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