src/jalview/gui/Jalview2XML.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer
   3  * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
   4  *
   5  * This program is free software; you can redistribute it and/or
   6  * modify it under the terms of the GNU General Public License
   7  * as published by the Free Software Foundation; either version 2
   8  * of the License, or (at your option) any later version.
   9  *
  10  * This program is distributed in the hope that it will be useful,
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  13  * GNU General Public License for more details.
  14  *
  15  * You should have received a copy of the GNU General Public License
  16  * along with this program; if not, write to the Free Software
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  18  */
  19 package jalview.gui;
  20
  21
  22 import jalview.schemes.*;
  23
  24 import jalview.gui.*;
  25
  26 import java.io.*;
  27
  28 import java.net.*;
  29
  30 import java.util.*;
  31
  32 import java.util.jar.*;
  33
  34 import javax.swing.*;
  35
  36 import org.exolab.castor.xml.*;
  37
  38 import jalview.schemabinding.version2.*;
  39
  40
  41
  42
  43 /**
  44  * DOCUMENT ME!
  45  *
  46  * @author $author$
  47  * @version $Revision$
  48  */
  49 public class Jalview2XML
  50 {
  51     // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE
  52     public void SaveState(File statefile)
  53     {
  54         long creation = System.currentTimeMillis();
  55         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
  56
  57         if (frames == null)
  58         {
  59             return;
  60         }
  61
  62         try
  63         {
  64             FileOutputStream fos = new FileOutputStream(statefile);
  65             JarOutputStream jout = new JarOutputStream(fos);
  66
  67             //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
  68             ////////////////////////////////////////////////////
  69             PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
  70                         "UTF-8"));
  71
  72             Vector shortNames = new Vector();
  73
  74             //REVERSE ORDER
  75             for (int i = frames.length - 1; i > -1; i--)
  76             {
  77                 if (frames[i] instanceof AlignFrame)
  78                 {
  79                     AlignFrame af = (AlignFrame) frames[i];
  80
  81                     String shortName = af.getTitle();
  82
  83                     if (shortName.indexOf(File.separatorChar) > -1)
  84                     {
  85                         shortName = shortName.substring(shortName.lastIndexOf(
  86                                     File.separatorChar) + 1);
  87                     }
  88
  89                     int count = 1;
  90
  91                     while (shortNames.contains(shortName))
  92                     {
  93                         if (shortName.endsWith("_" + (count - 1)))
  94                         {
  95                             shortName = shortName.substring(0,
  96                                     shortName.lastIndexOf("_"));
  97                         }
  98
  99                         shortName = shortName.concat("_" + count);
 100                         count++;
 101                     }
 102
 103                     shortNames.addElement(shortName);
 104
 105                     if (!shortName.endsWith(".xml"))
 106                     {
 107                         shortName = shortName + ".xml";
 108                     }
 109
 110                     SaveState(af, creation, shortName, jout, out);
 111                 }
 112             }
 113
 114             out.close();
 115             jout.close();
 116         }
 117         catch (Exception ex)
 118         {
 119             ex.printStackTrace();
 120         }
 121     }
 122
 123     // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
 124     public void SaveAlignment(AlignFrame af, String jarFile,
 125         String fileName)
 126     {
 127         try
 128         {
 129             FileOutputStream fos = new FileOutputStream(jarFile);
 130             JarOutputStream jout = new JarOutputStream(fos);
 131
 132             //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
 133             ////////////////////////////////////////////////////
 134             PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
 135                         "UTF-8"));
 136
 137             SaveState(af, System.currentTimeMillis(), fileName, jout, out);
 138             out.close();
 139             jout.close();
 140         }
 141         catch (Exception ex)
 142         {
 143           ex.printStackTrace();
 144         }
 145     }
 146
 147     /**
 148      * DOCUMENT ME!
 149      *
 150      * @param af DOCUMENT ME!
 151      * @param timeStamp DOCUMENT ME!
 152      * @param fileName DOCUMENT ME!
 153      * @param jout DOCUMENT ME!
 154      * @param out DOCUMENT ME!
 155      */
 156     public void SaveState(AlignFrame af, long timeStamp,
 157         String fileName, JarOutputStream jout, PrintWriter out)
 158     {
 159         Vector seqids = new Vector();
 160         Vector userColours = new Vector();
 161
 162         AlignViewport av = af.viewport;
 163
 164         JalviewModel object = new JalviewModel();
 165         object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
 166
 167         object.setCreationDate(new java.util.Date(timeStamp));
 168         object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
 169
 170         jalview.datamodel.AlignmentI jal = af.viewport.alignment;
 171         jalview.datamodel.AlignmentI jalhidden = null;
 172
 173         if(av.hasHiddenRows)
 174         {
 175           jalhidden = jal;
 176           jal = jal.getHiddenSequences().getFullAlignment();
 177         }
 178
 179
 180         SequenceSet vamsasSet = new SequenceSet();
 181         Sequence vamsasSeq;
 182         JalviewModelSequence jms = new JalviewModelSequence();
 183
 184         vamsasSet.setGapChar(jal.getGapCharacter() + "");
 185
 186         JSeq jseq;
 187         Vector pdbfiles = null;
 188
 189         //SAVE SEQUENCES
 190         int id = 0;
 191         for (int i = 0; i < jal.getHeight(); i++)
 192         {
 193             seqids.add(jal.getSequenceAt(i));
 194             vamsasSeq = new Sequence();
