src/jalview/commands/EditCommand.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   3  * Copyright (C) 2014 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 java.util.*;
  24
  25 import jalview.datamodel.*;
  26
  27 /**
  28  *
  29  * <p>
  30  * Title: EditCommmand
  31  * </p>
  32  *
  33  * <p>
  34  * Description: Essential information for performing undo and redo for cut/paste
  35  * insert/delete gap which can be stored in the HistoryList
  36  * </p>
  37  *
  38  * <p>
  39  * Copyright: Copyright (c) 2006
  40  * </p>
  41  *
  42  * <p>
  43  * Company: Dundee University
  44  * </p>
  45  *
  46  * @author not attributable
  47  * @version 1.0
  48  */
  49 public class EditCommand implements CommandI
  50 {
  51   public static final int INSERT_GAP = 0;
  52
  53   public static final int DELETE_GAP = 1;
  54
  55   public static final int CUT = 2;
  56
  57   public static final int PASTE = 3;
  58
  59   public static final int REPLACE = 4;
  60
  61   public static final int INSERT_NUC = 5;
  62
  63   Edit[] edits;
  64
  65   String description;
  66
  67   public EditCommand()
  68   {
  69   }
  70
  71   public EditCommand(String description)
  72   {
  73     this.description = description;
  74   }
  75
  76   public EditCommand(String description, int command, SequenceI[] seqs,
  77           int position, int number, AlignmentI al)
  78   {
  79     this.description = description;
  80     if (command == CUT || command == PASTE)
  81     {
  82       edits = new Edit[]
  83       { new Edit(command, seqs, position, number, al) };
  84     }
  85
  86     performEdit(0, null);
  87   }
  88
  89   public EditCommand(String description, int command, String replace,
  90           SequenceI[] seqs, int position, int number, AlignmentI al)
  91   {
  92     this.description = description;
  93     if (command == REPLACE)
  94     {
  95       edits = new Edit[]
  96       { new Edit(command, seqs, position, number, al, replace) };
  97     }
  98
  99     performEdit(0, null);
 100   }
 101
 102   @Override
 103   final public String getDescription()
 104   {
 105     return description;
 106   }
 107
 108   @Override
 109   public int getSize()
 110   {
 111     return edits == null ? 0 : edits.length;
 112   }
 113
 114   final public AlignmentI getAlignment()
 115   {
 116     return edits[0].al;
 117   }
 118
 119   /**
 120    * append a new editCommand Note. this shouldn't be called if the edit is an
 121    * operation affects more alignment objects than the one referenced in al (for
 122    * example, cut or pasting whole sequences). Use the form with an additional
 123    * AlignmentI[] views parameter.
 124    *
 125    * @param command
 126    * @param seqs
 127    * @param position
 128    * @param number
 129    * @param al
 130    * @param performEdit
 131    */
 132   final public void appendEdit(int command, SequenceI[] seqs, int position,
 133           int number, AlignmentI al, boolean performEdit)
 134   {
 135     appendEdit(command, seqs, position, number, al, performEdit, null);
 136   }
 137
 138   /**
 139    * append a new edit command with a set of alignment views that may be
 140    * operated on
 141    *
 142    * @param command
 143    * @param seqs
 144    * @param position
 145    * @param number
 146    * @param al
 147    * @param performEdit
 148    * @param views
 149    */
 150   final public void appendEdit(int command, SequenceI[] seqs, int position,
 151           int number, AlignmentI al, boolean performEdit, AlignmentI[] views)
 152   {
 153     Edit edit = new Edit(command, seqs, position, number,
 154             al.getGapCharacter());
 155     if (al.getHeight() == seqs.length)
 156     {
 157       edit.al = al;
 158       edit.fullAlignmentHeight = true;
 159     }
 160
 161     if (edits != null)
 162     {
 163       Edit[] temp = new Edit[edits.length + 1];
