X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=7ef2d59c3fd8c0eb6a7d041578400a2ad05eb0c7;hb=e2399fe0a610faf5dee11a68a8643c34e3ef2490;hp=4b55697aa815a1747b02f98fc3e1315ceac0ddf0;hpb=294cc8b0cf3d28310a95e1ffdb2a0f871304b70d;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 4b55697..7ef2d59 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -21,9 +21,7 @@
 package jalview.appletgui;
 
 import jalview.analysis.NJTree;
-import jalview.api.AlignExportSettingI;
 import jalview.api.AlignViewportI;
-import jalview.api.FeatureRenderer;
 import jalview.bin.JalviewLite;
 import jalview.commands.CommandI;
 import jalview.datamodel.AlignmentI;
@@ -59,10 +57,6 @@ public class AlignViewport extends AlignmentViewport implements
 
   private AnnotationColumnChooser annotationColumnSelectionState;
 
-  private FeatureRenderer featureRenderer;
-
-  private AlignExportSettingI exportSettings;
-
   public void finalize()
   {
     applet = null;
@@ -193,8 +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");
@@ -293,7 +292,6 @@ public class AlignViewport extends AlignmentViewport implements
     return font;
   }
 
-
   public void resetSeqLimits(int height)
   {
     setEndSeq(height / getCharHeight());
@@ -309,7 +307,6 @@ public class AlignViewport extends AlignmentViewport implements
     return currentTree;
   }
 
-
   boolean centreColumnLabels;
 
   public boolean getCentreColumnLabels()
@@ -331,8 +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);
   }
 
   /**
@@ -473,5 +470,4 @@ public class AlignViewport extends AlignmentViewport implements
     }
   }
 
-
 }