src/jalview/gui/Jalview2XML.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 package jalview.gui;\r
  20 \r
  21 \r
  22 import jalview.schemes.*;\r
  23 \r
  24 import jalview.gui.*;\r
  25 \r
  26 import java.io.*;\r
  27 \r
  28 import java.net.*;\r
  29 \r
  30 import java.util.*;\r
  31 \r
  32 import java.util.jar.*;\r
  33 \r
  34 import javax.swing.*;\r
  35 \r
  36 import org.exolab.castor.xml.*;\r
  37 \r
  38 import jalview.schemabinding.version2.*;\r
  39 \r
  40 \r
  41 \r
  42 \r
  43 /**\r
  44  * DOCUMENT ME!\r
  45  *\r
  46  * @author $author$\r
  47  * @version $Revision$\r
  48  */\r
  49 public class Jalview2XML\r
  50 {\r
  51     // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE\r
  52     public void SaveState(File statefile)\r
  53     {\r
  54         long creation = System.currentTimeMillis();\r
  55         JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
  56 \r
  57         if (frames == null)\r
  58         {\r
  59             return;\r
  60         }\r
  61 \r
  62         try\r
  63         {\r
  64             FileOutputStream fos = new FileOutputStream(statefile);\r
  65             JarOutputStream jout = new JarOutputStream(fos);\r
  66 \r
  67             //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS\r
  68             ////////////////////////////////////////////////////\r
  69             PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,\r
  70                         "UTF-8"));\r
  71 \r
  72             Vector shortNames = new Vector();\r
  73 \r
  74             //REVERSE ORDER\r
  75             for (int i = frames.length - 1; i > -1; i--)\r
  76             {\r
  77                 if (frames[i] instanceof AlignFrame)\r
  78                 {\r
  79                     AlignFrame af = (AlignFrame) frames[i];\r
  80 \r
  81                     String shortName = af.getTitle();\r
  82 \r
  83                     if (shortName.indexOf(File.separatorChar) > -1)\r
  84                     {\r
  85                         shortName = shortName.substring(shortName.lastIndexOf(\r
  86                                     File.separatorChar) + 1);\r
  87                     }\r
  88 \r
  89                     int count = 1;\r
  90 \r
  91                     while (shortNames.contains(shortName))\r
  92                     {\r
  93                         if (shortName.endsWith("_" + (count - 1)))\r
  94                         {\r
  95                             shortName = shortName.substring(0,\r
  96                                     shortName.lastIndexOf("_"));\r
  97                         }\r
  98 \r
  99                         shortName = shortName.concat("_" + count);\r
 100                         count++;\r
 101                     }\r
 102 \r
 103                     shortNames.addElement(shortName);\r
 104 \r
 105                     if (!shortName.endsWith(".xml"))\r
 106                     {\r
 107                         shortName = shortName + ".xml";\r
 108                     }\r
 109 \r
 110                     SaveState(af, creation, shortName, jout, out);\r
 111                 }\r
 112             }\r
 113 \r
 114             out.close();\r
 115             jout.close();\r
 116         }\r
 117         catch (Exception ex)\r
 118         {\r
 119             ex.printStackTrace();\r
 120         }\r
 121     }\r
 122 \r
 123     // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW\r
 124     public void SaveAlignment(AlignFrame af, String jarFile,\r
 125         String fileName)\r
 126     {\r
 127         try\r
 128         {\r
 129             FileOutputStream fos = new FileOutputStream(jarFile);\r
 130             JarOutputStream jout = new JarOutputStream(fos);\r
 131 \r
 132             //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS\r
 133             ////////////////////////////////////////////////////\r
 134             PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,\r
 135                         "UTF-8"));\r
 136 \r
 137             SaveState(af, System.currentTimeMillis(), fileName, jout, out);\r
 138             out.close();\r
 139             jout.close();\r
 140         }\r
 141         catch (Exception ex)\r
 142         {\r
 143           ex.printStackTrace();\r
 144         }\r
 145     }\r
 146 \r
 147     /**\r
 148      * DOCUMENT ME!\r
 149      *\r
 150      * @param af DOCUMENT ME!\r
 151      * @param timeStamp DOCUMENT ME!\r
 152      * @param fileName DOCUMENT ME!\r
 153      * @param jout DOCUMENT ME!\r
 154      * @param out DOCUMENT ME!\r
 155      */\r
 156     public void SaveState(AlignFrame af, long timeStamp,\r
 157         String fileName, JarOutputStream jout, PrintWriter out)\r
 158     {\r
 159         Vector seqids = new Vector();\r
 160         Vector userColours = new Vector();\r
 161 \r
 162         AlignViewport av = af.viewport;\r
 163 \r