 164       System.arraycopy(edits, 0, temp, 0, edits.length);
 165       edits = temp;
 166       edits[edits.length - 1] = edit;
 167     }
 168     else
 169     {
 170       edits = new Edit[]
 171       { edit };
 172     }
 173
 174     if (performEdit)
 175     {
 176       performEdit(edits.length - 1, views);
 177     }
 178   }
 179
 180   final void performEdit(int commandIndex, AlignmentI[] views)
 181   {
 182     int eSize = edits.length;
 183     for (int e = commandIndex; e < eSize; e++)
 184     {
 185       switch (edits[e].command)
 186       {
 187       case INSERT_GAP:
 188         insertGap(edits[e]);
 189         break;
 190       case DELETE_GAP:
 191         deleteGap(edits[e]);
 192         break;
 193       case CUT:
 194         cut(edits[e], views);
 195         break;
 196       case PASTE:
 197         paste(edits[e], views);
 198         break;
 199       case REPLACE:
 200         replace(edits[e]);
 201         break;
 202       // TODO:add deleteNuc for UNDO
 203       // case INSERT_NUC:
 204       // insertNuc(edits[e]);
 205       // break;
 206       }
 207     }
 208   }
 209
 210   @Override
 211   final public void doCommand(AlignmentI[] views)
 212   {
 213     performEdit(0, views);
 214   }
 215
 216   @Override
 217   final public void undoCommand(AlignmentI[] views)
 218   {
 219     for(Edit e : edits){
 220         switch (e.command)
 221         {
 222         case INSERT_GAP:
 223           deleteGap(e);
 224           break;
 225         case DELETE_GAP:
 226           insertGap(e);
 227           break;
 228         case CUT:
 229           paste(e, views);
 230           break;
 231         case PASTE:
 232           cut(e, views);
 233           break;
 234         case REPLACE:
 235           replace(e);
 236           break;
 237         }
 238     }
 239   }
 240
 241   final void insertGap(Edit command)
 242   {
 243
 244     for (int s = 0; s < command.seqs.length; s++)
 245     {
 246       command.seqs[s].insertCharAt(command.position, command.number,
 247               command.gapChar);
 248       // System.out.println("pos: "+command.position+" number: "+command.number);
 249     }
 250
 251     adjustAnnotations(command, true, false, null);
 252   }
 253
 254   //
 255   // final void insertNuc(Edit command)
 256   // {
 257   //
 258   // for (int s = 0; s < command.seqs.length; s++)
 259   // {
 260   // System.out.println("pos: "+command.position+" number: "+command.number);
 261   // command.seqs[s].insertCharAt(command.position, command.number,'A');
 262   // }
 263   //
 264   // adjustAnnotations(command, true, false, null);
 265   // }
 266
 267   final void deleteGap(Edit command)
 268   {
 269     for (int s = 0; s < command.seqs.length; s++)
 270     {
 271       command.seqs[s].deleteChars(command.position, command.position
 272               + command.number);
 273     }
 274
 275     adjustAnnotations(command, false, false, null);
 276   }
 277
 278   void cut(Edit command, AlignmentI[] views)
 279   {
 280     boolean seqDeleted = false;
 281     command.string = new char[command.seqs.length][];
 282
 283     for (int i = 0; i < command.seqs.length; i++)
 284     {
 285       if (command.seqs[i].getLength() > command.position)
 286       {
 287         command.string[i] = command.seqs[i].getSequence(command.position,
 288                 command.position + command.number);
 289         SequenceI oldds = command.seqs[i].getDatasetSequence();
 290         if (command.oldds != null && command.oldds[i] != null)
 291         {
 292           // we are redoing an undone cut.
 293           command.seqs[i].setDatasetSequence(null);
 294         }
 295         command.seqs[i].deleteChars(command.position, command.position
 296                 + command.number);
 297         if (command.oldds != null && command.oldds[i] != null)
 298         {
 299           // oldds entry contains the cut dataset sequence.
