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