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
 236     for (int s = 0; s < command.seqs.length; s++)
 237     {
 238       command.seqs[s].insertCharAt(command.position,
 239                                    command.number,
 240                                    command.gapChar);
 241     }
 242
 243     adjustAnnotations(command, true, false, null);
 244   }
 245
 246   final void deleteGap(Edit command)
 247   {
 248     for (int s = 0; s < command.seqs.length; s++)
 249     {
 250       command.seqs[s].deleteChars(command.position,
 251                                   command.position + command.number);
 252     }
 253
 254     adjustAnnotations(command, false, false, null);
 255   }
 256
 257   void cut(Edit command, AlignmentI[] views)
 258   {
 259     boolean seqDeleted=false;
 260     command.string = new char[command.seqs.length][];
 261
 262     for (int i = 0; i < command.seqs.length; i++)
 263     {
 264       if (command.seqs[i].getLength() > command.position)
 265       {
 266         command.string[i] = command.seqs[i].getSequence(command.position,
 267             command.position + command.number);
 268         SequenceI oldds = command.seqs[i].getDatasetSequence();
 269         if (command.oldds!=null && command.oldds[i]!=null)
 270         {
 271           // we are redoing an undone cut.
 272           command.seqs[i].setDatasetSequence(null);
 273         }
 274         command.seqs[i].deleteChars(command.position,
 275                 command.position + command.number);
 276         if (command.oldds!=null && command.oldds[i]!=null)
 277         {
 278           // oldds entry contains the cut dataset sequence.
 279           command.seqs[i].setDatasetSequence(command.oldds[i]);
 280           command.oldds[i] = oldds;
 281         } else {
 282           // modify the oldds if necessary
 283           if (oldds!=command.seqs[i].getDatasetSequence()
 284             || command.seqs[i].getSequenceFeatures() != null)
 285           {
 286             if (command.oldds==null)
 287             {
 288               command.oldds = new SequenceI[command.seqs.length];
 289             }
 290             command.oldds[i] = oldds;
 291             adjustFeatures(command, i,
 292                     command.seqs[i].findPosition(command.position),
 293                     command.seqs[i].findPosition(command.position +
 294                             command.number),
 295                             false);
 296           }
 297         }
 298       }
 299
 300       if (command.seqs[i].getLength() < 1)
 301       {
 302         command.al.deleteSequence(command.seqs[i]);
 303         seqDeleted=true;
 304       }
 305     }
 306
 307     adjustAnnotations(command, false, seqDeleted, views);
 308   }
 309
 310   void paste(Edit command, AlignmentI[] views)
 311   {
 312     StringBuffer tmp;
 313     boolean newDSNeeded;
 314     boolean newDSWasNeeded;
 315     int newstart,newend;
 316     boolean seqWasDeleted=false;
 317     int start = 0, end = 0;
 318
 319     for (int i = 0; i < command.seqs.length; i++)
 320     {
 321       newDSNeeded = false;
 322       newDSWasNeeded = command.oldds!=null && command.oldds[i]!=null;
 323       if (command.seqs[i].getLength() < 1)
 324       {
 325         // ie this sequence was deleted, we need to
 326         // read it to the alignment
 327         if (command.alIndex[i] < command.al.getHeight())
 328         {
 329           command.al.getSequences().insertElementAt(command.seqs[i],
 330               command.alIndex[i]);
 331         }
 332         else
 333         {
 334           command.al.addSequence(command.seqs[i]);
 335         }
 336         seqWasDeleted=true;
 337       }
 338       newstart = command.seqs[i].getStart();
 339       newend = command.seqs[i].getEnd();
 340
 341       tmp = new StringBuffer();
 342       tmp.append(command.seqs[i].getSequence());
 343       //Undo of a delete does not replace original dataset sequence on to alignment sequence.
