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().size();\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().elementAt(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                     an.setGraph(aa[i].isGraph);\r
 214                     an.setLabel(aa[i].label);\r
 215                     an.setProvenance(dummyProvenance());\r
 216 \r
 217                     AnnotationElement ae;\r
 218 \r
 219                     for (int a = 0; a < aa[i].annotations.length; a++)\r
 220                     {\r
 221                         if ((aa[i] == null) || (aa[i].annotations[a] == null))\r
 222                         {\r
 223                             continue;\r
 224                         }\r
 225 \r
 226                         ae = new AnnotationElement();\r
 227                         ae.setDescription(aa[i].annotations[a].description);\r
 228                         ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);\r
 229                         ae.setValue(aa[i].annotations[a].value);\r
 230                         ae.setPosition(a);\r
 231                         ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +\r
 232                             "");\r
 233                         an.addAnnotationElement(ae);\r
 234                     }\r
 235 \r
 236                     alignment.addAlignmentAnnotations(an);\r
 237                 }\r
 238             }\r
 239             ///////////////////////////////////////////////////////\r
 240 \r
 241 \r
 242           ////////////////////////////////////////////////\r
 243           ///SAVE THE TREES\r
 244           ///////////////////////////////////\r
 245           // FIND ANY ASSOCIATED TREES\r
 246           if (Desktop.desktop != null)\r
 247           {\r
 248             javax.swing.JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
 249 \r
 250             for (int t = 0; t < frames.length; t++)\r
 251             {\r
 252               if (frames[t] instanceof TreePanel)\r
 253               {\r
 254                 TreePanel tp = (TreePanel) frames[t];\r
 255 \r
 256                 if (tp.getAlignment() == jal)\r
 257                 {\r
 258                   Tree tree = new Tree();\r
 259                   tree.setTitle(tp.getTitle());\r
 260                   Newick newick = new Newick();\r
 261                   newick.setContent( tp.getTree().toString() );\r
 262                   newick.setTitle( tp.getTitle() );\r
 263                   newick.setId("t"+(time++));\r
 264                   tree.addNewick( newick );\r
 265                   tree.setProvenance(dummyProvenance());\r
 266                   alignment.addTree(tree);\r
 267                 }\r
 268               }\r
 269             }\r
 270           }\r
 271 \r
 272 \r
 273             JarEntry entry = new JarEntry("vamsas.xml");\r
 274             jout.putNextEntry(entry);\r
 275 \r
 276             vamsas.marshal(out);\r
 277 \r
 278             out.close();\r
 279             jout.close();\r
 280 \r
 281 \r
 282           }\r
 283           catch (Exception ex)\r
 284           {\r
 285             ex.printStackTrace();\r
 286           }\r
 287 \r
 288           return vamsas;\r
 289         }\r
 290 \r
 291         Tree jalview2VamsasTree()\r
 292         {\r
 293           Tree tree = new Tree();\r
 294 \r
 295           return tree;\r
 296         }\r
 297 \r
 298 \r
 299         public void load(String file)\r
 300         {\r
 301           VAMSAS vamsas = new VAMSAS() ;\r
 302 \r
 303           try\r
 304           {\r
 305             FileInputStream fis = new FileInputStream(file);\r
 306             JarInputStream jin = new JarInputStream(fis);\r
 307 \r
 308 \r
 309             ////////////////////////////////////////////////////\r
 310             //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS\r
 311             InputStreamReader in = new InputStreamReader(jin, "UTF-8");\r
 312             JarEntry jarentry = jin.getNextJarEntry();\r
 313             System.out.println("reading: "+jarentry.getName());\r
 314             vamsas = (VAMSAS) vamsas.unmarshal(in);\r
 315 \r
 316 \r
 317             /////////////////////////////////////\r
 318             /////LOAD DATASET\r
 319             DataSet dataset = vamsas.getDataSet(0);\r
 320 \r
 321             int i, iSize = dataset.getSequenceCount();\r
 322             jalview.datamodel.Sequence [] seqs = new jalview.datamodel.Sequence[iSize];\r
 323             DbRef [] dbref;\r
 324 \r
 325             for (i = 0; i < iSize ; i++)\r
 326             {\r
 327               seqs[i] = new jalview.datamodel.Sequence(\r
 328                   dataset.getSequence(i).getName(),\r
 329                   dataset.getSequence(i).getSequence(),\r
 330                    dataset.getSequence(i).getStart(),\r
 331                      dataset.getSequence(i).getEnd()  );\r
 332               seqs[i].setVamsasId(dataset.getSequence(i).getId());\r
 333 \r
 334               if (dataset.getDataSetAnnotations() != null)\r
 335               {\r
