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 \r
  22 import jalview.schemes.*;\r
  23 \r
  24 import jalview.gui.*;\r
  25 \r
  26 import java.io.*;\r
  27 \r
  28 import java.net.*;\r
  29 \r
  30 import java.util.*;\r
  31 \r
  32 import java.util.jar.*;\r
  33 \r
  34 import javax.swing.*;\r
  35 \r
  36 import org.exolab.castor.xml.*;\r
  37 \r
  38 import jalview.schemabinding.version2.*;\r
  39 \r
  40 \r
  41 \r
  42 \r
  43 /**\r
  44  * DOCUMENT ME!\r
  45  *\r
  46  * @author $author$\r
  47  * @version $Revision$\r
  48  */\r
  49 public class Jalview2XML\r
  50 {\r
  51     // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE\r
  52     public void SaveState(File statefile)\r
  53     {\r
  54         long creation = System.currentTimeMillis();\r
  55         JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
  56 \r
  57         if (frames == null)\r
  58         {\r
  59             return;\r
  60         }\r
  61 \r
  62         try\r
  63         {\r
  64             FileOutputStream fos = new FileOutputStream(statefile);\r
  65             JarOutputStream jout = new JarOutputStream(fos);\r
  66 \r
  67             //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS\r
  68             ////////////////////////////////////////////////////\r
  69             PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,\r
  70                         "UTF-8"));\r
  71 \r
  72             Vector shortNames = new Vector();\r
  73 \r
  74             //REVERSE ORDER\r
  75             for (int i = frames.length - 1; i > -1; i--)\r
  76             {\r
  77                 if (frames[i] instanceof AlignFrame)\r
  78                 {\r
  79                     AlignFrame af = (AlignFrame) frames[i];\r
  80 \r
  81                     String shortName = af.getTitle();\r
  82 \r
  83                     if (shortName.indexOf(File.separatorChar) > -1)\r
  84                     {\r
  85                         shortName = shortName.substring(shortName.lastIndexOf(\r
  86                                     File.separatorChar) + 1);\r
  87                     }\r
  88 \r
  89                     int count = 1;\r
  90 \r
  91                     while (shortNames.contains(shortName))\r
  92                     {\r
  93                         if (shortName.endsWith("_" + (count - 1)))\r
  94                         {\r
  95                             shortName = shortName.substring(0,\r
  96                                     shortName.lastIndexOf("_"));\r
  97                         }\r
  98 \r
  99                         shortName = shortName.concat("_" + count);\r
 100                         count++;\r
 101                     }\r
 102 \r
 103                     shortNames.addElement(shortName);\r
 104 \r
 105                     if (!shortName.endsWith(".xml"))\r
 106                     {\r
 107                         shortName = shortName + ".xml";\r
 108                     }\r
 109 \r
 110                     SaveState(af, creation, shortName, jout, out);\r
 111                 }\r
 112             }\r
 113 \r
 114             out.close();\r
 115             jout.close();\r
 116         }\r
 117         catch (Exception ex)\r
 118         {\r
 119             ex.printStackTrace();\r
 120         }\r
 121     }\r
 122 \r
 123     // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW\r
 124     public void SaveAlignment(AlignFrame af, String jarFile,\r
 125         String fileName)\r
 126     {\r
 127         try\r
 128         {\r
 129             FileOutputStream fos = new FileOutputStream(jarFile);\r
 130             JarOutputStream jout = new JarOutputStream(fos);\r
 131 \r
 132             //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS\r
 133             ////////////////////////////////////////////////////\r
 134             PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,\r
 135                         "UTF-8"));\r
 136 \r
 137             SaveState(af, System.currentTimeMillis(), fileName, jout, out);\r
 138             out.close();\r
 139             jout.close();\r
 140         }\r
 141         catch (Exception ex)\r
 142         {\r
 143           ex.printStackTrace();\r
 144         }\r
 145     }\r
 146 \r
 147     /**\r
 148      * DOCUMENT ME!\r
 149      *\r
 150      * @param af DOCUMENT ME!\r
 151      * @param timeStamp DOCUMENT ME!\r
 152      * @param fileName DOCUMENT ME!\r
 153      * @param jout DOCUMENT ME!\r
 154      * @param out DOCUMENT ME!\r
 155      */\r
 156     public void SaveState(AlignFrame af, long timeStamp,\r
 157         String fileName, JarOutputStream jout, PrintWriter out)\r
 158     {\r
 159         Vector seqids = new Vector();\r
 160         Vector userColours = new Vector();\r
 161 \r
 162         AlignViewport av = af.viewport;\r
 163 \r
 164         JalviewModel object = new JalviewModel();\r
 165         object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());\r
 166 \r
 167         object.setCreationDate(new java.util.Date(timeStamp));\r
 168         object.setVersion(jalview.bin.Cache.getProperty("VERSION"));\r
 169 \r
 170         jalview.datamodel.AlignmentI jal = af.viewport.alignment;\r
 171         jalview.datamodel.AlignmentI jalhidden = null;\r
 172 \r
 173         if(av.hasHiddenRows)\r
 174         {\r
 175           jalhidden = jal;\r
 176           jal = jal.getHiddenSequences().getFullAlignment();\r
 177         }\r
 178 \r
 179 \r
 180         SequenceSet vamsasSet = new SequenceSet();\r
 181         Sequence vamsasSeq;\r
 182         JalviewModelSequence jms = new JalviewModelSequence();\r
 183 \r
 184         vamsasSet.setGapChar(jal.getGapCharacter() + "");\r
 185 \r
 186         JSeq jseq;\r
 187 \r
 188         //SAVE SEQUENCES\r
 189         int id = 0;\r
 190         for (int i = 0; i < jal.getHeight(); i++)\r
 191         {\r
 192             seqids.add(jal.getSequenceAt(i));\r
 193             vamsasSeq = new Sequence();\r
 194             vamsasSeq.setId(id + "");\r
 195             vamsasSeq.setName(jal.getSequenceAt(i).getName());\r
 196             vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());\r
 197             vamsasSeq.setDescription(jal.getSequenceAt(i).getDescription());\r
 198 \r
 199             if(jal.getSequenceAt(i).getDatasetSequence().getDBRef()!=null)\r
 200             {\r
 201               jalview.datamodel.DBRefEntry [] dbrefs =\r
 202                   jal.getSequenceAt(i).getDatasetSequence().getDBRef();\r
 203 \r
 204               for(int d=0; d<dbrefs.length; d++)\r
 205               {\r
 206                 DBRef dbref = new DBRef();\r
 207                 dbref.setSource( dbrefs[d].getSource() );\r
