X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FEditCommand.java;h=c18b98ca6d32db4b1f0c2840aad0d29f00d52520;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=414cea71832a0d7e2d78174e6d08a51116fb62f5;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index 414cea7..c18b98c 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -1,19 +1,20 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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.
- * 
+ *  
  * 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;
 
@@ -55,6 +56,8 @@ public class EditCommand implements CommandI
 
   public static final int REPLACE = 4;
 
+  public static final int INSERT_NUC = 5;
+
   Edit[] edits;
 
   String description;
@@ -94,11 +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;
@@ -143,8 +148,8 @@ public class EditCommand implements CommandI
   final public void appendEdit(int command, SequenceI[] seqs, int position,
           int number, AlignmentI al, boolean performEdit, AlignmentI[] views)
   {
-    Edit edit = new Edit(command, seqs, position, number, al
-            .getGapCharacter());
+    Edit edit = new Edit(command, seqs, position, number,
+            al.getGapCharacter());
     if (al.getHeight() == seqs.length)
     {
       edit.al = al;
@@ -192,15 +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;
       }
     }
   }
 
+  @Override
   final public void doCommand(AlignmentI[] views)
   {
     performEdit(0, views);
   }
 
+  @Override
   final public void undoCommand(AlignmentI[] views)
   {
     int e = 0, eSize = edits.length;
@@ -234,11 +245,25 @@ public class EditCommand implements CommandI
     {
       command.seqs[s].insertCharAt(command.position, command.number,
               command.gapChar);
+      // 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 deleteGap(Edit command)
   {
     for (int s = 0; s < command.seqs.length; s++)
@@ -286,9 +311,12 @@ public class EditCommand implements CommandI
               command.oldds = new SequenceI[command.seqs.length];
             }
             command.oldds[i] = oldds;
-            adjustFeatures(command, i, command.seqs[i]
-                    .findPosition(command.position), command.seqs[i]
-                    .findPosition(command.position + command.number), false);
+            adjustFeatures(
+                    command,
+                    i,
+                    command.seqs[i].findPosition(command.position),
+                    command.seqs[i].findPosition(command.position
+                            + command.number), false);
           }
         }
       }
@@ -322,8 +350,11 @@ public class EditCommand implements CommandI
         // read it to the alignment
         if (command.alIndex[i] < command.al.getHeight())
         {
-          command.al.getSequences().insertElementAt(command.seqs[i],
-                  command.alIndex[i]);
+          List<SequenceI> sequences;
+          synchronized (sequences = command.al.getSequences())
+          {
+            sequences.add(command.alIndex[i], command.seqs[i]);
+          }
         }
         else
         {
@@ -424,6 +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,
@@ -438,9 +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;
     }
@@ -781,9 +854,8 @@ public class EditCommand implements CommandI
       if (command.editedFeatures != null
               && command.editedFeatures.containsKey(seq))
       {
-        sequence
-                .setSequenceFeatures((SequenceFeature[]) command.editedFeatures
-                        .get(seq));
+        sequence.setSequenceFeatures((SequenceFeature[]) command.editedFeatures
+                .get(seq));
       }
 
       return;