 336                 for (int dsa = 0; dsa < dataset.getDataSetAnnotationsCount(); dsa++)\r
 337                 {\r
 338                   if (dataset.getDataSetAnnotations(dsa).getSeqRef() ==\r
 339                       dataset.getSequence(i))\r
 340                   {\r
 341                     seqs[i].addSequenceFeature(new jalview.datamodel.\r
 342                                                SequenceFeature(\r
 343                         dataset.getDataSetAnnotations(dsa).getType(),\r
 344                         dataset.getDataSetAnnotations(dsa).getDescription(),\r
 345                         dataset.getDataSetAnnotations(dsa).getStatus(),\r
 346                         dataset.getDataSetAnnotations(dsa).getBegin(),\r
 347                         dataset.getDataSetAnnotations(dsa).getEnd()));\r
 348                   }\r
 349                 }\r
 350               }\r
 351               dbref = dataset.getSequence(i).getDbRef();\r
 352 \r
 353               if(dbref.length>0)\r
 354               {\r
 355                 for(int db=0; db<dbref.length; db++)\r
 356                 {\r
 357                   seqs[i].addDBRef( new jalview.datamodel.DBRefEntry\r
 358                       (\r
 359                            dbref[db].getSource().toString(),\r
 360                            dbref[db].getVersion().toString(),\r
 361                            dbref[db].getAccessionId().toString()));\r
 362                 }\r
 363               }\r
 364             }\r
 365             jalview.datamodel.Alignment jdataset = new jalview.datamodel.Alignment(seqs);\r
 366             ////////////////////////////////////////////////\r
 367 \r
 368 \r
 369             //////////////////////////////////////\r
 370             ////LOAD ALIGNMENT\r
 371             Alignment alignment = dataset.getAlignment(0);\r
 372             iSize = alignment.getAlignmentSequenceCount();\r
 373             seqs = new jalview.datamodel.Sequence[iSize];\r
 374             String id;\r
 375             int j, jSize = jdataset.getHeight();\r
 376             for (i = 0; i < iSize; i++)\r
 377             {\r
 378               seqs[i] = new jalview.datamodel.Sequence(\r
 379                   alignment.getAlignmentSequence(i).getName(),\r
 380                   alignment.getAlignmentSequence(i).getSequence(),\r
 381                   alignment.getAlignmentSequence(i).getStart(),\r
 382                   alignment.getAlignmentSequence(i).getEnd());\r
 383 \r
 384               id = ( (Sequence) alignment.getAlignmentSequence(i).getRefid()).getId();\r
 385 \r
 386              for(j=0; j<jSize; j++)\r
 387              {\r
 388                if(jdataset.getSequenceAt(j).getVamsasId().equals(id))\r
 389                {\r
 390                  seqs[i].setDatasetSequence( jdataset.getSequenceAt(j) );\r
 391                  break;\r
 392                }\r
 393              }\r
 394             }\r
 395             jalview.datamodel.Alignment jal = new jalview.datamodel.Alignment(seqs);\r
 396             jal.setDataset(jdataset);\r
 397             jal.getDataset().setProvenance(\r
 398                 getJalviewProvenance(dataset.getProvenance()));\r
 399             jal.setProvenance(\r
 400                 getJalviewProvenance(alignment.getProvenance()));\r
 401             //////////////////////////////////////////////\r
 402 \r
 403 \r
 404             ////////////////////////////////////////////\r
 405             ////LOAD ANNOTATIONS\r
 406             ////////////////////\r
 407             if (alignment.getAlignmentAnnotationsCount()>0)\r
 408             {\r
 409               AlignmentAnnotations[] an = alignment.getAlignmentAnnotations();\r
 410 \r
 411               for (j = 0; j < an.length; j++)\r
 412               {\r
 413                 boolean topaliBreakpoint = false;\r
 414 \r
 415                 AnnotationElement[] ae = an[j].getAnnotationElement();\r
 416                 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[jal.\r
 417                     getWidth()];\r
 418 \r
 419                 try{\r
 420 \r
 421                   for (int aa = 0; aa < ae.length; aa++)\r
 422                   {\r
 423                     String dc = ae[aa].getDisplayCharacter()==null ? "dc" : ae[aa].getDisplayCharacter();\r
 424                     String desc = ae[aa].getDescription()==null ? "desc" : ae[aa].getDescription();\r
 425                     String ss = ae[aa].getSecondaryStructure()==null ? "ss" : ae[aa].getSecondaryStructure();\r
 426                     float value = ae[aa].getValue();\r
 427 \r
 428                     if(an[j].getGraph())\r
 429                     {\r
 430                       dc = value+"";\r
 431                       desc = value + "";\r
 432                     }\r
 433                     anot[ae[aa].getPosition()-1] = new jalview.datamodel.\r
 434                         Annotation(dc,desc,ss.charAt(0),value);\r
 435 \r
 436                     if(desc.equals("TOPALi Partition Breakpoint"))\r
 437                       topaliBreakpoint = true;\r
 438 \r
 439                   }\r
