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