 195             vamsasSeq.setId(id + "");
 196             vamsasSeq.setName(jal.getSequenceAt(i).getName());
 197             vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());
 198             vamsasSeq.setDescription(jal.getSequenceAt(i).getDescription());
 199
 200             if(jal.getSequenceAt(i).getDatasetSequence().getDBRef()!=null)
 201             {
 202               jalview.datamodel.DBRefEntry [] dbrefs =
 203                   jal.getSequenceAt(i).getDatasetSequence().getDBRef();
 204
 205               for(int d=0; d<dbrefs.length; d++)
 206               {
 207                 DBRef dbref = new DBRef();
 208                 dbref.setSource( dbrefs[d].getSource() );
 209                 dbref.setVersion( dbrefs[d].getVersion());
 210                 dbref.setAccessionId(dbrefs[d].getAccessionId());
 211                 vamsasSeq.addDBRef(dbref);
 212               }
 213             }
 214
 215             jseq = new JSeq();
 216             jseq.setStart(jal.getSequenceAt(i).getStart());
 217             jseq.setEnd(jal.getSequenceAt(i).getEnd());
 218             jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());
 219
 220             jseq.setId(id);
 221
 222             if (av.hasHiddenRows)
 223             {
 224               jseq.setHidden(jalhidden.getHiddenSequences().isHidden(
 225                   jal.getSequenceAt(i)));
 226
 227               if(jal.getSequenceAt(i).getHiddenSequences()!=null)
 228               {
 229                 jalview.datamodel.SequenceI [] reps =
 230                     jal.getSequenceAt(i).getHiddenSequences().getSequencesInOrder(jal);
 231
 232                 for(int h=0; h<reps.length; h++)
 233                 {
 234                   jseq.addHiddenSequences(
 235                       jal.findIndex(reps[h])
 236                       );
 237                 }
 238               }
 239             }
 240
 241
 242             if(jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures()!=null)
 243             {
 244               jalview.datamodel.SequenceFeature[] sf
 245                   = jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
 246               int index = 0;
 247               while(index < sf.length)
 248               {
 249                 Features features = new Features();
 250
 251                 features.setBegin(sf[index].getBegin());
 252                 features.setEnd(sf[index].getEnd());
 253                 features.setDescription(sf[index].getDescription());
 254                 features.setType(sf[index].getType());
 255                 features.setFeatureGroup(sf[index].getFeatureGroup());
 256                 features.setScore(sf[index].getScore());
 257                 if(sf[index].links!=null)
 258                 {
 259                   for(int l=0; l<sf[index].links.size(); l++)
 260                   {
 261                     OtherData keyValue = new OtherData();
 262                     keyValue.setKey("LINK_"+l);
 263                     keyValue.setValue(sf[index].links.elementAt(l).toString());
 264                     features.addOtherData(keyValue);
 265                   }
 266                 }
 267                 if(sf[index].otherDetails!=null)
 268                 {
 269                   String key;
 270                   Enumeration keys = sf[index].otherDetails.keys();
 271                   while(keys.hasMoreElements())
 272                   {
 273                     key = keys.nextElement().toString();
 274                     OtherData keyValue = new OtherData();
 275                     keyValue.setKey( key );
 276                     keyValue.setValue(
 277                         sf[index].otherDetails.get(key).toString());
 278                     features.addOtherData(keyValue);
 279                   }
 280                 }
 281
 282                 jseq.addFeatures(features);
 283                 index ++;
 284               }
 285             }
 286
 287             if(jal.getSequenceAt(i).getDatasetSequence().getPDBId()!=null)
 288             {
 289               Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getPDBId().elements();
 290               while(en.hasMoreElements())
 291               {
 292                 Pdbids pdb = new Pdbids();
 293                 jalview.datamodel.PDBEntry entry
 294                    = (jalview.datamodel.PDBEntry)en.nextElement();
 295
 296                 pdb.setId(entry.getId());
 297                 pdb.setType(entry.getType());
 298
 299                 if(entry.getFile()!=null)
 300                 {
 301                   if(pdbfiles==null)
 302                     pdbfiles = new Vector();
 303
 304
 305                   if(!pdbfiles.contains(entry.getId()))
 306                   {
 307                     pdbfiles.addElement(entry.getId());
 308                     try
 309                     {
 310                       File file = new File(entry.getFile());
 311                       if(file.exists())
 312                       {
 313                         byte[] data = new byte[ (int) file.length()];
 314                         jout.putNextEntry(new JarEntry(entry.getId()));
 315                         DataInputStream dis = new DataInputStream(new
 316                             FileInputStream(file));
 317                         dis.readFully(data);
 318
 319                         DataOutputStream dout = new DataOutputStream(jout);
 320                         dout.write(data, 0, data.length);
 321                         jout.closeEntry();
 322                       }
 323                     }
 324                     catch (Exception ex)
 325                     {
 326                       ex.printStackTrace();
 327                     }
 328                   }
 329                 }
 330
 331
 332                 if(entry.getProperty()!=null)
 333                 {
 334                   PdbentryItem item = new PdbentryItem();
 335                   Hashtable properties = entry.getProperty();
 336                   Enumeration en2 = properties.keys();
 337                   while(en2.hasMoreElements())
 338                   {
 339                     Property prop = new Property();
 340                     String key = en2.nextElement().toString();
 341                     prop.setName(key);
 342                     prop.setValue( properties.get(key).toString() );
