src/jalview/io/VamsasDatastore.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2005 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 org.vamsas.objects.core.*;\r
  23 \r
  24 import jalview.gui.*;\r
  25 import java.io.*;\r
  26 import java.util.jar.*;\r
  27 import org.exolab.castor.xml.*;\r
  28 import org.exolab.castor.mapping.Mapping;\r
  29 \r
  30 /*\r
  31 \r
  32  static {\r
  33  org.exolab.castor.util.LocalConfiguration.getInstance().getProperties().setProperty(\r
  34  "org.exolab.castor.serializer", "org.apache.xml.serialize.XMLSerilazizer");\r
  35  }\r
  36 \r
  37 */\r
  38 \r
  39 public class VamsasDatastore\r
  40 {\r
  41         AlignViewport av;\r
  42         org.exolab.castor.types.Date date\r
  43               = new org.exolab.castor.types.Date(new java.util.Date());\r
  44 \r
  45         public VamsasDatastore(AlignViewport av)\r
  46         {\r
  47                 this.av = av;\r
  48         }\r
  49 \r
  50         public void store(String file)\r
  51         {\r
  52           storeVAMSAS(file);\r
  53         }\r
  54 \r
  55         public void storeJalview(String file, AlignFrame af)\r
  56         {\r
  57           try\r
  58           {\r
  59             // 1. Load the mapping information from the file\r
  60             Mapping map = new Mapping(getClass().getClassLoader());\r
  61             java.net.URL url = getClass().getResource("/jalview_mapping.xml");\r
  62             map.loadMapping(url);\r
  63 \r
  64             // 2. Unmarshal the data\r
  65             // Unmarshaller unmar = new Unmarshaller();\r
  66             //unmar.setIgnoreExtraElements(true);\r
  67             //unmar.setMapping(map);\r
  68             // uni = (UniprotFile) unmar.unmarshal(new FileReader(file));\r
  69 \r
  70             // 3. marshal the data with the total price back and print the XML in the console\r
  71               Marshaller marshaller = new Marshaller( new FileWriter(file) );\r
  72 \r
  73              marshaller.setMapping(map);\r
  74              marshaller.marshal(af);\r
  75           }\r
  76           catch (Exception e)\r
  77           {\r
  78             e.printStackTrace();\r
  79           }\r
  80         }\r
  81 \r
  82 \r
  83 \r
  84         public VAMSAS storeVAMSAS(String file)\r
  85         {\r
  86           long time = System.currentTimeMillis();\r
  87           VAMSAS vamsas = new VAMSAS();\r
  88 \r
  89           try\r
  90           {\r
  91             FileOutputStream fos = new FileOutputStream(file);\r
  92             JarOutputStream jout = new JarOutputStream(fos);\r
  93 \r
  94 \r
  95             ////////////////////////////////////////////////////\r
  96             //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS\r
  97             PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,\r
  98                 "UTF-8"));\r
  99 \r
 100             jalview.datamodel.AlignmentI jal = av.getAlignment();\r
 101 \r
 102 \r
 103             ///////////////////////////////////////////\r
 104             // SAVE THE DATASET\r
 105             DataSet dataset = new DataSet();\r
 106             vamsas.addDataSet(dataset);\r
 107 \r
 108             Sequence sequence;\r
 109             DbRef dbref;\r
 110             for (int i = 0; i < jal.getHeight(); i++)\r
 111             {\r
 112               sequence = new Sequence();\r
 113               sequence.setSequence(jal.getDataset().getSequenceAt(i).getSequence());\r
 114               sequence.setName(jal.getDataset().getSequenceAt(i).getName());\r
 115               sequence.setStart(jal.getDataset().getSequenceAt(i).getStart());\r
 116               sequence.setEnd(jal.getDataset().getSequenceAt(i).getEnd());\r
 117 \r
 118 \r
 119               if(jal.getDataset().getSequenceAt(i).getSequenceFeatures()!=null)\r
 120               {\r
 121                 int sfSize = jal.getDataset().getSequenceAt(i).getSequenceFeatures().length;\r
