src/jalview/commands/EditCommand.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  *\r
   5  * This program is free software; you can redistribute it and/or\r
   6  * modify it under the terms of the GNU General Public License\r
   7  * as published by the Free Software Foundation; either version 2\r
   8  * of the License, or (at your option) any later version.\r
   9  *\r
  10  * This program is distributed in the hope that it will be useful,\r
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13  * GNU General Public License for more details.\r
  14  *\r
  15  * You should have received a copy of the GNU General Public License\r
  16  * along with this program; if not, write to the Free Software\r
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18  */\r
  19 package jalview.commands;\r
  20 \r
  21 import jalview.datamodel.*;\r
  22 \r
  23 import java.util.Hashtable;\r
  24 \r
  25 /**\r
  26  *\r
  27  * <p>Title: EditCommmand</p>\r
  28  *\r
  29  * <p>Description: Essential information for performing\r
  30  * undo and redo for cut/paste insert/delete gap\r
  31  * which can be stored in the HistoryList </p>\r
  32  *\r
  33  * <p>Copyright: Copyright (c) 2006</p>\r
  34  *\r
  35  * <p>Company: Dundee University</p>\r
  36  *\r
  37  * @author not attributable\r
  38  * @version 1.0\r
  39  */\r
  40 public class EditCommand implements CommandI\r
  41 {\r
  42   public static final int INSERT_GAP = 0;\r
  43   public static final int DELETE_GAP = 1;\r
  44   public static final int CUT = 2;\r
  45   public static final int PASTE = 3;\r
  46 \r
  47   Edit[] edits;\r
  48 \r
  49   String description;\r
  50 \r
  51   public EditCommand()\r
  52   {}\r
  53 \r
  54   public EditCommand(String description)\r
  55   {\r
  56     this.description = description;\r
  57   }\r
  58 \r
  59   public EditCommand( String description,\r
  60                       int command,\r
  61                       SequenceI[] seqs,\r
  62                       int position,\r
  63                       int number,\r
  64                       AlignmentI al)\r
  65    {\r
  66      this.description = description;\r
  67      if ( command==CUT || command==PASTE)\r
  68      {\r
  69        edits = new Edit[]{new Edit(command, seqs, position, number, al)};\r
  70      }\r
  71 \r
  72      performEdit(0);\r
  73   }\r
  74 \r
  75 \r
  76   final public String getDescription()\r
  77   {\r
  78     return description;\r
  79   }\r
  80 \r
  81   public int getSize()\r
  82   {\r
  83     return edits==null?0:edits.length;\r
  84   }\r
  85 \r
  86   final public AlignmentI getAlignment()\r
  87   {\r
  88     return edits[0].al;\r
  89   }\r
  90 \r
  91 \r
  92   final public void appendEdit(int command,\r
  93                          SequenceI[] seqs,\r
  94                          int position,\r
  95                          int number,\r
  96                          AlignmentI al,\r
  97                          boolean performEdit)\r
  98   {\r
  99     Edit edit = new Edit(command, seqs, position, number, al.getGapCharacter());\r
 100     if(al.getHeight()==seqs.length)\r
 101     {\r
 102       edit.al = al;\r
 103       edit.fullAlignmentHeight = true;\r
 104     }\r
 105 \r
 106     if (edits != null)\r
 107     {\r
 108       Edit[] temp = new Edit[edits.length + 1];\r
 109       System.arraycopy(edits, 0, temp, 0, edits.length);\r
 110       edits = temp;\r
 111       edits[edits.length - 1] = edit;\r
 112     }\r
 113     else\r
 114       edits = new Edit[] {  edit  };\r
 115 \r
 116     if (performEdit)\r
 117       performEdit(edits.length - 1);\r
 118   }\r
 119 \r
 120   final void performEdit(int commandIndex)\r
 121   {\r
 122     int eSize = edits.length;\r
 123     for (int e = commandIndex; e < eSize; e++)\r
 124     {\r
 125       if (edits[e].command==INSERT_GAP)\r
 126       {\r
 127         insertGap(edits[e]);\r
 128       }\r
 129       else if (edits[e].command==DELETE_GAP)\r
 130       {\r
 131         deleteGap(edits[e]);\r
 132       }\r
 133       else if(edits[e].command==CUT)\r
 134       {\r
 135         cut(edits[e]);\r
 136       }\r
 137       else if(edits[e].command==PASTE)\r
 138       {\r
 139         paste(edits[e]);\r
 140       }\r
 141     }\r
 142   }\r
 143 \r
 144   final public void doCommand()\r
 145   {\r
 146     performEdit(0);\r
 147   }\r
 148 \r
 149   final public void undoCommand()\r
 150   {\r
