JAL-2541 it works!! it works!!!

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

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index 6484224..9be8d3f 100644 (file)
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -753,8 +753,7 @@ public class EditCommand implements CommandI
       tmp.append(oldstring.substring(end));
       command.seqs[i].setSequence(tmp.toString());
       command.string[i] = oldstring.substring(start, end).toCharArray();
-      String nogapold = jalview.analysis.AlignSeq.extractGaps(
-              jalview.util.Comparison.GapChars,
+      String nogapold = AlignSeq.extractGaps(Comparison.GapChars,
               new String(command.string[i]));
       if (!nogaprep.toLowerCase().equals(nogapold.toLowerCase()))
       {
@@ -903,8 +902,7 @@ public class EditCommand implements CommandI
                 }
                 // and then duplicate added annotation on every other alignment
                 // view
-                for (int vnum = 0; views != null
-                        && vnum < views.length; vnum++)
+                for (int vnum = 0; views != null && vnum < views.length; vnum++)
                 {
                   if (views[vnum] != command.al)
                   {
@@ -1461,6 +1459,10 @@ public class EditCommand implements CommandI
   protected static void cutFeatures(Edit command, SequenceI seq,
           int fromPosition, int toPosition, boolean cutIsInternal)
   {
+    if (!cutIsInternal)
+    {
+      return;
+    }
     List<SequenceFeature> added = new ArrayList<>();
     List<SequenceFeature> removed = new ArrayList<>();