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 jalview.io.*;\r
  22 \r
  23 import jalview.schemes.*;\r
  24 \r
  25 import java.io.*;\r
  26 \r
  27 import java.net.*;\r
  28 \r
  29 import java.util.*;\r
  30 \r
  31 import java.util.jar.*;\r
  32 \r
  33 import javax.swing.*;\r
  34 \r
  35 import jalview.binding.*;\r
  36 \r
  37 \r
  38 /**\r
  39  * DOCUMENT ME!\r
  40  *\r
  41  * @author $author$\r
  42  * @version $Revision$\r
  43  */\r
  44 public class Jalview2XML\r
  45 {\r
  46     // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE\r
  47     public static void SaveState(File statefile)\r
  48     {\r
  49         long creation = System.currentTimeMillis();\r
  50         JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
  51 \r
  52         if (frames == null)\r
  53         {\r
  54             return;\r
  55         }\r
  56 \r
  57         try\r
  58         {\r
  59             FileOutputStream fos = new FileOutputStream(statefile);\r
  60             JarOutputStream jout = new JarOutputStream(fos);\r
  61 \r
  62             //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS\r
  63             ////////////////////////////////////////////////////\r
  64             PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,\r
  65                         "UTF-8"));\r
  66 \r
  67             Vector shortNames = new Vector();\r
  68 \r
  69             //REVERSE ORDER\r
  70             for (int i = frames.length - 1; i > -1; i--)\r
  71             {\r
  72                 if (frames[i] instanceof AlignFrame)\r
  73                 {\r
  74                     AlignFrame af = (AlignFrame) frames[i];\r
  75 \r
  76                     String shortName = af.getTitle();\r
  77 \r
  78                     if (shortName.indexOf(File.separatorChar) > -1)\r
  79                     {\r
  80                         shortName = shortName.substring(shortName.lastIndexOf(\r
  81                                     File.separatorChar) + 1);\r
  82                     }\r
  83 \r
  84                     int count = 1;\r
  85 \r
  86                     while (shortNames.contains(shortName))\r
  87                     {\r
  88                         if (shortName.endsWith("_" + (count - 1)))\r
  89                         {\r
  90                             shortName = shortName.substring(0,\r
  91                                     shortName.lastIndexOf("_"));\r
  92                         }\r
  93 \r
  94                         shortName = shortName.concat("_" + count);\r
  95                         count++;\r
  96                     }\r
  97 \r
  98                     shortNames.addElement(shortName);\r
  99 \r
 100                     if (!shortName.endsWith(".xml"))\r
 101                     {\r
 102                         shortName = shortName + ".xml";\r
 103                     }\r
 104 \r
 105                     SaveState(af, creation, shortName, jout, out);\r
 106                 }\r
 107             }\r
 108 \r
 109             out.close();\r
 110             jout.close();\r
 111         }\r
 112         catch (Exception ex)\r
 113         {\r
 114             ex.printStackTrace();\r
 115         }\r
 116     }\r
 117 \r
 118     // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW\r
 119     public static void SaveAlignment(AlignFrame af, String jarFile,\r
 120         String fileName)\r
 121     {\r
 122         try\r
 123         {\r
 124             FileOutputStream fos = new FileOutputStream(jarFile);\r
 125             JarOutputStream jout = new JarOutputStream(fos);\r
 126 \r
 127             //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS\r
 128             ////////////////////////////////////////////////////\r
 129             PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,\r
 130                         "UTF-8"));\r
 131 \r
 132             SaveState(af, System.currentTimeMillis(), fileName, jout, out);\r
 133             out.close();\r
 134             jout.close();\r
 135         }\r
 136         catch (Exception ex)\r
 137         {\r
 138           ex.printStackTrace();\r
 139         }\r
 140     }\r
 141 \r
 142     /**\r
 143      * DOCUMENT ME!\r
 144      *\r
 145      * @param af DOCUMENT ME!\r
 146      * @param timeStamp DOCUMENT ME!\r
 147      * @param fileName DOCUMENT ME!\r
 148      * @param jout DOCUMENT ME!\r
 149      * @param out DOCUMENT ME!\r
 150      */\r
 151     public static void SaveState(AlignFrame af, long timeStamp,\r
 152         String fileName, JarOutputStream jout, PrintWriter out)\r
 153     {\r
 154         Vector seqids = new Vector();\r
 155         Vector userColours = new Vector();\r
 156 \r
 157         AlignViewport av = af.viewport;\r
 158 \r
 159         JalviewModel object = new JalviewModel();\r
