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                 Annotation an = new Annotation();\r
 311 \r
 312                 if (aa[i].label.equals("Quality") ||\r
 313                         aa[i].label.equals("Conservation") ||\r
 314                         aa[i].label.equals("Consensus"))\r
 315                 {\r
 316                     an.setLabel(aa[i].label);\r
 317                     an.setGraph(true);\r
 318                     vamsasSet.addAnnotation(an);\r
 319                     continue;\r
 320                 }\r
 321 \r
 322 \r
 323                 an.setDescription(aa[i].description);\r
 324 \r
 325                 if(aa[i].sequenceRef!=null)\r
 326                  {\r
 327                    an.setSequenceRef(aa[i].sequenceRef.getName());\r
 328                  }\r
 329 \r
 330                 if(aa[i].graph>0)\r
 331                 {\r
 332                   an.setGraph(true);\r
 333                   an.setGraphType(aa[i].graph);\r
 334                   an.setGraphGroup(aa[i].graphGroup);\r
 335                   if(aa[i].getThreshold()!=null)\r
 336                   {\r
 337                     ThresholdLine line = new ThresholdLine();\r
 338                     line.setLabel(aa[i].getThreshold().label);\r
 339                     line.setValue(aa[i].getThreshold().value);\r
 340                     line.setColour(aa[i].getThreshold().colour.getRGB());\r
 341                     an.setThresholdLine(line);\r
 342                   }\r
 343                 }\r
 344                 else\r
 345                   an.setGraph(false);\r
 346 \r
 347                 an.setLabel(aa[i].label);\r
 348 \r
 349                 AnnotationElement ae;\r
 350 \r
 351                 for (int a = 0; a < aa[i].annotations.length; a++)\r
 352                 {\r
 353                     if ((aa[i] == null) || (aa[i].annotations[a] == null))\r
 354                     {\r
 355                         continue;\r
 356                     }\r
 357 \r
 358                     ae = new AnnotationElement();\r
 359                     ae.setDescription(aa[i].annotations[a].description);\r
 360                     ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);\r
 361                     ae.setValue(aa[i].annotations[a].value);\r
 362                     ae.setPosition(a);\r
 363                     ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +\r
 364                         "");\r
 365 \r
 366                     if(aa[i].annotations[a].colour!=java.awt.Color.black)\r
 367                       ae.setColour(aa[i].annotations[a].colour.getRGB());\r
 368 \r
 369                     an.addAnnotationElement(ae);\r
 370                 }\r
 371 \r
 372                 vamsasSet.addAnnotation(an);\r
 373             }\r
 374         }\r
 375 \r
 376         //SAVE GROUPS\r
 377         if (jal.getGroups() != null)\r
 378         {\r
 379             JGroup[] groups = new JGroup[jal.getGroups().size()];\r
 380 \r
 381             for (int i = 0; i < groups.length; i++)\r
 382             {\r
 383                 groups[i] = new JGroup();\r
 384 \r
 385                 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()\r
 386                                                                                           .elementAt(i);\r
 387                 groups[i].setStart(sg.getStartRes());\r
 388                 groups[i].setEnd(sg.getEndRes());\r
 389                 groups[i].setName(sg.getName());\r
 390                 if(sg.cs!=null)\r
 391                 {\r
 392                   if (sg.cs.conservationApplied())\r
 393                   {\r
 394                     groups[i].setConsThreshold(sg.cs.getConservationInc());\r
 395 \r
 396                     if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
 397                     {\r
 398                       groups[i].setColour(SetUserColourScheme(sg.cs,\r
 399                           userColours,\r
 400                           jms));\r
 401                     }\r
 402                     else\r
 403                     {\r
 404                       groups[i].setColour(ColourSchemeProperty.getColourName(sg.\r
 405                           cs));\r
 406                     }\r
 407                   }\r
 408                   else if(sg.cs instanceof jalview.schemes.AnnotationColourGradient)\r
 409                   {\r
 410                     groups[i].setColour(\r
 411                         ColourSchemeProperty.getColourName(\r
 412                       ( (jalview.schemes.AnnotationColourGradient) sg.cs).getBaseColour()));\r
 413                   }\r
 414                   else if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
 415                   {\r