 343                     item.addProperty(prop);
 344                   }
 345                   pdb.addPdbentryItem(item);
 346                 }
 347
 348                 jseq.addPdbids(pdb);
 349               }
 350             }
 351
 352             jms.addJSeq(jseq);
 353             vamsasSet.addSequence(vamsasSeq);
 354             id++;
 355         }
 356
 357         //SAVE TREES
 358         ///////////////////////////////////
 359         if (af.viewport.currentTree != null)
 360         {
 361           // FIND ANY ASSOCIATED TREES
 362           // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
 363           if (Desktop.desktop != null)
 364           {
 365             JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 366
 367             for (int t = 0; t < frames.length; t++)
 368             {
 369               if (frames[t] instanceof TreePanel)
 370               {
 371                 TreePanel tp = (TreePanel) frames[t];
 372
 373                 if (tp.treeCanvas.av.alignment == jal)
 374                 {
 375                   Tree tree = new Tree();
 376                   tree.setTitle(tp.getTitle());
 377                   tree.setCurrentTree( (af.viewport.currentTree == tp.getTree()));
 378                   tree.setNewick(tp.getTree().toString());
 379                   tree.setThreshold(tp.treeCanvas.threshold);
 380
 381                   tree.setFitToWindow(tp.fitToWindow.getState());
 382                   tree.setFontName(tp.getTreeFont().getName());
 383                   tree.setFontSize(tp.getTreeFont().getSize());
 384                   tree.setFontStyle(tp.getTreeFont().getStyle());
 385                   tree.setMarkUnlinked(tp.placeholdersMenu.getState());
 386
 387                   tree.setShowBootstrap(tp.bootstrapMenu.getState());
 388                   tree.setShowDistances(tp.distanceMenu.getState());
 389
 390                   tree.setHeight(tp.getHeight());
 391                   tree.setWidth(tp.getWidth());
 392                   tree.setXpos(tp.getX());
 393                   tree.setYpos(tp.getY());
 394
 395                   jms.addTree(tree);
 396                 }
 397               }
 398             }
 399           }
 400         }
 401
 402         //SAVE ANNOTATIONS
 403         if (jal.getAlignmentAnnotation() != null)
 404         {
 405             jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
 406
 407             for (int i = 0; i < aa.length; i++)
 408             {
 409                 Annotation an = new Annotation();
 410
 411                 if (aa[i].label.equals("Quality") ||
 412                         aa[i].label.equals("Conservation") ||
 413                         aa[i].label.equals("Consensus"))
 414                 {
 415                     an.setLabel(aa[i].label);
 416                     an.setGraph(true);
 417                     vamsasSet.addAnnotation(an);
 418                     continue;
 419                 }
 420
 421
 422                 an.setDescription(aa[i].description);
 423
 424                 if(aa[i].sequenceRef!=null)
 425                  {
 426                    an.setSequenceRef(aa[i].sequenceRef.getName());
 427                  }
 428
 429                 if(aa[i].graph>0)
 430                 {
 431                   an.setGraph(true);
 432                   an.setGraphType(aa[i].graph);
 433                   an.setGraphGroup(aa[i].graphGroup);
 434                   if(aa[i].getThreshold()!=null)
 435                   {
 436                     ThresholdLine line = new ThresholdLine();
 437                     line.setLabel(aa[i].getThreshold().label);
 438                     line.setValue(aa[i].getThreshold().value);
 439                     line.setColour(aa[i].getThreshold().colour.getRGB());
 440                     an.setThresholdLine(line);
 441                   }
 442                 }
 443                 else
 444                   an.setGraph(false);
 445
 446                 an.setLabel(aa[i].label);
 447
 448                 AnnotationElement ae;
 449
 450                 for (int a = 0; a < aa[i].annotations.length; a++)
 451                 {
 452                     if ((aa[i] == null) || (aa[i].annotations[a] == null))
 453                     {
 454                         continue;
 455                     }
 456
 457                     ae = new AnnotationElement();
 458                     ae.setDescription(aa[i].annotations[a].description);
 459                     ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
 460                     ae.setValue(aa[i].annotations[a].value);
 461                     ae.setPosition(a);
 462                     ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
 463                         "");
 464
 465                     if(aa[i].annotations[a].colour!=java.awt.Color.black)
 466                       ae.setColour(aa[i].annotations[a].colour.getRGB());
 467
 468                     an.addAnnotationElement(ae);
 469                 }
 470
 471                 vamsasSet.addAnnotation(an);
 472             }
 473         }
 474
 475         //SAVE GROUPS
 476         if (jal.getGroups() != null)
 477         {
 478             JGroup[] groups = new JGroup[jal.getGroups().size()];
 479
 480             for (int i = 0; i < groups.length; i++)
 481             {
 482                 groups[i] = new JGroup();
 483
 484                 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()
 485                                                                                           .elementAt(i);
 486                 groups[i].setStart(sg.getStartRes());
 487                 groups[i].setEnd(sg.getEndRes());
 488                 groups[i].setName(sg.getName());
 489                 if(sg.cs!=null)
 490                 {
 491                   if (sg.cs.conservationApplied())
 492                   {
 493                     groups[i].setConsThreshold(sg.cs.getConservationInc());
 494
 495                     if (sg.cs instanceof jalview.schemes.UserColourScheme)
 496                     {
 497                       groups[i].setColour(SetUserColourScheme(sg.cs,
 498                           userColours,
 499                           jms));
 500                     }
 501                     else
 502                     {
 503                       groups[i].setColour(ColourSchemeProperty.getColourName(sg.
