X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=221f793d9c83fe1ad7d492c3fa9c404b8c6a5978;hb=6666fd8b18b395d444e7f4c76016231f5a4d3669;hp=5cabda3639d999f4c7bf19f3a4a913be93f63a7e;hpb=4f094851cd2247ea2d982e7829a6f5b663042573;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 5cabda3..221f793 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -22,6 +22,7 @@ package jalview.appletgui;
 
 import jalview.analysis.AlignmentSorter;
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.analysis.NJTree;
 import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
 import jalview.api.AlignViewportI;
@@ -284,6 +285,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     if (viewport.getAlignment().isNucleotide())
     {
+      conservationMenuItem.setEnabled(false);
+      clustalColour.setEnabled(false);
+      BLOSUM62Colour.setEnabled(false);
+      zappoColour.setEnabled(false);
+      taylorColour.setEnabled(false);
+      hydrophobicityColour.setEnabled(false);
+      helixColour.setEnabled(false);
+      strandColour.setEnabled(false);
+      turnColour.setEnabled(false);
+      buriedColour.setEnabled(false);
       viewport.updateStrucConsensus(alignPanel);
       if (viewport.getAlignment().hasRNAStructure())
       {
@@ -2795,22 +2806,26 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   public void averageDistanceTreeMenuItem_actionPerformed()
   {
-    NewTreePanel("AV", "PID", "Average distance tree using PID");
+    NewTreePanel(NJTree.AVERAGE_DISTANCE, "PID",
+            "Average distance tree using PID");
   }
 
   public void neighbourTreeMenuItem_actionPerformed()
   {
-    NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
+    NewTreePanel(NJTree.NEIGHBOUR_JOINING, "PID",
+            "Neighbour joining tree using PID");
   }
 
   protected void njTreeBlosumMenuItem_actionPerformed()
   {
-    NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
+    NewTreePanel(NJTree.NEIGHBOUR_JOINING, "BL",
+            "Neighbour joining tree using BLOSUM62");
   }
 
   protected void avTreeBlosumMenuItem_actionPerformed()
   {
-    NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
+    NewTreePanel(NJTree.AVERAGE_DISTANCE, "BL",
+            "Average distance tree using BLOSUM62");
   }
 
   void NewTreePanel(String type, String pwType, String title)