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 jalview.datamodel.AlignmentAnnotation;
  24 import jalview.datamodel.AlignmentI;
  25 import jalview.datamodel.Annotation;
  26 import jalview.datamodel.Sequence;
  27 import jalview.datamodel.SequenceFeature;
  28 import jalview.datamodel.SequenceI;
  29
  30 import java.util.ArrayList;
  31 import java.util.Hashtable;
  32 import java.util.List;
  33 import java.util.ListIterator;
  34
  35 /**
  36  *
  37  * <p>
  38  * Title: EditCommmand
  39  * </p>
  40  *
  41  * <p>
  42  * Description: Essential information for performing undo and redo for cut/paste
  43  * insert/delete gap which can be stored in the HistoryList
  44  * </p>
  45  *
  46  * <p>
  47  * Copyright: Copyright (c) 2006
  48  * </p>
  49  *
  50  * <p>
  51  * Company: Dundee University
  52  * </p>
  53  *
  54  * @author not attributable
  55  * @version 1.0
  56  */
  57 public class EditCommand implements CommandI
  58 {
  59   public enum Action
  60   {
  61     INSERT_GAP, DELETE_GAP, CUT, PASTE, REPLACE, INSERT_NUC
  62   };
  63
  64   private List<Edit> edits = new ArrayList<Edit>();
  65
  66   String description;
  67
  68   public EditCommand()
  69   {
  70   }
  71
  72   public EditCommand(String description)
  73   {
  74     this.description = description;
  75   }
  76
  77   public EditCommand(String description, Action command, SequenceI[] seqs,
  78           int position, int number, AlignmentI al)
  79   {
  80     this.description = description;
  81     if (command == Action.CUT || command == Action.PASTE)
  82     {
  83       setEdit(new Edit(command, seqs, position, number, al));
  84     }
  85
  86     performEdit(0, null);
  87   }
  88
  89   public EditCommand(String description, Action command, String replace,
  90           SequenceI[] seqs, int position, int number, AlignmentI al)
  91   {
  92     this.description = description;
  93     if (command == Action.REPLACE)
  94     {
  95       setEdit(new Edit(command, seqs, position, number, al, replace));
  96     }
  97
  98     performEdit(0, null);
  99   }
 100
 101   /**
 102    * Set the list of edits to the specified item (only).
 103    *
 104    * @param e
 105    */
 106   protected void setEdit(Edit e)
 107   {
 108     edits.clear();
 109     edits.add(e);
 110   }
 111
 112   /**
 113    * Add the given edit command to the stored list of commands.
 114    *
 115    * @param e
 116    */
 117   protected void addEdit(Edit e)
 118   {
 119     edits.add(e);
 120   }
 121
 122   /**
 123    * Clear the list of stored edit commands.
 124    *
 125    */
 126   protected void clearEdits()
 127   {
 128     edits.clear();
 129   }
 130
 131   /**
 132    * Returns the i'th stored Edit command.
 133    *
 134    * @param i
 135    * @return
 136    */
 137   protected Edit getEdit(int i)
 138   {
 139     if (i >= 0 && i < edits.size())
 140     {
 141       return edits.get(i);
 142     }
 143     return null;
 144   }
 145
 146   @Override
 147   final public String getDescription()
 148   {
 149     return description;
 150   }
 151
 152   @Override
 153   public int getSize()
 154   {
 155     return edits.size();
 156   }
 157
 158   /**
 159    * Return the alignment for the first edit (or null if no edit).
 160    *
 161    * @return
 162    */
 163   final public AlignmentI getAlignment()
 164   {
 165     return (edits.isEmpty() ? null : edits.get(0).al);
 166   }
 167
 168   /**
 169    * append a new editCommand Note. this shouldn't be called if the edit is an
 170    * operation affects more alignment objects than the one referenced in al (for
 171    * example, cut or pasting whole sequences). Use the form with an additional
 172    * AlignmentI[] views parameter.
