src/jalview/gui/Jalview2XML.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  *\r
   5  * This program is free software; you can redistribute it and/or\r
   6  * modify it under the terms of the GNU General Public License\r
   7  * as published by the Free Software Foundation; either version 2\r
   8  * of the License, or (at your option) any later version.\r
   9  *\r
  10  * This program is distributed in the hope that it will be useful,\r
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13  * GNU General Public License for more details.\r
  14  *\r
  15  * You should have received a copy of the GNU General Public License\r
  16  * along with this program; if not, write to the Free Software\r
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18  */\r
  19 package jalview.gui;\r
  20 \r
  21 import jalview.io.*;\r
  22 \r
  23 import jalview.schemes.*;\r
  24 \r
  25 import java.io.*;\r
  26 \r
  27 import java.net.*;\r
  28 \r
  29 import java.util.*;\r
  30 \r
  31 import java.util.jar.*;\r
  32 \r
  33 import javax.swing.*;\r
  34 \r
  35 import jalview.binding.*;\r
  36 \r
  37 \r
  38 /**\r
  39  * DOCUMENT ME!\r
  40  *\r
  41  * @author $author$\r
  42  * @version $Revision$\r
  43  */\r
  44 public class Jalview2XML\r
  45 {\r
  46     // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE\r
  47     public static void SaveState(File statefile)\r
  48     {\r
  49         long creation = System.currentTimeMillis();\r
  50         JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
  51 \r
  52         if (frames == null)\r
  53         {\r
  54             return;\r
  55         }\r
  56 \r
  57         try\r
  58         {\r
  59             FileOutputStream fos = new FileOutputStream(statefile);\r
  60             JarOutputStream jout = new JarOutputStream(fos);\r
  61 \r
  62             //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS\r
  63             ////////////////////////////////////////////////////\r
  64             PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,\r
  65                         "UTF-8"));\r
  66 \r
  67             Vector shortNames = new Vector();\r
  68 \r
  69             //REVERSE ORDER\r
  70             for (int i = frames.length - 1; i > -1; i--)\r
  71             {\r
  72                 if (frames[i] instanceof AlignFrame)\r
  73                 {\r
  74                     AlignFrame af = (AlignFrame) frames[i];\r
  75 \r
  76                     String shortName = af.getTitle();\r
  77 \r
  78                     if (shortName.indexOf(File.separatorChar) > -1)\r
  79                     {\r
  80                         shortName = shortName.substring(shortName.lastIndexOf(\r
  81                                     File.separatorChar) + 1);\r
  82                     }\r
  83 \r
  84                     int count = 1;\r
  85 \r
  86                     while (shortNames.contains(shortName))\r
  87                     {\r
  88                         if (shortName.endsWith("_" + (count - 1)))\r
  89                         {\r
  90                             shortName = shortName.substring(0,\r
  91                                     shortName.lastIndexOf("_"));\r
  92                         }\r
  93 \r
  94                         shortName = shortName.concat("_" + count);\r
  95                         count++;\r
  96                     }\r
  97 \r
  98                     shortNames.addElement(shortName);\r
  99 \r
 100                     if (!shortName.endsWith(".xml"))\r
 101                     {\r
 102                         shortName = shortName + ".xml";\r
 103                     }\r
 104 \r
 105                     SaveState(af, creation, shortName, jout, out);\r
 106                 }\r
 107             }\r
 108 \r
 109             out.close();\r
 110             jout.close();\r
 111         }\r
 112         catch (Exception ex)\r
 113         {\r
 114             ex.printStackTrace();\r
 115         }\r
 116     }\r
 117 \r
 118     // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW\r
 119     public static void SaveAlignment(AlignFrame af, String jarFile,\r
