src/jalview/gui/Jalview2XML.java

   1 package jalview.gui;\r
   2 \r
   3 import java.io.*;\r
   4 import java.util.*;\r
   5 import java.util.jar.*;\r
   6 \r
   7 import jalview.binding.*;\r
   8 import jalview.schemes.*;\r
   9 import javax.swing.JInternalFrame;\r
  10 import java.net.URL;\r
  11 \r
  12 \r
  13 public class Jalview2XML\r
  14 {\r
  15 \r
  16   // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE\r
  17   public static void SaveState(File statefile)\r
  18   {\r
  19       long creation = System.currentTimeMillis();\r
  20       JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
  21       if(frames==null)\r
  22         return;\r
  23 \r
  24       try{\r
  25         FileOutputStream fos = new FileOutputStream(statefile);\r
  26         JarOutputStream jout = new JarOutputStream(fos);\r
  27         //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS\r
  28         ////////////////////////////////////////////////////\r
  29         PrintWriter out = new PrintWriter(new OutputStreamWriter(jout, "UTF-8"));\r
  30 \r
  31         Vector shortNames = new Vector();\r
  32         //REVERSE ORDER\r
  33         for (int i = frames.length-1; i > -1; i--)\r
  34         {\r
  35           if (frames[i] instanceof AlignFrame)\r
  36           {\r
  37             AlignFrame af = (AlignFrame) frames[i];\r
  38 \r
  39             String shortName = af.getTitle();\r
  40 \r
  41             if(shortName.indexOf(File.separatorChar)>-1)\r
  42               shortName = shortName.substring(\r
  43                     shortName.lastIndexOf(File.separatorChar)+1);\r
  44 \r
  45             int count=1;\r
  46             while( shortNames.contains(shortName) )\r
  47             {\r
  48               if(shortName.endsWith("_"+(count-1)))\r
  49                 shortName = shortName.substring(0, shortName.lastIndexOf("_"));\r
  50 \r
  51               shortName = shortName.concat("_"+count);\r
  52               count++;\r
  53             }\r
  54             shortNames.addElement(shortName);\r
  55 \r
  56             if(!shortName.endsWith(".xml"))\r
  57               shortName = shortName+".xml";\r
  58 \r
  59             SaveState( af, creation, shortName, jout, out);\r
  60            }\r
  61         }\r
  62         out.close();\r
  63         jout.close();\r
  64       }\r
  65       catch(Exception ex){ex.printStackTrace();}\r
  66   }\r
  67 \r
  68   // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW\r
  69   public static void SaveState( AlignFrame af, String jarFile, String fileName)\r
  70   {\r
  71     try{\r
  72       FileOutputStream fos = new FileOutputStream(jarFile);\r
  73       JarOutputStream jout = new JarOutputStream(fos);\r
  74       //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS\r
  75       ////////////////////////////////////////////////////\r
  76       PrintWriter out = new PrintWriter(new OutputStreamWriter(jout, "UTF-8"));\r
  77 \r
  78       SaveState(af, System.currentTimeMillis(), fileName, jout, out);\r
  79       out.close();\r
  80       jout.close();\r
  81     }catch(Exception ex){}\r
  82   }\r
  83 \r
  84   public static void SaveState( AlignFrame af, long timeStamp,\r
  85       String fileName, JarOutputStream jout, PrintWriter out)\r
  86   {\r
  87 \r
  88     Vector seqids = new Vector();\r
  89     Vector userColours = new Vector();\r
  90 \r
  91     AlignViewport av = af.viewport;\r
  92 \r
  93     JalviewModel object = new JalviewModel();\r
  94     object.setVamsasModel( new VamsasModel() );\r
  95 \r
  96     object.setCreationDate( new java.util.Date(timeStamp) );\r
  97 \r
  98     jalview.datamodel.AlignmentI jal = af.viewport.alignment;\r
