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 java.net.URL;\r
  26 import jalview.schemes.*;\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 \r
 168   SequenceI refSeq = null;\r
 169   Hashtable annotationsHash = new Hashtable();\r
 170   public boolean readAnnotationFile(AlignmentI al,\r
 171                                     String file,\r
 172                                     String protocol)\r
 173   {\r
 174     try\r
 175     {\r
 176       BufferedReader in = null;\r
 177       if (protocol.equals(AppletFormatAdapter.FILE))\r
 178       {\r
 179         in = new BufferedReader(new FileReader(file));\r
 180       }\r
 181       else if (protocol.equals(AppletFormatAdapter.URL))\r
 182       {\r
 183         URL url = new URL(file);\r
 184         in = new BufferedReader(new InputStreamReader(url.openStream()));\r
 185       }\r
 186      else if (protocol.equals(AppletFormatAdapter.PASTE))\r
 187       {\r
 188         in = new BufferedReader(new StringReader(file));\r
 189       }\r
 190       else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))\r
 191       {\r
 192         java.io.InputStream is = getClass().getResourceAsStream("/" + file);\r
 193         if (is != null)\r
 194         {\r
 195           in = new BufferedReader(new java.io.InputStreamReader(is));\r
 196         }\r
 197     }\r
 198 \r
 199       String line, label, description, token;\r
 200       int graphStyle, index;\r
 201       int refSeqIndex = 1;\r
 202       int existingAnnotations = 0;\r
 203       if(al.getAlignmentAnnotation()!=null)\r
 204        existingAnnotations = al.getAlignmentAnnotation().length;\r
 205 \r
 206       int alWidth = al.getWidth();\r
 207 \r
 208       StringTokenizer st;\r
 209       Annotation[] annotations;\r
 210       AlignmentAnnotation annotation = null;\r
 211 \r
 212       // First confirm this is an Annotation file\r
 213       boolean jvAnnotationFile = false;\r
 214       while ( (line = in.readLine()) != null)\r
 215       {\r
 216         if (line.indexOf("#") == 0 )\r
 217           continue;\r
 218 \r
 219         if (line.indexOf("JALVIEW_ANNOTATION") > -1)\r
 220         {\r
 221           jvAnnotationFile = true;\r
 222           break;\r
 223         }\r
 224       }\r
 225 \r
 226       if(!jvAnnotationFile)\r
 227       {\r
 228         in.close();\r
 229         return false;\r
 230       }\r
 231 \r
 232       while ( (line = in.readLine()) != null)\r
 233       {\r
 234         if(line.indexOf("#")==0\r
 235            || line.indexOf("JALVIEW_ANNOTATION")>-1\r
 236            || line.length()==0)\r
 237           continue;\r
 238 \r
 239         st = new StringTokenizer(line, "\t");\r
 240         token = st.nextToken();\r
 241         if(token.equalsIgnoreCase("COLOUR"))\r
 242         {\r
 243           colourAnnotations(al, st.nextToken(), st.nextToken());\r
 244           continue;\r
 245         }\r
 246 \r
 247         else if(token.equalsIgnoreCase("COMBINE") )\r
 248         {\r
 249           combineAnnotations(al, st);\r
 250           continue;\r
 251         }\r
 252 \r
 253         else if (token.equalsIgnoreCase("GRAPHLINE"))\r
 254         {\r
 255           addLine(al, st);\r
 256           continue;\r
 257         }\r
 258 \r
 259 \r
 260         else if(token.equalsIgnoreCase("SEQUENCE_REF") )\r
 261         {\r
 262           refSeq = al.findName(st.nextToken());\r
 263           try{\r
 264             refSeqIndex = Integer.parseInt(st.nextToken());\r
 265             if(refSeqIndex<1)\r
 266             {\r
 267               refSeqIndex = 1;\r
 268               System.out.println("WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile");\r
