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 import java.util.jar.*;\r
  31 \r
  32 import javax.swing.*;\r
  33 \r
  34 import jalview.binding.*;\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                 if(sg.cs!=null)\r
 298                 {\r
 299                   if (sg.cs.conservationApplied())\r
 300                   {\r
 301                     groups[i].setConsThreshold(sg.cs.getConservationInc());\r
 302 \r
 303                     if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
 304                     {\r
 305                       groups[i].setColour(SetUserColourScheme(sg.cs,\r
 306                           userColours,\r
 307                           jms));\r
 308                     }\r
 309                     else\r
 310                     {\r
 311                       groups[i].setColour(ColourSchemeProperty.getColourName(sg.\r
 312                           cs));\r
 313                     }\r
 314                   }\r
 315                   else if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
 316                   {\r
 317                     groups[i].setColour(SetUserColourScheme(sg.cs, userColours,\r
 318                         jms));\r
 319                   }\r
 320                   else\r
 321                   {\r
 322                     groups[i].setColour(ColourSchemeProperty.getColourName(\r
 323                         sg.cs));\r
 324                   }\r
 325 \r
 326                   groups[i].setPidThreshold(sg.cs.getThreshold());\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!=null)\r
 369         {\r
 370           if (cs.conservationApplied())\r
 371           {\r
 372             view.setConsThreshold(cs.getConservationInc());\r
 373             if (cs instanceof jalview.schemes.UserColourScheme)\r
 374               view.setBgColour(SetUserColourScheme(cs, userColours, jms));\r
 375           }\r
 376 \r
 377           if (cs instanceof ResidueColourScheme)\r
 378           {\r
 379             view.setPidThreshold(cs.getThreshold());\r
 380           }\r
 381         }\r
 382 \r
 383         view.setConservationSelected(av.getConservationSelected());\r
 384         view.setPidSelected(av.getAbovePIDThreshold());\r
 385         view.setFontName(av.font.getName());\r
 386         view.setFontSize(av.font.getSize());\r
 387         view.setFontStyle(av.font.getStyle());\r
 388         view.setRenderGaps(av.renderGaps);\r
 389         view.setShowAnnotation(av.getShowAnnotation());\r
 390         view.setShowBoxes(av.getShowBoxes());\r
 391         view.setShowColourText(av.getColourText());\r
 392         view.setShowConservation(av.showConservation);\r
 393         view.setShowFullId(av.getShowFullId());\r
 394         view.setShowIdentity(av.showIdentity);\r
 395         view.setShowQuality(av.showQuality);\r
 396         view.setShowSequenceFeatures(av.showSequenceFeatures);\r
 397         view.setShowText(av.getShowText());\r
 398         view.setWrapAlignment(av.getWrapAlignment());\r
 399 \r
 400         jms.addViewport(view);\r
 401 \r
 402         object.setJalviewModelSequence(jms);\r
 403         object.getVamsasModel().addSequenceSet(vamsasSet);\r
 404 \r
 405         try\r
 406         {\r
 407             if (!fileName.endsWith(".xml"))\r
 408             {\r
 409                 fileName = fileName + ".xml";\r
 410             }\r
 411 \r
 412             JarEntry entry = new JarEntry(fileName);\r
 413             jout.putNextEntry(entry);\r
 414 \r
 415             object.marshal(out);\r
 416         }\r
 417         catch (Exception ex)\r
 418         {\r
 419             ex.printStackTrace();\r
 420         }\r
 421     }\r
 422 \r
 423     static String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,\r
 424         Vector userColours, JalviewModelSequence jms)\r
 425     {\r
 426         String id = null;\r
 427         jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;\r
 428 \r
 429         if (!userColours.contains(ucs))\r
 430         {\r
 431             userColours.add(ucs);\r
 432 \r
 433             java.awt.Color[] colours = ucs.getColours();\r
 434             jalview.binding.UserColours uc = new jalview.binding.UserColours();\r
 435             jalview.binding.UserColourScheme jbucs = new jalview.binding.UserColourScheme();\r
 436 \r
 437             for (int i = 0; i < colours.length; i++)\r
 438             {\r
 439                 jalview.binding.Colour col = new jalview.binding.Colour();\r
 440                 col.setRGB(jalview.util.Format.getHexString(colours[i]));\r
 441                 jbucs.addColour(col);\r
 442             }\r
 443 \r
 444             id = "ucs" + userColours.indexOf(ucs);\r
 445             uc.setId(id);\r
 446             uc.setUserColourScheme(jbucs);\r
 447             jms.addUserColours(uc);\r
