JAL-353 updated patch for undo successive remove redundant sequences

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

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index ed9e551..b39d1dd 100644 (file)
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -1,26 +1,34 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 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;
 
 /**
  * 
@@ -213,28 +221,26 @@ public class EditCommand implements CommandI
 
   @Override
   final public void undoCommand(AlignmentI[] views)
-  {
-    int e = 0, eSize = edits.length;
-    for (e = eSize - 1; e > -1; e--)
-    {
-      switch (edits[e].command)
-      {
-      case INSERT_GAP:
-        deleteGap(edits[e]);
-        break;
-      case DELETE_GAP:
-        insertGap(edits[e]);
-        break;
-      case CUT:
-        paste(edits[e], views);
-        break;
-      case PASTE:
-        cut(edits[e], views);
-        break;
-      case REPLACE:
-        replace(edits[e]);
-        break;
-      }
+  { 
+    for(Edit e : edits){
+       switch (e.command)
+        {
+        case INSERT_GAP:
+          deleteGap(e);
+          break;
+        case DELETE_GAP:
+          insertGap(e);
+          break;
+        case CUT:
+          paste(e, views);
+          break;
+        case PASTE:
+          cut(e, views);
+          break;
+        case REPLACE:
+          replace(e);
+          break;
+        }
     }
   }
 
@@ -353,7 +359,9 @@ public class EditCommand implements CommandI
           List<SequenceI> sequences;
           synchronized (sequences = command.al.getSequences())
           {
-            sequences.add(command.alIndex[i], command.seqs[i]);
+            // 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]);
           }
         }
         else
@@ -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)