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