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