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         }\r
 138     }\r
 139 \r
 140     /**\r
 141      * DOCUMENT ME!\r
 142      *\r
 143      * @param af DOCUMENT ME!\r
 144      * @param timeStamp DOCUMENT ME!\r
 145      * @param fileName DOCUMENT ME!\r
 146      * @param jout DOCUMENT ME!\r
 147      * @param out DOCUMENT ME!\r
 148      */\r
 149     public static void SaveState(AlignFrame af, long timeStamp,\r
 150         String fileName, JarOutputStream jout, PrintWriter out)\r
 151     {\r
 152         Vector seqids = new Vector();\r
 153         Vector userColours = new Vector();\r
 154 \r
 155         AlignViewport av = af.viewport;\r
 156 \r
 157         JalviewModel object = new JalviewModel();\r
 158         object.setVamsasModel(new VamsasModel());\r
 159 \r
 160         object.setCreationDate(new java.util.Date(timeStamp));\r
 161         object.setVersion(jalview.bin.Cache.getProperty("VERSION"));\r
 162 \r
 163         jalview.datamodel.AlignmentI jal = af.viewport.alignment;\r
 164 \r
 165         SequenceSet vamsasSet = new SequenceSet();\r
 166         Sequence vamsasSeq;\r
 167         JalviewModelSequence jms = new JalviewModelSequence();\r
 168 \r
 169         vamsasSet.setGapChar(jal.getGapCharacter() + "");\r
 170 \r
 171         JSeq jseq;\r
 172 \r
 173         //SAVE SEQUENCES\r
 174         int id = 0;\r
 175 \r
 176         for (int i = 0; i < jal.getHeight(); i++)\r
 177         {\r
 178             seqids.add(jal.getSequenceAt(i));\r
 179 \r
 180             vamsasSeq = new Sequence();\r
 181             vamsasSeq.setId(id + "");\r
 182             vamsasSeq.setName(jal.getSequenceAt(i).getName());\r
 183             vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());\r
 184 \r
 185             jseq = new JSeq();\r
 186             jseq.setStart(jal.getSequenceAt(i).getStart());\r
 187             jseq.setEnd(jal.getSequenceAt(i).getEnd());\r
 188 \r
 189             jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());\r
 190 \r
 191             jseq.setId(id);\r
 192 \r
 193             jms.addJSeq(jseq);\r
 194             vamsasSet.addSequence(vamsasSeq);\r
 195             id++;\r
 196         }\r
 197 \r
 198         //SAVE TREES\r
 199         ///////////////////////////////////\r
 200         if (af.viewport.currentTree != null)\r
 201         {\r
 202             // FIND ANY ASSOCIATED TREES\r
 203             JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
 204 \r
 205             for (int t = 0; t < frames.length; t++)\r
 206             {\r
 207                 if (frames[t] instanceof TreePanel)\r
 208                 {\r
 209                     TreePanel tp = (TreePanel) frames[t];\r
 210 \r
 211                     if (tp.treeCanvas.av.alignment == jal)\r
 212                     {\r
 213                         Tree tree = new Tree();\r
 214                         tree.setTitle(tp.getTitle());\r
 215                         tree.setCurrentTree((af.viewport.currentTree == tp.getTree()));\r
 216                         tree.setNewick(tp.getTree().toString());\r
 217                         tree.setThreshold(tp.treeCanvas.threshold);\r
 218 \r
 219                         tree.setFitToWindow(tp.fitToWindow.getState());\r
 220                         tree.setFontSize(tp.treeCanvas.fontSize);\r
 221                         tree.setMarkUnlinked(tp.placeholdersMenu.getState());\r
 222                         tree.setShowBootstrap(tp.bootstrapMenu.getState());\r
 223                         tree.setShowDistances(tp.distanceMenu.getState());\r
 224 \r
 225                         tree.setHeight(tp.getHeight());\r
 226                         tree.setWidth(tp.getWidth());\r
 227                         tree.setXpos(tp.getX());\r
 228                         tree.setYpos(tp.getY());\r
 229 \r
 230                         jms.addTree(tree);\r
 231                     }\r
 232                 }\r
 233             }\r
 234         }\r
 235 \r
 236         //SAVE ANNOTATIONS\r
 237         if (jal.getAlignmentAnnotation() != null)\r
 238         {\r
