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