 208                 dbref.setVersion( dbrefs[d].getVersion());\r
 209                 dbref.setAccessionId(dbrefs[d].getAccessionId());\r
 210                 vamsasSeq.addDBRef(dbref);\r
 211               }\r
 212             }\r
 213 \r
 214             jseq = new JSeq();\r
 215             jseq.setStart(jal.getSequenceAt(i).getStart());\r
 216             jseq.setEnd(jal.getSequenceAt(i).getEnd());\r
 217             jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());\r
 218 \r
 219             jseq.setId(id);\r
 220 \r
 221             if (av.hasHiddenRows)\r
 222             {\r
 223               jseq.setHidden(jalhidden.getHiddenSequences().isHidden(\r
 224                   jal.getSequenceAt(i)));\r
 225 \r
 226               if(jal.getSequenceAt(i).getHiddenSequences()!=null)\r
 227               {\r
 228                 jalview.datamodel.SequenceI [] reps =\r
 229                     jal.getSequenceAt(i).getHiddenSequences().getSequencesInOrder(jal);\r
 230 \r
 231                 for(int h=0; h<reps.length; h++)\r
 232                 {\r
 233                   jseq.addHiddenSequences(\r
 234                       jal.findIndex(reps[h])\r
 235                       );\r
 236                 }\r
 237               }\r
 238             }\r
 239 \r
 240 \r
 241             if(jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures()!=null)\r
 242             {\r
 243               jalview.datamodel.SequenceFeature[] sf\r
 244                   = jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
 245               int index = 0;\r
 246               while(index < sf.length)\r
 247               {\r
 248                 Features features = new Features();\r
 249 \r
 250                 features.setBegin(sf[index].getBegin());\r
 251                 features.setEnd(sf[index].getEnd());\r
 252                 features.setDescription(sf[index].getDescription());\r
 253                 features.setType(sf[index].getType());\r
 254                 features.setFeatureGroup(sf[index].getFeatureGroup());\r
 255                 jseq.addFeatures(features);\r
 256                 index ++;\r
 257               }\r
 258             }\r
 259 \r
 260             if(jal.getSequenceAt(i).getDatasetSequence().getPDBId()!=null)\r
 261             {\r
 262               Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getPDBId().elements();\r
 263               while(en.hasMoreElements())\r
 264               {\r
 265                 Pdbids pdb = new Pdbids();\r
 266                 jalview.datamodel.PDBEntry entry\r
 267                    = (jalview.datamodel.PDBEntry)en.nextElement();\r
 268 \r
 269                 pdb.setId(entry.getId());\r
 270                 pdb.setType(entry.getType());\r
 271 \r
 272                 if(entry.getProperty()!=null)\r
 273                 {\r
 274                   PdbentryItem item = new PdbentryItem();\r
 275                   Hashtable properties = entry.getProperty();\r
 276                   Enumeration en2 = properties.keys();\r
 277                   while(en2.hasMoreElements())\r
 278                   {\r
 279                     Property prop = new Property();\r
 280                     String key = en2.nextElement().toString();\r
 281                     prop.setName(key);\r
 282                     prop.setValue( properties.get(key).toString() );\r
 283                     item.addProperty(prop);\r
 284                   }\r
 285                   pdb.addPdbentryItem(item);\r
 286                 }\r
 287 \r
 288                 jseq.addPdbids(pdb);\r
 289               }\r
 290             }\r
 291 \r
 292             jms.addJSeq(jseq);\r
 293             vamsasSet.addSequence(vamsasSeq);\r
 294             id++;\r
 295         }\r
 296 \r
 297         //SAVE TREES\r
 298         ///////////////////////////////////\r
 299         if (af.viewport.currentTree != null)\r
 300         {\r
 301           // FIND ANY ASSOCIATED TREES\r
 302           // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT\r
 303           if (Desktop.desktop != null)\r
 304           {\r
 305             JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
 306 \r
 307             for (int t = 0; t < frames.length; t++)\r
 308             {\r
 309               if (frames[t] instanceof TreePanel)\r
 310               {\r
 311                 TreePanel tp = (TreePanel) frames[t];\r
 312 \r
 313                 if (tp.treeCanvas.av.alignment == jal)\r
 314                 {\r
 315                   Tree tree = new Tree();\r
 316                   tree.setTitle(tp.getTitle());\r
 317                   tree.setCurrentTree( (af.viewport.currentTree == tp.getTree()));\r
 318                   tree.setNewick(tp.getTree().toString());\r
 319                   tree.setThreshold(tp.treeCanvas.threshold);\r
 320 \r
 321                   tree.setFitToWindow(tp.fitToWindow.getState());\r
 322                   tree.setFontName(tp.getTreeFont().getName());\r
 323                   tree.setFontSize(tp.getTreeFont().getSize());\r
 324                   tree.setFontStyle(tp.getTreeFont().getStyle());\r
 325                   tree.setMarkUnlinked(tp.placeholdersMenu.getState());\r
 326 \r
 327                   tree.setShowBootstrap(tp.bootstrapMenu.getState());\r
 328                   tree.setShowDistances(tp.distanceMenu.getState());\r
 329 \r
 330                   tree.setHeight(tp.getHeight());\r
 331                   tree.setWidth(tp.getWidth());\r
 332                   tree.setXpos(tp.getX());\r
 333                   tree.setYpos(tp.getY());\r
 334 \r
 335                   jms.addTree(tree);\r
 336                 }\r
 337               }\r
 338             }\r
 339           }\r
 340         }\r
 341 \r
 342         //SAVE ANNOTATIONS\r
 343         if (jal.getAlignmentAnnotation() != null)\r
 344         {\r
 345             jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();\r
 346 \r
 347             for (int i = 0; i < aa.length; i++)\r
 348             {\r
 349                 Annotation an = new Annotation();\r
 350 \r
 351                 if (aa[i].label.equals("Quality") ||\r
 352                         aa[i].label.equals("Conservation") ||\r
 353                         aa[i].label.equals("Consensus"))\r
 354                 {\r
 355                     an.setLabel(aa[i].label);\r
 356                     an.setGraph(true);\r
 357                     vamsasSet.addAnnotation(an);\r
 358                     continue;\r
 359                 }\r
 360 \r
 361 \r
 362                 an.setDescription(aa[i].description);\r
 363 \r
 364                 if(aa[i].sequenceRef!=null)\r
 365                  {\r
 366                    an.setSequenceRef(aa[i].sequenceRef.getName());\r