 300           command.seqs[i].setDatasetSequence(command.oldds[i]);
 301           command.oldds[i] = oldds;
 302         }
 303         else
 304         {
 305           // modify the oldds if necessary
 306           if (oldds != command.seqs[i].getDatasetSequence()
 307                   || command.seqs[i].getSequenceFeatures() != null)
 308           {
 309             if (command.oldds == null)
 310             {
 311               command.oldds = new SequenceI[command.seqs.length];
 312             }
 313             command.oldds[i] = oldds;
 314             adjustFeatures(
 315                     command,
 316                     i,
 317                     command.seqs[i].findPosition(command.position),
 318                     command.seqs[i].findPosition(command.position
 319                             + command.number), false);
 320           }
 321         }
 322       }
 323
 324       if (command.seqs[i].getLength() < 1)
 325       {
 326         command.al.deleteSequence(command.seqs[i]);
 327         seqDeleted = true;
 328       }
 329     }
 330
 331     adjustAnnotations(command, false, seqDeleted, views);
 332   }
 333
 334   void paste(Edit command, AlignmentI[] views)
 335   {
 336     StringBuffer tmp;
 337     boolean newDSNeeded;
 338     boolean newDSWasNeeded;
 339     int newstart, newend;
 340     boolean seqWasDeleted = false;
 341     int start = 0, end = 0;
 342
 343     for (int i = 0; i < command.seqs.length; i++)
 344     {
 345       newDSNeeded = false;
 346       newDSWasNeeded = command.oldds != null && command.oldds[i] != null;
 347       if (command.seqs[i].getLength() < 1)
 348       {
 349         // ie this sequence was deleted, we need to
 350         // read it to the alignment
 351         if (command.alIndex[i] < command.al.getHeight())
 352         {
 353           List<SequenceI> sequences;
 354           synchronized (sequences = command.al.getSequences())
 355           {
 356             sequences.add(command.alIndex[i] < 0 ? 0 : command.alIndex[i], command.seqs[i]);
 357           }
 358         }
 359         else
 360         {
 361           command.al.addSequence(command.seqs[i]);
 362         }
 363         seqWasDeleted = true;
 364       }
 365       newstart = command.seqs[i].getStart();
 366       newend = command.seqs[i].getEnd();
 367
 368       tmp = new StringBuffer();
 369       tmp.append(command.seqs[i].getSequence());
 370       // Undo of a delete does not replace original dataset sequence on to
 371       // alignment sequence.
 372
 373       if (command.string != null && command.string[i] != null)
 374       {
 375         if (command.position >= tmp.length())
 376         {
 377           // This occurs if padding is on, and residues
 378           // are removed from end of alignment
 379           int length = command.position - tmp.length();
 380           while (length > 0)
 381           {
 382             tmp.append(command.gapChar);
 383             length--;
 384           }
 385         }
 386         tmp.insert(command.position, command.string[i]);
 387         for (int s = 0; s < command.string[i].length; s++)
 388         {
 389           if (jalview.schemes.ResidueProperties.aaIndex[command.string[i][s]] != 23)
 390           {
 391             if (!newDSNeeded)
 392             {
 393               newDSNeeded = true;
 394               start = command.seqs[i].findPosition(command.position);
 395               end = command.seqs[i].findPosition(command.position
 396                       + command.number);
 397             }
 398             if (command.seqs[i].getStart() == start)
 399               newstart--;
 400             else
 401               newend++;
 402           }
 403         }
 404         command.string[i] = null;
 405       }
 406
 407       command.seqs[i].setSequence(tmp.toString());
 408       command.seqs[i].setStart(newstart);
 409       command.seqs[i].setEnd(newend);
 410       if (newDSNeeded)
 411       {
 412         if (command.seqs[i].getDatasetSequence() != null)
 413         {
 414           SequenceI ds;
 415           if (newDSWasNeeded)
 416           {
 417             ds = command.oldds[i];
 418           }
 419           else
 420           {
 421             // make a new DS sequence
 422             // use new ds mechanism here
 423             ds = new Sequence(command.seqs[i].getName(),
 424                     jalview.analysis.AlignSeq.extractGaps(
 425                             jalview.util.Comparison.GapChars,
 426                             command.seqs[i].getSequenceAsString()),
 427                     command.seqs[i].getStart(), command.seqs[i].getEnd());
 428             ds.setDescription(command.seqs[i].getDescription());
 429           }
 430           if (command.oldds == null)
 431           {
 432             command.oldds = new SequenceI[command.seqs.length];
 433           }
 434           command.oldds[i] = command.seqs[i].getDatasetSequence();
 435           command.seqs[i].setDatasetSequence(ds);
 436         }
 437         adjustFeatures(command, i, start, end, true);
 438       }
 439     }
 440     adjustAnnotations(command, true, seqWasDeleted, views);
 441
 442     command.string = null;
 443   }
 444
 445   void replace(Edit command)
 446   {
 447     StringBuffer tmp;
 448     String oldstring;
 449     int start = command.position;
 450     int end = command.number;
 451     // TODO TUTORIAL - Fix for replacement with different length of sequence (or
 452     // whole sequence)
 453     // TODO Jalview 2.4 bugfix change to an aggregate command - original
 454     // sequence string is cut, new string is pasted in.
