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.setType(sf[index].getType());\r
 214                 features.setFeatureGroup(sf[index].getFeatureGroup());\r
 215                 jseq.addFeatures(features);\r
 216                 index ++;\r
 217               }\r
 218             }\r
 219 \r
 220             if(jal.getSequenceAt(i).getDatasetSequence().getPDBId()!=null)\r
 221             {\r
 222               Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getPDBId().elements();\r
 223               while(en.hasMoreElements())\r
 224               {\r
 225                 Pdbids pdb = new Pdbids();\r
 226                 jalview.datamodel.PDBEntry entry\r
 227                    = (jalview.datamodel.PDBEntry)en.nextElement();\r
 228 \r
 229                 pdb.setId(entry.getId());\r
 230                 pdb.setType(entry.getType());\r
 231 \r
 232                 if(entry.getProperty()!=null)\r
 233                 {\r
 234                   PdbentryItem item = new PdbentryItem();\r
 235                   Hashtable properties = entry.getProperty();\r
 236                   Enumeration en2 = properties.keys();\r
 237                   while(en2.hasMoreElements())\r
 238                   {\r
 239                     Property prop = new Property();\r
 240                     String key = en2.nextElement().toString();\r
 241                     prop.setName(key);\r
 242                     prop.setValue( properties.get(key).toString() );\r
 243                     item.addProperty(prop);\r
 244                   }\r
 245                   pdb.addPdbentryItem(item);\r
 246                 }\r
 247 \r
 248                 jseq.addPdbids(pdb);\r
 249               }\r
 250             }\r
 251 \r
 252             jms.addJSeq(jseq);\r
 253             vamsasSet.addSequence(vamsasSeq);\r
 254             id++;\r
 255         }\r
 256 \r
 257         //SAVE TREES\r
 258         ///////////////////////////////////\r
 259         if (af.viewport.currentTree != null)\r
 260         {\r
 261           // FIND ANY ASSOCIATED TREES\r
 262           // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT\r
 263           if (Desktop.desktop != null)\r
 264           {\r
 265             JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
 266 \r
 267             for (int t = 0; t < frames.length; t++)\r
 268             {\r
 269               if (frames[t] instanceof TreePanel)\r
 270               {\r
 271                 TreePanel tp = (TreePanel) frames[t];\r
 272 \r
 273                 if (tp.treeCanvas.av.alignment == jal)\r
 274                 {\r
 275                   Tree tree = new Tree();\r
 276                   tree.setTitle(tp.getTitle());\r
 277                   tree.setCurrentTree( (af.viewport.currentTree == tp.getTree()));\r
 278                   tree.setNewick(tp.getTree().toString());\r
 279                   tree.setThreshold(tp.treeCanvas.threshold);\r
 280 \r
 281                   tree.setFitToWindow(tp.fitToWindow.getState());\r
 282                   tree.setFontName(tp.getTreeFont().getName());\r
 283                   tree.setFontSize(tp.getTreeFont().getSize());\r
 284                   tree.setFontStyle(tp.getTreeFont().getStyle());\r
 285                   tree.setMarkUnlinked(tp.placeholdersMenu.getState());\r
 286 \r
 287                   tree.setShowBootstrap(tp.bootstrapMenu.getState());\r
 288                   tree.setShowDistances(tp.distanceMenu.getState());\r
 289 \r
 290                   tree.setHeight(tp.getHeight());\r
 291                   tree.setWidth(tp.getWidth());\r
 292                   tree.setXpos(tp.getX());\r
 293                   tree.setYpos(tp.getY());\r
 294 \r
 295                   jms.addTree(tree);\r
 296                 }\r
 297               }\r
 298             }\r
 299           }\r
 300         }\r
 301 \r
 302         //SAVE ANNOTATIONS\r
 303         if (jal.getAlignmentAnnotation() != null)\r
 304         {\r
 305             jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();\r
 306 \r
 307             for (int i = 0; i < aa.length; i++)\r
 308             {\r
 309                 Annotation an = new Annotation();\r
 310 \r
 311                 if (aa[i].label.equals("Quality") ||\r
 312                         aa[i].label.equals("Conservation") ||\r
 313                         aa[i].label.equals("Consensus"))\r
 314                 {\r
 315                     an.setLabel(aa[i].label);\r
 316                     an.setGraph(true);\r
 317                     vamsasSet.addAnnotation(an);\r
 318                     continue;\r
 319                 }\r
 320 \r
 321 \r
 322                 an.setDescription(aa[i].description);\r
 323 \r
 324                 if(aa[i].sequenceRef!=null)\r
 325                  {\r
 326                    an.setSequenceRef(aa[i].sequenceRef.getName());\r
 327                  }\r
 328 \r
 329                 if(aa[i].graph>0)\r
 330                 {\r
 331                   an.setGraph(true);\r
 332                   an.setGraphType(aa[i].graph);\r
 333                   an.setGraphGroup(aa[i].graphGroup);\r
 334                   if(aa[i].getThreshold()!=null)\r
 335                   {\r
 336                     ThresholdLine line = new ThresholdLine();\r
