X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FEditCommand.java;h=b39d1ddb69302035d183b18778a8c6939ee39b46;hb=9157d82cb9213d9071c15203dddf96ae9081dfbe;hp=ed356dcd33779b51ffb13268276cd37f6ac267d6;hpb=714af52b3db1dfa2420b0782ef64248b7404adf9;p=jalview.git

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index ed356dc..b39d1dd 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -1,402 +1,1009 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.commands;
-
-import jalview.datamodel.*;
-
-import java.util.Hashtable;
-
-/**
- *
- * <p>Title: EditCommmand</p>
- *
- * <p>Description: Essential information for performing
- * undo and redo for cut/paste insert/delete gap
- * which can be stored in the HistoryList </p>
- *
- * <p>Copyright: Copyright (c) 2006</p>
- *
- * <p>Company: Dundee University</p>
- *
- * @author not attributable
- * @version 1.0
- */
-public class EditCommand implements CommandI
-{
-  public static final int INSERT_GAP = 0;
-  public static final int DELETE_GAP = 1;
-  public static final int CUT = 2;
-  public static final int PASTE = 3;
-
-  Edit[] edits;
-
-  String description;
-
-  public EditCommand()
-  {}
-
-  public EditCommand(String description)
-  {
-    this.description = description;
-  }
-
-  public EditCommand( String description,
-                      int command,
-                      SequenceI[] seqs,
-                      int position,
-                      int number,
-                      AlignmentI al)
-   {
-     this.description = description;
-     if ( command==CUT || command==PASTE)
-     {
-       edits = new Edit[]{new Edit(command, seqs, position, number, al)};
-     }
-
-     performEdit(0);
-  }
-
-
-  public String getDescription()
-  {
-    return description;
-  }
-
-  public int getSize()
-  {
-    return edits==null?0:edits.length;
-  }
-
-  public AlignmentI getAlignment()
-  {
-    return edits[0].al;
-  }
-
-
-  public void appendEdit(int command,
-                         SequenceI[] seqs,
-                         int position,
-                         int number,
-                         AlignmentI al,
-                         boolean performEdit)
-  {
-    Edit edit = new Edit(command, seqs, position, number, al.getGapCharacter());
-    if(al.getHeight()==seqs.length)
-    {
-      edit.al = al;
-      edit.fullAlignmentHeight = true;
-    }
-
-    if (edits != null)
-    {
-      Edit[] temp = new Edit[edits.length + 1];
-      System.arraycopy(edits, 0, temp, 0, edits.length);
-      edits = temp;
-      edits[edits.length - 1] = edit;
-    }
-    else
-      edits = new Edit[] {  edit  };
-
-    if (performEdit)
-      performEdit(edits.length - 1);
-  }
-
-  void performEdit(int commandIndex)
-  {
-    int eSize = edits.length;
-    for (int e = commandIndex; e < eSize; e++)
-    {
-      if (edits[e].command==INSERT_GAP)
-      {
-        insertGap(edits[e]);
-      }
-      else if (edits[e].command==DELETE_GAP)
-      {
-        deleteGap(edits[e]);
-      }
-      else if(edits[e].command==CUT)
-      {
-        cut(edits[e]);
-      }
-      else if(edits[e].command==PASTE)
-      {
-        paste(edits[e]);
-      }
-    }
-  }
-
-  public void doCommand()
-  {
-    performEdit(0);
-  }
-
-  public void undoCommand()
-  {
-    int e = 0, eSize = edits.length;
-    for (e = eSize-1; e > -1; e--)
-    {
-      if (edits[e].command==INSERT_GAP)
-      {
-        deleteGap(edits[e]);
-      }
-      else if (edits[e].command==DELETE_GAP)
-      {
-        insertGap(edits[e]);
-      }
-      else if (edits[e].command==CUT)
-      {
-        paste(edits[e]);
-      }
-      else if (edits[e].command==PASTE)
-      {
-        cut(edits[e]);
-      }
-    }
-  }
-
-  void insertGap(Edit command)
-  {
-    for(int s=0; s<command.seqs.length; s++)
-    {
-        command.seqs[s].insertCharAt(command.position,
-                                     command.number,
-                                     command.gapChar);
-    }
-
-    if (command.fullAlignmentHeight)
-    {
-      adjustAnnotations(command, true);