 120         String fileName)\r
 121     {\r
 122         try\r
 123         {\r
 124             FileOutputStream fos = new FileOutputStream(jarFile);\r
 125             JarOutputStream jout = new JarOutputStream(fos);\r
 126 \r
 127             //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS\r
 128             ////////////////////////////////////////////////////\r
 129             PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,\r
 130                         "UTF-8"));\r
 131 \r
 132             SaveState(af, System.currentTimeMillis(), fileName, jout, out);\r
 133             out.close();\r
 134             jout.close();\r
 135         }\r
 136         catch (Exception ex)\r
 137         {\r
 138           ex.printStackTrace();\r
 139         }\r
 140     }\r
 141 \r
 142     /**\r
 143      * DOCUMENT ME!\r
 144      *\r
 145      * @param af DOCUMENT ME!\r
 146      * @param timeStamp DOCUMENT ME!\r
 147      * @param fileName DOCUMENT ME!\r
 148      * @param jout DOCUMENT ME!\r
 149      * @param out DOCUMENT ME!\r
 150      */\r
 151     public static void SaveState(AlignFrame af, long timeStamp,\r
 152         String fileName, JarOutputStream jout, PrintWriter out)\r
 153     {\r
 154         Vector seqids = new Vector();\r
 155         Vector userColours = new Vector();\r
 156 \r
 157         AlignViewport av = af.viewport;\r
 158 \r
 159         JalviewModel object = new JalviewModel();\r
 160         object.setVamsasModel(new jalview.binding.VamsasModel());\r
 161 \r
 162         object.setCreationDate(new java.util.Date(timeStamp));\r
 163         object.setVersion(jalview.bin.Cache.getProperty("VERSION"));\r
 164 \r
 165         jalview.datamodel.AlignmentI jal = af.viewport.alignment;\r
 166 \r
 167         SequenceSet vamsasSet = new SequenceSet();\r
 168         Sequence vamsasSeq;\r
 169         JalviewModelSequence jms = new JalviewModelSequence();\r
 170 \r
 171         vamsasSet.setGapChar(jal.getGapCharacter() + "");\r
 172 \r
 173         JSeq jseq;\r
 174 \r
 175         //SAVE SEQUENCES\r
 176         int id = 0;\r
 177 \r
 178         for (int i = 0; i < jal.getHeight(); i++)\r
 179         {\r
 180             seqids.add(jal.getSequenceAt(i));\r
 181 \r
 182             vamsasSeq = new Sequence();\r
 183             vamsasSeq.setId(id + "");\r
 184             vamsasSeq.setName(jal.getSequenceAt(i).getName());\r
 185             vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());\r
 186 \r
 187             jseq = new JSeq();\r
 188             jseq.setStart(jal.getSequenceAt(i).getStart());\r
 189             jseq.setEnd(jal.getSequenceAt(i).getEnd());\r
 190 \r
 191             jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());\r
 192 \r
 193             jseq.setId(id);\r
 194 \r
 195             jms.addJSeq(jseq);\r
 196             vamsasSet.addSequence(vamsasSeq);\r
 197             id++;\r
 198         }\r
 199 \r
 200         //SAVE TREES\r
 201         ///////////////////////////////////\r
 202         if (af.viewport.currentTree != null)\r
 203         {\r
 204           // FIND ANY ASSOCIATED TREES\r
 205           // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT\r
 206           if (Desktop.desktop != null)\r
 207           {\r
 208             JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
 209 \r
 210             for (int t = 0; t < frames.length; t++)\r
 211             {\r
 212               if (frames[t] instanceof TreePanel)\r
 213               {\r
 214                 TreePanel tp = (TreePanel) frames[t];\r
 215 \r
 216                 if (tp.treeCanvas.av.alignment == jal)\r
 217                 {\r
 218                   Tree tree = new Tree();\r
 219                   tree.setTitle(tp.getTitle());\r
 220                   tree.setCurrentTree( (af.viewport.currentTree == tp.getTree()));\r
 221                   tree.setNewick(tp.getTree().toString());\r
 222                   tree.setThreshold(tp.treeCanvas.threshold);\r
 223 \r
 224                   tree.setFitToWindow(tp.fitToWindow.getState());\r