 367                  }\r
 368 \r
 369                 if(aa[i].graph>0)\r
 370                 {\r
 371                   an.setGraph(true);\r
 372                   an.setGraphType(aa[i].graph);\r
 373                   an.setGraphGroup(aa[i].graphGroup);\r
 374                   if(aa[i].getThreshold()!=null)\r
 375                   {\r
 376                     ThresholdLine line = new ThresholdLine();\r
 377                     line.setLabel(aa[i].getThreshold().label);\r
 378                     line.setValue(aa[i].getThreshold().value);\r
 379                     line.setColour(aa[i].getThreshold().colour.getRGB());\r
 380                     an.setThresholdLine(line);\r
 381                   }\r
 382                 }\r
 383                 else\r
 384                   an.setGraph(false);\r
 385 \r
 386                 an.setLabel(aa[i].label);\r
 387 \r
 388                 AnnotationElement ae;\r
 389 \r
 390                 for (int a = 0; a < aa[i].annotations.length; a++)\r
 391                 {\r
 392                     if ((aa[i] == null) || (aa[i].annotations[a] == null))\r
 393                     {\r
 394                         continue;\r
 395                     }\r
 396 \r
 397                     ae = new AnnotationElement();\r
 398                     ae.setDescription(aa[i].annotations[a].description);\r
 399                     ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);\r
 400                     ae.setValue(aa[i].annotations[a].value);\r
 401                     ae.setPosition(a);\r
 402                     ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +\r
 403                         "");\r
 404 \r
 405                     if(aa[i].annotations[a].colour!=java.awt.Color.black)\r
 406                       ae.setColour(aa[i].annotations[a].colour.getRGB());\r
 407 \r
 408                     an.addAnnotationElement(ae);\r
 409                 }\r
 410 \r
 411                 vamsasSet.addAnnotation(an);\r
 412             }\r
 413         }\r
 414 \r
 415         //SAVE GROUPS\r
 416         if (jal.getGroups() != null)\r
 417         {\r
 418             JGroup[] groups = new JGroup[jal.getGroups().size()];\r
 419 \r
 420             for (int i = 0; i < groups.length; i++)\r
 421             {\r
 422                 groups[i] = new JGroup();\r
 423 \r
 424                 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()\r
 425                                                                                           .elementAt(i);\r
 426                 groups[i].setStart(sg.getStartRes());\r
 427                 groups[i].setEnd(sg.getEndRes());\r
 428                 groups[i].setName(sg.getName());\r
 429                 if(sg.cs!=null)\r
 430                 {\r
 431                   if (sg.cs.conservationApplied())\r
 432                   {\r
 433                     groups[i].setConsThreshold(sg.cs.getConservationInc());\r
 434 \r
 435                     if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
 436                     {\r
 437                       groups[i].setColour(SetUserColourScheme(sg.cs,\r
 438                           userColours,\r
 439                           jms));\r
 440                     }\r
 441                     else\r
 442                     {\r
 443                       groups[i].setColour(ColourSchemeProperty.getColourName(sg.\r
 444                           cs));\r
 445                     }\r
 446                   }\r
 447                   else if(sg.cs instanceof jalview.schemes.AnnotationColourGradient)\r
 448                   {\r
 449                     groups[i].setColour(\r
 450                         ColourSchemeProperty.getColourName(\r
 451                       ( (jalview.schemes.AnnotationColourGradient) sg.cs).getBaseColour()));\r
 452                   }\r
 453                   else if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
 454                   {\r
 455                     groups[i].setColour(SetUserColourScheme(sg.cs, userColours,\r
 456                         jms));\r
 457                   }\r
 458                   else\r
 459                   {\r
 460                     groups[i].setColour(ColourSchemeProperty.getColourName(\r
 461                         sg.cs));\r
 462                   }\r
 463 \r
 464                   groups[i].setPidThreshold(sg.cs.getThreshold());\r
 465                 }\r
 466 \r
 467                 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());\r
 468                 groups[i].setDisplayBoxes(sg.getDisplayBoxes());\r
 469                 groups[i].setDisplayText(sg.getDisplayText());\r
 470                 groups[i].setColourText(sg.getColourText());\r
 471 \r
 472                 for (int s = 0; s < sg.getSize(false); s++)\r
 473                 {\r
 474                     jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.getSequenceAt(s);\r
 475                     int index = seqids.indexOf(seq);\r
 476                     groups[i].addSeq(index);\r
 477                 }\r
 478             }\r
 479 \r
 480             jms.setJGroup(groups);\r
 481         }\r
 482 \r
 483 \r
 484         ///////////SAVE VIEWPORT\r
 485         Viewport view = new Viewport();\r
 486         view.setTitle(af.getTitle());\r
 487         view.setXpos(af.getX());\r
 488         view.setYpos(af.getY());\r
 489         view.setWidth(af.getWidth());\r
 490         view.setHeight(af.getHeight());\r
 491         view.setStartRes(av.startRes);\r
 492         view.setStartSeq(av.startSeq);\r
 493 \r
 494         if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)\r
 495         {\r
 496             view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),\r
 497                     userColours, jms));\r
 498         }\r
 499         else if(av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)\r
 500         {\r
 501            jalview.schemes.AnnotationColourGradient acg\r
 502               = (jalview.schemes.AnnotationColourGradient)av.getGlobalColourScheme();\r
 503 \r
 504             AnnotationColours ac = new AnnotationColours();\r
 505             ac.setAboveThreshold(acg.getAboveThreshold());\r
 506             ac.setThreshold(acg.getAnnotationThreshold());\r
 507             ac.setAnnotation(acg.getAnnotation());\r
 508             if(acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)\r
 509               ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),\r
 510                     userColours, jms));\r
 511             else\r
 512               ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));\r
 513 \r
 514             ac.setMaxColour(acg.getMaxColour().getRGB());\r