-    }
-  }
-
-  void deleteGap(Edit command)
-  {
-    for (int s = 0; s < command.seqs.length; s++)
-    {
-      command.seqs[s].deleteChars(command.position, command.position+command.number);
-    }
-
-    if (command.fullAlignmentHeight)
-    {
-      adjustAnnotations(command, false);
-    }
-  }
-
-  void cut(Edit command)
-  {
-    command.string = new char [command.seqs.length][];
-
-    for(int i=0; i<command.seqs.length; i++)
-    {
-      if(command.seqs[i].getLength()>command.position)
-      {
-        command.string[i] = command.seqs[i].getSequence(command.position,
-            command.position + command.number);
-
-        command.seqs[i].deleteChars(command.position,
-                                    command.position + command.number);
-      }
-
-      if(command.seqs[i].getLength()<1)
-      {
-        command.al.deleteSequence(command.seqs[i]);
-      }
-    }
-
-    if (command.fullAlignmentHeight)
-    {
-      adjustAnnotations(command, false);
-    }
-
-  }
-
-  void paste(Edit command)
-  {
-    StringBuffer tmp;
-    for(int i=0; i<command.seqs.length; i++)
-    {
-      if(command.seqs[i].getLength()<1)
-      {
-        // ie this sequence was deleted, we need to
-        // read it to the alignment
-        if (command.alIndex[i] < command.al.getHeight())
-          command.al.getSequences().insertElementAt(command.seqs[i],
-              command.alIndex[i]);
-        else
-          command.al.addSequence(command.seqs[i]);
-      }
-      tmp = new StringBuffer();
-      tmp.append(command.seqs[i].getSequence());
-
-      if(command.string!=null && command.string[i]!=null)
-      {
-        if(command.position>=tmp.length())
-        {
-          //This occurs if padding is on, and residues
-          //are removed from end of alignment
-          int length = command.position-tmp.length();
-          while (length > 0)
-          {
-            tmp.append(command.gapChar);
-            length--;
-          }
-        }
-        tmp.insert(command.position, command.string[i]);
-        command.string[i] = null;
-      }
-      command.seqs[i].setSequence(tmp.toString());
-    }
-
-    if (command.fullAlignmentHeight)
-    {
-      adjustAnnotations(command, true);
-    }
-
-    command.string = null;
-  }
-
-
-  void adjustAnnotations(Edit command, boolean insert)
-  {
-    AlignmentAnnotation [] annotations = command.al.getAlignmentAnnotation();
-    if(annotations!=null)
-    {
-      if(!insert)
-        command.deletedAnnotations = new Hashtable();
-
-      int aSize, tSize;
-      Annotation [] temp;
-      for (int a = 0; a < annotations.length; a++)
-      {
-        if(annotations[a].autoCalculated)
-        {
-          continue;
-        }
-
-        aSize = annotations[a].annotations.length;
-        if(insert)
-          tSize = aSize + command.number;
-        else
-          tSize = aSize - command.number;
-
-        temp = new Annotation[tSize];
-
-        if(insert)
-        {
-          System.arraycopy(annotations[a].annotations,
-              0, temp, 0, command.position);
-
-          if(command.deletedAnnotations!=null
-             && command.deletedAnnotations.containsKey(annotations[a].annotationId))
-          {
-            Annotation [] restore = (Annotation [])
-                command.deletedAnnotations.get(annotations[a].annotationId);
-
-            System.arraycopy(restore,
-                             0,
-                             temp,
-                             command.position,
-                             command.number);
-
-          }
-
-          System.arraycopy(annotations[a].annotations,
-              command.position, temp,
-              command.position+command.number,
-              aSize - command.position);
-        }
-        else
-        {
-          if(command.position < annotations[a].annotations.length)
-          {
-            System.arraycopy(annotations[a].annotations,
-                             0, temp, 0, command.position);
-