 160         object.setVamsasModel(new jalview.binding.VamsasModel());\r
 161 \r
 162         object.setCreationDate(new java.util.Date(timeStamp));\r
 163         object.setVersion(jalview.bin.Cache.getProperty("VERSION"));\r
 164 \r
 165         jalview.datamodel.AlignmentI jal = af.viewport.alignment;\r
 166 \r
 167         SequenceSet vamsasSet = new SequenceSet();\r
 168         Sequence vamsasSeq;\r
 169         JalviewModelSequence jms = new JalviewModelSequence();\r
 170 \r
 171         vamsasSet.setGapChar(jal.getGapCharacter() + "");\r
 172 \r
 173         JSeq jseq;\r
 174 \r
 175         //SAVE SEQUENCES\r
 176         int id = 0;\r
 177 \r
 178         for (int i = 0; i < jal.getHeight(); i++)\r
 179         {\r
 180             seqids.add(jal.getSequenceAt(i));\r
 181 \r
 182             vamsasSeq = new Sequence();\r
 183             vamsasSeq.setId(id + "");\r
 184             vamsasSeq.setName(jal.getSequenceAt(i).getName());\r
 185             vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());\r
 186             vamsasSeq.setDescription(jal.getSequenceAt(i).getDescription());\r
 187 \r
 188             jseq = new JSeq();\r
 189             jseq.setStart(jal.getSequenceAt(i).getStart());\r
 190             jseq.setEnd(jal.getSequenceAt(i).getEnd());\r
 191 \r
 192             jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());\r
 193 \r
 194             jseq.setId(id);\r
 195 \r
 196             if(jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures()!=null)\r
 197             {\r
 198               Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures().elements();\r
 199               while(en.hasMoreElements())\r
 200               {\r
 201                 Features features = new Features();\r
 202                 jalview.datamodel.SequenceFeature sf\r
 203                    = (jalview.datamodel.SequenceFeature)en.nextElement();\r
 204 \r
 205                 features.setBegin(sf.getBegin());\r
 206                 features.setEnd(sf.getEnd());\r
 207                 features.setDescription(sf.getDescription());\r
 208                 features.setStatus(sf.getStatus());\r
 209                 features.setType(sf.getType());\r
 210                 features.setFeatureGroup(sf.getFeatureGroup());\r
 211                 jseq.addFeatures(features);\r
 212               }\r
 213             }\r
 214 \r
 215             if(jal.getSequenceAt(i).getDatasetSequence().getPDBId()!=null)\r
 216             {\r
 217               Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getPDBId().elements();\r
 218               while(en.hasMoreElements())\r
 219               {\r
 220                 Pdbids pdb = new Pdbids();\r
 221                 jalview.datamodel.PDBEntry entry\r
 222                    = (jalview.datamodel.PDBEntry)en.nextElement();\r
 223 \r
 224                 pdb.setId(entry.getId());\r
 225                 pdb.setType(entry.getType());\r
 226 \r
 227                 if(entry.getProperty()!=null)\r
 228                 {\r
 229                   PdbentryItem item = new PdbentryItem();\r
 230                   Hashtable properties = entry.getProperty();\r
 231                   Enumeration en2 = properties.keys();\r
 232                   while(en2.hasMoreElements())\r
 233                   {\r
 234                     Property prop = new Property();\r
 235                     String key = en2.nextElement().toString();\r
 236                     prop.setName(key);\r
 237                     prop.setValue( properties.get(key).toString() );\r
 238                     item.addProperty(prop);\r
 239                   }\r
 240                   pdb.addPdbentryItem(item);\r
 241                 }\r
 242 \r
 243                 jseq.addPdbids(pdb);\r
 244               }\r
 245             }\r
 246 \r
 247             jms.addJSeq(jseq);\r
 248             vamsasSet.addSequence(vamsasSeq);\r
 249             id++;\r
 250         }\r
 251 \r
 252         //SAVE TREES\r
 253         ///////////////////////////////////\r
 254         if (af.viewport.currentTree != null)\r
 255         {\r
 256           // FIND ANY ASSOCIATED TREES\r
 257           // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT\r
 258           if (Desktop.desktop != null)\r
 259           {\r
 260             JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
 261 \r
 262             for (int t = 0; t < frames.length; t++)\r
 263             {\r
 264               if (frames[t] instanceof TreePanel)\r
 265               {\r
 266                 TreePanel tp = (TreePanel) frames[t];\r
 267 \r
 268                 if (tp.treeCanvas.av.alignment == jal)\r
 269                 {\r
 270                   Tree tree = new Tree();\r
 271                   tree.setTitle(tp.getTitle());\r