 448         }\r
 449 \r
 450         return id;\r
 451     }\r
 452 \r
 453     static jalview.schemes.UserColourScheme GetUserColourScheme(\r
 454         JalviewModelSequence jms, String id)\r
 455     {\r
 456         UserColours[] uc = jms.getUserColours();\r
 457         UserColours colours = null;\r
 458 \r
 459         for (int i = 0; i < uc.length; i++)\r
 460         {\r
 461             if (uc[i].getId().equals(id))\r
 462             {\r
 463                 colours = uc[i];\r
 464 \r
 465                 break;\r
 466             }\r
 467         }\r
 468 \r
 469         int csize = colours.getUserColourScheme().getColourCount();\r
 470         java.awt.Color[] newColours = new java.awt.Color[csize];\r
 471 \r
 472         for (int i = 0; i < csize; i++)\r
 473         {\r
 474             newColours[i] = new java.awt.Color(Integer.parseInt(\r
 475                         colours.getUserColourScheme().getColour(i).getRGB(), 16));\r
 476         }\r
 477 \r
 478         return new jalview.schemes.UserColourScheme(newColours);\r
 479     }\r
 480 \r
 481     /**\r
 482      * DOCUMENT ME!\r
 483      *\r
 484      * @param file DOCUMENT ME!\r
 485      */\r
 486     public static AlignFrame LoadJalviewAlign(String file)\r
 487     {\r
 488         JalviewModel object = new JalviewModel();\r
 489         jalview.gui.AlignFrame af = null;\r
 490 \r
 491         try\r
 492         {\r
 493             //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING\r
 494             URL url = null;\r
 495 \r
 496             if (file.startsWith("http://"))\r
 497             {\r
 498                 url = new URL(file);\r
 499             }\r
 500 \r
 501             JarInputStream jin = null;\r
 502             JarEntry jarentry = null;\r
 503             int entryCount = 1;\r
 504 \r
 505             do\r
 506             {\r
 507                 if (url != null)\r
 508                 {\r
 509                     jin = new JarInputStream(url.openStream());\r
 510                 }\r
 511                 else\r
 512                 {\r
 513                     jin = new JarInputStream(new FileInputStream(file));\r
 514                 }\r
 515 \r
 516                 for (int i = 0; i < entryCount; i++)\r
 517                 {\r
 518                     jarentry = jin.getNextJarEntry();\r
 519                 }\r
 520 \r
 521                 if (jarentry != null)\r
 522                 {\r
 523                     InputStreamReader in = new InputStreamReader(jin, "UTF-8");\r
 524                     object = (JalviewModel) object.unmarshal(in);\r
 525                     af = LoadFromObject(object);\r
 526                     entryCount++;\r
 527                 }\r
 528             }\r
 529             while (jarentry != null);\r
 530         }\r
 531         catch (Exception ex)\r
 532         {\r
 533           ex.printStackTrace();\r
 534             System.err.println("Exception whilst loading jalview XML file : " +\r
 535                 ex + "\n");\r
 536              JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 537                                       "Couldn't locate " + file,\r
 538                                       "URL not found",\r
 539                                       JOptionPane.WARNING_MESSAGE);\r
 540 \r
 541         }\r
 542 \r
 543         return af;\r
 544     }\r
 545 \r
 546     static AlignFrame LoadFromObject(JalviewModel object)\r
 547     {\r
 548         Vector seqids = new Vector();\r
 549         SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);\r
 550         Sequence[] vamsasSeq = vamsasSet.getSequence();\r
 551 \r
 552         JalviewModelSequence jms = object.getJalviewModelSequence();\r
 553 \r
 554         //////////////////////////////////\r
 555         //LOAD SEQUENCES\r
 556         jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];\r
 557         JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();\r
 558 \r
 559         for (int i = 0; i < vamsasSeq.length; i++)\r
 560         {\r
 561             jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),\r
 562                     vamsasSeq[i].getSequence());\r
 563 \r
 564             jseqs[i].setStart(JSEQ[i].getStart());\r
 565             jseqs[i].setEnd(JSEQ[i].getEnd());\r
 566             jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));\r
 567             seqids.add(jseqs[i]);\r
 568         }\r
 569 \r
 570         /////////////////////////////////\r
 571         jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);\r
 572 \r
 573         /////////////////////////////////\r
 574         //////////////////////////////////\r
 575         //LOAD ANNOTATIONS\r
 576         if (vamsasSet.getAnnotation() != null)\r
 577         {\r
 578             Annotation[] an = vamsasSet.getAnnotation();\r
