Make sure sequence is in mouse over alignment

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 3f3c3dd..4951516 100644 (file)
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -502,7 +502,8 @@ public class AppletJmol extends Frame
     {
       for (int m = 0; m < mapping.length; m++)
       {
-        if (mapping[m].getSequence() == sequence[s])
+        if (mapping[m].getSequence() == sequence[s]
+            && ap.av.alignment.findIndex(sequence[s])>-1)
         {
           for (int r = 0; r < sequence[s].getLength(); r++)
           {