src/jalview/io/AnnotationFile.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 \r
  20 package jalview.io;\r
  21 \r
  22 import java.io.*;\r
  23 import jalview.datamodel.*;\r
  24 import java.util.*;\r
  25 import jalview.schemes.UserColourScheme;\r
  26 import java.net.URL;\r
  27 \r
  28 \r
  29 public class AnnotationFile\r
  30 {\r
  31 \r
  32   public String printAnnotations(AlignmentAnnotation [] annotations)\r
  33   {\r
  34     StringBuffer text = new StringBuffer(\r
  35       "JALVIEW_ANNOTATION\n"\r
  36       +"# Created: "\r
  37       +new java.util.Date()+"\n\n");\r
  38 \r
  39     AlignmentAnnotation row;\r
  40     String comma;\r
  41     SequenceI seqref = null;\r
  42 \r
  43     StringBuffer colours = new StringBuffer();\r
  44     StringBuffer graphLine = new StringBuffer();\r
  45 \r
  46     Hashtable graphGroup = new Hashtable();\r
  47 \r
  48     java.awt.Color color;\r
  49 \r
  50     for(int i=0; i<annotations.length; i++)\r
  51     {\r
  52       row = annotations[i];\r
  53 \r
  54       if(!row.visible)\r
  55         continue;\r
  56 \r
  57       color = null;\r
  58 \r
  59       if( row.sequenceRef == null)\r
  60       {\r
  61         if(seqref!=null)\r
  62           text.append("\nSEQUENCE_REF\tALIGNMENT\n");\r
  63 \r
  64         seqref = null;\r
  65       }\r
  66 \r
  67       else if (seqref == null || seqref != row.sequenceRef)\r
  68       {\r
  69         seqref = row.sequenceRef;\r
  70         text.append("\nSEQUENCE_REF\t" + seqref.getName() + "\n");\r
  71       }\r
  72 \r
  73 \r
  74       if( row.graph == AlignmentAnnotation.NO_GRAPH)\r
  75       {\r
  76           text.append("NO_GRAPH\t");\r
  77       }\r
  78       else\r
  79       {\r
  80         if( row.graph == AlignmentAnnotation.BAR_GRAPH)\r
  81           text.append("BAR_GRAPH\t");\r
  82         else if(row.graph == AlignmentAnnotation.LINE_GRAPH)\r
  83           text.append("LINE_GRAPH\t");\r
  84 \r
  85         if(row.getThreshold()!=null)\r
  86             graphLine.append("GRAPHLINE\t"\r
  87                              + row.label + "\t"\r
  88                              + row.getThreshold().value + "\t"\r
  89                              + row.getThreshold().label + "\t"\r
  90                              + jalview.util.Format.getHexString(\r
  91                                  row.getThreshold().colour)+"\n"\r
  92                 );\r
  93 \r
  94           if(row.graphGroup>-1)\r
  95           {\r
  96             String key = String.valueOf(row.graphGroup);\r
  97             if(graphGroup.containsKey(key))\r
  98               graphGroup.put(key, graphGroup.get(key)\r
  99                              +"\t"+row.label);\r
 100             else\r
 101               graphGroup.put(key, row.label);\r
 102           }\r
 103       }\r
 104 \r
 105       text.append(row.label+"\t");\r
 106       if(row.description!=null)\r
 107         text.append(row.description+"\t");\r
 108 \r
 109       for(int j=0; j<row.annotations.length; j++)\r
 110       {\r
 111         if (seqref != null && jalview.util.Comparison.isGap(seqref.getCharAt(j)))\r
 112           continue;\r
 113 \r
 114         if(row.annotations[j]!=null)\r
 115         {\r
 116           comma = "";\r
 117           if (row.annotations[j].secondaryStructure!=' ')\r
 118           {\r
 119             text.append(comma + row.annotations[j].secondaryStructure);\r
 120             comma = ",";\r
 121           }\r
 122           if (row.annotations[j].displayCharacter.length() > 0\r
 123                   && !row.annotations[j].displayCharacter.equals(" "))\r
 124               {\r
 125                 text.append(comma + row.annotations[j].displayCharacter);\r