 225                   tree.setFontName(tp.getTreeFont().getName());\r
 226                   tree.setFontSize(tp.getTreeFont().getSize());\r
 227                   tree.setFontStyle(tp.getTreeFont().getStyle());\r
 228                   tree.setMarkUnlinked(tp.placeholdersMenu.getState());\r
 229 \r
 230                   tree.setShowBootstrap(tp.bootstrapMenu.getState());\r
 231                   tree.setShowDistances(tp.distanceMenu.getState());\r
 232 \r
 233                   tree.setHeight(tp.getHeight());\r
 234                   tree.setWidth(tp.getWidth());\r
 235                   tree.setXpos(tp.getX());\r
 236                   tree.setYpos(tp.getY());\r
 237 \r
 238                   jms.addTree(tree);\r
 239                 }\r
 240               }\r
 241             }\r
 242           }\r
 243         }\r
 244 \r
 245         //SAVE ANNOTATIONS\r
 246         if (jal.getAlignmentAnnotation() != null)\r
 247         {\r
 248             jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();\r
 249 \r
 250             for (int i = 0; i < aa.length; i++)\r
 251             {\r
 252                 if (aa[i].label.equals("Quality") ||\r
 253                         aa[i].label.equals("Conservation") ||\r
 254                         aa[i].label.equals("Consensus"))\r
 255                 {\r
 256                     continue;\r
 257                 }\r
 258 \r
 259                 Annotation an = new Annotation();\r
 260                 an.setDescription(aa[i].description);\r
 261                 an.setGraph(aa[i].isGraph);\r
 262                 an.setLabel(aa[i].label);\r
 263 \r
 264                 AnnotationElement ae;\r
 265 \r
 266                 for (int a = 0; a < aa[i].annotations.length; a++)\r
 267                 {\r
 268                     if ((aa[i] == null) || (aa[i].annotations[a] == null))\r
 269                     {\r
 270                         continue;\r
 271                     }\r
 272 \r
 273                     ae = new AnnotationElement();\r
 274                     ae.setDescription(aa[i].annotations[a].description);\r
 275                     ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);\r
 276                     ae.setValue(aa[i].annotations[a].value);\r
 277                     ae.setPosition(a);\r
 278                     ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +\r
 279                         "");\r
 280                     an.addAnnotationElement(ae);\r
 281                 }\r
 282 \r
 283                 vamsasSet.addAnnotation(an);\r
 284             }\r
 285         }\r
 286 \r
 287         //SAVE GROUPS\r
 288         if (jal.getGroups() != null)\r
 289         {\r
 290             JGroup[] groups = new JGroup[jal.getGroups().size()];\r
 291 \r
 292             for (int i = 0; i < groups.length; i++)\r
 293             {\r
 294                 groups[i] = new JGroup();\r
 295 \r
 296                 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()\r
 297                                                                                           .elementAt(i);\r
 298                 groups[i].setStart(sg.getStartRes());\r
 299                 groups[i].setEnd(sg.getEndRes());\r
 300                 groups[i].setName(sg.getName());\r
 301                 if(sg.cs!=null)\r
 302                 {\r
 303                   if (sg.cs.conservationApplied())\r
 304                   {\r
 305                     groups[i].setConsThreshold(sg.cs.getConservationInc());\r
 306 \r
 307                     if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
 308                     {\r
 309                       groups[i].setColour(SetUserColourScheme(sg.cs,\r
 310                           userColours,\r
 311                           jms));\r
 312                     }\r
 313                     else\r
 314                     {\r
 315                       groups[i].setColour(ColourSchemeProperty.getColourName(sg.\r
 316                           cs));\r
 317                     }\r
 318                   }\r
 319                   else if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