 515             ac.setMinColour(acg.getMinColour().getRGB());\r
 516             view.setAnnotationColours(ac);\r
 517             view.setBgColour("AnnotationColourGradient");\r
 518         }\r
 519         else\r
 520         {\r
 521             view.setBgColour(ColourSchemeProperty.getColourName(\r
 522                     av.getGlobalColourScheme()));\r
 523         }\r
 524 \r
 525         ColourSchemeI cs = av.getGlobalColourScheme();\r
 526 \r
 527         if(cs!=null)\r
 528         {\r
 529           if (cs.conservationApplied())\r
 530           {\r
 531             view.setConsThreshold(cs.getConservationInc());\r
 532             if (cs instanceof jalview.schemes.UserColourScheme)\r
 533               view.setBgColour(SetUserColourScheme(cs, userColours, jms));\r
 534           }\r
 535 \r
 536           if (cs instanceof ResidueColourScheme)\r
 537           {\r
 538             view.setPidThreshold(cs.getThreshold());\r
 539           }\r
 540         }\r
 541 \r
 542         view.setConservationSelected(av.getConservationSelected());\r
 543         view.setPidSelected(av.getAbovePIDThreshold());\r
 544         view.setFontName(av.font.getName());\r
 545         view.setFontSize(av.font.getSize());\r
 546         view.setFontStyle(av.font.getStyle());\r
 547         view.setRenderGaps(av.renderGaps);\r
 548         view.setShowAnnotation(av.getShowAnnotation());\r
 549         view.setShowBoxes(av.getShowBoxes());\r
 550         view.setShowColourText(av.getColourText());\r
 551         view.setShowConservation(av.showConservation);\r
 552         view.setShowFullId(av.getShowJVSuffix());\r
 553         view.setShowIdentity(av.showIdentity);\r
 554         view.setShowQuality(av.showQuality);\r
 555         view.setShowSequenceFeatures(av.showSequenceFeatures);\r
 556         view.setShowText(av.getShowText());\r
 557         view.setWrapAlignment(av.getWrapAlignment());\r
 558 \r
 559         if(av.featuresDisplayed!=null)\r
 560         {\r
 561           jalview.schemabinding.version2.FeatureSettings fs\r
 562               = new jalview.schemabinding.version2.FeatureSettings();\r
 563 \r
 564           String [] renderOrder =\r
 565               af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;\r
 566           for(int ro=0; ro<renderOrder.length; ro++)\r
 567           {\r
 568             Setting setting = new Setting();\r
 569             setting.setType(renderOrder[ro]);\r
 570             setting.setColour(\r
 571                 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).getRGB()\r
 572                 );\r
 573 \r
 574             setting.setDisplay(\r
 575                 av.featuresDisplayed.containsKey(renderOrder[ro])\r
 576                 );\r
 577 \r
 578             fs.addSetting(setting);\r
 579 \r
 580           }\r
 581           jms.setFeatureSettings(fs);\r
 582 \r
 583         }\r
 584 \r
 585         if(av.hasHiddenColumns)\r
 586         {\r
 587           for(int c=0; c<av.getColumnSelection().getHiddenColumns().size(); c++)\r
 588           {\r
 589             int [] region = (int[]) av.getColumnSelection().getHiddenColumns().elementAt(c);\r
 590             HiddenColumns hc = new HiddenColumns();\r
 591             hc.setStart(region[0]);\r
 592             hc.setEnd(region[1]);\r
 593             view.addHiddenColumns(hc);\r
 594           }\r
 595         }\r
 596 \r
 597         if(av.hasHiddenRows)\r
 598         {\r
 599         //  av.alignment.getHiddenSequences().get\r
 600       //    HiddenSequences hs = new HiddenSequences();\r
 601       //    hs.ad\r
 602       //    view.addHiddenSequences();\r
 603       //    av.showAllHiddenSeqs();.alignment.getHiddenSequences().\r
 604         }\r
 605 \r
 606         jms.addViewport(view);\r
 607 \r
 608 \r
 609         object.setJalviewModelSequence(jms);\r
 610         object.getVamsasModel().addSequenceSet(vamsasSet);\r
 611 \r
 612         try\r
 613         {\r
 614             if (!fileName.endsWith(".xml"))\r
 615             {\r
 616                 fileName = fileName + ".xml";\r
 617             }\r
 618 \r
 619             JarEntry entry = new JarEntry(fileName);\r
 620             jout.putNextEntry(entry);\r
 621 \r
 622             object.marshal(out);\r
 623         }\r
 624         catch (Exception ex)\r
 625         {\r
 626             ex.printStackTrace();\r
 627         }\r
 628     }\r
 629 \r
 630     String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,\r
 631         Vector userColours, JalviewModelSequence jms)\r
 632     {\r
 633         String id = null;\r
 634         jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;\r
 635 \r
 636         if (!userColours.contains(ucs))\r
 637         {\r
 638             userColours.add(ucs);\r
 639 \r
 640             java.awt.Color[] colours = ucs.getColours();\r
 641             jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();\r
 642             jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();\r
 643 \r
 644             for (int i = 0; i < colours.length; i++)\r
 645             {\r
 646                 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();\r
 647                 col.setRGB(jalview.util.Format.getHexString(colours[i]));\r
 648                 jbucs.addColour(col);\r
 649             }\r
 650 \r
 651             id = "ucs" + userColours.indexOf(ucs);\r
 652             uc.setId(id);\r
 653             uc.setUserColourScheme(jbucs);\r
 654             jms.addUserColours(uc);\r
 655         }\r
 656 \r
 657         return id;\r
 658     }\r
 659 \r
 660    jalview.schemes.UserColourScheme GetUserColourScheme(\r
 661         JalviewModelSequence jms, String id)\r
 662     {\r
 663         UserColours[] uc = jms.getUserColours();\r
 664         UserColours colours = null;\r
 665 \r
 666         for (int i = 0; i < uc.length; i++)\r
 667         {\r
 668             if (uc[i].getId().equals(id))\r
 669             {\r
 670                 colours = uc[i];\r
 671 \r
 672                 break;\r
 673             }\r
 674         }\r
 675 \r
 676         int csize = colours.getUserColourScheme().getColourCount();\r
 677         java.awt.Color[] newColours = new java.awt.Color[csize];\r
 678 \r
 679         for (int i = 0; i < csize; i++)\r
 680         {\r
 681             newColours[i] = new java.awt.Color(Integer.parseInt(\r
 682                         colours.getUserColourScheme().getColour(i).getRGB(), 16));\r
 683         }\r
 684 \r
 685         return new jalview.schemes.UserColourScheme(newColours);\r
 686     }\r
 687 \r
 688     /**\r
 689      * DOCUMENT ME!\r
 690      *\r
 691      * @param file DOCUMENT ME!\r