 173    *
 174    * @param command
 175    * @param seqs
 176    * @param position
 177    * @param number
 178    * @param al
 179    * @param performEdit
 180    */
 181   final public void appendEdit(Action command, SequenceI[] seqs,
 182           int position,
 183           int number, AlignmentI al, boolean performEdit)
 184   {
 185     appendEdit(command, seqs, position, number, al, performEdit, null);
 186   }
 187
 188   /**
 189    * append a new edit command with a set of alignment views that may be
 190    * operated on
 191    *
 192    * @param command
 193    * @param seqs
 194    * @param position
 195    * @param number
 196    * @param al
 197    * @param performEdit
 198    * @param views
 199    */
 200   final public void appendEdit(Action command, SequenceI[] seqs,
 201           int position,
 202           int number, AlignmentI al, boolean performEdit, AlignmentI[] views)
 203   {
 204     Edit edit = new Edit(command, seqs, position, number,
 205             al.getGapCharacter());
 206     if (al.getHeight() == seqs.length)
 207     {
 208       edit.al = al;
 209       edit.fullAlignmentHeight = true;
 210     }
 211
 212     edits.add(edit);
 213
 214     if (performEdit)
 215     {
 216       performEdit(edit, views);
 217     }
 218   }
 219
 220   /**
 221    * Execute all the edit commands, starting at the given commandIndex
 222    *
 223    * @param commandIndex
 224    * @param views
 225    */
 226   final void performEdit(int commandIndex, AlignmentI[] views)
 227   {
 228     ListIterator<Edit> iterator = edits.listIterator(commandIndex);
 229     while (iterator.hasNext())
 230     {
 231       Edit edit = iterator.next();
 232       performEdit(edit, views);
 233     }
 234   }
 235
 236   /**
 237    * Execute one edit command in all the specified alignment views
 238    *
 239    * @param edit
 240    * @param views
 241    */
 242   protected void performEdit(Edit edit, AlignmentI[] views)
 243   {
 244     switch (edit.command)
 245     {
 246     case INSERT_GAP:
 247       insertGap(edit);
 248       break;
 249     case DELETE_GAP:
 250       deleteGap(edit);
 251       break;
 252     case CUT:
 253       cut(edit, views);
 254       break;
 255     case PASTE:
 256       paste(edit, views);
 257       break;
 258     case REPLACE:
 259       replace(edit);
 260       break;
 261     case INSERT_NUC:
 262       // TODO:add deleteNuc for UNDO
 263       // case INSERT_NUC:
 264       // insertNuc(edits[e]);
 265       break;
 266     default:
 267       break;
 268     }
 269   }
 270
 271   @Override
 272   final public void doCommand(AlignmentI[] views)
 273   {
 274     performEdit(0, views);
 275   }
 276
 277   /**
 278    * Undo the stored list of commands, in reverse order.
 279    */
 280   @Override
 281   final public void undoCommand(AlignmentI[] views)
 282   {
 283     ListIterator<Edit> iterator = edits.listIterator(edits.size());
 284     while (iterator.hasPrevious())
 285     {
 286       Edit e = iterator.previous();
 287       switch (e.command)
 288       {
 289       case INSERT_GAP:
 290         deleteGap(e);
 291         break;
 292       case DELETE_GAP:
 293         insertGap(e);
 294         break;
 295       case CUT:
 296         paste(e, views);
 297         break;
 298       case PASTE:
 299         cut(e, views);
 300         break;
 301       case REPLACE:
 302         replace(e);
 303         break;
 304       case INSERT_NUC:
 305         // not implemented
 306         break;
 307       default:
 308         break;
 309       }
 310     }
 311   }
 312
 313   /**
 314    * Insert gap(s) in sequences as specified by the command, and adjust
 315    * annotations.
 316    *
 317    * @param command
 318    */
 319   final private void insertGap(Edit command)
 320   {
 321
 322     for (int s = 0; s < command.seqs.length; s++)
 323     {
 324       command.seqs[s].insertCharAt(command.position, command.number,
 325               command.gapChar);
 326       // System.out.println("pos: "+command.position+" number: "+command.number);
 327     }
 328
 329     adjustAnnotations(command, true, false, null);
 330   }
 331
 332   //
 333   // final void insertNuc(Edit command)
 334   // {
 335   //
 336   // for (int s = 0; s < command.seqs.length; s++)
 337   // {
 338   // System.out.println("pos: "+command.position+" number: "+command.number);
 339   // command.seqs[s].insertCharAt(command.position, command.number,'A');
 340   // }
 341   //
 342   // adjustAnnotations(command, true, false, null);
 343   // }
 344
 345   /**
 346    * Delete gap(s) in sequences as specified by the command, and adjust
 347    * annotations.
