src/jalview/io/FeaturesFile.java

   1 /*\r
   2 * Jalview - A Sequence Alignment Editor and Viewer\r
   3 * Copyright (C) 2005 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.io;\r
  20 \r
  21 import jalview.datamodel.*;\r
  22 \r
  23 import java.io.*;\r
  24 import java.util.*;\r
  25 import jalview.schemes.UserColourScheme;\r
  26 \r
  27 \r
  28 /**\r
  29  * DOCUMENT ME!\r
  30  *\r
  31  * @author $author$\r
  32  * @version $Revision$\r
  33  */\r
  34 public class FeaturesFile extends AlignFile\r
  35 {\r
  36     /**\r
  37      * Creates a new FeaturesFile object.\r
  38      */\r
  39     public FeaturesFile()\r
  40     {\r
  41     }\r
  42 \r
  43     /**\r
  44      * Creates a new FeaturesFile object.\r
  45      *\r
  46      * @param inStr DOCUMENT ME!\r
  47      */\r
  48     public FeaturesFile(String inStr)\r
  49     {\r
  50         super(inStr);\r
  51     }\r
  52 \r
  53     /**\r
  54      * Creates a new FeaturesFile object.\r
  55      *\r
  56      * @param inFile DOCUMENT ME!\r
  57      * @param type DOCUMENT ME!\r
  58      *\r
  59      * @throws IOException DOCUMENT ME!\r
  60      */\r
  61     public FeaturesFile(String inFile, String type)\r
  62        throws IOException\r
  63     {\r
  64         super(inFile, type);\r
  65     }\r
  66 \r
  67     /**\r
  68      * The Application can render HTML, but the applet will\r
  69      * remove HTML tags and replace links with %LINK%\r
  70      * Both need to read links in HTML however\r
  71      *\r
  72      * @throws IOException DOCUMENT ME!\r
  73      */\r
  74     public boolean parse(AlignmentI align,\r
  75                          Hashtable colours,\r
  76                          boolean removeHTML)\r
  77     {\r
  78       return parse(align, colours, null, removeHTML);\r
  79     }\r
  80     /**\r
  81      * The Application can render HTML, but the applet will\r
  82      * remove HTML tags and replace links with %LINK%\r
  83      * Both need to read links in HTML however\r
  84      *\r
  85      * @throws IOException DOCUMENT ME!\r
  86      */\r
  87     public boolean parse(AlignmentI align,\r
  88                          Hashtable colours,\r
  89                          Hashtable featureLink,\r
  90                          boolean removeHTML)\r
  91     {\r
  92       String line = null;\r
  93       try\r
  94       {\r
  95         SequenceI seq = null;\r
  96         String type, desc, token=null;\r
  97 \r
  98         int index, start, end;\r
  99         float score;\r
 100         StringTokenizer st;\r
 101         SequenceFeature sf;\r
 102         String featureGroup = null, groupLink = null;\r
 103         Hashtable typeLink = new Hashtable();\r
 104 \r
 105         boolean GFFFile = true;\r
 106 \r
 107         while ( (line = nextLine()) != null)\r
 108         {\r
 109           if(line.startsWith("#"))\r
 110             continue;\r
 111 \r
 112           st = new StringTokenizer(line, "\t");\r
 113           if (st.countTokens()>1 && st.countTokens() < 4 )\r
 114           {\r
 115             GFFFile = false;\r
 116             type = st.nextToken();\r
 117             if (type.equalsIgnoreCase("startgroup"))\r
 118             {\r
 119               featureGroup = st.nextToken();\r
 120               if (st.hasMoreElements())\r
 121               {\r
 122                 groupLink = st.nextToken();\r
 123                 featureLink.put(featureGroup, groupLink);\r
 124               }\r
 125             }\r
 126             else if (type.equalsIgnoreCase("endgroup"))\r
 127             {\r
 128               //We should check whether this is the current group,\r
 129               //but at present theres no way of showing more than 1 group\r
 130               st.nextToken();\r
 131               featureGroup = null;\r
 132               groupLink = null;\r
 133             }\r
 134             else\r
 135             {\r
 136               UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
 137               colours.put(type, ucs.findColour("A"));\r
 138               if (st.hasMoreElements())\r
 139               {\r
 140                 String link = st.nextToken();\r
 141                 typeLink.put(type, link);\r
 142                 if(featureLink==null)\r
 143                   featureLink = new Hashtable();\r
 144                 featureLink.put(type, link);\r
 145               }\r
 146 \r
 147             }\r
 148             continue;\r
 149           }\r
 150 \r
 151           while (st.hasMoreElements())\r
 152           {\r
 153 \r
 154             if(GFFFile)\r
 155             {\r
 156               // Still possible this is an old Jalview file,\r
 157               // which does not have type colours at the beginning\r
 158               token = st.nextToken();\r
 159               seq = align.findName(token);\r
 160               if(seq != null)\r
 161               {\r
 162                 desc = st.nextToken();\r
 163                 type = st.nextToken();\r
 164                 start = Integer.parseInt(st.nextToken());\r
