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 /**\r
  24  *\r
  25  * <p>Title: EditCommmand</p>\r
  26  *\r
  27  * <p>Description: Essential information for performing\r
  28  * undo and redo for cut/paste insert/delete gap\r
  29  * which can be stored in the HistoryList </p>\r
  30  *\r
  31  * <p>Copyright: Copyright (c) 2006</p>\r
  32  *\r
  33  * <p>Company: Dundee University</p>\r
  34  *\r
  35  * @author not attributable\r
  36  * @version 1.0\r
  37  */\r
  38 public class EditCommand implements CommandI\r
  39 {\r
  40   public static String INSERT_GAP = "InsertGap";\r
  41   public static String DELETE_GAP = "DeleteGap";\r
  42   public static String CUT = "Cut";\r
  43   public static String PASTE = "Paste";\r
  44 \r
  45   Edit[] edits;\r
  46 \r
  47   String description;\r
  48 \r
  49   public EditCommand()\r
  50   {}\r
  51 \r
  52   public EditCommand(String description)\r
  53   {\r
  54     this.description = description;\r
  55   }\r
  56 \r
  57   public EditCommand(String description,\r
  58                      String command,\r
  59                      SequenceI[] seqs,\r
  60                      int position,\r
  61                      int number,\r
  62                      char gapChar)\r
  63   {\r
  64     this.description = description;\r
  65 \r
  66     if (command.equalsIgnoreCase(INSERT_GAP)\r
  67         || command.equalsIgnoreCase(DELETE_GAP))\r
  68     {\r
  69       edits = new Edit[] { new Edit(command, seqs, position, number, gapChar)};\r
  70     }\r
  71 \r
  72     performEdit(0);\r
  73   }\r
  74 \r
  75   public EditCommand( String description,\r
  76                       String command,\r
  77                       SequenceI[] seqs,\r
  78                       int position,\r
  79                       int number,\r
  80                       AlignmentI al)\r
  81    {\r
  82      this.description = description;\r
  83      if ( command.equalsIgnoreCase(CUT) || command.equalsIgnoreCase(PASTE))\r
  84      {\r
  85        edits = new Edit[]{new Edit(command, seqs, position, number, al)};\r
  86      }\r
  87 \r
  88      performEdit(0);\r
  89   }\r
  90 \r
  91 \r
  92   public String getDescription()\r
  93   {\r
  94     return description;\r
  95   }\r
  96 \r
  97   public int getSize()\r
  98   {\r
  99     return edits==null?0:edits.length;\r
 100   }\r
 101 \r
 102 \r
 103   public void appendEdit(String command,\r
 104                          SequenceI[] seqs,\r
 105                          int position,\r
 106                          int number,\r
 107                          char gapChar,\r
 108                          boolean performEdit)\r
 109   {\r
 110     Edit edit = new Edit(command, seqs, position, number, gapChar);\r
 111 \r
 112     if (edits != null)\r
 113     {\r
 114       Edit[] temp = new Edit[edits.length + 1];\r
 115       System.arraycopy(edits, 0, temp, 0, edits.length);\r
 116       edits = temp;\r
 117       edits[edits.length - 1] = edit;\r
 118     }\r
 119     else\r
 120       edits = new Edit[] {  edit  };\r
 121 \r
 122     if (performEdit)\r
 123       performEdit(edits.length - 1);\r
 124   }\r
 125 \r
 126   void performEdit(int commandIndex)\r
 127   {\r
 128     int eSize = edits.length;\r
 129     for (int e = commandIndex; e < eSize; e++)\r
 130     {\r
 131       if (edits[e].command.equals(INSERT_GAP))\r
 132       {\r
 133         insertGap(edits[e]);\r
 134       }\r
 135       else if (edits[e].command.equals(DELETE_GAP))\r
 136       {\r
 137         deleteGap(edits[e]);\r
 138       }\r
 139       else if(edits[e].command.equals(CUT))\r
 140       {\r
 141         cut(edits[e]);\r
 142       }\r
 143       else if(edits[e].command.equals(PASTE))\r
 144       {\r
 145         paste(edits[e]);\r
 146       }\r
 147     }\r
 148   }\r
 149 \r
 150   public void doCommand()\r
 151   {\r
 152     performEdit(0);\r
 153   }\r
 154 \r
 155   public void undoCommand()\r
 156   {\r
 157     int e = 0, eSize = edits.length;\r
 158     for (e = eSize-1; e > -1; e--)\r
