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             adjustFeatures(
 559                     command,
 560                     i,
 561                     sequence.findPosition(command.position),
 562                     sequence.findPosition(command.position + command.number),
 563                     false);
 564           }
 565         }
 566       }
 567
 568       if (sequence.getLength() < 1)
 569       {
 570         command.al.deleteSequence(sequence);
 571         seqDeleted = true;
 572       }
 573     }
 574
 575     adjustAnnotations(command, false, seqDeleted, views);
 576   }
 577
 578   /**
 579    * Perform the given Paste command. This may be to add cut or copied sequences
 580    * to an alignment, or to undo a 'Cut' action on a region of the alignment.
 581    *
 582    * @param command
 583    * @param views
 584    */
 585   static void paste(Edit command, AlignmentI[] views)
 586   {
 587     StringBuffer tmp;
 588     boolean newDSNeeded;
 589     boolean newDSWasNeeded;
 590     int newstart, newend;
 591     boolean seqWasDeleted = false;
 592     int start = 0, end = 0;
 593
 594     for (int i = 0; i < command.seqs.length; i++)
 595     {
 596       newDSNeeded = false;
 597       newDSWasNeeded = command.oldds != null && command.oldds[i] != null;
 598       if (command.seqs[i].getLength() < 1)
 599       {
 600         // ie this sequence was deleted, we need to
 601         // readd it to the alignment
 602         if (command.alIndex[i] < command.al.getHeight())
 603         {
 604           List<SequenceI> sequences;
 605           synchronized (sequences = command.al.getSequences())
 606           {
 607             if (!(command.alIndex[i] < 0))
 608             {
 609               sequences.add(command.alIndex[i], command.seqs[i]);
 610             }
 611           }
 612         }
 613         else
 614         {
 615           command.al.addSequence(command.seqs[i]);
 616         }
 617         seqWasDeleted = true;
 618       }
 619       newstart = command.seqs[i].getStart();
 620       newend = command.seqs[i].getEnd();
 621
 622       tmp = new StringBuffer();
 623       tmp.append(command.seqs[i].getSequence());
 624       // Undo of a delete does not replace original dataset sequence on to
 625       // alignment sequence.
 626
 627       if (command.string != null && command.string[i] != null)
 628       {
 629         if (command.position >= tmp.length())
 630         {
 631           // This occurs if padding is on, and residues
 632           // are removed from end of alignment
 633           int length = command.position - tmp.length();
 634           while (length > 0)
 635           {
 636             tmp.append(command.gapChar);
 637             length--;
 638           }
 639         }
 640         tmp.insert(command.position, command.string[i]);
 641         for (int s = 0; s < command.string[i].length; s++)
 642         {
 643           if (jalview.schemes.ResidueProperties.aaIndex[command.string[i][s]] != 23)
 644           {
 645             if (!newDSNeeded)
 646             {
 647               newDSNeeded = true;
 648               start = command.seqs[i].findPosition(command.position);
 649               end = command.seqs[i].findPosition(command.position
 650                       + command.number);
 651             }
 652             if (command.seqs[i].getStart() == start)
 653             {
 654               newstart--;
 655             }
 656             else
 657             {
 658               newend++;
 659             }
 660           }
 661         }
 662         command.string[i] = null;
 663       }
 664
 665       command.seqs[i].setSequence(tmp.toString());
 666       command.seqs[i].setStart(newstart);
 667       command.seqs[i].setEnd(newend);
 668       if (newDSNeeded)
 669       {
 670         if (command.seqs[i].getDatasetSequence() != null)
 671         {
 672           SequenceI ds;
 673           if (newDSWasNeeded)
 674           {
 675             ds = command.oldds[i];
 676           }
 677           else
 678           {
 679             // make a new DS sequence
 680             // use new ds mechanism here
 681             ds = new Sequence(command.seqs[i].getName(),
 682                     jalview.analysis.AlignSeq.extractGaps(
 683                             jalview.util.Comparison.GapChars,
 684                             command.seqs[i].getSequenceAsString()),
 685                     command.seqs[i].getStart(), command.seqs[i].getEnd());
 686             ds.setDescription(command.seqs[i].getDescription());
 687           }
 688           if (command.oldds == null)
 689           {
 690             command.oldds = new SequenceI[command.seqs.length];
 691           }
 692           command.oldds[i] = command.seqs[i].getDatasetSequence();
 693           command.seqs[i].setDatasetSequence(ds);
 694         }
 695         adjustFeatures(command, i, start, end, true);
 696       }
 697     }
 698     adjustAnnotations(command, true, seqWasDeleted, views);
 699
 700     command.string = null;
 701   }
 702
 703   static void replace(Edit command)
 704   {
 705     StringBuffer tmp;
 706     String oldstring;
 707     int start = command.position;
 708     int end = command.number;
 709     // TODO TUTORIAL - Fix for replacement with different length of sequence (or
 710     // whole sequence)
 711     // TODO Jalview 2.4 bugfix change to an aggregate command - original
 712     // sequence string is cut, new string is pasted in.
