src/jalview/commands/EditCommand.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer
   3  * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
   4  *
   5  * This program is free software; you can redistribute it and/or
   6  * modify it under the terms of the GNU General Public License
   7  * as published by the Free Software Foundation; either version 2
   8  * of the License, or (at your option) any later version.
   9  *
  10  * This program is distributed in the hope that it will be useful,
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  13  * GNU General Public License for more details.
  14  *
  15  * You should have received a copy of the GNU General Public License
  16  * along with this program; if not, write to the Free Software
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  18  */
  19 package jalview.commands;
  20
  21 import java.util.*;
  22
  23 import jalview.datamodel.*;
  24
  25 /**
  26  *
  27  * <p>Title: EditCommmand</p>
  28  *
  29  * <p>Description: Essential information for performing
  30  * undo and redo for cut/paste insert/delete gap
  31  * which can be stored in the HistoryList </p>
  32  *
  33  * <p>Copyright: Copyright (c) 2006</p>
  34  *
  35  * <p>Company: Dundee University</p>
  36  *
  37  * @author not attributable
  38  * @version 1.0
  39  */
  40 public class EditCommand
  41     implements CommandI
  42 {
  43   public static final int INSERT_GAP = 0;
  44   public static final int DELETE_GAP = 1;
  45   public static final int CUT = 2;
  46   public static final int PASTE = 3;
  47   public static final int REPLACE = 4;
  48
  49   Edit[] edits;
  50
  51   String description;
  52
  53   public EditCommand()
  54   {}
  55
  56   public EditCommand(String description)
  57   {
  58     this.description = description;
  59   }
  60
  61   public EditCommand(String description,
  62                      int command,
  63                      SequenceI[] seqs,
  64                      int position,
  65                      int number,
  66                      AlignmentI al)
  67   {
  68     this.description = description;
  69     if (command == CUT || command == PASTE)
  70     {
  71       edits = new Edit[]
  72           {
  73           new Edit(command, seqs, position, number, al)};
  74     }
  75
  76     performEdit(0, null);
  77   }
  78
  79   public EditCommand(String description,
  80                      int command,
  81                      String replace,
  82                      SequenceI[] seqs,
  83                      int position,
  84                      int number,
  85                      AlignmentI al)
  86   {
  87     this.description = description;
  88     if (command == REPLACE)
  89     {
  90       edits = new Edit[]
  91           { new Edit(command, seqs, position, number, al, replace)};
  92     }
  93
  94     performEdit(0, null);
  95   }
  96
  97   final public String getDescription()
  98   {
  99     return description;
 100   }
 101
 102   public int getSize()
 103   {
 104     return edits == null ? 0 : edits.length;
 105   }
 106
 107   final public AlignmentI getAlignment()
 108   {
 109     return edits[0].al;
 110   }
 111
 112   /**
 113    * append a new editCommand
 114    * Note. this shouldn't be called if the edit is an operation affects more alignment objects than the one referenced
 115    * in al (for example, cut or pasting whole sequences). Use the form with an additional AlignmentI[] views parameter.
