src/jalview/commands/EditCommand.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2007 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 java.util.*;\r
  22 \r
  23 import jalview.datamodel.*;\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\r
  41     implements CommandI\r
  42 {\r
  43   public static final int INSERT_GAP = 0;\r
  44   public static final int DELETE_GAP = 1;\r
  45   public static final int CUT = 2;\r
  46   public static final int PASTE = 3;\r
  47 \r
  48   Edit[] edits;\r
  49 \r
  50   String description;\r
  51 \r
  52   public EditCommand()\r
  53   {}\r
  54 \r
  55   public EditCommand(String description)\r
  56   {\r
  57     this.description = description;\r
  58   }\r
  59 \r
  60   public EditCommand(String description,\r
  61                      int command,\r
  62                      SequenceI[] seqs,\r
  63                      int position,\r
  64                      int number,\r
  65                      AlignmentI al)\r
  66   {\r
  67     this.description = description;\r
  68     if (command == CUT || command == PASTE)\r
  69     {\r
  70       edits = new Edit[]\r
  71           {\r
  72           new Edit(command, seqs, position, number, al)};\r
  73     }\r
  74 \r
  75     performEdit(0);\r
  76   }\r
  77 \r
  78   final public String getDescription()\r
  79   {\r
  80     return description;\r
  81   }\r
  82 \r
  83   public int getSize()\r
  84   {\r
  85     return edits == null ? 0 : edits.length;\r
  86   }\r
  87 \r
  88   final public AlignmentI getAlignment()\r
  89   {\r
  90     return edits[0].al;\r
  91   }\r
  92 \r
  93   final public void appendEdit(int command,\r
  94                                SequenceI[] seqs,\r
  95                                int position,\r
  96                                int number,\r
  97                                AlignmentI al,\r
  98                                boolean performEdit)\r
  99   {\r
 100     Edit edit = new Edit(command, seqs, position, number, al.getGapCharacter());\r
 101     if (al.getHeight() == seqs.length)\r
 102     {\r
 103       edit.al = al;\r
 104       edit.fullAlignmentHeight = true;\r
 105     }\r
 106 \r
 107     if (edits != null)\r
 108     {\r
 109       Edit[] temp = new Edit[edits.length + 1];\r
 110       System.arraycopy(edits, 0, temp, 0, edits.length);\r
 111       edits = temp;\r
 112       edits[edits.length - 1] = edit;\r
 113     }\r
 114     else\r
 115     {\r
 116       edits = new Edit[]\r
 117           {\r
 118           edit};\r
 119     }\r
 120 \r
 121     if (performEdit)\r
 122     {\r
 123       performEdit(edits.length - 1);\r
 124     }\r
 125   }\r
 126 \r
 127   final void performEdit(int commandIndex)\r
 128   {\r
 129     int eSize = edits.length;\r
 130     for (int e = commandIndex; e < eSize; e++)\r
 131     {\r
 132       if (edits[e].command == INSERT_GAP)\r
 133       {\r
 134         insertGap(edits[e]);\r
 135       }\r
 136       else if (edits[e].command == DELETE_GAP)\r
 137       {\r
 138         deleteGap(edits[e]);\r
 139       }\r
 140       else if (edits[e].command == CUT)\r
 141       {\r
 142         cut(edits[e]);\r
 143       }\r
 144       else if (edits[e].command == PASTE)\r
 145       {\r
 146         paste(edits[e]);\r
 147       }\r
 148     }\r
 149   }\r
 150 \r
 151   final public void doCommand()\r
 152   {\r
 153     performEdit(0);\r
 154   }\r
 155 \r
 156   final public void undoCommand()\r
 157   {\r
 158     int e = 0, eSize = edits.length;\r
 159     for (e = eSize - 1; e > -1; e--)\r
 160     {\r
 161       if (edits[e].command == INSERT_GAP)\r
 162       {\r
 163         deleteGap(edits[e]);\r
 164       }\r
 165       else if (edits[e].command == DELETE_GAP)\r
 166       {\r
 167         insertGap(edits[e]);\r
 168       }\r
 169       else if (edits[e].command == CUT)\r
 170       {\r
 171         paste(edits[e]);\r
 172       }\r