 713     command.number = start + command.string[0].length;
 714     for (int i = 0; i < command.seqs.length; i++)
 715     {
 716       boolean newDSWasNeeded = command.oldds != null
 717               && command.oldds[i] != null;
 718
 719       /**
 720        * cut addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT,
 721        * cut, sg.getStartRes(), sg.getEndRes()-sg.getStartRes()+1,
 722        * viewport.alignment));
 723        *
 724        */
 725       /**
 726        * then addHistoryItem(new EditCommand( "Add sequences",
 727        * EditCommand.PASTE, sequences, 0, alignment.getWidth(), alignment) );
 728        *
 729        */
 730       oldstring = command.seqs[i].getSequenceAsString();
 731       tmp = new StringBuffer(oldstring.substring(0, start));
 732       tmp.append(command.string[i]);
 733       String nogaprep = jalview.analysis.AlignSeq.extractGaps(
 734               jalview.util.Comparison.GapChars, new String(
 735                       command.string[i]));
 736       int ipos = command.seqs[i].findPosition(start)
 737               - command.seqs[i].getStart();
 738       tmp.append(oldstring.substring(end));
 739       command.seqs[i].setSequence(tmp.toString());
 740       command.string[i] = oldstring.substring(start, end).toCharArray();
 741       String nogapold = jalview.analysis.AlignSeq.extractGaps(
 742               jalview.util.Comparison.GapChars, new String(
 743                       command.string[i]));
 744       if (!nogaprep.toLowerCase().equals(nogapold.toLowerCase()))
 745       {
 746         if (newDSWasNeeded)
 747         {
 748           SequenceI oldds = command.seqs[i].getDatasetSequence();
 749           command.seqs[i].setDatasetSequence(command.oldds[i]);
 750           command.oldds[i] = oldds;
 751         }
 752         else
 753         {
 754           if (command.oldds == null)
 755           {
 756             command.oldds = new SequenceI[command.seqs.length];
 757           }
 758           command.oldds[i] = command.seqs[i].getDatasetSequence();
 759           SequenceI newds = new Sequence(
 760                   command.seqs[i].getDatasetSequence());
 761           String fullseq, osp = newds.getSequenceAsString();
 762           fullseq = osp.substring(0, ipos) + nogaprep
 763                   + osp.substring(ipos + nogaprep.length());
 764           newds.setSequence(fullseq.toUpperCase());
 765           // TODO: JAL-1131 ensure newly created dataset sequence is added to
 766           // the set of
 767           // dataset sequences associated with the alignment.
 768           // TODO: JAL-1131 fix up any annotation associated with new dataset
 769           // sequence to ensure that original sequence/annotation relationships
 770           // are preserved.