 344
 345       if (command.string != null && command.string[i] != null)
 346       {
 347         if (command.position >= tmp.length())
 348         {
 349           //This occurs if padding is on, and residues
 350           //are removed from end of alignment
 351           int length = command.position - tmp.length();
 352           while (length > 0)
 353           {
 354             tmp.append(command.gapChar);
 355             length--;
 356           }
 357         }
 358         tmp.insert(command.position, command.string[i]);
 359         for (int s = 0; s < command.string[i].length; s++)
 360         {
 361           if (jalview.schemes.ResidueProperties.aaIndex[command.string[i][s]] !=
 362               23)
 363           {
 364             if (!newDSNeeded)
 365             {
 366               newDSNeeded = true;
 367               start = command.seqs[i].findPosition(command.position);
 368               end = command.seqs[i].findPosition(command.position +
 369                                                command.number);
 370             }
 371             if (command.seqs[i].getStart()==start)
 372               newstart--;
 373             else
 374               newend++;
 375           }
 376         }
 377         command.string[i] = null;
 378       }
 379
 380       command.seqs[i].setSequence(tmp.toString());
 381       command.seqs[i].setStart(newstart);
 382       command.seqs[i].setEnd(newend);
 383       if (newDSNeeded)
 384       {
 385         if (command.seqs[i].getDatasetSequence() != null)
 386         {
 387           SequenceI ds;
 388           if (newDSWasNeeded)
 389           {
 390             ds = command.oldds[i];
 391           } else {
 392             // make a new DS sequence
 393             // use new ds mechanism here
 394             ds= new Sequence(command.seqs[i].getName(),
 395                                      jalview.analysis.AlignSeq.extractGaps(
 396                                          jalview.util.Comparison.GapChars,
 397                                          command.seqs[i].getSequenceAsString()
 398                                      ),
 399                                      command.seqs[i].getStart(),
 400                                      command.seqs[i].getEnd());
 401             ds.setDescription(command.seqs[i].getDescription());
 402           }
 403           if (command.oldds==null)
 404           {
 405             command.oldds = new SequenceI[command.seqs.length];
 406           }
 407           command.oldds[i]=command.seqs[i].getDatasetSequence();
 408           command.seqs[i].setDatasetSequence(ds);
 409         }
 410         adjustFeatures(command, i, start, end, true);
 411       }
 412     }
 413     adjustAnnotations(command, true, seqWasDeleted, views);
 414
 415     command.string = null;
 416   }
 417
 418   void replace(Edit command)
 419   {
 420     StringBuffer tmp;
 421     String oldstring;
 422     int start = command.position;
 423     int end = command.number;
 424     // TODO TUTORIAL - Fix for replacement with different length of sequence (or whole sequence)
 425     // TODO Jalview 2.4 bugfix change to an aggregate command - original sequence string is cut, new string is pasted in.
 426     command.number = start + command.string[0].length;
 427     for (int i = 0; i < command.seqs.length; i++)
 428     {
 429       /**  cut
 430        *     addHistoryItem(new EditCommand("Cut Sequences",
 431                                       EditCommand.CUT,
 432                                       cut,
 433                                       sg.getStartRes(),
 434                                       sg.getEndRes()-sg.getStartRes()+1,
 435                                       viewport.alignment));
 436
 437        */
 438       /** then
 439        *        addHistoryItem(new EditCommand(
 440                "Add sequences",
 441                EditCommand.PASTE,
 442                sequences,
 443                0,
 444                alignment.getWidth(),
 445                alignment)
 446               );
 447
 448        */
 449       oldstring = command.seqs[i].getSequenceAsString();
 450       tmp = new StringBuffer(oldstring.substring(0, start));
 451       tmp.append(command.string[i]);
 452       tmp.append(oldstring.substring(end));
 453       command.seqs[i].setSequence(tmp.toString());
 454       command.string[i] = oldstring.substring(start, end).toCharArray();
 455       tmp = null;
 456       oldstring = null;
 457     }
 458   }
 459
 460   final void adjustAnnotations(Edit command, boolean insert, boolean modifyVisibility, AlignmentI[] views)
 461   {
 462     AlignmentAnnotation[] annotations = null;
 463
 464     if (modifyVisibility && !insert)
 465     {
 466       // only occurs if a sequence was added or deleted.
 467       command.deletedAnnotationRows = new Hashtable();
 468     }
 469     if (command.fullAlignmentHeight)
 470     {
 471       annotations = command.al.getAlignmentAnnotation();
 472     }
 473     else
 474     {
 475       int aSize = 0;
 476       AlignmentAnnotation[] tmp;
 477       for (int s = 0; s < command.seqs.length; s++)
 478       {
 479         if (modifyVisibility)
 480         {
 481           // Rows are only removed or added to sequence object.