 504                           cs));
 505                     }
 506                   }
 507                   else if(sg.cs instanceof jalview.schemes.AnnotationColourGradient)
 508                   {
 509                     groups[i].setColour(
 510                         ColourSchemeProperty.getColourName(
 511                       ( (jalview.schemes.AnnotationColourGradient) sg.cs).getBaseColour()));
 512                   }
 513                   else if (sg.cs instanceof jalview.schemes.UserColourScheme)
 514                   {
 515                     groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
 516                         jms));
 517                   }
 518                   else
 519                   {
 520                     groups[i].setColour(ColourSchemeProperty.getColourName(
 521                         sg.cs));
 522                   }
 523
 524                   groups[i].setPidThreshold(sg.cs.getThreshold());
 525                 }
 526
 527                 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
 528                 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
 529                 groups[i].setDisplayText(sg.getDisplayText());
 530                 groups[i].setColourText(sg.getColourText());
 531
 532                 for (int s = 0; s < sg.getSize(false); s++)
 533                 {
 534                     jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.getSequenceAt(s);
 535                     int index = seqids.indexOf(seq);
 536                     groups[i].addSeq(index);
 537                 }
 538             }
 539
 540             jms.setJGroup(groups);
 541         }
 542
 543
 544         ///////////SAVE VIEWPORT
 545         Viewport view = new Viewport();
 546         view.setTitle(af.getTitle());
 547         view.setXpos(af.getX());
 548         view.setYpos(af.getY());
 549         view.setWidth(af.getWidth());
 550         view.setHeight(af.getHeight());
 551         view.setStartRes(av.startRes);
 552         view.setStartSeq(av.startSeq);
 553
 554         if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
 555         {
 556             view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
 557                     userColours, jms));
 558         }
 559         else if(av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
 560         {
 561            jalview.schemes.AnnotationColourGradient acg
 562               = (jalview.schemes.AnnotationColourGradient)av.getGlobalColourScheme();
 563
 564             AnnotationColours ac = new AnnotationColours();
 565             ac.setAboveThreshold(acg.getAboveThreshold());
 566             ac.setThreshold(acg.getAnnotationThreshold());
 567             ac.setAnnotation(acg.getAnnotation());
 568             if(acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
 569               ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
 570                     userColours, jms));
 571             else
 572               ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
 573
 574             ac.setMaxColour(acg.getMaxColour().getRGB());
 575             ac.setMinColour(acg.getMinColour().getRGB());
 576             view.setAnnotationColours(ac);
 577             view.setBgColour("AnnotationColourGradient");
 578         }
 579         else
 580         {
 581             view.setBgColour(ColourSchemeProperty.getColourName(
 582                     av.getGlobalColourScheme()));
 583         }
 584
 585         ColourSchemeI cs = av.getGlobalColourScheme();
 586
 587         if(cs!=null)
 588         {
 589           if (cs.conservationApplied())
 590           {
 591             view.setConsThreshold(cs.getConservationInc());
 592             if (cs instanceof jalview.schemes.UserColourScheme)
 593               view.setBgColour(SetUserColourScheme(cs, userColours, jms));
 594           }
 595
 596           if (cs instanceof ResidueColourScheme)
 597           {
 598             view.setPidThreshold(cs.getThreshold());
 599           }
 600         }
 601
 602         view.setConservationSelected(av.getConservationSelected());
 603         view.setPidSelected(av.getAbovePIDThreshold());
 604         view.setFontName(av.font.getName());
 605         view.setFontSize(av.font.getSize());
 606         view.setFontStyle(av.font.getStyle());
 607         view.setRenderGaps(av.renderGaps);
 608         view.setShowAnnotation(av.getShowAnnotation());
 609         view.setShowBoxes(av.getShowBoxes());
 610         view.setShowColourText(av.getColourText());
 611         view.setShowConservation(av.showConservation);
 612         view.setShowFullId(av.getShowJVSuffix());
 613         view.setShowIdentity(av.showIdentity);
 614         view.setShowQuality(av.showQuality);
 615         view.setShowSequenceFeatures(av.showSequenceFeatures);
 616         view.setShowText(av.getShowText());
 617         view.setWrapAlignment(av.getWrapAlignment());
 618
 619         if(av.featuresDisplayed!=null)
 620         {
 621           jalview.schemabinding.version2.FeatureSettings fs
 622               = new jalview.schemabinding.version2.FeatureSettings();
 623
 624           String [] renderOrder =
 625               af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
 626
 627           Vector settingsAdded = new Vector();
 628           for(int ro=0; ro<renderOrder.length; ro++)
 629           {
 630             Setting setting = new Setting();
 631             setting.setType(renderOrder[ro]);
 632             setting.setColour(
 633                 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).getRGB()
 634                 );
 635
 636             setting.setDisplay(
 637                 av.featuresDisplayed.containsKey(renderOrder[ro])
 638                 );
 639
 640             fs.addSetting(setting);
 641             settingsAdded.addElement(renderOrder[ro]);
 642           }
 643
 644           //Make sure we save none displayed feature settings
 645           Enumeration en =
 646               af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
 647           while(en.hasMoreElements())
 648           {
 649             String key = en.nextElement().toString();
 650             if(settingsAdded.contains(key))
 651               continue;
 652
 653             Setting setting = new Setting();
 654             setting.setType(key);
 655             setting.setColour(
 656                 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()
 657                 );
 658
 659             setting.setDisplay(false);
 660
 661             fs.addSetting(setting);
 662             settingsAdded.addElement(key);
 663           }
 664
 665           jms.setFeatureSettings(fs);
 666
 667         }
 668
 669         if(av.hasHiddenColumns)
 670         {
 671           for(int c=0; c<av.getColumnSelection().getHiddenColumns().size(); c++)
 672           {
 673             int [] region = (int[]) av.getColumnSelection().getHiddenColumns().elementAt(c);
 674             HiddenColumns hc = new HiddenColumns();
 675             hc.setStart(region[0]);
 676             hc.setEnd(region[1]);
 677             view.addHiddenColumns(hc);
 678           }
 679         }
 680
 681         jms.addViewport(view);
 682
 683
 684         object.setJalviewModelSequence(jms);
 685         object.getVamsasModel().addSequenceSet(vamsasSet);
 686
 687         try
 688         {
 689             if (!fileName.endsWith(".xml"))
 690             {
 691                 fileName = fileName + ".xml";
 692             }
 693
 694             JarEntry entry = new JarEntry(fileName);
 695             jout.putNextEntry(entry);
 696
 697             object.marshal(out);
 698         }
 699         catch (Exception ex)
 700         {
 701             ex.printStackTrace();
 702         }
 703     }
 704
 705     String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
 706         Vector userColours, JalviewModelSequence jms)
 707     {
 708         String id = null;
 709         jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
 710
 711         if (!userColours.contains(ucs))
 712         {
 713             userColours.add(ucs);
 714
 715             java.awt.Color[] colours = ucs.getColours();
 716             jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
 717             jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
 718
 719             for (int i = 0; i < colours.length; i++)
 720             {
 721                 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
 722                 col.setRGB(jalview.util.Format.getHexString(colours[i]));
 723                 jbucs.addColour(col);
 724             }
 725
 726             id = "ucs" + userColours.indexOf(ucs);
 727             uc.setId(id);
 728             uc.setUserColourScheme(jbucs);
 729             jms.addUserColours(uc);
 730         }
 731
 732         return id;
 733     }
 734
 735    jalview.schemes.UserColourScheme GetUserColourScheme(
 736         JalviewModelSequence jms, String id)
 737     {
 738         UserColours[] uc = jms.getUserColours();
 739         UserColours colours = null;
 740
 741         for (int i = 0; i < uc.length; i++)
 742         {
 743             if (uc[i].getId().equals(id))
 744             {
 745                 colours = uc[i];
 746
 747                 break;
 748             }
 749         }
 750
 751         int csize = colours.getUserColourScheme().getColourCount();
 752         java.awt.Color[] newColours = new java.awt.Color[csize];
 753
 754         for (int i = 0; i < csize; i++)
 755         {
 756             newColours[i] = new java.awt.Color(Integer.parseInt(
 757                         colours.getUserColourScheme().getColour(i).getRGB(), 16));
 758         }
 759
 760         return new jalview.schemes.UserColourScheme(newColours);
 761     }
 762
 763     /**
 764      * DOCUMENT ME!