 337                     line.setLabel(aa[i].getThreshold().label);\r
 338                     line.setValue(aa[i].getThreshold().value);\r
 339                     line.setColour(aa[i].getThreshold().colour.getRGB());\r
 340                     an.setThresholdLine(line);\r
 341                   }\r
 342                 }\r
 343                 else\r
 344                   an.setGraph(false);\r
 345 \r
 346                 an.setLabel(aa[i].label);\r
 347 \r
 348                 AnnotationElement ae;\r
 349 \r
 350                 for (int a = 0; a < aa[i].annotations.length; a++)\r
 351                 {\r
 352                     if ((aa[i] == null) || (aa[i].annotations[a] == null))\r
 353                     {\r
 354                         continue;\r
 355                     }\r
 356 \r
 357                     ae = new AnnotationElement();\r
 358                     ae.setDescription(aa[i].annotations[a].description);\r
 359                     ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);\r
 360                     ae.setValue(aa[i].annotations[a].value);\r
 361                     ae.setPosition(a);\r
 362                     ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +\r
 363                         "");\r
 364 \r
 365                     if(aa[i].annotations[a].colour!=java.awt.Color.black)\r
 366                       ae.setColour(aa[i].annotations[a].colour.getRGB());\r
 367 \r
 368                     an.addAnnotationElement(ae);\r
 369                 }\r
 370 \r
 371                 vamsasSet.addAnnotation(an);\r
 372             }\r
 373         }\r
 374 \r
 375         //SAVE GROUPS\r
 376         if (jal.getGroups() != null)\r
 377         {\r
 378             JGroup[] groups = new JGroup[jal.getGroups().size()];\r
 379 \r
 380             for (int i = 0; i < groups.length; i++)\r
 381             {\r
 382                 groups[i] = new JGroup();\r
 383 \r
 384                 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()\r
 385                                                                                           .elementAt(i);\r
 386                 groups[i].setStart(sg.getStartRes());\r
 387                 groups[i].setEnd(sg.getEndRes());\r
 388                 groups[i].setName(sg.getName());\r
 389                 if(sg.cs!=null)\r
 390                 {\r
 391                   if (sg.cs.conservationApplied())\r
 392                   {\r
 393                     groups[i].setConsThreshold(sg.cs.getConservationInc());\r
 394 \r
 395                     if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
 396                     {\r
 397                       groups[i].setColour(SetUserColourScheme(sg.cs,\r
 398                           userColours,\r
 399                           jms));\r
 400                     }\r
 401                     else\r
 402                     {\r
 403                       groups[i].setColour(ColourSchemeProperty.getColourName(sg.\r
 404                           cs));\r
 405                     }\r
 406                   }\r
 407                   else if(sg.cs instanceof jalview.schemes.AnnotationColourGradient)\r
 408                   {\r
 409                     groups[i].setColour(\r
 410                         ColourSchemeProperty.getColourName(\r
 411                       ( (jalview.schemes.AnnotationColourGradient) sg.cs).getBaseColour()));\r
 412                   }\r
 413                   else if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
 414                   {\r
 415                     groups[i].setColour(SetUserColourScheme(sg.cs, userColours,\r
 416                         jms));\r
 417                   }\r
 418                   else\r
 419                   {\r
 420                     groups[i].setColour(ColourSchemeProperty.getColourName(\r
 421                         sg.cs));\r
 422                   }\r
 423 \r
 424                   groups[i].setPidThreshold(sg.cs.getThreshold());\r
 425                 }\r
 426 \r
 427                 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());\r
 428                 groups[i].setDisplayBoxes(sg.getDisplayBoxes());\r
 429                 groups[i].setDisplayText(sg.getDisplayText());\r
 430                 groups[i].setColourText(sg.getColourText());\r
 431 \r
 432                 for (int s = 0; s < sg.getSize(false); s++)\r
 433                 {\r
 434                     jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.getSequenceAt(s);\r
 435                     int index = seqids.indexOf(seq);\r
 436                     groups[i].addSeq(index);\r
 437                 }\r
 438             }\r
 439 \r
 440             jms.setJGroup(groups);\r
 441         }\r
 442 \r
 443 \r
 444         ///////////SAVE VIEWPORT\r
 445         Viewport view = new Viewport();\r
 446         view.setTitle(af.getTitle());\r
 447         view.setXpos(af.getX());\r
 448         view.setYpos(af.getY());\r
 449         view.setWidth(af.getWidth());\r
 450         view.setHeight(af.getHeight());\r
 451         view.setStartRes(av.startRes);\r
 452         view.setStartSeq(av.startSeq);\r
 453 \r
 454         if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)\r
 455         {\r
