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     int e = 0, eSize = edits.length;
 220     for (e = eSize - 1; e > -1; e--)
 221     {
 222       switch (edits[e].command)
 223       {
 224       case INSERT_GAP:
 225         deleteGap(edits[e]);
 226         break;
 227       case DELETE_GAP:
 228         insertGap(edits[e]);
 229         break;
 230       case CUT:
 231         paste(edits[e], views);
 232         break;
 233       case PASTE:
 234         cut(edits[e], views);
 235         break;
 236       case REPLACE:
 237         replace(edits[e]);
 238         break;
 239       }
 240     }
 241   }
 242
 243   final void insertGap(Edit command)
 244   {
 245
 246     for (int s = 0; s < command.seqs.length; s++)
 247     {
 248       command.seqs[s].insertCharAt(command.position, command.number,
 249               command.gapChar);
 250       // System.out.println("pos: "+command.position+" number: "+command.number);
 251     }
 252
 253     adjustAnnotations(command, true, false, null);
 254   }
 255
 256   //
 257   // final void insertNuc(Edit command)
 258   // {
 259   //
 260   // for (int s = 0; s < command.seqs.length; s++)
 261   // {
 262   // System.out.println("pos: "+command.position+" number: "+command.number);
 263   // command.seqs[s].insertCharAt(command.position, command.number,'A');
 264   // }
 265   //
 266   // adjustAnnotations(command, true, false, null);
 267   // }
 268
 269   final void deleteGap(Edit command)
 270   {
 271     for (int s = 0; s < command.seqs.length; s++)
 272     {
 273       command.seqs[s].deleteChars(command.position, command.position
 274               + command.number);
 275     }
 276
 277     adjustAnnotations(command, false, false, null);
 278   }
 279
 280   void cut(Edit command, AlignmentI[] views)
 281   {
 282     boolean seqDeleted = false;
 283     command.string = new char[command.seqs.length][];
 284
 285     for (int i = 0; i < command.seqs.length; i++)
 286     {
 287       if (command.seqs[i].getLength() > command.position)
 288       {
 289         command.string[i] = command.seqs[i].getSequence(command.position,
 290                 command.position + command.number);
 291         SequenceI oldds = command.seqs[i].getDatasetSequence();
 292         if (command.oldds != null && command.oldds[i] != null)
 293         {
 294           // we are redoing an undone cut.
 295           command.seqs[i].setDatasetSequence(null);
 296         }
 297         command.seqs[i].deleteChars(command.position, command.position
 298                 + command.number);
 299         if (command.oldds != null && command.oldds[i] != null)
 300         {
 301           // oldds entry contains the cut dataset sequence.
 302           command.seqs[i].setDatasetSequence(command.oldds[i]);
 303           command.oldds[i] = oldds;
 304         }
 305         else
 306         {
 307           // modify the oldds if necessary
 308           if (oldds != command.seqs[i].getDatasetSequence()
 309                   || command.seqs[i].getSequenceFeatures() != null)
 310           {
 311             if (command.oldds == null)
 312             {
 313               command.oldds = new SequenceI[command.seqs.length];
 314             }
 315             command.oldds[i] = oldds;
 316             adjustFeatures(
 317                     command,
 318                     i,
 319                     command.seqs[i].findPosition(command.position),
 320                     command.seqs[i].findPosition(command.position
 321                             + command.number), false);
 322           }
 323         }
 324       }
 325
 326       if (command.seqs[i].getLength() < 1)
 327       {
 328         command.al.deleteSequence(command.seqs[i]);
 329         seqDeleted = true;
 330       }
 331     }
 332
 333     adjustAnnotations(command, false, seqDeleted, views);
 334   }
 335
 336   void paste(Edit command, AlignmentI[] views)
 337   {
 338     StringBuffer tmp;
 339     boolean newDSNeeded;
 340     boolean newDSWasNeeded;
 341     int newstart, newend;
 342     boolean seqWasDeleted = false;
 343     int start = 0, end = 0;
 344
 345     for (int i = 0; i < command.seqs.length; i++)
 346     {
 347       newDSNeeded = false;
 348       newDSWasNeeded = command.oldds != null && command.oldds[i] != null;
 349       if (command.seqs[i].getLength() < 1)
 350       {
 351         // ie this sequence was deleted, we need to
 352         // read it to the alignment
 353         if (command.alIndex[i] < command.al.getHeight())
 354         {
 355           List<SequenceI> sequences;
 356           synchronized (sequences = command.al.getSequences())
 357           {
 358             sequences.add(command.alIndex[i], command.seqs[i]);
 359           }
 360         }
 361         else
 362         {
 363           command.al.addSequence(command.seqs[i]);
 364         }
 365         seqWasDeleted = true;
 366       }
 367       newstart = command.seqs[i].getStart();
 368       newend = command.seqs[i].getEnd();
 369
 370       tmp = new StringBuffer();
 371       tmp.append(command.seqs[i].getSequence());
 372       // Undo of a delete does not replace original dataset sequence on to
 373       // alignment sequence.