 173       else if (edits[e].command == PASTE)\r
 174       {\r
 175         cut(edits[e]);\r
 176       }\r
 177     }\r
 178   }\r
 179 \r
 180   final void insertGap(Edit command)\r
 181   {\r
 182     for (int s = 0; s < command.seqs.length; s++)\r
 183     {\r
 184       command.seqs[s].insertCharAt(command.position,\r
 185                                    command.number,\r
 186                                    command.gapChar);\r
 187     }\r
 188 \r
 189     adjustAnnotations(command, true);\r
 190   }\r
 191 \r
 192   final void deleteGap(Edit command)\r
 193   {\r
 194     for (int s = 0; s < command.seqs.length; s++)\r
 195     {\r
 196       command.seqs[s].deleteChars(command.position,\r
 197                                   command.position + command.number);\r
 198     }\r
 199 \r
 200     adjustAnnotations(command, false);\r
 201   }\r
 202 \r
 203   void cut(Edit command)\r
 204   {\r
 205     command.string = new char[command.seqs.length][];\r
 206 \r
 207     for (int i = 0; i < command.seqs.length; i++)\r
 208     {\r
 209       if (command.seqs[i].getLength() > command.position)\r
 210       {\r
 211         command.string[i] = command.seqs[i].getSequence(command.position,\r
 212             command.position + command.number);\r
 213 \r
 214         if (command.seqs[i].getDatasetSequence() != null\r
 215             || command.seqs[i].getSequenceFeatures() != null)\r
 216         {\r
 217           for (int s = command.position; s < command.position + command.number;\r
 218                s++)\r
 219           {\r
 220             if (jalview.schemes.ResidueProperties\r
 221                 .aaIndex[command.seqs[i].getCharAt(s)] != 23)\r
 222             {\r
 223               adjustFeatures(command, i,\r
 224                              command.seqs[i].findPosition(command.position),\r
 225                              command.seqs[i].findPosition(command.position +\r
 226                   command.number),\r
 227                              false);\r
 228               break;\r
 229             }\r
 230           }\r
 231         }\r
 232         command.seqs[i].deleteChars(command.position,\r
 233                                     command.position + command.number);\r
 234       }\r
 235 \r
 236       if (command.seqs[i].getLength() < 1)\r
 237       {\r
 238         command.al.deleteSequence(command.seqs[i]);\r
 239       }\r
 240     }\r
 241 \r
 242     adjustAnnotations(command, false);\r
 243   }\r
 244 \r
 245   void paste(Edit command)\r
 246   {\r
 247     StringBuffer tmp;\r
 248     boolean newDSNeeded;\r
 249     int start = 0, end = 0;\r
 250 \r
 251     for (int i = 0; i < command.seqs.length; i++)\r
 252     {\r
 253       newDSNeeded = false;\r
 254       if (command.seqs[i].getLength() < 1)\r
 255       {\r
 256         // ie this sequence was deleted, we need to\r
 257         // read it to the alignment\r
 258         if (command.alIndex[i] < command.al.getHeight())\r
 259         {\r
 260           command.al.getSequences().insertElementAt(command.seqs[i],\r
 261               command.alIndex[i]);\r
 262         }\r
 263         else\r
 264         {\r
 265           command.al.addSequence(command.seqs[i]);\r
 266         }\r
 267       }\r
 268       tmp = new StringBuffer();\r
 269       tmp.append(command.seqs[i].getSequence());\r
 270 \r
 271       if (command.string != null && command.string[i] != null)\r
 272       {\r
 273         if (command.position >= tmp.length())\r
 274         {\r
 275           //This occurs if padding is on, and residues\r
 276           //are removed from end of alignment\r
 277           int length = command.position - tmp.length();\r
 278           while (length > 0)\r
 279           {\r
 280             tmp.append(command.gapChar);\r
 281             length--;\r
 282           }\r
 283         }\r
 284         tmp.insert(command.position, command.string[i]);\r
 285 \r
 286         for (int s = 0; s < command.string[i].length; s++)\r