 692      */\r
 693     public AlignFrame LoadJalviewAlign(String file)\r
 694     {\r
 695 \r
 696         jalview.gui.AlignFrame af = null;\r
 697 \r
 698         try\r
 699         {\r
 700             //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING\r
 701             URL url = null;\r
 702 \r
 703             if (file.startsWith("http://"))\r
 704             {\r
 705                 url = new URL(file);\r
 706             }\r
 707 \r
 708             JarInputStream jin = null;\r
 709             JarEntry jarentry = null;\r
 710             int entryCount = 1;\r
 711 \r
 712             do\r
 713             {\r
 714                 if (url != null)\r
 715                 {\r
 716                     jin = new JarInputStream(url.openStream());\r
 717                 }\r
 718                 else\r
 719                 {\r
 720                     jin = new JarInputStream(new FileInputStream(file));\r
 721                 }\r
 722 \r
 723                 for (int i = 0; i < entryCount; i++)\r
 724                 {\r
 725                     jarentry = jin.getNextJarEntry();\r
 726 \r
 727                   }\r
 728 \r
 729 \r
 730                   class NoDescIDResolver implements IDResolver\r
 731                   {\r
 732                     public Object resolve(String idref)\r
 733                     {\r
 734                       System.out.println(idref+" used");\r
 735                       return null;\r
 736                     }\r
 737                   }\r
 738 \r
 739 \r
 740                 if (jarentry != null)\r
 741                 {\r
 742                     InputStreamReader in = new InputStreamReader(jin, "UTF-8");\r
 743                     JalviewModel object = new JalviewModel();\r
 744 \r
 745                     Unmarshaller unmar = new Unmarshaller(object);\r
 746                     unmar.setValidation(false);\r
 747                     object = (JalviewModel) unmar.unmarshal( in );\r
 748 \r
 749                     af = LoadFromObject(object);\r
 750                     entryCount++;\r
 751                 }\r
 752             }\r
 753             while (jarentry != null);\r
 754         }\r
 755         catch(java.net.UnknownHostException ex)\r
 756         {\r
 757           ex.printStackTrace();\r
 758           System.err.println("Couldn't locate Jalview XML file : " +\r
 759               ex + "\n");\r
 760            JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 761                                     "Couldn't locate " + file,\r
 762                                     "URL not found",\r
 763                                     JOptionPane.WARNING_MESSAGE);\r
 764 \r
 765         }\r
 766         catch (Exception ex)\r
 767         {\r
 768           //Is Version 1 Jar file?\r
 769           af =  new Jalview2XML_V1().LoadJalviewAlign(file);\r
 770 \r
 771           if(af!=null)\r
 772           {\r
 773             System.out.println("Successfully loaded archive file");\r
 774             return af;\r
 775           }\r
 776           ex.printStackTrace();\r
 777             System.err.println("Exception whilst loading jalview XML file : " +\r
 778                 ex + "\n");\r
 779              JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 780                                       "Error loading  " + file,\r
 781                                       "Error loading Jalview file",\r
 782                                       JOptionPane.WARNING_MESSAGE);\r
 783 \r
 784         }\r
 785 \r
 786         return af;\r
 787     }\r
 788 \r
 789     AlignFrame LoadFromObject(JalviewModel object)\r
 790     {\r
 791         Vector seqids = new Vector();\r
 792         SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);\r
 793         Sequence[] vamsasSeq = vamsasSet.getSequence();\r
 794 \r
 795         JalviewModelSequence jms = object.getJalviewModelSequence();\r
 796 \r
 797         //////////////////////////////////\r
 798         //LOAD SEQUENCES\r
 799         Vector hiddenSeqs = null;\r
 800         jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];\r
 801         JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();\r
 802         for (int i = 0; i < vamsasSeq.length; i++)\r
 803         {\r
 804             jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),\r
 805                     vamsasSeq[i].getSequence());\r
 806             jseqs[i].setDescription( vamsasSeq[i].getDescription() );\r
 807 \r
 808             if(JSEQ[i].getHidden())\r
 809             {\r
 810               if(hiddenSeqs == null)\r
 811                 hiddenSeqs = new Vector();\r
 812               hiddenSeqs.addElement(jseqs[i]);\r
 813             }\r
 814             jseqs[i].setStart(JSEQ[i].getStart());\r
 815             jseqs[i].setEnd(JSEQ[i].getEnd());\r
 816             jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));\r
 817             seqids.add(jseqs[i]);\r
 818         }\r
 819 \r
 820         ///SequenceFeatures are added to the DatasetSequence,\r
 821         // so we must create the dataset before loading features\r
 822         /////////////////////////////////\r
 823         jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);\r
 824         al.setDataset(null);\r
 825         /////////////////////////////////\r
 826 \r
 827 \r
 828         for (int i = 0; i < vamsasSeq.length; i++)\r
 829         {\r
 830           if (JSEQ[i].getFeaturesCount() > 0)\r
 831           {\r
 832             Features[] features = JSEQ[i].getFeatures();\r
 833             for (int f = 0; f < features.length; f++)\r
 834             {\r
 835               jalview.datamodel.SequenceFeature sf\r
 836                   = new jalview.datamodel.SequenceFeature(features[f].getType(),\r
 837                   features[f].getDescription(), features[f].getStatus(),\r
 838                   features[f].getBegin(), features[f].getEnd(),\r
 839                   features[f].getFeatureGroup());\r
 840 \r
 841               al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);\r
 842             }\r
 843           }\r
 844           if (JSEQ[i].getPdbidsCount() > 0)\r
 845           {\r
 846             Pdbids[] ids = JSEQ[i].getPdbids();\r
 847             for (int p = 0; p < ids.length; p++)\r
 848             {\r
 849               jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();\r
 850               entry.setId(ids[p].getId());\r
 851               entry.setType(ids[p].getType());\r
 852               al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);\r
 853             }\r
 854 \r
 855           }\r
 856           if(vamsasSeq[i].getDBRefCount()>0)\r
 857           {\r