  99 \r
 100     SequenceSet vamsasSet = new SequenceSet();\r
 101     Sequence vamsasSeq;\r
 102     JalviewModelSequence jms = new JalviewModelSequence();\r
 103 \r
 104     vamsasSet.setGapChar(jal.getGapCharacter()+"");\r
 105 \r
 106     JSeq jseq;\r
 107 \r
 108 \r
 109     //SAVE SEQUENCES\r
 110     int id = 0;\r
 111     for(int i=0; i<jal.getHeight(); i++)\r
 112     {\r
 113       seqids.add(jal.getSequenceAt(i));\r
 114 \r
 115       vamsasSeq = new Sequence( );\r
 116       vamsasSeq.setId(id+"");\r
 117       vamsasSeq.setName(jal.getSequenceAt(i).getName());\r
 118       vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());\r
 119 \r
 120       jseq = new JSeq();\r
 121       jseq.setStart(jal.getSequenceAt(i).getStart());\r
 122       jseq.setEnd(jal.getSequenceAt(i).getEnd());\r
 123 \r
 124       jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());\r
 125 \r
 126       jseq.setId( id );\r
 127 \r
 128       jms.addJSeq(jseq);\r
 129       vamsasSet.addSequence(vamsasSeq);\r
 130       id++;\r
 131     }\r
 132 \r
 133     //SAVE TREES\r
 134     if(af.viewport.currentTree!=null)\r
 135     {\r
 136       object.getVamsasModel().addTree(af.viewport.currentTree.toString());\r
 137     }\r
 138 \r
 139     //SAVE ANNOTATIONS\r
 140     if(jal.getAlignmentAnnotation()!=null)\r
 141     {\r
 142 \r
 143       jalview.datamodel.AlignmentAnnotation [] aa = jal.getAlignmentAnnotation();\r
 144       for(int i=0; i<aa.length; i++)\r
 145       {\r
 146         if(aa[i].label.equals("Quality")\r
 147         || aa[i].label.equals("Conservation")\r
 148         || aa[i].label.equals("Consensus"))\r
 149        {    continue;}\r
 150 \r
 151         Annotation an = new Annotation();\r
 152         an.setDescription(aa[i].description);\r
 153         an.setGraph(aa[i].isGraph);\r
 154         an.setLabel(aa[i].label);\r
 155 \r
 156         AnnotationElement ae;\r
 157 \r
 158         for(int a=0; a<aa[i].annotations.length; a++)\r
 159         {\r
 160           if(aa[i]==null || aa[i].annotations[a]==null)\r
 161             continue;\r
 162 \r
 163           ae = new AnnotationElement();\r
 164           ae.setDescription(aa[i].annotations[a].description);\r
 165           ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);\r
 166           ae.setValue(aa[i].annotations[a].value);\r
 167           ae.setPosition(a);\r
 168           ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure+"");\r
 169           an.addAnnotationElement(ae);\r
 170         }\r
 171 \r
 172         vamsasSet.addAnnotation(an);\r
 173       }\r
 174 \r
 175     }\r
 176 \r
 177     //SAVE GROUPS\r
 178     if(jal.getGroups()!=null)\r
 179     {\r
 180       JGroup [] groups = new JGroup[jal.getGroups().size()];\r
 181       for(int i=0; i<groups.length; i++)\r
 182       {\r
 183         groups[i] = new JGroup();\r
 184         jalview.datamodel.SequenceGroup sg\r
 185             = (jalview.datamodel.SequenceGroup)jal.getGroups().elementAt(i);\r
 186         groups[i].setStart( sg.getStartRes() );\r
 187         groups[i].setEnd( sg.getEndRes() );\r
 188         groups[i].setName( sg.getName());\r
 189 \r
 190         if(sg.cs instanceof ConservationColourScheme)\r
 191           groups[i].setConsThreshold( ((ConservationColourScheme)sg.cs).inc);\r
 192 \r
 193         if (sg.cs instanceof ResidueColourScheme)\r
 194           groups[i].setPidThreshold( ( (ResidueColourScheme) sg.cs).getThreshold());\r
 195         else if (sg.cs instanceof ScoreColourScheme)\r
 196           groups[i].setPidThreshold( ( (ScoreColourScheme) sg.cs).getThreshold());\r
 197 \r
 198 \r
 199         if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
