src/jalview/commands/EditCommand.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.commands;
  22
  23 import jalview.datamodel.AlignmentAnnotation;
  24 import jalview.datamodel.AlignmentI;
  25 import jalview.datamodel.Annotation;
  26 import jalview.datamodel.Sequence;
  27 import jalview.datamodel.SequenceFeature;
  28 import jalview.datamodel.SequenceI;
  29 import jalview.util.ReverseListIterator;
  30 import jalview.util.StringUtils;
  31
  32 import java.util.ArrayList;
  33 import java.util.HashMap;
  34 import java.util.Hashtable;
  35 import java.util.Iterator;
  36 import java.util.List;
  37 import java.util.ListIterator;
  38 import java.util.Map;
  39
  40 /**
  41  *
  42  * <p>
  43  * Title: EditCommmand
  44  * </p>
  45  *
  46  * <p>
  47  * Description: Essential information for performing undo and redo for cut/paste
  48  * insert/delete gap which can be stored in the HistoryList
  49  * </p>
  50  *
  51  * <p>
  52  * Copyright: Copyright (c) 2006
  53  * </p>
  54  *
  55  * <p>
  56  * Company: Dundee University
  57  * </p>
  58  *
  59  * @author not attributable
  60  * @version 1.0
  61  */
  62 public class EditCommand implements CommandI
  63 {
  64   public enum Action
  65   {
  66     INSERT_GAP
  67     {
  68       @Override
  69       public Action getUndoAction()
  70       {
  71         return DELETE_GAP;
  72       }
  73     },
  74     DELETE_GAP
  75     {
  76       @Override
  77       public Action getUndoAction()
  78       {
  79         return INSERT_GAP;
  80       }
  81     },
  82     CUT
  83     {
  84       @Override
  85       public Action getUndoAction()
  86       {
  87         return PASTE;
  88       }
  89     },
  90     PASTE
  91     {
  92       @Override
  93       public Action getUndoAction()
  94       {
  95         return CUT;
  96       }
  97     },
  98     REPLACE
  99     {
 100       @Override
 101       public Action getUndoAction()
 102       {
 103         return REPLACE;
 104       }
 105     },
 106     INSERT_NUC
 107     {
 108       @Override
 109       public Action getUndoAction()
 110       {
 111         return null;
 112       }
 113     };
 114     public abstract Action getUndoAction();
 115   };
 116
 117   private List<Edit> edits = new ArrayList<Edit>();
 118
 119   String description;
 120
 121   public EditCommand()
 122   {
 123   }
 124
 125   public EditCommand(String description)
 126   {
 127     this.description = description;
 128   }
 129
 130   public EditCommand(String description, Action command, SequenceI[] seqs,
 131           int position, int number, AlignmentI al)
 132   {
 133     this.description = description;
 134     if (command == Action.CUT || command == Action.PASTE)
 135     {
 136       setEdit(new Edit(command, seqs, position, number, al));
 137     }
 138
 139     performEdit(0, null);
 140   }
 141
 142   public EditCommand(String description, Action command, String replace,
 143           SequenceI[] seqs, int position, int number, AlignmentI al)
 144   {
 145     this.description = description;
 146     if (command == Action.REPLACE)
 147     {
 148       setEdit(new Edit(command, seqs, position, number, al, replace));
 149     }
 150
 151     performEdit(0, null);
 152   }
 153
 154   /**
 155    * Set the list of edits to the specified item (only).
 156    *
 157    * @param e
 158    */
 159   protected void setEdit(Edit e)
 160   {
 161     edits.clear();
 162     edits.add(e);
 163   }
 164
 165   /**
 166    * Add the given edit command to the stored list of commands. If simply
 167    * expanding the range of the last command added, then modify it instead of
 168    * adding a new command.
 169    *
 170    * @param e
 171    */
 172   public void addEdit(Edit e)
 173   {
 174     if (!expandEdit(edits, e))
 175     {
 176       edits.add(e);
 177     }
 178   }
 179
 180   /**
 181    * Returns true if the new edit is incorporated by updating (expanding the
 182    * range of) the last edit on the list, else false. We can 'expand' the last
 183    * edit if the new one is the same action, on the same sequences, and acts on
 184    * a contiguous range. This is the case where a mouse drag generates a series
 185    * of contiguous gap insertions or deletions.
 186    *
 187    * @param edits
 188    * @param e
 189    * @return
 190    */
 191   protected static boolean expandEdit(List<Edit> edits, Edit e)
 192   {
 193     if (edits == null || edits.isEmpty())
 194     {
 195       return false;
 196     }
 197     Edit lastEdit = edits.get(edits.size() - 1);
 198     Action action = e.command;
 199     if (lastEdit.command != action)
 200     {
 201       return false;
 202     }
 203
 204     /*
 205      * Both commands must act on the same sequences - compare the underlying
 206      * dataset sequences, rather than the aligned sequences, which change as
 207      * they are edited.