 858             for(int d=0; d<vamsasSeq[i].getDBRefCount(); d++)\r
 859             {\r
 860               jalview.datamodel.DBRefEntry entry =\r
 861                   new jalview.datamodel.DBRefEntry(\r
 862                       vamsasSeq[i].getDBRef(d).getSource(),\r
 863                       vamsasSeq[i].getDBRef(d).getVersion(),\r
 864                       vamsasSeq[i].getDBRef(d).getAccessionId()\r
 865                       );\r
 866               al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);\r
 867             }\r
 868 \r
 869           }\r
 870         }\r
 871 \r
 872 \r
 873 \r
 874          /////////////////////////////////\r
 875         //////////////////////////////////\r
 876         //LOAD ANNOTATIONS\r
 877         boolean hideQuality = true,\r
 878             hideConservation = true,\r
 879             hideConsensus = true;\r
 880 \r
 881         if (vamsasSet.getAnnotation() != null)\r
 882         {\r
 883             Annotation[] an = vamsasSet.getAnnotation();\r
 884 \r
 885             for (int i = 0; i < an.length; i++)\r
 886             {\r
 887                if (an[i].getLabel().equals("Quality"))\r
 888                 {\r
 889                  hideQuality = false;\r
 890                  continue;\r
 891                 }\r
 892                else if(an[i].getLabel().equals("Conservation"))\r
 893                {\r
 894                  hideConservation = false;\r
 895                  continue;\r
 896                }\r
 897                else if(an[i].getLabel().equals("Consensus"))\r
 898                {\r
 899                  hideConsensus = false;\r
 900                  continue;\r
 901                }\r
 902 \r
 903                 AnnotationElement[] ae = an[i].getAnnotationElement();\r
 904                 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];\r
 905 \r
 906                 for (int aa = 0; aa < ae.length; aa++)\r
 907                 {\r
 908                     anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),\r
 909                             ae[aa].getDescription(),\r
 910                             ae[aa].getSecondaryStructure().length()==0?' ':ae[aa].getSecondaryStructure().charAt(0),\r
 911                             ae[aa].getValue());\r
 912                     anot[ae[aa].getPosition()].colour = new java.awt.Color( ae[aa].getColour() );\r
 913                 }\r
 914 \r
 915                 jalview.datamodel.AlignmentAnnotation jaa = null;\r
 916 \r
 917                 if (an[i].getGraph())\r
 918                 {\r
 919                   jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
 920                       an[i].getDescription(), anot, 0, 0,\r
 921                       an[i].getGraphType());\r
 922 \r
 923                   jaa.graphGroup = an[i].getGraphGroup();\r
 924 \r
 925                   if (an[i].getThresholdLine() != null)\r
 926                   {\r
 927                     jaa.setThreshold(new jalview.datamodel.GraphLine(\r
 928                                   an[i].getThresholdLine().getValue(),\r
 929                                   an[i].getThresholdLine().getLabel(),\r
 930                                 new java.awt.Color(an[i].getThresholdLine().getColour()))\r
 931                              );\r
 932 \r
 933                   }\r
 934 \r
 935                 }\r
 936                 else\r
 937                 {\r
 938                     jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
 939                             an[i].getDescription(), anot);\r
 940                 }\r
 941 \r
 942                 if(an[i].getSequenceRef()!=null)\r
 943                 {\r
 944                   jaa.createSequenceMapping(\r
 945                       al.findName(an[i].getSequenceRef()), 1\r
 946                       );\r
 947                   al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);\r
 948                 }\r
 949 \r
 950                 al.addAnnotation(jaa);\r
 951             }\r
 952         }\r
 953 \r
 954 \r
 955         //  af.changeColour() );\r
 956         /////////////////////////\r
 957         //LOAD GROUPS\r
 958         if (jms.getJGroupCount() > 0)\r
 959         {\r
 960             JGroup[] groups = jms.getJGroup();\r
 961 \r
 962             for (int i = 0; i < groups.length; i++)\r
 963             {\r
 964                 ColourSchemeI cs = null;\r
 965 \r
 966                 if (groups[i].getColour() != null)\r
 967                 {\r
 968                     if (groups[i].getColour().startsWith("ucs"))\r
 969                     {\r
 970                         cs = GetUserColourScheme(jms, groups[i].getColour());\r
 971                     }\r
 972                     else\r
 973                     {\r
 974                         cs = ColourSchemeProperty.getColour(al,\r
 975                                 groups[i].getColour());\r
 976                     }\r
 977 \r
 978                     if(cs!=null)\r
 979                       cs.setThreshold(groups[i].getPidThreshold(), true);\r
 980                 }\r
 981 \r
 982                 Vector seqs = new Vector();\r
 983                 int[] ids = groups[i].getSeq();\r
 984 \r
 985                 for (int s = 0; s < ids.length; s++)\r
 986                 {\r
 987                     seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(\r
 988                             ids[s]));\r
 989                 }\r
 990 \r
 991                 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,\r
 992                         groups[i].getName(), cs, groups[i].getDisplayBoxes(),\r
 993                         groups[i].getDisplayText(), groups[i].getColourText(),\r
 994                         groups[i].getStart(), groups[i].getEnd());\r
 995 \r
 996                 sg.setOutlineColour(new java.awt.Color(\r
 997                         groups[i].getOutlineColour()));\r
 998 \r
 999                 if (groups[i].getConsThreshold() != 0)\r
1000                 {\r
1001                     jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",\r
1002                             ResidueProperties.propHash, 3, sg.getSequences(false), 0,\r
1003                             sg.getWidth() - 1);\r
1004                     c.calculate();\r
1005                     c.verdict(false, 25);\r
1006                     sg.cs.setConservation(c);\r
1007                 }\r
1008 \r
1009                 al.addGroup(sg);\r
1010             }\r
1011         }\r
1012 \r
1013 \r
1014         /////////////////////////////////\r
1015         // LOAD VIEWPORT\r
1016         Viewport[] views = jms.getViewport();\r
1017         Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER\r
1018 \r