 122 \r
 123                 for (int sf = 0; sf < sfSize; sf++)\r
 124                 {\r
 125                   jalview.datamodel.SequenceFeature feature =\r
 126                       (jalview.datamodel.SequenceFeature)\r
 127                       jal.getDataset().getSequenceAt(i).getSequenceFeatures()[sf];\r
 128 \r
 129                   DataSetAnnotations dsa = new DataSetAnnotations();\r
 130                   dsa.setType(feature.getType());\r
 131                   dsa.setBegin(feature.getBegin());\r
 132                   dsa.setEnd(feature.getEnd());\r
 133                   dsa.setDescription(feature.getDescription());\r
 134                   dsa.setStatus(feature.getStatus());\r
 135                   dsa.addProvenance(dummyProvenance());\r
 136                   dsa.setSeqRef(sequence);\r
 137                   dsa.setId("sf"+(time++));\r
 138                   dataset.addDataSetAnnotations(dsa);\r
 139                 }\r
 140               }\r
 141 \r
 142               if(jal.getDataset().getSequenceAt(i).getDBRef()!=null)\r
 143               {\r
 144                 java.util.Vector entries = jal.getDataset().getSequenceAt(i).getDBRef();\r
 145                 jalview.datamodel.DBRefEntry dbentry;\r
 146                 for(int db=0; db<entries.size(); db++)\r
 147                 {\r
 148                   dbentry = (jalview.datamodel.DBRefEntry)entries.elementAt(db);\r
 149                   dbref = new DbRef();\r
 150                   dbref.setAccessionId( dbentry.getAccessionId() );\r
 151                   dbref.setSource( dbentry.getSource() );\r
 152                   dbref.setVersion( dbentry.getVersion() );\r
 153                   dbref.setId("db"+(time++));\r
 154                   sequence.addDbRef(dbref);\r
 155                 }\r
 156 \r
 157               }\r
 158 \r
 159 \r
 160               if(jal.getDataset().getSequenceAt(i).getVamsasId()==null)\r
 161                 sequence.setId("ds" + (time++));\r
 162               else\r
 163                 sequence.setId(jal.getDataset().getSequenceAt(i).getVamsasId());\r
 164 \r
 165               dataset.addSequence(sequence);\r
 166             }\r
 167             // dataset.setProvenance(getVamsasProvenance(jal.getDataset().getProvenance()));\r
 168             //////////////////////////////////////////////\r
 169 \r
 170 \r
 171             //////////////////////////////////////////////\r
 172             //Save the Alignments\r
 173             Alignment alignment = new Alignment();\r
 174             alignment.setGapChar(av.getGapCharacter() + "");\r
 175             AlignmentSequence alseq = null;\r
 176             for (int i = 0; i < jal.getHeight(); i++)\r
 177             {\r
 178               alseq = new AlignmentSequence();\r
 179               alseq.setSequence(\r
 180                   jal.getSequenceAt(i).getSequence()\r
 181                   );\r
 182               alseq.setName(jal.getSequenceAt(i).getName());\r
 183               alseq.setStart(jal.getSequenceAt(i).getStart());\r
 184               alseq.setEnd(jal.getSequenceAt(i).getEnd());\r
 185               alseq.setRefid(dataset.getSequence(i));\r
 186               alseq.setId("as" + (time++));\r
 187               alignment.addAlignmentSequence(alseq);\r
 188             }\r
 189             // alignment.setProvenance(getVamsasProvenance(jal.getProvenance()));\r
 190             dataset.addAlignment(alignment);\r
 191             //////////////////////////////////////////////\r
 192 \r
 193 \r
 194 \r
 195             //////////////////////////////////////////////\r
 196             //SAVE ANNOTATIONS\r
 197             if (jal.getAlignmentAnnotation() != null)\r
 198             {\r
 199                 jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();\r
 200 \r
 201                 for (int i = 0; i < aa.length; i++)\r
 202                 {\r
 203                     if (aa[i].label.equals("Quality") ||\r