 208      */
 209     if (lastEdit.seqs.length != e.seqs.length)
 210     {
 211       return false;
 212     }
 213     for (int i = 0; i < e.seqs.length; i++)
 214     {
 215       if (lastEdit.seqs[i].getDatasetSequence() != e.seqs[i]
 216               .getDatasetSequence())
 217       {
 218         return false;
 219       }
 220     }
 221
 222     /**
 223      * Check a contiguous edit; either
 224      * <ul>
 225      * <li>a new Insert <n> positions to the right of the last <insert n>, or</li>
 226      * <li>a new Delete <n> gaps which is <n> positions to the left of the last
 227      * delete.</li>
 228      * </ul>
 229      */
 230     boolean contiguous = (action == Action.INSERT_GAP && e.position == lastEdit.position
 231             + lastEdit.number)
 232             || (action == Action.DELETE_GAP && e.position + e.number == lastEdit.position);
 233     if (contiguous)
 234     {
 235       /*
 236        * We are just expanding the range of the last edit. For delete gap, also
 237        * moving the start position left.
 238        */
 239       lastEdit.number += e.number;
 240       lastEdit.seqs = e.seqs;
 241       if (action == Action.DELETE_GAP)
 242       {
 243         lastEdit.position--;
 244       }
 245       return true;
 246     }
 247     return false;
 248   }
 249
 250   /**
 251    * Clear the list of stored edit commands.
 252    *
 253    */
 254   protected void clearEdits()
 255   {
 256     edits.clear();
 257   }
 258
 259   /**
 260    * Returns the i'th stored Edit command.
 261    *
 262    * @param i
 263    * @return
 264    */
 265   protected Edit getEdit(int i)
 266   {
 267     if (i >= 0 && i < edits.size())
 268     {
 269       return edits.get(i);
 270     }
 271     return null;
 272   }
 273
 274   @Override
 275   final public String getDescription()
 276   {
 277     return description;
 278   }
 279
 280   @Override
 281   public int getSize()
 282   {
 283     return edits.size();
 284   }
 285
 286   /**
 287    * Return the alignment for the first edit (or null if no edit).
 288    *
 289    * @return
 290    */
 291   final public AlignmentI getAlignment()
 292   {
 293     return (edits.isEmpty() ? null : edits.get(0).al);
 294   }
 295
 296   /**
 297    * append a new editCommand Note. this shouldn't be called if the edit is an
 298    * operation affects more alignment objects than the one referenced in al (for
 299    * example, cut or pasting whole sequences). Use the form with an additional
 300    * AlignmentI[] views parameter.
 301    *
 302    * @param command
 303    * @param seqs
 304    * @param position
 305    * @param number
 306    * @param al
 307    * @param performEdit
 308    */
 309   final public void appendEdit(Action command, SequenceI[] seqs,
 310           int position, int number, AlignmentI al, boolean performEdit)
 311   {
 312     appendEdit(command, seqs, position, number, al, performEdit, null);
 313   }
 314
 315   /**
 316    * append a new edit command with a set of alignment views that may be
 317    * operated on
 318    *
 319    * @param command
 320    * @param seqs
 321    * @param position
 322    * @param number
 323    * @param al
 324    * @param performEdit
 325    * @param views
 326    */
 327   final public void appendEdit(Action command, SequenceI[] seqs,
 328           int position, int number, AlignmentI al, boolean performEdit,
 329           AlignmentI[] views)
 330   {
 331     Edit edit = new Edit(command, seqs, position, number,
 332             al.getGapCharacter());
 333     if (al.getHeight() == seqs.length)
 334     {
 335       edit.al = al;
 336       edit.fullAlignmentHeight = true;
 337     }
 338
 339     addEdit(edit);
 340
 341     if (performEdit)
 342     {
 343       performEdit(edit, views);
 344     }
 345   }
 346
 347   /**
 348    * Overloaded method that accepts an Edit object with additional parameters.
 349    *
 350    * @param edit
 351    * @param al
 352    * @param performEdit
 353    * @param views
 354    */
 355   final public void appendEdit(Edit edit, AlignmentI al,
 356           boolean performEdit, AlignmentI[] views)
 357   {
 358     if (al.getHeight() == edit.seqs.length)
 359     {
 360       edit.al = al;
 361       edit.fullAlignmentHeight = true;
 362     }
 363
 364     addEdit(edit);
 365
 366     if (performEdit)
 367     {
 368       performEdit(edit, views);
 369     }
 370   }
 371
 372   /**
 373    * Execute all the edit commands, starting at the given commandIndex
 374    *
 375    * @param commandIndex
 376    * @param views
 377    */
 378   public final void performEdit(int commandIndex, AlignmentI[] views)
 379   {
 380     ListIterator<Edit> iterator = edits.listIterator(commandIndex);
 381     while (iterator.hasNext())
 382     {
 383       Edit edit = iterator.next();
 384       performEdit(edit, views);
 385     }
 386   }
 387
 388   /**
 389    * Execute one edit command in all the specified alignment views
 390    *
 391    * @param edit
 392    * @param views
 393    */
 394   protected static void performEdit(Edit edit, AlignmentI[] views)
 395   {
 396     switch (edit.command)
 397     {
 398     case INSERT_GAP:
 399       insertGap(edit);
 400       break;
 401     case DELETE_GAP:
 402       deleteGap(edit);
 403       break;
 404     case CUT:
 405       cut(edit, views);
 406       break;
 407     case PASTE:
 408       paste(edit, views);
 409       break;
 410     case REPLACE:
 411       replace(edit);
 412       break;
 413     case INSERT_NUC:
 414       // TODO:add deleteNuc for UNDO
 415       // case INSERT_NUC:
 416       // insertNuc(edits[e]);
 417       break;
 418     default:
 419       break;
 420     }
 421   }
 422
 423   @Override
 424   final public void doCommand(AlignmentI[] views)
 425   {
 426     performEdit(0, views);
 427   }
 428
 429   /**
 430    * Undo the stored list of commands, in reverse order.