 771           command.seqs[i].setDatasetSequence(newds);
 772
 773         }
 774       }
 775       tmp = null;
 776       oldstring = null;
 777     }
 778   }
 779
 780   final static void adjustAnnotations(Edit command, boolean insert,
 781           boolean modifyVisibility, AlignmentI[] views)
 782   {
 783     AlignmentAnnotation[] annotations = null;
 784
 785     if (modifyVisibility && !insert)
 786     {
 787       // only occurs if a sequence was added or deleted.
 788       command.deletedAnnotationRows = new Hashtable<SequenceI, AlignmentAnnotation[]>();
 789     }
 790     if (command.fullAlignmentHeight)
 791     {
 792       annotations = command.al.getAlignmentAnnotation();
 793     }
 794     else
 795     {
 796       int aSize = 0;
 797       AlignmentAnnotation[] tmp;
 798       for (int s = 0; s < command.seqs.length; s++)
 799       {
 800         if (modifyVisibility)
 801         {
 802           // Rows are only removed or added to sequence object.
 803           if (!insert)
 804           {
 805             // remove rows
 806             tmp = command.seqs[s].getAnnotation();
 807             if (tmp != null)
 808             {
 809               int alen = tmp.length;
 810               for (int aa = 0; aa < tmp.length; aa++)
 811               {
 812                 if (!command.al.deleteAnnotation(tmp[aa]))
 813                 {
 814                   // strip out annotation not in the current al (will be put
 815                   // back on insert in all views)
 816                   tmp[aa] = null;
 817                   alen--;
 818                 }
 819               }
 820               command.seqs[s].setAlignmentAnnotation(null);
 821               if (alen != tmp.length)
 822               {
 823                 // save the non-null annotation references only
 824                 AlignmentAnnotation[] saved = new AlignmentAnnotation[alen];
 825                 for (int aa = 0, aapos = 0; aa < tmp.length; aa++)
 826                 {
 827                   if (tmp[aa] != null)
 828                   {
 829                     saved[aapos++] = tmp[aa];
 830                     tmp[aa] = null;
 831                   }
 832                 }
 833                 tmp = saved;
 834                 command.deletedAnnotationRows.put(command.seqs[s], saved);
 835                 // and then remove any annotation in the other views
 836                 for (int alview = 0; views != null && alview < views.length; alview++)
 837                 {
 838                   if (views[alview] != command.al)
 839                   {
 840                     AlignmentAnnotation[] toremove = views[alview]
 841                             .getAlignmentAnnotation();
 842                     if (toremove == null || toremove.length == 0)
 843                     {
 844                       continue;
 845                     }
 846                     // remove any alignment annotation on this sequence that's
 847                     // on that alignment view.
 848                     for (int aa = 0; aa < toremove.length; aa++)
 849                     {
 850                       if (toremove[aa].sequenceRef == command.seqs[s])
 851                       {
 852                         views[alview].deleteAnnotation(toremove[aa]);
 853                       }
 854                     }
 855                   }
 856                 }
 857               }
 858               else
 859               {
 860                 // save all the annotation
 861                 command.deletedAnnotationRows.put(command.seqs[s], tmp);
 862               }
 863             }
 864           }
 865           else
 866           {
 867             // recover rows
 868             if (command.deletedAnnotationRows != null
 869                     && command.deletedAnnotationRows
 870                             .containsKey(command.seqs[s]))
 871             {
 872               AlignmentAnnotation[] revealed = command.deletedAnnotationRows
 873                       .get(command.seqs[s]);
 874               command.seqs[s].setAlignmentAnnotation(revealed);
 875               if (revealed != null)
 876               {
 877                 for (int aa = 0; aa < revealed.length; aa++)
 878                 {
 879                   // iterate through al adding original annotation
 880                   command.al.addAnnotation(revealed[aa]);
 881                 }
 882                 for (int aa = 0; aa < revealed.length; aa++)
 883                 {
 884                   command.al.setAnnotationIndex(revealed[aa], aa);
 885                 }
 886                 // and then duplicate added annotation on every other alignment