 116    * @param command
 117    * @param seqs
 118    * @param position
 119    * @param number
 120    * @param al
 121    * @param performEdit
 122    */
 123   final public void appendEdit(int command,
 124           SequenceI[] seqs,
 125           int position,
 126           int number,
 127           AlignmentI al,
 128           boolean performEdit)
 129   {
 130     appendEdit(command, seqs, position, number, al, performEdit, null);
 131   }
 132   /**
 133    * append a new edit command with a set of alignment views that may be operated on
 134    * @param command
 135    * @param seqs
 136    * @param position
 137    * @param number
 138    * @param al
 139    * @param performEdit
 140    * @param views
 141    */
 142   final public void appendEdit(int command,
 143                                SequenceI[] seqs,
 144                                int position,
 145                                int number,
 146                                AlignmentI al,
 147                                boolean performEdit, AlignmentI[] views)
 148   {
 149     Edit edit = new Edit(command, seqs, position, number, al.getGapCharacter());
 150     if (al.getHeight() == seqs.length)
 151     {
 152       edit.al = al;
 153       edit.fullAlignmentHeight = true;
 154     }
 155
 156     if (edits != null)
 157     {
 158       Edit[] temp = new Edit[edits.length + 1];
 159       System.arraycopy(edits, 0, temp, 0, edits.length);
 160       edits = temp;
 161       edits[edits.length - 1] = edit;
 162     }
 163     else
 164     {
 165       edits = new Edit[]
 166           {
 167           edit};
 168     }
 169
 170     if (performEdit)
 171     {
 172       performEdit(edits.length - 1, views);
 173     }
 174   }
 175
 176   final void performEdit(int commandIndex, AlignmentI[] views)
 177   {
 178     int eSize = edits.length;
 179     for (int e = commandIndex; e < eSize; e++)
 180     {
 181       switch(edits[e].command)
 182       {
 183         case INSERT_GAP:
 184         insertGap(edits[e]);
 185           break;
 186         case DELETE_GAP:
 187         deleteGap(edits[e]);
 188           break;
 189         case CUT:
 190         cut(edits[e], views);
 191           break;
 192         case PASTE:
 193         paste(edits[e], views);
 194           break;
 195         case REPLACE:
 196           replace(edits[e]);
 197           break;
 198       }
 199     }
 200   }
 201
 202   final public void doCommand(AlignmentI[] views)
 203   {
 204     performEdit(0,views);
 205   }
 206
 207   final public void undoCommand(AlignmentI[] views)
 208   {
 209     int e = 0, eSize = edits.length;
 210     for (e = eSize - 1; e > -1; e--)
 211     {
 212       switch (edits[e].command)
 213       {
 214         case INSERT_GAP:
 215         deleteGap(edits[e]);
 216           break;
 217         case DELETE_GAP:
 218         insertGap(edits[e]);
 219           break;
 220         case CUT:
 221         paste(edits[e], views);
 222           break;
 223         case PASTE:
 224         cut(edits[e], views);
 225           break;
 226         case REPLACE:
 227           replace(edits[e]);
 228           break;
 229       }
 230     }
 231   }
 232
 233   final void insertGap(Edit command)
 234   {
 235     for (int s = 0; s < command.seqs.length; s++)
 236     {
 237       command.seqs[s].insertCharAt(command.position,
 238                                    command.number,
 239                                    command.gapChar);
 240     }
 241
 242     adjustAnnotations(command, true, false, null);
 243   }
 244
 245   final void deleteGap(Edit command)
 246   {
 247     for (int s = 0; s < command.seqs.length; s++)
 248     {
 249       command.seqs[s].deleteChars(command.position,
 250                                   command.position + command.number);
 251     }
 252
 253     adjustAnnotations(command, false, false, null);
 254   }
 255
 256   void cut(Edit command, AlignmentI[] views)
 257   {
 258     boolean seqDeleted=false;
 259     command.string = new char[command.seqs.length][];
 260
 261     for (int i = 0; i < command.seqs.length; i++)
 262     {
 263       if (command.seqs[i].getLength() > command.position)
 264       {
 265         command.string[i] = command.seqs[i].getSequence(command.position,
 266             command.position + command.number);
 267
 268         if (command.seqs[i].getDatasetSequence() != null
 269             || command.seqs[i].getSequenceFeatures() != null)
 270         {
 271           for (int s = command.position; s < command.position + command.number;
 272                s++)
 273           {
 274             if (jalview.schemes.ResidueProperties
 275                 .aaIndex[command.seqs[i].getCharAt(s)] != 23)
 276             {
 277               adjustFeatures(command, i,
 278                              command.seqs[i].findPosition(command.position),
 279                              command.seqs[i].findPosition(command.position +
 280                   command.number),
 281                              false);
