Merge branch 'develop' into features/JAL-1705_ensembl

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

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index e4e3e17..7ef2d59 100644 (file)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -187,8 +187,13 @@ public class AlignViewport extends AlignmentViewport implements
 
     if (applet != null)
     {
-      String colour = applet.getParameter("defaultColour");
-
+      String colour = al.isNucleotide() ? applet
+              .getParameter("defaultColourNuc") : applet
+              .getParameter("defaultColourProt");
+      if (colour == null)
+      {
+        colour = applet.getParameter("defaultColour");
+      }
       if (colour == null)
       {
         colour = applet.getParameter("userDefinedColour");
@@ -287,7 +292,6 @@ public class AlignViewport extends AlignmentViewport implements
     return font;
   }
 
-
   public void resetSeqLimits(int height)
   {
     setEndSeq(height / getCharHeight());
@@ -303,7 +307,6 @@ public class AlignViewport extends AlignmentViewport implements
     return currentTree;
   }
 
-
   boolean centreColumnLabels;
 
   public boolean getCentreColumnLabels()
@@ -325,8 +328,8 @@ public class AlignViewport extends AlignmentViewport implements
   public void sendSelection()
   {
     getStructureSelectionManager().sendSelection(
-                    new SequenceGroup(getSelectionGroup()),
-                    new ColumnSelection(getColumnSelection()), this);
+            new SequenceGroup(getSelectionGroup()),
+            new ColumnSelection(getColumnSelection()), this);
   }
 
   /**
@@ -467,5 +470,4 @@ public class AlignViewport extends AlignmentViewport implements
     }
   }
 
-
 }