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.setName(ResidueProperties.aa[i]);
 723                 col.setRGB(jalview.util.Format.getHexString(colours[i]));
 724                 jbucs.addColour(col);
 725             }
 726             if(ucs.getLowerCaseColours()!=null)
 727             {
 728               colours = ucs.getLowerCaseColours();
 729               for (int i = 0; i < colours.length; i++)
 730              {
 731                  jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
 732                  col.setName(ResidueProperties.aa[i].toLowerCase());
 733                  col.setRGB(jalview.util.Format.getHexString(colours[i]));
 734                  jbucs.addColour(col);
 735              }
 736             }
 737
 738             id = "ucs" + userColours.indexOf(ucs);
 739             uc.setId(id);
 740             uc.setUserColourScheme(jbucs);
 741             jms.addUserColours(uc);
 742         }
 743
 744         return id;
 745     }
 746
 747    jalview.schemes.UserColourScheme GetUserColourScheme(
 748         JalviewModelSequence jms, String id)
 749     {
 750         UserColours[] uc = jms.getUserColours();
 751         UserColours colours = null;
 752
 753         for (int i = 0; i < uc.length; i++)
 754         {
 755             if (uc[i].getId().equals(id))
 756             {
 757                 colours = uc[i];
 758
 759                 break;
 760             }
 761         }
 762
 763         java.awt.Color[] newColours = new java.awt.Color[24];
 764
 765         for (int i = 0; i < 24; i++)
 766         {
 767             newColours[i] = new java.awt.Color(Integer.parseInt(
 768                         colours.getUserColourScheme().getColour(i).getRGB(), 16));
 769         }
 770
 771         jalview.schemes.UserColourScheme ucs =
 772             new jalview.schemes.UserColourScheme(newColours);
 773
 774         if (colours.getUserColourScheme().getColourCount() > 24)
 775         {
 776           newColours = new java.awt.Color[23];
 777           for (int i = 0; i < 23; i++)
 778           {
 779             newColours[i] = new java.awt.Color(Integer.parseInt(
 780                 colours.getUserColourScheme().getColour(i+24).getRGB(), 16));
 781           }
 782           ucs.setLowerCaseColours(newColours);
 783         }
 784
 785         return ucs;
 786     }
 787
 788     /**
 789      * DOCUMENT ME!
 790      *
 791      * @param file DOCUMENT ME!
 792      */
 793     public AlignFrame LoadJalviewAlign(final String file)
 794     {
 795         jalview.gui.AlignFrame af = null;
 796         try
 797         {
 798             //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
 799             URL url = null;
 800
 801             if (file.startsWith("http://"))
 802             {
 803                 url = new URL(file);
 804             }
 805
 806             JarInputStream jin = null;
 807             JarEntry jarentry = null;
 808             int entryCount = 1;
 809
 810             do
 811             {
 812                 if (url != null)
 813                 {
 814                     jin = new JarInputStream(url.openStream());
 815                 }
 816                 else
 817                 {
 818                     jin = new JarInputStream(new FileInputStream(file));
 819                 }
 820
 821                 for (int i = 0; i < entryCount; i++)
 822                 {
 823                     jarentry = jin.getNextJarEntry();
 824                 }
 825
 826                 if (jarentry != null && jarentry.getName().endsWith(".xml"))
 827                 {
 828                     InputStreamReader in = new InputStreamReader(jin, "UTF-8");
 829                     JalviewModel object = new JalviewModel();
 830
 831                     Unmarshaller unmar = new Unmarshaller(object);
 832                     unmar.setValidation(false);
 833                     object = (JalviewModel) unmar.unmarshal( in );
 834
 835                     af = LoadFromObject(object, file);
 836                     entryCount++;
 837                 }
 838                 else if (jarentry != null)
 839                 {
 840                   //Some other file here.
 841                   entryCount++;
 842                 }
 843             }
 844             while (jarentry != null);
 845         }
 846         catch(java.net.UnknownHostException ex)
 847         {
 848           ex.printStackTrace();
 849           System.err.println("Couldn't locate Jalview XML file : " +
 850               ex + "\n");
 851
 852           javax.swing.SwingUtilities.invokeLater(new Runnable()
 853           {
 854             public void run()
 855             {
 856               JOptionPane.showInternalMessageDialog(Desktop.desktop,
 857                   "Couldn't locate " + file,
 858                   "URL not found",
 859                   JOptionPane.WARNING_MESSAGE);
 860             }
 861           });
 862         }
 863         catch (Exception ex)
 864         {
 865
 866           //Is Version 1 Jar file?