 204                             aa[i].label.equals("Conservation") ||\r
 205                             aa[i].label.equals("Consensus"))\r
 206                     {\r
 207                         continue;\r
 208                     }\r
 209 \r
 210                     AlignmentAnnotations an = new AlignmentAnnotations();\r
 211 \r
 212                     an.setDescription(aa[i].description);\r
 213                     // JBPNote - have to deal with the many lines for one graph thing\r
 214                     if (aa[i].graph>0)\r
 215                         an.setGraph(true); //aa[i].graph);\r
 216                     // JBPNote - store graphGroup in the Jalview specific bits.\r
 217                     an.setLabel(aa[i].label);\r
 218                     an.setProvenance(dummyProvenance());\r
 219 \r
 220                     AnnotationElement ae;\r
 221 \r
 222                     for (int a = 0; a < aa[i].annotations.length; a++)\r
 223                     {\r
 224                         if ((aa[i] == null) || (aa[i].annotations[a] == null))\r
 225                         {\r
 226                             continue;\r
 227                         }\r
 228 \r
 229                         ae = new AnnotationElement();\r
 230                         ae.setDescription(aa[i].annotations[a].description);\r
 231                         ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);\r
 232                         ae.setValue(aa[i].annotations[a].value);\r
 233                         ae.setPosition(a);\r
 234                         ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +\r
 235                             "");\r
 236                         an.addAnnotationElement(ae);\r
 237                     }\r
 238 \r
 239                     alignment.addAlignmentAnnotations(an);\r
 240                 }\r
 241             }\r
 242             ///////////////////////////////////////////////////////\r
 243 \r
 244 \r
 245           ////////////////////////////////////////////////\r
 246           ///SAVE THE TREES\r
 247           ///////////////////////////////////\r
 248           // FIND ANY ASSOCIATED TREES\r
 249           if (Desktop.desktop != null)\r
 250           {\r
 251             javax.swing.JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
 252 \r
 253             for (int t = 0; t < frames.length; t++)\r
 254             {\r
 255               if (frames[t] instanceof TreePanel)\r
 256               {\r
 257                 TreePanel tp = (TreePanel) frames[t];\r
 258 \r
 259                 if (tp.getAlignment() == jal)\r
 260                 {\r
 261                   Tree tree = new Tree();\r
 262                   tree.setTitle(tp.getTitle());\r
 263                   Newick newick = new Newick();\r
 264                   newick.setContent( tp.getTree().toString() );\r
 265                   newick.setTitle( tp.getTitle() );\r
 266                   newick.setId("t"+(time++));\r
 267                   tree.addNewick( newick );\r
 268                   tree.setProvenance(dummyProvenance());\r
 269                   alignment.addTree(tree);\r
 270                 }\r
 271               }\r
 272             }\r
 273           }\r
 274 \r
 275 \r
 276             JarEntry entry = new JarEntry("vamsas.xml");\r
 277             jout.putNextEntry(entry);\r
 278 \r
 279             vamsas.marshal(out);\r
 280 \r
 281             out.close();\r
 282             jout.close();\r
 283 \r
 284 \r
 285           }\r
 286           catch (Exception ex)\r
 287           {\r
 288             ex.printStackTrace();\r
 289           }\r
 290 \r
 291           return vamsas;\r
 292         }\r
 293 \r
 294         Tree jalview2VamsasTree()\r
 295         {\r
 296           Tree tree = new Tree();\r
 297 \r
 298           return tree;\r
 299         }\r
 300 \r
 301 \r
 302         public void load(String file)\r
 303         {\r
 304           VAMSAS vamsas = new VAMSAS() ;\r