 440                 }catch(Exception ex)\r
 441                 {\r
 442                   ex.printStackTrace();\r
 443                   System.out.println("problem parsing annotations\n"+ex);}\r
 444 \r
 445                 jalview.datamodel.AlignmentAnnotation jaa = null;\r
 446 \r
 447                 if (an[j].getGraph())\r
 448                 {\r
 449                   jaa = new jalview.datamodel.AlignmentAnnotation(an[j].getLabel(),\r
 450                       an[j].getDescription(), anot, 0, 0, 1);\r
 451                 }\r
 452                 else\r
 453                 {\r
 454                   String label = an[j].getLabel();\r
 455                   if(topaliBreakpoint)\r
 456                     label = "TOPALi Partition Breakpoint";\r
 457                   jaa = new jalview.datamodel.AlignmentAnnotation(label,\r
 458                       an[j].getDescription(), anot);\r
 459                 }\r
 460 \r
 461                 jal.addAnnotation(jaa);\r
 462               }\r
 463             }\r
 464             /////////////////////////////////\r
 465 \r
 466             AlignFrame alignFrame = new AlignFrame(jal);\r
 467             jalview.gui.Desktop.addInternalFrame(alignFrame, "VAMSAS LOAD",\r
 468                                                  AlignFrame.NEW_WINDOW_WIDTH,\r
 469                                                  AlignFrame.NEW_WINDOW_HEIGHT);\r
 470 \r
 471             //LOAD TREES\r
 472             ///////////////////////////////////////\r
 473             if (alignment.getTreeCount() > 0)\r
 474             {\r
 475                 for (int t = 0; t < alignment.getTreeCount(); t++)\r
 476                 {\r
 477                   Tree tree = alignment.getTree(t);\r
 478 \r
 479                   alignFrame.ShowNewickTree(\r
 480                       new jalview.io.NewickFile(tree.getNewick(0).getContent()),\r
 481                       tree.getNewick(0).getTitle(),\r
 482                       600, 500,\r
 483                       t * 20 + 50, t * 20 + 50);\r
 484                 }\r
 485             }\r
 486 \r
 487 \r
 488             in.close();\r
 489             jin.close();\r
 490           }\r
 491           catch (Exception ex)\r
 492           {\r
 493             ex.printStackTrace();\r
 494           }\r
 495 \r
 496 \r
 497         }\r
 498 \r
 499 \r
 500 \r
 501         Provenance getVamsasProvenance(jalview.datamodel.Provenance jprov)\r
 502         {\r
 503           jalview.datamodel.ProvenanceEntry [] entries = null;\r
 504 \r
 505 \r
 506           Provenance prov = new Provenance();\r
 507           org.exolab.castor.types.Date date = new org.exolab.castor.types.Date(\r
 508       new java.util.Date());\r
 509           Entry provEntry;\r
 510 \r
 511           if(jprov!=null)\r
 512           {\r
 513             entries = jprov.getEntries();\r
 514             for (int i = 0; i < entries.length; i++)\r
 515             {\r
 516               provEntry = new Entry();\r
 517               try\r
 518               {\r
 519                 date = new org.exolab.castor.types.Date(entries[i].getDate());\r
 520               }\r
 521               catch (Exception ex)\r
 522               {\r
 523                 ex.printStackTrace();\r
 524 \r
 525                 date = new org.exolab.castor.types.Date(entries[i].getDate());\r
 526               }\r
 527               provEntry.setDate(date);\r
 528               provEntry.setUser(entries[i].getUser());\r
 529               provEntry.setAction(entries[i].getAction());\r
 530               prov.addEntry(provEntry);\r
 531             }\r
 532           }\r
 533           else\r
 534           {\r
 535             provEntry = new Entry();\r
 536             provEntry.setDate(date);\r
 537             provEntry.setUser(System.getProperty("user.name"));\r
 538             provEntry.setAction("Jalview");\r
 539             prov.addEntry(provEntry);\r
 540           }\r
 541 \r
 542           return prov;\r
 543         }\r
 544 \r
 545         jalview.datamodel.Provenance getJalviewProvenance(Provenance prov)\r
 546         {\r
 547 \r
 548           jalview.datamodel.Provenance jprov = new jalview.datamodel.Provenance();\r
 549           for (int i = 0; i < prov.getEntryCount(); i++)\r
 550           {\r
 551             jprov.addEntry(\r
 552                 prov.getEntry(i).getUser(),\r
 553                 prov.getEntry(i).getAction(),\r
 554                 prov.getEntry(i).getDate().toDate(),\r
 555                 prov.getEntry(i).getId()\r
 556                 );\r
 557           }\r
 558 \r
 559           return jprov;\r
 560         }\r
 561 \r
 562         Provenance dummyProvenance()\r
 563         {\r
 564           Provenance prov = new Provenance();\r
 565           Entry entry = new Entry();\r
 566           entry.setAction("Jalview");\r
 567           entry.setDate(new org.exolab.castor.types.Date(new java.util.Date()));\r
 568           entry.setUser(System.getProperty("user.name"));\r
 569           prov.addEntry(entry);\r
 570           return prov;\r
 571         }\r
 572 \r
 573 }\r