 287         {\r
 288           if (jalview.schemes.ResidueProperties.aaIndex[command.string[i][s]] !=\r
 289               23)\r
 290           {\r
 291             newDSNeeded = true;\r
 292             start = command.seqs[i].findPosition(command.position);\r
 293             end = command.seqs[i].findPosition(command.position +\r
 294                                                command.number);\r
 295             break;\r
 296           }\r
 297         }\r
 298         command.string[i] = null;\r
 299       }\r
 300 \r
 301       command.seqs[i].setSequence(tmp.toString());\r
 302 \r
 303       if (newDSNeeded)\r
 304       {\r
 305         if (command.seqs[i].getDatasetSequence() != null)\r
 306         {\r
 307           Sequence ds = new Sequence(command.seqs[i].getName(),\r
 308                                      jalview.analysis.AlignSeq.extractGaps(\r
 309                                          jalview.util.Comparison.GapChars,\r
 310                                          command.seqs[i].getSequenceAsString()\r
 311                                      ),\r
 312                                      command.seqs[i].getStart(),\r
 313                                      command.seqs[i].getEnd());\r
 314           ds.setDescription(command.seqs[i].getDescription());\r
 315           command.seqs[i].setDatasetSequence(ds);\r
 316         }\r
 317 \r
 318         adjustFeatures(command, i, start, end, true);\r
 319       }\r
 320     }\r
 321 \r
 322     adjustAnnotations(command, true);\r
 323 \r
 324     command.string = null;\r
 325   }\r
 326 \r
 327   final void adjustAnnotations(Edit command, boolean insert)\r
 328   {\r
 329 \r
 330     AlignmentAnnotation[] annotations = null;\r
 331 \r
 332     if (command.fullAlignmentHeight)\r
 333     {\r
 334       annotations = command.al.getAlignmentAnnotation();\r
 335     }\r
 336     else\r
 337     {\r
 338       int aSize = 0;\r
 339       AlignmentAnnotation[] tmp;\r
 340       for (int s = 0; s < command.seqs.length; s++)\r
 341       {\r
 342         if (command.seqs[s].getAnnotation() == null)\r
 343         {\r
 344           continue;\r
 345         }\r
 346 \r
 347         if (aSize == 0)\r
 348         {\r
 349           annotations = command.seqs[s].getAnnotation();\r
 350         }\r
 351         else\r
 352         {\r
 353           tmp = new AlignmentAnnotation\r
 354               [aSize + command.seqs[s].getAnnotation().length];\r
 355 \r
 356           System.arraycopy(annotations, 0, tmp, 0, aSize);\r
 357 \r
 358           System.arraycopy(command.seqs[s].getAnnotation(),\r
 359                            0, tmp, aSize,\r
 360                            command.seqs[s].getAnnotation().length);\r
 361 \r
 362           annotations = tmp;\r
 363         }\r
 364 \r
 365         aSize = annotations.length;\r
 366       }\r
 367     }\r
 368 \r
 369     if (annotations == null)\r
 370     {\r
 371       return;\r
 372     }\r
 373 \r
 374     if (!insert)\r
 375     {\r
 376       command.deletedAnnotations = new Hashtable();\r
 377     }\r
 378 \r
 379     int aSize;\r
 380     Annotation[] temp;\r
 381     for (int a = 0; a < annotations.length; a++)\r
 382     {\r
 383       if (annotations[a].autoCalculated)\r
 384       {\r
 385         continue;\r
 386       }\r
 387 \r
 388       int tSize = 0;\r
 389 \r
 390       aSize = annotations[a].annotations.length;\r
 391       if (insert)\r
 392       {\r
 393         temp = new Annotation[aSize + command.number];\r
 394       }\r
 395       else\r
 396       {\r
 397         if (command.position < aSize)\r
 398         {\r
 399           if (command.position + command.number > aSize)\r
 400           {\r
 401             tSize = aSize;\r
 402           }\r
 403           else\r
 404           {\r
 405             tSize = aSize - command.number + command.position;\r
 406           }\r
 407         }\r