 579 \r
 580             for (int i = 0; i < an.length; i++)\r
 581             {\r
 582                 AnnotationElement[] ae = an[i].getAnnotationElement();\r
 583                 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];\r
 584 \r
 585                 for (int aa = 0; aa < ae.length; aa++)\r
 586                 {\r
 587                     anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),\r
 588                             ae[aa].getDescription(),\r
 589                             ae[aa].getSecondaryStructure().charAt(0),\r
 590                             ae[aa].getValue());\r
 591                 }\r
 592 \r
 593                 jalview.datamodel.AlignmentAnnotation jaa = null;\r
 594 \r
 595                 if (an[i].getGraph())\r
 596                 {\r
 597                     jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
 598                             an[i].getDescription(), anot, 0, 0, 1);\r
 599                 }\r
 600                 else\r
 601                 {\r
 602                     jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
 603                             an[i].getDescription(), anot);\r
 604                 }\r
 605 \r
 606                 al.addAnnotation(jaa);\r
 607             }\r
 608         }\r
 609 \r
 610         /////////////////////////////////\r
 611         // LOAD VIEWPORT\r
 612         Viewport[] views = jms.getViewport();\r
 613         Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER\r
 614 \r
 615         AlignFrame af = new AlignFrame(al);\r
 616 \r
 617         //  af.changeColour() );\r
 618         /////////////////////////\r
 619         //LOAD GROUPS\r
 620         if (jms.getJGroupCount() > 0)\r
 621         {\r
 622             JGroup[] groups = jms.getJGroup();\r
 623 \r
 624             for (int i = 0; i < groups.length; i++)\r
 625             {\r
 626                 ColourSchemeI cs = null;\r
 627 \r
 628                 if (groups[i].getColour() != null)\r
 629                 {\r
 630                     if (groups[i].getColour().startsWith("ucs"))\r
 631                     {\r
 632                         cs = GetUserColourScheme(jms, groups[i].getColour());\r
 633                     }\r
 634                     else\r
 635                     {\r
 636                         cs = ColourSchemeProperty.getColour(al,\r
 637                                 groups[i].getColour());\r
 638                     }\r
 639 \r
 640                     cs.setThreshold(groups[i].getPidThreshold(), true);\r
 641                 }\r
 642 \r
 643                 Vector seqs = new Vector();\r
 644                 int[] ids = groups[i].getSeq();\r
 645 \r
 646                 for (int s = 0; s < ids.length; s++)\r
 647                 {\r
 648                     seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(\r
 649                             ids[s]));\r
 650                 }\r
 651 \r
 652                 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,\r
 653                         groups[i].getName(), cs, groups[i].getDisplayBoxes(),\r
 654                         groups[i].getDisplayText(), groups[i].getColourText(),\r
 655                         groups[i].getStart(), groups[i].getEnd());\r
 656 \r
 657                 sg.setOutlineColour(new java.awt.Color(\r
 658                         groups[i].getOutlineColour()));\r
 659 \r
 660                 if (groups[i].getConsThreshold() != 0)\r
 661                 {\r
 662                     jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",\r
 663                             ResidueProperties.propHash, 3, sg.sequences, 0,\r
 664                             sg.getWidth() - 1);\r
 665                     c.calculate();\r
 666                     c.verdict(false, 25);\r
 667                     sg.cs.setConservation(c);\r
 668                 }\r
 669 \r
 670                 al.addGroup(sg);\r
 671             }\r
 672         }\r
 673 \r
 674 \r
 675         af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),\r
 676             view.getHeight());\r
 677         af.viewport.setStartRes(view.getStartRes());\r
 678         af.viewport.setStartSeq(view.getStartSeq());\r
 679         af.viewport.showConservation = view.getShowConservation();\r
 680         af.viewport.showQuality = view.getShowQuality();\r
 681         af.viewport.showIdentity = view.getShowIdentity();\r
 682         af.viewport.setAbovePIDThreshold(view.getPidSelected());\r
 683         af.abovePIDThreshold.setSelected(view.getPidSelected());\r
 684         af.viewport.setColourText(view.getShowColourText());\r
 685         af.colourTextMenuItem.setSelected(view.getShowColourText());\r
 686         af.viewport.setConservationSelected(view.getConservationSelected());\r