 765      *
 766      * @param file DOCUMENT ME!
 767      */
 768     public AlignFrame LoadJalviewAlign(final String file)
 769     {
 770         jalview.gui.AlignFrame af = null;
 771         try
 772         {
 773             //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
 774             URL url = null;
 775
 776             if (file.startsWith("http://"))
 777             {
 778                 url = new URL(file);
 779             }
 780
 781             JarInputStream jin = null;
 782             JarEntry jarentry = null;
 783             int entryCount = 1;
 784
 785             do
 786             {
 787                 if (url != null)
 788                 {
 789                     jin = new JarInputStream(url.openStream());
 790                 }
 791                 else
 792                 {
 793                     jin = new JarInputStream(new FileInputStream(file));
 794                 }
 795
 796                 for (int i = 0; i < entryCount; i++)
 797                 {
 798                     jarentry = jin.getNextJarEntry();
 799                 }
 800
 801                 if (jarentry != null && jarentry.getName().endsWith(".xml"))
 802                 {
 803                     InputStreamReader in = new InputStreamReader(jin, "UTF-8");
 804                     JalviewModel object = new JalviewModel();
 805
 806                     Unmarshaller unmar = new Unmarshaller(object);
 807                     unmar.setValidation(false);
 808                     object = (JalviewModel) unmar.unmarshal( in );
 809
 810                     af = LoadFromObject(object, file);
 811                     entryCount++;
 812                 }
 813                 else if (jarentry != null)
 814                 {
 815                   //Some other file here.
 816                   entryCount++;
 817                 }
 818             }
 819             while (jarentry != null);
 820         }
 821         catch(java.net.UnknownHostException ex)
 822         {
 823           ex.printStackTrace();
 824           System.err.println("Couldn't locate Jalview XML file : " +
 825               ex + "\n");
 826
 827           javax.swing.SwingUtilities.invokeLater(new Runnable()
 828           {
 829             public void run()
 830             {
 831               JOptionPane.showInternalMessageDialog(Desktop.desktop,
 832                   "Couldn't locate " + file,
 833                   "URL not found",
 834                   JOptionPane.WARNING_MESSAGE);
 835             }
 836           });
 837         }
 838         catch (Exception ex)
 839         {
 840
 841           //Is Version 1 Jar file?
 842           af =  new Jalview2XML_V1().LoadJalviewAlign(file);
 843
 844           if(af!=null)
 845           {
 846             System.out.println("Successfully loaded archive file");
 847             return af;
 848           }
 849           ex.printStackTrace();
 850             System.err.println("Exception whilst loading jalview XML file : " +
 851                 ex + "\n");
 852             javax.swing.SwingUtilities.invokeLater(new Runnable()
 853             {
 854               public void run()
 855               {
 856
 857                 JOptionPane.showInternalMessageDialog(Desktop.desktop,
 858                     "Error loading  " + file,
 859                     "Error loading Jalview file",
 860                     JOptionPane.WARNING_MESSAGE);
 861               }});
 862         }
 863
 864         return af;
 865     }
 866
 867     String loadPDBFile(String file, String pdbId)
 868     {
 869       System.out.println("load file "+file);
 870       try
 871       {
 872         JarInputStream jin = null;
 873
 874         if (file.startsWith("http://"))
 875         {
 876           jin = new JarInputStream(new URL(file).openStream());
 877         }
 878         else
 879         {
 880           jin = new JarInputStream(new FileInputStream(file));
 881         }
 882
 883         JarEntry entry = null;
 884         do
 885         {
 886           entry = jin.getNextJarEntry();
 887         }
 888         while (!entry.getName().equals(pdbId));
 889
 890         BufferedReader in = new BufferedReader(new InputStreamReader(jin));
 891         File outFile = File.createTempFile("jalview_pdb", ".txt");
 892         outFile.deleteOnExit();
 893         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
 894         String data;
 895
 896         while ( (data = in.readLine()) != null)
 897         {
 898           out.println(data);
 899         }
 900         out.close();
 901         return outFile.getAbsolutePath();
 902
 903       }
 904       catch (Exception ex)
 905       {
 906         ex.printStackTrace();
 907       }
 908
 909       return null;
 910     }
 911
 912
 913     AlignFrame LoadFromObject(JalviewModel object, String file)
 914     {
 915         Vector seqids = new Vector();
 916         SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
 917         Sequence[] vamsasSeq = vamsasSet.getSequence();
 918
 919         JalviewModelSequence jms = object.getJalviewModelSequence();
 920
 921         //////////////////////////////////
 922         //LOAD SEQUENCES
 923         Vector hiddenSeqs = null;
 924         jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
 925         JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
 926         for (int i = 0; i < vamsasSeq.length; i++)
 927         {
 928             jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
 929                     vamsasSeq[i].getSequence());
 930             jseqs[i].setDescription( vamsasSeq[i].getDescription() );
 931
 932             if(JSEQ[i].getHidden())
 933             {
 934               if(hiddenSeqs == null)
 935                 hiddenSeqs = new Vector();
 936               hiddenSeqs.addElement(jseqs[i]);
 937             }
 938             jseqs[i].setStart(JSEQ[i].getStart());
 939             jseqs[i].setEnd(JSEQ[i].getEnd());
 940             jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));
 941             seqids.add(jseqs[i]);
 942         }
 943
 944         ///SequenceFeatures are added to the DatasetSequence,
 945         // so we must create the dataset before loading features
 946         /////////////////////////////////
 947         jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
 948         al.setDataset(null);
 949         /////////////////////////////////
 950
 951
 952         Hashtable pdbloaded = new Hashtable();
 953         for (int i = 0; i < vamsasSeq.length; i++)
 954         {
 955           if (JSEQ[i].getFeaturesCount() > 0)
 956           {
 957             Features[] features = JSEQ[i].getFeatures();
 958             for (int f = 0; f < features.length; f++)
 959             {