 431    */
 432   @Override
 433   final public void undoCommand(AlignmentI[] views)
 434   {
 435     ListIterator<Edit> iterator = edits.listIterator(edits.size());
 436     while (iterator.hasPrevious())
 437     {
 438       Edit e = iterator.previous();
 439       switch (e.command)
 440       {
 441       case INSERT_GAP:
 442         deleteGap(e);
 443         break;
 444       case DELETE_GAP:
 445         insertGap(e);
 446         break;
 447       case CUT:
 448         paste(e, views);
 449         break;
 450       case PASTE:
 451         cut(e, views);
 452         break;
 453       case REPLACE:
 454         replace(e);
 455         break;
 456       case INSERT_NUC:
 457         // not implemented
 458         break;
 459       default:
 460         break;
 461       }
 462     }
 463   }
 464
 465   /**
 466    * Insert gap(s) in sequences as specified by the command, and adjust
 467    * annotations.
 468    *
 469    * @param command
 470    */
 471   final private static void insertGap(Edit command)
 472   {
 473
 474     for (int s = 0; s < command.seqs.length; s++)
 475     {
 476       command.seqs[s].insertCharAt(command.position, command.number,
 477               command.gapChar);
 478       // System.out.println("pos: "+command.position+" number: "+command.number);
 479     }
 480
 481     adjustAnnotations(command, true, false, null);
 482   }
 483
 484   //
 485   // final void insertNuc(Edit command)
 486   // {
 487   //
 488   // for (int s = 0; s < command.seqs.length; s++)
 489   // {
 490   // System.out.println("pos: "+command.position+" number: "+command.number);
 491   // command.seqs[s].insertCharAt(command.position, command.number,'A');
 492   // }
 493   //
 494   // adjustAnnotations(command, true, false, null);
 495   // }
 496
 497   /**
 498    * Delete gap(s) in sequences as specified by the command, and adjust
 499    * annotations.
 500    *
 501    * @param command
 502    */
 503   final static private void deleteGap(Edit command)
 504   {
 505     for (int s = 0; s < command.seqs.length; s++)
 506     {
 507       command.seqs[s].deleteChars(command.position, command.position
 508               + command.number);
 509     }
 510
 511     adjustAnnotations(command, false, false, null);
 512   }
 513
 514   /**
 515    * Carry out a Cut action. The cut characters are saved in case Undo is
 516    * requested.
 517    *
 518    * @param command
 519    * @param views
 520    */
 521   static void cut(Edit command, AlignmentI[] views)
 522   {
 523     boolean seqDeleted = false;
 524     command.string = new char[command.seqs.length][];
 525
 526     for (int i = 0; i < command.seqs.length; i++)
 527     {
 528       final SequenceI sequence = command.seqs[i];
 529       if (sequence.getLength() > command.position)
 530       {
 531         command.string[i] = sequence.getSequence(command.position,
 532                 command.position + command.number);
 533         SequenceI oldds = sequence.getDatasetSequence();
 534         if (command.oldds != null && command.oldds[i] != null)
 535         {
 536           // we are redoing an undone cut.
 537           sequence.setDatasetSequence(null);
 538         }
 539         sequence.deleteChars(command.position, command.position
 540                 + command.number);
 541         if (command.oldds != null && command.oldds[i] != null)
 542         {
 543           // oldds entry contains the cut dataset sequence.
 544           sequence.setDatasetSequence(command.oldds[i]);
 545           command.oldds[i] = oldds;
 546         }
 547         else
 548         {
 549           // modify the oldds if necessary
 550           if (oldds != sequence.getDatasetSequence()
 551                   || sequence.getSequenceFeatures() != null)
 552           {
 553             if (command.oldds == null)
 554             {
 555               command.oldds = new SequenceI[command.seqs.length];
 556             }
 557             command.oldds[i] = oldds;
 558             // FIXME JAL-2541 JAL-2526 get correct positions if on a gap
 559             adjustFeatures(
 560                     command,
 561                     i,
 562                     sequence.findPosition(command.position),
 563                     sequence.findPosition(command.position + command.number),
 564                     false);
 565           }
 566         }
 567       }
 568
 569       if (sequence.getLength() < 1)
 570       {
 571         command.al.deleteSequence(sequence);
 572         seqDeleted = true;
 573       }
 574     }
 575
 576     adjustAnnotations(command, false, seqDeleted, views);
 577   }
 578
 579   /**
 580    * Perform the given Paste command. This may be to add cut or copied sequences
 581    * to an alignment, or to undo a 'Cut' action on a region of the alignment.