 164         JalviewModel object = new JalviewModel();\r
 165         object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());\r
 166 \r
 167         object.setCreationDate(new java.util.Date(timeStamp));\r
 168         object.setVersion(jalview.bin.Cache.getProperty("VERSION"));\r
 169 \r
 170         jalview.datamodel.AlignmentI jal = af.viewport.alignment;\r
 171 \r
 172         SequenceSet vamsasSet = new SequenceSet();\r
 173         Sequence vamsasSeq;\r
 174         JalviewModelSequence jms = new JalviewModelSequence();\r
 175 \r
 176         vamsasSet.setGapChar(jal.getGapCharacter() + "");\r
 177 \r
 178         JSeq jseq;\r
 179 \r
 180         //SAVE SEQUENCES\r
 181         int id = 0;\r
 182 \r
 183         for (int i = 0; i < jal.getHeight(); i++)\r
 184         {\r
 185             seqids.add(jal.getSequenceAt(i));\r
 186 \r
 187             vamsasSeq = new Sequence();\r
 188             vamsasSeq.setId(id + "");\r
 189             vamsasSeq.setName(jal.getSequenceAt(i).getName());\r
 190             vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());\r
 191             vamsasSeq.setDescription(jal.getSequenceAt(i).getDescription());\r
 192 \r
 193             jseq = new JSeq();\r
 194             jseq.setStart(jal.getSequenceAt(i).getStart());\r
 195             jseq.setEnd(jal.getSequenceAt(i).getEnd());\r
 196 \r
 197             jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());\r
 198 \r
 199             jseq.setId(id);\r
 200 \r
 201             if(jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures()!=null)\r
 202             {\r
 203               jalview.datamodel.SequenceFeature[] sf\r
 204                   = jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
 205               int index = 0;\r
 206               while(index < sf.length)\r
 207               {\r
 208                 Features features = new Features();\r
 209 \r
 210                 features.setBegin(sf[index].getBegin());\r
 211                 features.setEnd(sf[index].getEnd());\r
 212                 features.setDescription(sf[index].getDescription());\r
 213                 features.setStatus(sf[index].getStatus());\r
 214                 features.setType(sf[index].getType());\r
 215                 features.setFeatureGroup(sf[index].getFeatureGroup());\r
 216                 jseq.addFeatures(features);\r
 217                 index ++;\r
 218               }\r
 219             }\r
 220 \r
 221             if(jal.getSequenceAt(i).getDatasetSequence().getPDBId()!=null)\r
 222             {\r
 223               Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getPDBId().elements();\r
 224               while(en.hasMoreElements())\r
 225               {\r
 226                 Pdbids pdb = new Pdbids();\r
 227                 jalview.datamodel.PDBEntry entry\r
 228                    = (jalview.datamodel.PDBEntry)en.nextElement();\r
 229 \r
 230                 pdb.setId(entry.getId());\r
 231                 pdb.setType(entry.getType());\r
 232 \r
 233                 if(entry.getProperty()!=null)\r
 234                 {\r
 235                   PdbentryItem item = new PdbentryItem();\r
 236                   Hashtable properties = entry.getProperty();\r
 237                   Enumeration en2 = properties.keys();\r
 238                   while(en2.hasMoreElements())\r
 239                   {\r
 240                     Property prop = new Property();\r
 241                     String key = en2.nextElement().toString();\r
 242                     prop.setName(key);\r
 243                     prop.setValue( properties.get(key).toString() );\r
 244                     item.addProperty(prop);\r
 245                   }\r
 246                   pdb.addPdbentryItem(item);\r
 247                 }\r
 248 \r
 249                 jseq.addPdbids(pdb);\r
 250               }\r
 251             }\r
 252 \r
 253             jms.addJSeq(jseq);\r
 254             vamsasSet.addSequence(vamsasSeq);\r
 255             id++;\r
 256         }\r
 257 \r
 258         //SAVE TREES\r
 259         ///////////////////////////////////\r
 260         if (af.viewport.currentTree != null)\r
 261         {\r
 262           // FIND ANY ASSOCIATED TREES\r
 263           // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT\r
 264           if (Desktop.desktop != null)\r
 265           {\r
 266             JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
 267 \r
 268             for (int t = 0; t < frames.length; t++)\r
 269             {\r
 270               if (frames[t] instanceof TreePanel)\r
 271               {\r
 272                 TreePanel tp = (TreePanel) frames[t];\r
 273 \r
 274                 if (tp.treeCanvas.av.alignment == jal)\r
 275                 {\r
 276                   Tree tree = new Tree();\r
 277                   tree.setTitle(tp.getTitle());\r
 278                   tree.setCurrentTree( (af.viewport.currentTree == tp.getTree()));\r
