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