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   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   public AlignmentI getAlignment()\r
  87   {\r
  88     return edits[0].al;\r
  89   }\r
  90 \r
  91 \r
  92   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   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   public void doCommand()\r
 145   {\r
 146     performEdit(0);\r
 147   }\r
 148 \r
 149   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   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   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         command.seqs[i].deleteChars(command.position,\r
 207                                     command.position + command.number);\r
 208       }\r
 209 \r
 210       if(command.seqs[i].getLength()<1)\r
 211       {\r
 212         command.al.deleteSequence(command.seqs[i]);\r
 213       }\r
 214     }\r
 215 \r
 216     adjustAnnotations(command, false);\r
 217   }\r
 218 \r
 219   void paste(Edit command)\r
 220   {\r
 221     StringBuffer tmp;\r
 222     for(int i=0; i<command.seqs.length; i++)\r
 223     {\r
 224       if(command.seqs[i].getLength()<1)\r
 225       {\r
 226         // ie this sequence was deleted, we need to\r
 227         // read it to the alignment\r
 228         if (command.alIndex[i] < command.al.getHeight())\r
 229           command.al.getSequences().insertElementAt(command.seqs[i],\r
 230               command.alIndex[i]);\r
 231         else\r
 232           command.al.addSequence(command.seqs[i]);\r
 233       }\r
 234       tmp = new StringBuffer();\r
 235       tmp.append(command.seqs[i].getSequence());\r
 236 \r
 237       if(command.string!=null && command.string[i]!=null)\r
 238       {\r
 239         if(command.position>=tmp.length())\r
 240         {\r
 241           //This occurs if padding is on, and residues\r
 242           //are removed from end of alignment\r
 243           int length = command.position-tmp.length();\r
 244           while (length > 0)\r
 245           {\r
 246             tmp.append(command.gapChar);\r
 247             length--;\r
 248           }\r
 249         }\r
 250         tmp.insert(command.position, command.string[i]);\r
 251         command.string[i] = null;\r
 252       }\r
 253       command.seqs[i].setSequence(tmp.toString());\r
 254     }\r
 255 \r
 256 \r
 257     adjustAnnotations(command, true);\r
 258 \r
 259     command.string = null;\r
 260   }\r
 261 \r
 262 \r
 263   void adjustAnnotations(Edit command, boolean insert)\r
 264   {\r
 265 \r
 266     AlignmentAnnotation [] annotations = null;\r
 267 \r
 268     if (command.fullAlignmentHeight)\r
 269     {\r
 270       annotations = command.al.getAlignmentAnnotation();\r
 271     }\r
 272     else\r
 273     {\r
 274       int aSize = 0;\r
 275       AlignmentAnnotation [] tmp;\r
 276       for(int s=0; s<command.seqs.length; s++)\r
 277       {\r
 278         if(command.seqs[s].getAnnotation()==null)\r
 279           continue;\r
 280 \r
 281         if (aSize == 0)\r
 282             annotations = command.seqs[s].getAnnotation();\r
 283         else\r
 284         {\r
 285           tmp = new AlignmentAnnotation\r
 286               [aSize + command.seqs[s].getAnnotation().length];\r
 287 \r
 288           System.arraycopy(annotations,0,tmp,0,aSize);\r
 289 \r
 290           System.arraycopy(command.seqs[s].getAnnotation(),\r
 291               0,tmp,aSize,command.seqs[s].getAnnotation().length);\r
 292 \r
 293           annotations = tmp;\r
 294         }\r
 295 \r
 296 \r
 297         aSize = annotations.length;\r
 298       }\r
 299     }\r
 300 \r
 301     if(annotations==null)\r
 302       return;\r
 303 \r
 304 \r
 305       if(!insert)\r
 306         command.deletedAnnotations = new Hashtable();\r
 307 \r
 308       int aSize, tSize;\r
 309       Annotation [] temp;\r
 310       for (int a = 0; a < annotations.length; a++)\r
 311       {\r
 312         if(annotations[a].autoCalculated)\r
 313         {\r
 314           continue;\r
 315         }\r
 316 \r