 416                     groups[i].setColour(SetUserColourScheme(sg.cs, userColours,\r
 417                         jms));\r
 418                   }\r
 419                   else\r
 420                   {\r
 421                     groups[i].setColour(ColourSchemeProperty.getColourName(\r
 422                         sg.cs));\r
 423                   }\r
 424 \r
 425                   groups[i].setPidThreshold(sg.cs.getThreshold());\r
 426                 }\r
 427 \r
 428                 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());\r
 429                 groups[i].setDisplayBoxes(sg.getDisplayBoxes());\r
 430                 groups[i].setDisplayText(sg.getDisplayText());\r
 431                 groups[i].setColourText(sg.getColourText());\r
 432 \r
 433                 for (int s = 0; s < sg.getSize(); s++)\r
 434                 {\r
 435                     jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.getSequenceAt(s);\r
 436                     int index = seqids.indexOf(seq);\r
 437                     groups[i].addSeq(index);\r
 438                 }\r
 439             }\r
 440 \r
 441             jms.setJGroup(groups);\r
 442         }\r
 443 \r
 444 \r
 445         ///////////SAVE VIEWPORT\r
 446         Viewport view = new Viewport();\r
 447         view.setTitle(af.getTitle());\r
 448         view.setXpos(af.getX());\r
 449         view.setYpos(af.getY());\r
 450         view.setWidth(af.getWidth());\r
 451         view.setHeight(af.getHeight());\r
 452         view.setStartRes(av.startRes);\r
 453         view.setStartSeq(av.startSeq);\r
 454 \r
 455         if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)\r
 456         {\r
 457             view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),\r
 458                     userColours, jms));\r
 459         }\r
 460         else if(av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)\r
 461         {\r
 462            jalview.schemes.AnnotationColourGradient acg\r
 463               = (jalview.schemes.AnnotationColourGradient)av.getGlobalColourScheme();\r
 464 \r
 465             AnnotationColours ac = new AnnotationColours();\r
 466             ac.setAboveThreshold(acg.getAboveThreshold());\r
 467             ac.setThreshold(acg.getAnnotationThreshold());\r
 468             ac.setAnnotation(acg.getAnnotation());\r
 469             if(acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)\r
 470               ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),\r
 471                     userColours, jms));\r
 472             else\r
 473               ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));\r
 474 \r
 475             ac.setMaxColour(acg.getMaxColour().getRGB());\r
 476             ac.setMinColour(acg.getMinColour().getRGB());\r
 477             view.setAnnotationColours(ac);\r
 478             view.setBgColour("AnnotationColourGradient");\r
 479         }\r
 480         else\r
 481         {\r
 482             view.setBgColour(ColourSchemeProperty.getColourName(\r
 483                     av.getGlobalColourScheme()));\r
 484         }\r
 485 \r
 486         ColourSchemeI cs = av.getGlobalColourScheme();\r
 487 \r
 488         if(cs!=null)\r
 489         {\r
 490           if (cs.conservationApplied())\r
 491           {\r
 492             view.setConsThreshold(cs.getConservationInc());\r
 493             if (cs instanceof jalview.schemes.UserColourScheme)\r
 494               view.setBgColour(SetUserColourScheme(cs, userColours, jms));\r
 495           }\r
 496 \r
 497           if (cs instanceof ResidueColourScheme)\r
 498           {\r
 499             view.setPidThreshold(cs.getThreshold());\r
 500           }\r
 501         }\r
 502 \r
 503         view.setConservationSelected(av.getConservationSelected());\r
 504         view.setPidSelected(av.getAbovePIDThreshold());\r
 505         view.setFontName(av.font.getName());\r
 506         view.setFontSize(av.font.getSize());\r
 507         view.setFontStyle(av.font.getStyle());\r
 508         view.setRenderGaps(av.renderGaps);\r
 509         view.setShowAnnotation(av.getShowAnnotation());\r
 510         view.setShowBoxes(av.getShowBoxes());\r
 511         view.setShowColourText(av.getColourText());\r
 512         view.setShowConservation(av.showConservation);\r
 513         view.setShowFullId(av.getShowJVSuffix());\r
 514         view.setShowIdentity(av.showIdentity);\r
 515         view.setShowQuality(av.showQuality);\r
 516         view.setShowSequenceFeatures(av.showSequenceFeatures);\r
 517         view.setShowText(av.getShowText());\r
 518         view.setWrapAlignment(av.getWrapAlignment());\r
 519 \r
 520         if(av.featuresDisplayed!=null)\r
 521         {\r
 522           jalview.schemabinding.version2.FeatureSettings fs\r
