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