 282               break;
 283             }
 284           }
 285         }
 286         command.seqs[i].deleteChars(command.position,
 287                                     command.position + command.number);
 288       }
 289
 290       if (command.seqs[i].getLength() < 1)
 291       {
 292         command.al.deleteSequence(command.seqs[i]);
 293         seqDeleted=true;
 294       }
 295     }
 296
 297     adjustAnnotations(command, false, seqDeleted, views);
 298   }
 299
 300   void paste(Edit command, AlignmentI[] views)
 301   {
 302     StringBuffer tmp;
 303     boolean newDSNeeded;
 304     boolean seqWasDeleted=false;
 305     int start = 0, end = 0;
 306
 307     for (int i = 0; i < command.seqs.length; i++)
 308     {
 309       newDSNeeded = false;
 310       if (command.seqs[i].getLength() < 1)
 311       {
 312         // ie this sequence was deleted, we need to
 313         // read it to the alignment
 314         if (command.alIndex[i] < command.al.getHeight())
 315         {
 316           command.al.getSequences().insertElementAt(command.seqs[i],
 317               command.alIndex[i]);
 318         }
 319         else
 320         {
 321           command.al.addSequence(command.seqs[i]);
 322         }
 323         seqWasDeleted=true;
 324       }
 325       tmp = new StringBuffer();
 326       tmp.append(command.seqs[i].getSequence());
 327
 328       if (command.string != null && command.string[i] != null)
 329       {
 330         if (command.position >= tmp.length())
 331         {
 332           //This occurs if padding is on, and residues
 333           //are removed from end of alignment
 334           int length = command.position - tmp.length();
 335           while (length > 0)
 336           {
 337             tmp.append(command.gapChar);
 338             length--;
 339           }
 340         }
 341         tmp.insert(command.position, command.string[i]);
 342
 343         for (int s = 0; s < command.string[i].length; s++)
 344         {
 345           if (jalview.schemes.ResidueProperties.aaIndex[command.string[i][s]] !=
 346               23)
 347           {
 348             newDSNeeded = true;
 349             start = command.seqs[i].findPosition(command.position);
 350             end = command.seqs[i].findPosition(command.position +
 351                                                command.number);
 352             break;
 353           }
 354         }
 355         command.string[i] = null;
 356       }
 357
 358       command.seqs[i].setSequence(tmp.toString());
 359
 360       if (newDSNeeded)
 361       {
 362         if (command.seqs[i].getDatasetSequence() != null)
 363         { // use new ds mechanism here
 364           Sequence ds = new Sequence(command.seqs[i].getName(),
 365                                      jalview.analysis.AlignSeq.extractGaps(
 366                                          jalview.util.Comparison.GapChars,
 367                                          command.seqs[i].getSequenceAsString()
 368                                      ),
 369                                      command.seqs[i].getStart(),
 370                                      command.seqs[i].getEnd());
 371           ds.setDescription(command.seqs[i].getDescription());
 372           command.seqs[i].setDatasetSequence(ds);
 373         }
 374
 375         adjustFeatures(command, i, start, end, true);
 376       }
 377     }
 378     adjustAnnotations(command, true, seqWasDeleted, views);
 379
 380     command.string = null;
 381   }
 382
 383   void replace(Edit command)
 384   {
 385     StringBuffer tmp;
 386     String oldstring;
 387     int start = command.position;
 388     int end = command.number;
 389
 390     command.number = start + command.string[0].length;
 391     for (int i = 0; i < command.seqs.length; i++)
 392     {
 393       oldstring = command.seqs[i].getSequenceAsString();
 394       tmp = new StringBuffer(oldstring.substring(0, start));
 395       tmp.append(command.string[i]);
 396       tmp.append(oldstring.substring(end));
 397       command.seqs[i].setSequence(tmp.toString());
 398       command.string[i] = oldstring.substring(start, end).toCharArray();
 399       tmp = null;
 400       oldstring = null;
 401     }
 402   }
 403
 404   final void adjustAnnotations(Edit command, boolean insert, boolean modifyVisibility, AlignmentI[] views)
 405   {
 406
 407     AlignmentAnnotation[] annotations = null;
 408
 409     if (modifyVisibility && !insert)
 410     {
 411       // only occurs if a sequence was added or deleted.
 412       command.deletedAnnotationRows = new Hashtable();
 413     }
 414     if (command.fullAlignmentHeight)
 415     {
 416       annotations = command.al.getAlignmentAnnotation();
 417     }
 418     else
 419     {
 420       int aSize = 0;
 421       AlignmentAnnotation[] tmp;
 422       for (int s = 0; s < command.seqs.length; s++)
 423       {
 424         if (modifyVisibility)
 425         {
 426           // Rows are only removed or added to sequence object.
