src/jalview/commands/EditCommand.java

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