 320                   {\r
 321                     groups[i].setColour(SetUserColourScheme(sg.cs, userColours,\r
 322                         jms));\r
 323                   }\r
 324                   else\r
 325                   {\r
 326                     groups[i].setColour(ColourSchemeProperty.getColourName(\r
 327                         sg.cs));\r
 328                   }\r
 329 \r
 330                   groups[i].setPidThreshold(sg.cs.getThreshold());\r
 331                 }\r
 332 \r
 333                 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());\r
 334                 groups[i].setDisplayBoxes(sg.getDisplayBoxes());\r
 335                 groups[i].setDisplayText(sg.getDisplayText());\r
 336                 groups[i].setColourText(sg.getColourText());\r
 337 \r
 338                 for (int s = 0; s < sg.getSize(); s++)\r
 339                 {\r
 340                     jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.getSequenceAt(s);\r
 341                     int index = seqids.indexOf(seq);\r
 342                     groups[i].addSeq(index);\r
 343                 }\r
 344             }\r
 345 \r
 346             jms.setJGroup(groups);\r
 347         }\r
 348 \r
 349         ///////////SAVE VIEWPORT\r
 350         Viewport view = new Viewport();\r
 351         view.setTitle(af.getTitle());\r
 352         view.setXpos(af.getX());\r
 353         view.setYpos(af.getY());\r
 354         view.setWidth(af.getWidth());\r
 355         view.setHeight(af.getHeight());\r
 356         view.setStartRes(av.startRes);\r
 357         view.setStartSeq(av.startSeq);\r
 358 \r
 359         if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)\r
 360         {\r
 361             view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),\r
 362                     userColours, jms));\r
 363         }\r
 364         else\r
 365         {\r
 366             view.setBgColour(ColourSchemeProperty.getColourName(\r
 367                     av.getGlobalColourScheme()));\r
 368         }\r
 369 \r
 370         ColourSchemeI cs = av.getGlobalColourScheme();\r
 371 \r
 372         if(cs!=null)\r
 373         {\r
 374           if (cs.conservationApplied())\r
 375           {\r
 376             view.setConsThreshold(cs.getConservationInc());\r
 377             if (cs instanceof jalview.schemes.UserColourScheme)\r
 378               view.setBgColour(SetUserColourScheme(cs, userColours, jms));\r
 379           }\r
 380 \r
 381           if (cs instanceof ResidueColourScheme)\r
 382           {\r
 383             view.setPidThreshold(cs.getThreshold());\r
 384           }\r
 385         }\r
 386 \r
 387         view.setConservationSelected(av.getConservationSelected());\r
 388         view.setPidSelected(av.getAbovePIDThreshold());\r
 389         view.setFontName(av.font.getName());\r
 390         view.setFontSize(av.font.getSize());\r
 391         view.setFontStyle(av.font.getStyle());\r
 392         view.setRenderGaps(av.renderGaps);\r
 393         view.setShowAnnotation(av.getShowAnnotation());\r
 394         view.setShowBoxes(av.getShowBoxes());\r
 395         view.setShowColourText(av.getColourText());\r
 396         view.setShowConservation(av.showConservation);\r
 397         view.setShowFullId(av.getShowJVSuffix());\r
 398         view.setShowIdentity(av.showIdentity);\r
 399         view.setShowQuality(av.showQuality);\r
 400         view.setShowSequenceFeatures(av.showSequenceFeatures);\r
 401         view.setShowText(av.getShowText());\r
 402         view.setWrapAlignment(av.getWrapAlignment());\r
 403 \r
 404         jms.addViewport(view);\r
 405 \r
 406         object.setJalviewModelSequence(jms);\r
 407         object.getVamsasModel().addSequenceSet(vamsasSet);\r
 408 \r
 409         try\r
 410         {\r
 411             if (!fileName.endsWith(".xml"))\r
 412             {\r
 413                 fileName = fileName + ".xml";\r
 414             }\r
 415 \r
 416             JarEntry entry = new JarEntry(fileName);\r
 417             jout.putNextEntry(entry);\r
 418 \r
 419             object.marshal(out);\r
 420         }\r