 427           if (!insert) {
 428             // remove rows
 429             tmp = command.seqs[s].getAnnotation();
 430             if (tmp!=null) {
 431               int alen=tmp.length;
 432               for (int aa =0; aa<tmp.length; aa++)
 433               {
 434                 if (!command.al.deleteAnnotation(tmp[aa]))
 435                 {
 436                   // strip out annotation not in the current al (will be put back on insert in all views)
 437                   tmp[aa] = null;
 438                   alen--;
 439                 }
 440               }
 441               command.seqs[s].setAlignmentAnnotation(null);
 442               if (alen!=tmp.length)
 443               {
 444                 // save the non-null annotation references only
 445                 AlignmentAnnotation[] saved = new AlignmentAnnotation[alen];
 446                 for (int aa=0,aapos=0;aa<tmp.length;aa++)
 447                 {
 448                   if (tmp[aa]!=null)
 449                   {
 450                     saved[aapos++] = tmp[aa];
 451                     tmp[aa] = null;
 452                   }
 453                 }
 454                 tmp = saved;
 455                 command.deletedAnnotationRows.put(command.seqs[s], saved);
 456                 // and then remove any annotation in the other views
 457                 for (int alview=0; views!=null && alview<views.length; alview++)
 458                 {
 459                   if (views[alview]!=command.al)
 460                   {
 461                     AlignmentAnnotation[] toremove = views[alview].getAlignmentAnnotation();
 462                     if (toremove==null || toremove.length==0)
 463                     {
 464                       continue;
 465                     }
 466                     // remove any alignment annotation on this sequence that's on that alignment view.
 467                     for (int aa = 0; aa<toremove.length; aa++)
 468                     {
 469                       if (toremove[aa].sequenceRef==command.seqs[s])
 470                       {
 471                         views[alview].deleteAnnotation(toremove[aa]);
 472                       }
 473                     }
 474                   }
 475                 }
 476               } else {
 477                 // save all the annotation
 478                 command.deletedAnnotationRows.put(command.seqs[s], tmp);
 479               }
 480             }
 481           } else {
 482             // recover rows
 483             if (command.deletedAnnotationRows!=null && command.deletedAnnotationRows.containsKey(command.seqs[s]))
 484             {
 485               AlignmentAnnotation[] revealed = (AlignmentAnnotation[]) command.deletedAnnotationRows.get(command.seqs[s]);
 486               command.seqs[s].setAlignmentAnnotation(revealed);
 487               if (revealed!=null) {
 488                 for (int aa =0; aa<revealed.length; aa++)
 489                 {
 490                   // iterate through al adding original annotation
 491                   command.al.addAnnotation(revealed[aa]);
 492                 }
 493                 for (int aa =0; aa<revealed.length; aa++)
 494                 {
 495                   command.al.setAnnotationIndex(revealed[aa], aa);
 496                 }
 497                 // and then duplicate added annotation on every other alignment view
 498                 for (int vnum=0; views!=null && vnum<views.length; vnum++)
 499                 {
 500                   if (views[vnum]!=command.al)
 501                   {
 502                     int avwidth = views[vnum].getWidth()+1;
 503                     // duplicate in this view
 504                     for (int a=0; a<revealed.length; a++)
 505                     {
 506                       AlignmentAnnotation newann = new AlignmentAnnotation(revealed[a]);
 507                       command.seqs[s].addAlignmentAnnotation(newann);
 508                       newann.padAnnotation(avwidth);
 509                       views[vnum].addAnnotation(newann);
 510                       views[vnum].setAnnotationIndex(newann, a);
 511                     }
 512                   }
 513                 }
 514               }
 515             }
 516           }
 517           continue;
 518         }
 519
 520         if (command.seqs[s].getAnnotation() == null)
 521         {
 522           continue;
 523         }
 524
 525         if (aSize == 0)
 526         {
 527           annotations = command.seqs[s].getAnnotation();
 528         }
 529         else
 530         {
 531           tmp = new AlignmentAnnotation
 532               [aSize + command.seqs[s].getAnnotation().length];
 533
 534           System.arraycopy(annotations, 0, tmp, 0, aSize);
 535
 536           System.arraycopy(command.seqs[s].getAnnotation(),
 537                            0, tmp, aSize,
 538                            command.seqs[s].getAnnotation().length);
 539
 540           annotations = tmp;
 541         }
 542         aSize = annotations.length;
 543       }
 544     }
 545
 546     if (annotations == null)
 547     {
 548       return;
 549     }
 550
 551     if (!insert)
 552     {
 553       command.deletedAnnotations = new Hashtable();
 554     }
 555
 556     int aSize;
 557     Annotation[] temp;
 558     for (int a = 0; a < annotations.length; a++)
 559     {
 560       if (annotations[a].autoCalculated)
 561       {
 562         continue;
 563       }
 564
 565       int tSize = 0;
 566       if (annotations[a].annotations == null)
 567       {
 568         // nothing to edit here ?