 960               jalview.datamodel.SequenceFeature sf
 961                   = new jalview.datamodel.SequenceFeature(features[f].getType(),
 962                   features[f].getDescription(), features[f].getStatus(),
 963                   features[f].getBegin(), features[f].getEnd(),
 964                   features[f].getFeatureGroup());
 965
 966               sf.setScore(features[f].getScore());
 967               for(int od=0; od<features[f].getOtherDataCount(); od++)
 968               {
 969                 OtherData keyValue = features[f].getOtherData(od);
 970                 if(keyValue.getKey().startsWith("LINK"))
 971                   sf.addLink(keyValue.getValue());
 972                 else
 973                   sf.setValue(keyValue.getKey(), keyValue.getValue());
 974
 975               }
 976
 977               al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
 978             }
 979           }
 980           if (JSEQ[i].getPdbidsCount() > 0)
 981           {
 982             Pdbids[] ids = JSEQ[i].getPdbids();
 983             for (int p = 0; p < ids.length; p++)
 984             {
 985               jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
 986               entry.setId(ids[p].getId());
 987               entry.setType(ids[p].getType());
 988               if (ids[p].getFile() != null)
 989               {
 990                 if (!pdbloaded.containsKey(ids[p].getFile()))
 991                 {
 992                   String tmppdb = loadPDBFile(file, ids[p].getId());
 993                   entry.setFile(tmppdb);
 994                   pdbloaded.put(ids[p].getId(), tmppdb);
 995                 }
 996                 else
 997                   entry.setFile(pdbloaded.get(ids[p].getId()).toString());
 998               }
 999
1000               al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1001             }
1002           }
1003           if(vamsasSeq[i].getDBRefCount()>0)
1004           {
1005             for(int d=0; d<vamsasSeq[i].getDBRefCount(); d++)
1006             {
1007               jalview.datamodel.DBRefEntry entry =
1008                   new jalview.datamodel.DBRefEntry(
1009                       vamsasSeq[i].getDBRef(d).getSource(),
1010                       vamsasSeq[i].getDBRef(d).getVersion(),
1011                       vamsasSeq[i].getDBRef(d).getAccessionId()
1012                       );
1013               al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);
1014             }
1015
1016           }
1017         }
1018
1019
1020
1021          /////////////////////////////////
1022         //////////////////////////////////
1023         //LOAD ANNOTATIONS
1024         boolean hideQuality = true,
1025             hideConservation = true,
1026             hideConsensus = true;
1027
1028         if (vamsasSet.getAnnotation() != null)
1029         {
1030             Annotation[] an = vamsasSet.getAnnotation();
1031
1032             for (int i = 0; i < an.length; i++)
1033             {
1034                if (an[i].getLabel().equals("Quality"))
1035                 {
1036                  hideQuality = false;
1037                  continue;
1038                 }
1039                else if(an[i].getLabel().equals("Conservation"))
1040                {
1041                  hideConservation = false;
1042                  continue;
1043                }
1044                else if(an[i].getLabel().equals("Consensus"))
1045                {
1046                  hideConsensus = false;
1047                  continue;
1048                }
1049
1050                 AnnotationElement[] ae = an[i].getAnnotationElement();
1051                 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];
1052
1053                 for (int aa = 0; aa < ae.length; aa++)
1054                 {
1055                     anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),
1056                             ae[aa].getDescription(),
1057                             ae[aa].getSecondaryStructure().length()==0?' ':ae[aa].getSecondaryStructure().charAt(0),
1058                             ae[aa].getValue());
1059                     anot[ae[aa].getPosition()].colour = new java.awt.Color( ae[aa].getColour() );
1060                 }
1061
1062                 jalview.datamodel.AlignmentAnnotation jaa = null;
1063
1064                 if (an[i].getGraph())
1065                 {
1066                   jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1067                       an[i].getDescription(), anot, 0, 0,
1068                       an[i].getGraphType());
1069
1070                   jaa.graphGroup = an[i].getGraphGroup();
1071
1072                   if (an[i].getThresholdLine() != null)
1073                   {
1074                     jaa.setThreshold(new jalview.datamodel.GraphLine(
1075                                   an[i].getThresholdLine().getValue(),
1076                                   an[i].getThresholdLine().getLabel(),
1077                                 new java.awt.Color(an[i].getThresholdLine().getColour()))
1078                              );
1079
1080                   }
1081
1082                 }
1083                 else
1084                 {
1085                     jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1086                             an[i].getDescription(), anot);
1087                 }
1088
1089                 if(an[i].getSequenceRef()!=null)
1090                 {
1091                   jaa.createSequenceMapping(
1092                       al.findName(an[i].getSequenceRef()), 1
1093                       );
1094                   al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
1095                 }
1096
1097                 al.addAnnotation(jaa);
1098             }
1099         }
1100
1101
1102         //  af.changeColour() );
1103         /////////////////////////
1104         //LOAD GROUPS
1105         if (jms.getJGroupCount() > 0)
1106         {
1107             JGroup[] groups = jms.getJGroup();
1108
1109             for (int i = 0; i < groups.length; i++)
1110             {
1111                 ColourSchemeI cs = null;
1112
1113                 if (groups[i].getColour() != null)
1114                 {
1115                     if (groups[i].getColour().startsWith("ucs"))
1116                     {
1117                         cs = GetUserColourScheme(jms, groups[i].getColour());
1118                     }
1119                     else
1120                     {
1121                         cs = ColourSchemeProperty.getColour(al,
1122                                 groups[i].getColour());
1123                     }
1124
1125                     if(cs!=null)
1126                       cs.setThreshold(groups[i].getPidThreshold(), true);
1127                 }
1128