 239             jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();\r
 240 \r
 241             for (int i = 0; i < aa.length; i++)\r
 242             {\r
 243                 if (aa[i].label.equals("Quality") ||\r
 244                         aa[i].label.equals("Conservation") ||\r
 245                         aa[i].label.equals("Consensus"))\r
 246                 {\r
 247                     continue;\r
 248                 }\r
 249 \r
 250                 Annotation an = new Annotation();\r
 251                 an.setDescription(aa[i].description);\r
 252                 an.setGraph(aa[i].isGraph);\r
 253                 an.setLabel(aa[i].label);\r
 254 \r
 255                 AnnotationElement ae;\r
 256 \r
 257                 for (int a = 0; a < aa[i].annotations.length; a++)\r
 258                 {\r
 259                     if ((aa[i] == null) || (aa[i].annotations[a] == null))\r
 260                     {\r
 261                         continue;\r
 262                     }\r
 263 \r
 264                     ae = new AnnotationElement();\r
 265                     ae.setDescription(aa[i].annotations[a].description);\r
 266                     ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);\r
 267                     ae.setValue(aa[i].annotations[a].value);\r
 268                     ae.setPosition(a);\r
 269                     ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +\r
 270                         "");\r
 271                     an.addAnnotationElement(ae);\r
 272                 }\r
 273 \r
 274                 vamsasSet.addAnnotation(an);\r
 275             }\r
 276         }\r
 277 \r
 278         //SAVE GROUPS\r
 279         if (jal.getGroups() != null)\r
 280         {\r
 281             JGroup[] groups = new JGroup[jal.getGroups().size()];\r
 282 \r
 283             for (int i = 0; i < groups.length; i++)\r
 284             {\r
 285                 groups[i] = new JGroup();\r
 286 \r
 287                 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()\r
 288                                                                                           .elementAt(i);\r
 289                 groups[i].setStart(sg.getStartRes());\r
 290                 groups[i].setEnd(sg.getEndRes());\r
 291                 groups[i].setName(sg.getName());\r
 292 \r
 293                 if (sg.cs instanceof ConservationColourScheme)\r
 294                 {\r
 295                     groups[i].setConsThreshold(((ConservationColourScheme) sg.cs).inc);\r
 296                 }\r
 297 \r
 298                 if (sg.cs instanceof ResidueColourScheme)\r
 299                 {\r
 300                     groups[i].setPidThreshold(((ResidueColourScheme) sg.cs).getThreshold());\r
 301                 }\r
 302                 else if (sg.cs instanceof ScoreColourScheme)\r
 303                 {\r
 304                     groups[i].setPidThreshold(((ScoreColourScheme) sg.cs).getThreshold());\r
 305                 }\r
 306 \r
 307                 if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
 308                 {\r
 309                     groups[i].setColour(SetUserColourScheme(sg.cs, userColours,\r
 310                             jms));\r
 311                 }\r
 312                 else\r
 313                 {\r
 314                     groups[i].setColour(ColourSchemeProperty.getColourName(\r
 315                             sg.cs));\r
 316                 }\r
 317 \r
 318                 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());\r
 319                 groups[i].setDisplayBoxes(sg.getDisplayBoxes());\r
 320                 groups[i].setDisplayText(sg.getDisplayText());\r
 321                 groups[i].setColourText(sg.getColourText());\r
 322 \r
 323                 for (int s = 0; s < sg.getSize(); s++)\r
 324                 {\r
 325                     jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.getSequenceAt(s);\r
 326                     int index = seqids.indexOf(seq);\r
 327                     groups[i].addSeq(index);\r
 328                 }\r
 329             }\r