 523               = new jalview.schemabinding.version2.FeatureSettings();\r
 524 \r
 525           String [] renderOrder =\r
 526               af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;\r
 527           for(int ro=0; ro<renderOrder.length; ro++)\r
 528           {\r
 529             Setting setting = new Setting();\r
 530             setting.setType(renderOrder[ro]);\r
 531             setting.setColour(\r
 532                 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).getRGB()\r
 533                 );\r
 534 \r
 535             setting.setDisplay(\r
 536                 av.featuresDisplayed.containsKey(renderOrder[ro])\r
 537                 );\r
 538 \r
 539             fs.addSetting(setting);\r
 540 \r
 541           }\r
 542           jms.setFeatureSettings(fs);\r
 543 \r
 544         }\r
 545 \r
 546         jms.addViewport(view);\r
 547 \r
 548 \r
 549         object.setJalviewModelSequence(jms);\r
 550         object.getVamsasModel().addSequenceSet(vamsasSet);\r
 551 \r
 552         try\r
 553         {\r
 554             if (!fileName.endsWith(".xml"))\r
 555             {\r
 556                 fileName = fileName + ".xml";\r
 557             }\r
 558 \r
 559             JarEntry entry = new JarEntry(fileName);\r
 560             jout.putNextEntry(entry);\r
 561 \r
 562             object.marshal(out);\r
 563         }\r
 564         catch (Exception ex)\r
 565         {\r
 566             ex.printStackTrace();\r
 567         }\r
 568     }\r
 569 \r
 570     String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,\r
 571         Vector userColours, JalviewModelSequence jms)\r
 572     {\r
 573         String id = null;\r
 574         jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;\r
 575 \r
 576         if (!userColours.contains(ucs))\r
 577         {\r
 578             userColours.add(ucs);\r
 579 \r
 580             java.awt.Color[] colours = ucs.getColours();\r
 581             jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();\r
 582             jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();\r
 583 \r
 584             for (int i = 0; i < colours.length; i++)\r
 585             {\r
 586                 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();\r
 587                 col.setRGB(jalview.util.Format.getHexString(colours[i]));\r
 588                 jbucs.addColour(col);\r
 589             }\r
 590 \r
 591             id = "ucs" + userColours.indexOf(ucs);\r
 592             uc.setId(id);\r
 593             uc.setUserColourScheme(jbucs);\r
 594             jms.addUserColours(uc);\r
 595         }\r
 596 \r
 597         return id;\r
 598     }\r
 599 \r
 600    jalview.schemes.UserColourScheme GetUserColourScheme(\r
 601         JalviewModelSequence jms, String id)\r
 602     {\r
 603         UserColours[] uc = jms.getUserColours();\r
 604         UserColours colours = null;\r
 605 \r
 606         for (int i = 0; i < uc.length; i++)\r
 607         {\r
 608             if (uc[i].getId().equals(id))\r
 609             {\r
 610                 colours = uc[i];\r
 611 \r
 612                 break;\r
 613             }\r
 614         }\r
 615 \r
 616         int csize = colours.getUserColourScheme().getColourCount();\r
 617         java.awt.Color[] newColours = new java.awt.Color[csize];\r
 618 \r
 619         for (int i = 0; i < csize; i++)\r
 620         {\r
 621             newColours[i] = new java.awt.Color(Integer.parseInt(\r
 622                         colours.getUserColourScheme().getColour(i).getRGB(), 16));\r
 623         }\r
 624 \r
 625         return new jalview.schemes.UserColourScheme(newColours);\r
 626     }\r
 627 \r
 628     /**\r
 629      * DOCUMENT ME!\r
 630      *\r
 631      * @param file DOCUMENT ME!\r
 632      */\r
 633     public AlignFrame LoadJalviewAlign(String file)\r
 634     {\r
 635 \r
 636         jalview.gui.AlignFrame af = null;\r
 637 \r
 638         try\r
 639         {\r
 640             //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING\r
 641             URL url = null;\r
 642 \r
 643             if (file.startsWith("http://"))\r
 644             {\r
 645                 url = new URL(file);\r
 646             }\r
 647 \r
 648             JarInputStream jin = null;\r
 649             JarEntry jarentry = null;\r
 650             int entryCount = 1;\r
 651 \r
 652             do\r
 653             {\r
 654                 if (url != null)\r
 655                 {\r
 656                     jin = new JarInputStream(url.openStream());\r
 657                 }\r
 658                 else\r
 659                 {\r
 660                     jin = new JarInputStream(new FileInputStream(file));\r
 661                 }\r
 662 \r