1129                 Vector seqs = new Vector();
1130                 int[] ids = groups[i].getSeq();
1131
1132                 for (int s = 0; s < ids.length; s++)
1133                 {
1134                     seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(
1135                             ids[s]));
1136                 }
1137
1138                 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,
1139                         groups[i].getName(), cs, groups[i].getDisplayBoxes(),
1140                         groups[i].getDisplayText(), groups[i].getColourText(),
1141                         groups[i].getStart(), groups[i].getEnd());
1142
1143                 sg.setOutlineColour(new java.awt.Color(
1144                         groups[i].getOutlineColour()));
1145
1146                 if (groups[i].getConsThreshold() != 0)
1147                 {
1148                     jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
1149                             ResidueProperties.propHash, 3, sg.getSequences(false), 0,
1150                             sg.getWidth() - 1);
1151                     c.calculate();
1152                     c.verdict(false, 25);
1153                     sg.cs.setConservation(c);
1154                 }
1155
1156                 al.addGroup(sg);
1157             }
1158         }
1159
1160
1161         /////////////////////////////////
1162         // LOAD VIEWPORT
1163         Viewport[] views = jms.getViewport();
1164         Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
1165
1166
1167         AlignFrame af = new AlignFrame(al);
1168
1169         if(hiddenSeqs!=null)
1170         {
1171           for(int s=0; s<JSEQ.length; s++)
1172           {
1173             for(int r=0; r<JSEQ[s].getHiddenSequencesCount(); r++)
1174             {
1175               al.getSequenceAt(s).addHiddenSequence(
1176                   al.getSequenceAt( JSEQ[s].getHiddenSequences(r)  )
1177                   );
1178             }
1179           }
1180
1181           for(int s=0; s<hiddenSeqs.size(); s++)
1182           {
1183               af.viewport.hideSequence(
1184                 (jalview.datamodel.SequenceI)hiddenSeqs.elementAt(s));
1185           }
1186         }
1187
1188
1189         if(hideConsensus || hideQuality || hideConservation)
1190         {
1191           int hSize = al.getAlignmentAnnotation().length;
1192           for (int h = 0; h < hSize; h++)
1193           {
1194             if (
1195                 (hideConsensus &&
1196                  al.getAlignmentAnnotation()[h].label.equals("Consensus"))
1197                 ||
1198                 (hideQuality &&
1199                  al.getAlignmentAnnotation()[h].label.equals("Quality"))
1200                 ||
1201                 (hideConservation &&
1202                  al.getAlignmentAnnotation()[h].label.equals("Conservation")))
1203             {
1204               al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
1205               hSize--;
1206               h--;
1207             }
1208           }
1209           af.alignPanel.adjustAnnotationHeight();
1210         }
1211
1212         af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
1213             view.getHeight());
1214         af.viewport.setStartRes(view.getStartRes());
1215         af.viewport.setStartSeq(view.getStartSeq());
1216         af.viewport.setShowAnnotation(view.getShowAnnotation());
1217         af.viewport.showConservation = view.getShowConservation();
1218         af.viewport.showQuality = view.getShowQuality();
1219         af.viewport.showIdentity = view.getShowIdentity();
1220         af.viewport.setAbovePIDThreshold(view.getPidSelected());
1221         af.abovePIDThreshold.setSelected(view.getPidSelected());
1222         af.viewport.setColourText(view.getShowColourText());
1223         af.colourTextMenuItem.setSelected(view.getShowColourText());
1224         af.viewport.setConservationSelected(view.getConservationSelected());
1225         af.conservationMenuItem.setSelected(view.getConservationSelected());
1226
1227         af.viewport.setShowJVSuffix(view.getShowFullId());
1228         af.seqLimits.setSelected(view.getShowFullId());
1229
1230         af.viewport.setFont(new java.awt.Font(view.getFontName(),
1231                 view.getFontStyle(), view.getFontSize()));
1232         af.alignPanel.fontChanged();
1233
1234         af.viewport.setRenderGaps(view.getRenderGaps());
1235         af.renderGapsMenuItem.setSelected(view.getRenderGaps());
1236
1237         af.viewport.setWrapAlignment(view.getWrapAlignment());
1238         af.wrapMenuItem.setSelected(view.getWrapAlignment());
1239
1240         af.alignPanel.setWrapAlignment(view.getWrapAlignment());
1241
1242         af.annotationPanelMenuItem.setState(view.getShowAnnotation());
1243         af.viewport.setShowAnnotation(view.getShowAnnotation());
1244         af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
1245
1246         af.viewport.setShowBoxes(view.getShowBoxes());
1247         af.viewBoxesMenuItem.setSelected(view.getShowBoxes());
1248         af.viewport.setShowText(view.getShowText());
1249         af.viewTextMenuItem.setSelected(view.getShowText());
1250
1251         ColourSchemeI cs = null;
1252
1253         if (view.getBgColour() != null)
1254         {
1255             if (view.getBgColour().startsWith("ucs"))
1256             {
1257                 cs = GetUserColourScheme(jms, view.getBgColour());
1258             }
1259             else if(view.getBgColour().startsWith("Annotation"))
1260             {
1261               //int find annotation
1262               for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
1263               {
1264                 if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
1265                     equals(view.getAnnotationColours().getAnnotation()))
1266                 {
1267                   if (af.viewport.alignment.getAlignmentAnnotation()[i].
1268                       getThreshold() == null)
1269                   {
1270                     af.viewport.alignment.getAlignmentAnnotation()[i].
1271                         setThreshold(
1272                             new jalview.datamodel.GraphLine(
1273                                 view.getAnnotationColours().getThreshold(),
1274                                 "Threshold", java.awt.Color.black)
1275
1276                         );
1277                   }
1278
1279
1280                   if (view.getAnnotationColours().getColourScheme().equals(
1281                       "None"))
1282                   {
1283                     cs = new AnnotationColourGradient(
1284                         af.viewport.alignment.getAlignmentAnnotation()[i],
1285                         new java.awt.Color(view.getAnnotationColours().