 200           groups[i].setColour(SetUserColourScheme(sg.cs, userColours, jms));\r
 201         else\r
 202           groups[i].setColour(ColourSchemeProperty.getColourName(sg.cs));\r
 203 \r
 204         groups[i].setOutlineColour(sg.getOutlineColour().getRGB());\r
 205         groups[i].setDisplayBoxes(sg.getDisplayBoxes());\r
 206         groups[i].setDisplayText(sg.getDisplayText());\r
 207         groups[i].setColourText(sg.getColourText());\r
 208 \r
 209         for(int s=0; s<sg.getSize(); s++)\r
 210         {\r
 211           jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence)sg.getSequenceAt(s);\r
 212           int index = seqids.indexOf(seq);\r
 213           groups[i].addSeq(index);\r
 214         }\r
 215 \r
 216       }\r
 217       jms.setJGroup(groups);\r
 218 \r
 219     }\r
 220 \r
 221     ///////////SAVE VIEWPORT\r
 222     Viewport view = new Viewport();\r
 223    view.setTitle(af.getTitle());\r
 224    view.setXpos(af.getX());\r
 225    view.setYpos(af.getY());\r
 226    view.setWidth(af.getWidth());\r
 227    view.setHeight(af.getHeight());\r
 228    view.setStartRes(av.startRes);\r
 229    view.setStartSeq(av.startSeq);\r
 230 \r
 231 \r
 232  if( av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)\r
 233    view.setBgColour( SetUserColourScheme(av.getGlobalColourScheme(),\r
 234                                          userColours, jms) );\r
 235  else\r
 236    view.setBgColour( ColourSchemeProperty.getColourName\r
 237                      ( av.getGlobalColourScheme()));\r
 238 \r
 239    ColourSchemeI cs = av.getGlobalColourScheme();\r
 240    if(cs instanceof ConservationColourScheme)\r
 241      view.setConsThreshold( ((ConservationColourScheme)cs).inc);\r
 242 \r
 243    if (cs instanceof ResidueColourScheme)\r
 244      view.setPidThreshold( ( (ResidueColourScheme) cs).getThreshold());\r
 245   else if (cs instanceof ScoreColourScheme)\r
 246      view.setPidThreshold( ( (ScoreColourScheme) cs).getThreshold());\r
 247 \r
 248 \r
 249    view.setConservationSelected(av.getConservationSelected());\r
 250    view.setPidSelected(av.getAbovePIDThreshold());\r
 251    view.setFontName(av.font.getFontName());\r
 252    view.setFontSize(av.font.getSize());\r
 253    view.setFontStyle(av.font.getStyle());\r
 254    view.setRenderGaps(av.renderGaps);\r
 255    view.setShowAnnotation(av.getShowAnnotation());\r
 256    view.setShowBoxes(av.getShowBoxes());\r
 257    view.setShowColourText(av.getColourText());\r
 258    view.setShowConservation(av.showConservation);\r
 259    view.setShowFullId(av.getShowFullId());\r
 260    view.setShowIdentity(av.showIdentity);\r
 261    view.setShowQuality(av.showQuality);\r
 262    view.setShowSequenceFeatures(av.showSequenceFeatures);\r
 263    view.setShowText(av.getShowText());\r
 264    view.setWrapAlignment(av.getWrapAlignment());\r
 265 \r
 266    jms.addViewport( view );\r
 267 \r
 268     object.setJalviewModelSequence(jms);\r
 269     object.getVamsasModel().addSequenceSet(vamsasSet);\r
 270 \r
 271 \r
 272     try\r
 273     {\r
 274      if(!fileName.endsWith(".xml"))\r
 275               fileName = fileName+".xml";\r
 276 \r
 277      JarEntry entry = new JarEntry(fileName);\r
 278      jout.putNextEntry(entry);\r
 279 \r
 280       object.marshal(out);\r
 281     }\r
 282     catch (Exception ex)\r
 283     {\r
 284       ex.printStackTrace();\r
 285     }\r
 286   }\r
 287 \r
 288   static String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,\r
 289                                     Vector userColours,\r
 290                                     JalviewModelSequence jms)\r
 291   {\r
 292     String id=null;\r
