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