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 \r
  84     AlignViewport av = af.viewport;\r
  85 \r
  86     JalviewModel object = new JalviewModel();\r
  87     object.setVamsasModel( new VamsasModel() );\r
  88 \r
  89     object.setCreationDate( new java.util.Date(timeStamp) );\r
  90 \r
  91     jalview.datamodel.AlignmentI jal = af.viewport.alignment;\r
  92 \r
  93     SequenceSet vamsasSet = new SequenceSet();\r
  94     Sequence vamsasSeq;\r
  95     JalviewModelSequence jms = new JalviewModelSequence();\r
  96 \r
  97     vamsasSet.setGapChar(jal.getGapCharacter()+"");\r
  98 \r
  99     JSeq jseq;\r
 100 \r
 101 \r
 102     //SAVE SEQUENCES\r
 103     int id = 0;\r
 104     for(int i=0; i<jal.getHeight(); i++)\r
 105     {\r
 106       seqids.add(jal.getSequenceAt(i));\r
 107 \r
 108       vamsasSeq = new Sequence( );\r
 109       vamsasSeq.setId(id+"");\r
 110       vamsasSeq.setName(jal.getSequenceAt(i).getName());\r
 111       vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());\r
 112 \r
 113       jseq = new JSeq();\r
 114       jseq.setStart(jal.getSequenceAt(i).getStart());\r
 115       jseq.setEnd(jal.getSequenceAt(i).getEnd());\r
 116 \r
 117       jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());\r
 118 \r
 119       jseq.setId( id );\r
 120 \r
 121       jms.addJSeq(jseq);\r
 122       vamsasSet.addSequence(vamsasSeq);\r
 123       id++;\r
 124     }\r
 125 \r
 126     //SAVE TREES\r
 127     if(af.viewport.currentTree!=null)\r
 128     {\r
 129       object.getVamsasModel().addTree(af.viewport.currentTree.toString());\r
 130     }\r
 131 \r
 132     //SAVE ANNOTATIONS\r
 133     if(jal.getAlignmentAnnotation()!=null)\r
 134     {\r
 135 \r
 136       jalview.datamodel.AlignmentAnnotation [] aa = jal.getAlignmentAnnotation();\r
 137       for(int i=0; i<aa.length; i++)\r
 138       {\r
 139         if(aa[i].label.equals("Quality")\r
 140         || aa[i].label.equals("Conservation")\r
 141         || aa[i].label.equals("Consensus"))\r
 142        {    continue;}\r
 143 \r
 144         Annotation an = new Annotation();\r
 145         an.setDescription(aa[i].description);\r
 146         an.setGraph(aa[i].isGraph);\r
 147         an.setLabel(aa[i].label);\r
 148 \r
 149         AnnotationElement ae;\r
 150 \r
 151         for(int a=0; a<aa[i].annotations.length; a++)\r
 152         {\r
 153           if(aa[i]==null || aa[i].annotations[a]==null)\r
 154             continue;\r
 155 \r
 156           ae = new AnnotationElement();\r
 157           ae.setDescription(aa[i].annotations[a].description);\r
 158           ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);\r
 159           ae.setValue(aa[i].annotations[a].value);\r
 160           ae.setPosition(a);\r
 161           ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure+"");\r
 162           an.addAnnotationElement(ae);\r
 163         }\r
 164 \r
 165         vamsasSet.addAnnotation(an);\r
 166       }\r
 167 \r
 168     }\r
 169 \r
 170     //SAVE GROUPS\r
 171     if(jal.getGroups()!=null)\r
 172     {\r
 173       JGroup [] groups = new JGroup[jal.getGroups().size()];\r
 174       for(int i=0; i<groups.length; i++)\r
 175       {\r
 176         groups[i] = new JGroup();\r
 177         jalview.datamodel.SequenceGroup sg\r
 178             = (jalview.datamodel.SequenceGroup)jal.getGroups().elementAt(i);\r
 179         groups[i].setStart( sg.getStartRes() );\r
 180         groups[i].setEnd( sg.getEndRes() );\r
 181         groups[i].setName( sg.getName());\r
 182 \r
 183         if(sg.cs instanceof ConservationColourScheme)\r
 184           groups[i].setConsThreshold( ((ConservationColourScheme)sg.cs).inc);\r
 185 \r
 186         if (sg.cs instanceof ResidueColourScheme)\r
 187           groups[i].setPidThreshold( ( (ResidueColourScheme) sg.cs).getThreshold());\r
 188        else if (sg.cs instanceof ScoreColourScheme)\r