1019 \r
1020         AlignFrame af = new AlignFrame(al);\r
1021 \r
1022         if(hiddenSeqs!=null)\r
1023         {\r
1024           for(int s=0; s<JSEQ.length; s++)\r
1025           {\r
1026             for(int r=0; r<JSEQ[s].getHiddenSequencesCount(); r++)\r
1027             {\r
1028               al.getSequenceAt(s).addHiddenSequence(\r
1029                   al.getSequenceAt( JSEQ[s].getHiddenSequences(r)  )\r
1030                   );\r
1031             }\r
1032           }\r
1033 \r
1034           for(int s=0; s<hiddenSeqs.size(); s++)\r
1035           {\r
1036               af.viewport.hideSequence(\r
1037                 (jalview.datamodel.SequenceI)hiddenSeqs.elementAt(s));\r
1038           }\r
1039         }\r
1040 \r
1041 \r
1042         if(hideConsensus || hideQuality || hideConservation)\r
1043         {\r
1044           int hSize = al.getAlignmentAnnotation().length;\r
1045           for (int h = 0; h < hSize; h++)\r
1046           {\r
1047             if (\r
1048                 (hideConsensus &&\r
1049                  al.getAlignmentAnnotation()[h].label.equals("Consensus"))\r
1050                 ||\r
1051                 (hideQuality &&\r
1052                  al.getAlignmentAnnotation()[h].label.equals("Quality"))\r
1053                 ||\r
1054                 (hideConservation &&\r
1055                  al.getAlignmentAnnotation()[h].label.equals("Conservation")))\r
1056             {\r
1057               al.deleteAnnotation(al.getAlignmentAnnotation()[h]);\r
1058               hSize--;\r
1059               h--;\r
1060             }\r
1061           }\r
1062           af.alignPanel.adjustAnnotationHeight();\r
1063         }\r
1064 \r
1065         af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),\r
1066             view.getHeight());\r
1067         af.viewport.setStartRes(view.getStartRes());\r
1068         af.viewport.setStartSeq(view.getStartSeq());\r
1069         af.viewport.setShowAnnotation(view.getShowAnnotation());\r
1070         af.viewport.showConservation = view.getShowConservation();\r
1071         af.viewport.showQuality = view.getShowQuality();\r
1072         af.viewport.showIdentity = view.getShowIdentity();\r
1073         af.viewport.setAbovePIDThreshold(view.getPidSelected());\r
1074         af.abovePIDThreshold.setSelected(view.getPidSelected());\r
1075         af.viewport.setColourText(view.getShowColourText());\r
1076         af.colourTextMenuItem.setSelected(view.getShowColourText());\r
1077         af.viewport.setConservationSelected(view.getConservationSelected());\r
1078         af.conservationMenuItem.setSelected(view.getConservationSelected());\r
1079 \r
1080         af.viewport.setShowJVSuffix(view.getShowFullId());\r
1081         af.seqLimits.setSelected(view.getShowFullId());\r
1082 \r
1083         af.viewport.setFont(new java.awt.Font(view.getFontName(),\r
1084                 view.getFontStyle(), view.getFontSize()));\r
1085         af.alignPanel.fontChanged();\r
1086 \r
1087         af.viewport.setRenderGaps(view.getRenderGaps());\r
1088         af.renderGapsMenuItem.setSelected(view.getRenderGaps());\r
1089 \r
1090         af.viewport.setWrapAlignment(view.getWrapAlignment());\r
1091         af.wrapMenuItem.setSelected(view.getWrapAlignment());\r
1092 \r
1093         if (view.getWrapAlignment())\r
1094         {\r
1095             af.alignPanel.setWrapAlignment(view.getWrapAlignment());\r
1096         }\r
1097         else\r
1098         {\r
1099             af.annotationPanelMenuItem.setState(view.getShowAnnotation());\r
1100             af.viewport.setShowAnnotation(view.getShowAnnotation());\r
1101             af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\r
1102         }\r
1103 \r
1104         af.viewport.setShowBoxes(view.getShowBoxes());\r
1105         af.viewBoxesMenuItem.setSelected(view.getShowBoxes());\r
1106         af.viewport.setShowText(view.getShowText());\r
1107         af.viewTextMenuItem.setSelected(view.getShowText());\r
1108 \r
1109         ColourSchemeI cs = null;\r
1110 \r
1111         if (view.getBgColour() != null)\r
1112         {\r
1113             if (view.getBgColour().startsWith("ucs"))\r
1114             {\r
1115                 cs = GetUserColourScheme(jms, view.getBgColour());\r
1116             }\r
1117             else if(view.getBgColour().startsWith("Annotation"))\r
1118             {\r
1119               //int find annotation\r
1120               for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)\r
1121               {\r
1122                 if (af.viewport.alignment.getAlignmentAnnotation()[i].label.\r
1123                     equals(view.getAnnotationColours().getAnnotation()))\r
1124                 {\r
1125                   if (af.viewport.alignment.getAlignmentAnnotation()[i].\r
1126                       getThreshold() == null)\r
1127                   {\r
1128                     af.viewport.alignment.getAlignmentAnnotation()[i].\r
1129                         setThreshold(\r
1130                             new jalview.datamodel.GraphLine(\r
1131                                 view.getAnnotationColours().getThreshold(),\r
1132                                 "Threshold", java.awt.Color.black)\r
1133 \r
1134                         );\r
1135                   }\r
1136 \r
1137 \r
1138                   if (view.getAnnotationColours().getColourScheme().equals(\r
1139                       "None"))\r
1140                   {\r
1141                     cs = new AnnotationColourGradient(\r
1142                         af.viewport.alignment.getAlignmentAnnotation()[i],\r
1143                         new java.awt.Color(view.getAnnotationColours().\r
1144                                            getMinColour()),\r
1145                         new java.awt.Color(view.getAnnotationColours().\r
1146                                            getMaxColour()),\r
1147                         view.getAnnotationColours().getAboveThreshold());\r
1148                   }\r
1149                   else if (view.getAnnotationColours().getColourScheme().\r
1150                            startsWith("ucs"))\r
1151                   {\r
1152                      cs = new AnnotationColourGradient(\r
1153                          af.viewport.alignment.getAlignmentAnnotation()[i],\r
1154                          GetUserColourScheme(jms, view.getAnnotationColours().\r
1155                                                         getColourScheme()),\r
1156                          view.getAnnotationColours().getAboveThreshold()\r
1157                          );\r
1158                    }\r
1159                    else\r
1160                    {\r
1161                      cs = new AnnotationColourGradient(\r