 269             }\r
 270           }\r
 271           catch(Exception ex)\r
 272           {\r
 273             refSeqIndex = 1;\r
 274           }\r
 275 \r
 276           continue;\r
 277         }\r
 278 \r
 279         else if(token.equalsIgnoreCase("SEQUENCE_GROUP"))\r
 280         {\r
 281           addGroup(al, st);\r
 282           continue;\r
 283         }\r
 284 \r
 285         else if(token.equalsIgnoreCase("PROPERTIES"))\r
 286         {\r
 287           addProperties(al, st);\r
 288           continue;\r
 289         }\r
 290 \r
 291 \r
 292         graphStyle = AlignmentAnnotation.getGraphValueFromString(token);\r
 293         label = st.nextToken();\r
 294 \r
 295         if(st.countTokens()>1)\r
 296           description = st.nextToken();\r
 297         else\r
 298           description = null;\r
 299 \r
 300         line = st.nextToken();\r
 301 \r
 302         st = new StringTokenizer(line, "|", true);\r
 303         annotations = new Annotation[alWidth];\r
 304 \r
 305         index = 0;\r
 306         boolean emptyColumn = true;\r
 307 \r
 308 \r
 309         while (st.hasMoreElements() && index<alWidth)\r
 310         {\r
 311           token = st.nextToken().trim();\r
 312           if(token.equals("|"))\r
 313           {\r
 314             if(emptyColumn)\r
 315               index++;\r
 316 \r
 317             emptyColumn = true;\r
 318           }\r
 319           else\r
 320           {\r
 321             annotations[index++] = parseAnnotation(token);\r
 322             emptyColumn = false;\r
 323           }\r
 324         }\r
 325 \r
 326        annotation = new AlignmentAnnotation(label,\r
 327                                           description,\r
 328                                           annotations,\r
 329                                           0,\r
 330                                           0,\r
 331                                           graphStyle);\r
 332 \r
 333        if(refSeq!=null)\r
 334        {\r
 335          annotation.createSequenceMapping(refSeq, refSeqIndex, false);\r
 336          refSeq.addAlignmentAnnotation(annotation);\r
 337        }\r
 338 \r
 339        al.addAnnotation(annotation);\r
 340 \r
 341        al.setAnnotationIndex(annotation,  al.getAlignmentAnnotation().length - existingAnnotations-1);\r
 342       }\r
 343 \r
 344     }catch(Exception ex)\r
 345     {\r
 346       ex.printStackTrace();\r
 347       System.out.println("Problem reading annotation file: "+ex);\r
 348       return false;\r
 349     }\r
 350     return true;\r
 351   }\r
 352 \r
 353   Annotation parseAnnotation(String string)\r
 354   {\r
 355     String desc = null, displayChar="";\r
 356     char ss = ' '; // secondaryStructure\r
 357     float value = 0;\r
 358     boolean parsedValue = false;\r
 359     StringTokenizer st = new StringTokenizer(string, ",");\r
 360     String token;\r
 361     while(st.hasMoreTokens())\r
 362     {\r
 363       token = st.nextToken().trim();\r
 364       if(token.length()==0)\r
 365         continue;\r
 366 \r
 367       if(!parsedValue)\r
 368       {\r
 369         try{\r
 370           displayChar = token;\r
 371           value = new Float(token).floatValue();\r
 372           parsedValue = true;\r
 373           continue;\r
 374         }catch(NumberFormatException ex){}\r
 375       }\r
 376 \r
 377       if(token.equals("H") || token.equals("E"))\r
 378       {\r
 379         // Either this character represents a helix or sheet\r
 380         // or an integer which can be displayed\r
 381         ss = token.charAt(0);\r
 382         if(displayChar.equals(token.substring(0,1)))\r