 189          groups[i].setPidThreshold( ( (ScoreColourScheme) sg.cs).getThreshold());\r
 190 \r
 191 \r
 192         groups[i].setColour( ColourSchemeProperty.getColourName(sg.cs) );\r
 193         groups[i].setOutlineColour(sg.getOutlineColour().getRGB());\r
 194         groups[i].setDisplayBoxes(sg.getDisplayBoxes());\r
 195         groups[i].setDisplayText(sg.getDisplayText());\r
 196         groups[i].setColourText(sg.getColourText());\r
 197 \r
 198         for(int s=0; s<sg.getSize(); s++)\r
 199         {\r
 200           jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence)sg.getSequenceAt(s);\r
 201           int index = seqids.indexOf(seq);\r
 202           groups[i].addSeq(index);\r
 203         }\r
 204 \r
 205       }\r
 206 \r
 207       jms.setJGroup(groups);\r
 208 \r
 209     }\r
 210 \r
 211     ///////////SAVE VIEWPORT\r
 212     Viewport view = new Viewport();\r
 213    view.setTitle(af.getTitle());\r
 214    view.setXpos(af.getX());\r
 215    view.setYpos(af.getY());\r
 216    view.setWidth(af.getWidth());\r
 217    view.setHeight(af.getHeight());\r
 218    view.setStartRes(av.startRes);\r
 219    view.setStartSeq(av.startSeq);\r
 220    view.setBgColour( ColourSchemeProperty.getColourName\r
 221                      ( av.getGlobalColourScheme()));\r
 222 \r
 223    ColourSchemeI cs = av.getGlobalColourScheme();\r
 224    if(cs instanceof ConservationColourScheme)\r
 225      view.setConsThreshold( ((ConservationColourScheme)cs).inc);\r
 226 \r
 227    if (cs instanceof ResidueColourScheme)\r
 228      view.setPidThreshold( ( (ResidueColourScheme) cs).getThreshold());\r
 229   else if (cs instanceof ScoreColourScheme)\r
 230      view.setPidThreshold( ( (ScoreColourScheme) cs).getThreshold());\r
 231 \r
 232 \r
 233    view.setConservationSelected(av.getConservationSelected());\r
 234    view.setPidSelected(av.getAbovePIDThreshold());\r
 235    view.setFontName(av.font.getFontName());\r
 236    view.setFontSize(av.font.getSize());\r
 237    view.setFontStyle(av.font.getStyle());\r
 238    view.setRenderGaps(av.renderGaps);\r
 239    view.setShowAnnotation(av.getShowAnnotation());\r
 240    view.setShowBoxes(av.getShowBoxes());\r
 241    view.setShowColourText(av.getColourText());\r
 242    view.setShowConservation(av.showConservation);\r
 243    view.setShowFullId(av.getShowFullId());\r
 244    view.setShowIdentity(av.showIdentity);\r
 245    view.setShowQuality(av.showQuality);\r
 246    view.setShowSequenceFeatures(av.showSequenceFeatures);\r
 247    view.setShowText(av.getShowText());\r
 248    view.setWrapAlignment(av.getWrapAlignment());\r
 249 \r
 250    jms.addViewport( view );\r
 251 \r
 252     object.setJalviewModelSequence(jms);\r
 253     object.getVamsasModel().addSequenceSet(vamsasSet);\r
 254 \r
 255 \r
 256     try\r
 257     {\r
 258      if(!fileName.endsWith(".xml"))\r
 259               fileName = fileName+".xml";\r
 260 \r
 261      JarEntry entry = new JarEntry(fileName);\r
 262      jout.putNextEntry(entry);\r
 263 \r
 264       object.marshal(out);\r
 265     }\r
 266     catch (Exception ex)\r
 267     {\r
 268       ex.printStackTrace();\r
 269     }\r
 270   }\r
 271 \r
 272 \r
 273   public static void LoadJalviewAlign(String file)\r
 274   {\r
 275     JalviewModel object = new JalviewModel();\r
 276     try{\r
 277       //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING\r
 278       JarInputStream jin = new JarInputStream(new FileInputStream(file));\r
 279       JarEntry jarentry=null;\r
 280       int entryCount = 1;\r
 281       do{\r
 282         jin = new JarInputStream(new FileInputStream(file));\r
 283         for(int i=0; i<entryCount; i++)\r
 284           jarentry = jin.getNextJarEntry();\r
 285 \r
 286         if(jarentry!=null)\r
 287         {\r
 288           InputStreamReader in = new InputStreamReader(jin, "UTF-8");\r
 289           object = (JalviewModel) object.unmarshal(in);\r