 348    *
 349    * @param command
 350    */
 351   final private void deleteGap(Edit command)
 352   {
 353     for (int s = 0; s < command.seqs.length; s++)
 354     {
 355       command.seqs[s].deleteChars(command.position, command.position
 356               + command.number);
 357     }
 358
 359     adjustAnnotations(command, false, false, null);
 360   }
 361
 362   /**
 363    * Carry out a Cut action. The cut characters are saved in case Undo is
 364    * requested.
 365    *
 366    * @param command
 367    * @param views
 368    */
 369   void cut(Edit command, AlignmentI[] views)
 370   {
 371     boolean seqDeleted = false;
 372     command.string = new char[command.seqs.length][];
 373
 374     for (int i = 0; i < command.seqs.length; i++)
 375     {
 376       final SequenceI sequence = command.seqs[i];
 377       if (sequence.getLength() > command.position)
 378       {
 379         command.string[i] = sequence.getSequence(command.position,
 380                 command.position + command.number);
 381         SequenceI oldds = sequence.getDatasetSequence();
 382         if (command.oldds != null && command.oldds[i] != null)
 383         {
 384           // we are redoing an undone cut.
 385           sequence.setDatasetSequence(null);
 386         }
 387         sequence.deleteChars(command.position, command.position
 388                 + command.number);
 389         if (command.oldds != null && command.oldds[i] != null)
 390         {
 391           // oldds entry contains the cut dataset sequence.
 392           sequence.setDatasetSequence(command.oldds[i]);
 393           command.oldds[i] = oldds;
 394         }
 395         else
 396         {
 397           // modify the oldds if necessary
 398           if (oldds != sequence.getDatasetSequence()
 399                   || sequence.getSequenceFeatures() != null)
 400           {
 401             if (command.oldds == null)
 402             {
 403               command.oldds = new SequenceI[command.seqs.length];
 404             }
 405             command.oldds[i] = oldds;
 406             adjustFeatures(
 407                     command,
 408                     i,
 409                     sequence.findPosition(command.position),
 410                     sequence.findPosition(command.position
 411                             + command.number), false);
 412           }
 413         }
 414       }
 415
 416       if (sequence.getLength() < 1)
 417       {
 418         command.al.deleteSequence(sequence);
 419         seqDeleted = true;
 420       }
 421     }
 422
 423     adjustAnnotations(command, false, seqDeleted, views);
 424   }
 425
 426   /**
 427    * Perform the given Paste command. This may be to add cut or copied sequences
 428    * to an alignment, or to undo a 'Cut' action on a region of the alignment.
 429    *
 430    * @param command
 431    * @param views
 432    */
 433   void paste(Edit command, AlignmentI[] views)
 434   {
 435     StringBuffer tmp;
 436     boolean newDSNeeded;
 437     boolean newDSWasNeeded;
 438     int newstart, newend;
 439     boolean seqWasDeleted = false;
 440     int start = 0, end = 0;
 441
 442     for (int i = 0; i < command.seqs.length; i++)
 443     {
 444       newDSNeeded = false;
 445       newDSWasNeeded = command.oldds != null && command.oldds[i] != null;
 446       if (command.seqs[i].getLength() < 1)
 447       {
 448         // ie this sequence was deleted, we need to
 449         // read it to the alignment
 450         if (command.alIndex[i] < command.al.getHeight())
 451         {
 452           List<SequenceI> sequences;
 453           synchronized (sequences = command.al.getSequences())
 454           {
 455             if (!(command.alIndex[i] < 0))
 456             {
 457               sequences.add(command.alIndex[i], command.seqs[i]);
 458             }
 459           }
 460         }
 461         else
 462         {
 463           command.al.addSequence(command.seqs[i]);
 464         }
 465         seqWasDeleted = true;
 466       }
 467       newstart = command.seqs[i].getStart();
 468       newend = command.seqs[i].getEnd();
 469
 470       tmp = new StringBuffer();
 471       tmp.append(command.seqs[i].getSequence());
 472       // Undo of a delete does not replace original dataset sequence on to
 473       // alignment sequence.