 279                   tree.setNewick(tp.getTree().toString());\r
 280                   tree.setThreshold(tp.treeCanvas.threshold);\r
 281 \r
 282                   tree.setFitToWindow(tp.fitToWindow.getState());\r
 283                   tree.setFontName(tp.getTreeFont().getName());\r
 284                   tree.setFontSize(tp.getTreeFont().getSize());\r
 285                   tree.setFontStyle(tp.getTreeFont().getStyle());\r
 286                   tree.setMarkUnlinked(tp.placeholdersMenu.getState());\r
 287 \r
 288                   tree.setShowBootstrap(tp.bootstrapMenu.getState());\r
 289                   tree.setShowDistances(tp.distanceMenu.getState());\r
 290 \r
 291                   tree.setHeight(tp.getHeight());\r
 292                   tree.setWidth(tp.getWidth());\r
 293                   tree.setXpos(tp.getX());\r
 294                   tree.setYpos(tp.getY());\r
 295 \r
 296                   jms.addTree(tree);\r
 297                 }\r
 298               }\r
 299             }\r
 300           }\r
 301         }\r
 302 \r
 303         //SAVE ANNOTATIONS\r
 304         if (jal.getAlignmentAnnotation() != null)\r
 305         {\r
 306             jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();\r
 307 \r
 308             for (int i = 0; i < aa.length; i++)\r
 309             {\r
 310                 if (aa[i].label.equals("Quality") ||\r
 311                         aa[i].label.equals("Conservation") ||\r
 312                         aa[i].label.equals("Consensus"))\r
 313                 {\r
 314                     continue;\r
 315                 }\r
 316 \r
 317                 Annotation an = new Annotation();\r
 318                 an.setDescription(aa[i].description);\r
 319                 if(aa[i].graph>0)\r
 320                 {\r
 321                   an.setGraph(true);\r
 322                   an.setGraphType(aa[i].graph);\r
 323                 }\r
 324                 else\r
 325                   an.setGraph(false);\r
 326 \r
 327                 an.setLabel(aa[i].label);\r
 328 \r
 329                 AnnotationElement ae;\r
 330 \r
 331                 for (int a = 0; a < aa[i].annotations.length; a++)\r
 332                 {\r
 333                     if ((aa[i] == null) || (aa[i].annotations[a] == null))\r
 334                     {\r
 335                         continue;\r
 336                     }\r
 337 \r
 338                     ae = new AnnotationElement();\r
 339                     ae.setDescription(aa[i].annotations[a].description);\r
 340                     ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);\r
 341                     ae.setValue(aa[i].annotations[a].value);\r
 342                     ae.setPosition(a);\r
 343                     ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +\r
 344                         "");\r
 345                     an.addAnnotationElement(ae);\r
 346                 }\r
 347 \r
 348                 vamsasSet.addAnnotation(an);\r
 349             }\r
 350         }\r
 351 \r
 352         //SAVE GROUPS\r
 353         if (jal.getGroups() != null)\r
 354         {\r
 355             JGroup[] groups = new JGroup[jal.getGroups().size()];\r
 356 \r
 357             for (int i = 0; i < groups.length; i++)\r
 358             {\r
 359                 groups[i] = new JGroup();\r
 360 \r
 361                 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()\r
 362                                                                                           .elementAt(i);\r
 363                 groups[i].setStart(sg.getStartRes());\r
 364                 groups[i].setEnd(sg.getEndRes());\r
 365                 groups[i].setName(sg.getName());\r
 366                 if(sg.cs!=null)\r
 367                 {\r
 368                   if (sg.cs.conservationApplied())\r
 369                   {\r
 370                     groups[i].setConsThreshold(sg.cs.getConservationInc());\r
 371 \r
 372                     if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
 373                     {\r
 374                       groups[i].setColour(SetUserColourScheme(sg.cs,\r
 375                           userColours,\r
 376                           jms));\r
 377                     }\r
 378                     else\r
 379                     {\r
 380                       groups[i].setColour(ColourSchemeProperty.getColourName(sg.\r
 381                           cs));\r
 382                     }\r
 383                   }\r
 384                   else if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
 385                   {\r
 386                     groups[i].setColour(SetUserColourScheme(sg.cs, userColours,\r
 387                         jms));\r
 388                   }\r
 389                   else\r
 390                   {\r
 391                     groups[i].setColour(ColourSchemeProperty.getColourName(\r