1162                          af.viewport.alignment.getAlignmentAnnotation()[i],\r
1163                          ColourSchemeProperty.getColour(al,\r
1164                          view.getAnnotationColours().getColourScheme()),\r
1165                          view.getAnnotationColours().getAboveThreshold()\r
1166                          );\r
1167                    }\r
1168 \r
1169                   // Also use these settings for all the groups\r
1170                   if (al.getGroups() != null)\r
1171                     for (int g = 0; g < al.getGroups().size(); g++)\r
1172                     {\r
1173                       jalview.datamodel.SequenceGroup sg\r
1174                           = (jalview.datamodel.SequenceGroup)al.getGroups().elementAt(g);\r
1175 \r
1176                       if(sg.cs == null)\r
1177                         continue;\r
1178 \r
1179 \r
1180                   /*    if (view.getAnnotationColours().getColourScheme().equals("None"))\r
1181                       {\r
1182                         sg.cs = new AnnotationColourGradient(\r
1183                             af.viewport.alignment.getAlignmentAnnotation()[i],\r
1184                             new java.awt.Color(view.getAnnotationColours().\r
1185                                                getMinColour()),\r
1186                             new java.awt.Color(view.getAnnotationColours().\r
1187                                                getMaxColour()),\r
1188                             view.getAnnotationColours().getAboveThreshold());\r
1189                       }\r
1190                       else*/\r
1191                       {\r
1192                         sg.cs = new AnnotationColourGradient(\r
1193                             af.viewport.alignment.getAlignmentAnnotation()[i],\r
1194                             sg.cs,\r
1195                             view.getAnnotationColours().getAboveThreshold()\r
1196                             );\r
1197                       }\r
1198 \r
1199                     }\r
1200 \r
1201 \r
1202                   break;\r
1203                 }\r
1204 \r
1205               }\r
1206             }\r
1207             else\r
1208             {\r
1209                 cs = ColourSchemeProperty.getColour(al, view.getBgColour());\r
1210             }\r
1211 \r
1212             if(cs!=null)\r
1213             {\r
1214               cs.setThreshold(view.getPidThreshold(), true);\r
1215               cs.setConsensus(af.viewport.vconsensus);\r
1216             }\r
1217         }\r
1218 \r
1219         af.setColourSelected(view.getBgColour());\r
1220         af.viewport.setGlobalColourScheme(cs);\r
1221         af.viewport.setColourAppliesToAllGroups(false);\r
1222         af.changeColour(cs);\r
1223         if (view.getConservationSelected() && cs!=null)\r
1224         {\r
1225           cs.setConservationInc(view.getConsThreshold());\r
1226         }\r
1227 \r
1228         af.viewport.setColourAppliesToAllGroups(true);\r
1229 \r
1230         if (view.getShowSequenceFeatures())\r
1231         {\r
1232            af.viewport.showSequenceFeatures = true;\r
1233            af.showSeqFeatures.setSelected(true);\r
1234         }\r
1235 \r
1236         if(jms.getFeatureSettings()!=null)\r
1237         {\r
1238           af.viewport.featuresDisplayed = new Hashtable();\r
1239           String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];\r
1240          for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)\r
1241          {\r
1242            Setting setting = jms.getFeatureSettings().getSetting(fs);\r
1243 \r
1244            af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),\r
1245                new java.awt.Color(setting.getColour()));\r
1246 \r
1247            renderOrder[fs] = setting.getType();\r
1248 \r
1249            if(setting.getDisplay())\r
1250              af.viewport.featuresDisplayed.put(\r
1251                  setting.getType(), new Integer(setting.getColour()));\r
1252          }\r
1253          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;\r
1254         }\r
1255 \r
1256         if (view.getHiddenColumnsCount() > 0)\r
1257         {\r
1258           for (int c = 0; c < view.getHiddenColumnsCount(); c++)\r
1259           {\r
1260               af.viewport.hideColumns(\r
1261                 view.getHiddenColumns(c).getStart(),\r
1262                 view.getHiddenColumns(c).getEnd()+1\r
1263                 );\r
1264           }\r
1265         }\r
1266 \r
1267 \r
1268         Desktop.addInternalFrame(af, view.getTitle(),\r
1269              view.getWidth(), view.getHeight());\r
1270 \r
1271         //LOAD TREES\r
1272         ///////////////////////////////////////\r
1273         if (jms.getTreeCount() > 0)\r
1274         {\r
1275             try\r
1276             {\r
1277                 for (int t = 0; t < jms.getTreeCount(); t++)\r
1278                 {\r
1279 \r
1280                     Tree tree = jms.getTree(t);\r
1281 \r
1282                     TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(\r
1283                                 tree.getNewick()), tree.getTitle(),\r
1284                                 tree.getWidth(), tree.getHeight(),\r
1285                                 tree.getXpos(), tree.getYpos());\r
1286 \r
1287                     tp.fitToWindow.setState(tree.getFitToWindow());\r
1288                     tp.fitToWindow_actionPerformed(null);\r
1289 \r
1290                     if(tree.getFontName()!=null)\r
1291                       tp.setTreeFont(new java.awt.Font(tree.getFontName(),\r
1292                                           tree.getFontStyle(),\r
1293                                           tree.getFontSize()));\r
1294                     else\r
1295                       tp.setTreeFont(new java.awt.Font(view.getFontName(),\r
1296                                             view.getFontStyle(),\r
1297                                             tree.getFontSize()));\r
1298 \r
1299                     tp.showPlaceholders(tree.getMarkUnlinked());\r
1300                     tp.showBootstrap(tree.getShowBootstrap());\r
1301                     tp.showDistances(tree.getShowDistances());\r
1302 \r
1303                     tp.treeCanvas.threshold = tree.getThreshold();\r
1304 \r
1305                     if (tree.getCurrentTree())\r
1306                       af.viewport.setCurrentTree(tp.getTree());\r
1307                 }\r
1308 \r
1309             }\r
1310             catch (Exception ex)\r
1311             {\r
1312                 ex.printStackTrace();\r
1313             }\r
1314 \r
1315         }\r
1316 \r
1317         return af;\r
1318     }\r
1319 }\r
1320 \r