 474
 475       if (command.string != null && command.string[i] != null)
 476       {
 477         if (command.position >= tmp.length())
 478         {
 479           // This occurs if padding is on, and residues
 480           // are removed from end of alignment
 481           int length = command.position - tmp.length();
 482           while (length > 0)
 483           {
 484             tmp.append(command.gapChar);
 485             length--;
 486           }
 487         }
 488         tmp.insert(command.position, command.string[i]);
 489         for (int s = 0; s < command.string[i].length; s++)
 490         {
 491           if (jalview.schemes.ResidueProperties.aaIndex[command.string[i][s]] != 23)
 492           {
 493             if (!newDSNeeded)
 494             {
 495               newDSNeeded = true;
 496               start = command.seqs[i].findPosition(command.position);
 497               end = command.seqs[i].findPosition(command.position
 498                       + command.number);
 499             }
 500             if (command.seqs[i].getStart() == start)
 501             {
 502               newstart--;
 503             }
 504             else
 505             {
 506               newend++;
 507             }
 508           }
 509         }
 510         command.string[i] = null;
 511       }
 512
 513       command.seqs[i].setSequence(tmp.toString());
 514       command.seqs[i].setStart(newstart);
 515       command.seqs[i].setEnd(newend);
 516       if (newDSNeeded)
 517       {
 518         if (command.seqs[i].getDatasetSequence() != null)
 519         {
 520           SequenceI ds;
 521           if (newDSWasNeeded)
 522           {
 523             ds = command.oldds[i];
 524           }
 525           else
 526           {
 527             // make a new DS sequence
 528             // use new ds mechanism here
 529             ds = new Sequence(command.seqs[i].getName(),
 530                     jalview.analysis.AlignSeq.extractGaps(
 531                             jalview.util.Comparison.GapChars,
 532                             command.seqs[i].getSequenceAsString()),
 533                     command.seqs[i].getStart(), command.seqs[i].getEnd());
 534             ds.setDescription(command.seqs[i].getDescription());
 535           }
 536           if (command.oldds == null)
 537           {
 538             command.oldds = new SequenceI[command.seqs.length];
 539           }
 540           command.oldds[i] = command.seqs[i].getDatasetSequence();
 541           command.seqs[i].setDatasetSequence(ds);
 542         }
 543         adjustFeatures(command, i, start, end, true);
 544       }
 545     }
 546     adjustAnnotations(command, true, seqWasDeleted, views);
 547
 548     command.string = null;
 549   }
 550
 551   void replace(Edit command)
 552   {
 553     StringBuffer tmp;
 554     String oldstring;
 555     int start = command.position;
 556     int end = command.number;
 557     // TODO TUTORIAL - Fix for replacement with different length of sequence (or
 558     // whole sequence)
 559     // TODO Jalview 2.4 bugfix change to an aggregate command - original
 560     // sequence string is cut, new string is pasted in.