 455     command.number = start + command.string[0].length;
 456     for (int i = 0; i < command.seqs.length; i++)
 457     {
 458       boolean newDSWasNeeded = command.oldds != null
 459               && command.oldds[i] != null;
 460
 461       /**
 462        * cut addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT,
 463        * cut, sg.getStartRes(), sg.getEndRes()-sg.getStartRes()+1,
 464        * viewport.alignment));
 465        *
 466        */
 467       /**
 468        * then addHistoryItem(new EditCommand( "Add sequences",
 469        * EditCommand.PASTE, sequences, 0, alignment.getWidth(), alignment) );
 470        *
 471        */
 472       oldstring = command.seqs[i].getSequenceAsString();
 473       tmp = new StringBuffer(oldstring.substring(0, start));
 474       tmp.append(command.string[i]);
 475       String nogaprep = jalview.analysis.AlignSeq.extractGaps(
 476               jalview.util.Comparison.GapChars, new String(
 477                       command.string[i]));
 478       int ipos = command.seqs[i].findPosition(start)
 479               - command.seqs[i].getStart();
 480       tmp.append(oldstring.substring(end));
 481       command.seqs[i].setSequence(tmp.toString());
 482       command.string[i] = oldstring.substring(start, end).toCharArray();
 483       String nogapold = jalview.analysis.AlignSeq.extractGaps(
 484               jalview.util.Comparison.GapChars, new String(
 485                       command.string[i]));
 486       if (!nogaprep.toLowerCase().equals(nogapold.toLowerCase()))
 487       {
 488         if (newDSWasNeeded)
 489         {
 490           SequenceI oldds = command.seqs[i].getDatasetSequence();
 491           command.seqs[i].setDatasetSequence(command.oldds[i]);
 492           command.oldds[i] = oldds;
 493         }
 494         else
 495         {
 496           if (command.oldds == null)
 497           {
 498             command.oldds = new SequenceI[command.seqs.length];
 499           }
 500           command.oldds[i] = command.seqs[i].getDatasetSequence();
 501           SequenceI newds = new Sequence(
 502                   command.seqs[i].getDatasetSequence());
 503           String fullseq, osp = newds.getSequenceAsString();
 504           fullseq = osp.substring(0, ipos) + nogaprep
 505                   + osp.substring(ipos + nogaprep.length());
 506           newds.setSequence(fullseq.toUpperCase());
 507           // TODO: JAL-1131 ensure newly created dataset sequence is added to
 508           // the set of
 509           // dataset sequences associated with the alignment.
 510           // TODO: JAL-1131 fix up any annotation associated with new dataset
 511           // sequence to ensure that original sequence/annotation relationships
 512           // are preserved.
 513           command.seqs[i].setDatasetSequence(newds);
 514
 515         }
 516       }
 517       tmp = null;
 518       oldstring = null;
 519     }
 520   }
 521
 522   final void adjustAnnotations(Edit command, boolean insert,
 523           boolean modifyVisibility, AlignmentI[] views)
 524   {
 525     AlignmentAnnotation[] annotations = null;
 526
 527     if (modifyVisibility && !insert)
 528     {
 529       // only occurs if a sequence was added or deleted.
 530       command.deletedAnnotationRows = new Hashtable();
 531     }
 532     if (command.fullAlignmentHeight)
 533     {
 534       annotations = command.al.getAlignmentAnnotation();
 535     }
 536     else
 537     {
 538       int aSize = 0;
 539       AlignmentAnnotation[] tmp;
 540       for (int s = 0; s < command.seqs.length; s++)
 541       {
 542         if (modifyVisibility)
 543         {
 544           // Rows are only removed or added to sequence object.