 392                         sg.cs));\r
 393                   }\r
 394 \r
 395                   groups[i].setPidThreshold(sg.cs.getThreshold());\r
 396                 }\r
 397 \r
 398                 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());\r
 399                 groups[i].setDisplayBoxes(sg.getDisplayBoxes());\r
 400                 groups[i].setDisplayText(sg.getDisplayText());\r
 401                 groups[i].setColourText(sg.getColourText());\r
 402 \r
 403                 for (int s = 0; s < sg.getSize(); s++)\r
 404                 {\r
 405                     jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.getSequenceAt(s);\r
 406                     int index = seqids.indexOf(seq);\r
 407                     groups[i].addSeq(index);\r
 408                 }\r
 409             }\r
 410 \r
 411             jms.setJGroup(groups);\r
 412         }\r
 413 \r
 414 \r
 415         ///////////SAVE VIEWPORT\r
 416         Viewport view = new Viewport();\r
 417         view.setTitle(af.getTitle());\r
 418         view.setXpos(af.getX());\r
 419         view.setYpos(af.getY());\r
 420         view.setWidth(af.getWidth());\r
 421         view.setHeight(af.getHeight());\r
 422         view.setStartRes(av.startRes);\r
 423         view.setStartSeq(av.startSeq);\r
 424 \r
 425         if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)\r
 426         {\r
 427             view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),\r
 428                     userColours, jms));\r
 429         }\r
 430         else\r
 431         {\r
 432             view.setBgColour(ColourSchemeProperty.getColourName(\r
 433                     av.getGlobalColourScheme()));\r
 434         }\r
 435 \r
 436         ColourSchemeI cs = av.getGlobalColourScheme();\r
 437 \r
 438         if(cs!=null)\r
 439         {\r
 440           if (cs.conservationApplied())\r
 441           {\r
 442             view.setConsThreshold(cs.getConservationInc());\r
 443             if (cs instanceof jalview.schemes.UserColourScheme)\r
 444               view.setBgColour(SetUserColourScheme(cs, userColours, jms));\r
 445           }\r
 446 \r
 447           if (cs instanceof ResidueColourScheme)\r
 448           {\r
 449             view.setPidThreshold(cs.getThreshold());\r
 450           }\r
 451         }\r
 452 \r
 453         view.setConservationSelected(av.getConservationSelected());\r
 454         view.setPidSelected(av.getAbovePIDThreshold());\r
 455         view.setFontName(av.font.getName());\r
 456         view.setFontSize(av.font.getSize());\r
 457         view.setFontStyle(av.font.getStyle());\r
 458         view.setRenderGaps(av.renderGaps);\r
 459         view.setShowAnnotation(av.getShowAnnotation());\r
 460         view.setShowBoxes(av.getShowBoxes());\r
 461         view.setShowColourText(av.getColourText());\r
 462         view.setShowConservation(av.showConservation);\r
 463         view.setShowFullId(av.getShowJVSuffix());\r
 464         view.setShowIdentity(av.showIdentity);\r
 465         view.setShowQuality(av.showQuality);\r
 466         view.setShowSequenceFeatures(av.showSequenceFeatures);\r
 467         view.setShowText(av.getShowText());\r
 468         view.setWrapAlignment(av.getWrapAlignment());\r
 469 \r
 470         if(av.featuresDisplayed!=null)\r
 471         {\r
 472           jalview.schemabinding.version2.FeatureSettings fs\r
 473               = new jalview.schemabinding.version2.FeatureSettings();\r
 474 \r
 475           Enumeration e = af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();\r
 476           while (e.hasMoreElements())\r
 477           {\r
 478             String type = e.nextElement().toString();\r
 479             Setting setting = new Setting();\r
 480             setting.setType(type);\r
 481             setting.setColour(\r
 482                 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(type).getRGB()\r
 483                 );\r
 484 \r
 485             setting.setDisplay(\r
 486                 av.featuresDisplayed.containsKey(type)\r
 487                 );\r
 488 \r
 489             fs.addSetting(setting);\r
 490 \r
 491           }\r
 492           jms.setFeatureSettings(fs);\r
 493 \r
 494         }\r
 495 \r
 496         jms.addViewport(view);\r
 497 \r
 498 \r
 499         object.setJalviewModelSequence(jms);\r
 500         object.getVamsasModel().addSequenceSet(vamsasSet);\r
 501 \r
 502         try\r
 503         {\r
 504             if (!fileName.endsWith(".xml"))\r
 505             {\r
 506                 fileName = fileName + ".xml";\r
 507             }\r
 508 \r
 509             JarEntry entry = new JarEntry(fileName);\r
 510             jout.putNextEntry(entry);\r
 511 \r
 512             object.marshal(out);\r
 513         }\r
 514         catch (Exception ex)\r
 515         {\r
 516             ex.printStackTrace();\r