 421         catch (Exception ex)\r
 422         {\r
 423             ex.printStackTrace();\r
 424         }\r
 425     }\r
 426 \r
 427     static String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,\r
 428         Vector userColours, JalviewModelSequence jms)\r
 429     {\r
 430         String id = null;\r
 431         jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;\r
 432 \r
 433         if (!userColours.contains(ucs))\r
 434         {\r
 435             userColours.add(ucs);\r
 436 \r
 437             java.awt.Color[] colours = ucs.getColours();\r
 438             jalview.binding.UserColours uc = new jalview.binding.UserColours();\r
 439             jalview.binding.UserColourScheme jbucs = new jalview.binding.UserColourScheme();\r
 440 \r
 441             for (int i = 0; i < colours.length; i++)\r
 442             {\r
 443                 jalview.binding.Colour col = new jalview.binding.Colour();\r
 444                 col.setRGB(jalview.util.Format.getHexString(colours[i]));\r
 445                 jbucs.addColour(col);\r
 446             }\r
 447 \r
 448             id = "ucs" + userColours.indexOf(ucs);\r
 449             uc.setId(id);\r
 450             uc.setUserColourScheme(jbucs);\r
 451             jms.addUserColours(uc);\r
 452         }\r
 453 \r
 454         return id;\r
 455     }\r
 456 \r
 457     static jalview.schemes.UserColourScheme GetUserColourScheme(\r
 458         JalviewModelSequence jms, String id)\r
 459     {\r
 460         UserColours[] uc = jms.getUserColours();\r
 461         UserColours colours = null;\r
 462 \r
 463         for (int i = 0; i < uc.length; i++)\r
 464         {\r
 465             if (uc[i].getId().equals(id))\r
 466             {\r
 467                 colours = uc[i];\r
 468 \r
 469                 break;\r
 470             }\r
 471         }\r
 472 \r
 473         int csize = colours.getUserColourScheme().getColourCount();\r
 474         java.awt.Color[] newColours = new java.awt.Color[csize];\r
 475 \r
 476         for (int i = 0; i < csize; i++)\r
 477         {\r
 478             newColours[i] = new java.awt.Color(Integer.parseInt(\r
 479                         colours.getUserColourScheme().getColour(i).getRGB(), 16));\r
 480         }\r
 481 \r
 482         return new jalview.schemes.UserColourScheme(newColours);\r
 483     }\r
 484 \r
 485     /**\r
 486      * DOCUMENT ME!\r
 487      *\r
 488      * @param file DOCUMENT ME!\r
 489      */\r
 490     public static AlignFrame LoadJalviewAlign(String file)\r
 491     {\r
 492         JalviewModel object = new JalviewModel();\r
 493         jalview.gui.AlignFrame af = null;\r
 494 \r
 495         try\r
 496         {\r
 497             //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING\r
 498             URL url = null;\r
 499 \r
 500             if (file.startsWith("http://"))\r
 501             {\r
 502                 url = new URL(file);\r
 503             }\r
 504 \r
 505             JarInputStream jin = null;\r
 506             JarEntry jarentry = null;\r
 507             int entryCount = 1;\r
 508 \r
 509             do\r
 510             {\r
 511                 if (url != null)\r
 512                 {\r
 513                     jin = new JarInputStream(url.openStream());\r
 514                 }\r
 515                 else\r
 516                 {\r
 517                     jin = new JarInputStream(new FileInputStream(file));\r
 518                 }\r
 519 \r
 520                 for (int i = 0; i < entryCount; i++)\r
 521                 {\r
 522                     jarentry = jin.getNextJarEntry();\r
 523                 }\r
 524 \r
 525                 if (jarentry != null)\r
 526                 {\r
 527                     InputStreamReader in = new InputStreamReader(jin, "UTF-8");\r
 528                     object = (JalviewModel) object.unmarshal(in);\r
 529                     af = LoadFromObject(object);\r
 530                     entryCount++;\r
 531                 }\r
 532             }\r
 533             while (jarentry != null);\r
 534         }\r
 535         catch(java.net.UnknownHostException ex)\r