 663                 for (int i = 0; i < entryCount; i++)\r
 664                 {\r
 665                     jarentry = jin.getNextJarEntry();\r
 666 \r
 667                   }\r
 668 \r
 669 \r
 670                   class NoDescIDResolver implements IDResolver\r
 671                   {\r
 672                     public Object resolve(String idref)\r
 673                     {\r
 674                       System.out.println(idref+" used");\r
 675                       return null;\r
 676                     }\r
 677                   }\r
 678 \r
 679 \r
 680                 if (jarentry != null)\r
 681                 {\r
 682                     InputStreamReader in = new InputStreamReader(jin, "UTF-8");\r
 683                     JalviewModel object = new JalviewModel();\r
 684 \r
 685                     Unmarshaller unmar = new Unmarshaller(object);\r
 686                     unmar.setValidation(false);\r
 687                     object = (JalviewModel) unmar.unmarshal( in );\r
 688 \r
 689                     af = LoadFromObject(object);\r
 690                     entryCount++;\r
 691                 }\r
 692             }\r
 693             while (jarentry != null);\r
 694         }\r
 695         catch(java.net.UnknownHostException ex)\r
 696         {\r
 697           ex.printStackTrace();\r
 698           System.err.println("Couldn't locate Jalview XML file : " +\r
 699               ex + "\n");\r
 700            JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 701                                     "Couldn't locate " + file,\r
 702                                     "URL not found",\r
 703                                     JOptionPane.WARNING_MESSAGE);\r
 704 \r
 705         }\r
 706         catch (Exception ex)\r
 707         {\r
 708           //Is Version 1 Jar file?\r
 709           af =  new Jalview2XML_V1().LoadJalviewAlign(file);\r
 710 \r
 711           if(af!=null)\r
 712           {\r
 713             System.out.println("Successfully loaded archive file");\r
 714             return af;\r
 715           }\r
 716           ex.printStackTrace();\r
 717             System.err.println("Exception whilst loading jalview XML file : " +\r
 718                 ex + "\n");\r
 719              JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 720                                       "Error loading  " + file,\r
 721                                       "Error loading Jalview file",\r
 722                                       JOptionPane.WARNING_MESSAGE);\r
 723 \r
 724         }\r
 725 \r
 726         return af;\r
 727     }\r
 728 \r
 729     AlignFrame LoadFromObject(JalviewModel object)\r
 730     {\r
 731         Vector seqids = new Vector();\r
 732         SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);\r
 733         Sequence[] vamsasSeq = vamsasSet.getSequence();\r
 734 \r
 735         JalviewModelSequence jms = object.getJalviewModelSequence();\r
 736 \r
 737         //////////////////////////////////\r
 738         //LOAD SEQUENCES\r
 739         jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];\r
 740         JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();\r
 741         for (int i = 0; i < vamsasSeq.length; i++)\r
 742         {\r
 743             jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),\r
 744                     vamsasSeq[i].getSequence());\r
 745             jseqs[i].setDescription( vamsasSeq[i].getDescription() );\r
 746 \r
 747             jseqs[i].setStart(JSEQ[i].getStart());\r
 748             jseqs[i].setEnd(JSEQ[i].getEnd());\r
 749             jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));\r
 750             seqids.add(jseqs[i]);\r
 751         }\r
 752 \r
 753         ///SequenceFeatures are added to the DatasetSequence,\r
 754         // so we must create the dataset before loading features\r
 755         /////////////////////////////////\r
 756         jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);\r
 757         al.setDataset(null);\r
 758         /////////////////////////////////\r
 759 \r
 760         for (int i = 0; i < vamsasSeq.length; i++)\r
 761         {\r
 762           if (JSEQ[i].getFeaturesCount() > 0)\r
 763           {\r
 764             Features[] features = JSEQ[i].getFeatures();\r
 765             for (int f = 0; f < features.length; f++)\r
 766             {\r
 767               jalview.datamodel.SequenceFeature sf\r
 768                   = new jalview.datamodel.SequenceFeature(features[f].getType(),\r
 769                   features[f].getDescription(), features[f].getStatus(),\r
 770                   features[f].getBegin(), features[f].getEnd(),\r
 771                   features[f].getFeatureGroup());\r
 772 \r
 773               al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);\r