 517         }\r
 518     }\r
 519 \r
 520     String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,\r
 521         Vector userColours, JalviewModelSequence jms)\r
 522     {\r
 523         String id = null;\r
 524         jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;\r
 525 \r
 526         if (!userColours.contains(ucs))\r
 527         {\r
 528             userColours.add(ucs);\r
 529 \r
 530             java.awt.Color[] colours = ucs.getColours();\r
 531             jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();\r
 532             jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();\r
 533 \r
 534             for (int i = 0; i < colours.length; i++)\r
 535             {\r
 536                 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();\r
 537                 col.setRGB(jalview.util.Format.getHexString(colours[i]));\r
 538                 jbucs.addColour(col);\r
 539             }\r
 540 \r
 541             id = "ucs" + userColours.indexOf(ucs);\r
 542             uc.setId(id);\r
 543             uc.setUserColourScheme(jbucs);\r
 544             jms.addUserColours(uc);\r
 545         }\r
 546 \r
 547         return id;\r
 548     }\r
 549 \r
 550    jalview.schemes.UserColourScheme GetUserColourScheme(\r
 551         JalviewModelSequence jms, String id)\r
 552     {\r
 553         UserColours[] uc = jms.getUserColours();\r
 554         UserColours colours = null;\r
 555 \r
 556         for (int i = 0; i < uc.length; i++)\r
 557         {\r
 558             if (uc[i].getId().equals(id))\r
 559             {\r
 560                 colours = uc[i];\r
 561 \r
 562                 break;\r
 563             }\r
 564         }\r
 565 \r
 566         int csize = colours.getUserColourScheme().getColourCount();\r
 567         java.awt.Color[] newColours = new java.awt.Color[csize];\r
 568 \r
 569         for (int i = 0; i < csize; i++)\r
 570         {\r
 571             newColours[i] = new java.awt.Color(Integer.parseInt(\r
 572                         colours.getUserColourScheme().getColour(i).getRGB(), 16));\r
 573         }\r
 574 \r
 575         return new jalview.schemes.UserColourScheme(newColours);\r
 576     }\r
 577 \r
 578     /**\r
 579      * DOCUMENT ME!\r
 580      *\r
 581      * @param file DOCUMENT ME!\r
 582      */\r
 583     public AlignFrame LoadJalviewAlign(String file)\r
 584     {\r
 585 \r
 586         jalview.gui.AlignFrame af = null;\r
 587 \r
 588         try\r
 589         {\r
 590             //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING\r
 591             URL url = null;\r
 592 \r
 593             if (file.startsWith("http://"))\r
 594             {\r
 595                 url = new URL(file);\r
 596             }\r
 597 \r
 598             JarInputStream jin = null;\r
 599             JarEntry jarentry = null;\r
 600             int entryCount = 1;\r
 601 \r
 602             do\r
 603             {\r
 604                 if (url != null)\r
 605                 {\r
 606                     jin = new JarInputStream(url.openStream());\r
 607                 }\r
 608                 else\r
 609                 {\r
 610                     jin = new JarInputStream(new FileInputStream(file));\r
 611                 }\r
 612 \r
 613                 for (int i = 0; i < entryCount; i++)\r
 614                 {\r
 615                     jarentry = jin.getNextJarEntry();\r
 616 \r
 617                   }\r
 618 \r
 619 \r
 620                   class NoDescIDResolver implements IDResolver\r
 621                   {\r
 622                     public Object resolve(String idref)\r
 623                     {\r
 624                       System.out.println(idref+" used");\r
 625                       return null;\r
 626                     }\r
 627                   }\r
 628 \r
 629 \r
 630                 if (jarentry != null)\r
 631                 {\r
 632                     InputStreamReader in = new InputStreamReader(jin, "UTF-8");\r
 633                     JalviewModel object = new JalviewModel();\r
 634 \r
 635                     Unmarshaller unmar = new Unmarshaller(object);\r
 636                     object = (JalviewModel) unmar.unmarshal( in );\r
 637 \r
 638                     af = LoadFromObject(object);\r
 639                     entryCount++;\r
 640                 }\r
 641             }\r
 642             while (jarentry != null);\r
 643         }\r
 644         catch(java.net.UnknownHostException ex)\r
 645         {\r
 646           ex.printStackTrace();\r
 647           System.err.println("Couldn't locate Jalview XML file : " +\r
 648               ex + "\n");\r
 649            JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 650                                     "Couldn't locate " + file,\r
 651                                     "URL not found",\r
 652                                     JOptionPane.WARNING_MESSAGE);\r
 653 \r