 482           if (!insert) {
 483             // remove rows
 484             tmp = command.seqs[s].getAnnotation();
 485             if (tmp!=null) {
 486               int alen=tmp.length;
 487               for (int aa =0; aa<tmp.length; aa++)
 488               {
 489                 if (!command.al.deleteAnnotation(tmp[aa]))
 490                 {
 491                   // strip out annotation not in the current al (will be put back on insert in all views)
 492                   tmp[aa] = null;
 493                   alen--;
 494                 }
 495               }
 496               command.seqs[s].setAlignmentAnnotation(null);
 497               if (alen!=tmp.length)
 498               {
 499                 // save the non-null annotation references only
 500                 AlignmentAnnotation[] saved = new AlignmentAnnotation[alen];
 501                 for (int aa=0,aapos=0;aa<tmp.length;aa++)
 502                 {
 503                   if (tmp[aa]!=null)
 504                   {
 505                     saved[aapos++] = tmp[aa];
 506                     tmp[aa] = null;
 507                   }
 508                 }
 509                 tmp = saved;
 510                 command.deletedAnnotationRows.put(command.seqs[s], saved);
 511                 // and then remove any annotation in the other views
 512                 for (int alview=0; views!=null && alview<views.length; alview++)
 513                 {
 514                   if (views[alview]!=command.al)
 515                   {
 516                     AlignmentAnnotation[] toremove = views[alview].getAlignmentAnnotation();
 517                     if (toremove==null || toremove.length==0)
 518                     {
 519                       continue;
 520                     }
 521                     // remove any alignment annotation on this sequence that's on that alignment view.
 522                     for (int aa = 0; aa<toremove.length; aa++)
 523                     {
 524                       if (toremove[aa].sequenceRef==command.seqs[s])
 525                       {
 526                         views[alview].deleteAnnotation(toremove[aa]);
 527                       }
 528                     }
 529                   }
 530                 }
 531               } else {
 532                 // save all the annotation
 533                 command.deletedAnnotationRows.put(command.seqs[s], tmp);
 534               }
 535             }
 536           } else {
 537             // recover rows
 538             if (command.deletedAnnotationRows!=null && command.deletedAnnotationRows.containsKey(command.seqs[s]))
 539             {
 540               AlignmentAnnotation[] revealed = (AlignmentAnnotation[]) command.deletedAnnotationRows.get(command.seqs[s]);
 541               command.seqs[s].setAlignmentAnnotation(revealed);
 542               if (revealed!=null) {
 543                 for (int aa =0; aa<revealed.length; aa++)
 544                 {
 545                   // iterate through al adding original annotation
 546                   command.al.addAnnotation(revealed[aa]);
 547                 }
 548                 for (int aa =0; aa<revealed.length; aa++)
 549                 {
 550                   command.al.setAnnotationIndex(revealed[aa], aa);
 551                 }
 552                 // and then duplicate added annotation on every other alignment view
 553                 for (int vnum=0; views!=null && vnum<views.length; vnum++)
 554                 {
 555                   if (views[vnum]!=command.al)
 556                   {
 557                     int avwidth = views[vnum].getWidth()+1;
 558                     // duplicate in this view
 559                     for (int a=0; a<revealed.length; a++)
 560                     {
 561                       AlignmentAnnotation newann = new AlignmentAnnotation(revealed[a]);
 562                       command.seqs[s].addAlignmentAnnotation(newann);
 563                       newann.padAnnotation(avwidth);
 564                       views[vnum].addAnnotation(newann);
 565                       views[vnum].setAnnotationIndex(newann, a);
 566                     }
 567                   }
 568                 }
 569               }
 570             }
 571           }
 572           continue;
 573         }
 574
 575         if (command.seqs[s].getAnnotation() == null)
 576         {
 577           continue;
 578         }
 579
 580         if (aSize == 0)
 581         {
 582           annotations = command.seqs[s].getAnnotation();
 583         }
 584         else
 585         {
 586           tmp = new AlignmentAnnotation
 587               [aSize + command.seqs[s].getAnnotation().length];
 588
 589           System.arraycopy(annotations, 0, tmp, 0, aSize);
 590
 591           System.arraycopy(command.seqs[s].getAnnotation(),
 592                            0, tmp, aSize,
 593                            command.seqs[s].getAnnotation().length);
