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