 290           LoadFromObject(object);\r
 291           entryCount++;\r
 292         }\r
 293       }while(jarentry!=null);\r
 294 \r
 295     }\r
 296     catch(Exception ex)\r
 297     {   System.out.println("HERE"+ex); return; }\r
 298 \r
 299   }\r
 300 \r
 301   static void LoadFromObject(JalviewModel object)\r
 302   {\r
 303      Vector seqids = new Vector();\r
 304      SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);\r
 305      Sequence [] vamsasSeq = vamsasSet.getSequence();\r
 306 \r
 307      JalviewModelSequence jms = object.getJalviewModelSequence();\r
 308      //////////////////////////////////\r
 309      //LOAD SEQUENCES\r
 310      jalview.datamodel.Sequence [] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];\r
 311      JSeq [] JSEQ = object.getJalviewModelSequence().getJSeq();\r
 312      for(int i=0; i<vamsasSeq.length; i++)\r
 313      {\r
 314        jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),\r
 315                                                  vamsasSeq[i].getSequence());\r
 316 \r
 317        jseqs[i].setStart( JSEQ[i].getStart());\r
 318        jseqs[i].setEnd( JSEQ[i].getEnd());\r
 319        jseqs[i].setColor( new java.awt.Color(JSEQ[i].getColour()) );\r
 320        seqids.add(jseqs[i]);\r
 321      }\r
 322 \r
 323      /////////////////////////////////\r
 324      jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);\r
 325      /////////////////////////////////\r
 326 \r
 327      //////////////////////////////////\r
 328      //LOAD ANNOTATIONS\r
 329      if(vamsasSet.getAnnotation()!=null)\r
 330      {\r
 331        Annotation[] an = vamsasSet.getAnnotation();\r
 332        for (int i = 0; i < an.length; i++)\r
 333        {\r
 334          AnnotationElement[] ae = an[i].getAnnotationElement();\r
 335          jalview.datamodel.Annotation anot[]\r
 336              = new jalview.datamodel.Annotation[al.getWidth()];\r
 337          for (int aa = 0; aa < ae.length; aa++)\r
 338          {\r
 339            anot[ae[aa].getPosition()]\r
 340                = new jalview.datamodel.Annotation(\r
 341                    ae[aa].getDisplayCharacter(),\r
 342                    ae[aa].getDescription(),\r
 343                    ae[aa].getSecondaryStructure().charAt(0),\r
 344                    ae[aa].getValue()\r
 345                );\r
 346          }\r
 347 \r
 348 \r
 349           jalview.datamodel.AlignmentAnnotation jaa = null;\r
 350           if(an[i].getGraph())\r
 351             jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
 352                                         an[i].getDescription(), anot,\r
 353                                         0,0,1);\r
 354           else\r
 355             jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
 356                                         an[i].getDescription(), anot);\r
 357           al.addAnnotation(jaa);\r
 358        }\r
 359      }\r
 360 \r
 361       /////////////////////////////////\r
 362       // LOAD VIEWPORT\r
 363       Viewport[] views = jms.getViewport();\r
 364       Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER\r
 365 \r
 366       AlignFrame af = new AlignFrame(al);\r
 367     //  af.changeColour() );\r
 368 \r
 369     /////////////////////////\r
 370     //LOAD GROUPS\r
 371     if (jms.getJGroupCount()>0)\r
 372     {\r
 373       JGroup[] groups = jms.getJGroup();\r
 374       for (int i = 0; i < groups.length; i++)\r
 375       {\r
 376        ColourSchemeI cs = ColourSchemeProperty.getColour(al, groups[i].getColour() );\r
 377        if (cs instanceof ResidueColourScheme)\r
 378          ( (ResidueColourScheme) cs).setThreshold(groups[i].getPidThreshold());\r
 379        else if (cs instanceof ScoreColourScheme)\r
 380       ( (ScoreColourScheme) cs).setThreshold(groups[i].getPidThreshold());\r
 381 \r
 382         jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup\r