 456             view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),\r
 457                     userColours, jms));\r
 458         }\r
 459         else if(av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)\r
 460         {\r
 461            jalview.schemes.AnnotationColourGradient acg\r
 462               = (jalview.schemes.AnnotationColourGradient)av.getGlobalColourScheme();\r
 463 \r
 464             AnnotationColours ac = new AnnotationColours();\r
 465             ac.setAboveThreshold(acg.getAboveThreshold());\r
 466             ac.setThreshold(acg.getAnnotationThreshold());\r
 467             ac.setAnnotation(acg.getAnnotation());\r
 468             if(acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)\r
 469               ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),\r
 470                     userColours, jms));\r
 471             else\r
 472               ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));\r
 473 \r
 474             ac.setMaxColour(acg.getMaxColour().getRGB());\r
 475             ac.setMinColour(acg.getMinColour().getRGB());\r
 476             view.setAnnotationColours(ac);\r
 477             view.setBgColour("AnnotationColourGradient");\r
 478         }\r
 479         else\r
 480         {\r
 481             view.setBgColour(ColourSchemeProperty.getColourName(\r
 482                     av.getGlobalColourScheme()));\r
 483         }\r
 484 \r
 485         ColourSchemeI cs = av.getGlobalColourScheme();\r
 486 \r
 487         if(cs!=null)\r
 488         {\r
 489           if (cs.conservationApplied())\r
 490           {\r
 491             view.setConsThreshold(cs.getConservationInc());\r
 492             if (cs instanceof jalview.schemes.UserColourScheme)\r
 493               view.setBgColour(SetUserColourScheme(cs, userColours, jms));\r
 494           }\r
 495 \r
 496           if (cs instanceof ResidueColourScheme)\r
 497           {\r
 498             view.setPidThreshold(cs.getThreshold());\r
 499           }\r
 500         }\r
 501 \r
 502         view.setConservationSelected(av.getConservationSelected());\r
 503         view.setPidSelected(av.getAbovePIDThreshold());\r
 504         view.setFontName(av.font.getName());\r
 505         view.setFontSize(av.font.getSize());\r
 506         view.setFontStyle(av.font.getStyle());\r
 507         view.setRenderGaps(av.renderGaps);\r
 508         view.setShowAnnotation(av.getShowAnnotation());\r
 509         view.setShowBoxes(av.getShowBoxes());\r
 510         view.setShowColourText(av.getColourText());\r
 511         view.setShowConservation(av.showConservation);\r
 512         view.setShowFullId(av.getShowJVSuffix());\r
 513         view.setShowIdentity(av.showIdentity);\r
 514         view.setShowQuality(av.showQuality);\r
 515         view.setShowSequenceFeatures(av.showSequenceFeatures);\r
 516         view.setShowText(av.getShowText());\r
 517         view.setWrapAlignment(av.getWrapAlignment());\r
 518 \r
 519         if(av.featuresDisplayed!=null)\r
 520         {\r
 521           jalview.schemabinding.version2.FeatureSettings fs\r
 522               = new jalview.schemabinding.version2.FeatureSettings();\r
 523 \r
 524           String [] renderOrder =\r
 525               af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;\r
 526           for(int ro=0; ro<renderOrder.length; ro++)\r
 527           {\r
 528             Setting setting = new Setting();\r
 529             setting.setType(renderOrder[ro]);\r
 530             setting.setColour(\r
 531                 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).getRGB()\r
 532                 );\r
 533 \r
 534             setting.setDisplay(\r
 535                 av.featuresDisplayed.containsKey(renderOrder[ro])\r
 536                 );\r
 537 \r
 538             fs.addSetting(setting);\r
 539 \r
 540           }\r
 541           jms.setFeatureSettings(fs);\r
 542 \r
 543         }\r
 544 \r
 545         jms.addViewport(view);\r
 546 \r
 547 \r
 548         object.setJalviewModelSequence(jms);\r
 549         object.getVamsasModel().addSequenceSet(vamsasSet);\r
 550 \r
 551         try\r
 552         {\r
 553             if (!fileName.endsWith(".xml"))\r
 554             {\r
 555                 fileName = fileName + ".xml";\r
 556             }\r
 557 \r
 558             JarEntry entry = new JarEntry(fileName);\r
 559             jout.putNextEntry(entry);\r
 560 \r
 561             object.marshal(out);\r
 562         }\r
 563         catch (Exception ex)\r
 564         {\r
 565             ex.printStackTrace();\r
 566         }\r
 567     }\r
 568 \r
 569     String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,\r
 570         Vector userColours, JalviewModelSequence jms)\r
 571     {\r
 572         String id = null;\r
 573         jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;\r
 574 \r
 575         if (!userColours.contains(ucs))\r
 576         {\r
 577             userColours.add(ucs);\r
 578 \r
 579             java.awt.Color[] colours = ucs.getColours();\r
 580             jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();\r
 581             jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();\r
 582 \r
 583             for (int i = 0; i < colours.length; i++)\r
 584             {\r