 408         else\r
 409         {\r
 410           tSize = aSize;\r
 411         }\r
 412 \r
 413         if (tSize < 0)\r
 414         {\r
 415           tSize = aSize;\r
 416         }\r
 417         temp = new Annotation[tSize];\r
 418 \r
 419       }\r
 420 \r
 421       if (insert)\r
 422       {\r
 423         if (command.position < annotations[a].annotations.length)\r
 424         {\r
 425           System.arraycopy(annotations[a].annotations,\r
 426                            0, temp, 0, command.position);\r
 427 \r
 428           if (command.deletedAnnotations != null\r
 429               &&\r
 430               command.deletedAnnotations.containsKey(annotations[a].\r
 431               annotationId))\r
 432           {\r
 433             Annotation[] restore = (Annotation[])\r
 434                 command.deletedAnnotations.get(annotations[a].annotationId);\r
 435 \r
 436             System.arraycopy(restore,\r
 437                              0,\r
 438                              temp,\r
 439                              command.position,\r
 440                              command.number);\r
 441 \r
 442           }\r
 443 \r
 444           System.arraycopy(annotations[a].annotations,\r
 445                            command.position, temp,\r
 446                            command.position + command.number,\r
 447                            aSize - command.position);\r
 448         }\r
 449         else\r
 450         {\r
 451           if (command.deletedAnnotations != null\r
 452               &&\r
 453               command.deletedAnnotations.containsKey(annotations[a].\r
 454               annotationId))\r
 455           {\r
 456             Annotation[] restore = (Annotation[])\r
 457                 command.deletedAnnotations.get(annotations[a].annotationId);\r
 458 \r
 459             temp = new Annotation[annotations[a].annotations.length +\r
 460                 restore.length];\r
 461             System.arraycopy(annotations[a].annotations,\r
 462                              0, temp, 0,\r
 463                              annotations[a].annotations.length);\r
 464             System.arraycopy(restore, 0, temp,\r
 465                              annotations[a].annotations.length, restore.length);\r
 466           }\r
 467           else\r
 468           {\r
 469             temp = annotations[a].annotations;\r
 470           }\r
 471         }\r
 472       }\r
 473       else\r
 474       {\r
 475         if (tSize != aSize || command.position < 2)\r
 476         {\r
 477           System.arraycopy(annotations[a].annotations,\r
 478                            0, temp, 0, command.position);\r
 479 \r
 480           Annotation[] deleted = new Annotation[command.number];\r
 481           System.arraycopy(annotations[a].annotations,\r
 482                            command.position, deleted, 0, command.number);\r
 483 \r
 484           command.deletedAnnotations.put(annotations[a].annotationId,\r
 485                                          deleted);\r
 486 \r
 487           System.arraycopy(annotations[a].annotations,\r
 488                            command.position + command.number,\r
 489                            temp, command.position,\r
 490                            aSize - command.position - command.number);\r
 491         }\r
 492         else\r
 493         {\r
 494           int dSize = aSize - command.position;\r
 495 \r
 496           if (dSize > 0)\r
 497           {\r
 498             Annotation[] deleted = new Annotation[command.number];\r
 499             System.arraycopy(annotations[a].annotations,\r
 500                              command.position, deleted, 0, dSize);\r
 501 \r
 502             command.deletedAnnotations.put(annotations[a].annotationId,\r
 503                                            deleted);\r
 504 \r
 505             tSize = Math.min(annotations[a].annotations.length,\r
 506                              command.position);\r