 374
 375       if (command.string != null && command.string[i] != null)
 376       {
 377         if (command.position >= tmp.length())
 378         {
 379           // This occurs if padding is on, and residues
 380           // are removed from end of alignment
 381           int length = command.position - tmp.length();
 382           while (length > 0)
 383           {
 384             tmp.append(command.gapChar);
 385             length--;
 386           }
 387         }
 388         tmp.insert(command.position, command.string[i]);
 389         for (int s = 0; s < command.string[i].length; s++)
 390         {
 391           if (jalview.schemes.ResidueProperties.aaIndex[command.string[i][s]] != 23)
 392           {
 393             if (!newDSNeeded)
 394             {
 395               newDSNeeded = true;
 396               start = command.seqs[i].findPosition(command.position);
 397               end = command.seqs[i].findPosition(command.position
 398                       + command.number);
 399             }
 400             if (command.seqs[i].getStart() == start)
 401               newstart--;
 402             else
 403               newend++;
 404           }
 405         }
 406         command.string[i] = null;
 407       }
 408
 409       command.seqs[i].setSequence(tmp.toString());
 410       command.seqs[i].setStart(newstart);
 411       command.seqs[i].setEnd(newend);
 412       if (newDSNeeded)
 413       {
 414         if (command.seqs[i].getDatasetSequence() != null)
 415         {
 416           SequenceI ds;
 417           if (newDSWasNeeded)
 418           {
 419             ds = command.oldds[i];
 420           }
 421           else
 422           {
 423             // make a new DS sequence
 424             // use new ds mechanism here
 425             ds = new Sequence(command.seqs[i].getName(),
 426                     jalview.analysis.AlignSeq.extractGaps(
 427                             jalview.util.Comparison.GapChars,
 428                             command.seqs[i].getSequenceAsString()),
 429                     command.seqs[i].getStart(), command.seqs[i].getEnd());
 430             ds.setDescription(command.seqs[i].getDescription());
 431           }
 432           if (command.oldds == null)
 433           {
 434             command.oldds = new SequenceI[command.seqs.length];
 435           }
 436           command.oldds[i] = command.seqs[i].getDatasetSequence();
 437           command.seqs[i].setDatasetSequence(ds);
 438         }
 439         adjustFeatures(command, i, start, end, true);
 440       }
 441     }
 442     adjustAnnotations(command, true, seqWasDeleted, views);
 443
 444     command.string = null;
 445   }
 446
 447   void replace(Edit command)
 448   {
 449     StringBuffer tmp;
 450     String oldstring;
 451     int start = command.position;
 452     int end = command.number;
 453     // TODO TUTORIAL - Fix for replacement with different length of sequence (or
 454     // whole sequence)
 455     // TODO Jalview 2.4 bugfix change to an aggregate command - original
 456     // sequence string is cut, new string is pasted in.