 561     command.number = start + command.string[0].length;
 562     for (int i = 0; i < command.seqs.length; i++)
 563     {
 564       boolean newDSWasNeeded = command.oldds != null
 565               && command.oldds[i] != null;
 566
 567       /**
 568        * cut addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT,
 569        * cut, sg.getStartRes(), sg.getEndRes()-sg.getStartRes()+1,
 570        * viewport.alignment));
 571        *
 572        */
 573       /**
 574        * then addHistoryItem(new EditCommand( "Add sequences",
 575        * EditCommand.PASTE, sequences, 0, alignment.getWidth(), alignment) );
 576        *
 577        */
 578       oldstring = command.seqs[i].getSequenceAsString();
 579       tmp = new StringBuffer(oldstring.substring(0, start));
 580       tmp.append(command.string[i]);
 581       String nogaprep = jalview.analysis.AlignSeq.extractGaps(
 582               jalview.util.Comparison.GapChars, new String(
 583                       command.string[i]));
 584       int ipos = command.seqs[i].findPosition(start)
 585               - command.seqs[i].getStart();
 586       tmp.append(oldstring.substring(end));
 587       command.seqs[i].setSequence(tmp.toString());
 588       command.string[i] = oldstring.substring(start, end).toCharArray();
 589       String nogapold = jalview.analysis.AlignSeq.extractGaps(
 590               jalview.util.Comparison.GapChars, new String(
 591                       command.string[i]));
 592       if (!nogaprep.toLowerCase().equals(nogapold.toLowerCase()))
 593       {
 594         if (newDSWasNeeded)
 595         {
 596           SequenceI oldds = command.seqs[i].getDatasetSequence();
 597           command.seqs[i].setDatasetSequence(command.oldds[i]);
 598           command.oldds[i] = oldds;
 599         }
 600         else
 601         {
 602           if (command.oldds == null)
 603           {
 604             command.oldds = new SequenceI[command.seqs.length];
 605           }
 606           command.oldds[i] = command.seqs[i].getDatasetSequence();
 607           SequenceI newds = new Sequence(
 608                   command.seqs[i].getDatasetSequence());
 609           String fullseq, osp = newds.getSequenceAsString();
 610           fullseq = osp.substring(0, ipos) + nogaprep
 611                   + osp.substring(ipos + nogaprep.length());
 612           newds.setSequence(fullseq.toUpperCase());
 613           // TODO: JAL-1131 ensure newly created dataset sequence is added to
 614           // the set of
 615           // dataset sequences associated with the alignment.
 616           // TODO: JAL-1131 fix up any annotation associated with new dataset
 617           // sequence to ensure that original sequence/annotation relationships
 618           // are preserved.
 619           command.seqs[i].setDatasetSequence(newds);
 620
 621         }
 622       }
 623       tmp = null;
 624       oldstring = null;
 625     }
 626   }
 627
 628   final void adjustAnnotations(Edit command, boolean insert,
 629           boolean modifyVisibility, AlignmentI[] views)
 630   {
 631     AlignmentAnnotation[] annotations = null;
 632
 633     if (modifyVisibility && !insert)
 634     {
 635       // only occurs if a sequence was added or deleted.
 636       command.deletedAnnotationRows = new Hashtable<SequenceI, AlignmentAnnotation[]>();
 637     }
 638     if (command.fullAlignmentHeight)
 639     {
 640       annotations = command.al.getAlignmentAnnotation();
 641     }
 642     else
 643     {
 644       int aSize = 0;
 645       AlignmentAnnotation[] tmp;
 646       for (int s = 0; s < command.seqs.length; s++)
 647       {
 648         if (modifyVisibility)
 649         {
 650           // Rows are only removed or added to sequence object.
 651           if (!insert)
 652           {
 653             // remove rows
 654             tmp = command.seqs[s].getAnnotation();
 655             if (tmp != null)
 656             {
 657               int alen = tmp.length;
 658               for (int aa = 0; aa < tmp.length; aa++)
 659               {
 660                 if (!command.al.deleteAnnotation(tmp[aa]))
 661                 {
 662                   // strip out annotation not in the current al (will be put
 663                   // back on insert in all views)
 664                   tmp[aa] = null;
 665                   alen--;
 666                 }
 667               }
 668               command.seqs[s].setAlignmentAnnotation(null);
 669               if (alen != tmp.length)
 670               {
 671                 // save the non-null annotation references only
 672                 AlignmentAnnotation[] saved = new AlignmentAnnotation[alen];
 673                 for (int aa = 0, aapos = 0; aa < tmp.length; aa++)
 674                 {
 675                   if (tmp[aa] != null)
 676                   {
 677                     saved[aapos++] = tmp[aa];
 678                     tmp[aa] = null;
 679                   }
 680                 }
 681                 tmp = saved;
 682                 command.deletedAnnotationRows.put(command.seqs[s], saved);
 683                 // and then remove any annotation in the other views
 684                 for (int alview = 0; views != null && alview < views.length; alview++)
 685                 {
 686                   if (views[alview] != command.al)
 687                   {
 688                     AlignmentAnnotation[] toremove = views[alview]
 689                             .getAlignmentAnnotation();
 690                     if (toremove == null || toremove.length == 0)
 691                     {
 692                       continue;
 693                     }
 694                     // remove any alignment annotation on this sequence that's
 695                     // on that alignment view.