 507             temp = new Annotation[tSize];\r
 508             System.arraycopy(annotations[a].annotations,\r
 509                              0, temp, 0, tSize);\r
 510           }\r
 511           else\r
 512           {\r
 513             temp = annotations[a].annotations;\r
 514           }\r
 515         }\r
 516       }\r
 517 \r
 518       annotations[a].annotations = temp;\r
 519     }\r
 520   }\r
 521 \r
 522   final void adjustFeatures(Edit command, int index, int i, int j,\r
 523                             boolean insert)\r
 524   {\r
 525     SequenceI seq = command.seqs[index];\r
 526     SequenceI sequence = seq.getDatasetSequence();\r
 527     if (sequence == null)\r
 528     {\r
 529       sequence = seq;\r
 530     }\r
 531 \r
 532     if (insert)\r
 533     {\r
 534       if (command.editedFeatures != null\r
 535           && command.editedFeatures.containsKey(seq))\r
 536       {\r
 537         sequence.setSequenceFeatures(\r
 538             (SequenceFeature[]) command.editedFeatures.get(seq)\r
 539             );\r
 540       }\r
 541 \r
 542       return;\r
 543     }\r
 544 \r
 545     SequenceFeature[] sf = sequence.getSequenceFeatures();\r
 546 \r
 547     if (sf == null)\r
 548     {\r
 549       return;\r
 550     }\r
 551 \r
 552     SequenceFeature[] oldsf = new SequenceFeature[sf.length];\r
 553 \r
 554     int cSize = j - i;\r
 555 \r
 556     for (int s = 0; s < sf.length; s++)\r
 557     {\r
 558       SequenceFeature copy = new SequenceFeature(sf[s]);\r
 559 \r
 560       oldsf[s] = copy;\r
 561 \r
 562       if (sf[s].getEnd() < i)\r
 563       {\r
 564         continue;\r
 565       }\r
 566 \r
 567       if (sf[s].getBegin() > j)\r
 568       {\r
 569         sf[s].setBegin(copy.getBegin() - cSize);\r
 570         sf[s].setEnd(copy.getEnd() - cSize);\r
 571         continue;\r
 572       }\r
 573 \r
 574       if (sf[s].getBegin() >= i)\r
 575       {\r
 576         sf[s].setBegin(i);\r
 577       }\r
 578 \r
 579       if (sf[s].getEnd() < j)\r
 580       {\r
 581         sf[s].setEnd(j - 1);\r
 582       }\r
 583 \r
 584       sf[s].setEnd(sf[s].getEnd() - (cSize));\r
 585 \r
 586       if (sf[s].getBegin() > sf[s].getEnd())\r
 587       {\r
 588         sequence.deleteFeature(sf[s]);\r
 589       }\r
 590     }\r
 591 \r
 592     if (command.editedFeatures == null)\r
 593     {\r
 594       command.editedFeatures = new Hashtable();\r
 595     }\r
 596 \r
 597     command.editedFeatures.put(seq, oldsf);\r
 598 \r
 599   }\r
 600 \r
 601   class Edit\r
 602   {\r
 603     boolean fullAlignmentHeight = false;\r
 604     Hashtable deletedAnnotations;\r
 605     Hashtable editedFeatures;\r
 606     AlignmentI al;\r
 607     int command;\r
 608     char[][] string;\r
 609     SequenceI[] seqs;\r
 610     int[] alIndex;\r
 611     int position, number;\r
 612     char gapChar;\r
 613 \r
 614     Edit(int command,\r
 615          SequenceI[] seqs,\r
 616          int position,\r
 617          int number,\r
 618          char gapChar)\r
 619     {\r
 620       this.command = command;\r
 621       this.seqs = seqs;\r
 622       this.position = position;\r
 623       this.number = number;\r
 624       this.gapChar = gapChar;\r
 625     }\r
 626 \r
 627     Edit(int command,\r
 628          SequenceI[] seqs,\r
 629          int position,\r
 630          int number,\r
 631          AlignmentI al)\r
 632     {\r
 633       this.gapChar = al.getGapCharacter();\r
 634       this.command = command;\r
 635       this.seqs = seqs;\r
 636       this.position = position;\r
 637       this.number = number;\r
 638       this.al = al;\r
 639 \r
 640       alIndex = new int[seqs.length];\r
 641       for (int i = 0; i < seqs.length; i++)\r
 642       {\r
 643         alIndex[i] = al.findIndex(seqs[i]);\r
 644       }\r
 645 \r
 646       fullAlignmentHeight = (al.getHeight() == seqs.length);\r
 647     }\r
 648   }\r
 649 \r
 650 }\r