X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FEditCommand.java;h=61e2595a4c0e340aae6e02e4c80bfae8ba028954;hb=6de402db90987d3645f3429d9073c13678d8e980;hp=0c833d0bca6427ed4d998b6dca8c48479ceee658;hpb=e88632fe0e6a74b1a9519cf9e58e769ad406e066;p=jalview.git

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index 0c833d0..61e2595 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -1,432 +1,865 @@
-/*
- * 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);
-    }
-
-    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);
-    }
-
-    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]);
-      }
-    }
-
-    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());
-    }
-
-
-    adjustAnnotations(command, true);
-
-    command.string = null;
-  }
-
-
-  void adjustAnnotations(Edit command, boolean insert)
-  {
-
-    AlignmentAnnotation [] annotations = null;
-
-    if (command.fullAlignmentHeight)
-    {
-      annotations = command.al.getAlignmentAnnotation();
-    }
-    else
-    {
-      int aSize = 0;
-      AlignmentAnnotation [] tmp;
-      for(int s=0; s<command.seqs.length; s++)
-      {
-        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, 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)
-        {
-          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
-            temp = annotations[a].annotations;
-        }
-        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
+ * Copyright (C) 2007 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 java.util.*;
+
+import jalview.datamodel.*;
+
+/**
+ *
+ * <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;
+
+  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);
+  }
+
+  final public String getDescription()
+  {
+    return description;
+  }
+
+  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;
+      }
+    }
+  }
+
+  final public void doCommand(AlignmentI[] views)
+  {
+    performEdit(0,views);
+  }
+
+  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;
+      }
+    }
+  }
+
+  final void insertGap(Edit command)
+  {
+
+    for (int s = 0; s < command.seqs.length; s++)
+    {
+      command.seqs[s].insertCharAt(command.position,
+                                   command.number,
+                                   command.gapChar);
+    }
+
+    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);
+
+        if (command.seqs[i].getDatasetSequence() != null
+            || command.seqs[i].getSequenceFeatures() != null)
+        {
+          for (int s = command.position; s < command.position + command.number;
+               s++)
+          {
+            if (jalview.schemes.ResidueProperties
+                .aaIndex[command.seqs[i].getCharAt(s)] != 23)
+            {
+              adjustFeatures(command, i,
+                             command.seqs[i].findPosition(command.position),
+                             command.seqs[i].findPosition(command.position +
+                  command.number),
+                             false);
+              break;
+            }
+          }
+        }
+        command.seqs[i].deleteChars(command.position,
+                                    command.position + command.number);
+      }
+
+      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 seqWasDeleted=false;
+    int start = 0, end = 0;
+
+    for (int i = 0; i < command.seqs.length; i++)
+    {
+      newDSNeeded = false;
+      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]);
+        }
+        seqWasDeleted=true;
+      }
+      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]);
+
+        for (int s = 0; s < command.string[i].length; s++)
+        {
+          if (jalview.schemes.ResidueProperties.aaIndex[command.string[i][s]] !=
+              23)
+          {
+            newDSNeeded = true;
+            start = command.seqs[i].findPosition(command.position);
+            end = command.seqs[i].findPosition(command.position +
+                                               command.number);
+            break;
+          }
+        }
+        command.string[i] = null;
+      }
+
+      command.seqs[i].setSequence(tmp.toString());
+
+      if (newDSNeeded)
+      {
+        if (command.seqs[i].getDatasetSequence() != null)
+        { // use new ds mechanism here
+          Sequence 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());
+          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;
+
+    command.number = start + command.string[0].length;
+    for (int i = 0; i < command.seqs.length; i++)
+    {
+      oldstring = command.seqs[i].getSequenceAsString();
+      tmp = new StringBuffer(oldstring.substring(0, start));
+      tmp.append(command.string[i]);
+      tmp.append(oldstring.substring(end));
+      command.seqs[i].setSequence(tmp.toString());
+      command.string[i] = oldstring.substring(start, end).toCharArray();
+      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
+  {
+    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);
+    }
+  }
+}