 594
 595           annotations = tmp;
 596         }
 597         aSize = annotations.length;
 598       }
 599     }
 600
 601     if (annotations == null)
 602     {
 603       return;
 604     }
 605
 606     if (!insert)
 607     {
 608       command.deletedAnnotations = new Hashtable();
 609     }
 610
 611     int aSize;
 612     Annotation[] temp;
 613     for (int a = 0; a < annotations.length; a++)
 614     {
 615       if (annotations[a].autoCalculated || annotations[a].annotations == null)
 616       {
 617         continue;
 618       }
 619
 620       int tSize = 0;
 621
 622       aSize = annotations[a].annotations.length;
 623       if (insert)
 624       {
 625         temp = new Annotation[aSize + command.number];
 626         if(annotations[a].padGaps)
 627           for (int aa = 0; aa < temp.length; aa++)
 628           {
 629             temp[aa] = new Annotation(
 630                 command.gapChar+"",
 631                 null, ' ', 0);
 632           }
 633       }
 634       else
 635       {
 636         if (command.position < aSize)
 637         {
 638           if (command.position + command.number >= aSize)
 639           {
 640             tSize = aSize;
 641           }
 642           else
 643           {
 644             tSize = aSize - command.number;
 645           }
 646         }
 647         else
 648         {
 649           tSize = aSize;
 650         }
 651
 652         if (tSize < 0)
 653         {
 654           tSize = aSize;
 655         }
 656         temp = new Annotation[tSize];
 657       }
 658
 659
 660       if (insert)
 661       {
 662         if (command.position < annotations[a].annotations.length)
 663         {
 664           System.arraycopy(annotations[a].annotations,
 665                            0, temp, 0, command.position);
 666
 667           if (command.deletedAnnotations != null
 668               &&
 669               command.deletedAnnotations.containsKey(annotations[a].
 670               annotationId))
 671           {
 672             Annotation[] restore = (Annotation[])
 673                 command.deletedAnnotations.get(annotations[a].annotationId);
 674
 675             System.arraycopy(restore,
 676                              0,
 677                              temp,
 678                              command.position,
 679                              command.number);
 680
 681           }
 682
 683           System.arraycopy(annotations[a].annotations,
 684                            command.position, temp,
 685                            command.position + command.number,
 686                            aSize - command.position);
 687         }
 688         else
 689         {
 690           if (command.deletedAnnotations != null
 691               &&
 692               command.deletedAnnotations.containsKey(annotations[a].
 693               annotationId))
 694           {
 695             Annotation[] restore = (Annotation[])
 696                 command.deletedAnnotations.get(annotations[a].annotationId);
 697
 698             temp = new Annotation[annotations[a].annotations.length +
 699                 restore.length];
 700             System.arraycopy(annotations[a].annotations,
 701                              0, temp, 0,
 702                              annotations[a].annotations.length);
 703             System.arraycopy(restore, 0, temp,
 704                              annotations[a].annotations.length, restore.length);
 705           }
 706           else
 707           {
 708             temp = annotations[a].annotations;
 709           }
 710         }
 711       }
 712       else
 713       {
 714         if (tSize != aSize || command.position < 2)
 715         {
 716           int copylen = Math.min(command.position, annotations[a].annotations.length);
 717           if (copylen>0)
 718             System.arraycopy(annotations[a].annotations,
 719                            0, temp, 0, copylen); //command.position);
 720
 721           Annotation[] deleted = new Annotation[command.number];
 722           if (copylen>=command.position) {
 723             copylen = Math.min(command.number, annotations[a].annotations.length-command.position);
 724             if (copylen>0)
 725             {
 726               System.arraycopy(annotations[a].annotations,
 727                       command.position, deleted, 0, copylen); // command.number);
 728             }
 729           }
 730
 731           command.deletedAnnotations.put(annotations[a].annotationId,
 732                                          deleted);
 733           if (annotations[a].annotations.length>command.position+command.number) {
 734             System.arraycopy(annotations[a].annotations,
 735                            command.position + command.number,
 736                            temp, command.position,
 737                            annotations[a].annotations.length - command.position - command.number); // aSize