 457     command.number = start + command.string[0].length;
 458     for (int i = 0; i < command.seqs.length; i++)
 459     {
 460       boolean newDSWasNeeded = command.oldds != null
 461               && command.oldds[i] != null;
 462
 463       /**
 464        * cut addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT,
 465        * cut, sg.getStartRes(), sg.getEndRes()-sg.getStartRes()+1,
 466        * viewport.alignment));
 467        *
 468        */
 469       /**
 470        * then addHistoryItem(new EditCommand( "Add sequences",
 471        * EditCommand.PASTE, sequences, 0, alignment.getWidth(), alignment) );
 472        *
 473        */
 474       oldstring = command.seqs[i].getSequenceAsString();
 475       tmp = new StringBuffer(oldstring.substring(0, start));
 476       tmp.append(command.string[i]);
 477       String nogaprep = jalview.analysis.AlignSeq.extractGaps(
 478               jalview.util.Comparison.GapChars, new String(
 479                       command.string[i]));
 480       int ipos = command.seqs[i].findPosition(start)
 481               - command.seqs[i].getStart();
 482       tmp.append(oldstring.substring(end));
 483       command.seqs[i].setSequence(tmp.toString());
 484       command.string[i] = oldstring.substring(start, end).toCharArray();
 485       String nogapold = jalview.analysis.AlignSeq.extractGaps(
 486               jalview.util.Comparison.GapChars, new String(
 487                       command.string[i]));
 488       if (!nogaprep.toLowerCase().equals(nogapold.toLowerCase()))
 489       {
 490         if (newDSWasNeeded)
 491         {
 492           SequenceI oldds = command.seqs[i].getDatasetSequence();
 493           command.seqs[i].setDatasetSequence(command.oldds[i]);
 494           command.oldds[i] = oldds;
 495         }
 496         else
 497         {
 498           if (command.oldds == null)
 499           {
 500             command.oldds = new SequenceI[command.seqs.length];
 501           }
 502           command.oldds[i] = command.seqs[i].getDatasetSequence();
 503           SequenceI newds = new Sequence(
 504                   command.seqs[i].getDatasetSequence());
 505           String fullseq, osp = newds.getSequenceAsString();
 506           fullseq = osp.substring(0, ipos) + nogaprep
 507                   + osp.substring(ipos + nogaprep.length());
 508           newds.setSequence(fullseq.toUpperCase());
 509           // TODO: JAL-1131 ensure newly created dataset sequence is added to
 510           // the set of
 511           // dataset sequences associated with the alignment.
 512           // TODO: JAL-1131 fix up any annotation associated with new dataset
 513           // sequence to ensure that original sequence/annotation relationships
 514           // are preserved.
 515           command.seqs[i].setDatasetSequence(newds);
 516
 517         }
 518       }
 519       tmp = null;
 520       oldstring = null;
 521     }
 522   }
 523
 524   final void adjustAnnotations(Edit command, boolean insert,
 525           boolean modifyVisibility, AlignmentI[] views)
 526   {
 527     AlignmentAnnotation[] annotations = null;
 528
 529     if (modifyVisibility && !insert)
 530     {
 531       // only occurs if a sequence was added or deleted.
 532       command.deletedAnnotationRows = new Hashtable();
 533     }
 534     if (command.fullAlignmentHeight)
 535     {
 536       annotations = command.al.getAlignmentAnnotation();
 537     }
 538     else
 539     {
 540       int aSize = 0;
 541       AlignmentAnnotation[] tmp;
 542       for (int s = 0; s < command.seqs.length; s++)
 543       {
 544         if (modifyVisibility)
 545         {
 546           // Rows are only removed or added to sequence object.
 547           if (!insert)
 548           {
 549             // remove rows
 550             tmp = command.seqs[s].getAnnotation();
 551             if (tmp != null)
 552             {
 553               int alen = tmp.length;
 554               for (int aa = 0; aa < tmp.length; aa++)
 555               {
 556                 if (!command.al.deleteAnnotation(tmp[aa]))
 557                 {
 558                   // strip out annotation not in the current al (will be put
 559                   // back on insert in all views)
 560                   tmp[aa] = null;
 561                   alen--;
 562                 }
 563               }
 564               command.seqs[s].setAlignmentAnnotation(null);
 565               if (alen != tmp.length)
 566               {
 567                 // save the non-null annotation references only
 568                 AlignmentAnnotation[] saved = new AlignmentAnnotation[alen];
 569                 for (int aa = 0, aapos = 0; aa < tmp.length; aa++)
 570                 {
 571                   if (tmp[aa] != null)
 572                   {
 573                     saved[aapos++] = tmp[aa];
 574                     tmp[aa] = null;
 575                   }
 576                 }
 577                 tmp = saved;
 578                 command.deletedAnnotationRows.put(command.seqs[s], saved);
 579                 // and then remove any annotation in the other views
 580                 for (int alview = 0; views != null && alview < views.length; alview++)
 581                 {
 582                   if (views[alview] != command.al)
 583                   {
 584                     AlignmentAnnotation[] toremove = views[alview]
 585                             .getAlignmentAnnotation();
 586                     if (toremove == null || toremove.length == 0)
 587                     {
 588                       continue;
 589                     }
 590                     // remove any alignment annotation on this sequence that's
 591                     // on that alignment view.