-            Annotation[] deleted = new Annotation[command.number];
-            System.arraycopy(annotations[a].annotations,
-                             command.position, deleted, 0, command.number);
-
-            command.deletedAnnotations.put(annotations[a].annotationId,
-                                           deleted);
-
-            System.arraycopy(annotations[a].annotations,
-                             command.position + command.number,
-                             temp, command.position,
-                             aSize - command.position - command.number);
-          }
-          else
-            temp = annotations[a].annotations;
-        }
-
-        annotations[a].annotations = temp;
-     }
-    }
-  }
-
-
-  class Edit
-  {
-    boolean fullAlignmentHeight = false;
-    Hashtable deletedAnnotations;
-    AlignmentI al;
-    int command;
-    char [][] string;
-    SequenceI[] seqs;
-    int [] alIndex;
-    int position, number;
-    char gapChar;
-
-    Edit(int command,
-         SequenceI[] seqs,
-         int position,
-         int number,
-         char gapChar)
-    {
-      this.command = command;
-      this.seqs = seqs;
-      this.position = position;
-      this.number = number;
-      this.gapChar = gapChar;
-    }
-
-
-    Edit(int command,
-         SequenceI[] seqs,
-         int position,
-         int number,
-         AlignmentI al)
-    {
-      this.gapChar = al.getGapCharacter();
-      this.command = command;
-      this.seqs = seqs;
-      this.position = position;
-      this.number = number;
-      this.al = al;
-
-      alIndex = new int[seqs.length];
-      for(int i=0; i<seqs.length; i++)
-        alIndex[i] = al.findIndex(seqs[i]);
-
-      fullAlignmentHeight = (al.getHeight()==seqs.length);
-
-    }
-
-  }
-
-}
+/*
+ * 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;
+
+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 java.util.Hashtable;
+import java.util.List;
+
+/**
+ * 
+ * <p>
+ * Title: EditCommmand
+ * </p>
+ * 
+ * <p>
+ * Description: Essential information for performing undo and redo for cut/paste
+ * insert/delete gap which can be stored in the HistoryList
+ * </p>
+ * 
+ * <p>
+ * Copyright: Copyright (c) 2006
+ * </p>
+ * 
+ * <p>
+ * Company: Dundee University
+ * </p>
+ * 
+ * @author not attributable
+ * @version 1.0
+ */
+public class EditCommand implements CommandI
+{
+  public static final int INSERT_GAP = 0;
+
+  public static final int DELETE_GAP = 1;
+
+  public static final int CUT = 2;
+
+  public static final int PASTE = 3;
+
+  public static final int REPLACE = 4;
+
+  public static final int INSERT_NUC = 5;
+
+  Edit[] edits;
+
+  String description;
+
+  public EditCommand()
+  {
+  }
+
+  public EditCommand(String description)
+  {
+    this.description = description;
+  }
+
+  public EditCommand(String description, int command, SequenceI[] seqs,
+          int position, int number, AlignmentI al)
+  {
+    this.description = description;
+    if (command == CUT || command == PASTE)
+    {
+      edits = new Edit[]
+      { new Edit(command, seqs, position, number, al) };
+    }
+
+    performEdit(0, null);
+  }
+
+  public EditCommand(String description, int command, String replace,
+          SequenceI[] seqs, int position, int number, AlignmentI al)
+  {
+    this.description = description;
+    if (command == REPLACE)
+    {
+      edits = new Edit[]
+      { new Edit(command, seqs, position, number, al, replace) };
+    }
+
+    performEdit(0, null);
+  }
+
+  @Override
+  final public String getDescription()
+  {
+    return description;
+  }
+
+  @Override
+  public int getSize()
+  {
+    return edits == null ? 0 : edits.length;
+  }
+
+  final public AlignmentI getAlignment()
+  {
+    return edits[0].al;
+  }
+
+  /**
+   * append a new editCommand Note. this shouldn't be called if the edit is an
+   * operation affects more alignment objects than the one referenced in al (for
+   * example, cut or pasting whole sequences). Use the form with an additional
+   * AlignmentI[] views parameter.