 887                 // view
 888                 for (int vnum = 0; views != null && vnum < views.length; vnum++)
 889                 {
 890                   if (views[vnum] != command.al)
 891                   {
 892                     int avwidth = views[vnum].getWidth() + 1;
 893                     // duplicate in this view
 894                     for (int a = 0; a < revealed.length; a++)
 895                     {
 896                       AlignmentAnnotation newann = new AlignmentAnnotation(
 897                               revealed[a]);
 898                       command.seqs[s].addAlignmentAnnotation(newann);
 899                       newann.padAnnotation(avwidth);
 900                       views[vnum].addAnnotation(newann);
 901                       views[vnum].setAnnotationIndex(newann, a);
 902                     }
 903                   }
 904                 }
 905               }
 906             }
 907           }
 908           continue;
 909         }
 910
 911         if (command.seqs[s].getAnnotation() == null)
 912         {
 913           continue;
 914         }
 915
 916         if (aSize == 0)
 917         {
 918           annotations = command.seqs[s].getAnnotation();
 919         }
 920         else
 921         {
 922           tmp = new AlignmentAnnotation[aSize
 923                   + command.seqs[s].getAnnotation().length];
 924
 925           System.arraycopy(annotations, 0, tmp, 0, aSize);
 926
 927           System.arraycopy(command.seqs[s].getAnnotation(), 0, tmp, aSize,
 928                   command.seqs[s].getAnnotation().length);
 929
 930           annotations = tmp;
 931         }
 932         aSize = annotations.length;
 933       }
 934     }
 935
 936     if (annotations == null)
 937     {
 938       return;
 939     }
 940
 941     if (!insert)
 942     {
 943       command.deletedAnnotations = new Hashtable<String, Annotation[]>();
 944     }
 945
 946     int aSize;
 947     Annotation[] temp;
 948     for (int a = 0; a < annotations.length; a++)
 949     {
 950       if (annotations[a].autoCalculated
 951               || annotations[a].annotations == null)
 952       {
 953         continue;
 954       }
 955
 956       int tSize = 0;
 957
 958       aSize = annotations[a].annotations.length;
 959       if (insert)
 960       {
 961         temp = new Annotation[aSize + command.number];
 962         if (annotations[a].padGaps)
 963         {
 964           for (int aa = 0; aa < temp.length; aa++)
 965           {
 966             temp[aa] = new Annotation(command.gapChar + "", null, ' ', 0);
 967           }
 968         }
 969       }
 970       else
 971       {
 972         if (command.position < aSize)
 973         {
 974           if (command.position + command.number >= aSize)
 975           {
 976             tSize = aSize;
 977           }
 978           else
 979           {
 980             tSize = aSize - command.number;
 981           }
 982         }
 983         else
 984         {
 985           tSize = aSize;
 986         }
 987
 988         if (tSize < 0)
 989         {
 990           tSize = aSize;
 991         }
 992         temp = new Annotation[tSize];
 993       }
 994
 995       if (insert)
 996       {
 997         if (command.position < annotations[a].annotations.length)
 998         {
 999           System.arraycopy(annotations[a].annotations, 0, temp, 0,
1000                   command.position);
1001
1002           if (command.deletedAnnotations != null
1003                   && command.deletedAnnotations
1004                           .containsKey(annotations[a].annotationId))
1005           {
1006             Annotation[] restore = command.deletedAnnotations
1007                     .get(annotations[a].annotationId);
1008
1009             System.arraycopy(restore, 0, temp, command.position,
1010                     command.number);
1011
1012           }
1013
1014           System.arraycopy(annotations[a].annotations, command.position,
1015                   temp, command.position + command.number, aSize
1016                           - command.position);
1017         }
1018         else
1019         {
1020           if (command.deletedAnnotations != null
1021                   && command.deletedAnnotations
1022                           .containsKey(annotations[a].annotationId))
1023           {
1024             Annotation[] restore = command.deletedAnnotations
1025                     .get(annotations[a].annotationId);
1026
1027             temp = new Annotation[annotations[a].annotations.length
1028                     + restore.length];
1029             System.arraycopy(annotations[a].annotations, 0, temp, 0,