 330 \r
 331             jms.setJGroup(groups);\r
 332         }\r
 333 \r
 334         ///////////SAVE VIEWPORT\r
 335         Viewport view = new Viewport();\r
 336         view.setTitle(af.getTitle());\r
 337         view.setXpos(af.getX());\r
 338         view.setYpos(af.getY());\r
 339         view.setWidth(af.getWidth());\r
 340         view.setHeight(af.getHeight());\r
 341         view.setStartRes(av.startRes);\r
 342         view.setStartSeq(av.startSeq);\r
 343 \r
 344         if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)\r
 345         {\r
 346             view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),\r
 347                     userColours, jms));\r
 348         }\r
 349         else\r
 350         {\r
 351             view.setBgColour(ColourSchemeProperty.getColourName(\r
 352                     av.getGlobalColourScheme()));\r
 353         }\r
 354 \r
 355         ColourSchemeI cs = av.getGlobalColourScheme();\r
 356 \r
 357         if (cs instanceof ConservationColourScheme)\r
 358         {\r
 359             view.setConsThreshold(((ConservationColourScheme) cs).inc);\r
 360         }\r
 361 \r
 362         if (cs instanceof ResidueColourScheme)\r
 363         {\r
 364             view.setPidThreshold(((ResidueColourScheme) cs).getThreshold());\r
 365         }\r
 366         else if (cs instanceof ScoreColourScheme)\r
 367         {\r
 368             view.setPidThreshold(((ScoreColourScheme) cs).getThreshold());\r
 369         }\r
 370 \r
 371         view.setConservationSelected(av.getConservationSelected());\r
 372         view.setPidSelected(av.getAbovePIDThreshold());\r
 373         view.setFontName(av.font.getFontName());\r
 374         view.setFontSize(av.font.getSize());\r
 375         view.setFontStyle(av.font.getStyle());\r
 376         view.setRenderGaps(av.renderGaps);\r
 377         view.setShowAnnotation(av.getShowAnnotation());\r
 378         view.setShowBoxes(av.getShowBoxes());\r
 379         view.setShowColourText(av.getColourText());\r
 380         view.setShowConservation(av.showConservation);\r
 381         view.setShowFullId(av.getShowFullId());\r
 382         view.setShowIdentity(av.showIdentity);\r
 383         view.setShowQuality(av.showQuality);\r
 384         view.setShowSequenceFeatures(av.showSequenceFeatures);\r
 385         view.setShowText(av.getShowText());\r
 386         view.setWrapAlignment(av.getWrapAlignment());\r
 387 \r
 388         jms.addViewport(view);\r
 389 \r
 390         object.setJalviewModelSequence(jms);\r
 391         object.getVamsasModel().addSequenceSet(vamsasSet);\r
 392 \r
 393         try\r
 394         {\r
 395             if (!fileName.endsWith(".xml"))\r
 396             {\r
 397                 fileName = fileName + ".xml";\r
 398             }\r
 399 \r
 400             JarEntry entry = new JarEntry(fileName);\r
 401             jout.putNextEntry(entry);\r
 402 \r
 403             object.marshal(out);\r
 404         }\r
 405         catch (Exception ex)\r
 406         {\r
 407             ex.printStackTrace();\r
 408         }\r
 409     }\r
 410 \r
 411     static String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,\r
 412         Vector userColours, JalviewModelSequence jms)\r
 413     {\r
 414         String id = null;\r
 415         jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;\r
 416 \r
 417         if (!userColours.contains(ucs))\r
 418         {\r
 419             userColours.add(ucs);\r
 420 \r
 421             java.awt.Color[] colours = ucs.getColours();\r
 422             jalview.binding.UserColours uc = new jalview.binding.UserColours();\r
 423             jalview.binding.UserColourScheme jbucs = new jalview.binding.UserColourScheme();\r
 424 \r
 425             for (int i = 0; i < colours.length; i++)\r
 426             {\r
 427                 jalview.binding.Colour col = new jalview.binding.Colour();\r
 428                 col.setRGB(jalview.util.Format.getHexString(colours[i]));\r
 429                 jbucs.addColour(col);\r
 430             }\r
 431 \r
 432             id = "ucs" + userColours.indexOf(ucs);\r
