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