 592                     for (int aa = 0; aa < toremove.length; aa++)
 593                     {
 594                       if (toremove[aa].sequenceRef == command.seqs[s])
 595                       {
 596                         views[alview].deleteAnnotation(toremove[aa]);
 597                       }
 598                     }
 599                   }
 600                 }
 601               }
 602               else
 603               {
 604                 // save all the annotation
 605                 command.deletedAnnotationRows.put(command.seqs[s], tmp);
 606               }
 607             }
 608           }
 609           else
 610           {
 611             // recover rows
 612             if (command.deletedAnnotationRows != null
 613                     && command.deletedAnnotationRows
 614                             .containsKey(command.seqs[s]))
 615             {
 616               AlignmentAnnotation[] revealed = (AlignmentAnnotation[]) command.deletedAnnotationRows
 617                       .get(command.seqs[s]);
 618               command.seqs[s].setAlignmentAnnotation(revealed);
 619               if (revealed != null)
 620               {
 621                 for (int aa = 0; aa < revealed.length; aa++)
 622                 {
 623                   // iterate through al adding original annotation
 624                   command.al.addAnnotation(revealed[aa]);
 625                 }
 626                 for (int aa = 0; aa < revealed.length; aa++)
 627                 {
 628                   command.al.setAnnotationIndex(revealed[aa], aa);
 629                 }
 630                 // and then duplicate added annotation on every other alignment
 631                 // view
 632                 for (int vnum = 0; views != null && vnum < views.length; vnum++)
 633                 {
 634                   if (views[vnum] != command.al)
 635                   {
 636                     int avwidth = views[vnum].getWidth() + 1;
 637                     // duplicate in this view
 638                     for (int a = 0; a < revealed.length; a++)
 639                     {
 640                       AlignmentAnnotation newann = new AlignmentAnnotation(
 641                               revealed[a]);
 642                       command.seqs[s].addAlignmentAnnotation(newann);
 643                       newann.padAnnotation(avwidth);
 644                       views[vnum].addAnnotation(newann);
 645                       views[vnum].setAnnotationIndex(newann, a);
 646                     }
 647                   }
 648                 }
 649               }
 650             }
 651           }
 652           continue;
 653         }
 654
 655         if (command.seqs[s].getAnnotation() == null)
 656         {
 657           continue;
 658         }
 659
 660         if (aSize == 0)
 661         {
 662           annotations = command.seqs[s].getAnnotation();
 663         }
 664         else
 665         {
 666           tmp = new AlignmentAnnotation[aSize
 667                   + command.seqs[s].getAnnotation().length];
 668
 669           System.arraycopy(annotations, 0, tmp, 0, aSize);
 670
 671           System.arraycopy(command.seqs[s].getAnnotation(), 0, tmp, aSize,
 672                   command.seqs[s].getAnnotation().length);
 673
 674           annotations = tmp;
 675         }
 676         aSize = annotations.length;
 677       }
 678     }
 679
 680     if (annotations == null)
 681     {
 682       return;
 683     }
 684
 685     if (!insert)
 686     {
 687       command.deletedAnnotations = new Hashtable();
 688     }
 689
 690     int aSize;
 691     Annotation[] temp;
 692     for (int a = 0; a < annotations.length; a++)
 693     {
 694       if (annotations[a].autoCalculated
 695               || annotations[a].annotations == null)
 696       {
 697         continue;
 698       }
 699
 700       int tSize = 0;
 701
 702       aSize = annotations[a].annotations.length;
 703       if (insert)
 704       {
 705         temp = new Annotation[aSize + command.number];
 706         if (annotations[a].padGaps)
 707           for (int aa = 0; aa < temp.length; aa++)
 708           {
 709             temp[aa] = new Annotation(command.gapChar + "", null, ' ', 0);
 710           }
 711       }
 712       else