 272                   tree.setCurrentTree( (af.viewport.currentTree == tp.getTree()));\r
 273                   tree.setNewick(tp.getTree().toString());\r
 274                   tree.setThreshold(tp.treeCanvas.threshold);\r
 275 \r
 276                   tree.setFitToWindow(tp.fitToWindow.getState());\r
 277                   tree.setFontName(tp.getTreeFont().getName());\r
 278                   tree.setFontSize(tp.getTreeFont().getSize());\r
 279                   tree.setFontStyle(tp.getTreeFont().getStyle());\r
 280                   tree.setMarkUnlinked(tp.placeholdersMenu.getState());\r
 281 \r
 282                   tree.setShowBootstrap(tp.bootstrapMenu.getState());\r
 283                   tree.setShowDistances(tp.distanceMenu.getState());\r
 284 \r
 285                   tree.setHeight(tp.getHeight());\r
 286                   tree.setWidth(tp.getWidth());\r
 287                   tree.setXpos(tp.getX());\r
 288                   tree.setYpos(tp.getY());\r
 289 \r
 290                   jms.addTree(tree);\r
 291                 }\r
 292               }\r
 293             }\r
 294           }\r
 295         }\r
 296 \r
 297         //SAVE ANNOTATIONS\r
 298         if (jal.getAlignmentAnnotation() != null)\r
 299         {\r
 300             jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();\r
 301 \r
 302             for (int i = 0; i < aa.length; i++)\r
 303             {\r
 304                 if (aa[i].label.equals("Quality") ||\r
 305                         aa[i].label.equals("Conservation") ||\r
 306                         aa[i].label.equals("Consensus"))\r
 307                 {\r
 308                     continue;\r
 309                 }\r
 310 \r
 311                 Annotation an = new Annotation();\r
 312                 an.setDescription(aa[i].description);\r
 313                 if(aa[i].graph>0)\r
 314                 {\r
 315                   an.setGraph(true);\r
 316                   an.setGraphType(aa[i].graph);\r
 317                 }\r
 318                 an.setLabel(aa[i].label);\r
 319 \r
 320                 AnnotationElement ae;\r
 321 \r
 322                 for (int a = 0; a < aa[i].annotations.length; a++)\r
 323                 {\r
 324                     if ((aa[i] == null) || (aa[i].annotations[a] == null))\r
 325                     {\r
 326                         continue;\r
 327                     }\r
 328 \r
 329                     ae = new AnnotationElement();\r
 330                     ae.setDescription(aa[i].annotations[a].description);\r
 331                     ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);\r
 332                     ae.setValue(aa[i].annotations[a].value);\r
 333                     ae.setPosition(a);\r
 334                     ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +\r
 335                         "");\r
 336                     an.addAnnotationElement(ae);\r
 337                 }\r
 338 \r
 339                 vamsasSet.addAnnotation(an);\r
 340             }\r
 341         }\r
 342 \r
 343         //SAVE GROUPS\r
 344         if (jal.getGroups() != null)\r
 345         {\r
 346             JGroup[] groups = new JGroup[jal.getGroups().size()];\r
 347 \r
 348             for (int i = 0; i < groups.length; i++)\r
 349             {\r
 350                 groups[i] = new JGroup();\r
 351 \r
 352                 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()\r
 353                                                                                           .elementAt(i);\r
 354                 groups[i].setStart(sg.getStartRes());\r
 355                 groups[i].setEnd(sg.getEndRes());\r
 356                 groups[i].setName(sg.getName());\r
 357                 if(sg.cs!=null)\r
 358                 {\r
 359                   if (sg.cs.conservationApplied())\r
 360                   {\r
 361                     groups[i].setConsThreshold(sg.cs.getConservationInc());\r
 362 \r
 363                     if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
 364                     {\r
 365                       groups[i].setColour(SetUserColourScheme(sg.cs,\r
 366                           userColours,\r
 367                           jms));\r
 368                     }\r
 369                     else\r
 370                     {\r
 371                       groups[i].setColour(ColourSchemeProperty.getColourName(sg.\r
 372                           cs));\r
 373                     }\r
 374                   }\r
 375                   else if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
 376                   {\r
 377                     groups[i].setColour(SetUserColourScheme(sg.cs, userColours,\r
 378                         jms));\r
 379                   }\r