 293     jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme)cs;\r
 294     if (!userColours.contains(ucs))\r
 295     {\r
 296       userColours.add(ucs);\r
 297       java.awt.Color [] colours = ucs.getColours();\r
 298       jalview.binding.UserColours uc = new jalview.binding.UserColours();\r
 299       jalview.binding.UserColourScheme jbucs = new jalview.binding.UserColourScheme();\r
 300       for(int i=0; i<colours.length; i++)\r
 301       {\r
 302              jalview.binding.Colour col = new jalview.binding.Colour();\r
 303              col.setRGB( jalview.util.Format.getHexString(colours[i]) );\r
 304              jbucs.addColour(col);\r
 305       }\r
 306       id = "ucs"+userColours.indexOf(ucs);\r
 307       uc.setId(id);\r
 308       uc.setUserColourScheme(jbucs);\r
 309       jms.addUserColours(uc);\r
 310     }\r
 311     return id;\r
 312   }\r
 313 \r
 314   static jalview.schemes.UserColourScheme GetUserColourScheme(JalviewModelSequence jms, String id)\r
 315   {\r
 316     UserColours [] uc = jms.getUserColours();\r
 317     UserColours colours=null;\r
 318     for(int i=0; i<uc.length; i++)\r
 319     {\r
 320        if(uc[i].getId().equals(id))\r
 321        {  colours = uc[i]; break;  }\r
 322     }\r
 323     int csize = colours.getUserColourScheme().getColourCount();\r
 324     java.awt.Color [] newColours = new java.awt.Color[csize];\r
 325 \r
 326     for(int i=0; i<csize;i++)\r
 327       newColours[i] = new java.awt.Color(\r
 328         Integer.parseInt( colours.getUserColourScheme().getColour(i).getRGB(), 16) );\r
 329 \r
 330     return  new jalview.schemes.UserColourScheme(newColours);\r
 331 \r
 332   }\r
 333 \r
 334 \r
 335   public static void LoadJalviewAlign(String file)\r
 336   {\r
 337     JalviewModel object = new JalviewModel();\r
 338     try{\r
 339       //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING\r
 340 \r
 341       URL url = null;\r
 342       if( file.startsWith("http://"))\r
 343        url = new URL(file);\r
 344 \r
 345       JarInputStream jin = null;\r
 346       JarEntry jarentry=null;\r
 347       int entryCount = 1;\r
 348       do{\r
 349         if (url != null)\r
 350           jin = new JarInputStream(url.openStream());\r
 351         else\r
 352           jin = new JarInputStream(new FileInputStream(file));\r
 353 \r
 354         for(int i=0; i<entryCount; i++)\r
 355           jarentry = jin.getNextJarEntry();\r
 356 \r
 357         if(jarentry!=null)\r
 358         {\r
 359           InputStreamReader in = new InputStreamReader(jin, "UTF-8");\r
 360           object = (JalviewModel) object.unmarshal(in);\r
 361           LoadFromObject(object);\r
 362           entryCount++;\r
 363         }\r
 364       }while(jarentry!=null);\r
 365 \r
 366     }\r
 367     catch(Exception ex)\r
 368     {   System.err.println("Exception whilst loading jalview XML file : "+ex+"\n");\r
 369      ex.printStackTrace(); return; }\r
 370 \r
 371   }\r
 372 \r
 373   static void LoadFromObject(JalviewModel object)\r
 374   {\r
 375      Vector seqids = new Vector();\r
 376      SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);\r
 377      Sequence [] vamsasSeq = vamsasSet.getSequence();\r
 378 \r
 379      JalviewModelSequence jms = object.getJalviewModelSequence();\r
 380      //////////////////////////////////\r
 381      //LOAD SEQUENCES\r
 382      jalview.datamodel.Sequence [] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];\r
 383      JSeq [] JSEQ = object.getJalviewModelSequence().getJSeq();\r
 384      for(int i=0; i<vamsasSeq.length; i++)\r
 385      {\r
 386        jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),\r
