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