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, String file)\r
 168   {\r
 169     try\r
 170     {\r
 171       BufferedReader in = null;\r
 172       java.io.InputStream is = getClass().getResourceAsStream("/" + file);\r
 173       if (is != null)\r
 174       {\r
 175         in = new BufferedReader(new java.io.InputStreamReader(is));\r
 176       }\r
 177       else\r
 178       {\r
 179         try\r
 180         {\r
 181           URL url = new URL(file);\r
 182           in = new BufferedReader(new InputStreamReader(url.openStream()));\r
 183         }\r
 184         catch (java.net.MalformedURLException ex)\r
 185         {\r
 186           in = new BufferedReader(new FileReader(file));\r
 187         }\r
 188       }\r
 189 \r
 190       String line, label, description, token;\r
 191       int graphStyle, index;\r
 192       SequenceI refSeq = null;\r
 193       int refSeqIndex = 1;\r
 194       int existingAnnotations = 0;\r
 195       if(al.getAlignmentAnnotation()!=null)\r
 196        existingAnnotations = al.getAlignmentAnnotation().length;\r
 197 \r
 198       int alWidth = al.getWidth();\r
 199 \r
 200       StringTokenizer st;\r
 201       Annotation[] annotations;\r
 202       AlignmentAnnotation annotation = null;\r
 203 \r
 204       // First confirm this is an Annotation file\r
 205       boolean jvAnnotationFile = false;\r
 206       while ( (line = in.readLine()) != null)\r
 207       {\r
 208         if (line.indexOf("#") == 0 )\r
 209           continue;\r
 210 \r
 211         if (line.indexOf("JALVIEW_ANNOTATION") > -1)\r
 212         {\r
 213           jvAnnotationFile = true;\r
 214           break;\r
 215         }\r
 216       }\r
 217 \r
 218       if(!jvAnnotationFile)\r
 219       {\r
 220         in.close();\r
 221         return false;\r
 222       }\r
 223 \r
 224       while ( (line = in.readLine()) != null)\r
 225       {\r
 226         if(line.indexOf("#")==0\r
 227            || line.indexOf("JALVIEW_ANNOTATION")>-1\r
 228            || line.length()==0)\r
 229           continue;\r
 230 \r
 231         st = new StringTokenizer(line, "\t");\r
 232         token = st.nextToken();\r
 233         if(token.equalsIgnoreCase("COLOUR"))\r
 234         {\r
 235           colourAnnotations(al, st.nextToken(), st.nextToken());\r
 236           continue;\r
 237         }\r
 238 \r
 239         if(token.equalsIgnoreCase("COMBINE") )\r
 240         {\r
 241           combineAnnotations(al, st);\r
 242           continue;\r
 243         }\r
 244 \r
 245         if (token.equalsIgnoreCase("GRAPHLINE"))\r
 246         {\r
 247           addLine(al, st);\r
 248           continue;\r
 249         }\r
 250 \r
 251 \r
 252         if(token.equalsIgnoreCase("SEQUENCE_REF") )\r
 253         {\r
 254           refSeq = al.findName(st.nextToken());\r
 255           try{\r
 256             refSeqIndex = Integer.parseInt(st.nextToken());\r
 257             if(refSeqIndex<1)\r
 258             {\r
 259               refSeqIndex = 1;\r
 260               System.out.println("WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile");\r
 261             }\r
 262           }\r
 263           catch(Exception ex)\r
 264           {\r
 265             refSeqIndex = 1;\r
 266           }\r
 267 \r
 268           continue;\r
 269         }\r
 270 \r
 271 \r
 272         graphStyle = AlignmentAnnotation.getGraphValueFromString(token);\r
 273         label = st.nextToken();\r
 274 \r
 275         if(st.countTokens()>1)\r
 276           description = st.nextToken();\r
 277         else\r
 278           description = null;\r
 279 \r
 280         line = st.nextToken();\r
 281 \r
 282         st = new StringTokenizer(line, "|", true);\r
 283         annotations = new Annotation[alWidth];\r
 284 \r
 285         index = 0;\r
 286         boolean emptyColumn = true;\r
 287 \r
 288 \r
 289         while (st.hasMoreElements() && index<alWidth)\r
 290         {\r
 291           token = st.nextToken().trim();\r
 292           if(token.equals("|"))\r
 293           {\r
 294             if(emptyColumn)\r
 295               index++;\r
 296 \r
 297             emptyColumn = true;\r
 298           }\r
 299           else\r
 300           {\r
 301             annotations[index++] = parseAnnotation(token);\r
 302             emptyColumn = false;\r
 303           }\r
 304         }\r
 305 \r
 306        annotation = new AlignmentAnnotation(label,\r
 307                                           description,\r
 308                                           annotations,\r
 309                                           0,\r
 310                                           0,\r
 311                                           graphStyle);\r
 312 \r
 313        if(refSeq!=null)\r
 314        {\r