 654         }\r
 655         catch (Exception ex)\r
 656         {\r
 657           //Is Version 1 Jar file?\r
 658           af =  new Jalview2XML_V1().LoadJalviewAlign(file);\r
 659 \r
 660           if(af!=null)\r
 661           {\r
 662             System.out.println("Successfuly loaded archive file");\r
 663             return af;\r
 664           }\r
 665           ex.printStackTrace();\r
 666             System.err.println("Exception whilst loading jalview XML file : " +\r
 667                 ex + "\n");\r
 668              JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 669                                       "Error loading  " + file,\r
 670                                       "Error loading Jalview file",\r
 671                                       JOptionPane.WARNING_MESSAGE);\r
 672 \r
 673         }\r
 674 \r
 675         return af;\r
 676     }\r
 677 \r
 678     AlignFrame LoadFromObject(JalviewModel object)\r
 679     {\r
 680         Vector seqids = new Vector();\r
 681         SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);\r
 682         Sequence[] vamsasSeq = vamsasSet.getSequence();\r
 683 \r
 684         JalviewModelSequence jms = object.getJalviewModelSequence();\r
 685 \r
 686         //////////////////////////////////\r
 687         //LOAD SEQUENCES\r
 688         jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];\r
 689         JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();\r
 690         for (int i = 0; i < vamsasSeq.length; i++)\r
 691         {\r
 692             jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),\r
 693                     vamsasSeq[i].getSequence());\r
 694             jseqs[i].setDescription( vamsasSeq[i].getDescription() );\r
 695 \r
 696             jseqs[i].setStart(JSEQ[i].getStart());\r
 697             jseqs[i].setEnd(JSEQ[i].getEnd());\r
 698             jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));\r
 699             seqids.add(jseqs[i]);\r
 700         }\r
 701 \r
 702         ///SequenceFeatures are added to the DatasetSequence,\r
 703         // so we must create the dataset before loading features\r
 704         /////////////////////////////////\r
 705         jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);\r
 706         al.setDataset(null);\r
 707         /////////////////////////////////\r
 708 \r
 709         for (int i = 0; i < vamsasSeq.length; i++)\r
 710         {\r
 711           if (JSEQ[i].getFeaturesCount() > 0)\r
 712           {\r
 713             Features[] features = JSEQ[i].getFeatures();\r
 714             for (int f = 0; f < features.length; f++)\r
 715             {\r
 716               jalview.datamodel.SequenceFeature sf\r
 717                   = new jalview.datamodel.SequenceFeature(features[f].getType(),\r
 718                   features[f].getDescription(), features[f].getStatus(),\r
 719                   features[f].getBegin(), features[f].getEnd(),\r
 720                   features[f].getFeatureGroup());\r
 721 \r
 722               al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);\r
 723             }\r
 724           }\r
 725           if (JSEQ[i].getPdbidsCount() > 0)\r
 726           {\r
 727             Pdbids[] ids = JSEQ[i].getPdbids();\r
 728             for (int p = 0; p < ids.length; p++)\r
 729             {\r
 730               jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();\r
 731               entry.setId(ids[p].getId());\r
 732               entry.setType(ids[p].getType());\r
 733               al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);\r
 734             }\r
 735 \r
 736           }\r
 737         }\r
 738 \r
 739          /////////////////////////////////\r
 740         //////////////////////////////////\r
 741         //LOAD ANNOTATIONS\r
 742         if (vamsasSet.getAnnotation() != null)\r
 743         {\r
 744             Annotation[] an = vamsasSet.getAnnotation();\r
 745 \r
 746             for (int i = 0; i < an.length; i++)\r
 747             {\r
 748                 AnnotationElement[] ae = an[i].getAnnotationElement();\r
 749                 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];\r
 750 \r
 751                 for (int aa = 0; aa < ae.length; aa++)\r
 752                 {\r
 753                     anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),\r
 754                             ae[aa].getDescription(),\r
 755                             ae[aa].getSecondaryStructure().charAt(0),\r
 756                             ae[aa].getValue());\r
 757                 }\r
 758 \r
 759                 jalview.datamodel.AlignmentAnnotation jaa = null;\r
 760 \r
 761                 if (an[i].getGraph())\r
 762                 {\r
 763                     jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
 764                             an[i].getDescription(), anot, 0, 0,\r