 713       {
 714         if (command.position < aSize)
 715         {
 716           if (command.position + command.number >= aSize)
 717           {
 718             tSize = aSize;
 719           }
 720           else
 721           {
 722             tSize = aSize - command.number;
 723           }
 724         }
 725         else
 726         {
 727           tSize = aSize;
 728         }
 729
 730         if (tSize < 0)
 731         {
 732           tSize = aSize;
 733         }
 734         temp = new Annotation[tSize];
 735       }
 736
 737       if (insert)
 738       {
 739         if (command.position < annotations[a].annotations.length)
 740         {
 741           System.arraycopy(annotations[a].annotations, 0, temp, 0,
 742                   command.position);
 743
 744           if (command.deletedAnnotations != null
 745                   && command.deletedAnnotations
 746                           .containsKey(annotations[a].annotationId))
 747           {
 748             Annotation[] restore = (Annotation[]) command.deletedAnnotations
 749                     .get(annotations[a].annotationId);
 750
 751             System.arraycopy(restore, 0, temp, command.position,
 752                     command.number);
 753
 754           }
 755
 756           System.arraycopy(annotations[a].annotations, command.position,
 757                   temp, command.position + command.number, aSize
 758                           - command.position);
 759         }
 760         else
 761         {
 762           if (command.deletedAnnotations != null
 763                   && command.deletedAnnotations
 764                           .containsKey(annotations[a].annotationId))
 765           {
 766             Annotation[] restore = (Annotation[]) command.deletedAnnotations
 767                     .get(annotations[a].annotationId);
 768
 769             temp = new Annotation[annotations[a].annotations.length
 770                     + restore.length];
 771             System.arraycopy(annotations[a].annotations, 0, temp, 0,
 772                     annotations[a].annotations.length);
 773             System.arraycopy(restore, 0, temp,
 774                     annotations[a].annotations.length, restore.length);
 775           }
 776           else
 777           {
 778             temp = annotations[a].annotations;
 779           }
 780         }
 781       }
 782       else
 783       {
 784         if (tSize != aSize || command.position < 2)
 785         {
 786           int copylen = Math.min(command.position,
 787                   annotations[a].annotations.length);
 788           if (copylen > 0)
 789             System.arraycopy(annotations[a].annotations, 0, temp, 0,
 790                     copylen); // command.position);
 791
 792           Annotation[] deleted = new Annotation[command.number];
 793           if (copylen >= command.position)
 794           {
 795             copylen = Math.min(command.number,
 796                     annotations[a].annotations.length - command.position);
 797             if (copylen > 0)
 798             {
 799               System.arraycopy(annotations[a].annotations,
 800                       command.position, deleted, 0, copylen); // command.number);
 801             }
 802           }
 803
 804           command.deletedAnnotations.put(annotations[a].annotationId,
 805                   deleted);
 806           if (annotations[a].annotations.length > command.position
 807                   + command.number)
 808           {
 809             System.arraycopy(annotations[a].annotations, command.position
 810                     + command.number, temp, command.position,
 811                     annotations[a].annotations.length - command.position
 812                             - command.number); // aSize
 813           }
 814         }
 815         else
 816         {
 817           int dSize = aSize - command.position;
 818
 819           if (dSize > 0)
 820           {
 821             Annotation[] deleted = new Annotation[command.number];
 822             System.arraycopy(annotations[a].annotations, command.position,
 823                     deleted, 0, dSize);
 824
 825             command.deletedAnnotations.put(annotations[a].annotationId,
 826                     deleted);