 585                 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();\r
 586                 col.setRGB(jalview.util.Format.getHexString(colours[i]));\r
 587                 jbucs.addColour(col);\r
 588             }\r
 589 \r
 590             id = "ucs" + userColours.indexOf(ucs);\r
 591             uc.setId(id);\r
 592             uc.setUserColourScheme(jbucs);\r
 593             jms.addUserColours(uc);\r
 594         }\r
 595 \r
 596         return id;\r
 597     }\r
 598 \r
 599    jalview.schemes.UserColourScheme GetUserColourScheme(\r
 600         JalviewModelSequence jms, String id)\r
 601     {\r
 602         UserColours[] uc = jms.getUserColours();\r
 603         UserColours colours = null;\r
 604 \r
 605         for (int i = 0; i < uc.length; i++)\r
 606         {\r
 607             if (uc[i].getId().equals(id))\r
 608             {\r
 609                 colours = uc[i];\r
 610 \r
 611                 break;\r
 612             }\r
 613         }\r
 614 \r
 615         int csize = colours.getUserColourScheme().getColourCount();\r
 616         java.awt.Color[] newColours = new java.awt.Color[csize];\r
 617 \r
 618         for (int i = 0; i < csize; i++)\r
 619         {\r
 620             newColours[i] = new java.awt.Color(Integer.parseInt(\r
 621                         colours.getUserColourScheme().getColour(i).getRGB(), 16));\r
 622         }\r
 623 \r
 624         return new jalview.schemes.UserColourScheme(newColours);\r
 625     }\r
 626 \r
 627     /**\r
 628      * DOCUMENT ME!\r
 629      *\r
 630      * @param file DOCUMENT ME!\r
 631      */\r
 632     public AlignFrame LoadJalviewAlign(String file)\r
 633     {\r
 634 \r
 635         jalview.gui.AlignFrame af = null;\r
 636 \r
 637         try\r
 638         {\r
 639             //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING\r
 640             URL url = null;\r
 641 \r
 642             if (file.startsWith("http://"))\r
 643             {\r
 644                 url = new URL(file);\r
 645             }\r
 646 \r
 647             JarInputStream jin = null;\r
 648             JarEntry jarentry = null;\r
 649             int entryCount = 1;\r
 650 \r
 651             do\r
 652             {\r
 653                 if (url != null)\r
 654                 {\r
 655                     jin = new JarInputStream(url.openStream());\r
 656                 }\r
 657                 else\r
 658                 {\r
 659                     jin = new JarInputStream(new FileInputStream(file));\r
 660                 }\r
 661 \r
 662                 for (int i = 0; i < entryCount; i++)\r
 663                 {\r
 664                     jarentry = jin.getNextJarEntry();\r
 665 \r
 666                   }\r
 667 \r
 668 \r
 669                   class NoDescIDResolver implements IDResolver\r
 670                   {\r
 671                     public Object resolve(String idref)\r
 672                     {\r
 673                       System.out.println(idref+" used");\r
 674                       return null;\r
 675                     }\r
 676                   }\r
 677 \r
 678 \r
 679                 if (jarentry != null)\r
 680                 {\r
 681                     InputStreamReader in = new InputStreamReader(jin, "UTF-8");\r
 682                     JalviewModel object = new JalviewModel();\r
 683 \r
 684                     Unmarshaller unmar = new Unmarshaller(object);\r
 685                     unmar.setValidation(false);\r
 686                     object = (JalviewModel) unmar.unmarshal( in );\r
 687 \r
 688                     af = LoadFromObject(object);\r
 689                     entryCount++;\r
 690                 }\r
 691             }\r
 692             while (jarentry != null);\r
 693         }\r
 694         catch(java.net.UnknownHostException ex)\r
 695         {\r
 696           ex.printStackTrace();\r
 697           System.err.println("Couldn't locate Jalview XML file : " +\r
 698               ex + "\n");\r
 699            JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 700                                     "Couldn't locate " + file,\r
 701                                     "URL not found",\r
 702                                     JOptionPane.WARNING_MESSAGE);\r
 703 \r
 704         }\r
 705         catch (Exception ex)\r
 706         {\r
 707           //Is Version 1 Jar file?\r
 708           af =  new Jalview2XML_V1().LoadJalviewAlign(file);\r
 709 \r
 710           if(af!=null)\r
 711           {\r
 712             System.out.println("Successfully loaded archive file");\r
 713             return af;\r
 714           }\r
 715           ex.printStackTrace();\r
 716             System.err.println("Exception whilst loading jalview XML file : " +\r
 717                 ex + "\n");\r
 718              JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 719                                       "Error loading  " + file,\r
 720                                       "Error loading Jalview file",\r
 721                                       JOptionPane.WARNING_MESSAGE);\r
 722 \r
 723         }\r
 724 \r
 725         return af;\r
 726     }\r
 727 \r
 728     AlignFrame LoadFromObject(JalviewModel object)\r
 729     {\r
 730         Vector seqids = new Vector();\r