 765                             an[i].getGraphType());\r
 766                 }\r
 767                 else\r
 768                 {\r
 769                     jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
 770                             an[i].getDescription(), anot);\r
 771                 }\r
 772 \r
 773                 al.addAnnotation(jaa);\r
 774             }\r
 775         }\r
 776 \r
 777 \r
 778         /////////////////////////////////\r
 779         // LOAD VIEWPORT\r
 780         Viewport[] views = jms.getViewport();\r
 781         Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER\r
 782 \r
 783         AlignFrame af = new AlignFrame(al);\r
 784 \r
 785 \r
 786         //  af.changeColour() );\r
 787         /////////////////////////\r
 788         //LOAD GROUPS\r
 789         if (jms.getJGroupCount() > 0)\r
 790         {\r
 791             JGroup[] groups = jms.getJGroup();\r
 792 \r
 793             for (int i = 0; i < groups.length; i++)\r
 794             {\r
 795                 ColourSchemeI cs = null;\r
 796 \r
 797                 if (groups[i].getColour() != null)\r
 798                 {\r
 799                     if (groups[i].getColour().startsWith("ucs"))\r
 800                     {\r
 801                         cs = GetUserColourScheme(jms, groups[i].getColour());\r
 802                     }\r
 803                     else\r
 804                     {\r
 805                         cs = ColourSchemeProperty.getColour(al,\r
 806                                 groups[i].getColour());\r
 807                     }\r
 808 \r
 809                     cs.setThreshold(groups[i].getPidThreshold(), true);\r
 810                 }\r
 811 \r
 812                 Vector seqs = new Vector();\r
 813                 int[] ids = groups[i].getSeq();\r
 814 \r
 815                 for (int s = 0; s < ids.length; s++)\r
 816                 {\r
 817                     seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(\r
 818                             ids[s]));\r
 819                 }\r
 820 \r
 821                 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,\r
 822                         groups[i].getName(), cs, groups[i].getDisplayBoxes(),\r
 823                         groups[i].getDisplayText(), groups[i].getColourText(),\r
 824                         groups[i].getStart(), groups[i].getEnd());\r
 825 \r
 826                 sg.setOutlineColour(new java.awt.Color(\r
 827                         groups[i].getOutlineColour()));\r
 828 \r
 829                 if (groups[i].getConsThreshold() != 0)\r
 830                 {\r
 831                     jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",\r
 832                             ResidueProperties.propHash, 3, sg.sequences, 0,\r
 833                             sg.getWidth() - 1);\r
 834                     c.calculate();\r
 835                     c.verdict(false, 25);\r
 836                     sg.cs.setConservation(c);\r
 837                 }\r
 838 \r
 839                 al.addGroup(sg);\r
 840             }\r
 841         }\r
 842 \r
 843 \r
 844 \r
 845         af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),\r
 846             view.getHeight());\r
 847         af.viewport.setStartRes(view.getStartRes());\r
 848         af.viewport.setStartSeq(view.getStartSeq());\r
 849         af.viewport.setShowAnnotation(view.getShowAnnotation());\r
 850         af.viewport.showConservation = view.getShowConservation();\r
 851         af.viewport.showQuality = view.getShowQuality();\r
 852         af.viewport.showIdentity = view.getShowIdentity();\r
 853         af.viewport.setAbovePIDThreshold(view.getPidSelected());\r
 854         af.abovePIDThreshold.setSelected(view.getPidSelected());\r
 855         af.viewport.setColourText(view.getShowColourText());\r
 856         af.colourTextMenuItem.setSelected(view.getShowColourText());\r
 857         af.viewport.setConservationSelected(view.getConservationSelected());\r
 858         af.conservationMenuItem.setSelected(view.getConservationSelected());\r
 859 \r
 860         af.viewport.setShowJVSuffix(view.getShowFullId());\r
 861         af.seqLimits.setSelected(view.getShowFullId());\r
 862 \r
 863         af.viewport.setFont(new java.awt.Font(view.getFontName(),\r
 864                 view.getFontStyle(), view.getFontSize()));\r
 865         af.alignPanel.fontChanged();\r
 866 \r
 867         af.viewport.setRenderGaps(view.getRenderGaps());\r
 868         af.renderGapsMenuItem.setSelected(view.getRenderGaps());\r
 869 \r
 870         af.viewport.setWrapAlignment(view.getWrapAlignment());\r
 871         af.wrapMenuItem.setSelected(view.getWrapAlignment());\r
 872 \r
 873         if (view.getWrapAlignment())\r
 874         {\r
 875             af.alignPanel.setWrapAlignment(view.getWrapAlignment());\r
 876         }\r
 877         else\r
 878         {\r
