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      * DOCUMENT ME!\r
  69      *\r
  70      * @throws IOException DOCUMENT ME!\r
  71      */\r
  72     public boolean parse(AlignmentI align,  Hashtable colours)\r
  73         throws IOException\r
  74     {\r
  75       String line = null;\r
  76       try\r
  77       {\r
  78         SequenceI seq = null;\r
  79         String type, desc, token=null;\r
  80 \r
  81         int index, start, end;\r
  82         float score;\r
  83         StringTokenizer st;\r
  84         SequenceFeature sf;\r
  85         String featureGroup = null;\r
  86 \r
  87         boolean GFFFile = true;\r
  88 \r
  89         while ( (line = nextLine()) != null)\r
  90         {\r
  91           if(line.startsWith("#"))\r
  92             continue;\r
  93 \r
  94           st = new StringTokenizer(line, "\t");\r
  95           if (st.countTokens()>1 && st.countTokens() < 4 )\r
  96           {\r
  97             GFFFile = false;\r
  98             type = st.nextToken();\r
  99             if (type.equalsIgnoreCase("startgroup"))\r
 100             {\r
 101               featureGroup = st.nextToken();\r
 102             }\r
 103             else if (type.equalsIgnoreCase("endgroup"))\r
 104             {\r
 105               //We should check whether this is the current group,\r
 106               //but at present theres no way of showing more than 1 group\r
 107               st.nextToken();\r
 108               featureGroup = null;\r
 109             }\r
 110             else\r
 111             {\r
 112               UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
 113               colours.put(type, ucs.findColour("A"));\r
 114             }\r
 115             continue;\r
 116           }\r
 117 \r
 118           while (st.hasMoreElements())\r
 119           {\r
 120 \r
 121             if(GFFFile)\r
 122             {\r
 123               // Still possible this is an old Jalview file,\r
 124               // which does not have type colours at the beginning\r
 125               token = st.nextToken();\r
 126               seq = align.findName(token);\r
 127               if(seq != null)\r
 128               {\r
 129                 desc = st.nextToken();\r
 130                 type = st.nextToken();\r
 131                 start = Integer.parseInt(st.nextToken());\r
 132                 end = Integer.parseInt(st.nextToken());\r
 133                 try\r
 134                 {\r
 135                   score = Float.parseFloat(st.nextToken());\r
 136                 }\r
 137                 catch (NumberFormatException ex)\r
 138                 {\r
 139                   score = 0;\r
 140                 }\r
 141 \r
 142                 sf = new SequenceFeature(type, desc, start, end, score, null);\r
 143 \r
 144                 try\r
 145                 {\r
 146                   sf.setValue("STRAND", st.nextToken());\r
 147                   sf.setValue("FRAME", st.nextToken());\r
 148                 }\r
 149                 catch (Exception ex)\r
 150                 {}\r
 151 \r
 152                 seq.getDatasetSequence().addSequenceFeature(sf);\r
 153 \r
 154                 break;\r
 155               }\r
 156             }\r
 157 \r
 158             if(GFFFile && seq==null)\r
 159             {\r
 160               desc = token;\r
 161             }\r
 162             else\r
 163               desc = st.nextToken();\r
 164 \r
 165 \r
 166             token = st.nextToken();\r
 167             if (!token.equals("ID_NOT_SPECIFIED"))\r
 168             {\r
 169               seq = align.findName(token);\r
 170               st.nextToken();\r
 171             }\r
 172             else\r
 173             {\r
 174               try{\r
 175                 index = Integer.parseInt(st.nextToken());\r
 176                 seq = align.getSequenceAt(index);\r
 177               }\r
 178               catch(NumberFormatException ex)\r
 179               {\r
 180                 seq = null;\r
 181               }\r
 182             }\r
 183 \r
 184             if(seq==null)\r
 185             {\r
 186               System.out.println("Sequence not found: "+line);\r
 187               break;\r
 188             }\r
 189 \r
 190             start = Integer.parseInt(st.nextToken());\r
 191             end = Integer.parseInt(st.nextToken());\r
 192 \r
 193             type = st.nextToken();\r
 194 \r
 195             if (!colours.containsKey(type))\r
 196             {\r
 197               // Probably the old style groups file\r
 198               UserColourScheme ucs = new UserColourScheme(type);\r
 199               colours.put(type, ucs.findColour("A"));\r
 200             }\r
 201 \r
 202             sf = new SequenceFeature(type, desc, "", start, end, featureGroup);\r
 203 \r
 204             seq.getDatasetSequence().addSequenceFeature(sf);\r
 205 \r
 206             //If we got here, its not a GFFFile\r
 207             GFFFile = false;\r
 208           }\r
 209         }\r
 210       }\r
 211       catch (Exception ex)\r
 212       {\r
 213         System.out.println(line);\r
 214         ex.printStackTrace();\r
 215         System.out.println("Error parsing groups file: " + ex +"\n"+line);\r
 216         return false;\r
 217       }\r
 218 \r
 219       return true;\r
 220 \r
 221     }\r
 222 \r