 151     int e = 0, eSize = edits.length;\r
 152     for (e = eSize-1; e > -1; e--)\r
 153     {\r
 154       if (edits[e].command==INSERT_GAP)\r
 155       {\r
 156         deleteGap(edits[e]);\r
 157       }\r
 158       else if (edits[e].command==DELETE_GAP)\r
 159       {\r
 160         insertGap(edits[e]);\r
 161       }\r
 162       else if (edits[e].command==CUT)\r
 163       {\r
 164         paste(edits[e]);\r
 165       }\r
 166       else if (edits[e].command==PASTE)\r
 167       {\r
 168         cut(edits[e]);\r
 169       }\r
 170     }\r
 171   }\r
 172 \r
 173   final void insertGap(Edit command)\r
 174   {\r
 175     for(int s=0; s<command.seqs.length; s++)\r
 176     {\r
 177         command.seqs[s].insertCharAt(command.position,\r
 178                                      command.number,\r
 179                                      command.gapChar);\r
 180     }\r
 181 \r
 182     adjustAnnotations(command, true);\r
 183   }\r
 184 \r
 185   final void deleteGap(Edit command)\r
 186   {\r
 187     for (int s = 0; s < command.seqs.length; s++)\r
 188     {\r
 189       command.seqs[s].deleteChars(command.position, command.position+command.number);\r
 190     }\r
 191 \r
 192     adjustAnnotations(command, false);\r
 193   }\r
 194 \r
 195   void cut(Edit command)\r
 196   {\r
 197     command.string = new char [command.seqs.length][];\r
 198 \r
 199     for(int i=0; i<command.seqs.length; i++)\r
 200     {\r
 201       if(command.seqs[i].getLength()>command.position)\r
 202       {\r
 203         command.string[i] = command.seqs[i].getSequence(command.position,\r
 204             command.position + command.number);\r
 205 \r
 206         if(command.seqs[i].getDatasetSequence()!=null\r
 207         || command.seqs[i].getSequenceFeatures()!=null)\r
 208         {\r
 209           for (int s = command.position; s < command.position + command.number; s++)\r
 210           {\r
 211             if (jalview.schemes.ResidueProperties\r
 212                 .aaIndex[command.seqs[i].getCharAt(s)] != 23)\r
 213             {\r
 214               adjustFeatures(command, i,\r
 215                              command.seqs[i].findPosition(command.position),\r
 216                              command.seqs[i].findPosition(command.position +\r
 217                                                           command.number),\r
 218                              false);\r
 219               break;\r
 220             }\r
 221           }\r
 222         }\r
 223         command.seqs[i].deleteChars(command.position,\r
 224                                     command.position + command.number);\r
 225       }\r
 226 \r
 227       if(command.seqs[i].getLength()<1)\r
 228       {\r
 229         command.al.deleteSequence(command.seqs[i]);\r
 230       }\r
 231     }\r
 232 \r
 233     adjustAnnotations(command, false);\r
 234   }\r
 235 \r
 236   void paste(Edit command)\r
 237   {\r
 238     StringBuffer tmp;\r
 239     boolean newDSNeeded;\r
 240     int start=0, end=0;\r
 241 \r
 242     for(int i=0; i<command.seqs.length; i++)\r
 243     {\r
 244       newDSNeeded = false;\r
 245       if(command.seqs[i].getLength()<1)\r
 246       {\r
 247         // ie this sequence was deleted, we need to\r
 248         // read it to the alignment\r
 249         if (command.alIndex[i] < command.al.getHeight())\r
 250           command.al.getSequences().insertElementAt(command.seqs[i],\r
 251               command.alIndex[i]);\r
 252         else\r
 253           command.al.addSequence(command.seqs[i]);\r
 254       }\r
 255       tmp = new StringBuffer();\r
 256       tmp.append(command.seqs[i].getSequence());\r
 257 \r
 258       if(command.string!=null && command.string[i]!=null)\r
 259       {\r
 260         if(command.position>=tmp.length())\r
 261         {\r
 262           //This occurs if padding is on, and residues\r
 263           //are removed from end of alignment\r
 264           int length = command.position-tmp.length();\r
 265           while (length > 0)\r
 266           {\r
 267             tmp.append(command.gapChar);\r
 268             length--;\r
 269           }\r
 270         }\r
 271         tmp.insert(command.position, command.string[i]);\r
 272 \r
 273         for (int s = 0; s < command.string[i].length; s++)\r
 274         {\r
 275           if (jalview.schemes.ResidueProperties.aaIndex[command.string[i][s]] != 23)\r
 276           {\r
 277             newDSNeeded = true;\r