 317         aSize = annotations[a].annotations.length;\r
 318         if(insert)\r
 319           tSize = aSize + command.number;\r
 320         else\r
 321           tSize = aSize - command.number;\r
 322 \r
 323         temp = new Annotation[tSize];\r
 324 \r
 325         if(insert)\r
 326         {\r
 327           if(command.position < annotations[a].annotations.length)\r
 328           {\r
 329             System.arraycopy(annotations[a].annotations,\r
 330                              0, temp, 0, command.position);\r
 331 \r
 332             if (command.deletedAnnotations != null\r
 333                 &&\r
 334                 command.deletedAnnotations.containsKey(annotations[a].annotationId))\r
 335             {\r
 336               Annotation[] restore = (Annotation[])\r
 337                   command.deletedAnnotations.get(annotations[a].annotationId);\r
 338 \r
 339               System.arraycopy(restore,\r
 340                                0,\r
 341                                temp,\r
 342                                command.position,\r
 343                                command.number);\r
 344 \r
 345             }\r
 346 \r
 347             System.arraycopy(annotations[a].annotations,\r
 348                              command.position, temp,\r
 349                              command.position + command.number,\r
 350                              aSize - command.position);\r
 351           }\r
 352           else\r
 353             temp = annotations[a].annotations;\r
 354         }\r
 355         else\r
 356         {\r
 357           if(command.position < annotations[a].annotations.length)\r
 358           {\r
 359             System.arraycopy(annotations[a].annotations,\r
 360                              0, temp, 0, command.position);\r
 361 \r
 362             Annotation[] deleted = new Annotation[command.number];\r
 363             System.arraycopy(annotations[a].annotations,\r
 364                              command.position, deleted, 0, command.number);\r
 365 \r
 366             command.deletedAnnotations.put(annotations[a].annotationId,\r
 367                                            deleted);\r
 368 \r
 369             System.arraycopy(annotations[a].annotations,\r
 370                              command.position + command.number,\r
 371                              temp, command.position,\r
 372                              aSize - command.position - command.number);\r
 373           }\r
 374           else\r
 375             temp = annotations[a].annotations;\r
 376         }\r
 377 \r
 378         annotations[a].annotations = temp;\r
 379      }\r
 380   }\r
 381 \r
 382 \r
 383   class Edit\r
 384   {\r
 385     boolean fullAlignmentHeight = false;\r
 386     Hashtable deletedAnnotations;\r
 387     AlignmentI al;\r
 388     int command;\r
 389     char [][] string;\r
 390     SequenceI[] seqs;\r
 391     int [] alIndex;\r
 392     int position, number;\r
 393     char gapChar;\r
 394 \r
 395     Edit(int command,\r
 396          SequenceI[] seqs,\r
 397          int position,\r
 398          int number,\r
 399          char gapChar)\r
 400     {\r
 401       this.command = command;\r
 402       this.seqs = seqs;\r
 403       this.position = position;\r
 404       this.number = number;\r
 405       this.gapChar = gapChar;\r
 406     }\r
 407 \r
 408 \r
 409     Edit(int command,\r
 410          SequenceI[] seqs,\r
 411          int position,\r
 412          int number,\r
 413          AlignmentI al)\r
 414     {\r
 415       this.gapChar = al.getGapCharacter();\r
 416       this.command = command;\r
 417       this.seqs = seqs;\r
 418       this.position = position;\r
 419       this.number = number;\r
 420       this.al = al;\r
 421 \r
 422       alIndex = new int[seqs.length];\r
 423       for(int i=0; i<seqs.length; i++)\r
 424       {\r
 425         alIndex[i] = al.findIndex(seqs[i]);\r
 426       }\r
 427 \r
 428       fullAlignmentHeight = (al.getHeight()==seqs.length);\r
 429     }\r
 430   }\r
 431 \r
 432 }\r