 433             uc.setId(id);\r
 434             uc.setUserColourScheme(jbucs);\r
 435             jms.addUserColours(uc);\r
 436         }\r
 437 \r
 438         return id;\r
 439     }\r
 440 \r
 441     static jalview.schemes.UserColourScheme GetUserColourScheme(\r
 442         JalviewModelSequence jms, String id)\r
 443     {\r
 444         UserColours[] uc = jms.getUserColours();\r
 445         UserColours colours = null;\r
 446 \r
 447         for (int i = 0; i < uc.length; i++)\r
 448         {\r
 449             if (uc[i].getId().equals(id))\r
 450             {\r
 451                 colours = uc[i];\r
 452 \r
 453                 break;\r
 454             }\r
 455         }\r
 456 \r
 457         int csize = colours.getUserColourScheme().getColourCount();\r
 458         java.awt.Color[] newColours = new java.awt.Color[csize];\r
 459 \r
 460         for (int i = 0; i < csize; i++)\r
 461         {\r
 462             newColours[i] = new java.awt.Color(Integer.parseInt(\r
 463                         colours.getUserColourScheme().getColour(i).getRGB(), 16));\r
 464         }\r
 465 \r
 466         return new jalview.schemes.UserColourScheme(newColours);\r
 467     }\r
 468 \r
 469     /**\r
 470      * DOCUMENT ME!\r
 471      *\r
 472      * @param file DOCUMENT ME!\r
 473      */\r
 474     public static AlignFrame LoadJalviewAlign(String file)\r
 475     {\r
 476         JalviewModel object = new JalviewModel();\r
 477         jalview.gui.AlignFrame af = null;\r
 478 \r
 479         try\r
 480         {\r
 481             //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING\r
 482             URL url = null;\r
 483 \r
 484             if (file.startsWith("http://"))\r
 485             {\r
 486                 url = new URL(file);\r
 487             }\r
 488 \r
 489             JarInputStream jin = null;\r
 490             JarEntry jarentry = null;\r
 491             int entryCount = 1;\r
 492 \r
 493             do\r
 494             {\r
 495                 if (url != null)\r
 496                 {\r
 497                     jin = new JarInputStream(url.openStream());\r
 498                 }\r
 499                 else\r
 500                 {\r
 501                     jin = new JarInputStream(new FileInputStream(file));\r
 502                 }\r
 503 \r
 504                 for (int i = 0; i < entryCount; i++)\r
 505                 {\r
 506                     jarentry = jin.getNextJarEntry();\r
 507                 }\r
 508 \r
 509                 if (jarentry != null)\r
 510                 {\r
 511                     InputStreamReader in = new InputStreamReader(jin, "UTF-8");\r
 512                     object = (JalviewModel) object.unmarshal(in);\r
 513                     af = LoadFromObject(object);\r
 514                     entryCount++;\r
 515                 }\r
 516             }\r
 517             while (jarentry != null);\r
 518         }\r
 519         catch (Exception ex)\r
 520         {\r
 521             System.err.println("Exception whilst loading jalview XML file : " +\r
 522                 ex + "\n");\r
 523              JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 524                                       "Couldn't locate " + file,\r
 525                                       "URL not found",\r
 526                                       JOptionPane.WARNING_MESSAGE);\r
 527 \r
 528         }\r
 529 \r
 530         return af;\r
 531     }\r
 532 \r
 533     static AlignFrame LoadFromObject(JalviewModel object)\r
 534     {\r
 535         Vector seqids = new Vector();\r
 536         SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);\r
 537         Sequence[] vamsasSeq = vamsasSet.getSequence();\r
 538 \r
 539         JalviewModelSequence jms = object.getJalviewModelSequence();\r
 540 \r
 541         //////////////////////////////////\r
 542         //LOAD SEQUENCES\r
 543         jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];\r
 544         JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();\r
 545 \r
 546         for (int i = 0; i < vamsasSeq.length; i++)\r