 223 \r
 224     /**\r
 225      * DOCUMENT ME!\r
 226      *\r
 227      * @param s DOCUMENT ME!\r
 228      * @param len DOCUMENT ME!\r
 229      * @param gaps DOCUMENT ME!\r
 230      * @param displayId DOCUMENT ME!\r
 231      *\r
 232      * @return DOCUMENT ME!\r
 233      */\r
 234     public String printJalviewFormat(SequenceI [] seqs,\r
 235                                      Hashtable visible)\r
 236     {\r
 237         StringBuffer out = new StringBuffer();\r
 238         SequenceFeature [] next;\r
 239 \r
 240         if(visible==null || visible.size()<1)\r
 241           return "No Features Visible";\r
 242 \r
 243         Enumeration en = visible.keys();\r
 244         String type;\r
 245         int color;\r
 246         while( en.hasMoreElements() )\r
 247         {\r
 248           type = en.nextElement().toString();\r
 249           color = Integer.parseInt( visible.get(type).toString() );\r
 250           out.append(type + "\t"\r
 251                      + jalview.util.Format.getHexString(\r
 252                          new java.awt.Color(color)  )\r
 253                      +"\n");\r
 254         }\r
 255 \r
 256         //Work out which groups are both present and visible\r
 257         Vector groups = new Vector();\r
 258         int groupIndex = 0;\r
 259 \r
 260         for(int i=0; i<seqs.length; i++)\r
 261         {\r
 262           next = seqs[i].getSequenceFeatures();\r
 263           if(next!=null)\r
 264           {\r
 265             for(int j=0; j<next.length; j++)\r
 266             {\r
 267               if (!visible.containsKey(next[j].type))\r
 268                 continue;\r
 269 \r
 270               if (    next[j].featureGroup != null\r
 271                   && !groups.contains(next[j].featureGroup))\r
 272                 groups.addElement(next[j].featureGroup);\r
 273             }\r
 274           }\r
 275         }\r
 276 \r
 277         String group = null;\r
 278 \r
 279         do\r
 280         {\r
 281           if (groups.size() > 0)\r
 282           {\r
 283             group = groups.elementAt(groupIndex).toString();\r
 284             out.append("\nSTARTGROUP\t" + group + "\n");\r
 285           }\r
 286 \r
 287 \r
 288           for (int i = 0; i < seqs.length; i++)\r
 289           {\r
 290             next = seqs[i].getSequenceFeatures();\r
 291             if (next != null)\r
 292             {\r
 293               for (int j = 0; j < next.length; j++)\r
 294               {\r
 295                 if (!visible.containsKey(next[j].type))\r
 296                   continue;\r
 297 \r
 298                 if (group != null && !next[j].featureGroup.equals(group))\r
 299                   continue;\r
 300 \r
 301                 if(next[j].description==null || next[j].description.equals(""))\r
 302                   out.append(next[j].type+"\t");\r
 303                 else\r
 304                   out.append(next[j].description + "\t");\r
 305 \r
 306                 out.append(  seqs[i].getName() + "\t-1\t"\r
 307                            + next[j].begin + "\t"\r
 308                            + next[j].end + "\t"\r
 309                            + next[j].type + "\n"\r
 310                     );\r
 311               }\r
 312             }\r
 313           }\r
 314 \r
 315           if(groups.size()>0)\r
 316           {\r
 317             out.append("ENDGROUP\t"+group+"\n");\r
 318           }\r
 319 \r
 320           groupIndex++;\r
 321         }\r
 322         while(groupIndex < groups.size());\r
 323 \r
 324 \r
 325       return out.toString();\r
 326     }\r
 327 \r
 328     public String printGFFFormat(SequenceI [] seqs, Hashtable visible)\r
 329     {\r
 330       StringBuffer out = new StringBuffer();\r
 331       SequenceFeature [] next;\r
 332 \r
 333       for(int i=0; i<seqs.length; i++)\r
 334       {\r
 335         if(seqs[i].getSequenceFeatures()!=null)\r
 336         {\r
 337           next = seqs[i].getSequenceFeatures();\r
 338           for(int j=0; j<next.length; j++)\r
 339           {\r
 340             if(!visible.containsKey(next[j].type))\r
 341               continue;\r
 342 \r
 343             out.append(seqs[i].getName() + "\t"\r
 344                        + next[j].description + "\t"\r
 345                        + next[j].type  + "\t"\r
 346                        + next[j].begin + "\t"\r
 347                        + next[j].end   + "\t"\r
 348                        + next[j].score + "\t"\r
 349                       );\r
 350 \r
 351             if(next[j].getValue("STRAND")!=null)\r
 352               out.append(next[j].getValue("STRAND")+"\t");\r
 353             else\r
 354               out.append(".\t");\r
 355             if(next[j].getValue("FRAME")!=null)\r
 356               out.append(next[j].getValue("FRAME")+"\n");\r
 357             else\r
 358               out.append(".\n");\r
 359 \r
 360           }\r
 361         }\r
 362       }\r
 363 \r
 364       return out.toString();\r
 365     }\r
 366 \r
 367     public void parse()\r
 368     {\r
 369       //IGNORED\r
 370     }\r
 371 \r
 372     /**\r
 373      * DOCUMENT ME!\r
 374      *\r
 375      * @return DOCUMENT ME!\r
 376      */\r
 377     public String print()\r
 378     {\r
 379         return "USE printGFFFormat() or printJalviewFormat()";\r
 380     }\r
 381 }\r