 536         {\r
 537           ex.printStackTrace();\r
 538           System.err.println("Couldn't locate Jalview XML file : " +\r
 539               ex + "\n");\r
 540            JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 541                                     "Couldn't locate " + file,\r
 542                                     "URL not found",\r
 543                                     JOptionPane.WARNING_MESSAGE);\r
 544 \r
 545         }\r
 546         catch (Exception ex)\r
 547         {\r
 548           ex.printStackTrace();\r
 549             System.err.println("Exception whilst loading jalview XML file : " +\r
 550                 ex + "\n");\r
 551              JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 552                                       "Error loading  " + file,\r
 553                                       "Error loading Jalview file",\r
 554                                       JOptionPane.WARNING_MESSAGE);\r
 555 \r
 556         }\r
 557 \r
 558         return af;\r
 559     }\r
 560 \r
 561     static AlignFrame LoadFromObject(JalviewModel object)\r
 562     {\r
 563         Vector seqids = new Vector();\r
 564         SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);\r
 565         Sequence[] vamsasSeq = vamsasSet.getSequence();\r
 566 \r
 567         JalviewModelSequence jms = object.getJalviewModelSequence();\r
 568 \r
 569         //////////////////////////////////\r
 570         //LOAD SEQUENCES\r
 571         jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];\r
 572         JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();\r
 573 \r
 574         for (int i = 0; i < vamsasSeq.length; i++)\r
 575         {\r
 576             jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),\r
 577                     vamsasSeq[i].getSequence());\r
 578 \r
 579             jseqs[i].setStart(JSEQ[i].getStart());\r
 580             jseqs[i].setEnd(JSEQ[i].getEnd());\r
 581             jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));\r
 582             seqids.add(jseqs[i]);\r
 583         }\r
 584 \r
 585         /////////////////////////////////\r
 586         jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);\r
 587 \r
 588         /////////////////////////////////\r
 589         //////////////////////////////////\r
 590         //LOAD ANNOTATIONS\r
 591         if (vamsasSet.getAnnotation() != null)\r
 592         {\r
 593             Annotation[] an = vamsasSet.getAnnotation();\r
 594 \r
 595             for (int i = 0; i < an.length; i++)\r
 596             {\r
 597                 AnnotationElement[] ae = an[i].getAnnotationElement();\r
 598                 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];\r
 599 \r
 600                 for (int aa = 0; aa < ae.length; aa++)\r
 601                 {\r
 602                     anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),\r
 603                             ae[aa].getDescription(),\r
 604                             ae[aa].getSecondaryStructure().charAt(0),\r
 605                             ae[aa].getValue());\r
 606                 }\r
 607 \r
 608                 jalview.datamodel.AlignmentAnnotation jaa = null;\r
 609 \r
 610                 if (an[i].getGraph())\r
 611                 {\r
 612                     jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
 613                             an[i].getDescription(), anot, 0, 0, 1);\r
 614                 }\r
 615                 else\r
 616                 {\r
 617                     jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
 618                             an[i].getDescription(), anot);\r
 619                 }\r
 620 \r
 621                 al.addAnnotation(jaa);\r
 622             }\r
 623         }\r
 624 \r
 625         /////////////////////////////////\r
 626         // LOAD VIEWPORT\r
 627         Viewport[] views = jms.getViewport();\r
 628         Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER\r
 629 \r
 630         AlignFrame af = new AlignFrame(al);\r
 631 \r
 632         //  af.changeColour() );\r