 731         SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);\r
 732         Sequence[] vamsasSeq = vamsasSet.getSequence();\r
 733 \r
 734         JalviewModelSequence jms = object.getJalviewModelSequence();\r
 735 \r
 736         //////////////////////////////////\r
 737         //LOAD SEQUENCES\r
 738         jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];\r
 739         JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();\r
 740         for (int i = 0; i < vamsasSeq.length; i++)\r
 741         {\r
 742             jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),\r
 743                     vamsasSeq[i].getSequence());\r
 744             jseqs[i].setDescription( vamsasSeq[i].getDescription() );\r
 745 \r
 746             jseqs[i].setStart(JSEQ[i].getStart());\r
 747             jseqs[i].setEnd(JSEQ[i].getEnd());\r
 748             jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));\r
 749             seqids.add(jseqs[i]);\r
 750         }\r
 751 \r
 752         ///SequenceFeatures are added to the DatasetSequence,\r
 753         // so we must create the dataset before loading features\r
 754         /////////////////////////////////\r
 755         jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);\r
 756         al.setDataset(null);\r
 757         /////////////////////////////////\r
 758 \r
 759         for (int i = 0; i < vamsasSeq.length; i++)\r
 760         {\r
 761           if (JSEQ[i].getFeaturesCount() > 0)\r
 762           {\r
 763             Features[] features = JSEQ[i].getFeatures();\r
 764             for (int f = 0; f < features.length; f++)\r
 765             {\r
 766               jalview.datamodel.SequenceFeature sf\r
 767                   = new jalview.datamodel.SequenceFeature(features[f].getType(),\r
 768                   features[f].getDescription(), features[f].getStatus(),\r
 769                   features[f].getBegin(), features[f].getEnd(),\r
 770                   features[f].getFeatureGroup());\r
 771 \r
 772               al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);\r
 773             }\r
 774           }\r
 775           if (JSEQ[i].getPdbidsCount() > 0)\r
 776           {\r
 777             Pdbids[] ids = JSEQ[i].getPdbids();\r
 778             for (int p = 0; p < ids.length; p++)\r
 779             {\r
 780               jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();\r
 781               entry.setId(ids[p].getId());\r
 782               entry.setType(ids[p].getType());\r
 783               al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);\r
 784             }\r
 785 \r
 786           }\r
 787         }\r
 788 \r
 789 \r
 790          /////////////////////////////////\r
 791         //////////////////////////////////\r
 792         //LOAD ANNOTATIONS\r
 793         boolean hideQuality = true,\r
 794             hideConservation = true,\r
 795             hideConsensus = true;\r
 796 \r
 797         if (vamsasSet.getAnnotation() != null)\r
 798         {\r
 799             Annotation[] an = vamsasSet.getAnnotation();\r
 800 \r
 801             for (int i = 0; i < an.length; i++)\r
 802             {\r
 803                if (an[i].getLabel().equals("Quality"))\r
 804                 {\r
 805                  hideQuality = false;\r
 806                  continue;\r
 807                 }\r
 808                else if(an[i].getLabel().equals("Conservation"))\r
 809                {\r
 810                  hideConservation = false;\r
 811                  continue;\r
 812                }\r
 813                else if(an[i].getLabel().equals("Consensus"))\r
 814                {\r
 815                  hideConsensus = false;\r
 816                  continue;\r
 817                }\r
 818 \r
 819                 AnnotationElement[] ae = an[i].getAnnotationElement();\r
 820                 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];\r
 821 \r
 822                 for (int aa = 0; aa < ae.length; aa++)\r
 823                 {\r
 824                     anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),\r
 825                             ae[aa].getDescription(),\r
 826                             ae[aa].getSecondaryStructure().length()==0?' ':ae[aa].getSecondaryStructure().charAt(0),\r
 827                             ae[aa].getValue());\r
 828                     anot[ae[aa].getPosition()].colour = new java.awt.Color( ae[aa].getColour() );\r
 829                 }\r
 830 \r
 831                 jalview.datamodel.AlignmentAnnotation jaa = null;\r
 832 \r
 833                 if (an[i].getGraph())\r
 834                 {\r
 835                   jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
 836                       an[i].getDescription(), anot, 0, 0,\r
 837                       an[i].getGraphType());\r
 838 \r
 839                   jaa.graphGroup = an[i].getGraphGroup();\r
 840 \r
 841                   if (an[i].getThresholdLine() != null)\r
 842                   {\r
 843                     jaa.setThreshold(new jalview.datamodel.GraphLine(\r
 844                                   an[i].getThresholdLine().getValue(),\r
 845                                   an[i].getThresholdLine().getLabel(),\r
 846                                 new java.awt.Color(an[i].getThresholdLine().getColour()))\r