 547         {\r
 548             jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),\r
 549                     vamsasSeq[i].getSequence());\r
 550 \r
 551             jseqs[i].setStart(JSEQ[i].getStart());\r
 552             jseqs[i].setEnd(JSEQ[i].getEnd());\r
 553             jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));\r
 554             seqids.add(jseqs[i]);\r
 555         }\r
 556 \r
 557         /////////////////////////////////\r
 558         jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);\r
 559 \r
 560         /////////////////////////////////\r
 561         //////////////////////////////////\r
 562         //LOAD ANNOTATIONS\r
 563         if (vamsasSet.getAnnotation() != null)\r
 564         {\r
 565             Annotation[] an = vamsasSet.getAnnotation();\r
 566 \r
 567             for (int i = 0; i < an.length; i++)\r
 568             {\r
 569                 AnnotationElement[] ae = an[i].getAnnotationElement();\r
 570                 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];\r
 571 \r
 572                 for (int aa = 0; aa < ae.length; aa++)\r
 573                 {\r
 574                     anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),\r
 575                             ae[aa].getDescription(),\r
 576                             ae[aa].getSecondaryStructure().charAt(0),\r
 577                             ae[aa].getValue());\r
 578                 }\r
 579 \r
 580                 jalview.datamodel.AlignmentAnnotation jaa = null;\r
 581 \r
 582                 if (an[i].getGraph())\r
 583                 {\r
 584                     jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
 585                             an[i].getDescription(), anot, 0, 0, 1);\r
 586                 }\r
 587                 else\r
 588                 {\r
 589                     jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
 590                             an[i].getDescription(), anot);\r
 591                 }\r
 592 \r
 593                 al.addAnnotation(jaa);\r
 594             }\r
 595         }\r
 596 \r
 597         /////////////////////////////////\r
 598         // LOAD VIEWPORT\r
 599         Viewport[] views = jms.getViewport();\r
 600         Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER\r
 601 \r
 602         AlignFrame af = new AlignFrame(al);\r
 603 \r
 604         //  af.changeColour() );\r
 605         /////////////////////////\r
 606         //LOAD GROUPS\r
 607         if (jms.getJGroupCount() > 0)\r
 608         {\r
 609             JGroup[] groups = jms.getJGroup();\r
 610 \r
 611             for (int i = 0; i < groups.length; i++)\r
 612             {\r
 613                 ColourSchemeI cs = null;\r
 614 \r
 615                 if (groups[i].getColour() != null)\r
 616                 {\r
 617                     if (groups[i].getColour().startsWith("ucs"))\r
 618                     {\r
 619                         cs = GetUserColourScheme(jms, groups[i].getColour());\r
 620                     }\r
 621                     else\r
 622                     {\r
 623                         cs = ColourSchemeProperty.getColour(al,\r
 624                                 groups[i].getColour());\r
 625                     }\r
 626 \r
 627                     if (cs instanceof ResidueColourScheme)\r
 628                     {\r
 629                         ((ResidueColourScheme) cs).setThreshold(groups[i].getPidThreshold());\r
 630                     }\r
 631                     else if (cs instanceof ScoreColourScheme)\r
 632                     {\r
 633                         ((ScoreColourScheme) cs).setThreshold(groups[i].getPidThreshold());\r
 634                     }\r
 635                 }\r
 636 \r
 637                 Vector seqs = new Vector();\r
 638                 int[] ids = groups[i].getSeq();\r
 639 \r
 640                 for (int s = 0; s < ids.length; s++)\r
 641                 {\r
 642                     seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(\r
 643                             ids[s]));\r