 774             }\r
 775           }\r
 776           if (JSEQ[i].getPdbidsCount() > 0)\r
 777           {\r
 778             Pdbids[] ids = JSEQ[i].getPdbids();\r
 779             for (int p = 0; p < ids.length; p++)\r
 780             {\r
 781               jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();\r
 782               entry.setId(ids[p].getId());\r
 783               entry.setType(ids[p].getType());\r
 784               al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);\r
 785             }\r
 786 \r
 787           }\r
 788         }\r
 789 \r
 790 \r
 791          /////////////////////////////////\r
 792         //////////////////////////////////\r
 793         //LOAD ANNOTATIONS\r
 794         boolean hideQuality = true,\r
 795             hideConservation = true,\r
 796             hideConsensus = true;\r
 797 \r
 798         if (vamsasSet.getAnnotation() != null)\r
 799         {\r
 800             Annotation[] an = vamsasSet.getAnnotation();\r
 801 \r
 802             for (int i = 0; i < an.length; i++)\r
 803             {\r
 804                if (an[i].getLabel().equals("Quality"))\r
 805                 {\r
 806                  hideQuality = false;\r
 807                  continue;\r
 808                 }\r
 809                else if(an[i].getLabel().equals("Conservation"))\r
 810                {\r
 811                  hideConservation = false;\r
 812                  continue;\r
 813                }\r
 814                else if(an[i].getLabel().equals("Consensus"))\r
 815                {\r
 816                  hideConsensus = false;\r
 817                  continue;\r
 818                }\r
 819 \r
 820                 AnnotationElement[] ae = an[i].getAnnotationElement();\r
 821                 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];\r
 822 \r
 823                 for (int aa = 0; aa < ae.length; aa++)\r
 824                 {\r
 825                     anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),\r
 826                             ae[aa].getDescription(),\r
 827                             ae[aa].getSecondaryStructure().length()==0?' ':ae[aa].getSecondaryStructure().charAt(0),\r
 828                             ae[aa].getValue());\r
 829                     anot[ae[aa].getPosition()].colour = new java.awt.Color( ae[aa].getColour() );\r
 830                 }\r
 831 \r
 832                 jalview.datamodel.AlignmentAnnotation jaa = null;\r
 833 \r
 834                 if (an[i].getGraph())\r
 835                 {\r
 836                   jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
 837                       an[i].getDescription(), anot, 0, 0,\r
 838                       an[i].getGraphType());\r
 839 \r
 840                   jaa.graphGroup = an[i].getGraphGroup();\r
 841 \r
 842                   if (an[i].getThresholdLine() != null)\r
 843                   {\r
 844                     jaa.setThreshold(new jalview.datamodel.GraphLine(\r
 845                                   an[i].getThresholdLine().getValue(),\r
 846                                   an[i].getThresholdLine().getLabel(),\r
 847                                 new java.awt.Color(an[i].getThresholdLine().getColour()))\r
 848                              );\r
 849 \r
 850                   }\r
 851 \r
 852                 }\r
 853                 else\r
 854                 {\r
 855                     jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
 856                             an[i].getDescription(), anot);\r
 857                 }\r
 858 \r
 859                 if(an[i].getSequenceRef()!=null)\r
 860                 {\r
 861                   jaa.createSequenceMapping(\r
 862                       al.findName(an[i].getSequenceRef()), 1\r
 863                       );\r
 864                   al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);\r
 865                 }\r
 866 \r
 867                 al.addAnnotation(jaa);\r
 868             }\r
 869         }\r
 870 \r
 871 \r
 872         //  af.changeColour() );\r
 873         /////////////////////////\r
 874         //LOAD GROUPS\r
 875         if (jms.getJGroupCount() > 0)\r
 876         {\r
 877             JGroup[] groups = jms.getJGroup();\r
 878 \r
 879             for (int i = 0; i < groups.length; i++)\r
 880             {\r
 881                 ColourSchemeI cs = null;\r
 882 \r
 883                 if (groups[i].getColour() != null)\r
 884                 {\r
 885                     if (groups[i].getColour().startsWith("ucs"))\r
 886                     {\r
 887                         cs = GetUserColourScheme(jms, groups[i].getColour());\r
 888                     }\r
 889                     else\r