 847                              );\r
 848 \r
 849                   }\r
 850 \r
 851                 }\r
 852                 else\r
 853                 {\r
 854                     jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
 855                             an[i].getDescription(), anot);\r
 856                 }\r
 857 \r
 858                 if(an[i].getSequenceRef()!=null)\r
 859                 {\r
 860                   jaa.createSequenceMapping(\r
 861                       al.findName(an[i].getSequenceRef()), 1\r
 862                       );\r
 863                   al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);\r
 864                 }\r
 865 \r
 866                 al.addAnnotation(jaa);\r
 867             }\r
 868         }\r
 869 \r
 870 \r
 871         //  af.changeColour() );\r
 872         /////////////////////////\r
 873         //LOAD GROUPS\r
 874         if (jms.getJGroupCount() > 0)\r
 875         {\r
 876             JGroup[] groups = jms.getJGroup();\r
 877 \r
 878             for (int i = 0; i < groups.length; i++)\r
 879             {\r
 880                 ColourSchemeI cs = null;\r
 881 \r
 882                 if (groups[i].getColour() != null)\r
 883                 {\r
 884                     if (groups[i].getColour().startsWith("ucs"))\r
 885                     {\r
 886                         cs = GetUserColourScheme(jms, groups[i].getColour());\r
 887                     }\r
 888                     else\r
 889                     {\r
 890                         cs = ColourSchemeProperty.getColour(al,\r
 891                                 groups[i].getColour());\r
 892                     }\r
 893 \r
 894                     if(cs!=null)\r
 895                       cs.setThreshold(groups[i].getPidThreshold(), true);\r
 896                 }\r
 897 \r
 898                 Vector seqs = new Vector();\r
 899                 int[] ids = groups[i].getSeq();\r
 900 \r
 901                 for (int s = 0; s < ids.length; s++)\r
 902                 {\r
 903                     seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(\r
 904                             ids[s]));\r
 905                 }\r
 906 \r
 907                 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,\r
 908                         groups[i].getName(), cs, groups[i].getDisplayBoxes(),\r
 909                         groups[i].getDisplayText(), groups[i].getColourText(),\r
 910                         groups[i].getStart(), groups[i].getEnd());\r
 911 \r
 912                 sg.setOutlineColour(new java.awt.Color(\r
 913                         groups[i].getOutlineColour()));\r
 914 \r
 915                 if (groups[i].getConsThreshold() != 0)\r
 916                 {\r
 917                     jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",\r
 918                             ResidueProperties.propHash, 3, sg.getSequences(false), 0,\r
 919                             sg.getWidth() - 1);\r
 920                     c.calculate();\r
 921                     c.verdict(false, 25);\r
 922                     sg.cs.setConservation(c);\r
 923                 }\r
 924 \r
 925                 al.addGroup(sg);\r
 926             }\r
 927         }\r
 928 \r
 929 \r
 930         /////////////////////////////////\r
 931         // LOAD VIEWPORT\r
 932         Viewport[] views = jms.getViewport();\r
 933         Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER\r
 934 \r
 935         AlignFrame af = new AlignFrame(al);\r
 936         if(hideConsensus || hideQuality || hideConservation)\r
 937         {\r
 938           int hSize = al.getAlignmentAnnotation().length;\r
 939           for (int h = 0; h < hSize; h++)\r
 940           {\r
 941             if (\r
 942                 (hideConsensus &&\r
 943                  al.getAlignmentAnnotation()[h].label.equals("Consensus"))\r
 944                 ||\r
 945                 (hideQuality &&\r
 946                  al.getAlignmentAnnotation()[h].label.equals("Quality"))\r
 947                 ||\r
 948                 (hideConservation &&\r
 949                  al.getAlignmentAnnotation()[h].label.equals("Conservation")))\r
 950             {\r
 951               al.deleteAnnotation(al.getAlignmentAnnotation()[h]);\r
 952               hSize--;\r
 953               h--;\r
 954             }\r
 955           }\r
 956           af.alignPanel.adjustAnnotationHeight();\r
 957         }\r
 958 \r
 959         af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),\r
 960             view.getHeight());\r
 961         af.viewport.setStartRes(view.getStartRes());\r
 962         af.viewport.setStartSeq(view.getStartSeq());\r
 963         af.viewport.setShowAnnotation(view.getShowAnnotation());\r
 964         af.viewport.showConservation = view.getShowConservation();\r
 965         af.viewport.showQuality = view.getShowQuality();\r
 966         af.viewport.showIdentity = view.getShowIdentity();\r
 967         af.viewport.setAbovePIDThreshold(view.getPidSelected());\r
 968         af.abovePIDThreshold.setSelected(view.getPidSelected());\r
 969         af.viewport.setColourText(view.getShowColourText());\r
 970         af.colourTextMenuItem.setSelected(view.getShowColourText());\r