 159     {\r
 160       if (edits[e].command.equals(INSERT_GAP))\r
 161       {\r
 162         deleteGap(edits[e]);\r
 163       }\r
 164       else if (edits[e].command.equals(DELETE_GAP))\r
 165       {\r
 166         insertGap(edits[e]);\r
 167       }\r
 168       else if (edits[e].command.equals(CUT))\r
 169       {\r
 170         paste(edits[e]);\r
 171       }\r
 172       else if (edits[e].command.equals(PASTE))\r
 173       {\r
 174         cut(edits[e]);\r
 175       }\r
 176     }\r
 177   }\r
 178 \r
 179   void insertGap(Edit command)\r
 180   {\r
 181     for(int s=0; s<command.seqs.length; s++)\r
 182     {\r
 183         command.seqs[s].insertCharAt(command.position,\r
 184                                      command.number,\r
 185                                      command.gapChar);\r
 186     }\r
 187   }\r
 188 \r
 189   void deleteGap(Edit command)\r
 190   {\r
 191     for (int s = 0; s < command.seqs.length; s++)\r
 192     {\r
 193       command.seqs[s].deleteChars(command.position, command.position+command.number);\r
 194     }\r
 195   }\r
 196 \r
 197   void cut(Edit command)\r
 198   {\r
 199     command.string = new String [command.seqs.length];\r
 200 \r
 201     for(int i=0; i<command.seqs.length; i++)\r
 202     {\r
 203       if(command.seqs[i].getLength()>command.position)\r
 204       {\r
 205         command.string[i] = command.seqs[i].getSequence(command.position,\r
 206             command.position + command.number);\r
 207 \r
 208         System.out.println("CUT:"+command.string[i]+":");\r
 209 \r
 210         command.seqs[i].deleteChars(command.position,\r
 211                                     command.position + command.number);\r
 212       }\r
 213 \r
 214       if(command.seqs[i].getLength()<1)\r
 215       {\r
 216         command.al.deleteSequence(command.seqs[i]);\r
 217       }\r
 218     }\r
 219   }\r
 220 \r
 221   void paste(Edit command)\r
 222   {\r
 223     StringBuffer tmp;\r
 224     for(int i=0; i<command.seqs.length; i++)\r
 225     {\r
 226       if(command.seqs[i].getLength()<1)\r
 227       {\r
 228         // ie this sequence was deleted, we need to\r
 229         // read it to the alignment\r
 230         if (command.alIndex[i] < command.al.getHeight())\r
 231           command.al.getSequences().insertElementAt(command.seqs[i],\r
 232               command.alIndex[i]);\r
 233         else\r
 234           command.al.addSequence(command.seqs[i]);\r
 235       }\r
 236       tmp = new StringBuffer(command.seqs[i].getSequence());\r
 237 \r
 238       if(command.string!=null && command.string[i]!=null)\r
 239       {\r
 240         tmp.insert(command.position, command.string[i]);\r
 241         command.string[i] = null;\r
 242       }\r
 243       command.seqs[i].setSequence(tmp.toString());\r
 244     }\r
 245 \r
 246     command.string = null;\r
 247   }\r
 248 \r
 249   class Edit\r
 250   {\r
 251     AlignmentI al;\r
 252     String command;\r
 253     String [] string;\r
 254     SequenceI[] seqs;\r
 255     int [] alIndex;\r
 256     int position, number;\r
 257     char gapChar;\r
 258 \r
 259     Edit(String command,\r
 260          SequenceI[] seqs,\r
 261          int position,\r
 262          int number,\r
 263          char gapChar)\r
 264     {\r
 265       this.command = command;\r
 266       this.seqs = seqs;\r
 267       this.position = position;\r
 268       this.number = number;\r
 269       this.gapChar = gapChar;\r
 270     }\r
 271 \r
 272 \r
 273     Edit(String command,\r
 274          SequenceI[] seqs,\r
 275          int position,\r
 276          int number,\r
 277          AlignmentI al)\r
 278     {\r
 279       this.command = command;\r
 280       this.seqs = seqs;\r
 281       this.position = position;\r
 282       this.number = number;\r
 283       this.al = al;\r
 284       alIndex = new int[seqs.length];\r
 285       for(int i=0; i<seqs.length; i++)\r
 286         alIndex[i] = al.findIndex(seqs[i]);\r
 287     }\r
 288 \r
 289   }\r
 290 \r
 291 }\r