 383                 (groups[i].getName(),\r
 384                  cs,\r
 385                  groups[i].getDisplayBoxes(),\r
 386                  groups[i].getDisplayText(),\r
 387                  groups[i].getColourText(),\r
 388                  groups[i].getStart(),\r
 389                  groups[i].getEnd()) ;\r
 390         sg.setOutlineColour( new java.awt.Color(groups[i].getOutlineColour()));\r
 391         int [] ids = groups[i].getSeq();\r
 392         for(int s=0; s<ids.length; s++)\r
 393             sg.addSequence( (jalview.datamodel.SequenceI)seqids.elementAt( ids[s] ));\r
 394 \r
 395         if(groups[i].getConsThreshold()!=0)\r
 396         {\r
 397           jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",\r
 398               ResidueProperties.propHash, 3,\r
 399               sg.sequences, 0,\r
 400               sg.getWidth() - 1);\r
 401           c.calculate();\r
 402           c.verdict(false, 25);\r
 403           cs = new ConservationColourScheme(c, cs);\r
 404           sg.cs = cs;\r
 405         }\r
 406 \r
 407 \r
 408         al.addGroup(sg);\r
 409       }\r
 410     }\r
 411 \r
 412 \r
 413     Desktop.addInternalFrame(af, view.getTitle(), AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);\r
 414     af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view.getHeight());\r
 415     af.viewport.setStartRes( view.getStartRes() );\r
 416     af.viewport.setStartSeq( view.getStartSeq() );\r
 417     af.viewport.showConservation = view.getShowConservation();\r
 418     af.viewport.showQuality = view.getShowQuality();\r
 419     af.viewport.showIdentity= view.getShowIdentity();\r
 420     af.viewport.setAbovePIDThreshold( view.getPidSelected() );\r
 421     af.viewport.setColourText( view.getShowColourText() );\r
 422     af.viewport.setConservationSelected( view.getConservationSelected());\r
 423     af.viewport.setShowFullId( view.getShowFullId());\r
 424     af.viewport.setFont( new java.awt.Font( view.getFontName(),\r
 425                                             view.getFontStyle(),\r
 426                                             view.getFontSize()));\r
 427     af.alignPanel.fontChanged();\r
 428     af.viewport.setRenderGaps( view.getRenderGaps() );\r
 429 \r
 430     af.viewport.setWrapAlignment( view.getWrapAlignment() );\r
 431     if(view.getWrapAlignment())\r
 432     {\r
 433       af.alignPanel.setWrapAlignment(view.getWrapAlignment());\r
 434     }\r
 435     else\r
 436     {\r
 437       af.viewport.setShowAnnotation(view.getShowAnnotation());\r
 438       af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\r
 439     }\r
 440 \r
 441     af.viewport.setShowBoxes( view.getShowBoxes() );\r
 442     af.viewport.setShowText( view.getShowText() );\r
 443 \r
 444     af.viewport.setGlobalColourScheme( ColourSchemeProperty.getColour(al, view.getBgColour()));\r
 445     af.viewport.setColourAppliesToAllGroups(false);\r
 446     af.changeColour( af.viewport.getGlobalColourScheme() );\r
 447     af.viewport.setColourAppliesToAllGroups(true);\r
 448 \r
 449     ColourSchemeI cs = af.viewport.getGlobalColourScheme();\r
 450     if(cs instanceof ConservationColourScheme)\r
 451       ( (ConservationColourScheme) cs).inc = view.getConsThreshold();\r
 452 \r
 453     if (cs instanceof ResidueColourScheme)\r
 454       ( (ResidueColourScheme) cs).setThreshold(view.getPidThreshold());\r
 455     else if (cs instanceof ScoreColourScheme)\r
 456       ( (ScoreColourScheme) cs).setThreshold(view.getPidThreshold());\r
 457 \r
 458     //LOAD TREES - THIS RELEASE ONLY ALLOWS 1 TREE\r
 459     if(object.getVamsasModel().getTreeCount()>0)\r
 460     {\r
 461       try{\r
 462         af.ShowNewickTree(new jalview.io.NewickFile(\r
 463             (String)object.getVamsasModel().getTree(0)), "Tree");\r
 464       }catch(Exception ex){ex.printStackTrace();}\r
 465     }\r
 466 \r
 467   }\r
 468 }\r
 469 \r
 470 \r
 471 \r