1286                                            getMinColour()),
1287                         new java.awt.Color(view.getAnnotationColours().
1288                                            getMaxColour()),
1289                         view.getAnnotationColours().getAboveThreshold());
1290                   }
1291                   else if (view.getAnnotationColours().getColourScheme().
1292                            startsWith("ucs"))
1293                   {
1294                      cs = new AnnotationColourGradient(
1295                          af.viewport.alignment.getAlignmentAnnotation()[i],
1296                          GetUserColourScheme(jms, view.getAnnotationColours().
1297                                                         getColourScheme()),
1298                          view.getAnnotationColours().getAboveThreshold()
1299                          );
1300                    }
1301                    else
1302                    {
1303                      cs = new AnnotationColourGradient(
1304                          af.viewport.alignment.getAlignmentAnnotation()[i],
1305                          ColourSchemeProperty.getColour(al,
1306                          view.getAnnotationColours().getColourScheme()),
1307                          view.getAnnotationColours().getAboveThreshold()
1308                          );
1309                    }
1310
1311                   // Also use these settings for all the groups
1312                   if (al.getGroups() != null)
1313                     for (int g = 0; g < al.getGroups().size(); g++)
1314                     {
1315                       jalview.datamodel.SequenceGroup sg
1316                           = (jalview.datamodel.SequenceGroup)al.getGroups().elementAt(g);
1317
1318                       if(sg.cs == null)
1319                         continue;
1320
1321
1322                   /*    if (view.getAnnotationColours().getColourScheme().equals("None"))
1323                       {
1324                         sg.cs = new AnnotationColourGradient(
1325                             af.viewport.alignment.getAlignmentAnnotation()[i],
1326                             new java.awt.Color(view.getAnnotationColours().
1327                                                getMinColour()),
1328                             new java.awt.Color(view.getAnnotationColours().
1329                                                getMaxColour()),
1330                             view.getAnnotationColours().getAboveThreshold());
1331                       }
1332                       else*/
1333                       {
1334                         sg.cs = new AnnotationColourGradient(
1335                             af.viewport.alignment.getAlignmentAnnotation()[i],
1336                             sg.cs,
1337                             view.getAnnotationColours().getAboveThreshold()
1338                             );
1339                       }
1340
1341                     }
1342
1343
1344                   break;
1345                 }
1346
1347               }
1348             }
1349             else
1350             {
1351                 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
1352             }
1353
1354             if(cs!=null)
1355             {
1356               cs.setThreshold(view.getPidThreshold(), true);
1357               cs.setConsensus(af.viewport.vconsensus);
1358             }
1359         }
1360
1361         af.setColourSelected(view.getBgColour());
1362         af.viewport.setGlobalColourScheme(cs);
1363         af.viewport.setColourAppliesToAllGroups(false);
1364         af.changeColour(cs);
1365         if (view.getConservationSelected() && cs!=null)
1366         {
1367           cs.setConservationInc(view.getConsThreshold());
1368         }
1369
1370         af.viewport.setColourAppliesToAllGroups(true);
1371
1372         if (view.getShowSequenceFeatures())
1373         {
1374            af.viewport.showSequenceFeatures = true;
1375            af.showSeqFeatures.setSelected(true);
1376         }
1377
1378         if(jms.getFeatureSettings()!=null)
1379         {
1380           af.viewport.featuresDisplayed = new Hashtable();
1381           String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];
1382          for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)
1383          {
1384            Setting setting = jms.getFeatureSettings().getSetting(fs);
1385
1386            af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),
1387                new java.awt.Color(setting.getColour()));
1388
1389            renderOrder[fs] = setting.getType();
1390
1391            if(setting.getDisplay())
1392              af.viewport.featuresDisplayed.put(
1393                  setting.getType(), new Integer(setting.getColour()));
1394          }
1395          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
1396         }
1397
1398         if (view.getHiddenColumnsCount() > 0)
1399         {
1400           for (int c = 0; c < view.getHiddenColumnsCount(); c++)
1401           {
1402               af.viewport.hideColumns(
1403                 view.getHiddenColumns(c).getStart(),
1404                 view.getHiddenColumns(c).getEnd() //+1
1405                 );
1406           }
1407         }
1408
1409
1410         Desktop.addInternalFrame(af, view.getTitle(),
1411              view.getWidth(), view.getHeight());
1412
1413         //LOAD TREES
1414         ///////////////////////////////////////
1415         if (jms.getTreeCount() > 0)
1416         {
1417             try
1418             {
1419                 for (int t = 0; t < jms.getTreeCount(); t++)
1420                 {
1421
1422                     Tree tree = jms.getTree(t);
1423
1424                     TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
1425                                 tree.getNewick()), tree.getTitle(),
1426                                 tree.getWidth(), tree.getHeight(),
1427                                 tree.getXpos(), tree.getYpos());
1428
1429                     tp.fitToWindow.setState(tree.getFitToWindow());
1430                     tp.fitToWindow_actionPerformed(null);
1431
1432                     if(tree.getFontName()!=null)
1433                       tp.setTreeFont(new java.awt.Font(tree.getFontName(),
1434                                           tree.getFontStyle(),
1435                                           tree.getFontSize()));
1436                     else
1437                       tp.setTreeFont(new java.awt.Font(view.getFontName(),
1438                                             view.getFontStyle(),
1439                                             tree.getFontSize()));
1440
1441                     tp.showPlaceholders(tree.getMarkUnlinked());
1442                     tp.showBootstrap(tree.getShowBootstrap());
1443                     tp.showDistances(tree.getShowDistances());
1444
1445                     tp.treeCanvas.threshold = tree.getThreshold();
1446
1447                     if (tree.getCurrentTree())
1448                       af.viewport.setCurrentTree(tp.getTree());
1449                 }
1450
1451             }
1452             catch (Exception ex)
1453             {
1454                 ex.printStackTrace();
1455             }
1456
1457         }
1458
1459         return af;
1460     }
1461 }
1462