 867           af =  new Jalview2XML_V1().LoadJalviewAlign(file);
 868
 869           if(af!=null)
 870           {
 871             System.out.println("Successfully loaded archive file");
 872             return af;
 873           }
 874           ex.printStackTrace();
 875             System.err.println("Exception whilst loading jalview XML file : " +
 876                 ex + "\n");
 877             javax.swing.SwingUtilities.invokeLater(new Runnable()
 878             {
 879               public void run()
 880               {
 881
 882                 JOptionPane.showInternalMessageDialog(Desktop.desktop,
 883                     "Error loading  " + file,
 884                     "Error loading Jalview file",
 885                     JOptionPane.WARNING_MESSAGE);
 886               }});
 887         }
 888
 889         return af;
 890     }
 891
 892     String loadPDBFile(String file, String pdbId)
 893     {
 894       System.out.println("load file "+file);
 895       try
 896       {
 897         JarInputStream jin = null;
 898
 899         if (file.startsWith("http://"))
 900         {
 901           jin = new JarInputStream(new URL(file).openStream());
 902         }
 903         else
 904         {
 905           jin = new JarInputStream(new FileInputStream(file));
 906         }
 907
 908         JarEntry entry = null;
 909         do
 910         {
 911           entry = jin.getNextJarEntry();
 912         }
 913         while (!entry.getName().equals(pdbId));
 914
 915         BufferedReader in = new BufferedReader(new InputStreamReader(jin));
 916         File outFile = File.createTempFile("jalview_pdb", ".txt");
 917         outFile.deleteOnExit();
 918         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
 919         String data;
 920
 921         while ( (data = in.readLine()) != null)
 922         {
 923           out.println(data);
 924         }
 925         out.close();
 926         return outFile.getAbsolutePath();
 927
 928       }
 929       catch (Exception ex)
 930       {
 931         ex.printStackTrace();
 932       }
 933
 934       return null;
 935     }
 936
 937
 938     AlignFrame LoadFromObject(JalviewModel object, String file)
 939     {
 940         Vector seqids = new Vector();
 941         SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
 942         Sequence[] vamsasSeq = vamsasSet.getSequence();
 943
 944         JalviewModelSequence jms = object.getJalviewModelSequence();
 945
 946         //////////////////////////////////
 947         //LOAD SEQUENCES
 948         Vector hiddenSeqs = null;
 949         jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
 950         JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
 951         for (int i = 0; i < vamsasSeq.length; i++)
 952         {
 953             jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
 954                     vamsasSeq[i].getSequence());
 955             jseqs[i].setDescription( vamsasSeq[i].getDescription() );
 956
 957             if(JSEQ[i].getHidden())
 958             {
 959               if(hiddenSeqs == null)
 960                 hiddenSeqs = new Vector();
 961               hiddenSeqs.addElement(jseqs[i]);
 962             }
 963             jseqs[i].setStart(JSEQ[i].getStart());
 964             jseqs[i].setEnd(JSEQ[i].getEnd());
 965             jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));
 966             seqids.add(jseqs[i]);
 967         }
 968
 969         ///SequenceFeatures are added to the DatasetSequence,
 970         // so we must create the dataset before loading features
 971         /////////////////////////////////
 972         jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
 973         al.setDataset(null);
 974         /////////////////////////////////
 975
 976
 977         Hashtable pdbloaded = new Hashtable();
 978         for (int i = 0; i < vamsasSeq.length; i++)
 979         {
 980           if (JSEQ[i].getFeaturesCount() > 0)
 981           {
 982             Features[] features = JSEQ[i].getFeatures();
 983             for (int f = 0; f < features.length; f++)
 984             {
 985               jalview.datamodel.SequenceFeature sf
 986                   = new jalview.datamodel.SequenceFeature(features[f].getType(),
 987                   features[f].getDescription(), features[f].getStatus(),
 988                   features[f].getBegin(), features[f].getEnd(),
 989                   features[f].getFeatureGroup());
 990
 991               sf.setScore(features[f].getScore());
 992               for(int od=0; od<features[f].getOtherDataCount(); od++)
 993               {
 994                 OtherData keyValue = features[f].getOtherData(od);
 995                 if(keyValue.getKey().startsWith("LINK"))
 996                   sf.addLink(keyValue.getValue());
 997                 else
 998                   sf.setValue(keyValue.getKey(), keyValue.getValue());
 999
1000               }
1001
1002               al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1003             }
1004           }
1005           if (JSEQ[i].getPdbidsCount() > 0)
1006           {
1007             Pdbids[] ids = JSEQ[i].getPdbids();
1008             for (int p = 0; p < ids.length; p++)
1009             {
1010               jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
1011               entry.setId(ids[p].getId());
1012               entry.setType(ids[p].getType());
1013               if (ids[p].getFile() != null)
1014               {
1015                 if (!pdbloaded.containsKey(ids[p].getFile()))
1016                 {
1017                   String tmppdb = loadPDBFile(file, ids[p].getId());
1018                   entry.setFile(tmppdb);
1019                   pdbloaded.put(ids[p].getId(), tmppdb);
1020                 }
1021                 else
1022                   entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1023               }
1024
1025               al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1026             }
1027           }
1028           if(vamsasSeq[i].getDBRefCount()>0)
1029           {
1030             for(int d=0; d<vamsasSeq[i].getDBRefCount(); d++)
1031             {
1032               jalview.datamodel.DBRefEntry entry =
