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