 738           }
 739         }
 740         else
 741         {
 742           int dSize = aSize - command.position;
 743
 744           if (dSize > 0)
 745           {
 746             Annotation[] deleted = new Annotation[command.number];
 747             System.arraycopy(annotations[a].annotations,
 748                              command.position, deleted, 0, dSize);
 749
 750             command.deletedAnnotations.put(annotations[a].annotationId,
 751                                            deleted);
 752
 753             tSize = Math.min(annotations[a].annotations.length,
 754                              command.position);
 755             temp = new Annotation[tSize];
 756             System.arraycopy(annotations[a].annotations,
 757                              0, temp, 0, tSize);
 758           }
 759           else
 760           {
 761             temp = annotations[a].annotations;
 762           }
 763         }
 764       }
 765
 766       annotations[a].annotations = temp;
 767     }
 768   }
 769
 770   final void adjustFeatures(Edit command, int index, int i, int j,
 771                             boolean insert)
 772   {
 773     SequenceI seq = command.seqs[index];
 774     SequenceI sequence = seq.getDatasetSequence();
 775     if (sequence == null)
 776     {
 777       sequence = seq;
 778     }
 779
 780     if (insert)
 781     {
 782       if (command.editedFeatures != null
 783           && command.editedFeatures.containsKey(seq))
 784       {
 785         sequence.setSequenceFeatures(
 786             (SequenceFeature[]) command.editedFeatures.get(seq)
 787             );
 788       }
 789
 790       return;
 791     }
 792
 793     SequenceFeature[] sf = sequence.getSequenceFeatures();
 794
 795     if (sf == null)
 796     {
 797       return;
 798     }
 799
 800     SequenceFeature[] oldsf = new SequenceFeature[sf.length];
 801
 802     int cSize = j - i;
 803
 804     for (int s = 0; s < sf.length; s++)
 805     {
 806       SequenceFeature copy = new SequenceFeature(sf[s]);
 807
 808       oldsf[s] = copy;
 809
 810       if (sf[s].getEnd() < i)
 811       {
 812         continue;
 813       }
 814
 815       if (sf[s].getBegin() > j)
 816       {
 817         sf[s].setBegin(copy.getBegin() - cSize);
 818         sf[s].setEnd(copy.getEnd() - cSize);
 819         continue;
 820       }
 821
 822       if (sf[s].getBegin() >= i)
 823       {
 824         sf[s].setBegin(i);
 825       }
 826
 827       if (sf[s].getEnd() < j)
 828       {
 829         sf[s].setEnd(j - 1);
 830       }
 831
 832       sf[s].setEnd(sf[s].getEnd() - (cSize));
 833
 834       if (sf[s].getBegin() > sf[s].getEnd())
 835       {
 836         sequence.deleteFeature(sf[s]);
 837       }
 838     }
 839
 840     if (command.editedFeatures == null)
 841     {
 842       command.editedFeatures = new Hashtable();
 843     }
 844
 845     command.editedFeatures.put(seq, oldsf);
 846
 847   }
 848
 849   class Edit
 850   {
 851     public SequenceI[] oldds;
 852     boolean fullAlignmentHeight = false;
 853     Hashtable deletedAnnotationRows;
 854     Hashtable deletedAnnotations;
 855     Hashtable editedFeatures;
 856     AlignmentI al;
 857     int command;
 858     char[][] string;
 859     SequenceI[] seqs;
 860     int[] alIndex;
 861     int position, number;
 862     char gapChar;
 863
 864     Edit(int command,
 865          SequenceI[] seqs,
 866          int position,
 867          int number,
 868          char gapChar)
 869     {
 870       this.command = command;
 871       this.seqs = seqs;
 872       this.position = position;
 873       this.number = number;
 874       this.gapChar = gapChar;
 875     }
 876
 877     Edit(int command,
 878          SequenceI[] seqs,
 879          int position,
 880          int number,
 881          AlignmentI al)
 882     {
 883       this.gapChar = al.getGapCharacter();
 884       this.command = command;
 885       this.seqs = seqs;
 886       this.position = position;
 887       this.number = number;
 888       this.al = al;
 889
 890       alIndex = new int[seqs.length];
 891       for (int i = 0; i < seqs.length; i++)
 892       {
 893         alIndex[i] = al.findIndex(seqs[i]);
 894       }
 895
 896       fullAlignmentHeight = (al.getHeight() == seqs.length);
 897     }
 898
 899     Edit(int command,
 900          SequenceI[] seqs,
 901          int position,
 902          int number,
 903          AlignmentI al,
 904          String replace)
 905     {
 906       this.command = command;
 907       this.seqs = seqs;
 908       this.position = position;
 909       this.number = number;
 910       this.al = al;
 911       this.gapChar = al.getGapCharacter();
 912       string = new char[seqs.length][];
 913       for (int i = 0; i < seqs.length; i++)
 914       {
 915         string[i] = replace.toCharArray();
 916       }
 917
 918       fullAlignmentHeight = (al.getHeight() == seqs.length);
 919     }
 920   }
 921 }