 305 \r
 306           try\r
 307           {\r
 308             FileInputStream fis = new FileInputStream(file);\r
 309             JarInputStream jin = new JarInputStream(fis);\r
 310 \r
 311 \r
 312             ////////////////////////////////////////////////////\r
 313             //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS\r
 314             InputStreamReader in = new InputStreamReader(jin, "UTF-8");\r
 315             JarEntry jarentry = jin.getNextJarEntry();\r
 316             System.out.println("reading: "+jarentry.getName());\r
 317             vamsas = (VAMSAS) vamsas.unmarshal(in);\r
 318 \r
 319 \r
 320             /////////////////////////////////////\r
 321             /////LOAD DATASET\r
 322             DataSet dataset = vamsas.getDataSet(0);\r
 323 \r
 324             int i, iSize = dataset.getSequenceCount();\r
 325             jalview.datamodel.Sequence [] seqs = new jalview.datamodel.Sequence[iSize];\r
 326             DbRef [] dbref;\r
 327 \r
 328             for (i = 0; i < iSize ; i++)\r
 329             {\r
 330               seqs[i] = new jalview.datamodel.Sequence(\r
 331                   dataset.getSequence(i).getName(),\r
 332                   dataset.getSequence(i).getSequence(),\r
 333                    dataset.getSequence(i).getStart(),\r
 334                      dataset.getSequence(i).getEnd()  );\r
 335               seqs[i].setVamsasId(dataset.getSequence(i).getId());\r
 336 \r
 337               if (dataset.getDataSetAnnotations() != null)\r
 338               {\r
 339                 for (int dsa = 0; dsa < dataset.getDataSetAnnotationsCount(); dsa++)\r
 340                 {\r
 341                   if (dataset.getDataSetAnnotations(dsa).getSeqRef() ==\r
 342                       dataset.getSequence(i))\r
 343                   {\r
 344                     seqs[i].addSequenceFeature(new jalview.datamodel.\r
 345                                                SequenceFeature(\r
 346                         dataset.getDataSetAnnotations(dsa).getType(),\r
 347                         dataset.getDataSetAnnotations(dsa).getDescription(),\r
 348                         dataset.getDataSetAnnotations(dsa).getStatus(),\r
 349                         dataset.getDataSetAnnotations(dsa).getBegin(),\r
 350                         dataset.getDataSetAnnotations(dsa).getEnd(),\r
 351                         "vamsas"));\r
 352                   }\r
 353                 }\r
 354               }\r
 355               dbref = dataset.getSequence(i).getDbRef();\r
 356 \r
 357               if(dbref.length>0)\r
 358               {\r
 359                 for(int db=0; db<dbref.length; db++)\r
 360                 {\r
 361                   seqs[i].addDBRef( new jalview.datamodel.DBRefEntry\r
 362                       (\r
 363                            dbref[db].getSource().toString(),\r
 364                            dbref[db].getVersion().toString(),\r
 365                            dbref[db].getAccessionId().toString()));\r
 366                 }\r
 367               }\r
 368             }\r
 369             jalview.datamodel.Alignment jdataset = new jalview.datamodel.Alignment(seqs);\r
 370             ////////////////////////////////////////////////\r
 371 \r
 372 \r
 373             //////////////////////////////////////\r
 374             ////LOAD ALIGNMENT\r
 375             Alignment alignment = dataset.getAlignment(0);\r
 376             iSize = alignment.getAlignmentSequenceCount();\r
 377             seqs = new jalview.datamodel.Sequence[iSize];\r
 378             String id;\r
 379             int j, jSize = jdataset.getHeight();\r
 380             for (i = 0; i < iSize; i++)\r
 381             {\r
 382               seqs[i] = new jalview.datamodel.Sequence(\r
 383                   alignment.getAlignmentSequence(i).getName(),\r
 384                   alignment.getAlignmentSequence(i).getSequence(),\r