 383           displayChar = "";\r
 384       }\r
 385       else if(desc==null)\r
 386         desc = token;\r
 387 \r
 388     }\r
 389 \r
 390     if(desc == null)\r
 391       desc = value+"";\r
 392 \r
 393     if(displayChar.length()>1 && desc.length()==1)\r
 394     {\r
 395       String tmp = displayChar;\r
 396       displayChar = desc;\r
 397       desc = tmp;\r
 398     }\r
 399 \r
 400     return new Annotation(displayChar, desc, ss, value);\r
 401   }\r
 402 \r
 403   void colourAnnotations(AlignmentI al, String label, String colour)\r
 404   {\r
 405     UserColourScheme ucs = new UserColourScheme(colour);\r
 406     Annotation[] annotations;\r
 407     for(int i=0; i<al.getAlignmentAnnotation().length; i++)\r
 408     {\r
 409       if(al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(label))\r
 410       {\r
 411         annotations = al.getAlignmentAnnotation()[i].annotations;\r
 412         for(int j=0; j<annotations.length; j++)\r
 413         {\r
 414           if(annotations[j]!=null)\r
 415             annotations[j].colour = ucs.findColour('A');\r
 416         }\r
 417       }\r
 418     }\r
 419   }\r
 420 \r
 421   void combineAnnotations(AlignmentI al, StringTokenizer st)\r
 422   {\r
 423     int graphGroup = -1;\r
 424     String group = st.nextToken();\r
 425     //First make sure we are not overwriting the graphIndex\r
 426     for(int i=0; i<al.getAlignmentAnnotation().length; i++)\r
 427     {\r
 428       if(al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))\r
 429       {\r
 430         graphGroup = al.getAlignmentAnnotation()[i].graphGroup +1;\r
 431         al.getAlignmentAnnotation()[i].graphGroup = graphGroup;\r
 432         break;\r
 433       }\r
 434     }\r
 435 \r
 436     //Now update groups\r
 437     while(st.hasMoreTokens())\r
 438     {\r
 439       group = st.nextToken();\r
 440       for(int i=0; i<al.getAlignmentAnnotation().length; i++)\r
 441       {\r
 442         if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))\r
 443         {\r
 444           al.getAlignmentAnnotation()[i].graphGroup = graphGroup;\r
 445           break;\r
 446         }\r
 447       }\r
 448     }\r
 449   }\r
 450 \r
 451   void addLine(AlignmentI al, StringTokenizer st)\r
 452   {\r
 453     String group = st.nextToken();\r
 454     AlignmentAnnotation annotation = null;\r
 455 \r
 456     for (int i = 0; i < al.getAlignmentAnnotation().length; i++)\r
 457     {\r
 458       if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))\r
 459       {\r
 460         annotation = al.getAlignmentAnnotation()[i];\r
 461         break;\r
 462       }\r
 463     }\r
 464 \r
 465     if(annotation==null)\r
 466       return;\r
 467     float value = new Float(st.nextToken()).floatValue();\r
 468     String label = st.hasMoreTokens() ?  st.nextToken() : null;\r
 469     java.awt.Color colour = null;\r
 470     if(st.hasMoreTokens())\r
 471     {\r
 472       UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
 473       colour = ucs.findColour('A');\r
 474     }\r
 475 \r
 476     annotation.setThreshold(new GraphLine(value, label, colour));\r
 477   }\r
 478 \r
 479   void addGroup(AlignmentI al, StringTokenizer st)\r
 480   {\r
 481     SequenceGroup sg = new SequenceGroup();\r
 482     sg.setName(st.nextToken());\r
 483     sg.setStartRes(Integer.parseInt(st.nextToken())-1);\r
 484     sg.setEndRes(Integer.parseInt(st.nextToken())-1);\r
 485 \r
 486     String index = st.nextToken();\r
 487     if(index.equals("-1"))\r
 488     {\r
 489       while (st.hasMoreElements())\r
 490       {\r