 569         continue;
 570       }
 571       aSize = annotations[a].annotations.length;
 572       if (insert)
 573       {
 574         temp = new Annotation[aSize + command.number];
 575         if(annotations[a].padGaps)
 576           for (int aa = 0; aa < temp.length; aa++)
 577           {
 578             temp[aa] = new Annotation(
 579                 command.gapChar+"",
 580                 null, ' ', 0);
 581           }
 582       }
 583       else
 584       {
 585         if (command.position < aSize)
 586         {
 587           if (command.position + command.number > aSize)
 588           {
 589             tSize = aSize;
 590           }
 591           else
 592           {
 593             tSize = aSize - command.number + command.position;
 594           }
 595         }
 596         else
 597         {
 598           tSize = aSize;
 599         }
 600
 601         if (tSize < 0)
 602         {
 603           tSize = aSize;
 604         }
 605         temp = new Annotation[tSize];
 606
 607       }
 608
 609       if (insert)
 610       {
 611         if (command.position < annotations[a].annotations.length)
 612         {
 613           System.arraycopy(annotations[a].annotations,
 614                            0, temp, 0, command.position);
 615
 616           if (command.deletedAnnotations != null
 617               &&
 618               command.deletedAnnotations.containsKey(annotations[a].
 619               annotationId))
 620           {
 621             Annotation[] restore = (Annotation[])
 622                 command.deletedAnnotations.get(annotations[a].annotationId);
 623
 624             System.arraycopy(restore,
 625                              0,
 626                              temp,
 627                              command.position,
 628                              command.number);
 629
 630           }
 631
 632           System.arraycopy(annotations[a].annotations,
 633                            command.position, temp,
 634                            command.position + command.number,
 635                            aSize - command.position);
 636         }
 637         else
 638         {
 639           if (command.deletedAnnotations != null
 640               &&
 641               command.deletedAnnotations.containsKey(annotations[a].
 642               annotationId))
 643           {
 644             Annotation[] restore = (Annotation[])
 645                 command.deletedAnnotations.get(annotations[a].annotationId);
 646
 647             temp = new Annotation[annotations[a].annotations.length +
 648                 restore.length];
 649             System.arraycopy(annotations[a].annotations,
 650                              0, temp, 0,
 651                              annotations[a].annotations.length);
 652             System.arraycopy(restore, 0, temp,
 653                              annotations[a].annotations.length, restore.length);
 654           }
 655           else
 656           {
 657             temp = annotations[a].annotations;
 658           }
 659         }
 660       }
 661       else
 662       {
 663         if (tSize != aSize || command.position < 2)
 664         {
 665           int copylen = Math.min(command.position, annotations[a].annotations.length);
 666           if (copylen>0)
 667             System.arraycopy(annotations[a].annotations,
 668                            0, temp, 0, copylen); //command.position);
 669
 670           Annotation[] deleted = new Annotation[command.number];
 671           if (copylen>=command.position) {
 672             copylen = Math.min(command.number, annotations[a].annotations.length-command.position);
 673             if (copylen>0)
 674             {
 675               System.arraycopy(annotations[a].annotations,
 676                       command.position, deleted, 0, copylen); // command.number);
 677             }
 678           }
 679
 680           command.deletedAnnotations.put(annotations[a].annotationId,
 681                                          deleted);
 682           if (annotations[a].annotations.length>command.position+command.number) {
 683             System.arraycopy(annotations[a].annotations,
 684                            command.position + command.number,
 685                            temp, command.position,
 686                            annotations[a].annotations.length - command.position - command.number); // aSize
 687           }
 688         }
 689         else
 690         {
 691           int dSize = aSize - command.position;
 692
 693           if (dSize > 0)
 694           {
 695             Annotation[] deleted = new Annotation[command.number];