 545           if (!insert)
 546           {
 547             // remove rows
 548             tmp = command.seqs[s].getAnnotation();
 549             if (tmp != null)
 550             {
 551               int alen = tmp.length;
 552               for (int aa = 0; aa < tmp.length; aa++)
 553               {
 554                 if (!command.al.deleteAnnotation(tmp[aa]))
 555                 {
 556                   // strip out annotation not in the current al (will be put
 557                   // back on insert in all views)
 558                   tmp[aa] = null;
 559                   alen--;
 560                 }
 561               }
 562               command.seqs[s].setAlignmentAnnotation(null);
 563               if (alen != tmp.length)
 564               {
 565                 // save the non-null annotation references only
 566                 AlignmentAnnotation[] saved = new AlignmentAnnotation[alen];
 567                 for (int aa = 0, aapos = 0; aa < tmp.length; aa++)
 568                 {
 569                   if (tmp[aa] != null)
 570                   {
 571                     saved[aapos++] = tmp[aa];
 572                     tmp[aa] = null;
 573                   }
 574                 }
 575                 tmp = saved;
 576                 command.deletedAnnotationRows.put(command.seqs[s], saved);
 577                 // and then remove any annotation in the other views
 578                 for (int alview = 0; views != null && alview < views.length; alview++)
 579                 {
 580                   if (views[alview] != command.al)
 581                   {
 582                     AlignmentAnnotation[] toremove = views[alview]
 583                             .getAlignmentAnnotation();
 584                     if (toremove == null || toremove.length == 0)
 585                     {
 586                       continue;
 587                     }
 588                     // remove any alignment annotation on this sequence that's
 589                     // on that alignment view.
 590                     for (int aa = 0; aa < toremove.length; aa++)
 591                     {
 592                       if (toremove[aa].sequenceRef == command.seqs[s])
 593                       {
 594                         views[alview].deleteAnnotation(toremove[aa]);
 595                       }
 596                     }
 597                   }
 598                 }
 599               }
 600               else
 601               {
 602                 // save all the annotation
 603                 command.deletedAnnotationRows.put(command.seqs[s], tmp);
 604               }
 605             }
 606           }
 607           else
 608           {
 609             // recover rows
 610             if (command.deletedAnnotationRows != null
 611                     && command.deletedAnnotationRows
 612                             .containsKey(command.seqs[s]))
 613             {
 614               AlignmentAnnotation[] revealed = (AlignmentAnnotation[]) command.deletedAnnotationRows
 615                       .get(command.seqs[s]);
 616               command.seqs[s].setAlignmentAnnotation(revealed);
 617               if (revealed != null)
 618               {
 619                 for (int aa = 0; aa < revealed.length; aa++)
 620                 {
 621                   // iterate through al adding original annotation
 622                   command.al.addAnnotation(revealed[aa]);
 623                 }
 624                 for (int aa = 0; aa < revealed.length; aa++)
 625                 {
 626                   command.al.setAnnotationIndex(revealed[aa], aa);
 627                 }
 628                 // and then duplicate added annotation on every other alignment
 629                 // view
 630                 for (int vnum = 0; views != null && vnum < views.length; vnum++)
 631                 {
 632                   if (views[vnum] != command.al)
 633                   {
 634                     int avwidth = views[vnum].getWidth() + 1;
 635                     // duplicate in this view
 636                     for (int a = 0; a < revealed.length; a++)
 637                     {
 638                       AlignmentAnnotation newann = new AlignmentAnnotation(
 639                               revealed[a]);
 640                       command.seqs[s].addAlignmentAnnotation(newann);
 641                       newann.padAnnotation(avwidth);
 642                       views[vnum].addAnnotation(newann);
 643                       views[vnum].setAnnotationIndex(newann, a);
 644                     }
 645                   }
 646                 }
 647               }
 648             }
 649           }
 650           continue;
 651         }
 652
 653         if (command.seqs[s].getAnnotation() == null)
 654         {
 655           continue;
 656         }
 657
 658         if (aSize == 0)
 659         {
 660           annotations = command.seqs[s].getAnnotation();
 661         }