+   * 
+   * @param command
+   * @param seqs
+   * @param position
+   * @param number
+   * @param al
+   * @param performEdit
+   */
+  final public void appendEdit(int command, SequenceI[] seqs, int position,
+          int number, AlignmentI al, boolean performEdit)
+  {
+    appendEdit(command, seqs, position, number, al, performEdit, null);
+  }
+
+  /**
+   * append a new edit command with a set of alignment views that may be
+   * operated on
+   * 
+   * @param command
+   * @param seqs
+   * @param position
+   * @param number
+   * @param al
+   * @param performEdit
+   * @param views
+   */
+  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());
+    if (al.getHeight() == seqs.length)
+    {
+      edit.al = al;
+      edit.fullAlignmentHeight = true;
+    }
+
+    if (edits != null)
+    {
+      Edit[] temp = new Edit[edits.length + 1];
+      System.arraycopy(edits, 0, temp, 0, edits.length);
+      edits = temp;
+      edits[edits.length - 1] = edit;
+    }
+    else
+    {
+      edits = new Edit[]
+      { edit };
+    }
+
+    if (performEdit)
+    {
+      performEdit(edits.length - 1, views);
+    }
+  }
+
+  final void performEdit(int commandIndex, AlignmentI[] views)
+  {
+    int eSize = edits.length;
+    for (int e = commandIndex; e < eSize; e++)
+    {
+      switch (edits[e].command)
+      {
+      case INSERT_GAP:
+        insertGap(edits[e]);
+        break;
+      case DELETE_GAP:
+        deleteGap(edits[e]);
+        break;
+      case CUT:
+        cut(edits[e], views);
+        break;
+      case PASTE:
+        paste(edits[e], views);
+        break;
+      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)
+  { 
+    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;
+        }
+    }
+  }
+
+  final void insertGap(Edit command)
+  {
+
+    for (int s = 0; s < command.seqs.length; s++)
+    {
+      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++)
+    {
+      command.seqs[s].deleteChars(command.position, command.position
+              + command.number);
+    }
+
+    adjustAnnotations(command, false, false, null);
+  }
+
+  void cut(Edit command, AlignmentI[] views)
+  {
+    boolean seqDeleted = false;
+    command.string = new char[command.seqs.length][];
+
+    for (int i = 0; i < command.seqs.length; i++)
+    {
+      if (command.seqs[i].getLength() > command.position)
+      {
+        command.string[i] = command.seqs[i].getSequence(command.position,
+                command.position + command.number);
+        SequenceI oldds = command.seqs[i].getDatasetSequence();
+        if (command.oldds != null && command.oldds[i] != null)
+        {
+          // we are redoing an undone cut.
+          command.seqs[i].setDatasetSequence(null);
+        }
+        command.seqs[i].deleteChars(command.position, command.position
+                + command.number);
+        if (command.oldds != null && command.oldds[i] != null)
+        {
+          // oldds entry contains the cut dataset sequence.
+          command.seqs[i].setDatasetSequence(command.oldds[i]);
+          command.oldds[i] = oldds;
+        }
+        else
+        {
+          // modify the oldds if necessary
+          if (oldds != command.seqs[i].getDatasetSequence()
+                  || command.seqs[i].getSequenceFeatures() != null)
+          {
+            if (command.oldds == null)
+            {
+              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);
+          }
+        }
+      }
+
+      if (command.seqs[i].getLength() < 1)
+      {
+        command.al.deleteSequence(command.seqs[i]);
+        seqDeleted = true;
+      }
+    }
+
+    adjustAnnotations(command, false, seqDeleted, views);
+  }
+
+  void paste(Edit command, AlignmentI[] views)
+  {
+    StringBuffer tmp;
+    boolean newDSNeeded;
+    boolean newDSWasNeeded;
+    int newstart, newend;
+    boolean seqWasDeleted = false;
+    int start = 0, end = 0;
+
+    for (int i = 0; i < command.seqs.length; i++)
+    {
+      newDSNeeded = false;
+      newDSWasNeeded = command.oldds != null && command.oldds[i] != null;
+      if (command.seqs[i].getLength() < 1)
+      {
+        // ie this sequence was deleted, we need to
+        // read it to the alignment
+        if (command.alIndex[i] < command.al.getHeight())
+        {
+          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]);
+          }
+        }
+        else
+        {
+          command.al.addSequence(command.seqs[i]);
+        }
+        seqWasDeleted = true;
+      }
+      newstart = command.seqs[i].getStart();
+      newend = command.seqs[i].getEnd();
+
+      tmp = new StringBuffer();
+      tmp.append(command.seqs[i].getSequence());
+      // Undo of a delete does not replace original dataset sequence on to
+      // alignment sequence.