 165                 end = Integer.parseInt(st.nextToken());\r
 166                 try\r
 167                 {\r
 168                   score = Float.parseFloat(st.nextToken());\r
 169                 }\r
 170                 catch (NumberFormatException ex)\r
 171                 {\r
 172                   score = 0;\r
 173                 }\r
 174 \r
 175                 sf = new SequenceFeature(type, desc, start, end, score, null);\r
 176 \r
 177                 try\r
 178                 {\r
 179                   sf.setValue("STRAND", st.nextToken());\r
 180                   sf.setValue("FRAME", st.nextToken());\r
 181                 }\r
 182                 catch (Exception ex)\r
 183                 {}\r
 184 \r
 185                 seq.getDatasetSequence().addSequenceFeature(sf);\r
 186 \r
 187                 break;\r
 188               }\r
 189             }\r
 190 \r
 191             if(GFFFile && seq==null)\r
 192             {\r
 193               desc = token;\r
 194             }\r
 195             else\r
 196               desc = st.nextToken();\r
 197 \r
 198 \r
 199             token = st.nextToken();\r
 200             if (!token.equals("ID_NOT_SPECIFIED"))\r
 201             {\r
 202               seq = align.findName(token);\r
 203               st.nextToken();\r
 204             }\r
 205             else\r
 206             {\r
 207               try{\r
 208                 index = Integer.parseInt(st.nextToken());\r
 209                 seq = align.getSequenceAt(index);\r
 210               }\r
 211               catch(NumberFormatException ex)\r
 212               {\r
 213                 seq = null;\r
 214               }\r
 215             }\r
 216 \r
 217             if(seq==null)\r
 218             {\r
 219               System.out.println("Sequence not found: "+line);\r
 220               break;\r
 221             }\r
 222 \r
 223             start = Integer.parseInt(st.nextToken());\r
 224             end = Integer.parseInt(st.nextToken());\r
 225 \r
 226             type = st.nextToken();\r
 227 \r
 228             if (!colours.containsKey(type))\r
 229             {\r
 230               // Probably the old style groups file\r
 231               UserColourScheme ucs = new UserColourScheme(type);\r
 232               colours.put(type, ucs.findColour("A"));\r
 233             }\r
 234 \r
 235             sf = new SequenceFeature(type, desc, "", start, end, featureGroup);\r
 236 \r
 237             seq.addSequenceFeature(sf);\r
 238 \r
 239             if(groupLink!=null && removeHTML)\r
 240             {\r
 241               sf.addLink(groupLink);\r
 242               sf.description += "%LINK%";\r
 243             }\r
 244             if(typeLink.containsKey(type) && removeHTML)\r
 245             {\r
 246               sf.addLink(typeLink.get(type).toString());\r
 247               sf.description += "%LINK%";\r
 248             }\r
 249 \r
 250             parseDescriptionHTML(sf, removeHTML);\r
 251 \r
 252             //If we got here, its not a GFFFile\r
 253             GFFFile = false;\r
 254           }\r
 255         }\r
 256       }\r
 257       catch (Exception ex)\r
 258       {\r
 259         System.out.println(line);\r
 260         ex.printStackTrace();\r
 261         System.out.println("Error parsing feature file: " + ex +"\n"+line);\r
 262         return false;\r
 263       }\r
 264 \r
 265       return true;\r
 266     }\r
 267 \r
 268     void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)\r
 269     {\r
 270       StringBuffer sb = new StringBuffer();\r
 271       StringTokenizer st = new StringTokenizer(sf.getDescription(), "<");\r
 272       String token,  link;\r
 273       while(st.hasMoreElements())\r
 274       {\r
 275         token = st.nextToken("<>");\r
 276         if(token.equalsIgnoreCase("html") || token.startsWith("/"))\r
 277           continue;\r
 278 \r
 279         if(token.startsWith("a href="))\r
 280         {\r
 281           link = token.substring(token.indexOf("\"")+1, token.length()-1);\r
 282           String label = st.nextToken("<>");\r
 283           sf.addLink(label+"|"+link);\r
 284           sb.append(label+"%LINK%");\r
 285         }\r
 286         else if(token.equalsIgnoreCase("br"))\r
 287           sb.append("\n");\r
 288         else\r
 289           sb.append(token);\r
 290       }\r
 291 \r
 292       if(removeHTML)\r
 293         sf.description = sb.toString();\r
 294   }\r
 295 \r
 296     /**\r
 297      * DOCUMENT ME!\r
 298      *\r
 299      * @param s DOCUMENT ME!\r
 300      * @param len DOCUMENT ME!\r
 301      * @param gaps DOCUMENT ME!\r
 302      * @param displayId DOCUMENT ME!\r
 303      *\r
 304      * @return DOCUMENT ME!\r
 305      */\r
 306     public String printJalviewFormat(SequenceI [] seqs,\r
 307                                      Hashtable visible)\r
 308     {\r
 309         StringBuffer out = new StringBuffer();\r
 310         SequenceFeature [] next;\r
 311 \r
 312         if(visible==null || visible.size()<1)\r
 313           return "No Features Visible";\r