 385                   alignment.getAlignmentSequence(i).getStart(),\r
 386                   alignment.getAlignmentSequence(i).getEnd());\r
 387 \r
 388               id = ( (Sequence) alignment.getAlignmentSequence(i).getRefid()).getId();\r
 389 \r
 390              for(j=0; j<jSize; j++)\r
 391              {\r
 392                if(jdataset.getSequenceAt(j).getVamsasId().equals(id))\r
 393                {\r
 394                  seqs[i].setDatasetSequence( jdataset.getSequenceAt(j) );\r
 395                  break;\r
 396                }\r
 397              }\r
 398             }\r
 399             jalview.datamodel.Alignment jal = new jalview.datamodel.Alignment(seqs);\r
 400             jal.setDataset(jdataset);\r
 401             /*jal.getDataset().setProvenance(\r
 402                 getJalviewProvenance(dataset.getProvenance()));\r
 403             jal.setProvenance(\r
 404                 getJalviewProvenance(alignment.getProvenance()));\r
 405             */\r
 406              //////////////////////////////////////////////\r
 407 \r
 408 \r
 409             ////////////////////////////////////////////\r
 410             ////LOAD ANNOTATIONS\r
 411             ////////////////////\r
 412             if (alignment.getAlignmentAnnotationsCount()>0)\r
 413             {\r
 414               AlignmentAnnotations[] an = alignment.getAlignmentAnnotations();\r
 415 \r
 416               for (j = 0; j < an.length; j++)\r
 417               {\r
 418                 boolean topaliBreakpoint = false;\r
 419 \r
 420                 AnnotationElement[] ae = an[j].getAnnotationElement();\r
 421                 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[jal.\r
 422                     getWidth()];\r
 423 \r
 424                 try{\r
 425 \r
 426                   for (int aa = 0; aa < ae.length; aa++)\r
 427                   {\r
 428                     String dc = ae[aa].getDisplayCharacter()==null ? "dc" : ae[aa].getDisplayCharacter();\r
 429                     String desc = ae[aa].getDescription()==null ? "desc" : ae[aa].getDescription();\r
 430                     String ss = ae[aa].getSecondaryStructure()==null ? "ss" : ae[aa].getSecondaryStructure();\r
 431                     float value = ae[aa].getValue();\r
 432 \r
 433                     if(an[j].getGraph())\r
 434                     {\r
 435                       dc = value+"";\r
 436                       desc = value + "";\r
 437                     }\r
 438                     anot[ae[aa].getPosition()-1] = new jalview.datamodel.\r
 439                         Annotation(dc,desc,ss.charAt(0),value);\r
 440 \r
 441                     if(desc.equals("TOPALi Partition Breakpoint"))\r
 442                       topaliBreakpoint = true;\r
 443 \r
 444                   }\r
 445                 }catch(Exception ex)\r
 446                 {\r
 447                   ex.printStackTrace();\r
 448                   System.out.println("problem parsing annotations\n"+ex);}\r
 449 \r
 450                 jalview.datamodel.AlignmentAnnotation jaa = null;\r
 451 \r
 452                 if (an[j].getGraph())\r
 453                 {\r
 454                   jaa = new jalview.datamodel.AlignmentAnnotation(an[j].getLabel(),\r
 455                       an[j].getDescription(), anot, 0, 0, 1);\r
 456                 }\r
 457                 else\r
 458                 {\r
 459                   String label = an[j].getLabel();\r
 460                   if(topaliBreakpoint)\r
 461                     label = "TOPALi Partition Breakpoint";\r
 462                   jaa = new jalview.datamodel.AlignmentAnnotation(label,\r
 463                       an[j].getDescription(), anot);\r
 464                 }\r
 465 \r
 466                 jal.addAnnotation(jaa);\r
 467               }\r
 468             }\r
 469             /////////////////////////////////\r
 470 \r
 471             AlignFrame alignFrame = new AlignFrame(jal);\r
