Merge branch 'patch/JAL-3700_JAL-3748_JAL-3763_for_2_11_1_3' into releases/Release_2_...

[jalview.git] / src / jalview / commands / EditCommand.java

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index f80bd4a..aae72d6 100644 (file)
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -838,7 +838,7 @@ public class EditCommand implements CommandI
             // old ds and edited ds are different, so
             // create the new dataset sequence
             SequenceI newds = new Sequence(oldds);
-            newds.setSequence(fullseq);
+            newds.setSequence(fullseq.toUpperCase());
 
             if (command.oldds == null)
             {
@@ -1484,6 +1484,12 @@ public class EditCommand implements CommandI
 
     private char gapChar;
 
+    /*
+     * flag that identifies edits inserted to balance 
+     * user edits in a 'locked editing' region
+     */
+    private boolean systemGenerated;
+
     public Edit(Action cmd, SequenceI[] sqs, int pos, int count,
             char gap)
     {
@@ -1556,6 +1562,16 @@ public class EditCommand implements CommandI
     {
       return gapChar;
     }
+
+    public void setSystemGenerated(boolean b)
+    {
+      systemGenerated = b;
+    }
+
+    public boolean isSystemGenerated()
+    {
+      return systemGenerated;
+    }
   }
 
   /**