 696                     for (int aa = 0; aa < toremove.length; aa++)
 697                     {
 698                       if (toremove[aa].sequenceRef == command.seqs[s])
 699                       {
 700                         views[alview].deleteAnnotation(toremove[aa]);
 701                       }
 702                     }
 703                   }
 704                 }
 705               }
 706               else
 707               {
 708                 // save all the annotation
 709                 command.deletedAnnotationRows.put(command.seqs[s], tmp);
 710               }
 711             }
 712           }
 713           else
 714           {
 715             // recover rows
 716             if (command.deletedAnnotationRows != null
 717                     && command.deletedAnnotationRows
 718                             .containsKey(command.seqs[s]))
 719             {
 720               AlignmentAnnotation[] revealed = command.deletedAnnotationRows
 721                       .get(command.seqs[s]);
 722               command.seqs[s].setAlignmentAnnotation(revealed);
 723               if (revealed != null)
 724               {
 725                 for (int aa = 0; aa < revealed.length; aa++)
 726                 {
 727                   // iterate through al adding original annotation
 728                   command.al.addAnnotation(revealed[aa]);
 729                 }
 730                 for (int aa = 0; aa < revealed.length; aa++)
 731                 {
 732                   command.al.setAnnotationIndex(revealed[aa], aa);
 733                 }
 734                 // and then duplicate added annotation on every other alignment
 735                 // view
 736                 for (int vnum = 0; views != null && vnum < views.length; vnum++)
 737                 {
 738                   if (views[vnum] != command.al)
 739                   {
 740                     int avwidth = views[vnum].getWidth() + 1;
 741                     // duplicate in this view
 742                     for (int a = 0; a < revealed.length; a++)
 743                     {
 744                       AlignmentAnnotation newann = new AlignmentAnnotation(
 745                               revealed[a]);
 746                       command.seqs[s].addAlignmentAnnotation(newann);
 747                       newann.padAnnotation(avwidth);
 748                       views[vnum].addAnnotation(newann);
 749                       views[vnum].setAnnotationIndex(newann, a);
 750                     }
 751                   }
 752                 }
 753               }
 754             }
 755           }
 756           continue;
 757         }
 758
 759         if (command.seqs[s].getAnnotation() == null)
 760         {
 761           continue;
 762         }
 763
 764         if (aSize == 0)
 765         {
 766           annotations = command.seqs[s].getAnnotation();
 767         }
 768         else
 769         {
 770           tmp = new AlignmentAnnotation[aSize
 771                   + command.seqs[s].getAnnotation().length];
 772
 773           System.arraycopy(annotations, 0, tmp, 0, aSize);
 774
 775           System.arraycopy(command.seqs[s].getAnnotation(), 0, tmp, aSize,
 776                   command.seqs[s].getAnnotation().length);
 777
 778           annotations = tmp;
 779         }
 780         aSize = annotations.length;
 781       }
 782     }
 783
 784     if (annotations == null)
 785     {
 786       return;
 787     }
 788
 789     if (!insert)
 790     {
 791       command.deletedAnnotations = new Hashtable<String, Annotation[]>();
 792     }
 793
 794     int aSize;
 795     Annotation[] temp;
 796     for (int a = 0; a < annotations.length; a++)
 797     {
 798       if (annotations[a].autoCalculated
 799               || annotations[a].annotations == null)
 800       {
 801         continue;
 802       }
 803
 804       int tSize = 0;
 805
 806       aSize = annotations[a].annotations.length;
 807       if (insert)
 808       {
 809         temp = new Annotation[aSize + command.number];
 810         if (annotations[a].padGaps)
 811         {
 812           for (int aa = 0; aa < temp.length; aa++)
 813           {
 814             temp[aa] = new Annotation(command.gapChar + "", null, ' ', 0);
 815           }
 816         }
 817       }
 818       else
 819       {