 890                     {\r
 891                         cs = ColourSchemeProperty.getColour(al,\r
 892                                 groups[i].getColour());\r
 893                     }\r
 894 \r
 895                     if(cs!=null)\r
 896                       cs.setThreshold(groups[i].getPidThreshold(), true);\r
 897                 }\r
 898 \r
 899                 Vector seqs = new Vector();\r
 900                 int[] ids = groups[i].getSeq();\r
 901 \r
 902                 for (int s = 0; s < ids.length; s++)\r
 903                 {\r
 904                     seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(\r
 905                             ids[s]));\r
 906                 }\r
 907 \r
 908                 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,\r
 909                         groups[i].getName(), cs, groups[i].getDisplayBoxes(),\r
 910                         groups[i].getDisplayText(), groups[i].getColourText(),\r
 911                         groups[i].getStart(), groups[i].getEnd());\r
 912 \r
 913                 sg.setOutlineColour(new java.awt.Color(\r
 914                         groups[i].getOutlineColour()));\r
 915 \r
 916                 if (groups[i].getConsThreshold() != 0)\r
 917                 {\r
 918                     jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",\r
 919                             ResidueProperties.propHash, 3, sg.sequences, 0,\r
 920                             sg.getWidth() - 1);\r
 921                     c.calculate();\r
 922                     c.verdict(false, 25);\r
 923                     sg.cs.setConservation(c);\r
 924                 }\r
 925 \r
 926                 al.addGroup(sg);\r
 927             }\r
 928         }\r
 929 \r
 930 \r
 931         /////////////////////////////////\r
 932         // LOAD VIEWPORT\r
 933         Viewport[] views = jms.getViewport();\r
 934         Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER\r
 935 \r
 936         AlignFrame af = new AlignFrame(al);\r
 937         if(hideConsensus || hideQuality || hideConservation)\r
 938         {\r
 939           int hSize = al.getAlignmentAnnotation().length;\r
 940           for (int h = 0; h < hSize; h++)\r
 941           {\r
 942             if (\r
 943                 (hideConsensus &&\r
 944                  al.getAlignmentAnnotation()[h].label.equals("Consensus"))\r
 945                 ||\r
 946                 (hideQuality &&\r
 947                  al.getAlignmentAnnotation()[h].label.equals("Quality"))\r
 948                 ||\r
 949                 (hideConservation &&\r
 950                  al.getAlignmentAnnotation()[h].label.equals("Conservation")))\r
 951             {\r
 952               al.deleteAnnotation(al.getAlignmentAnnotation()[h]);\r
 953               hSize--;\r
 954               h--;\r
 955             }\r
 956           }\r
 957           af.alignPanel.adjustAnnotationHeight();\r
 958         }\r
 959 \r
 960         af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),\r
 961             view.getHeight());\r
 962         af.viewport.setStartRes(view.getStartRes());\r
 963         af.viewport.setStartSeq(view.getStartSeq());\r
 964         af.viewport.setShowAnnotation(view.getShowAnnotation());\r
 965         af.viewport.showConservation = view.getShowConservation();\r
 966         af.viewport.showQuality = view.getShowQuality();\r
 967         af.viewport.showIdentity = view.getShowIdentity();\r
 968         af.viewport.setAbovePIDThreshold(view.getPidSelected());\r
 969         af.abovePIDThreshold.setSelected(view.getPidSelected());\r
 970         af.viewport.setColourText(view.getShowColourText());\r
 971         af.colourTextMenuItem.setSelected(view.getShowColourText());\r
 972         af.viewport.setConservationSelected(view.getConservationSelected());\r
 973         af.conservationMenuItem.setSelected(view.getConservationSelected());\r
 974 \r
 975         af.viewport.setShowJVSuffix(view.getShowFullId());\r
 976         af.seqLimits.setSelected(view.getShowFullId());\r
 977 \r
 978         af.viewport.setFont(new java.awt.Font(view.getFontName(),\r
 979                 view.getFontStyle(), view.getFontSize()));\r
 980         af.alignPanel.fontChanged();\r
 981 \r
 982         af.viewport.setRenderGaps(view.getRenderGaps());\r
 983         af.renderGapsMenuItem.setSelected(view.getRenderGaps());\r
 984 \r
 985         af.viewport.setWrapAlignment(view.getWrapAlignment());\r
 986         af.wrapMenuItem.setSelected(view.getWrapAlignment());\r
 987 \r
 988         if (view.getWrapAlignment())\r
 989         {\r
 990             af.alignPanel.setWrapAlignment(view.getWrapAlignment());\r
 991         }\r
 992         else\r
 993         {\r