 380                   else\r
 381                   {\r
 382                     groups[i].setColour(ColourSchemeProperty.getColourName(\r
 383                         sg.cs));\r
 384                   }\r
 385 \r
 386                   groups[i].setPidThreshold(sg.cs.getThreshold());\r
 387                 }\r
 388 \r
 389                 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());\r
 390                 groups[i].setDisplayBoxes(sg.getDisplayBoxes());\r
 391                 groups[i].setDisplayText(sg.getDisplayText());\r
 392                 groups[i].setColourText(sg.getColourText());\r
 393 \r
 394                 for (int s = 0; s < sg.getSize(); s++)\r
 395                 {\r
 396                     jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.getSequenceAt(s);\r
 397                     int index = seqids.indexOf(seq);\r
 398                     groups[i].addSeq(index);\r
 399                 }\r
 400             }\r
 401 \r
 402             jms.setJGroup(groups);\r
 403         }\r
 404 \r
 405 \r
 406         ///////////SAVE VIEWPORT\r
 407         Viewport view = new Viewport();\r
 408         view.setTitle(af.getTitle());\r
 409         view.setXpos(af.getX());\r
 410         view.setYpos(af.getY());\r
 411         view.setWidth(af.getWidth());\r
 412         view.setHeight(af.getHeight());\r
 413         view.setStartRes(av.startRes);\r
 414         view.setStartSeq(av.startSeq);\r
 415 \r
 416         if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)\r
 417         {\r
 418             view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),\r
 419                     userColours, jms));\r
 420         }\r
 421         else\r
 422         {\r
 423             view.setBgColour(ColourSchemeProperty.getColourName(\r
 424                     av.getGlobalColourScheme()));\r
 425         }\r
 426 \r
 427         ColourSchemeI cs = av.getGlobalColourScheme();\r
 428 \r
 429         if(cs!=null)\r
 430         {\r
 431           if (cs.conservationApplied())\r
 432           {\r
 433             view.setConsThreshold(cs.getConservationInc());\r
 434             if (cs instanceof jalview.schemes.UserColourScheme)\r
 435               view.setBgColour(SetUserColourScheme(cs, userColours, jms));\r
 436           }\r
 437 \r
 438           if (cs instanceof ResidueColourScheme)\r
 439           {\r
 440             view.setPidThreshold(cs.getThreshold());\r
 441           }\r
 442         }\r
 443 \r
 444         view.setConservationSelected(av.getConservationSelected());\r
 445         view.setPidSelected(av.getAbovePIDThreshold());\r
 446         view.setFontName(av.font.getName());\r
 447         view.setFontSize(av.font.getSize());\r
 448         view.setFontStyle(av.font.getStyle());\r
 449         view.setRenderGaps(av.renderGaps);\r
 450         view.setShowAnnotation(av.getShowAnnotation());\r
 451         view.setShowBoxes(av.getShowBoxes());\r
 452         view.setShowColourText(av.getColourText());\r
 453         view.setShowConservation(av.showConservation);\r
 454         view.setShowFullId(av.getShowJVSuffix());\r
 455         view.setShowIdentity(av.showIdentity);\r
 456         view.setShowQuality(av.showQuality);\r
 457         view.setShowSequenceFeatures(av.showSequenceFeatures);\r
 458         view.setShowText(av.getShowText());\r
 459         view.setWrapAlignment(av.getWrapAlignment());\r
 460 \r
 461         if(af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed!=null)\r
 462         {\r
 463           jalview.binding.FeatureSettings fs = new jalview.binding.FeatureSettings();\r
 464 \r
 465           Enumeration e = af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();\r
 466           while (e.hasMoreElements())\r
 467           {\r
 468             String type = e.nextElement().toString();\r
 469             Setting setting = new Setting();\r
 470             setting.setType(type);\r
 471             setting.setColour(\r
 472                 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(type).getRGB()\r
 473                 );\r
 474             setting.setDisplay(\r
 475                 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed.contains(type)\r
 476                 );\r
 477 \r
 478             fs.addSetting(setting);\r
 479 \r
 480           }\r
 481           jms.setFeatureSettings(fs);\r
 482 \r
 483         }\r
 484 \r
 485         jms.addViewport(view);\r
 486 \r
 487 \r
 488         object.setJalviewModelSequence(jms);\r
 489         object.getVamsasModel().addSequenceSet(vamsasSet);\r
 490 \r
 491         try\r
 492         {\r
 493             if (!fileName.endsWith(".xml"))\r
 494             {\r
 495                 fileName = fileName + ".xml";\r
 496             }\r
 497 \r