 820         if (command.position < aSize)
 821         {
 822           if (command.position + command.number >= aSize)
 823           {
 824             tSize = aSize;
 825           }
 826           else
 827           {
 828             tSize = aSize - command.number;
 829           }
 830         }
 831         else
 832         {
 833           tSize = aSize;
 834         }
 835
 836         if (tSize < 0)
 837         {
 838           tSize = aSize;
 839         }
 840         temp = new Annotation[tSize];
 841       }
 842
 843       if (insert)
 844       {
 845         if (command.position < annotations[a].annotations.length)
 846         {
 847           System.arraycopy(annotations[a].annotations, 0, temp, 0,
 848                   command.position);
 849
 850           if (command.deletedAnnotations != null
 851                   && command.deletedAnnotations
 852                           .containsKey(annotations[a].annotationId))
 853           {
 854             Annotation[] restore = command.deletedAnnotations
 855                     .get(annotations[a].annotationId);
 856
 857             System.arraycopy(restore, 0, temp, command.position,
 858                     command.number);
 859
 860           }
 861
 862           System.arraycopy(annotations[a].annotations, command.position,
 863                   temp, command.position + command.number, aSize
 864                           - command.position);
 865         }
 866         else
 867         {
 868           if (command.deletedAnnotations != null
 869                   && command.deletedAnnotations
 870                           .containsKey(annotations[a].annotationId))
 871           {
 872             Annotation[] restore = command.deletedAnnotations
 873                     .get(annotations[a].annotationId);
 874
 875             temp = new Annotation[annotations[a].annotations.length
 876                     + restore.length];
 877             System.arraycopy(annotations[a].annotations, 0, temp, 0,
 878                     annotations[a].annotations.length);
 879             System.arraycopy(restore, 0, temp,
 880                     annotations[a].annotations.length, restore.length);
 881           }
 882           else
 883           {
 884             temp = annotations[a].annotations;
 885           }
 886         }
 887       }
 888       else
 889       {
 890         if (tSize != aSize || command.position < 2)
 891         {
 892           int copylen = Math.min(command.position,
 893                   annotations[a].annotations.length);
 894           if (copylen > 0)
 895            {
 896             System.arraycopy(annotations[a].annotations, 0, temp, 0,
 897                     copylen); // command.position);
 898           }
 899
 900           Annotation[] deleted = new Annotation[command.number];
 901           if (copylen >= command.position)
 902           {
 903             copylen = Math.min(command.number,
 904                     annotations[a].annotations.length - command.position);
 905             if (copylen > 0)
 906             {
 907               System.arraycopy(annotations[a].annotations,
 908                       command.position, deleted, 0, copylen); // command.number);
 909             }
 910           }
 911
 912           command.deletedAnnotations.put(annotations[a].annotationId,
 913                   deleted);
 914           if (annotations[a].annotations.length > command.position
 915                   + command.number)
 916           {
 917             System.arraycopy(annotations[a].annotations, command.position
 918                     + command.number, temp, command.position,
 919                     annotations[a].annotations.length - command.position
 920                             - command.number); // aSize
 921           }
 922         }
 923         else
 924         {
 925           int dSize = aSize - command.position;
 926
 927           if (dSize > 0)
 928           {
 929             Annotation[] deleted = new Annotation[command.number];
 930             System.arraycopy(annotations[a].annotations, command.position,
 931                     deleted, 0, dSize);
 932
 933             command.deletedAnnotations.put(annotations[a].annotationId,
 934                     deleted);
 935
 936             tSize = Math.min(annotations[a].annotations.length,