 126                 comma = ",";\r
 127               }\r
 128 \r
 129           if (row.annotations[j]!=null)\r
 130           {\r
 131             color = row.annotations[j].colour;\r
 132             if (row.annotations[j].value!=0f)\r
 133               text.append(comma + row.annotations[j].value);\r
 134           }\r
 135         }\r
 136         text.append("|");\r
 137       }\r
 138 \r
 139       text.append("\n");\r
 140 \r
 141       if(color!=null && color!=java.awt.Color.black)\r
 142       {\r
 143         colours.append("COLOUR\t"\r
 144                        +row.label+"\t"\r
 145                        +jalview.util.Format.getHexString(color)+"\n");\r
 146       }\r
 147 \r
 148     }\r
 149 \r
 150     text.append("\n");\r
 151 \r
 152     text.append(colours.toString());\r
 153     text.append(graphLine.toString());\r
 154     if(graphGroup.size()>0)\r
 155     {\r
 156       text.append("COMBINE\t");\r
 157       Enumeration en = graphGroup.elements();\r
 158       while(en.hasMoreElements())\r
 159       {\r
 160         text.append(en.nextElement()+"\n");\r
 161       }\r
 162     }\r
 163 \r
 164     return text.toString();\r
 165   }\r
 166 \r
 167   public boolean readAnnotationFile(AlignmentI al,\r
 168                                     String file,\r
 169                                     String protocol)\r
 170   {\r
 171     try\r
 172     {\r
 173       BufferedReader in = null;\r
 174       if (protocol.equals(AppletFormatAdapter.FILE))\r
 175       {\r
 176         in = new BufferedReader(new FileReader(file));\r
 177       }\r
 178       else if (protocol.equals(AppletFormatAdapter.URL))\r
 179       {\r
 180         URL url = new URL(file);\r
 181         in = new BufferedReader(new InputStreamReader(url.openStream()));\r
 182       }\r
 183      else if (protocol.equals(AppletFormatAdapter.PASTE))\r
 184       {\r
 185         in = new BufferedReader(new StringReader(file));\r
 186       }\r
 187       else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))\r
 188       {\r
 189         java.io.InputStream is = getClass().getResourceAsStream("/" + file);\r
 190         if (is != null)\r
 191         {\r
 192           in = new BufferedReader(new java.io.InputStreamReader(is));\r
 193         }\r
 194     }\r
 195 \r
 196       String line, label, description, token;\r
 197       int graphStyle, index;\r
 198       SequenceI refSeq = null;\r
 199       int refSeqIndex = 1;\r
 200       int existingAnnotations = 0;\r
 201       if(al.getAlignmentAnnotation()!=null)\r
 202        existingAnnotations = al.getAlignmentAnnotation().length;\r
 203 \r
 204       int alWidth = al.getWidth();\r
 205 \r
 206       StringTokenizer st;\r
 207       Annotation[] annotations;\r
 208       AlignmentAnnotation annotation = null;\r
 209 \r
 210       // First confirm this is an Annotation file\r
 211       boolean jvAnnotationFile = false;\r
 212       while ( (line = in.readLine()) != null)\r
 213       {\r
 214         if (line.indexOf("#") == 0 )\r
 215           continue;\r
 216 \r
 217         if (line.indexOf("JALVIEW_ANNOTATION") > -1)\r
 218         {\r
 219           jvAnnotationFile = true;\r
 220           break;\r
 221         }\r
 222       }\r
 223 \r
 224       if(!jvAnnotationFile)\r
 225       {\r
 226         in.close();\r
 227         return false;\r
 228       }\r
 229 \r
 230       while ( (line = in.readLine()) != null)\r
 231       {\r
 232         if(line.indexOf("#")==0\r
 233            || line.indexOf("JALVIEW_ANNOTATION")>-1\r
 234            || line.length()==0)\r
 235           continue;\r
 236 \r
 237         st = new StringTokenizer(line, "\t");\r
 238         token = st.nextToken();\r