 498             JarEntry entry = new JarEntry(fileName);\r
 499             jout.putNextEntry(entry);\r
 500 \r
 501             object.marshal(out);\r
 502         }\r
 503         catch (Exception ex)\r
 504         {\r
 505             ex.printStackTrace();\r
 506         }\r
 507     }\r
 508 \r
 509     static String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,\r
 510         Vector userColours, JalviewModelSequence jms)\r
 511     {\r
 512         String id = null;\r
 513         jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;\r
 514 \r
 515         if (!userColours.contains(ucs))\r
 516         {\r
 517             userColours.add(ucs);\r
 518 \r
 519             java.awt.Color[] colours = ucs.getColours();\r
 520             jalview.binding.UserColours uc = new jalview.binding.UserColours();\r
 521             jalview.binding.UserColourScheme jbucs = new jalview.binding.UserColourScheme();\r
 522 \r
 523             for (int i = 0; i < colours.length; i++)\r
 524             {\r
 525                 jalview.binding.Colour col = new jalview.binding.Colour();\r
 526                 col.setRGB(jalview.util.Format.getHexString(colours[i]));\r
 527                 jbucs.addColour(col);\r
 528             }\r
 529 \r
 530             id = "ucs" + userColours.indexOf(ucs);\r
 531             uc.setId(id);\r
 532             uc.setUserColourScheme(jbucs);\r
 533             jms.addUserColours(uc);\r
 534         }\r
 535 \r
 536         return id;\r
 537     }\r
 538 \r
 539     static jalview.schemes.UserColourScheme GetUserColourScheme(\r
 540         JalviewModelSequence jms, String id)\r
 541     {\r
 542         UserColours[] uc = jms.getUserColours();\r
 543         UserColours colours = null;\r
 544 \r
 545         for (int i = 0; i < uc.length; i++)\r
 546         {\r
 547             if (uc[i].getId().equals(id))\r
 548             {\r
 549                 colours = uc[i];\r
 550 \r
 551                 break;\r
 552             }\r
 553         }\r
 554 \r
 555         int csize = colours.getUserColourScheme().getColourCount();\r
 556         java.awt.Color[] newColours = new java.awt.Color[csize];\r
 557 \r
 558         for (int i = 0; i < csize; i++)\r
 559         {\r
 560             newColours[i] = new java.awt.Color(Integer.parseInt(\r
 561                         colours.getUserColourScheme().getColour(i).getRGB(), 16));\r
 562         }\r
 563 \r
 564         return new jalview.schemes.UserColourScheme(newColours);\r
 565     }\r
 566 \r
 567     /**\r
 568      * DOCUMENT ME!\r
 569      *\r
 570      * @param file DOCUMENT ME!\r
 571      */\r
 572     public static AlignFrame LoadJalviewAlign(String file)\r
 573     {\r
 574         JalviewModel object = new JalviewModel();\r
 575         jalview.gui.AlignFrame af = null;\r
 576 \r
 577         try\r
 578         {\r
 579             //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING\r
 580             URL url = null;\r
 581 \r
 582             if (file.startsWith("http://"))\r
 583             {\r
 584                 url = new URL(file);\r
 585             }\r
 586 \r
 587             JarInputStream jin = null;\r
 588             JarEntry jarentry = null;\r
 589             int entryCount = 1;\r
 590 \r
 591             do\r
 592             {\r
 593                 if (url != null)\r
 594                 {\r
 595                     jin = new JarInputStream(url.openStream());\r
 596                 }\r
 597                 else\r
 598                 {\r
 599                     jin = new JarInputStream(new FileInputStream(file));\r
 600                 }\r
 601 \r
 602                 for (int i = 0; i < entryCount; i++)\r
 603                 {\r
 604                     jarentry = jin.getNextJarEntry();\r
 605                 }\r
 606 \r
 607                 if (jarentry != null)\r
 608                 {\r
 609                     InputStreamReader in = new InputStreamReader(jin, "UTF-8");\r
 610                     object = (JalviewModel) object.unmarshal(in);\r
 611                     af = LoadFromObject(object);\r
 612                     entryCount++;\r
 613                 }\r
 614             }\r
 615             while (jarentry != null);\r
 616         }\r
 617         catch(java.net.UnknownHostException ex)\r
 618         {\r
 619           ex.printStackTrace();\r
 620           System.err.println("Couldn't locate Jalview XML file : " +\r
 621               ex + "\n");\r
 622            JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 623                                     "Couldn't locate " + file,\r
 624                                     "URL not found",\r
 625                                     JOptionPane.WARNING_MESSAGE);\r
 626 \r
 627         }\r
 628         catch (Exception ex)\r