 994             af.annotationPanelMenuItem.setState(view.getShowAnnotation());\r
 995             af.viewport.setShowAnnotation(view.getShowAnnotation());\r
 996             af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\r
 997         }\r
 998 \r
 999         af.viewport.setShowBoxes(view.getShowBoxes());\r
1000         af.viewBoxesMenuItem.setSelected(view.getShowBoxes());\r
1001         af.viewport.setShowText(view.getShowText());\r
1002         af.viewTextMenuItem.setSelected(view.getShowText());\r
1003 \r
1004         ColourSchemeI cs = null;\r
1005 \r
1006         if (view.getBgColour() != null)\r
1007         {\r
1008             if (view.getBgColour().startsWith("ucs"))\r
1009             {\r
1010                 cs = GetUserColourScheme(jms, view.getBgColour());\r
1011             }\r
1012             else if(view.getBgColour().startsWith("Annotation"))\r
1013             {\r
1014               //int find annotation\r
1015               for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)\r
1016               {\r
1017                 if (af.viewport.alignment.getAlignmentAnnotation()[i].label.\r
1018                     equals(view.getAnnotationColours().getAnnotation()))\r
1019                 {\r
1020                   if (af.viewport.alignment.getAlignmentAnnotation()[i].\r
1021                       getThreshold() == null)\r
1022                   {\r
1023                     af.viewport.alignment.getAlignmentAnnotation()[i].\r
1024                         setThreshold(\r
1025                             new jalview.datamodel.GraphLine(\r
1026                                 view.getAnnotationColours().getThreshold(),\r
1027                                 "Threshold", java.awt.Color.black)\r
1028 \r
1029                         );\r
1030                   }\r
1031 \r
1032 \r
1033                   if (view.getAnnotationColours().getColourScheme().equals(\r
1034                       "None"))\r
1035                   {\r
1036                     cs = new AnnotationColourGradient(\r
1037                         af.viewport.alignment.getAlignmentAnnotation()[i],\r
1038                         new java.awt.Color(view.getAnnotationColours().\r
1039                                            getMinColour()),\r
1040                         new java.awt.Color(view.getAnnotationColours().\r
1041                                            getMaxColour()),\r
1042                         view.getAnnotationColours().getAboveThreshold());\r
1043                   }\r
1044                   else if (view.getAnnotationColours().getColourScheme().\r
1045                            startsWith("ucs"))\r
1046                   {\r
1047                      cs = new AnnotationColourGradient(\r
1048                          af.viewport.alignment.getAlignmentAnnotation()[i],\r
1049                          GetUserColourScheme(jms, view.getAnnotationColours().\r
1050                                                         getColourScheme()),\r
1051                          view.getAnnotationColours().getAboveThreshold()\r
1052                          );\r
1053                    }\r
1054                    else\r
1055                    {\r
1056                      cs = new AnnotationColourGradient(\r
1057                          af.viewport.alignment.getAlignmentAnnotation()[i],\r
1058                          ColourSchemeProperty.getColour(al,\r
1059                          view.getAnnotationColours().getColourScheme()),\r
1060                          view.getAnnotationColours().getAboveThreshold()\r
1061                          );\r
1062                    }\r
1063 \r
1064                   // Also use these settings for all the groups\r
1065                   if (al.getGroups() != null)\r
1066                     for (int g = 0; g < al.getGroups().size(); g++)\r
1067                     {\r
1068                       jalview.datamodel.SequenceGroup sg\r
1069                           = (jalview.datamodel.SequenceGroup)al.getGroups().elementAt(g);\r
1070 \r
1071                       if(sg.cs == null)\r
1072                         continue;\r
1073 \r
1074 \r
1075                   /*    if (view.getAnnotationColours().getColourScheme().equals("None"))\r
1076                       {\r
1077                         sg.cs = new AnnotationColourGradient(\r
1078                             af.viewport.alignment.getAlignmentAnnotation()[i],\r
1079                             new java.awt.Color(view.getAnnotationColours().\r
1080                                                getMinColour()),\r
1081                             new java.awt.Color(view.getAnnotationColours().\r
1082                                                getMaxColour()),\r
1083                             view.getAnnotationColours().getAboveThreshold());\r
