -259,9 +268,7 @@ public class OverviewResColourFinderTest
 
     // gaps gap colour
     c = rcf.getBoxColour(shader, seq, 3);
-    assertEquals(
-            jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP,
-            c);
+    assertEquals(OverviewResColourFinder.OVERVIEW_DEFAULT_GAP, c);
 
     // non legacy colouring with colour scheme
     rcf = new OverviewResColourFinder(false, Color.blue, Color.red);