+
+      if (command.string != null && command.string[i] != null)
+      {
+        if (command.position >= tmp.length())
+        {
+          // This occurs if padding is on, and residues
+          // are removed from end of alignment
+          int length = command.position - tmp.length();
+          while (length > 0)
+          {
+            tmp.append(command.gapChar);
+            length--;
+          }
+        }
+        tmp.insert(command.position, command.string[i]);
+        for (int s = 0; s < command.string[i].length; s++)
+        {
+          if (jalview.schemes.ResidueProperties.aaIndex[command.string[i][s]] != 23)
+          {
+            if (!newDSNeeded)
+            {
+              newDSNeeded = true;
+              start = command.seqs[i].findPosition(command.position);
+              end = command.seqs[i].findPosition(command.position
+                      + command.number);
+            }
+            if (command.seqs[i].getStart() == start)
+            {
+              newstart--;
+            }
+            else
+            {
+              newend++;
+            }
+          }
+        }
+        command.string[i] = null;
+      }
+
+      command.seqs[i].setSequence(tmp.toString());
+      command.seqs[i].setStart(newstart);
+      command.seqs[i].setEnd(newend);
+      if (newDSNeeded)
+      {
+        if (command.seqs[i].getDatasetSequence() != null)
+        {
+          SequenceI ds;
+          if (newDSWasNeeded)
+          {
+            ds = command.oldds[i];
+          }
+          else
+          {
+            // make a new DS sequence
+            // use new ds mechanism here
+            ds = new Sequence(command.seqs[i].getName(),
+                    jalview.analysis.AlignSeq.extractGaps(
+                            jalview.util.Comparison.GapChars,
+                            command.seqs[i].getSequenceAsString()),
+                    command.seqs[i].getStart(), command.seqs[i].getEnd());
+            ds.setDescription(command.seqs[i].getDescription());
+          }
+          if (command.oldds == null)
+          {
+            command.oldds = new SequenceI[command.seqs.length];
+          }
+          command.oldds[i] = command.seqs[i].getDatasetSequence();
+          command.seqs[i].setDatasetSequence(ds);
+        }
+        adjustFeatures(command, i, start, end, true);
+      }
+    }
+    adjustAnnotations(command, true, seqWasDeleted, views);
+
+    command.string = null;
+  }
+
+  void replace(Edit command)
+  {
+    StringBuffer tmp;
+    String oldstring;
+    int start = command.position;
+    int end = command.number;
+    // TODO TUTORIAL - Fix for replacement with different length of sequence (or
+    // whole sequence)
+    // TODO Jalview 2.4 bugfix change to an aggregate command - original
+    // sequence string is cut, new string is pasted in.
+    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,
+       * viewport.alignment));
+       * 
+       */
+      /**
+       * then addHistoryItem(new EditCommand( "Add sequences",
+       * EditCommand.PASTE, sequences, 0, alignment.getWidth(), alignment) );
+       * 
+       */
+      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;
+    }
+  }
+
+  final void adjustAnnotations(Edit command, boolean insert,
+          boolean modifyVisibility, AlignmentI[] views)
+  {
+    AlignmentAnnotation[] annotations = null;
+
+    if (modifyVisibility && !insert)
+    {
+      // only occurs if a sequence was added or deleted.
