X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FEditCommand.java;fp=src%2Fjalview%2Fcommands%2FEditCommand.java;h=b9d32f79d5adc1c777e418056da131a5dcf94ed6;hb=ca8504cf9d10874dce9f07cf7a9d933853fe0dd0;hp=1a227c53d50b3380d7f1803b2cda1992717aaf42;hpb=775e7bc104584e88dddcea73fbf02c66f5200c16;p=jalview.git

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index 1a227c5..b9d32f7 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -24,6 +24,7 @@ import jalview.analysis.AlignSeq;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.ContiguousI;
 import jalview.datamodel.Range;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
@@ -526,8 +527,8 @@ public class EditCommand implements CommandI
         command.string[i] = sequence.getSequence(command.position,
                 command.position + command.number);
         SequenceI oldds = sequence.getDatasetSequence();
-        Range cutPositions = sequence.findPositions(command.position + 1,
-                command.position + command.number);
+        ContiguousI cutPositions = sequence.findPositions(
+                command.position + 1, command.position + command.number);
         boolean cutIsInternal = cutPositions != null
                 && sequence.getStart() != cutPositions
                 .getBegin() && sequence.getEnd() != cutPositions.getEnd();
@@ -763,9 +764,9 @@ public class EditCommand implements CommandI
        * EditCommand.PASTE, sequences, 0, alignment.getWidth(), alignment) );
        * 
        */
-
-      Range beforeEditedPositions = command.seqs[i].findPositions(1, start);
-      Range afterEditedPositions = command.seqs[i]
+      ContiguousI beforeEditedPositions = command.seqs[i].findPositions(1,
+              start);
+      ContiguousI afterEditedPositions = command.seqs[i]
               .findPositions(end + 1, command.seqs[i].getLength());
       
       oldstring = command.seqs[i].getSequenceAsString();
@@ -1483,6 +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)
     {
@@ -1555,6 +1562,16 @@ public class EditCommand implements CommandI
     {
       return gapChar;
     }
+
+    public void setSystemGenerated(boolean b)
+    {
+      systemGenerated = b;
+    }
+
+    public boolean isSystemGenerated()
+    {
+      return systemGenerated;
+    }
   }
 
   /**