 239         if(token.equalsIgnoreCase("COLOUR"))\r
 240         {\r
 241           colourAnnotations(al, st.nextToken(), st.nextToken());\r
 242           continue;\r
 243         }\r
 244 \r
 245         if(token.equalsIgnoreCase("COMBINE") )\r
 246         {\r
 247           combineAnnotations(al, st);\r
 248           continue;\r
 249         }\r
 250 \r
 251         if (token.equalsIgnoreCase("GRAPHLINE"))\r
 252         {\r
 253           addLine(al, st);\r
 254           continue;\r
 255         }\r
 256 \r
 257 \r
 258         if(token.equalsIgnoreCase("SEQUENCE_REF") )\r
 259         {\r
 260           refSeq = al.findName(st.nextToken());\r
 261           try{\r
 262             refSeqIndex = Integer.parseInt(st.nextToken());\r
 263             if(refSeqIndex<1)\r
 264             {\r
 265               refSeqIndex = 1;\r
 266               System.out.println("WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile");\r
 267             }\r
 268           }\r
 269           catch(Exception ex)\r
 270           {\r
 271             refSeqIndex = 1;\r
 272           }\r
 273 \r
 274           continue;\r
 275         }\r
 276 \r
 277 \r
 278         graphStyle = AlignmentAnnotation.getGraphValueFromString(token);\r
 279         label = st.nextToken();\r
 280 \r
 281         if(st.countTokens()>1)\r
 282           description = st.nextToken();\r
 283         else\r
 284           description = null;\r
 285 \r
 286         line = st.nextToken();\r
 287 \r
 288         st = new StringTokenizer(line, "|", true);\r
 289         annotations = new Annotation[alWidth];\r
 290 \r
 291         index = 0;\r
 292         boolean emptyColumn = true;\r
 293 \r
 294 \r
 295         while (st.hasMoreElements() && index<alWidth)\r
 296         {\r
 297           token = st.nextToken().trim();\r
 298           if(token.equals("|"))\r
 299           {\r
 300             if(emptyColumn)\r
 301               index++;\r
 302 \r
 303             emptyColumn = true;\r
 304           }\r
 305           else\r
 306           {\r
 307             annotations[index++] = parseAnnotation(token);\r
 308             emptyColumn = false;\r
 309           }\r
 310         }\r
 311 \r
 312        annotation = new AlignmentAnnotation(label,\r
 313                                           description,\r
 314                                           annotations,\r
 315                                           0,\r
 316                                           0,\r
 317                                           graphStyle);\r
 318 \r
 319        if(refSeq!=null)\r
 320        {\r
 321          annotation.createSequenceMapping(refSeq, refSeqIndex, false);\r
 322          refSeq.addAlignmentAnnotation(annotation);\r
 323        }\r
 324 \r
 325        al.addAnnotation(annotation);\r
 326 \r
 327        al.setAnnotationIndex(annotation,  al.getAlignmentAnnotation().length - existingAnnotations-1);\r
 328       }\r
 329 \r
 330     }catch(Exception ex)\r
 331     {\r
 332       ex.printStackTrace();\r
 333       System.out.println("Problem reading annotation file: "+ex);\r
 334       return false;\r
 335     }\r
 336     return true;\r
 337   }\r
 338 \r
 339   Annotation parseAnnotation(String string)\r
 340   {\r
 341     String desc = null, displayChar="";\r
 342     char ss = ' '; // secondaryStructure\r
 343     float value = 0;\r
 344     boolean parsedValue = false;\r
 345     StringTokenizer st = new StringTokenizer(string, ",");\r
 346     String token;\r
 347     while(st.hasMoreTokens())\r
 348     {\r
 349       token = st.nextToken().trim();\r
 350       if(token.length()==0)\r
 351         continue;\r
 352 \r
 353       if(!parsedValue)\r