 582    *
 583    * @param command
 584    * @param views
 585    */
 586   static void paste(Edit command, AlignmentI[] views)
 587   {
 588     StringBuffer tmp;
 589     boolean newDSNeeded;
 590     boolean newDSWasNeeded;
 591     int newstart, newend;
 592     boolean seqWasDeleted = false;
 593     int start = 0, end = 0;
 594
 595     for (int i = 0; i < command.seqs.length; i++)
 596     {
 597       newDSNeeded = false;
 598       newDSWasNeeded = command.oldds != null && command.oldds[i] != null;
 599       if (command.seqs[i].getLength() < 1)
 600       {
 601         // ie this sequence was deleted, we need to
 602         // readd it to the alignment
 603         if (command.alIndex[i] < command.al.getHeight())
 604         {
 605           List<SequenceI> sequences;
 606           synchronized (sequences = command.al.getSequences())
 607           {
 608             if (!(command.alIndex[i] < 0))
 609             {
 610               sequences.add(command.alIndex[i], command.seqs[i]);
 611             }
 612           }
 613         }
 614         else
 615         {
 616           command.al.addSequence(command.seqs[i]);
 617         }
 618         seqWasDeleted = true;
 619       }
 620       newstart = command.seqs[i].getStart();
 621       newend = command.seqs[i].getEnd();
 622
 623       tmp = new StringBuffer();
 624       tmp.append(command.seqs[i].getSequence());
 625       // Undo of a delete does not replace original dataset sequence on to
 626       // alignment sequence.
 627
 628       if (command.string != null && command.string[i] != null)
 629       {
 630         if (command.position >= tmp.length())
 631         {
 632           // This occurs if padding is on, and residues
 633           // are removed from end of alignment
 634           int length = command.position - tmp.length();
 635           while (length > 0)
 636           {
 637             tmp.append(command.gapChar);
 638             length--;
 639           }
 640         }
 641         tmp.insert(command.position, command.string[i]);
 642         for (int s = 0; s < command.string[i].length; s++)
 643         {
 644           if (jalview.schemes.ResidueProperties.aaIndex[command.string[i][s]] != 23)
 645           {
 646             if (!newDSNeeded)
 647             {
 648               newDSNeeded = true;
 649               start = command.seqs[i].findPosition(command.position);
 650               end = command.seqs[i].findPosition(command.position
 651                       + command.number);
 652             }
 653             if (command.seqs[i].getStart() == start)
 654             {
 655               newstart--;
 656             }
 657             else
 658             {
 659               newend++;
 660             }
 661           }
 662         }
 663         command.string[i] = null;
 664       }
 665
 666       command.seqs[i].setSequence(tmp.toString());
 667       command.seqs[i].setStart(newstart);
 668       command.seqs[i].setEnd(newend);
 669       if (newDSNeeded)
 670       {
 671         if (command.seqs[i].getDatasetSequence() != null)
 672         {
 673           SequenceI ds;
 674           if (newDSWasNeeded)
 675           {
 676             ds = command.oldds[i];
 677           }
 678           else
 679           {
 680             // make a new DS sequence
 681             // use new ds mechanism here
 682             ds = new Sequence(command.seqs[i].getName(),
 683                     jalview.analysis.AlignSeq.extractGaps(
 684                             jalview.util.Comparison.GapChars,
 685                             command.seqs[i].getSequenceAsString()),
 686                     command.seqs[i].getStart(), command.seqs[i].getEnd());
 687             ds.setDescription(command.seqs[i].getDescription());
 688           }
 689           if (command.oldds == null)
 690           {
 691             command.oldds = new SequenceI[command.seqs.length];
 692           }
 693           command.oldds[i] = command.seqs[i].getDatasetSequence();
 694           command.seqs[i].setDatasetSequence(ds);
 695         }
 696         adjustFeatures(command, i, start, end, true);
 697       }
 698     }
 699     adjustAnnotations(command, true, seqWasDeleted, views);
 700
 701     command.string = null;
 702   }
 703
 704   static void replace(Edit command)
 705   {
 706     StringBuffer tmp;
 707     String oldstring;
 708     int start = command.position;
 709     int end = command.number;
 710     // TODO TUTORIAL - Fix for replacement with different length of sequence (or
 711     // whole sequence)
 712     // TODO Jalview 2.4 bugfix change to an aggregate command - original
 713     // sequence string is cut, new string is pasted in.
 714     command.number = start + command.string[0].length;
 715     for (int i = 0; i < command.seqs.length; i++)
 716     {
 717       boolean newDSWasNeeded = command.oldds != null
 718               && command.oldds[i] != null;
 719
 720       /**
 721        * cut addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT,
 722        * cut, sg.getStartRes(), sg.getEndRes()-sg.getStartRes()+1,
 723        * viewport.alignment));
 724        *
 725        */
 726       /**
 727        * then addHistoryItem(new EditCommand( "Add sequences",
 728        * EditCommand.PASTE, sequences, 0, alignment.getWidth(), alignment) );
 729        *
 730        */
 731       oldstring = command.seqs[i].getSequenceAsString();
 732       tmp = new StringBuffer(oldstring.substring(0, start));
 733       tmp.append(command.string[i]);
 734       String nogaprep = jalview.analysis.AlignSeq.extractGaps(
 735               jalview.util.Comparison.GapChars, new String(
 736                       command.string[i]));
 737       int ipos = command.seqs[i].findPosition(start)
 738               - command.seqs[i].getStart();
 739       tmp.append(oldstring.substring(end));
 740       command.seqs[i].setSequence(tmp.toString());
 741       command.string[i] = oldstring.substring(start, end).toCharArray();
 742       String nogapold = jalview.analysis.AlignSeq.extractGaps(
 743               jalview.util.Comparison.GapChars, new String(
 744                       command.string[i]));
 745       if (!nogaprep.toLowerCase().equals(nogapold.toLowerCase()))
 746       {
 747         if (newDSWasNeeded)
 748         {
 749           SequenceI oldds = command.seqs[i].getDatasetSequence();
 750           command.seqs[i].setDatasetSequence(command.oldds[i]);
 751           command.oldds[i] = oldds;
 752         }
 753         else
 754         {
 755           if (command.oldds == null)
 756           {
 757             command.oldds = new SequenceI[command.seqs.length];
 758           }
 759           command.oldds[i] = command.seqs[i].getDatasetSequence();
 760           SequenceI newds = new Sequence(
 761                   command.seqs[i].getDatasetSequence());
 762           String fullseq, osp = newds.getSequenceAsString();
 763           fullseq = osp.substring(0, ipos) + nogaprep
 764                   + osp.substring(ipos + nogaprep.length());
 765           newds.setSequence(fullseq.toUpperCase());
 766           // TODO: JAL-1131 ensure newly created dataset sequence is added to
 767           // the set of
 768           // dataset sequences associated with the alignment.
