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