 278             start = command.seqs[i].findPosition(command.position);\r
 279             end = command.seqs[i].findPosition(command.position+command.number);\r
 280             break;\r
 281           }\r
 282         }\r
 283         command.string[i] = null;\r
 284       }\r
 285 \r
 286 \r
 287       command.seqs[i].setSequence(tmp.toString());\r
 288 \r
 289       if(newDSNeeded)\r
 290       {\r
 291         if (command.seqs[i].getDatasetSequence() != null)\r
 292         {\r
 293           Sequence ds = new Sequence(command.seqs[i].getName(),\r
 294                                      jalview.analysis.AlignSeq.extractGaps(\r
 295                                          jalview.util.Comparison.GapChars,\r
 296                                          command.seqs[i].getSequenceAsString()\r
 297                                      ),\r
 298                                      command.seqs[i].getStart(),\r
 299                                      command.seqs[i].getEnd());\r
 300           ds.setDescription(command.seqs[i].getDescription());\r
 301           command.seqs[i].setDatasetSequence(ds);\r
 302         }\r
 303 \r
 304         adjustFeatures(command, i, start, end, true);\r
 305       }\r
 306     }\r
 307 \r
 308 \r
 309     adjustAnnotations(command, true);\r
 310 \r
 311     command.string = null;\r
 312   }\r
 313 \r
 314 \r
 315   final void adjustAnnotations(Edit command, boolean insert)\r
 316   {\r
 317 \r
 318     AlignmentAnnotation [] annotations = null;\r
 319 \r
 320     if (command.fullAlignmentHeight)\r
 321     {\r
 322       annotations = command.al.getAlignmentAnnotation();\r
 323     }\r
 324     else\r
 325     {\r
 326       int aSize = 0;\r
 327       AlignmentAnnotation [] tmp;\r
 328       for(int s=0; s<command.seqs.length; s++)\r
 329       {\r
 330         if(command.seqs[s].getAnnotation()==null)\r
 331           continue;\r
 332 \r
 333         if (aSize == 0)\r
 334             annotations = command.seqs[s].getAnnotation();\r
 335         else\r
 336         {\r
 337           tmp = new AlignmentAnnotation\r
 338               [aSize + command.seqs[s].getAnnotation().length];\r
 339 \r
 340           System.arraycopy(annotations,0,tmp,0,aSize);\r
 341 \r
 342           System.arraycopy(command.seqs[s].getAnnotation(),\r
 343               0,tmp,aSize,command.seqs[s].getAnnotation().length);\r
 344 \r
 345           annotations = tmp;\r
 346         }\r
 347 \r
 348 \r
 349         aSize = annotations.length;\r
 350       }\r
 351     }\r
 352 \r
 353     if(annotations==null)\r
 354       return;\r
 355 \r
 356 \r
 357       if(!insert)\r
 358         command.deletedAnnotations = new Hashtable();\r
 359 \r
 360       int aSize, tSize;\r
 361       Annotation [] temp;\r
 362       for (int a = 0; a < annotations.length; a++)\r
 363       {\r
 364         if(annotations[a].autoCalculated)\r
 365         {\r
 366           continue;\r
 367         }\r
 368 \r
 369         aSize = annotations[a].annotations.length;\r
 370         if(insert)\r
 371           tSize = aSize + command.number;\r
 372         else\r
 373           tSize = aSize - command.number;\r
 374 \r
 375         temp = new Annotation[tSize];\r
 376 \r
 377         if(insert)\r
 378         {\r
 379           if(command.position < annotations[a].annotations.length)\r
 380           {\r
 381             System.arraycopy(annotations[a].annotations,\r
 382                              0, temp, 0, command.position);\r
 383 \r
 384             if (command.deletedAnnotations != null\r
 385                 &&\r
 386                 command.deletedAnnotations.containsKey(annotations[a].annotationId))\r
 387             {\r
 388               Annotation[] restore = (Annotation[])\r
 389                   command.deletedAnnotations.get(annotations[a].annotationId);\r
 390 \r
 391               System.arraycopy(restore,\r
 392                                0,\r
 393                                temp,\r
 394                                command.position,\r
 395                                command.number);\r
 396 \r
 397             }\r
 398 \r
 399             System.arraycopy(annotations[a].annotations,\r
 400                              command.position, temp,\r
 401                              command.position + command.number,\r
 402                              aSize - command.position);\r
 403           }\r
 404           else\r
 405             temp = annotations[a].annotations;\r