 879             af.annotationPanelMenuItem.setState(view.getShowAnnotation());\r
 880             af.viewport.setShowAnnotation(view.getShowAnnotation());\r
 881             af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\r
 882         }\r
 883 \r
 884         af.viewport.setShowBoxes(view.getShowBoxes());\r
 885         af.viewBoxesMenuItem.setSelected(view.getShowBoxes());\r
 886         af.viewport.setShowText(view.getShowText());\r
 887         af.viewTextMenuItem.setSelected(view.getShowText());\r
 888 \r
 889         ColourSchemeI cs = null;\r
 890 \r
 891         if (view.getBgColour() != null)\r
 892         {\r
 893             if (view.getBgColour().startsWith("ucs"))\r
 894             {\r
 895                 cs = GetUserColourScheme(jms, view.getBgColour());\r
 896             }\r
 897             else\r
 898             {\r
 899                 cs = ColourSchemeProperty.getColour(al, view.getBgColour());\r
 900             }\r
 901 \r
 902             if(cs!=null)\r
 903             {\r
 904               cs.setThreshold(view.getPidThreshold(), true);\r
 905               cs.setConsensus(af.viewport.vconsensus);\r
 906             }\r
 907         }\r
 908 \r
 909         af.setColourSelected(view.getBgColour());\r
 910         af.viewport.setGlobalColourScheme(cs);\r
 911         af.viewport.setColourAppliesToAllGroups(false);\r
 912         af.changeColour(cs);\r
 913         if (view.getConservationSelected() && cs!=null)\r
 914         {\r
 915           cs.setConservationInc(view.getConsThreshold());\r
 916         }\r
 917 \r
 918         af.viewport.setColourAppliesToAllGroups(true);\r
 919 \r
 920         if (view.getShowSequenceFeatures())\r
 921         {\r
 922            af.viewport.showSequenceFeatures = true;\r
 923            af.showSeqFeatures.setSelected(true);\r
 924         }\r
 925 \r
 926         if(jms.getFeatureSettings()!=null)\r
 927         {\r
 928           af.viewport.featuresDisplayed = new Hashtable();\r
 929           String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];\r
 930          for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)\r
 931          {\r
 932            Setting setting = jms.getFeatureSettings().getSetting(fs);\r
 933 \r
 934            af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),\r
 935                new java.awt.Color(setting.getColour()));\r
 936 \r
 937            renderOrder[fs] = setting.getType();\r
 938 \r
 939            if(setting.getDisplay())\r
 940              af.viewport.featuresDisplayed.put(\r
 941                  setting.getType(), new Integer(setting.getColour()));\r
 942          }\r
 943          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;\r
 944         }\r
 945 \r
 946 \r
 947         Desktop.addInternalFrame(af, view.getTitle(),\r
 948              view.getWidth(), view.getHeight());\r
 949 \r
 950         //LOAD TREES\r
 951         ///////////////////////////////////////\r
 952         if (jms.getTreeCount() > 0)\r
 953         {\r
 954             try\r
 955             {\r
 956                 for (int t = 0; t < jms.getTreeCount(); t++)\r
 957                 {\r
 958 \r
 959                     Tree tree = jms.getTree(t);\r
 960 \r
 961                     TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(\r
 962                                 tree.getNewick()), tree.getTitle(),\r
 963                                 tree.getWidth(), tree.getHeight(),\r
 964                                 tree.getXpos(), tree.getYpos());\r
 965 \r
 966                     tp.fitToWindow.setState(tree.getFitToWindow());\r
 967                     tp.fitToWindow_actionPerformed(null);\r
 968 \r
 969                     if(tree.getFontName()!=null)\r
 970                       tp.setTreeFont(new java.awt.Font(tree.getFontName(),\r
 971                                           tree.getFontStyle(),\r
 972                                           tree.getFontSize()));\r
 973                     else\r
 974                       tp.setTreeFont(new java.awt.Font(view.getFontName(),\r
 975                                             view.getFontStyle(),\r
 976                                             tree.getFontSize()));\r
 977 \r
 978                     tp.showPlaceholders(tree.getMarkUnlinked());\r
 979                     tp.showBootstrap(tree.getShowBootstrap());\r
 980                     tp.showDistances(tree.getShowDistances());\r
 981 \r
 982                     tp.treeCanvas.threshold = tree.getThreshold();\r
 983 \r
 984                     if (tree.getCurrentTree())\r
 985                       af.viewport.setCurrentTree(tp.getTree());\r
 986                 }\r
 987 \r
 988             }\r
 989             catch (Exception ex)\r
 990             {\r
 991                 ex.printStackTrace();\r
 992             }\r
 993 \r
 994         }\r
 995 \r
 996         return af;\r
 997     }\r
 998 }\r
 999 \r