 769           // TODO: JAL-1131 fix up any annotation associated with new dataset
 770           // sequence to ensure that original sequence/annotation relationships
 771           // are preserved.
 772           command.seqs[i].setDatasetSequence(newds);
 773
 774         }
 775       }
 776       tmp = null;
 777       oldstring = null;
 778     }
 779   }
 780
 781   final static void adjustAnnotations(Edit command, boolean insert,
 782           boolean modifyVisibility, AlignmentI[] views)
 783   {
 784     AlignmentAnnotation[] annotations = null;
 785
 786     if (modifyVisibility && !insert)
 787     {
 788       // only occurs if a sequence was added or deleted.
 789       command.deletedAnnotationRows = new Hashtable<SequenceI, AlignmentAnnotation[]>();
 790     }
 791     if (command.fullAlignmentHeight)
 792     {
 793       annotations = command.al.getAlignmentAnnotation();
 794     }
 795     else
 796     {
 797       int aSize = 0;
 798       AlignmentAnnotation[] tmp;
 799       for (int s = 0; s < command.seqs.length; s++)
 800       {
 801         if (modifyVisibility)
 802         {
 803           // Rows are only removed or added to sequence object.
 804           if (!insert)
 805           {
 806             // remove rows
 807             tmp = command.seqs[s].getAnnotation();
 808             if (tmp != null)
 809             {
 810               int alen = tmp.length;
 811               for (int aa = 0; aa < tmp.length; aa++)
 812               {
 813                 if (!command.al.deleteAnnotation(tmp[aa]))
 814                 {
 815                   // strip out annotation not in the current al (will be put
 816                   // back on insert in all views)
 817                   tmp[aa] = null;
 818                   alen--;
 819                 }
 820               }
 821               command.seqs[s].setAlignmentAnnotation(null);
 822               if (alen != tmp.length)
 823               {
 824                 // save the non-null annotation references only
 825                 AlignmentAnnotation[] saved = new AlignmentAnnotation[alen];
 826                 for (int aa = 0, aapos = 0; aa < tmp.length; aa++)
 827                 {
 828                   if (tmp[aa] != null)
 829                   {
 830                     saved[aapos++] = tmp[aa];
 831                     tmp[aa] = null;
 832                   }
 833                 }
 834                 tmp = saved;
 835                 command.deletedAnnotationRows.put(command.seqs[s], saved);
 836                 // and then remove any annotation in the other views
 837                 for (int alview = 0; views != null && alview < views.length; alview++)
 838                 {
 839                   if (views[alview] != command.al)
 840                   {
 841                     AlignmentAnnotation[] toremove = views[alview]
 842                             .getAlignmentAnnotation();
 843                     if (toremove == null || toremove.length == 0)
 844                     {
 845                       continue;
 846                     }
 847                     // remove any alignment annotation on this sequence that's
 848                     // on that alignment view.
