GetResidueBoxColour needs no colourscheme

[jalview.git] / src / jalview / appletgui / SequenceRenderer.java

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 217a67d..c68e85c 100755 (executable)
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -44,11 +44,24 @@ public class SequenceRenderer
     renderGaps = b;\r
   }\r
 \r
-  public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i)\r
+  public Color getResidueBoxColour(SequenceI seq, int i)\r
   {\r
-    getBoxColour(cs, seq, i);\r
+    allGroups = av.alignment.findAllGroups(seq);\r
+\r
+    if (inCurrentSequenceGroup(i))\r
+    {\r
+      if (currentSequenceGroup.getDisplayBoxes())\r
+      {\r
+        getBoxColour(currentSequenceGroup.cs, seq, i);\r
+      }\r
+    }\r
+    else if (av.getShowBoxes())\r
+    {\r
+        getBoxColour(av.globalColourScheme, seq, i);\r
+    }\r
+\r
     return resBoxColour;\r
-  }\r
+    }\r
 \r
   void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)\r
   {\r