 472             jalview.gui.Desktop.addInternalFrame(alignFrame, "VAMSAS LOAD",\r
 473                                                  AlignFrame.NEW_WINDOW_WIDTH,\r
 474                                                  AlignFrame.NEW_WINDOW_HEIGHT);\r
 475 \r
 476             //LOAD TREES\r
 477             ///////////////////////////////////////\r
 478             if (alignment.getTreeCount() > 0)\r
 479             {\r
 480                 for (int t = 0; t < alignment.getTreeCount(); t++)\r
 481                 {\r
 482                   Tree tree = alignment.getTree(t);\r
 483 \r
 484                   alignFrame.ShowNewickTree(\r
 485                       new jalview.io.NewickFile(tree.getNewick(0).getContent()),\r
 486                       tree.getNewick(0).getTitle(),\r
 487                       600, 500,\r
 488                       t * 20 + 50, t * 20 + 50);\r
 489                 }\r
 490             }\r
 491 \r
 492 \r
 493             in.close();\r
 494             jin.close();\r
 495           }\r
 496           catch (Exception ex)\r
 497           {\r
 498             ex.printStackTrace();\r
 499           }\r
 500 \r
 501 \r
 502         }\r
 503 \r
 504 \r
 505 \r
 506         Provenance getVamsasProvenance(jalview.datamodel.Provenance jprov)\r
 507         {\r
 508           jalview.datamodel.ProvenanceEntry [] entries = null;\r
 509 \r
 510 \r
 511           Provenance prov = new Provenance();\r
 512           org.exolab.castor.types.Date date = new org.exolab.castor.types.Date(\r
 513       new java.util.Date());\r
 514           Entry provEntry;\r
 515 \r
 516           if(jprov!=null)\r
 517           {\r
 518             entries = jprov.getEntries();\r
 519             for (int i = 0; i < entries.length; i++)\r
 520             {\r
 521               provEntry = new Entry();\r
 522               try\r
 523               {\r
 524                 date = new org.exolab.castor.types.Date(entries[i].getDate());\r
 525               }\r
 526               catch (Exception ex)\r
 527               {\r
 528                 ex.printStackTrace();\r
 529 \r
 530                 date = new org.exolab.castor.types.Date(entries[i].getDate());\r
 531               }\r
 532               provEntry.setDate(date);\r
 533               provEntry.setUser(entries[i].getUser());\r
 534               provEntry.setAction(entries[i].getAction());\r
 535               prov.addEntry(provEntry);\r
 536             }\r
 537           }\r
 538           else\r
 539           {\r
 540             provEntry = new Entry();\r
 541             provEntry.setDate(date);\r
 542             provEntry.setUser(System.getProperty("user.name"));\r
 543             provEntry.setAction("Jalview");\r
 544             prov.addEntry(provEntry);\r
 545           }\r
 546 \r
 547           return prov;\r
 548         }\r
 549 \r
 550         jalview.datamodel.Provenance getJalviewProvenance(Provenance prov)\r
 551         {\r
 552 \r
 553           jalview.datamodel.Provenance jprov = new jalview.datamodel.Provenance();\r
 554           for (int i = 0; i < prov.getEntryCount(); i++)\r
 555           {\r
 556             jprov.addEntry(\r
 557                 prov.getEntry(i).getUser(),\r
 558                 prov.getEntry(i).getAction(),\r
 559                 prov.getEntry(i).getDate().toDate(),\r
 560                 prov.getEntry(i).getId()\r
 561                 );\r
 562           }\r
 563 \r
 564           return jprov;\r
 565         }\r
 566 \r
 567         Provenance dummyProvenance()\r
 568         {\r
 569           Provenance prov = new Provenance();\r
 570           Entry entry = new Entry();\r
 571           entry.setAction("Jalview");\r
 572           entry.setDate(new org.exolab.castor.types.Date(new java.util.Date()));\r
 573           entry.setUser(System.getProperty("user.name"));\r
 574           prov.addEntry(entry);\r
 575           return prov;\r
 576         }\r
 577 \r
 578 }\r