X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fcommands%2FEditCommand.java;h=d0790c866cd19c2705c6ce02f615d13ecc6e23d9;hb=7c41e0253551a494219c4f1133a1aa2fe591b97a;hp=b9d32f79d5adc1c777e418056da131a5dcf94ed6;hpb=c793942b6430bba9d9b6795e4afd8a1907c022d7;p=jalview.git

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index b9d32f7..d0790c8 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -619,8 +619,8 @@ public class EditCommand implements CommandI
          */
         if (command.alIndex[i] < command.al.getHeight())
         {
-          List<SequenceI> sequences;
-          synchronized (sequences = command.al.getSequences())
+          List<SequenceI> sequences = command.al.getSequences();
+          synchronized (sequences)
           {
             if (!(command.alIndex[i] < 0))
             {
@@ -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)
             {
@@ -1444,45 +1444,45 @@ public class EditCommand implements CommandI
 
   public class Edit
   {
-    private SequenceI[] oldds;
+    SequenceI[] oldds;
 
     /**
      * start and end of sequence prior to edit
      */
-    private Range[] oldStartEnd;
+    Range[] oldStartEnd;
 
-    private boolean fullAlignmentHeight = false;
+    boolean fullAlignmentHeight = false;
 
-    private Map<SequenceI, AlignmentAnnotation[]> deletedAnnotationRows;
+    Map<SequenceI, AlignmentAnnotation[]> deletedAnnotationRows;
 
-    private Map<String, Annotation[]> deletedAnnotations;
+    Map<String, Annotation[]> deletedAnnotations;
 
     /*
      * features deleted by the cut (re-add on Undo)
      * (including the original of any shortened features)
      */
-    private Map<SequenceI, List<SequenceFeature>> deletedFeatures;
+    Map<SequenceI, List<SequenceFeature>> deletedFeatures;
 
     /*
      * shortened features added by the cut (delete on Undo)
      */
-    private Map<SequenceI, List<SequenceFeature>> truncatedFeatures;
+    Map<SequenceI, List<SequenceFeature>> truncatedFeatures;
 
-    private AlignmentI al;
+    AlignmentI al;
 
-    final private Action command;
+    final Action command;
 
     char[][] string;
 
     SequenceI[] seqs;
 
-    private int[] alIndex;
+    int[] alIndex;
 
-    private int position;
+    int position;
 
-    private int number;
+    int number;
 
-    private char gapChar;
+    char gapChar;
 
     /*
      * flag that identifies edits inserted to balance