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