1030                     annotations[a].annotations.length);
1031             System.arraycopy(restore, 0, temp,
1032                     annotations[a].annotations.length, restore.length);
1033           }
1034           else
1035           {
1036             temp = annotations[a].annotations;
1037           }
1038         }
1039       }
1040       else
1041       {
1042         if (tSize != aSize || command.position < 2)
1043         {
1044           int copylen = Math.min(command.position,
1045                   annotations[a].annotations.length);
1046           if (copylen > 0)
1047           {
1048             System.arraycopy(annotations[a].annotations, 0, temp, 0,
1049                     copylen); // command.position);
1050           }
1051
1052           Annotation[] deleted = new Annotation[command.number];
1053           if (copylen >= command.position)
1054           {
1055             copylen = Math.min(command.number,
1056                     annotations[a].annotations.length - command.position);
1057             if (copylen > 0)
1058             {
1059               System.arraycopy(annotations[a].annotations,
1060                       command.position, deleted, 0, copylen); // command.number);
1061             }
1062           }
1063
1064           command.deletedAnnotations.put(annotations[a].annotationId,
1065                   deleted);
1066           if (annotations[a].annotations.length > command.position
1067                   + command.number)
1068           {
1069             System.arraycopy(annotations[a].annotations, command.position
1070                     + command.number, temp, command.position,
1071                     annotations[a].annotations.length - command.position
1072                             - command.number); // aSize
1073           }
1074         }
1075         else
1076         {
1077           int dSize = aSize - command.position;
1078
1079           if (dSize > 0)
1080           {
1081             Annotation[] deleted = new Annotation[command.number];
1082             System.arraycopy(annotations[a].annotations, command.position,
1083                     deleted, 0, dSize);
1084
1085             command.deletedAnnotations.put(annotations[a].annotationId,
1086                     deleted);
1087
1088             tSize = Math.min(annotations[a].annotations.length,
1089                     command.position);
1090             temp = new Annotation[tSize];
1091             System.arraycopy(annotations[a].annotations, 0, temp, 0, tSize);
1092           }
1093           else
1094           {
1095             temp = annotations[a].annotations;
1096           }
1097         }
1098       }
1099
1100       annotations[a].annotations = temp;
1101     }
1102   }
1103
1104   final static void adjustFeatures(Edit command, int index, int i, int j,
1105           boolean insert)
1106   {
1107     SequenceI seq = command.seqs[index];
1108     SequenceI sequence = seq.getDatasetSequence();
1109     if (sequence == null)
1110     {
1111       sequence = seq;
1112     }
1113
1114     if (insert)
1115     {
1116       if (command.editedFeatures != null
1117               && command.editedFeatures.containsKey(seq))
1118       {
1119         sequence.setSequenceFeatures(command.editedFeatures.get(seq));
1120       }
1121
1122       return;
1123     }
1124
1125     SequenceFeature[] sf = sequence.getSequenceFeatures();
1126
1127     if (sf == null)
1128     {
1129       return;
1130     }
1131
1132     SequenceFeature[] oldsf = new SequenceFeature[sf.length];
1133
1134     int cSize = j - i;
1135
1136     for (int s = 0; s < sf.length; s++)
1137     {
1138       SequenceFeature copy = new SequenceFeature(sf[s]);
1139
1140       oldsf[s] = copy;
1141
1142       if (sf[s].getEnd() < i)
1143       {
1144         continue;
1145       }
1146
1147       if (sf[s].getBegin() > j)
1148       {
1149         sf[s].setBegin(copy.getBegin() - cSize);
1150         sf[s].setEnd(copy.getEnd() - cSize);
1151         continue;
1152       }
1153
1154       if (sf[s].getBegin() >= i)
1155       {
1156         sf[s].setBegin(i);
1157       }
1158
1159       if (sf[s].getEnd() < j)
1160       {
1161         sf[s].setEnd(j - 1);
1162       }
1163
1164       sf[s].setEnd(sf[s].getEnd() - (cSize));
1165
1166       if (sf[s].getBegin() > sf[s].getEnd())
1167       {
1168         sequence.deleteFeature(sf[s]);
1169       }
1170     }
1171
1172     if (command.editedFeatures == null)
1173     {
1174       command.editedFeatures = new Hashtable<SequenceI, SequenceFeature[]>();
1175     }
1176
1177     command.editedFeatures.put(seq, oldsf);
1178
1179   }
1180
1181   /**
1182    * Returns the list of edit commands wrapped by this object.