 387                                                  vamsasSeq[i].getSequence());\r
 388 \r
 389        jseqs[i].setStart( JSEQ[i].getStart());\r
 390        jseqs[i].setEnd( JSEQ[i].getEnd());\r
 391        jseqs[i].setColor( new java.awt.Color(JSEQ[i].getColour()) );\r
 392        seqids.add(jseqs[i]);\r
 393      }\r
 394 \r
 395      /////////////////////////////////\r
 396      jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);\r
 397      /////////////////////////////////\r
 398 \r
 399      //////////////////////////////////\r
 400      //LOAD ANNOTATIONS\r
 401      if(vamsasSet.getAnnotation()!=null)\r
 402      {\r
 403        Annotation[] an = vamsasSet.getAnnotation();\r
 404        for (int i = 0; i < an.length; i++)\r
 405        {\r
 406          AnnotationElement[] ae = an[i].getAnnotationElement();\r
 407          jalview.datamodel.Annotation anot[]\r
 408              = new jalview.datamodel.Annotation[al.getWidth()];\r
 409          for (int aa = 0; aa < ae.length; aa++)\r
 410          {\r
 411            anot[ae[aa].getPosition()]\r
 412                = new jalview.datamodel.Annotation(\r
 413                    ae[aa].getDisplayCharacter(),\r
 414                    ae[aa].getDescription(),\r
 415                    ae[aa].getSecondaryStructure().charAt(0),\r
 416                    ae[aa].getValue()\r
 417                );\r
 418          }\r
 419 \r
 420 \r
 421           jalview.datamodel.AlignmentAnnotation jaa = null;\r
 422           if(an[i].getGraph())\r
 423             jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
 424                                         an[i].getDescription(), anot,\r
 425                                         0,0,1);\r
 426           else\r
 427             jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
 428                                         an[i].getDescription(), anot);\r
 429           al.addAnnotation(jaa);\r
 430        }\r
 431      }\r
 432 \r
 433       /////////////////////////////////\r
 434       // LOAD VIEWPORT\r
 435       Viewport[] views = jms.getViewport();\r
 436       Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER\r
 437 \r
 438       AlignFrame af = new AlignFrame(al);\r
 439     //  af.changeColour() );\r
 440 \r
 441     /////////////////////////\r
 442     //LOAD GROUPS\r
 443     if (jms.getJGroupCount()>0)\r
 444     {\r
 445       JGroup[] groups = jms.getJGroup();\r
 446       for (int i = 0; i < groups.length; i++)\r
 447       {\r
 448        ColourSchemeI cs=null;\r
 449        if(groups[i].getColour()!=null)\r
 450        {\r
 451          if (groups[i].getColour().startsWith("ucs"))\r
 452            cs = GetUserColourScheme(jms, groups[i].getColour());\r
 453          else\r
 454            cs = ColourSchemeProperty.getColour(al, groups[i].getColour());\r
 455 \r
 456          if (cs instanceof ResidueColourScheme)\r
 457            ( (ResidueColourScheme) cs).setThreshold(groups[i].getPidThreshold());\r
 458          else if (cs instanceof ScoreColourScheme)\r
 459            ( (ScoreColourScheme) cs).setThreshold(groups[i].getPidThreshold());\r
 460        }\r
 461 \r
 462         jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup\r
 463                 (groups[i].getName(),\r
 464                  cs,\r
 465                  groups[i].getDisplayBoxes(),\r
 466                  groups[i].getDisplayText(),\r
 467                  groups[i].getColourText(),\r
 468                  groups[i].getStart(),\r
 469                  groups[i].getEnd()) ;\r
 470         sg.setOutlineColour( new java.awt.Color(groups[i].getOutlineColour()));\r
 471         int [] ids = groups[i].getSeq();\r
 472         for(int s=0; s<ids.length; s++)\r