 937                     command.position);
 938             temp = new Annotation[tSize];
 939             System.arraycopy(annotations[a].annotations, 0, temp, 0, tSize);
 940           }
 941           else
 942           {
 943             temp = annotations[a].annotations;
 944           }
 945         }
 946       }
 947
 948       annotations[a].annotations = temp;
 949     }
 950   }
 951
 952   final void adjustFeatures(Edit command, int index, int i, int j,
 953           boolean insert)
 954   {
 955     SequenceI seq = command.seqs[index];
 956     SequenceI sequence = seq.getDatasetSequence();
 957     if (sequence == null)
 958     {
 959       sequence = seq;
 960     }
 961
 962     if (insert)
 963     {
 964       if (command.editedFeatures != null
 965               && command.editedFeatures.containsKey(seq))
 966       {
 967         sequence.setSequenceFeatures(command.editedFeatures
 968                 .get(seq));
 969       }
 970
 971       return;
 972     }
 973
 974     SequenceFeature[] sf = sequence.getSequenceFeatures();
 975
 976     if (sf == null)
 977     {
 978       return;
 979     }
 980
 981     SequenceFeature[] oldsf = new SequenceFeature[sf.length];
 982
 983     int cSize = j - i;
 984
 985     for (int s = 0; s < sf.length; s++)
 986     {
 987       SequenceFeature copy = new SequenceFeature(sf[s]);
 988
 989       oldsf[s] = copy;
 990
 991       if (sf[s].getEnd() < i)
 992       {
 993         continue;
 994       }
 995
 996       if (sf[s].getBegin() > j)
 997       {
 998         sf[s].setBegin(copy.getBegin() - cSize);
 999         sf[s].setEnd(copy.getEnd() - cSize);
1000         continue;
1001       }
1002
1003       if (sf[s].getBegin() >= i)
1004       {
1005         sf[s].setBegin(i);
1006       }
1007
1008       if (sf[s].getEnd() < j)
1009       {
1010         sf[s].setEnd(j - 1);
1011       }
1012
1013       sf[s].setEnd(sf[s].getEnd() - (cSize));
1014
1015       if (sf[s].getBegin() > sf[s].getEnd())
1016       {
1017         sequence.deleteFeature(sf[s]);
1018       }
1019     }
1020
1021     if (command.editedFeatures == null)
1022     {
1023       command.editedFeatures = new Hashtable<SequenceI, SequenceFeature[]>();
1024     }
1025
1026     command.editedFeatures.put(seq, oldsf);
1027
1028   }
1029
1030   class Edit
1031   {
1032     public SequenceI[] oldds;
1033
1034     boolean fullAlignmentHeight = false;
1035
1036     Hashtable<SequenceI, AlignmentAnnotation[]> deletedAnnotationRows;
1037
1038     Hashtable<String, Annotation[]> deletedAnnotations;
1039
1040     Hashtable<SequenceI, SequenceFeature[]> editedFeatures;
1041
1042     AlignmentI al;
1043
1044     Action command;
1045
1046     char[][] string;
1047
1048     SequenceI[] seqs;
1049
1050     int[] alIndex;
1051
1052     int position, number;
1053
1054     char gapChar;
1055
1056     Edit(Action command, SequenceI[] seqs, int position, int number,
1057             char gapChar)
1058     {
1059       this.command = command;
1060       this.seqs = seqs;
1061       this.position = position;
1062       this.number = number;
1063       this.gapChar = gapChar;
1064     }
1065
1066     Edit(Action command, SequenceI[] seqs, int position, int number,
1067             AlignmentI al)
1068     {
1069       this.gapChar = al.getGapCharacter();
1070       this.command = command;
1071       this.seqs = seqs;
1072       this.position = position;
1073       this.number = number;
1074       this.al = al;
1075
1076       alIndex = new int[seqs.length];
1077       for (int i = 0; i < seqs.length; i++)
1078       {
1079         alIndex[i] = al.findIndex(seqs[i]);
1080       }
1081
1082       fullAlignmentHeight = (al.getHeight() == seqs.length);
1083     }
1084
1085     Edit(Action command, SequenceI[] seqs, int position, int number,
1086             AlignmentI al, String replace)
1087     {
1088       this.command = command;
1089       this.seqs = seqs;
1090       this.position = position;
1091       this.number = number;
1092       this.al = al;
1093       this.gapChar = al.getGapCharacter();
1094       string = new char[seqs.length][];
1095       for (int i = 0; i < seqs.length; i++)
1096       {
1097         string[i] = replace.toCharArray();
1098       }
1099
1100       fullAlignmentHeight = (al.getHeight() == seqs.length);
1101     }
1102   }
1103 }