 315          annotation.createSequenceMapping(refSeq, refSeqIndex, false);\r
 316          refSeq.addAlignmentAnnotation(annotation);\r
 317        }\r
 318 \r
 319        al.addAnnotation(annotation);\r
 320 \r
 321        al.setAnnotationIndex(annotation,  al.getAlignmentAnnotation().length - existingAnnotations-1);\r
 322       }\r
 323 \r
 324     }catch(Exception ex)\r
 325     {\r
 326       ex.printStackTrace();\r
 327       System.out.println("Problem reading annotation file: "+ex);\r
 328       return false;\r
 329     }\r
 330     return true;\r
 331   }\r
 332 \r
 333   Annotation parseAnnotation(String string)\r
 334   {\r
 335     String desc = null, displayChar="";\r
 336     char ss = ' '; // secondaryStructure\r
 337     float value = 0;\r
 338     boolean parsedValue = false;\r
 339     StringTokenizer st = new StringTokenizer(string, ",");\r
 340     String token;\r
 341     while(st.hasMoreTokens())\r
 342     {\r
 343       token = st.nextToken().trim();\r
 344       if(token.length()==0)\r
 345         continue;\r
 346 \r
 347       if(!parsedValue)\r
 348       {\r
 349         try{\r
 350           displayChar = token;\r
 351           value = new Float(token).floatValue();\r
 352           parsedValue = true;\r
 353           continue;\r
 354         }catch(NumberFormatException ex){}\r
 355       }\r
 356 \r
 357       if(token.equals("H") || token.equals("E"))\r
 358       {\r
 359         // Either this character represents a helix or sheet\r
 360         // or an integer which can be displayed\r
 361         ss = token.charAt(0);\r
 362         if(displayChar.equals(token.substring(0,1)))\r
 363           displayChar = "";\r
 364       }\r
 365       else if(desc==null)\r
 366         desc = token;\r
 367 \r
 368     }\r
 369 \r
 370     if(desc == null)\r
 371       desc = value+"";\r
 372 \r
 373     if(displayChar.length()>1 && desc.length()==1)\r
 374     {\r
 375       String tmp = displayChar;\r
 376       displayChar = desc;\r
 377       desc = tmp;\r
 378     }\r
 379 \r
 380     return new Annotation(displayChar, desc, ss, value);\r
 381   }\r
 382 \r
 383   void colourAnnotations(AlignmentI al, String label, String colour)\r
 384   {\r
 385     UserColourScheme ucs = new UserColourScheme(colour);\r
 386     Annotation[] annotations;\r
 387     for(int i=0; i<al.getAlignmentAnnotation().length; i++)\r
 388     {\r
 389       if(al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(label))\r
 390       {\r
 391         annotations = al.getAlignmentAnnotation()[i].annotations;\r
 392         for(int j=0; j<annotations.length; j++)\r
 393         {\r
 394           if(annotations[j]!=null)\r
 395             annotations[j].colour = ucs.findColour('A');\r
 396         }\r
 397       }\r
 398     }\r
 399   }\r
 400 \r
 401   void combineAnnotations(AlignmentI al, StringTokenizer st)\r
 402   {\r
 403     int graphGroup = -1;\r
 404     String group = st.nextToken();\r
 405     //First make sure we are not overwriting the graphIndex\r
 406     for(int i=0; i<al.getAlignmentAnnotation().length; i++)\r
 407     {\r
 408       if(al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))\r
 409       {\r
 410         graphGroup = al.getAlignmentAnnotation()[i].graphGroup +1;\r
 411         al.getAlignmentAnnotation()[i].graphGroup = graphGroup;\r
 412         break;\r
 413       }\r
 414     }\r
 415 \r
 416     //Now update groups\r
 417     while(st.hasMoreTokens())\r
 418     {\r
 419       group = st.nextToken();\r
 420       for(int i=0; i<al.getAlignmentAnnotation().length; i++)\r
 421       {\r
 422         if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))\r
 423         {\r
 424           al.getAlignmentAnnotation()[i].graphGroup = graphGroup;\r
 425           break;\r
 426         }\r
 427       }\r
 428     }\r
 429   }\r
 430 \r
 431   void addLine(AlignmentI al, StringTokenizer st)\r
 432   {\r
 433     String group = st.nextToken();\r
 434     AlignmentAnnotation annotation = null;\r
 435 \r
 436     for (int i = 0; i < al.getAlignmentAnnotation().length; i++)\r
 437     {\r
 438       if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))\r
 439       {\r
 440         annotation = al.getAlignmentAnnotation()[i];\r
 441         break;\r
 442       }\r
 443     }\r
 444 \r
 445     if(annotation==null)\r
 446       return;\r
 447     float value = new Float(st.nextToken()).floatValue();\r
 448     String label = st.hasMoreTokens() ?  st.nextToken() : null;\r
 449     java.awt.Color colour = null;\r
 450     if(st.hasMoreTokens())\r
 451     {\r
 452       UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
 453       colour = ucs.findColour('A');\r
 454     }\r
 455 \r
 456     annotation.setThreshold(new GraphLine(value, label, colour));\r
 457 \r
 458   }\r
 459 }\r