 971         af.viewport.setConservationSelected(view.getConservationSelected());\r
 972         af.conservationMenuItem.setSelected(view.getConservationSelected());\r
 973 \r
 974         af.viewport.setShowJVSuffix(view.getShowFullId());\r
 975         af.seqLimits.setSelected(view.getShowFullId());\r
 976 \r
 977         af.viewport.setFont(new java.awt.Font(view.getFontName(),\r
 978                 view.getFontStyle(), view.getFontSize()));\r
 979         af.alignPanel.fontChanged();\r
 980 \r
 981         af.viewport.setRenderGaps(view.getRenderGaps());\r
 982         af.renderGapsMenuItem.setSelected(view.getRenderGaps());\r
 983 \r
 984         af.viewport.setWrapAlignment(view.getWrapAlignment());\r
 985         af.wrapMenuItem.setSelected(view.getWrapAlignment());\r
 986 \r
 987         if (view.getWrapAlignment())\r
 988         {\r
 989             af.alignPanel.setWrapAlignment(view.getWrapAlignment());\r
 990         }\r
 991         else\r
 992         {\r
 993             af.annotationPanelMenuItem.setState(view.getShowAnnotation());\r
 994             af.viewport.setShowAnnotation(view.getShowAnnotation());\r
 995             af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\r
 996         }\r
 997 \r
 998         af.viewport.setShowBoxes(view.getShowBoxes());\r
 999         af.viewBoxesMenuItem.setSelected(view.getShowBoxes());\r
1000         af.viewport.setShowText(view.getShowText());\r
1001         af.viewTextMenuItem.setSelected(view.getShowText());\r
1002 \r
1003         ColourSchemeI cs = null;\r
1004 \r
1005         if (view.getBgColour() != null)\r
1006         {\r
1007             if (view.getBgColour().startsWith("ucs"))\r
1008             {\r
1009                 cs = GetUserColourScheme(jms, view.getBgColour());\r
1010             }\r
1011             else if(view.getBgColour().startsWith("Annotation"))\r
1012             {\r
1013               //int find annotation\r
1014               for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)\r
1015               {\r
1016                 if (af.viewport.alignment.getAlignmentAnnotation()[i].label.\r
1017                     equals(view.getAnnotationColours().getAnnotation()))\r
1018                 {\r
1019                   if (af.viewport.alignment.getAlignmentAnnotation()[i].\r
1020                       getThreshold() == null)\r
1021                   {\r
1022                     af.viewport.alignment.getAlignmentAnnotation()[i].\r
1023                         setThreshold(\r
1024                             new jalview.datamodel.GraphLine(\r
1025                                 view.getAnnotationColours().getThreshold(),\r
1026                                 "Threshold", java.awt.Color.black)\r
1027 \r
1028                         );\r
1029                   }\r
1030 \r
1031 \r
1032                   if (view.getAnnotationColours().getColourScheme().equals(\r
1033                       "None"))\r
1034                   {\r
1035                     cs = new AnnotationColourGradient(\r
1036                         af.viewport.alignment.getAlignmentAnnotation()[i],\r
1037                         new java.awt.Color(view.getAnnotationColours().\r
1038                                            getMinColour()),\r
1039                         new java.awt.Color(view.getAnnotationColours().\r
1040                                            getMaxColour()),\r
1041                         view.getAnnotationColours().getAboveThreshold());\r
1042                   }\r
1043                   else if (view.getAnnotationColours().getColourScheme().\r
1044                            startsWith("ucs"))\r
1045                   {\r
1046                      cs = new AnnotationColourGradient(\r
1047                          af.viewport.alignment.getAlignmentAnnotation()[i],\r
1048                          GetUserColourScheme(jms, view.getAnnotationColours().\r
1049                                                         getColourScheme()),\r
1050                          view.getAnnotationColours().getAboveThreshold()\r
1051                          );\r
1052                    }\r
1053                    else\r
1054                    {\r
1055                      cs = new AnnotationColourGradient(\r
1056                          af.viewport.alignment.getAlignmentAnnotation()[i],\r
1057                          ColourSchemeProperty.getColour(al,\r
1058                          view.getAnnotationColours().getColourScheme()),\r
1059                          view.getAnnotationColours().getAboveThreshold()\r
1060                          );\r
1061                    }\r
1062 \r
1063                   // Also use these settings for all the groups\r
1064                   if (al.getGroups() != null)\r
1065                     for (int g = 0; g < al.getGroups().size(); g++)\r
1066                     {\r
1067                       jalview.datamodel.SequenceGroup sg\r
1068                           = (jalview.datamodel.SequenceGroup)al.getGroups().elementAt(g);\r
1069 \r
1070                       if(sg.cs == null)\r
1071                         continue;\r
1072 \r
1073 \r
1074                   /*    if (view.getAnnotationColours().getColourScheme().equals("None"))\r
1075                       {\r
