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