 696             System.arraycopy(annotations[a].annotations,
 697                              command.position, deleted, 0, dSize);
 698
 699             command.deletedAnnotations.put(annotations[a].annotationId,
 700                                            deleted);
 701
 702             tSize = Math.min(annotations[a].annotations.length,
 703                              command.position);
 704             temp = new Annotation[tSize];
 705             System.arraycopy(annotations[a].annotations,
 706                              0, temp, 0, tSize);
 707           }
 708           else
 709           {
 710             temp = annotations[a].annotations;
 711           }
 712         }
 713       }
 714
 715       annotations[a].annotations = temp;
 716     }
 717   }
 718
 719   final void adjustFeatures(Edit command, int index, int i, int j,
 720                             boolean insert)
 721   {
 722     SequenceI seq = command.seqs[index];
 723     SequenceI sequence = seq.getDatasetSequence();
 724     if (sequence == null)
 725     {
 726       sequence = seq;
 727     }
 728
 729     if (insert)
 730     {
 731       if (command.editedFeatures != null
 732           && command.editedFeatures.containsKey(seq))
 733       {
 734         sequence.setSequenceFeatures(
 735             (SequenceFeature[]) command.editedFeatures.get(seq)
 736             );
 737       }
 738
 739       return;
 740     }
 741
 742     SequenceFeature[] sf = sequence.getSequenceFeatures();
 743
 744     if (sf == null)
 745     {
 746       return;
 747     }
 748
 749     SequenceFeature[] oldsf = new SequenceFeature[sf.length];
 750
 751     int cSize = j - i;
 752
 753     for (int s = 0; s < sf.length; s++)
 754     {
 755       SequenceFeature copy = new SequenceFeature(sf[s]);
 756
 757       oldsf[s] = copy;
 758
 759       if (sf[s].getEnd() < i)
 760       {
 761         continue;
 762       }
 763
 764       if (sf[s].getBegin() > j)
 765       {
 766         sf[s].setBegin(copy.getBegin() - cSize);
 767         sf[s].setEnd(copy.getEnd() - cSize);
 768         continue;
 769       }
 770
 771       if (sf[s].getBegin() >= i)
 772       {
 773         sf[s].setBegin(i);
 774       }
 775
 776       if (sf[s].getEnd() < j)
 777       {
 778         sf[s].setEnd(j - 1);
 779       }
 780
 781       sf[s].setEnd(sf[s].getEnd() - (cSize));
 782
 783       if (sf[s].getBegin() > sf[s].getEnd())
 784       {
 785         sequence.deleteFeature(sf[s]);
 786       }
 787     }
 788
 789     if (command.editedFeatures == null)
 790     {
 791       command.editedFeatures = new Hashtable();
 792     }
 793
 794     command.editedFeatures.put(seq, oldsf);
 795
 796   }
 797
 798   class Edit
 799   {
 800     boolean fullAlignmentHeight = false;
 801     Hashtable deletedAnnotationRows;
 802     Hashtable deletedAnnotations;
 803     Hashtable editedFeatures;
 804     AlignmentI al;
 805     int command;
 806     char[][] string;
 807     SequenceI[] seqs;
 808     int[] alIndex;
 809     int position, number;
 810     char gapChar;
 811
 812     Edit(int command,
 813          SequenceI[] seqs,
 814          int position,
 815          int number,
 816          char gapChar)
 817     {
 818       this.command = command;
 819       this.seqs = seqs;
 820       this.position = position;
 821       this.number = number;
 822       this.gapChar = gapChar;
 823     }
 824
 825     Edit(int command,
 826          SequenceI[] seqs,
 827          int position,
 828          int number,
 829          AlignmentI al)
 830     {
 831       this.gapChar = al.getGapCharacter();
 832       this.command = command;
 833       this.seqs = seqs;
 834       this.position = position;
 835       this.number = number;
 836       this.al = al;
 837
 838       alIndex = new int[seqs.length];
 839       for (int i = 0; i < seqs.length; i++)
 840       {
 841         alIndex[i] = al.findIndex(seqs[i]);
 842       }
 843
 844       fullAlignmentHeight = (al.getHeight() == seqs.length);
 845     }
 846
 847     Edit(int command,
 848          SequenceI[] seqs,
 849          int position,
 850          int number,
 851          AlignmentI al,
 852          String replace)
 853     {
 854       this.command = command;
 855       this.seqs = seqs;
 856       this.position = position;
 857       this.number = number;
 858       this.al = al;
 859       this.gapChar = al.getGapCharacter();
 860       string = new char[seqs.length][];
 861       for (int i = 0; i < seqs.length; i++)
 862       {
 863         string[i] = replace.toCharArray();
 864       }
 865
 866       fullAlignmentHeight = (al.getHeight() == seqs.length);
 867     }
 868   }
 869 }