 633         /////////////////////////\r
 634         //LOAD GROUPS\r
 635         if (jms.getJGroupCount() > 0)\r
 636         {\r
 637             JGroup[] groups = jms.getJGroup();\r
 638 \r
 639             for (int i = 0; i < groups.length; i++)\r
 640             {\r
 641                 ColourSchemeI cs = null;\r
 642 \r
 643                 if (groups[i].getColour() != null)\r
 644                 {\r
 645                     if (groups[i].getColour().startsWith("ucs"))\r
 646                     {\r
 647                         cs = GetUserColourScheme(jms, groups[i].getColour());\r
 648                     }\r
 649                     else\r
 650                     {\r
 651                         cs = ColourSchemeProperty.getColour(al,\r
 652                                 groups[i].getColour());\r
 653                     }\r
 654 \r
 655                     cs.setThreshold(groups[i].getPidThreshold(), true);\r
 656                 }\r
 657 \r
 658                 Vector seqs = new Vector();\r
 659                 int[] ids = groups[i].getSeq();\r
 660 \r
 661                 for (int s = 0; s < ids.length; s++)\r
 662                 {\r
 663                     seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(\r
 664                             ids[s]));\r
 665                 }\r
 666 \r
 667                 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,\r
 668                         groups[i].getName(), cs, groups[i].getDisplayBoxes(),\r
 669                         groups[i].getDisplayText(), groups[i].getColourText(),\r
 670                         groups[i].getStart(), groups[i].getEnd());\r
 671 \r
 672                 sg.setOutlineColour(new java.awt.Color(\r
 673                         groups[i].getOutlineColour()));\r
 674 \r
 675                 if (groups[i].getConsThreshold() != 0)\r
 676                 {\r
 677                     jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",\r
 678                             ResidueProperties.propHash, 3, sg.sequences, 0,\r
 679                             sg.getWidth() - 1);\r
 680                     c.calculate();\r
 681                     c.verdict(false, 25);\r
 682                     sg.cs.setConservation(c);\r
 683                 }\r
 684 \r
 685                 al.addGroup(sg);\r
 686             }\r
 687         }\r
 688 \r
 689 \r
 690         af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),\r
 691             view.getHeight());\r
 692         af.viewport.setStartRes(view.getStartRes());\r
 693         af.viewport.setStartSeq(view.getStartSeq());\r
 694         af.viewport.showConservation = view.getShowConservation();\r
 695         af.viewport.showQuality = view.getShowQuality();\r
 696         af.viewport.showIdentity = view.getShowIdentity();\r
 697         af.viewport.setAbovePIDThreshold(view.getPidSelected());\r
 698         af.abovePIDThreshold.setSelected(view.getPidSelected());\r
 699         af.viewport.setColourText(view.getShowColourText());\r
 700         af.colourTextMenuItem.setSelected(view.getShowColourText());\r
 701         af.viewport.setConservationSelected(view.getConservationSelected());\r
 702         af.conservationMenuItem.setSelected(view.getConservationSelected());\r
 703 \r
 704         af.viewport.setShowJVSuffix(view.getShowFullId());\r
 705         af.seqLimits.setSelected(view.getShowFullId());\r
 706 \r
 707         af.viewport.setFont(new java.awt.Font(view.getFontName(),\r
 708                 view.getFontStyle(), view.getFontSize()));\r
 709         af.alignPanel.fontChanged();\r
 710 \r
 711         af.viewport.setRenderGaps(view.getRenderGaps());\r
 712         af.renderGapsMenuItem.setSelected(view.getRenderGaps());\r
 713 \r
 714         af.viewport.setWrapAlignment(view.getWrapAlignment());\r
 715         af.wrapMenuItem.setSelected(view.getWrapAlignment());\r
 716 \r
 717         if (view.getWrapAlignment())\r
 718         {\r
 719             af.alignPanel.setWrapAlignment(view.getWrapAlignment());\r
 720         }\r
 721         else\r
 722         {\r