+      command.deletedAnnotationRows = new Hashtable();
+    }
+    if (command.fullAlignmentHeight)
+    {
+      annotations = command.al.getAlignmentAnnotation();
+    }
+    else
+    {
+      int aSize = 0;
+      AlignmentAnnotation[] tmp;
+      for (int s = 0; s < command.seqs.length; s++)
+      {
+        if (modifyVisibility)
+        {
+          // Rows are only removed or added to sequence object.
+          if (!insert)
+          {
+            // remove rows
+            tmp = command.seqs[s].getAnnotation();
+            if (tmp != null)
+            {
+              int alen = tmp.length;
+              for (int aa = 0; aa < tmp.length; aa++)
+              {
+                if (!command.al.deleteAnnotation(tmp[aa]))
+                {
+                  // strip out annotation not in the current al (will be put
+                  // back on insert in all views)
+                  tmp[aa] = null;
+                  alen--;
+                }
+              }
+              command.seqs[s].setAlignmentAnnotation(null);
+              if (alen != tmp.length)
+              {
+                // save the non-null annotation references only
+                AlignmentAnnotation[] saved = new AlignmentAnnotation[alen];
+                for (int aa = 0, aapos = 0; aa < tmp.length; aa++)
+                {
+                  if (tmp[aa] != null)
+                  {
+                    saved[aapos++] = tmp[aa];
+                    tmp[aa] = null;
+                  }
+                }
+                tmp = saved;
+                command.deletedAnnotationRows.put(command.seqs[s], saved);
+                // and then remove any annotation in the other views
+                for (int alview = 0; views != null && alview < views.length; alview++)
+                {
+                  if (views[alview] != command.al)
+                  {
+                    AlignmentAnnotation[] toremove = views[alview]
+                            .getAlignmentAnnotation();
+                    if (toremove == null || toremove.length == 0)
+                    {
+                      continue;
+                    }
+                    // remove any alignment annotation on this sequence that's
+                    // on that alignment view.
+                    for (int aa = 0; aa < toremove.length; aa++)
+                    {
+                      if (toremove[aa].sequenceRef == command.seqs[s])
+                      {
+                        views[alview].deleteAnnotation(toremove[aa]);
+                      }
+                    }
+                  }
+                }
+              }
+              else
+              {
+                // save all the annotation
+                command.deletedAnnotationRows.put(command.seqs[s], tmp);
+              }
+            }
+          }
+          else
+          {
+            // recover rows
+            if (command.deletedAnnotationRows != null
+                    && command.deletedAnnotationRows
+                            .containsKey(command.seqs[s]))
+            {
+              AlignmentAnnotation[] revealed = (AlignmentAnnotation[]) command.deletedAnnotationRows
+                      .get(command.seqs[s]);
+              command.seqs[s].setAlignmentAnnotation(revealed);
+              if (revealed != null)
+              {
+                for (int aa = 0; aa < revealed.length; aa++)
+                {
+                  // iterate through al adding original annotation
+                  command.al.addAnnotation(revealed[aa]);
+                }
+                for (int aa = 0; aa < revealed.length; aa++)
+                {
+                  command.al.setAnnotationIndex(revealed[aa], aa);
+                }
+                // and then duplicate added annotation on every other alignment
+                // view
+                for (int vnum = 0; views != null && vnum < views.length; vnum++)
+                {
+                  if (views[vnum] != command.al)
+                  {
+                    int avwidth = views[vnum].getWidth() + 1;
+                    // duplicate in this view
+                    for (int a = 0; a < revealed.length; a++)
+                    {
+                      AlignmentAnnotation newann = new AlignmentAnnotation(
+                              revealed[a]);
+                      command.seqs[s].addAlignmentAnnotation(newann);