 849                     for (int aa = 0; aa < toremove.length; aa++)
 850                     {
 851                       if (toremove[aa].sequenceRef == command.seqs[s])
 852                       {
 853                         views[alview].deleteAnnotation(toremove[aa]);
 854                       }
 855                     }
 856                   }
 857                 }
 858               }
 859               else
 860               {
 861                 // save all the annotation
 862                 command.deletedAnnotationRows.put(command.seqs[s], tmp);
 863               }
 864             }
 865           }
 866           else
 867           {
 868             // recover rows
 869             if (command.deletedAnnotationRows != null
 870                     && command.deletedAnnotationRows
 871                             .containsKey(command.seqs[s]))
 872             {
 873               AlignmentAnnotation[] revealed = command.deletedAnnotationRows
 874                       .get(command.seqs[s]);
 875               command.seqs[s].setAlignmentAnnotation(revealed);
 876               if (revealed != null)
 877               {
 878                 for (int aa = 0; aa < revealed.length; aa++)
 879                 {
 880                   // iterate through al adding original annotation
 881                   command.al.addAnnotation(revealed[aa]);
 882                 }
 883                 for (int aa = 0; aa < revealed.length; aa++)
 884                 {
 885                   command.al.setAnnotationIndex(revealed[aa], aa);
 886                 }
 887                 // and then duplicate added annotation on every other alignment
 888                 // view
 889                 for (int vnum = 0; views != null && vnum < views.length; vnum++)
 890                 {
 891                   if (views[vnum] != command.al)
 892                   {
 893                     int avwidth = views[vnum].getWidth() + 1;
 894                     // duplicate in this view
 895                     for (int a = 0; a < revealed.length; a++)
 896                     {
 897                       AlignmentAnnotation newann = new AlignmentAnnotation(
 898                               revealed[a]);
 899                       command.seqs[s].addAlignmentAnnotation(newann);
 900                       newann.padAnnotation(avwidth);
 901                       views[vnum].addAnnotation(newann);
 902                       views[vnum].setAnnotationIndex(newann, a);
 903                     }
 904                   }
 905                 }
 906               }
 907             }
 908           }
 909           continue;
 910         }
 911
 912         if (command.seqs[s].getAnnotation() == null)
 913         {
 914           continue;
 915         }
 916
 917         if (aSize == 0)
 918         {
 919           annotations = command.seqs[s].getAnnotation();
 920         }
 921         else
 922         {
 923           tmp = new AlignmentAnnotation[aSize
 924                   + command.seqs[s].getAnnotation().length];
 925
 926           System.arraycopy(annotations, 0, tmp, 0, aSize);
 927
 928           System.arraycopy(command.seqs[s].getAnnotation(), 0, tmp, aSize,
 929                   command.seqs[s].getAnnotation().length);
 930
 931           annotations = tmp;
 932         }
 933         aSize = annotations.length;
 934       }
 935     }
 936
 937     if (annotations == null)
 938     {
 939       return;
 940     }
 941
 942     if (!insert)
 943     {
 944       command.deletedAnnotations = new Hashtable<String, Annotation[]>();
 945     }
 946
 947     int aSize;
 948     Annotation[] temp;
 949     for (int a = 0; a < annotations.length; a++)
 950     {
 951       if (annotations[a].autoCalculated
 952               || annotations[a].annotations == null)
 953       {
 954         continue;
 955       }
 956
 957       int tSize = 0;
 958
 959       aSize = annotations[a].annotations.length;
 960       if (insert)
 961       {
 962         temp = new Annotation[aSize + command.number];
 963         if (annotations[a].padGaps)
 964         {
 965           for (int aa = 0; aa < temp.length; aa++)
 966           {
 967             temp[aa] = new Annotation(command.gapChar + "", null, ' ', 0);
 968           }
 969         }
 970       }
 971       else
 972       {
 973         if (command.position < aSize)
 974         {
 975           if (command.position + command.number >= aSize)
 976           {
 977             tSize = aSize;
 978           }
 979           else
 980           {
 981             tSize = aSize - command.number;
 982           }
 983         }
 984         else
 985         {
 986           tSize = aSize;
 987         }
 988
 989         if (tSize < 0)
 990         {
 991           tSize = aSize;
 992         }
 993         temp = new Annotation[tSize];
 994       }
 995
 996       if (insert)
 997       {
 998         if (command.position < annotations[a].annotations.length)
 999         {
1000           System.arraycopy(annotations[a].annotations, 0, temp, 0,
1001                   command.position);
1002
1003           if (command.deletedAnnotations != null
1004                   && command.deletedAnnotations
1005                           .containsKey(annotations[a].annotationId))
1006           {
1007             Annotation[] restore = command.deletedAnnotations
1008                     .get(annotations[a].annotationId);
1009
1010             System.arraycopy(restore, 0, temp, command.position,
1011                     command.number);
1012
1013           }
1014
1015           System.arraycopy(annotations[a].annotations, command.position,
1016                   temp, command.position + command.number, aSize
1017                           - command.position);
1018         }
1019         else
1020         {
1021           if (command.deletedAnnotations != null
1022                   && command.deletedAnnotations
1023                           .containsKey(annotations[a].annotationId))
1024           {
1025             Annotation[] restore = command.deletedAnnotations
1026                     .get(annotations[a].annotationId);
1027
1028             temp = new Annotation[annotations[a].annotations.length
1029                     + restore.length];
1030             System.arraycopy(annotations[a].annotations, 0, temp, 0,
1031                     annotations[a].annotations.length);
1032             System.arraycopy(restore, 0, temp,
1033                     annotations[a].annotations.length, restore.length);
1034           }
1035           else
1036           {
1037             temp = annotations[a].annotations;
1038           }
1039         }
1040       }
1041       else
1042       {
1043         if (tSize != aSize || command.position < 2)
1044         {
1045           int copylen = Math.min(command.position,
1046                   annotations[a].annotations.length);
1047           if (copylen > 0)
1048           {
1049             System.arraycopy(annotations[a].annotations, 0, temp, 0,
1050                     copylen); // command.position);
1051           }
1052