 629         {\r
 630           ex.printStackTrace();\r
 631             System.err.println("Exception whilst loading jalview XML file : " +\r
 632                 ex + "\n");\r
 633              JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 634                                       "Error loading  " + file,\r
 635                                       "Error loading Jalview file",\r
 636                                       JOptionPane.WARNING_MESSAGE);\r
 637 \r
 638         }\r
 639 \r
 640         return af;\r
 641     }\r
 642 \r
 643     static AlignFrame LoadFromObject(JalviewModel object)\r
 644     {\r
 645         Vector seqids = new Vector();\r
 646         SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);\r
 647         Sequence[] vamsasSeq = vamsasSet.getSequence();\r
 648 \r
 649         JalviewModelSequence jms = object.getJalviewModelSequence();\r
 650 \r
 651         //////////////////////////////////\r
 652         //LOAD SEQUENCES\r
 653         jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];\r
 654         JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();\r
 655         for (int i = 0; i < vamsasSeq.length; i++)\r
 656         {\r
 657             jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),\r
 658                     vamsasSeq[i].getSequence());\r
 659             jseqs[i].setDescription( vamsasSeq[i].getDescription() );\r
 660 \r
 661             jseqs[i].setStart(JSEQ[i].getStart());\r
 662             jseqs[i].setEnd(JSEQ[i].getEnd());\r
 663             jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));\r
 664             seqids.add(jseqs[i]);\r
 665         }\r
 666 \r
 667         ///SequenceFeatures are added to the DatasetSequence,\r
 668         // so we must create the dataset before loading features\r
 669         /////////////////////////////////\r
 670         jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);\r
 671         al.setDataset(null);\r
 672         /////////////////////////////////\r
 673 \r
 674         for (int i = 0; i < vamsasSeq.length; i++)\r
 675         {\r
 676           if (JSEQ[i].getFeaturesCount() > 0)\r
 677           {\r
 678             Features[] features = JSEQ[i].getFeatures();\r
 679             for (int f = 0; f < features.length; f++)\r
 680             {\r
 681               //features[f].getBegin()\r
 682               jalview.datamodel.SequenceFeature sf\r
 683                   = new jalview.datamodel.SequenceFeature(features[f].getType(),\r
 684                   features[f].getDescription(), features[f].getStatus(),\r
 685                   features[f].getBegin(), features[f].getEnd());\r
 686               sf.setFeatureGroup(features[f].getFeatureGroup());\r
 687               al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);\r
 688             }\r
 689           }\r
 690           if (JSEQ[i].getPdbidsCount() > 0)\r
 691           {\r
 692             Pdbids[] ids = JSEQ[i].getPdbids();\r
 693             for (int p = 0; p < ids.length; p++)\r
 694             {\r
 695               jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();\r
 696               entry.setId(ids[p].getId());\r
 697               entry.setType(ids[p].getType());\r
 698               al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);\r
 699             }\r
 700 \r
 701           }\r
 702         }\r
 703         /////////////////////////////////\r
 704         //////////////////////////////////\r
 705         //LOAD ANNOTATIONS\r
 706         if (vamsasSet.getAnnotation() != null)\r
 707         {\r
 708             Annotation[] an = vamsasSet.getAnnotation();\r
 709 \r
 710             for (int i = 0; i < an.length; i++)\r
 711             {\r
 712                 AnnotationElement[] ae = an[i].getAnnotationElement();\r
 713                 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];\r
 714 \r
 715                 for (int aa = 0; aa < ae.length; aa++)\r
 716                 {\r
 717                     anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),\r
 718                             ae[aa].getDescription(),\r
 719                             ae[aa].getSecondaryStructure().charAt(0),\r
 720                             ae[aa].getValue());\r
 721                 }\r
 722 \r
 723                 jalview.datamodel.AlignmentAnnotation jaa = null;\r
 724 \r
 725                 if (an[i].getGraph())\r
 726                 {\r
 727                     jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
 728                             an[i].getDescription(), anot, 0, 0,\r
 729                             an[i].getGraphType());\r
 730                 }\r
 731                 else\r
 732                 {\r
 733                     jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