 687         af.conservationMenuItem.setSelected(view.getConservationSelected());\r
 688 \r
 689         af.viewport.setShowFullId(view.getShowFullId());\r
 690         af.fullSeqId.setSelected(view.getShowFullId());\r
 691 \r
 692         af.viewport.setFont(new java.awt.Font(view.getFontName(),\r
 693                 view.getFontStyle(), view.getFontSize()));\r
 694         af.alignPanel.fontChanged();\r
 695 \r
 696         af.viewport.setRenderGaps(view.getRenderGaps());\r
 697         af.renderGapsMenuItem.setSelected(view.getRenderGaps());\r
 698 \r
 699         af.viewport.setWrapAlignment(view.getWrapAlignment());\r
 700         af.wrapMenuItem.setSelected(view.getWrapAlignment());\r
 701 \r
 702         if (view.getWrapAlignment())\r
 703         {\r
 704             af.alignPanel.setWrapAlignment(view.getWrapAlignment());\r
 705         }\r
 706         else\r
 707         {\r
 708             af.annotationPanelMenuItem.setState(view.getShowAnnotation());\r
 709             af.viewport.setShowAnnotation(view.getShowAnnotation());\r
 710             af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\r
 711         }\r
 712 \r
 713         af.viewport.setShowBoxes(view.getShowBoxes());\r
 714         af.viewBoxesMenuItem.setSelected(view.getShowBoxes());\r
 715         af.viewport.setShowText(view.getShowText());\r
 716         af.viewTextMenuItem.setSelected(view.getShowText());\r
 717 \r
 718         ColourSchemeI cs = null;\r
 719 \r
 720         if (view.getBgColour() != null)\r
 721         {\r
 722             if (view.getBgColour().startsWith("ucs"))\r
 723             {\r
 724                 cs = GetUserColourScheme(jms, view.getBgColour());\r
 725             }\r
 726             else\r
 727             {\r
 728                 cs = ColourSchemeProperty.getColour(al, view.getBgColour());\r
 729             }\r
 730 \r
 731             if(cs!=null)\r
 732             {\r
 733               cs.setThreshold(view.getPidThreshold(), true);\r
 734               cs.setConsensus(af.viewport.vconsensus);\r
 735             }\r
 736         }\r
 737 \r
 738         af.setColourSelected(view.getBgColour());\r
 739         af.viewport.setGlobalColourScheme(cs);\r
 740         af.viewport.setColourAppliesToAllGroups(false);\r
 741         af.changeColour(cs);\r
 742         if (view.getConservationSelected() && cs!=null)\r
 743         {\r
 744           cs.setConservationInc(view.getConsThreshold());\r
 745         }\r
 746 \r
 747         af.viewport.setColourAppliesToAllGroups(true);\r
 748 \r
 749         if (view.getShowSequenceFeatures())\r
 750         {\r
 751             af.viewport.showSequenceFeatures = true;\r
 752             af.sequenceFeatures.setSelected(true);\r
 753             new SequenceFeatureFetcher(al, af.alignPanel);\r
 754             al.featuresAdded = true;\r
 755         }\r
 756 \r
 757         Desktop.addInternalFrame(af, view.getTitle(),\r
 758              view.getWidth(), view.getHeight());\r
 759 \r
 760         //LOAD TREES\r
 761         ///////////////////////////////////////\r
 762         if (jms.getTreeCount() > 0)\r
 763         {\r
 764             try\r
 765             {\r
 766                 for (int t = 0; t < jms.getTreeCount(); t++)\r
 767                 {\r
 768 \r
 769                     Tree tree = jms.getTree(t);\r
 770 \r
 771                     TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(\r
 772                                 tree.getNewick()), tree.getTitle(),\r
 773                                 tree.getWidth(), tree.getHeight(),\r
 774                                 tree.getXpos(), tree.getYpos());\r
 775 \r
 776                     tp.fitToWindow.setState(tree.getFitToWindow());\r
 777                     tp.fitToWindow_actionPerformed(null);\r
 778                     tp.treeCanvas.fontSize = tree.getFontSize();\r
 779                     tp.fontSize.setText("Font Size - " + tree.getFontSize());\r
 780                     tp.placeholdersMenu.setState(tree.getMarkUnlinked());\r
 781                     tp.placeholdersMenu_actionPerformed(null);\r
 782                     tp.bootstrapMenu.setState(tree.getShowBootstrap());\r
 783                     tp.bootstrapMenu_actionPerformed(null);\r
 784                     tp.distanceMenu.setState(tree.getShowDistances());\r
 785                     tp.distanceMenu_actionPerformed(null);\r
 786                     tp.treeCanvas.threshold = tree.getThreshold();\r
 787 \r
 788                     if (tree.getCurrentTree())\r
 789                       af.viewport.setCurrentTree(tp.getTree());\r
 790                 }\r
 791 \r
 792             }\r
 793             catch (Exception ex)\r
 794             {\r
 795                 ex.printStackTrace();\r
 796             }\r
 797 \r
 798         }\r
 799 \r
 800         return af;\r
 801     }\r
 802 }\r