 662         else
 663         {
 664           tmp = new AlignmentAnnotation[aSize
 665                   + command.seqs[s].getAnnotation().length];
 666
 667           System.arraycopy(annotations, 0, tmp, 0, aSize);
 668
 669           System.arraycopy(command.seqs[s].getAnnotation(), 0, tmp, aSize,
 670                   command.seqs[s].getAnnotation().length);
 671
 672           annotations = tmp;
 673         }
 674         aSize = annotations.length;
 675       }
 676     }
 677
 678     if (annotations == null)
 679     {
 680       return;
 681     }
 682
 683     if (!insert)
 684     {
 685       command.deletedAnnotations = new Hashtable();
 686     }
 687
 688     int aSize;
 689     Annotation[] temp;
 690     for (int a = 0; a < annotations.length; a++)
 691     {
 692       if (annotations[a].autoCalculated
 693               || annotations[a].annotations == null)
 694       {
 695         continue;
 696       }
 697
 698       int tSize = 0;
 699
 700       aSize = annotations[a].annotations.length;
 701       if (insert)
 702       {
 703         temp = new Annotation[aSize + command.number];
 704         if (annotations[a].padGaps)
 705           for (int aa = 0; aa < temp.length; aa++)
 706           {
 707             temp[aa] = new Annotation(command.gapChar + "", null, ' ', 0);
 708           }
 709       }
 710       else
 711       {
 712         if (command.position < aSize)
 713         {
 714           if (command.position + command.number >= aSize)
 715           {
 716             tSize = aSize;
 717           }
 718           else
 719           {
 720             tSize = aSize - command.number;
 721           }
 722         }
 723         else
 724         {
 725           tSize = aSize;
 726         }
 727
 728         if (tSize < 0)
 729         {
 730           tSize = aSize;
 731         }
 732         temp = new Annotation[tSize];
 733       }
 734
 735       if (insert)
 736       {
 737         if (command.position < annotations[a].annotations.length)
 738         {
 739           System.arraycopy(annotations[a].annotations, 0, temp, 0,
 740                   command.position);
 741
 742           if (command.deletedAnnotations != null
 743                   && command.deletedAnnotations
 744                           .containsKey(annotations[a].annotationId))
 745           {
 746             Annotation[] restore = (Annotation[]) command.deletedAnnotations
 747                     .get(annotations[a].annotationId);
 748
 749             System.arraycopy(restore, 0, temp, command.position,
 750                     command.number);
 751
 752           }
 753
 754           System.arraycopy(annotations[a].annotations, command.position,
 755                   temp, command.position + command.number, aSize
 756                           - command.position);
 757         }
 758         else
 759         {
 760           if (command.deletedAnnotations != null
 761                   && command.deletedAnnotations
 762                           .containsKey(annotations[a].annotationId))
 763           {
 764             Annotation[] restore = (Annotation[]) command.deletedAnnotations
 765                     .get(annotations[a].annotationId);
 766
 767             temp = new Annotation[annotations[a].annotations.length
 768                     + restore.length];
 769             System.arraycopy(annotations[a].annotations, 0, temp, 0,
 770                     annotations[a].annotations.length);
 771             System.arraycopy(restore, 0, temp,
 772                     annotations[a].annotations.length, restore.length);
 773           }
 774           else
 775           {
 776             temp = annotations[a].annotations;
 777           }
 778         }
 779       }
 780       else
 781       {
 782         if (tSize != aSize || command.position < 2)
 783         {
 784           int copylen = Math.min(command.position,
 785                   annotations[a].annotations.length);
 786           if (copylen > 0)
 787             System.arraycopy(annotations[a].annotations, 0, temp, 0,
 788                     copylen); // command.position);
 789
 790           Annotation[] deleted = new Annotation[command.number];
 791           if (copylen >= command.position)
 792           {
 793             copylen = Math.min(command.number,
 794                     annotations[a].annotations.length - command.position);
 795             if (copylen > 0)
 796             {
 797               System.arraycopy(annotations[a].annotations,
 798                       command.position, deleted, 0, copylen); // command.number);
 799             }
 800           }
 801
 802           command.deletedAnnotations.put(annotations[a].annotationId,
 803                   deleted);
 804           if (annotations[a].annotations.length > command.position
 805                   + command.number)
 806           {
 807             System.arraycopy(annotations[a].annotations, command.position