 734                             an[i].getDescription(), anot);\r
 735                 }\r
 736 \r
 737                 al.addAnnotation(jaa);\r
 738             }\r
 739         }\r
 740 \r
 741         /////////////////////////////////\r
 742         // LOAD VIEWPORT\r
 743         Viewport[] views = jms.getViewport();\r
 744         Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER\r
 745 \r
 746         AlignFrame af = new AlignFrame(al);\r
 747 \r
 748 \r
 749         //  af.changeColour() );\r
 750         /////////////////////////\r
 751         //LOAD GROUPS\r
 752         if (jms.getJGroupCount() > 0)\r
 753         {\r
 754             JGroup[] groups = jms.getJGroup();\r
 755 \r
 756             for (int i = 0; i < groups.length; i++)\r
 757             {\r
 758                 ColourSchemeI cs = null;\r
 759 \r
 760                 if (groups[i].getColour() != null)\r
 761                 {\r
 762                     if (groups[i].getColour().startsWith("ucs"))\r
 763                     {\r
 764                         cs = GetUserColourScheme(jms, groups[i].getColour());\r
 765                     }\r
 766                     else\r
 767                     {\r
 768                         cs = ColourSchemeProperty.getColour(al,\r
 769                                 groups[i].getColour());\r
 770                     }\r
 771 \r
 772                     cs.setThreshold(groups[i].getPidThreshold(), true);\r
 773                 }\r
 774 \r
 775                 Vector seqs = new Vector();\r
 776                 int[] ids = groups[i].getSeq();\r
 777 \r
 778                 for (int s = 0; s < ids.length; s++)\r
 779                 {\r
 780                     seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(\r
 781                             ids[s]));\r
 782                 }\r
 783 \r
 784                 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,\r
 785                         groups[i].getName(), cs, groups[i].getDisplayBoxes(),\r
 786                         groups[i].getDisplayText(), groups[i].getColourText(),\r
 787                         groups[i].getStart(), groups[i].getEnd());\r
 788 \r
 789                 sg.setOutlineColour(new java.awt.Color(\r
 790                         groups[i].getOutlineColour()));\r
 791 \r
 792                 if (groups[i].getConsThreshold() != 0)\r
 793                 {\r
 794                     jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",\r
 795                             ResidueProperties.propHash, 3, sg.sequences, 0,\r
 796                             sg.getWidth() - 1);\r
 797                     c.calculate();\r
 798                     c.verdict(false, 25);\r
 799                     sg.cs.setConservation(c);\r
 800                 }\r
 801 \r
 802                 al.addGroup(sg);\r
 803             }\r
 804         }\r
 805 \r
 806 \r
 807         af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),\r
 808             view.getHeight());\r
 809         af.viewport.setStartRes(view.getStartRes());\r
 810         af.viewport.setStartSeq(view.getStartSeq());\r
 811         af.viewport.setShowAnnotation(view.getShowAnnotation());\r
 812         af.viewport.showConservation = view.getShowConservation();\r
 813         af.viewport.showQuality = view.getShowQuality();\r
 814         af.viewport.showIdentity = view.getShowIdentity();\r
 815         af.viewport.setAbovePIDThreshold(view.getPidSelected());\r
 816         af.abovePIDThreshold.setSelected(view.getPidSelected());\r
 817         af.viewport.setColourText(view.getShowColourText());\r
 818         af.colourTextMenuItem.setSelected(view.getShowColourText());\r
 819         af.viewport.setConservationSelected(view.getConservationSelected());\r
 820         af.conservationMenuItem.setSelected(view.getConservationSelected());\r
 821 \r
 822         af.viewport.setShowJVSuffix(view.getShowFullId());\r
 823         af.seqLimits.setSelected(view.getShowFullId());\r
 824 \r
 825         af.viewport.setFont(new java.awt.Font(view.getFontName(),\r
 826                 view.getFontStyle(), view.getFontSize()));\r
 827         af.alignPanel.fontChanged();\r
 828 \r
 829         af.viewport.setRenderGaps(view.getRenderGaps());\r
 830         af.renderGapsMenuItem.setSelected(view.getRenderGaps());\r
 831 \r
 832         af.viewport.setWrapAlignment(view.getWrapAlignment());\r
 833         af.wrapMenuItem.setSelected(view.getWrapAlignment());\r
 834 \r
 835         if (view.getWrapAlignment())\r
 836         {\r
 837             af.alignPanel.setWrapAlignment(view.getWrapAlignment());\r
 838         }\r
 839         else\r
 840         {\r
 841             af.annotationPanelMenuItem.setState(view.getShowAnnotation());\r