+                      newann.padAnnotation(avwidth);
+                      views[vnum].addAnnotation(newann);
+                      views[vnum].setAnnotationIndex(newann, a);
+                    }
+                  }
+                }
+              }
+            }
+          }
+          continue;
+        }
+
+        if (command.seqs[s].getAnnotation() == null)
+        {
+          continue;
+        }
+
+        if (aSize == 0)
+        {
+          annotations = command.seqs[s].getAnnotation();
+        }
+        else
+        {
+          tmp = new AlignmentAnnotation[aSize
+                  + command.seqs[s].getAnnotation().length];
+
+          System.arraycopy(annotations, 0, tmp, 0, aSize);
+
+          System.arraycopy(command.seqs[s].getAnnotation(), 0, tmp, aSize,
+                  command.seqs[s].getAnnotation().length);
+
+          annotations = tmp;
+        }
+        aSize = annotations.length;
+      }
+    }
+
+    if (annotations == null)
+    {
+      return;
+    }
+
+    if (!insert)
+    {
+      command.deletedAnnotations = new Hashtable();
+    }
+
+    int aSize;
+    Annotation[] temp;
+    for (int a = 0; a < annotations.length; a++)
+    {
+      if (annotations[a].autoCalculated
+              || annotations[a].annotations == null)
+      {
+        continue;
+      }
+
+      int tSize = 0;
+
+      aSize = annotations[a].annotations.length;
+      if (insert)
+      {
+        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
+      {
+        if (command.position < aSize)
+        {
+          if (command.position + command.number >= aSize)
+          {
+            tSize = aSize;
+          }
+          else
+          {
+            tSize = aSize - command.number;
+          }
+        }
+        else
+        {
+          tSize = aSize;
+        }
+
+        if (tSize < 0)
+        {
+          tSize = aSize;
+        }
+        temp = new Annotation[tSize];
+      }
+
+      if (insert)
+      {
+        if (command.position < annotations[a].annotations.length)
+        {
+          System.arraycopy(annotations[a].annotations, 0, temp, 0,
+                  command.position);
+
+          if (command.deletedAnnotations != null
+                  && command.deletedAnnotations
+                          .containsKey(annotations[a].annotationId))
+          {
+            Annotation[] restore = (Annotation[]) command.deletedAnnotations
+                    .get(annotations[a].annotationId);
+
+            System.arraycopy(restore, 0, temp, command.position,
+                    command.number);
+
+          }
+
+          System.arraycopy(annotations[a].annotations, command.position,
+                  temp, command.position + command.number, aSize
+                          - command.position);
+        }
+        else
+        {
+          if (command.deletedAnnotations != null
+                  && command.deletedAnnotations
+                          .containsKey(annotations[a].annotationId))
+          {
+            Annotation[] restore = (Annotation[]) command.deletedAnnotations
+                    .get(annotations[a].annotationId);
+
+            temp = new Annotation[annotations[a].annotations.length
+                    + restore.length];
+            System.arraycopy(annotations[a].annotations, 0, temp, 0,
+                    annotations[a].annotations.length);
+            System.arraycopy(restore, 0, temp,
+                    annotations[a].annotations.length, restore.length);
+          }
+          else
+          {
+            temp = annotations[a].annotations;
+          }
+        }
+      }
+      else
+      {
+        if (tSize != aSize || command.position < 2)
+        {
+          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)
+          {
+            copylen = Math.min(command.number,
+                    annotations[a].annotations.length - command.position);
+            if (copylen > 0)
+            {
+              System.arraycopy(annotations[a].annotations,
+                      command.position, deleted, 0, copylen); // command.number);
+            }
+          }
+
+          command.deletedAnnotations.put(annotations[a].annotationId,
+                  deleted);
+          if (annotations[a].annotations.length > command.position
+                  + command.number)
