merge

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 688ea53..84be0dd 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -60,7 +60,6 @@ import jalview.schemes.NucleotideColourScheme;
 import jalview.schemes.PIDColourScheme;
 import jalview.schemes.PurinePyrimidineColourScheme;
 import jalview.schemes.RNAHelicesColourChooser;
-import jalview.schemes.RNAInteractionColourScheme;
 import jalview.schemes.StrandColourScheme;
 import jalview.schemes.TCoffeeColourScheme;
 import jalview.schemes.TaylorColourScheme;
@@ -1230,10 +1229,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       changeColour(new PurinePyrimidineColourScheme());
     }
-    else if (source == RNAInteractionColour)
-    {
-      changeColour(new RNAInteractionColourScheme());
-    }
+    // else if (source == RNAInteractionColour)
+    // {
+    // changeColour(new RNAInteractionColourScheme());
+    // }
     else if (source == RNAHelixColour)
     {
       new RNAHelicesColourChooser(viewport, alignPanel);
@@ -3071,7 +3070,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   MenuItem purinePyrimidineColour = new MenuItem();
 
-  MenuItem RNAInteractionColour = new MenuItem();
+  // MenuItem RNAInteractionColour = new MenuItem();
 
   MenuItem RNAHelixColour = new MenuItem();
 
@@ -3441,9 +3440,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     purinePyrimidineColour.setLabel(MessageManager
             .getString("label.purine_pyrimidine"));
     purinePyrimidineColour.addActionListener(this);
-    RNAInteractionColour.setLabel(MessageManager
-            .getString("label.rna_interaction"));
-    RNAInteractionColour.addActionListener(this);
+    // RNAInteractionColour.setLabel(MessageManager
+    // .getString("label.rna_interaction"));
+    // RNAInteractionColour.addActionListener(this);
     RNAHelixColour.setLabel(MessageManager
             .getString("action.by_rna_helixes"));
     RNAHelixColour.addActionListener(this);

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 8a9c54b..9aa5735 100644 (file)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -20,6 +20,7 @@
  */
 package jalview.bin;
 
+import jalview.analysis.AlignmentUtils;
 import jalview.api.StructureSelectionManagerProvider;
 import jalview.appletgui.AlignFrame;
 import jalview.appletgui.AlignViewport;
@@ -1879,15 +1880,27 @@ public class JalviewLite extends Applet implements
      */
     public void addToDisplay(AlignFrame af, AlignFrame af2)
     {
-      if (af2 == null)
+      if (af2 != null)
       {
-        af.addToDisplay(embedded);
-      }
-      else
-      {
-        SplitFrame sf = new SplitFrame(af, af2);
-        sf.addToDisplay(embedded, JalviewLite.this);
+        AlignmentI al1 = af.viewport.getAlignment();
+        AlignmentI al2 = af2.viewport.getAlignment();
+        if (AlignmentUtils.isMappable(al1, al2))
+        {
+          SplitFrame sf = new SplitFrame(af, af2);
+          sf.addToDisplay(embedded, JalviewLite.this);
+          return;
+        }
+        else
+        {
+          String msg = "Could not map any sequence in " + af2.getTitle()
+                  + " as "
+                  + (al1.isNucleotide() ? "protein product" : "cDNA")
+                  + " for " + af.getTitle();
+          System.err.println(msg);
+        }
       }
+
+      af.addToDisplay(embedded);
     }
 
     /**