 644                 }\r
 645 \r
 646                 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,\r
 647                         groups[i].getName(), cs, groups[i].getDisplayBoxes(),\r
 648                         groups[i].getDisplayText(), groups[i].getColourText(),\r
 649                         groups[i].getStart(), groups[i].getEnd());\r
 650 \r
 651                 sg.setOutlineColour(new java.awt.Color(\r
 652                         groups[i].getOutlineColour()));\r
 653 \r
 654                 if (groups[i].getConsThreshold() != 0)\r
 655                 {\r
 656                     jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",\r
 657                             ResidueProperties.propHash, 3, sg.sequences, 0,\r
 658                             sg.getWidth() - 1);\r
 659                     c.calculate();\r
 660                     c.verdict(false, 25);\r
 661                     cs = new ConservationColourScheme(c, cs);\r
 662                     sg.cs = cs;\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             if (cs instanceof ConservationColourScheme)\r
 728             {\r
 729                 ((ConservationColourScheme) cs).inc = view.getConsThreshold();\r
 730             }\r
 731 \r
 732             if (cs instanceof ResidueColourScheme)\r
 733             {\r
 734                 ((ResidueColourScheme) cs).setThreshold(view.getPidThreshold());\r
 735             }\r
 736             else if (cs instanceof ScoreColourScheme)\r
 737             {\r
 738                 ((ScoreColourScheme) cs).setThreshold(view.getPidThreshold());\r
 739             }\r
 740         }\r
 741 \r
 742         af.viewport.setGlobalColourScheme(cs);\r
 743 \r
 744         af.viewport.setColourAppliesToAllGroups(false);\r
 745         af.changeColour(af.viewport.getGlobalColourScheme());\r
 746         af.viewport.setColourAppliesToAllGroups(true);\r
 747 \r
 748         if (view.getShowSequenceFeatures())\r
 749         {\r
 750             af.viewport.showSequenceFeatures = true;\r
 751             af.sequenceFeatures.setSelected(true);\r
 752             new SequenceFeatureFetcher(al, af.alignPanel);\r
 753             al.featuresAdded = true;\r
 754         }\r
 755 \r
 756         //LOAD TREES\r
 757         ///////////////////////////////////////\r
 758         if (jms.getTreeCount() > 0)\r
 759         {\r
 760             try\r
 761             {\r
 762                 for (int t = 0; t < jms.getTreeCount(); t++)\r
 763                 {\r
 764                     Tree tree = jms.getTree(t);\r
 765 \r
 766                     TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(\r
 767                                 tree.getNewick()), tree.getTitle());\r
 768 \r
 769                     tp.setBounds(tree.getXpos(), tree.getYpos(),\r
 770                         tree.getWidth(), tree.getHeight());\r
 771 \r
 772                     tp.fitToWindow.setState(tree.getFitToWindow());\r
 773                     tp.fitToWindow_actionPerformed(null);\r
 774                     tp.treeCanvas.fontSize = tree.getFontSize();\r
 775                     tp.fontSize.setText("Font Size - " + tree.getFontSize());\r
 776                     tp.placeholdersMenu.setState(tree.getMarkUnlinked());\r
 777                     tp.placeholdersMenu_actionPerformed(null);\r
 778                     tp.bootstrapMenu.setState(tree.getShowBootstrap());\r
 779                     tp.bootstrapMenu_actionPerformed(null);\r
 780                     tp.distanceMenu.setState(tree.getShowDistances());\r
 781                     tp.distanceMenu_actionPerformed(null);\r
 782                     tp.treeCanvas.threshold = tree.getThreshold();\r
 783 \r
 784                     if (tree.getCurrentTree())\r
 785                       af.viewport.setCurrentTree(tp.getTree());\r
 786                 }\r
 787             }\r
 788             catch (Exception ex)\r
 789             {\r
 790                 ex.printStackTrace();\r
 791             }\r
 792         }\r
 793         return af;\r
 794     }\r
 795 }\r