+          {
+            System.arraycopy(annotations[a].annotations, command.position
+                    + command.number, temp, command.position,
+                    annotations[a].annotations.length - command.position
+                            - command.number); // aSize
+          }
+        }
+        else
+        {
+          int dSize = aSize - command.position;
+
+          if (dSize > 0)
+          {
+            Annotation[] deleted = new Annotation[command.number];
+            System.arraycopy(annotations[a].annotations, command.position,
+                    deleted, 0, dSize);
+
+            command.deletedAnnotations.put(annotations[a].annotationId,
+                    deleted);
+
+            tSize = Math.min(annotations[a].annotations.length,
+                    command.position);
+            temp = new Annotation[tSize];
+            System.arraycopy(annotations[a].annotations, 0, temp, 0, tSize);
+          }
+          else
+          {
+            temp = annotations[a].annotations;
+          }
+        }
+      }
+
+      annotations[a].annotations = temp;
+    }
+  }
+
+  final void adjustFeatures(Edit command, int index, int i, int j,
+          boolean insert)
+  {
+    SequenceI seq = command.seqs[index];
+    SequenceI sequence = seq.getDatasetSequence();
+    if (sequence == null)
+    {
+      sequence = seq;
+    }
+
+    if (insert)
+    {
+      if (command.editedFeatures != null
+              && command.editedFeatures.containsKey(seq))
+      {
+        sequence.setSequenceFeatures((SequenceFeature[]) command.editedFeatures
+                .get(seq));
+      }
+
+      return;
+    }
+
+    SequenceFeature[] sf = sequence.getSequenceFeatures();
+
+    if (sf == null)
+    {
+      return;
+    }
+
+    SequenceFeature[] oldsf = new SequenceFeature[sf.length];
+
+    int cSize = j - i;
+
+    for (int s = 0; s < sf.length; s++)
+    {
+      SequenceFeature copy = new SequenceFeature(sf[s]);
+
+      oldsf[s] = copy;
+
+      if (sf[s].getEnd() < i)
+      {
+        continue;
+      }
+
+      if (sf[s].getBegin() > j)
+      {
+        sf[s].setBegin(copy.getBegin() - cSize);
+        sf[s].setEnd(copy.getEnd() - cSize);
+        continue;
+      }
+
+      if (sf[s].getBegin() >= i)
+      {
+        sf[s].setBegin(i);
+      }
+
+      if (sf[s].getEnd() < j)
+      {
+        sf[s].setEnd(j - 1);
+      }
+
+      sf[s].setEnd(sf[s].getEnd() - (cSize));
+
+      if (sf[s].getBegin() > sf[s].getEnd())
+      {
+        sequence.deleteFeature(sf[s]);
+      }
+    }
+
+    if (command.editedFeatures == null)
+    {
+      command.editedFeatures = new Hashtable();
+    }
+
+    command.editedFeatures.put(seq, oldsf);
+
+  }
+
+  class Edit
+  {
+    public SequenceI[] oldds;
+
+    boolean fullAlignmentHeight = false;
+
+    Hashtable deletedAnnotationRows;
+
+    Hashtable deletedAnnotations;
+
+    Hashtable editedFeatures;
+
+    AlignmentI al;
+
+    int command;
+
+    char[][] string;
+
+    SequenceI[] seqs;
+
+    int[] alIndex;
+
+    int position, number;
+
+    char gapChar;
+
+    Edit(int command, SequenceI[] seqs, int position, int number,
+            char gapChar)
+    {
+      this.command = command;
+      this.seqs = seqs;
+      this.position = position;
+      this.number = number;
+      this.gapChar = gapChar;
+    }
+
+    Edit(int command, SequenceI[] seqs, int position, int number,
+            AlignmentI al)
+    {
+      this.gapChar = al.getGapCharacter();
+      this.command = command;
+      this.seqs = seqs;
+      this.position = position;
+      this.number = number;
+      this.al = al;
+
+      alIndex = new int[seqs.length];
+      for (int i = 0; i < seqs.length; i++)
+      {
+        alIndex[i] = al.findIndex(seqs[i]);
+      }
+
+      fullAlignmentHeight = (al.getHeight() == seqs.length);
+    }
+
+    Edit(int command, SequenceI[] seqs, int position, int number,
+            AlignmentI al, String replace)
+    {
+      this.command = command;
+      this.seqs = seqs;
+      this.position = position;
+      this.number = number;
+      this.al = al;
+      this.gapChar = al.getGapCharacter();
+      string = new char[seqs.length][];
+      for (int i = 0; i < seqs.length; i++)
+      {
+        string[i] = replace.toCharArray();
+      }
+
+      fullAlignmentHeight = (al.getHeight() == seqs.length);
+    }
+  }
+}