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