 808                     + command.number, temp, command.position,
 809                     annotations[a].annotations.length - command.position
 810                             - command.number); // aSize
 811           }
 812         }
 813         else
 814         {
 815           int dSize = aSize - command.position;
 816
 817           if (dSize > 0)
 818           {
 819             Annotation[] deleted = new Annotation[command.number];
 820             System.arraycopy(annotations[a].annotations, command.position,
 821                     deleted, 0, dSize);
 822
 823             command.deletedAnnotations.put(annotations[a].annotationId,
 824                     deleted);
 825
 826             tSize = Math.min(annotations[a].annotations.length,
 827                     command.position);
 828             temp = new Annotation[tSize];
 829             System.arraycopy(annotations[a].annotations, 0, temp, 0, tSize);
 830           }
 831           else
 832           {
 833             temp = annotations[a].annotations;
 834           }
 835         }
 836       }
 837
 838       annotations[a].annotations = temp;
 839     }
 840   }
 841
 842   final void adjustFeatures(Edit command, int index, int i, int j,
 843           boolean insert)
 844   {
 845     SequenceI seq = command.seqs[index];
 846     SequenceI sequence = seq.getDatasetSequence();
 847     if (sequence == null)
 848     {
 849       sequence = seq;
 850     }
 851
 852     if (insert)
 853     {
 854       if (command.editedFeatures != null
 855               && command.editedFeatures.containsKey(seq))
 856       {
 857         sequence.setSequenceFeatures((SequenceFeature[]) command.editedFeatures
 858                 .get(seq));
 859       }
 860
 861       return;
 862     }
 863
 864     SequenceFeature[] sf = sequence.getSequenceFeatures();
 865
 866     if (sf == null)
 867     {
 868       return;
 869     }
 870
 871     SequenceFeature[] oldsf = new SequenceFeature[sf.length];
 872
 873     int cSize = j - i;
 874
 875     for (int s = 0; s < sf.length; s++)
 876     {
 877       SequenceFeature copy = new SequenceFeature(sf[s]);
 878
 879       oldsf[s] = copy;
 880
 881       if (sf[s].getEnd() < i)
 882       {
 883         continue;
 884       }
 885
 886       if (sf[s].getBegin() > j)
 887       {
 888         sf[s].setBegin(copy.getBegin() - cSize);
 889         sf[s].setEnd(copy.getEnd() - cSize);
 890         continue;
 891       }
 892
 893       if (sf[s].getBegin() >= i)
 894       {
 895         sf[s].setBegin(i);
 896       }
 897
 898       if (sf[s].getEnd() < j)
 899       {
 900         sf[s].setEnd(j - 1);
 901       }
 902
 903       sf[s].setEnd(sf[s].getEnd() - (cSize));
 904
 905       if (sf[s].getBegin() > sf[s].getEnd())
 906       {
 907         sequence.deleteFeature(sf[s]);
 908       }
 909     }
 910
 911     if (command.editedFeatures == null)
 912     {
 913       command.editedFeatures = new Hashtable();
 914     }
 915
 916     command.editedFeatures.put(seq, oldsf);
 917
 918   }
 919
 920   class Edit
 921   {
 922     public SequenceI[] oldds;
 923
 924     boolean fullAlignmentHeight = false;
 925
 926     Hashtable deletedAnnotationRows;
 927
 928     Hashtable deletedAnnotations;
 929
 930     Hashtable editedFeatures;
 931
 932     AlignmentI al;
 933
 934     int command;
 935
 936     char[][] string;
 937
 938     SequenceI[] seqs;
 939
 940     int[] alIndex;
 941
 942     int position, number;
 943
 944     char gapChar;
 945
 946     Edit(int command, SequenceI[] seqs, int position, int number,
 947             char gapChar)
 948     {
 949       this.command = command;
 950       this.seqs = seqs;
 951       this.position = position;
 952       this.number = number;
 953       this.gapChar = gapChar;
 954     }
 955
 956     Edit(int command, SequenceI[] seqs, int position, int number,
 957             AlignmentI al)
 958     {
 959       this.gapChar = al.getGapCharacter();
 960       this.command = command;
 961       this.seqs = seqs;
 962       this.position = position;
 963       this.number = number;
 964       this.al = al;
 965
 966       alIndex = new int[seqs.length];
 967       for (int i = 0; i < seqs.length; i++)
 968       {
 969         alIndex[i] = al.findIndex(seqs[i]);
 970       }
 971
 972       fullAlignmentHeight = (al.getHeight() == seqs.length);
 973     }
 974
 975     Edit(int command, SequenceI[] seqs, int position, int number,
 976             AlignmentI al, String replace)
 977     {
 978       this.command = command;
 979       this.seqs = seqs;
 980       this.position = position;
 981       this.number = number;
 982       this.al = al;
 983       this.gapChar = al.getGapCharacter();
 984       string = new char[seqs.length][];
 985       for (int i = 0; i < seqs.length; i++)
 986       {
 987         string[i] = replace.toCharArray();
 988       }
 989
 990       fullAlignmentHeight = (al.getHeight() == seqs.length);
 991     }
 992   }
 993 }