 314 \r
 315         Enumeration en = visible.keys();\r
 316         String type;\r
 317         int color;\r
 318         while( en.hasMoreElements() )\r
 319         {\r
 320           type = en.nextElement().toString();\r
 321           color = Integer.parseInt( visible.get(type).toString() );\r
 322           out.append(type + "\t"\r
 323                      + jalview.util.Format.getHexString(\r
 324                          new java.awt.Color(color)  )\r
 325                      +"\n");\r
 326         }\r
 327 \r
 328         //Work out which groups are both present and visible\r
 329         Vector groups = new Vector();\r
 330         int groupIndex = 0;\r
 331 \r
 332         for(int i=0; i<seqs.length; i++)\r
 333         {\r
 334           next = seqs[i].getSequenceFeatures();\r
 335           if(next!=null)\r
 336           {\r
 337             for(int j=0; j<next.length; j++)\r
 338             {\r
 339               if (!visible.containsKey(next[j].type))\r
 340                 continue;\r
 341 \r
 342               if (    next[j].featureGroup != null\r
 343                   && !groups.contains(next[j].featureGroup))\r
 344                 groups.addElement(next[j].featureGroup);\r
 345             }\r
 346           }\r
 347         }\r
 348 \r
 349         String group = null;\r
 350 \r
 351         do\r
 352         {\r
 353 \r
 354 \r
 355           if (groups.size() > 0 && groupIndex < groups.size())\r
 356           {\r
 357             group = groups.elementAt(groupIndex).toString();\r
 358             out.append("\nSTARTGROUP\t" + group + "\n");\r
 359           }\r
 360           else\r
 361             group = null;\r
 362 \r
 363           for (int i = 0; i < seqs.length; i++)\r
 364           {\r
 365             next = seqs[i].getSequenceFeatures();\r
 366             if (next != null)\r
 367             {\r
 368               for (int j = 0; j < next.length; j++)\r
 369               {\r
 370                 if (!visible.containsKey(next[j].type))\r
 371                   continue;\r
 372 \r
 373                 if (group != null\r
 374                     && (next[j].featureGroup==null\r
 375                         || !next[j].featureGroup.equals(group))\r
 376                   )\r
 377                   continue;\r
 378 \r
 379                 if(group==null && next[j].featureGroup!=null)\r
 380                   continue;\r
 381 \r
 382                 if(next[j].description==null || next[j].description.equals(""))\r
 383                   out.append(next[j].type+"\t");\r
 384                 else\r
 385                   out.append(next[j].description + "\t");\r
 386 \r
 387                 out.append(  seqs[i].getName() + "\t-1\t"\r
 388                            + next[j].begin + "\t"\r
 389                            + next[j].end + "\t"\r
 390                            + next[j].type + "\n"\r
 391                     );\r
 392               }\r
 393             }\r
 394           }\r
 395 \r
 396           if(group!=null)\r
 397           {\r
 398             out.append("ENDGROUP\t"+group+"\n");\r
 399             groupIndex++;\r
 400           }\r
 401           else\r
 402             break;\r
 403 \r
 404         }\r
 405         while(groupIndex < groups.size()+1);\r
 406 \r
 407 \r
 408       return out.toString();\r
 409     }\r
 410 \r
 411     public String printGFFFormat(SequenceI [] seqs, Hashtable visible)\r
 412     {\r
 413       StringBuffer out = new StringBuffer();\r
 414       SequenceFeature [] next;\r
 415 \r
 416       for(int i=0; i<seqs.length; i++)\r
 417       {\r
 418         if(seqs[i].getSequenceFeatures()!=null)\r
 419         {\r
 420           next = seqs[i].getSequenceFeatures();\r
 421           for(int j=0; j<next.length; j++)\r
 422           {\r
 423             if(!visible.containsKey(next[j].type))\r
 424               continue;\r
 425 \r
 426             out.append(seqs[i].getName() + "\t"\r
 427                        + next[j].description + "\t"\r
 428                        + next[j].type  + "\t"\r
 429                        + next[j].begin + "\t"\r
 430                        + next[j].end   + "\t"\r
 431                        + next[j].score + "\t"\r
 432                       );\r
 433 \r
 434             if(next[j].getValue("STRAND")!=null)\r
 435               out.append(next[j].getValue("STRAND")+"\t");\r
 436             else\r
 437               out.append(".\t");\r
 438             if(next[j].getValue("FRAME")!=null)\r
 439               out.append(next[j].getValue("FRAME")+"\n");\r
 440             else\r
 441               out.append(".\n");\r
 442 \r
 443           }\r
 444         }\r
 445       }\r
 446 \r
 447       return out.toString();\r
 448     }\r
 449 \r
 450     public void parse()\r
 451     {\r
 452       //IGNORED\r
 453     }\r
 454 \r
 455     /**\r
 456      * DOCUMENT ME!\r
 457      *\r
 458      * @return DOCUMENT ME!\r
 459      */\r
 460     public String print()\r
 461     {\r
 462         return "USE printGFFFormat() or printJalviewFormat()";\r
 463     }\r
 464 }\r