1053           Annotation[] deleted = new Annotation[command.number];
1054           if (copylen >= command.position)
1055           {
1056             copylen = Math.min(command.number,
1057                     annotations[a].annotations.length - command.position);
1058             if (copylen > 0)
1059             {
1060               System.arraycopy(annotations[a].annotations,
1061                       command.position, deleted, 0, copylen); // command.number);
1062             }
1063           }
1064
1065           command.deletedAnnotations.put(annotations[a].annotationId,
1066                   deleted);
1067           if (annotations[a].annotations.length > command.position
1068                   + command.number)
1069           {
1070             System.arraycopy(annotations[a].annotations, command.position
1071                     + command.number, temp, command.position,
1072                     annotations[a].annotations.length - command.position
1073                             - command.number); // aSize
1074           }
1075         }
1076         else
1077         {
1078           int dSize = aSize - command.position;
1079
1080           if (dSize > 0)
1081           {
1082             Annotation[] deleted = new Annotation[command.number];
1083             System.arraycopy(annotations[a].annotations, command.position,
1084                     deleted, 0, dSize);
1085
1086             command.deletedAnnotations.put(annotations[a].annotationId,
1087                     deleted);
1088
1089             tSize = Math.min(annotations[a].annotations.length,
1090                     command.position);
1091             temp = new Annotation[tSize];
1092             System.arraycopy(annotations[a].annotations, 0, temp, 0, tSize);
1093           }
1094           else
1095           {
1096             temp = annotations[a].annotations;
1097           }
1098         }
1099       }
1100
1101       annotations[a].annotations = temp;
1102     }
1103   }
1104
1105   final static void adjustFeatures(Edit command, int index, final int i,
1106           final int j, boolean insert)
1107   {
1108     SequenceI seq = command.seqs[index];
1109     SequenceI sequence = seq.getDatasetSequence();
1110     if (sequence == null)
1111     {
1112       sequence = seq;
1113     }
1114
1115     if (insert)
1116     {
1117       if (command.editedFeatures != null
1118               && command.editedFeatures.containsKey(seq))
1119       {
1120         sequence.setSequenceFeatures(command.editedFeatures.get(seq));
1121       }
1122
1123       return;
1124     }
1125
1126     List<SequenceFeature> sf = sequence.getFeatures()
1127             .getPositionalFeatures();
1128
1129     if (sf.isEmpty())
1130     {
1131       return;
1132     }
1133
1134     SequenceFeature[] oldsf = new SequenceFeature[sf.size()];
1135
1136     int cSize = j - i;
1137
1138     int s = 0;
1139     for (SequenceFeature feature : sf)
1140     {
1141       SequenceFeature copy = new SequenceFeature(feature);
1142
1143       oldsf[s++] = copy;
1144
1145       if (feature.getEnd() < i)
1146       {
1147         continue;
1148       }
1149
1150       if (feature.getBegin() > j)
1151       {
1152         int newBegin = copy.getBegin() - cSize;
1153         int newEnd = copy.getEnd() - cSize;
1154         SequenceFeature newSf = new SequenceFeature(feature, newBegin,
1155                 newEnd, feature.getFeatureGroup());
1156         sequence.deleteFeature(feature);
1157         sequence.addSequenceFeature(newSf);
1158         // feature.setBegin(newBegin);
1159         // feature.setEnd(newEnd);
1160         continue;
1161       }
1162
1163       int newBegin = feature.getBegin();
1164       int newEnd = feature.getEnd();
1165       if (newBegin >= i)
1166       {
1167         newBegin = i;
1168         // feature.setBegin(i);
1169       }
1170
1171       if (newEnd < j)
1172       {
1173         newEnd = j - 1;
1174         // feature.setEnd(j - 1);
1175       }
1176       newEnd = newEnd - cSize;
1177       // feature.setEnd(feature.getEnd() - (cSize));
1178
1179       sequence.deleteFeature(feature);
1180       if (newEnd >= newBegin)
1181       {
1182         sequence.addSequenceFeature(new SequenceFeature(feature, newBegin,
1183                 newEnd, feature.getFeatureGroup()));
1184       }
1185       // if (feature.getBegin() > feature.getEnd())
1186       // {
1187       // sequence.deleteFeature(feature);
1188       // }
1189     }
1190
1191     if (command.editedFeatures == null)
1192     {
1193       command.editedFeatures = new Hashtable<SequenceI, SequenceFeature[]>();
1194     }
1195
1196     command.editedFeatures.put(seq, oldsf);
1197
1198   }
1199
1200   /**
1201    * Returns the list of edit commands wrapped by this object.
1202    *
1203    * @return
1204    */
1205   public List<Edit> getEdits()
1206   {
1207     return this.edits;
1208   }
1209
1210   /**
1211    * Returns a map whose keys are the dataset sequences, and values their
1212    * aligned sequences before the command edit list was applied. The aligned
1213    * sequences are copies, which may be updated without affecting the originals.
1214    *
1215    * The command holds references to the aligned sequences (after editing). If
1216    * the command is an 'undo',then the prior state is simply the aligned state.
1217    * Otherwise, we have to derive the prior state by working backwards through
1218    * the edit list to infer the aligned sequences before editing.
1219    *
1220    * Note: an alternative solution would be to cache the 'before' state of each
1221    * edit, but this would be expensive in space in the common case that the
1222    * original is never needed (edits are not mirrored).
1223    *
1224    * @return
1225    * @throws IllegalStateException
1226    *           on detecting an edit command of a type that can't be unwound
1227    */
1228   public Map<SequenceI, SequenceI> priorState(boolean forUndo)
1229   {
1230     Map<SequenceI, SequenceI> result = new HashMap<SequenceI, SequenceI>();
1231     if (getEdits() == null)
1232     {
1233       return result;
1234     }
1235     if (forUndo)
1236     {
1237       for (Edit e : getEdits())
1238       {
1239         for (SequenceI seq : e.getSequences())
1240         {
1241           SequenceI ds = seq.getDatasetSequence();
1242           // SequenceI preEdit = result.get(ds);
1243           if (!result.containsKey(ds))
1244           {
1245             /*
1246              * copy sequence including start/end (but don't use copy constructor
1247              * as we don't need annotations)
1248              */
1249             SequenceI preEdit = new Sequence("", seq.getSequenceAsString(),
1250                     seq.getStart(), seq.getEnd());
1251             preEdit.setDatasetSequence(ds);
1252             result.put(ds, preEdit);
1253           }
1254         }
1255       }
1256       return result;
1257     }
1258
1259     /*
1260      * Work backwards through the edit list, deriving the sequences before each
1261      * was applied. The final result is the sequence set before any edits.