1183    *
1184    * @return
1185    */
1186   public List<Edit> getEdits()
1187   {
1188     return this.edits;
1189   }
1190
1191   /**
1192    * Returns a map whose keys are the dataset sequences, and values their
1193    * aligned sequences before the command edit list was applied. The aligned
1194    * sequences are copies, which may be updated without affecting the originals.
1195    *
1196    * The command holds references to the aligned sequences (after editing). If
1197    * the command is an 'undo',then the prior state is simply the aligned state.
1198    * Otherwise, we have to derive the prior state by working backwards through
1199    * the edit list to infer the aligned sequences before editing.
1200    *
1201    * Note: an alternative solution would be to cache the 'before' state of each
1202    * edit, but this would be expensive in space in the common case that the
1203    * original is never needed (edits are not mirrored).
1204    *
1205    * @return
1206    * @throws IllegalStateException
1207    *           on detecting an edit command of a type that can't be unwound
1208    */
1209   public Map<SequenceI, SequenceI> priorState(boolean forUndo)
1210   {
1211     Map<SequenceI, SequenceI> result = new HashMap<SequenceI, SequenceI>();
1212     if (getEdits() == null)
1213     {
1214       return result;
1215     }
1216     if (forUndo)
1217     {
1218       for (Edit e : getEdits())
1219       {
1220         for (SequenceI seq : e.getSequences())
1221         {
1222           SequenceI ds = seq.getDatasetSequence();
1223           // SequenceI preEdit = result.get(ds);
1224           if (!result.containsKey(ds))
1225           {
1226             /*
1227              * copy sequence including start/end (but don't use copy constructor
1228              * as we don't need annotations)
1229              */
1230             SequenceI preEdit = new Sequence("", seq.getSequenceAsString(),
1231                     seq.getStart(), seq.getEnd());
1232             preEdit.setDatasetSequence(ds);
1233             result.put(ds, preEdit);
1234           }
1235         }
1236       }
1237       return result;
1238     }
1239
1240     /*
1241      * Work backwards through the edit list, deriving the sequences before each
1242      * was applied. The final result is the sequence set before any edits.
1243      */
1244     Iterator<Edit> editList = new ReverseListIterator<Edit>(getEdits());
1245     while (editList.hasNext())
1246     {
1247       Edit oldEdit = editList.next();
1248       Action action = oldEdit.getAction();
1249       int position = oldEdit.getPosition();
1250       int number = oldEdit.getNumber();
1251       final char gap = oldEdit.getGapCharacter();
1252       for (SequenceI seq : oldEdit.getSequences())
1253       {
1254         SequenceI ds = seq.getDatasetSequence();
1255         SequenceI preEdit = result.get(ds);
1256         if (preEdit == null)
1257         {
1258           preEdit = new Sequence("", seq.getSequenceAsString(),
1259                   seq.getStart(), seq.getEnd());
1260           preEdit.setDatasetSequence(ds);
1261           result.put(ds, preEdit);
1262         }
1263         /*
1264          * 'Undo' this edit action on the sequence (updating the value in the
1265          * map).