 723             af.annotationPanelMenuItem.setState(view.getShowAnnotation());\r
 724             af.viewport.setShowAnnotation(view.getShowAnnotation());\r
 725             af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\r
 726         }\r
 727 \r
 728         af.viewport.setShowBoxes(view.getShowBoxes());\r
 729         af.viewBoxesMenuItem.setSelected(view.getShowBoxes());\r
 730         af.viewport.setShowText(view.getShowText());\r
 731         af.viewTextMenuItem.setSelected(view.getShowText());\r
 732 \r
 733         ColourSchemeI cs = null;\r
 734 \r
 735         if (view.getBgColour() != null)\r
 736         {\r
 737             if (view.getBgColour().startsWith("ucs"))\r
 738             {\r
 739                 cs = GetUserColourScheme(jms, view.getBgColour());\r
 740             }\r
 741             else\r
 742             {\r
 743                 cs = ColourSchemeProperty.getColour(al, view.getBgColour());\r
 744             }\r
 745 \r
 746             if(cs!=null)\r
 747             {\r
 748               cs.setThreshold(view.getPidThreshold(), true);\r
 749               cs.setConsensus(af.viewport.vconsensus);\r
 750             }\r
 751         }\r
 752 \r
 753         af.setColourSelected(view.getBgColour());\r
 754         af.viewport.setGlobalColourScheme(cs);\r
 755         af.viewport.setColourAppliesToAllGroups(false);\r
 756         af.changeColour(cs);\r
 757         if (view.getConservationSelected() && cs!=null)\r
 758         {\r
 759           cs.setConservationInc(view.getConsThreshold());\r
 760         }\r
 761 \r
 762         af.viewport.setColourAppliesToAllGroups(true);\r
 763 \r
 764         if (view.getShowSequenceFeatures())\r
 765         {\r
 766             af.viewport.showSequenceFeatures = true;\r
 767             af.sequenceFeatures.setSelected(true);\r
 768             new SequenceFeatureFetcher(al, af.alignPanel);\r
 769             al.featuresAdded = true;\r
 770         }\r
 771 \r
 772         Desktop.addInternalFrame(af, view.getTitle(),\r
 773              view.getWidth(), view.getHeight());\r
 774 \r
 775         //LOAD TREES\r
 776         ///////////////////////////////////////\r
 777         if (jms.getTreeCount() > 0)\r
 778         {\r
 779             try\r
 780             {\r
 781                 for (int t = 0; t < jms.getTreeCount(); t++)\r
 782                 {\r
 783 \r
 784                     Tree tree = jms.getTree(t);\r
 785 \r
 786                     TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(\r
 787                                 tree.getNewick()), tree.getTitle(),\r
 788                                 tree.getWidth(), tree.getHeight(),\r
 789                                 tree.getXpos(), tree.getYpos());\r
 790 \r
 791                     tp.fitToWindow.setState(tree.getFitToWindow());\r
 792                     tp.fitToWindow_actionPerformed(null);\r
 793 \r
 794                     if(tree.getFontName()!=null)\r
 795                       tp.setTreeFont(new java.awt.Font(tree.getFontName(),\r
 796                                           tree.getFontStyle(),\r
 797                                           tree.getFontSize()));\r
 798                     else\r
 799                       tp.setTreeFont(new java.awt.Font(view.getFontName(),\r
 800                                             view.getFontStyle(),\r
 801                                             tree.getFontSize()));\r
 802 \r
 803                     tp.showPlaceholders(tree.getMarkUnlinked());\r
 804                     tp.showBootstrap(tree.getShowBootstrap());\r
 805                     tp.showDistances(tree.getShowDistances());\r
 806 \r
 807                     tp.treeCanvas.threshold = tree.getThreshold();\r
 808 \r
 809                     if (tree.getCurrentTree())\r
 810                       af.viewport.setCurrentTree(tp.getTree());\r
 811                 }\r
 812 \r
 813             }\r
 814             catch (Exception ex)\r
 815             {\r
 816                 ex.printStackTrace();\r
 817             }\r
 818 \r
 819         }\r
 820 \r
 821         return af;\r
 822     }\r
 823 }\r