 842             af.viewport.setShowAnnotation(view.getShowAnnotation());\r
 843             af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\r
 844         }\r
 845 \r
 846         af.viewport.setShowBoxes(view.getShowBoxes());\r
 847         af.viewBoxesMenuItem.setSelected(view.getShowBoxes());\r
 848         af.viewport.setShowText(view.getShowText());\r
 849         af.viewTextMenuItem.setSelected(view.getShowText());\r
 850 \r
 851         ColourSchemeI cs = null;\r
 852 \r
 853         if (view.getBgColour() != null)\r
 854         {\r
 855             if (view.getBgColour().startsWith("ucs"))\r
 856             {\r
 857                 cs = GetUserColourScheme(jms, view.getBgColour());\r
 858             }\r
 859             else\r
 860             {\r
 861                 cs = ColourSchemeProperty.getColour(al, view.getBgColour());\r
 862             }\r
 863 \r
 864             if(cs!=null)\r
 865             {\r
 866               cs.setThreshold(view.getPidThreshold(), true);\r
 867               cs.setConsensus(af.viewport.vconsensus);\r
 868             }\r
 869         }\r
 870 \r
 871         af.setColourSelected(view.getBgColour());\r
 872         af.viewport.setGlobalColourScheme(cs);\r
 873         af.viewport.setColourAppliesToAllGroups(false);\r
 874         af.changeColour(cs);\r
 875         if (view.getConservationSelected() && cs!=null)\r
 876         {\r
 877           cs.setConservationInc(view.getConsThreshold());\r
 878         }\r
 879 \r
 880         af.viewport.setColourAppliesToAllGroups(true);\r
 881 \r
 882         if (view.getShowSequenceFeatures())\r
 883         {\r
 884            af.viewport.showSequenceFeatures = true;\r
 885            af.showSeqFeatures.setSelected(true);\r
 886         }\r
 887 \r
 888         if(jms.getFeatureSettings()!=null)\r
 889         {\r
 890           af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed = new Vector();\r
 891          // af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed!=null)\r
 892          // jalview.binding.FeatureSettings fs = new jalview.binding.FeatureSettings();\r
 893          for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)\r
 894          {\r
 895            Setting setting = jms.getFeatureSettings().getSetting(fs);\r
 896 \r
 897            af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),\r
 898                new java.awt.Color(setting.getColour()));\r
 899            if(setting.getDisplay())\r
 900              af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed.addElement(setting.getType());\r
 901          }\r
 902         }\r
 903 \r
 904         Desktop.addInternalFrame(af, view.getTitle(),\r
 905              view.getWidth(), view.getHeight());\r
 906 \r
 907         //LOAD TREES\r
 908         ///////////////////////////////////////\r
 909         if (jms.getTreeCount() > 0)\r
 910         {\r
 911             try\r
 912             {\r
 913                 for (int t = 0; t < jms.getTreeCount(); t++)\r
 914                 {\r
 915 \r
 916                     Tree tree = jms.getTree(t);\r
 917 \r
 918                     TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(\r
 919                                 tree.getNewick()), tree.getTitle(),\r
 920                                 tree.getWidth(), tree.getHeight(),\r
 921                                 tree.getXpos(), tree.getYpos());\r
 922 \r
 923                     tp.fitToWindow.setState(tree.getFitToWindow());\r
 924                     tp.fitToWindow_actionPerformed(null);\r
 925 \r
 926                     if(tree.getFontName()!=null)\r
 927                       tp.setTreeFont(new java.awt.Font(tree.getFontName(),\r
 928                                           tree.getFontStyle(),\r
 929                                           tree.getFontSize()));\r
 930                     else\r
 931                       tp.setTreeFont(new java.awt.Font(view.getFontName(),\r
 932                                             view.getFontStyle(),\r
 933                                             tree.getFontSize()));\r
 934 \r
 935                     tp.showPlaceholders(tree.getMarkUnlinked());\r
 936                     tp.showBootstrap(tree.getShowBootstrap());\r
 937                     tp.showDistances(tree.getShowDistances());\r
 938 \r
 939                     tp.treeCanvas.threshold = tree.getThreshold();\r
 940 \r
 941                     if (tree.getCurrentTree())\r
 942                       af.viewport.setCurrentTree(tp.getTree());\r
 943                 }\r
 944 \r
 945             }\r
 946             catch (Exception ex)\r
 947             {\r
 948                 ex.printStackTrace();\r
 949             }\r
 950 \r
 951         }\r
 952 \r
 953         return af;\r
 954     }\r
 955 }\r