 473             sg.addSequence( (jalview.datamodel.SequenceI)seqids.elementAt( ids[s] ));\r
 474 \r
 475         if(groups[i].getConsThreshold()!=0)\r
 476         {\r
 477           jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",\r
 478               ResidueProperties.propHash, 3,\r
 479               sg.sequences, 0,\r
 480               sg.getWidth() - 1);\r
 481           c.calculate();\r
 482           c.verdict(false, 25);\r
 483           cs = new ConservationColourScheme(c, cs);\r
 484           sg.cs = cs;\r
 485         }\r
 486 \r
 487 \r
 488         al.addGroup(sg);\r
 489       }\r
 490     }\r
 491 \r
 492 \r
 493     Desktop.addInternalFrame(af, view.getTitle(), AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);\r
 494     af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view.getHeight());\r
 495     af.viewport.setStartRes( view.getStartRes() );\r
 496     af.viewport.setStartSeq( view.getStartSeq() );\r
 497     af.viewport.showConservation = view.getShowConservation();\r
 498     af.viewport.showQuality = view.getShowQuality();\r
 499     af.viewport.showIdentity= view.getShowIdentity();\r
 500     af.viewport.setAbovePIDThreshold( view.getPidSelected() );\r
 501     af.viewport.setColourText( view.getShowColourText() );\r
 502     af.viewport.setConservationSelected( view.getConservationSelected());\r
 503     af.viewport.setShowFullId( view.getShowFullId());\r
 504     af.viewport.setFont( new java.awt.Font( view.getFontName(),\r
 505                                             view.getFontStyle(),\r
 506                                             view.getFontSize()));\r
 507     af.alignPanel.fontChanged();\r
 508     af.viewport.setRenderGaps( view.getRenderGaps() );\r
 509 \r
 510     af.viewport.setWrapAlignment( view.getWrapAlignment() );\r
 511     if(view.getWrapAlignment())\r
 512     {\r
 513       af.alignPanel.setWrapAlignment(view.getWrapAlignment());\r
 514     }\r
 515     else\r
 516     {\r
 517       af.viewport.setShowAnnotation(view.getShowAnnotation());\r
 518       af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\r
 519     }\r
 520 \r
 521     af.viewport.setShowBoxes( view.getShowBoxes() );\r
 522     af.viewport.setShowText( view.getShowText() );\r
 523 \r
 524     ColourSchemeI cs=null;\r
 525     if(view.getBgColour()!=null)\r
 526     {\r
 527 \r
 528       if (view.getBgColour().startsWith("ucs"))\r
 529         cs = GetUserColourScheme(jms, view.getBgColour());\r
 530       else\r
 531         cs = ColourSchemeProperty.getColour(al, view.getBgColour());\r
 532 \r
 533       if (cs instanceof ConservationColourScheme)\r
 534         ( (ConservationColourScheme) cs).inc = view.getConsThreshold();\r
 535 \r
 536       if (cs instanceof ResidueColourScheme)\r
 537         ( (ResidueColourScheme) cs).setThreshold(view.getPidThreshold());\r
 538       else if (cs instanceof ScoreColourScheme)\r
 539         ( (ScoreColourScheme) cs).setThreshold(view.getPidThreshold());\r
 540 \r
 541     }\r
 542     af.viewport.setGlobalColourScheme( cs );\r
 543 \r
 544 \r
 545     af.viewport.setColourAppliesToAllGroups(false);\r
 546     af.changeColour(af.viewport.getGlobalColourScheme());\r
 547     af.viewport.setColourAppliesToAllGroups(true);\r
 548 \r
 549 \r
 550     //LOAD TREES - THIS RELEASE ONLY ALLOWS 1 TREE\r
 551     if(object.getVamsasModel().getTreeCount()>0)\r
 552     {\r
 553       try{\r
 554         af.ShowNewickTree(new jalview.io.NewickFile(\r
 555             (String)object.getVamsasModel().getTree(0)), "Tree");\r
 556       }catch(Exception ex){ex.printStackTrace();}\r
 557     }\r
 558 \r
 559   }\r
 560 }\r
 561 \r
 562 \r
 563 \r