 354       {\r
 355         try{\r
 356           displayChar = token;\r
 357           value = new Float(token).floatValue();\r
 358           parsedValue = true;\r
 359           continue;\r
 360         }catch(NumberFormatException ex){}\r
 361       }\r
 362 \r
 363       if(token.equals("H") || token.equals("E"))\r
 364       {\r
 365         // Either this character represents a helix or sheet\r
 366         // or an integer which can be displayed\r
 367         ss = token.charAt(0);\r
 368         if(displayChar.equals(token.substring(0,1)))\r
 369           displayChar = "";\r
 370       }\r
 371       else if(desc==null)\r
 372         desc = token;\r
 373 \r
 374     }\r
 375 \r
 376     if(desc == null)\r
 377       desc = value+"";\r
 378 \r
 379     if(displayChar.length()>1 && desc.length()==1)\r
 380     {\r
 381       String tmp = displayChar;\r
 382       displayChar = desc;\r
 383       desc = tmp;\r
 384     }\r
 385 \r
 386     return new Annotation(displayChar, desc, ss, value);\r
 387   }\r
 388 \r
 389   void colourAnnotations(AlignmentI al, String label, String colour)\r
 390   {\r
 391     UserColourScheme ucs = new UserColourScheme(colour);\r
 392     Annotation[] annotations;\r
 393     for(int i=0; i<al.getAlignmentAnnotation().length; i++)\r
 394     {\r
 395       if(al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(label))\r
 396       {\r
 397         annotations = al.getAlignmentAnnotation()[i].annotations;\r
 398         for(int j=0; j<annotations.length; j++)\r
 399         {\r
 400           if(annotations[j]!=null)\r
 401             annotations[j].colour = ucs.findColour('A');\r
 402         }\r
 403       }\r
 404     }\r
 405   }\r
 406 \r
 407   void combineAnnotations(AlignmentI al, StringTokenizer st)\r
 408   {\r
 409     int graphGroup = -1;\r
 410     String group = st.nextToken();\r
 411     //First make sure we are not overwriting the graphIndex\r
 412     for(int i=0; i<al.getAlignmentAnnotation().length; i++)\r
 413     {\r
 414       if(al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))\r
 415       {\r
 416         graphGroup = al.getAlignmentAnnotation()[i].graphGroup +1;\r
 417         al.getAlignmentAnnotation()[i].graphGroup = graphGroup;\r
 418         break;\r
 419       }\r
 420     }\r
 421 \r
 422     //Now update groups\r
 423     while(st.hasMoreTokens())\r
 424     {\r
 425       group = st.nextToken();\r
 426       for(int i=0; i<al.getAlignmentAnnotation().length; i++)\r
 427       {\r
 428         if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))\r
 429         {\r
 430           al.getAlignmentAnnotation()[i].graphGroup = graphGroup;\r
 431           break;\r
 432         }\r
 433       }\r
 434     }\r
 435   }\r
 436 \r
 437   void addLine(AlignmentI al, StringTokenizer st)\r
 438   {\r
 439     String group = st.nextToken();\r
 440     AlignmentAnnotation annotation = null;\r
 441 \r
 442     for (int i = 0; i < al.getAlignmentAnnotation().length; i++)\r
 443     {\r
 444       if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))\r
 445       {\r
 446         annotation = al.getAlignmentAnnotation()[i];\r
 447         break;\r
 448       }\r
 449     }\r
 450 \r
 451     if(annotation==null)\r
 452       return;\r
 453     float value = new Float(st.nextToken()).floatValue();\r
 454     String label = st.hasMoreTokens() ?  st.nextToken() : null;\r
 455     java.awt.Color colour = null;\r
 456     if(st.hasMoreTokens())\r
 457     {\r
 458       UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
 459       colour = ucs.findColour('A');\r
 460     }\r
 461 \r
 462     annotation.setThreshold(new GraphLine(value, label, colour));\r
 463 \r
 464   }\r
 465 }\r