 491         sg.addSequence(al.findName(st.nextToken()), false);\r
 492       }\r
 493     }\r
 494     else\r
 495     {\r
 496       StringTokenizer st2 = new StringTokenizer(index, ",");\r
 497 \r
 498       while (st2.hasMoreTokens())\r
 499       {\r
 500         String tmp = st2.nextToken();\r
 501         if (tmp.equals("*"))\r
 502         {\r
 503           for (int i = 0; i < al.getHeight(); i++)\r
 504           {\r
 505             sg.addSequence(al.getSequenceAt(i), false);\r
 506           }\r
 507         }\r
 508         else if (tmp.indexOf("-") >= 0)\r
 509         {\r
 510           StringTokenizer st3 = new StringTokenizer(tmp, "-");\r
 511 \r
 512           int start = (Integer.parseInt(st3.nextToken()));\r
 513           int end = (Integer.parseInt(st3.nextToken()));\r
 514 \r
 515           if (end > start)\r
 516             for (int i = start; i <= end; i++)\r
 517               sg.addSequence(al.getSequenceAt(i-1), false);\r
 518         }\r
 519         else\r
 520         {\r
 521           sg.addSequence(al.getSequenceAt(Integer.parseInt(tmp)-1 ), false);\r
 522         }\r
 523       }\r
 524     }\r
 525 \r
 526     if(refSeq!=null)\r
 527     {\r
 528       sg.setStartRes( refSeq.findIndex( sg.getStartRes()+1 )-1 );\r
 529       sg.setEndRes(   refSeq.findIndex( sg.getEndRes() +1) -1 );\r
 530     }\r
 531 \r
 532 \r
 533     al.addGroup(sg);\r
 534     annotationsHash.put(sg.getName(), sg);\r
 535   }\r
 536 \r
 537   void addProperties(AlignmentI al, StringTokenizer st)\r
 538   {\r
 539 \r
 540     //So far we have only added groups to the annotationHash,\r
 541     //the idea is in the future properties can be added to\r
 542     //alignments, other annotations etc\r
 543     SequenceGroup sg = (SequenceGroup)annotationsHash.get(st.nextToken());\r
 544 \r
 545     if(sg!=null)\r
 546     {\r
 547       String keyValue, key, value;\r
 548       while(st.hasMoreTokens())\r
 549       {\r
 550         keyValue = st.nextToken();\r
 551         key = keyValue.substring(0,keyValue.indexOf("="));\r
 552         value=keyValue.substring(keyValue.indexOf("=")+1);\r
 553 \r
 554         if(key.equalsIgnoreCase("description"))\r
 555           sg.setDescription(value);\r
 556         else if(key.equalsIgnoreCase("colour"))\r
 557           sg.cs = ColourSchemeProperty.getColour(al, value);\r
 558         else if (key.equalsIgnoreCase("pidThreshold"))\r
 559           sg.cs.setThreshold(Integer.parseInt(value), false);//\r
 560         else if (key.equalsIgnoreCase("outlineColour"))\r
 561          {\r
 562            sg.setOutlineColour(new UserColourScheme(value).findColour('A'));\r
 563          }\r
 564 \r
 565          //Boolean.valueOf(string).booleanValue();\r
 566         else if (key.equalsIgnoreCase("displayBoxes"))\r
 567          sg.setDisplayBoxes( Boolean.valueOf(value).booleanValue() );\r
 568         else if (key.equalsIgnoreCase("displayText"))\r
 569          sg.setDisplayText( Boolean.valueOf(value).booleanValue() );\r
 570         else if (key.equalsIgnoreCase("colourText"))\r
 571          sg.setColourText( Boolean.valueOf(value).booleanValue() );\r
 572         else if (key.equalsIgnoreCase("textCol1"))\r
 573          {\r
 574            sg.textColour = new UserColourScheme(value).findColour('A');\r
 575          }\r
 576         else if (key.equalsIgnoreCase("textCol2"))\r
 577         {\r
 578           sg.textColour2 = new UserColourScheme(value).findColour('A');\r
 579         }\r
 580         else if (key.equalsIgnoreCase("textColThreshold"))\r
 581          sg.thresholdTextColour = Integer.parseInt(value);\r
 582 \r
 583       }\r
 584     }\r
 585   }\r
 586 }\r