 827
 828             tSize = Math.min(annotations[a].annotations.length,
 829                     command.position);
 830             temp = new Annotation[tSize];
 831             System.arraycopy(annotations[a].annotations, 0, temp, 0, tSize);
 832           }
 833           else
 834           {
 835             temp = annotations[a].annotations;
 836           }
 837         }
 838       }
 839
 840       annotations[a].annotations = temp;
 841     }
 842   }
 843
 844   final void adjustFeatures(Edit command, int index, int i, int j,
 845           boolean insert)
 846   {
 847     SequenceI seq = command.seqs[index];
 848     SequenceI sequence = seq.getDatasetSequence();
 849     if (sequence == null)
 850     {
 851       sequence = seq;
 852     }
 853
 854     if (insert)
 855     {
 856       if (command.editedFeatures != null
 857               && command.editedFeatures.containsKey(seq))
 858       {
 859         sequence.setSequenceFeatures((SequenceFeature[]) command.editedFeatures
 860                 .get(seq));
 861       }
 862
 863       return;
 864     }
 865
 866     SequenceFeature[] sf = sequence.getSequenceFeatures();
 867
 868     if (sf == null)
 869     {
 870       return;
 871     }
 872
 873     SequenceFeature[] oldsf = new SequenceFeature[sf.length];
 874
 875     int cSize = j - i;
 876
 877     for (int s = 0; s < sf.length; s++)
 878     {
 879       SequenceFeature copy = new SequenceFeature(sf[s]);
 880
 881       oldsf[s] = copy;
 882
 883       if (sf[s].getEnd() < i)
 884       {
 885         continue;
 886       }
 887
 888       if (sf[s].getBegin() > j)
 889       {
 890         sf[s].setBegin(copy.getBegin() - cSize);
 891         sf[s].setEnd(copy.getEnd() - cSize);
 892         continue;
 893       }
 894
 895       if (sf[s].getBegin() >= i)
 896       {
 897         sf[s].setBegin(i);
 898       }
 899
 900       if (sf[s].getEnd() < j)
 901       {
 902         sf[s].setEnd(j - 1);
 903       }
 904
 905       sf[s].setEnd(sf[s].getEnd() - (cSize));
 906
 907       if (sf[s].getBegin() > sf[s].getEnd())
 908       {
 909         sequence.deleteFeature(sf[s]);
 910       }
 911     }
 912
 913     if (command.editedFeatures == null)
 914     {
 915       command.editedFeatures = new Hashtable();
 916     }
 917
 918     command.editedFeatures.put(seq, oldsf);
 919
 920   }
 921
 922   class Edit
 923   {
 924     public SequenceI[] oldds;
 925
 926     boolean fullAlignmentHeight = false;
 927
 928     Hashtable deletedAnnotationRows;
 929
 930     Hashtable deletedAnnotations;
 931
 932     Hashtable editedFeatures;
 933
 934     AlignmentI al;
 935
 936     int command;
 937
 938     char[][] string;
 939
 940     SequenceI[] seqs;
 941
 942     int[] alIndex;
 943
 944     int position, number;
 945
 946     char gapChar;
 947
 948     Edit(int command, SequenceI[] seqs, int position, int number,
 949             char gapChar)
 950     {
 951       this.command = command;
 952       this.seqs = seqs;
 953       this.position = position;
 954       this.number = number;
 955       this.gapChar = gapChar;
 956     }
 957
 958     Edit(int command, SequenceI[] seqs, int position, int number,
 959             AlignmentI al)
 960     {
 961       this.gapChar = al.getGapCharacter();
 962       this.command = command;
 963       this.seqs = seqs;
 964       this.position = position;
 965       this.number = number;
 966       this.al = al;
 967
 968       alIndex = new int[seqs.length];
 969       for (int i = 0; i < seqs.length; i++)
 970       {
 971         alIndex[i] = al.findIndex(seqs[i]);
 972       }
 973
 974       fullAlignmentHeight = (al.getHeight() == seqs.length);
 975     }
 976
 977     Edit(int command, SequenceI[] seqs, int position, int number,
 978             AlignmentI al, String replace)
 979     {
 980       this.command = command;
 981       this.seqs = seqs;
 982       this.position = position;
 983       this.number = number;
 984       this.al = al;
 985       this.gapChar = al.getGapCharacter();
 986       string = new char[seqs.length][];
 987       for (int i = 0; i < seqs.length; i++)
 988       {
 989         string[i] = replace.toCharArray();
 990       }
 991
 992       fullAlignmentHeight = (al.getHeight() == seqs.length);
 993     }
 994   }
 995 }