1076                         sg.cs = new AnnotationColourGradient(\r
1077                             af.viewport.alignment.getAlignmentAnnotation()[i],\r
1078                             new java.awt.Color(view.getAnnotationColours().\r
1079                                                getMinColour()),\r
1080                             new java.awt.Color(view.getAnnotationColours().\r
1081                                                getMaxColour()),\r
1082                             view.getAnnotationColours().getAboveThreshold());\r
1083                       }\r
1084                       else*/\r
1085                       {\r
1086                         sg.cs = new AnnotationColourGradient(\r
1087                             af.viewport.alignment.getAlignmentAnnotation()[i],\r
1088                             sg.cs,\r
1089                             view.getAnnotationColours().getAboveThreshold()\r
1090                             );\r
1091                       }\r
1092 \r
1093                     }\r
1094 \r
1095 \r
1096                   break;\r
1097                 }\r
1098 \r
1099               }\r
1100             }\r
1101             else\r
1102             {\r
1103                 cs = ColourSchemeProperty.getColour(al, view.getBgColour());\r
1104             }\r
1105 \r
1106             if(cs!=null)\r
1107             {\r
1108               cs.setThreshold(view.getPidThreshold(), true);\r
1109               cs.setConsensus(af.viewport.vconsensus);\r
1110             }\r
1111         }\r
1112 \r
1113         af.setColourSelected(view.getBgColour());\r
1114         af.viewport.setGlobalColourScheme(cs);\r
1115         af.viewport.setColourAppliesToAllGroups(false);\r
1116         af.changeColour(cs);\r
1117         if (view.getConservationSelected() && cs!=null)\r
1118         {\r
1119           cs.setConservationInc(view.getConsThreshold());\r
1120         }\r
1121 \r
1122         af.viewport.setColourAppliesToAllGroups(true);\r
1123 \r
1124         if (view.getShowSequenceFeatures())\r
1125         {\r
1126            af.viewport.showSequenceFeatures = true;\r
1127            af.showSeqFeatures.setSelected(true);\r
1128         }\r
1129 \r
1130         if(jms.getFeatureSettings()!=null)\r
1131         {\r
1132           af.viewport.featuresDisplayed = new Hashtable();\r
1133           String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];\r
1134          for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)\r
1135          {\r
1136            Setting setting = jms.getFeatureSettings().getSetting(fs);\r
1137 \r
1138            af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),\r
1139                new java.awt.Color(setting.getColour()));\r
1140 \r
1141            renderOrder[fs] = setting.getType();\r
1142 \r
1143            if(setting.getDisplay())\r
1144              af.viewport.featuresDisplayed.put(\r
1145                  setting.getType(), new Integer(setting.getColour()));\r
1146          }\r
1147          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;\r
1148         }\r
1149 \r
1150 \r
1151         Desktop.addInternalFrame(af, view.getTitle(),\r
1152              view.getWidth(), view.getHeight());\r
1153 \r
1154         //LOAD TREES\r
1155         ///////////////////////////////////////\r
1156         if (jms.getTreeCount() > 0)\r
1157         {\r
1158             try\r
1159             {\r
1160                 for (int t = 0; t < jms.getTreeCount(); t++)\r
1161                 {\r
1162 \r
1163                     Tree tree = jms.getTree(t);\r
1164 \r
1165                     TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(\r
1166                                 tree.getNewick()), tree.getTitle(),\r
1167                                 tree.getWidth(), tree.getHeight(),\r
1168                                 tree.getXpos(), tree.getYpos());\r
1169 \r
1170                     tp.fitToWindow.setState(tree.getFitToWindow());\r
1171                     tp.fitToWindow_actionPerformed(null);\r
1172 \r
1173                     if(tree.getFontName()!=null)\r
1174                       tp.setTreeFont(new java.awt.Font(tree.getFontName(),\r
1175                                           tree.getFontStyle(),\r
1176                                           tree.getFontSize()));\r
1177                     else\r
1178                       tp.setTreeFont(new java.awt.Font(view.getFontName(),\r
1179                                             view.getFontStyle(),\r
1180                                             tree.getFontSize()));\r
1181 \r
1182                     tp.showPlaceholders(tree.getMarkUnlinked());\r
1183                     tp.showBootstrap(tree.getShowBootstrap());\r
1184                     tp.showDistances(tree.getShowDistances());\r
1185 \r
1186                     tp.treeCanvas.threshold = tree.getThreshold();\r
1187 \r
1188                     if (tree.getCurrentTree())\r
1189                       af.viewport.setCurrentTree(tp.getTree());\r
1190                 }\r
1191 \r
1192             }\r
1193             catch (Exception ex)\r
1194             {\r
1195                 ex.printStackTrace();\r
1196             }\r
1197 \r
1198         }\r
1199 \r
1200         return af;\r
1201     }\r
1202 }\r
1203 \r