1266          */
1267         if (ds != null)
1268         {
1269           if (action == Action.DELETE_GAP)
1270           {
1271             preEdit.setSequence(new String(StringUtils.insertCharAt(
1272                     preEdit.getSequence(), position, number, gap)));
1273           }
1274           else if (action == Action.INSERT_GAP)
1275           {
1276             preEdit.setSequence(new String(StringUtils.deleteChars(
1277                     preEdit.getSequence(), position, position + number)));
1278           }
1279           else
1280           {
1281             System.err.println("Can't undo edit action " + action);
1282             // throw new IllegalStateException("Can't undo edit action " +
1283             // action);
1284           }
1285         }
1286       }
1287     }
1288     return result;
1289   }
1290
1291   public class Edit
1292   {
1293     public SequenceI[] oldds;
1294
1295     boolean fullAlignmentHeight = false;
1296
1297     Hashtable<SequenceI, AlignmentAnnotation[]> deletedAnnotationRows;
1298
1299     Hashtable<String, Annotation[]> deletedAnnotations;
1300
1301     Hashtable<SequenceI, SequenceFeature[]> editedFeatures;
1302
1303     AlignmentI al;
1304
1305     Action command;
1306
1307     char[][] string;
1308
1309     SequenceI[] seqs;
1310
1311     int[] alIndex;
1312
1313     int position, number;
1314
1315     char gapChar;
1316
1317     public Edit(Action command, SequenceI[] seqs, int position, int number,
1318             char gapChar)
1319     {
1320       this.command = command;
1321       this.seqs = seqs;
1322       this.position = position;
1323       this.number = number;
1324       this.gapChar = gapChar;
1325     }
1326
1327     Edit(Action command, SequenceI[] seqs, int position, int number,
1328             AlignmentI al)
1329     {
1330       this.gapChar = al.getGapCharacter();
1331       this.command = command;
1332       this.seqs = seqs;
1333       this.position = position;
1334       this.number = number;
1335       this.al = al;
1336
1337       alIndex = new int[seqs.length];
1338       for (int i = 0; i < seqs.length; i++)
1339       {
1340         alIndex[i] = al.findIndex(seqs[i]);
1341       }
1342
1343       fullAlignmentHeight = (al.getHeight() == seqs.length);
1344     }
1345
1346     Edit(Action command, SequenceI[] seqs, int position, int number,
1347             AlignmentI al, String replace)
1348     {
1349       this.command = command;
1350       this.seqs = seqs;
1351       this.position = position;
1352       this.number = number;
1353       this.al = al;
1354       this.gapChar = al.getGapCharacter();
1355       string = new char[seqs.length][];
1356       for (int i = 0; i < seqs.length; i++)
1357       {
1358         string[i] = replace.toCharArray();
1359       }
1360
1361       fullAlignmentHeight = (al.getHeight() == seqs.length);
1362     }
1363
1364     public SequenceI[] getSequences()
1365     {
1366       return seqs;
1367     }
1368
1369     public int getPosition()
1370     {
1371       return position;
1372     }
1373
1374     public Action getAction()
1375     {
1376       return command;
1377     }
1378
1379     public int getNumber()
1380     {
1381       return number;
1382     }
1383
1384     public char getGapCharacter()
1385     {
1386       return gapChar;
1387     }
1388   }
1389
1390   /**
1391    * Returns an iterator over the list of edit commands which traverses the list
1392    * either forwards or backwards.
1393    *
1394    * @param forwards
1395    * @return
1396    */
1397   public Iterator<Edit> getEditIterator(boolean forwards)
1398   {
1399     if (forwards)
1400     {
1401       return getEdits().iterator();
1402     }
1403     else
1404     {
1405       return new ReverseListIterator<Edit>(getEdits());
1406     }
1407   }
1408 }