X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FEditCommand.java;h=b39d1ddb69302035d183b18778a8c6939ee39b46;hb=9157d82cb9213d9071c15203dddf96ae9081dfbe;hp=da2b552ff6c7313d834a3807caa273933f5f46d5;hpb=5ea448311ea011e104ffc4f86f48564d873ad56c;p=jalview.git

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index da2b552..b39d1dd 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -20,9 +20,15 @@
  */
 package jalview.commands;
 
-import java.util.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
 
-import jalview.datamodel.*;
+import java.util.Hashtable;
+import java.util.List;
 
 /**
  * 
@@ -353,6 +359,8 @@ public class EditCommand implements CommandI
           List<SequenceI> sequences;
           synchronized (sequences = command.al.getSequences())
           {
+            // int index = command.al.findIndex(command.seqs[i]);
+            // sequences.add(index, command.seqs[i]);
             sequences.add(command.alIndex[i] < 0 ? 0 : command.alIndex[i], command.seqs[i]);
           }
         }
@@ -396,9 +404,13 @@ public class EditCommand implements CommandI
                       + command.number);
             }
             if (command.seqs[i].getStart() == start)
+            {
               newstart--;
+            }
             else
+            {
               newend++;
+            }
           }
         }
         command.string[i] = null;
@@ -702,10 +714,12 @@ public class EditCommand implements CommandI
       {
         temp = new Annotation[aSize + command.number];
         if (annotations[a].padGaps)
+        {
           for (int aa = 0; aa < temp.length; aa++)
           {
             temp[aa] = new Annotation(command.gapChar + "", null, ' ', 0);
           }
+        }
       }
       else
       {
@@ -784,8 +798,10 @@ public class EditCommand implements CommandI
           int copylen = Math.min(command.position,
                   annotations[a].annotations.length);
           if (copylen > 0)
+           {
             System.arraycopy(annotations[a].annotations, 0, temp, 0,
                     copylen); // command.position);
+          }
 
           Annotation[] deleted = new Annotation[command.number];
           if (copylen >= command.position)