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