1262      */
1263     Iterator<Edit> editList = new ReverseListIterator<Edit>(getEdits());
1264     while (editList.hasNext())
1265     {
1266       Edit oldEdit = editList.next();
1267       Action action = oldEdit.getAction();
1268       int position = oldEdit.getPosition();
1269       int number = oldEdit.getNumber();
1270       final char gap = oldEdit.getGapCharacter();
1271       for (SequenceI seq : oldEdit.getSequences())
1272       {
1273         SequenceI ds = seq.getDatasetSequence();
1274         SequenceI preEdit = result.get(ds);
1275         if (preEdit == null)
1276         {
1277           preEdit = new Sequence("", seq.getSequenceAsString(),
1278                   seq.getStart(), seq.getEnd());
1279           preEdit.setDatasetSequence(ds);
1280           result.put(ds, preEdit);
1281         }
1282         /*
1283          * 'Undo' this edit action on the sequence (updating the value in the
1284          * map).
1285          */
1286         if (ds != null)
1287         {
1288           if (action == Action.DELETE_GAP)
1289           {
1290             preEdit.setSequence(new String(StringUtils.insertCharAt(
1291                     preEdit.getSequence(), position, number, gap)));
1292           }
1293           else if (action == Action.INSERT_GAP)
1294           {
1295             preEdit.setSequence(new String(StringUtils.deleteChars(
1296                     preEdit.getSequence(), position, position + number)));
1297           }
1298           else
1299           {
1300             System.err.println("Can't undo edit action " + action);
1301             // throw new IllegalStateException("Can't undo edit action " +
1302             // action);
1303           }
1304         }
1305       }
1306     }
1307     return result;
1308   }
1309
1310   public class Edit
1311   {
1312     public SequenceI[] oldds;
1313
1314     boolean fullAlignmentHeight = false;
1315
1316     Hashtable<SequenceI, AlignmentAnnotation[]> deletedAnnotationRows;
1317
1318     Hashtable<String, Annotation[]> deletedAnnotations;
1319
1320     Hashtable<SequenceI, SequenceFeature[]> editedFeatures;
1321
1322     AlignmentI al;
1323
1324     Action command;
1325
1326     char[][] string;
1327
1328     SequenceI[] seqs;
1329
1330     int[] alIndex;
1331
1332     int position, number;
1333
1334     char gapChar;
1335
1336     public Edit(Action command, SequenceI[] seqs, int position, int number,
1337             char gapChar)
1338     {
1339       this.command = command;
1340       this.seqs = seqs;
1341       this.position = position;
1342       this.number = number;
1343       this.gapChar = gapChar;
1344     }
1345
1346     Edit(Action command, SequenceI[] seqs, int position, int number,
1347             AlignmentI al)
1348     {
1349       this.gapChar = al.getGapCharacter();
1350       this.command = command;
1351       this.seqs = seqs;
1352       this.position = position;
1353       this.number = number;
1354       this.al = al;
1355
1356       alIndex = new int[seqs.length];
1357       for (int i = 0; i < seqs.length; i++)
1358       {
1359         alIndex[i] = al.findIndex(seqs[i]);
1360       }
1361
1362       fullAlignmentHeight = (al.getHeight() == seqs.length);
1363     }
1364
1365     Edit(Action command, SequenceI[] seqs, int position, int number,
1366             AlignmentI al, String replace)
1367     {
1368       this.command = command;
1369       this.seqs = seqs;
1370       this.position = position;
1371       this.number = number;
1372       this.al = al;
1373       this.gapChar = al.getGapCharacter();
1374       string = new char[seqs.length][];
1375       for (int i = 0; i < seqs.length; i++)
1376       {
1377         string[i] = replace.toCharArray();
1378       }
1379
1380       fullAlignmentHeight = (al.getHeight() == seqs.length);
1381     }
1382
1383     public SequenceI[] getSequences()
1384     {
1385       return seqs;
1386     }
1387
1388     public int getPosition()
1389     {
1390       return position;
1391     }
1392
1393     public Action getAction()
1394     {
1395       return command;
1396     }
1397
1398     public int getNumber()
1399     {
1400       return number;
1401     }
1402
1403     public char getGapCharacter()
1404     {
1405       return gapChar;
1406     }
1407   }
1408
1409   /**
1410    * Returns an iterator over the list of edit commands which traverses the list
1411    * either forwards or backwards.
1412    *
1413    * @param forwards
1414    * @return
1415    */
1416   public Iterator<Edit> getEditIterator(boolean forwards)
1417   {
1418     if (forwards)
1419     {
1420       return getEdits().iterator();
1421     }
1422     else
1423     {
1424       return new ReverseListIterator<Edit>(getEdits());
1425     }
1426   }
1427 }