JAL-1503 update version in GPL header

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

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index a8aa886..ba66e82 100644 (file)
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -1,19 +1,20 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * 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.
- * 
+ *  
  * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.commands;
 
@@ -54,8 +55,8 @@ public class EditCommand implements CommandI
   public static final int PASTE = 3;
 
   public static final int REPLACE = 4;
-  
-  public static final int INSERT_NUC=5;
+
+  public static final int INSERT_NUC = 5;
 
   Edit[] edits;
 
@@ -96,11 +97,13 @@ public class EditCommand implements CommandI
     performEdit(0, null);
   }
 
+  @Override
   final public String getDescription()
   {
     return description;
   }
 
+  @Override
   public int getSize()
   {
     return edits == null ? 0 : edits.length;
@@ -194,19 +197,21 @@ public class EditCommand implements CommandI
       case REPLACE:
         replace(edits[e]);
         break;
-        //TODO:add deleteNuc for UNDO
-//      case INSERT_NUC:
-//     insertNuc(edits[e]);
-//     break;
+      // TODO:add deleteNuc for UNDO
+      // case INSERT_NUC:
+      // insertNuc(edits[e]);
+      // break;
       }
     }
   }
 
+  @Override
   final public void doCommand(AlignmentI[] views)
   {
     performEdit(0, views);
   }
 
+  @Override
   final public void undoCommand(AlignmentI[] views)
   {
     int e = 0, eSize = edits.length;
@@ -229,7 +234,7 @@ public class EditCommand implements CommandI
       case REPLACE:
         replace(edits[e]);
         break;
-       }
+      }
     }
   }
 
@@ -240,23 +245,24 @@ public class EditCommand implements CommandI
     {
       command.seqs[s].insertCharAt(command.position, command.number,
               command.gapChar);
-//      System.out.println("pos: "+command.position+" number: "+command.number);
+      // System.out.println("pos: "+command.position+" number: "+command.number);
     }
 
     adjustAnnotations(command, true, false, null);
   }
-//  
-//  final void insertNuc(Edit command)
-//  {
-//
-//    for (int s = 0; s < command.seqs.length; s++)
-//    {
-//        System.out.println("pos: "+command.position+" number: "+command.number);
-//     command.seqs[s].insertCharAt(command.position, command.number,'A');
-//    }
-//
-//    adjustAnnotations(command, true, false, null);
-//  }
+
+  //
+  // final void insertNuc(Edit command)
+  // {
+  //
+  // for (int s = 0; s < command.seqs.length; s++)
+  // {
+  // System.out.println("pos: "+command.position+" number: "+command.number);
+  // command.seqs[s].insertCharAt(command.position, command.number,'A');
+  // }
+  //
+  // adjustAnnotations(command, true, false, null);
+  // }
 
   final void deleteGap(Edit command)
   {
@@ -345,7 +351,8 @@ public class EditCommand implements CommandI
         if (command.alIndex[i] < command.al.getHeight())
         {
           List<SequenceI> sequences;
-          synchronized (sequences=command.al.getSequences()) {
+          synchronized (sequences = command.al.getSequences())
+          {
             sequences.add(command.alIndex[i], command.seqs[i]);
           }
         }
@@ -448,6 +455,9 @@ public class EditCommand implements CommandI
     command.number = start + command.string[0].length;
     for (int i = 0; i < command.seqs.length; i++)
     {
+      boolean newDSWasNeeded = command.oldds != null
+              && command.oldds[i] != null;
+
       /**
        * cut addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT,
        * cut, sg.getStartRes(), sg.getEndRes()-sg.getStartRes()+1,
@@ -462,9 +472,48 @@ public class EditCommand implements CommandI
       oldstring = command.seqs[i].getSequenceAsString();
       tmp = new StringBuffer(oldstring.substring(0, start));
       tmp.append(command.string[i]);
+      String nogaprep = jalview.analysis.AlignSeq.extractGaps(
+              jalview.util.Comparison.GapChars, new String(
+                      command.string[i]));
+      int ipos = command.seqs[i].findPosition(start)
+              - command.seqs[i].getStart();
       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, new String(
+                      command.string[i]));
+      if (!nogaprep.toLowerCase().equals(nogapold.toLowerCase()))
+      {
+        if (newDSWasNeeded)
+        {
+          SequenceI oldds = command.seqs[i].getDatasetSequence();
+          command.seqs[i].setDatasetSequence(command.oldds[i]);
+          command.oldds[i] = oldds;
+        }
+        else
+        {
+          if (command.oldds == null)
+          {
+            command.oldds = new SequenceI[command.seqs.length];
+          }
+          command.oldds[i] = command.seqs[i].getDatasetSequence();
+          SequenceI newds = new Sequence(
+                  command.seqs[i].getDatasetSequence());
+          String fullseq, osp = newds.getSequenceAsString();
+          fullseq = osp.substring(0, ipos) + nogaprep
+                  + osp.substring(ipos + nogaprep.length());
+          newds.setSequence(fullseq.toUpperCase());
+          // TODO: JAL-1131 ensure newly created dataset sequence is added to
+          // the set of
+          // dataset sequences associated with the alignment.
+          // TODO: JAL-1131 fix up any annotation associated with new dataset
+          // sequence to ensure that original sequence/annotation relationships
+          // are preserved.
+          command.seqs[i].setDatasetSequence(newds);
+
+        }
+      }
       tmp = null;
       oldstring = null;
     }