src/jalview/gui/Jalview2XML.java

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