1084                       }\r
1085                       else*/\r
1086                       {\r
1087                         sg.cs = new AnnotationColourGradient(\r
1088                             af.viewport.alignment.getAlignmentAnnotation()[i],\r
1089                             sg.cs,\r
1090                             view.getAnnotationColours().getAboveThreshold()\r
1091                             );\r
1092                       }\r
1093 \r
1094                     }\r
1095 \r
1096 \r
1097                   break;\r
1098                 }\r
1099 \r
1100               }\r
1101             }\r
1102             else\r
1103             {\r
1104                 cs = ColourSchemeProperty.getColour(al, view.getBgColour());\r
1105             }\r
1106 \r
1107             if(cs!=null)\r
1108             {\r
1109               cs.setThreshold(view.getPidThreshold(), true);\r
1110               cs.setConsensus(af.viewport.vconsensus);\r
1111             }\r
1112         }\r
1113 \r
1114         af.setColourSelected(view.getBgColour());\r
1115         af.viewport.setGlobalColourScheme(cs);\r
1116         af.viewport.setColourAppliesToAllGroups(false);\r
1117         af.changeColour(cs);\r
1118         if (view.getConservationSelected() && cs!=null)\r
1119         {\r
1120           cs.setConservationInc(view.getConsThreshold());\r
1121         }\r
1122 \r
1123         af.viewport.setColourAppliesToAllGroups(true);\r
1124 \r
1125         if (view.getShowSequenceFeatures())\r
1126         {\r
1127            af.viewport.showSequenceFeatures = true;\r
1128            af.showSeqFeatures.setSelected(true);\r
1129         }\r
1130 \r
1131         if(jms.getFeatureSettings()!=null)\r
1132         {\r
1133           af.viewport.featuresDisplayed = new Hashtable();\r
1134           String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];\r
1135          for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)\r
1136          {\r
1137            Setting setting = jms.getFeatureSettings().getSetting(fs);\r
1138 \r
1139            af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),\r
1140                new java.awt.Color(setting.getColour()));\r
1141 \r
1142            renderOrder[fs] = setting.getType();\r
1143 \r
1144            if(setting.getDisplay())\r
1145              af.viewport.featuresDisplayed.put(\r
1146                  setting.getType(), new Integer(setting.getColour()));\r
1147          }\r
1148          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;\r
1149         }\r
1150 \r
1151 \r
1152         Desktop.addInternalFrame(af, view.getTitle(),\r
1153              view.getWidth(), view.getHeight());\r
1154 \r
1155         //LOAD TREES\r
1156         ///////////////////////////////////////\r
1157         if (jms.getTreeCount() > 0)\r
1158         {\r
1159             try\r
1160             {\r
1161                 for (int t = 0; t < jms.getTreeCount(); t++)\r
1162                 {\r
1163 \r
1164                     Tree tree = jms.getTree(t);\r
1165 \r
1166                     TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(\r
1167                                 tree.getNewick()), tree.getTitle(),\r
1168                                 tree.getWidth(), tree.getHeight(),\r
1169                                 tree.getXpos(), tree.getYpos());\r
1170 \r
1171                     tp.fitToWindow.setState(tree.getFitToWindow());\r
1172                     tp.fitToWindow_actionPerformed(null);\r
1173 \r
1174                     if(tree.getFontName()!=null)\r
1175                       tp.setTreeFont(new java.awt.Font(tree.getFontName(),\r
1176                                           tree.getFontStyle(),\r
1177                                           tree.getFontSize()));\r
1178                     else\r
1179                       tp.setTreeFont(new java.awt.Font(view.getFontName(),\r
1180                                             view.getFontStyle(),\r
1181                                             tree.getFontSize()));\r
1182 \r
1183                     tp.showPlaceholders(tree.getMarkUnlinked());\r
1184                     tp.showBootstrap(tree.getShowBootstrap());\r
1185                     tp.showDistances(tree.getShowDistances());\r
1186 \r
1187                     tp.treeCanvas.threshold = tree.getThreshold();\r
1188 \r
1189                     if (tree.getCurrentTree())\r
1190                       af.viewport.setCurrentTree(tp.getTree());\r
1191                 }\r
1192 \r
1193             }\r
1194             catch (Exception ex)\r
1195             {\r
1196                 ex.printStackTrace();\r
1197             }\r
1198 \r
1199         }\r
1200 \r
1201         return af;\r
1202     }\r
1203 }\r
1204 \r