 406         }\r
 407         else\r
 408         {\r
 409           if(command.position < annotations[a].annotations.length)\r
 410           {\r
 411             System.arraycopy(annotations[a].annotations,\r
 412                              0, temp, 0, command.position);\r
 413 \r
 414             Annotation[] deleted = new Annotation[command.number];\r
 415             System.arraycopy(annotations[a].annotations,\r
 416                              command.position, deleted, 0, command.number);\r
 417 \r
 418             command.deletedAnnotations.put(annotations[a].annotationId,\r
 419                                            deleted);\r
 420 \r
 421             System.arraycopy(annotations[a].annotations,\r
 422                              command.position + command.number,\r
 423                              temp, command.position,\r
 424                              aSize - command.position - command.number);\r
 425           }\r
 426           else\r
 427             temp = annotations[a].annotations;\r
 428         }\r
 429 \r
 430         annotations[a].annotations = temp;\r
 431      }\r
 432   }\r
 433 \r
 434   final void adjustFeatures(Edit command, int index, int i, int j, boolean insert)\r
 435   {\r
 436     SequenceI seq = command.seqs[index];\r
 437     SequenceI sequence = seq.getDatasetSequence();\r
 438     if(sequence==null)\r
 439       sequence = seq;\r
 440 \r
 441     if(insert)\r
 442     {\r
 443       if (command.editedFeatures != null\r
 444           && command.editedFeatures.containsKey(seq))\r
 445         sequence.setSequenceFeatures(\r
 446             (SequenceFeature[]) command.editedFeatures.get(seq)\r
 447             );\r
 448 \r
 449       return;\r
 450     }\r
 451 \r
 452 \r
 453     SequenceFeature [] sf = sequence.getSequenceFeatures();\r
 454 \r
 455 \r
 456     if(sf==null)\r
 457     {\r
 458       return;\r
 459     }\r
 460 \r
 461     SequenceFeature [] oldsf = new SequenceFeature[sf.length];\r
 462 \r
 463     int cSize = j - i;\r
 464 \r
 465     for (int s = 0; s < sf.length; s++)\r
 466     {\r
 467       SequenceFeature copy = new SequenceFeature(sf[s]);\r
 468 \r
 469       oldsf[s] = copy;\r
 470 \r
 471       if (sf[s].getEnd() < i)\r
 472         continue;\r
 473 \r
 474       if (sf[s].getBegin() > j)\r
 475       {\r
 476         sf[s].setBegin(copy.getBegin() - cSize);\r
 477         sf[s].setEnd(copy.getEnd() - cSize);\r
 478         continue;\r
 479       }\r
 480 \r
 481       if (sf[s].getBegin() >= i)\r
 482         sf[s].setBegin(i);\r
 483 \r
 484       if (sf[s].getEnd() < j)\r
 485         sf[s].setEnd(j - 1);\r
 486 \r
 487       sf[s].setEnd(sf[s].getEnd() - (cSize));\r
 488 \r
 489       if (sf[s].getBegin() > sf[s].getEnd())\r
 490         sequence.deleteFeature(sf[s]);\r
 491     }\r
 492 \r
 493     if (command.editedFeatures == null)\r
 494       command.editedFeatures = new Hashtable();\r
 495 \r
 496     command.editedFeatures.put(seq, oldsf);\r
 497 \r
 498   }\r
 499 \r
 500 \r
 501   class Edit\r
 502   {\r
 503     boolean fullAlignmentHeight = false;\r
 504     Hashtable deletedAnnotations;\r
 505     Hashtable editedFeatures;\r
 506     AlignmentI al;\r
 507     int command;\r
 508     char [][] string;\r
 509     SequenceI[] seqs;\r
 510     int [] alIndex;\r
 511     int position, number;\r
 512     char gapChar;\r
 513 \r
 514     Edit(int command,\r
 515          SequenceI[] seqs,\r
 516          int position,\r
 517          int number,\r
 518          char gapChar)\r
 519     {\r
 520       this.command = command;\r
 521       this.seqs = seqs;\r
 522       this.position = position;\r
 523       this.number = number;\r
 524       this.gapChar = gapChar;\r
 525     }\r
 526 \r
 527 \r
 528     Edit(int command,\r
 529          SequenceI[] seqs,\r
 530          int position,\r
 531          int number,\r
 532          AlignmentI al)\r
 533     {\r
 534       this.gapChar = al.getGapCharacter();\r
 535       this.command = command;\r
 536       this.seqs = seqs;\r
 537       this.position = position;\r
 538       this.number = number;\r
 539       this.al = al;\r
 540 \r
 541       alIndex = new int[seqs.length];\r
 542       for(int i=0; i<seqs.length; i++)\r
 543       {\r
 544         alIndex[i] = al.findIndex(seqs[i]);\r
 545       }\r
 546 \r
 547       fullAlignmentHeight = (al.getHeight()==seqs.length);\r
 548     }\r
 549   }\r
 550 \r
 551 }\r