1033                   new jalview.datamodel.DBRefEntry(
1034                       vamsasSeq[i].getDBRef(d).getSource(),
1035                       vamsasSeq[i].getDBRef(d).getVersion(),
1036                       vamsasSeq[i].getDBRef(d).getAccessionId()
1037                       );
1038               al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);
1039             }
1040
1041           }
1042         }
1043
1044
1045
1046          /////////////////////////////////
1047         //////////////////////////////////
1048         //LOAD ANNOTATIONS
1049         boolean hideQuality = true,
1050             hideConservation = true,
1051             hideConsensus = true;
1052
1053         if (vamsasSet.getAnnotation() != null)
1054         {
1055             Annotation[] an = vamsasSet.getAnnotation();
1056
1057             for (int i = 0; i < an.length; i++)
1058             {
1059                if (an[i].getLabel().equals("Quality"))
1060                 {
1061                  hideQuality = false;
1062                  continue;
1063                 }
1064                else if(an[i].getLabel().equals("Conservation"))
1065                {
1066                  hideConservation = false;
1067                  continue;
1068                }
1069                else if(an[i].getLabel().equals("Consensus"))
1070                {
1071                  hideConsensus = false;
1072                  continue;
1073                }
1074
1075                 AnnotationElement[] ae = an[i].getAnnotationElement();
1076                 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];
1077
1078                 for (int aa = 0; aa < ae.length; aa++)
1079                 {
1080                     anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),
1081                             ae[aa].getDescription(),
1082                             ae[aa].getSecondaryStructure().length()==0?' ':ae[aa].getSecondaryStructure().charAt(0),
1083                             ae[aa].getValue());
1084                     anot[ae[aa].getPosition()].colour = new java.awt.Color( ae[aa].getColour() );
1085                 }
1086
1087                 jalview.datamodel.AlignmentAnnotation jaa = null;
1088
1089                 if (an[i].getGraph())
1090                 {
1091                   jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1092                       an[i].getDescription(), anot, 0, 0,
1093                       an[i].getGraphType());
1094
1095                   jaa.graphGroup = an[i].getGraphGroup();
1096
1097                   if (an[i].getThresholdLine() != null)
1098                   {
1099                     jaa.setThreshold(new jalview.datamodel.GraphLine(
1100                                   an[i].getThresholdLine().getValue(),
1101                                   an[i].getThresholdLine().getLabel(),
1102                                 new java.awt.Color(an[i].getThresholdLine().getColour()))
1103                              );
1104
1105                   }
1106
1107                 }
1108                 else
1109                 {
1110                     jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1111                             an[i].getDescription(), anot);
1112                 }
1113
1114                 if(an[i].getSequenceRef()!=null)
1115                 {
1116                   jaa.createSequenceMapping(
1117                       al.findName(an[i].getSequenceRef()), 1, true
1118                       );
1119                   al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
1120                 }
1121
1122                 al.addAnnotation(jaa);
1123             }
1124         }
1125
1126
1127         //  af.changeColour() );
1128         /////////////////////////
1129         //LOAD GROUPS
1130         if (jms.getJGroupCount() > 0)
1131         {
1132             JGroup[] groups = jms.getJGroup();
1133
1134             for (int i = 0; i < groups.length; i++)
1135             {
1136                 ColourSchemeI cs = null;
1137
1138                 if (groups[i].getColour() != null)
1139                 {
1140                     if (groups[i].getColour().startsWith("ucs"))
1141                     {
1142                         cs = GetUserColourScheme(jms, groups[i].getColour());
1143                     }
1144                     else
1145                     {
1146                         cs = ColourSchemeProperty.getColour(al,
1147                                 groups[i].getColour());
1148                     }
1149
1150                     if(cs!=null)
1151                       cs.setThreshold(groups[i].getPidThreshold(), true);
1152                 }
1153
1154                 Vector seqs = new Vector();
1155                 int[] ids = groups[i].getSeq();
1156
1157                 for (int s = 0; s < ids.length; s++)
1158                 {
1159                     seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(
1160                             ids[s]));
1161                 }
1162
1163                 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,
1164                         groups[i].getName(), cs, groups[i].getDisplayBoxes(),
1165                         groups[i].getDisplayText(), groups[i].getColourText(),
1166                         groups[i].getStart(), groups[i].getEnd());
1167
1168                 sg.setOutlineColour(new java.awt.Color(
1169                         groups[i].getOutlineColour()));
1170
1171                 if (groups[i].getConsThreshold() != 0)
1172                 {
1173                     jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
1174                             ResidueProperties.propHash, 3, sg.getSequences(false), 0,
1175                             sg.getWidth() - 1);
1176                     c.calculate();
1177                     c.verdict(false, 25);
1178                     sg.cs.setConservation(c);
1179                 }
1180
1181                 al.addGroup(sg);
1182             }
1183         }
1184
1185
1186         /////////////////////////////////
1187         // LOAD VIEWPORT
1188         Viewport[] views = jms.getViewport();
1189         Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
1190
1191
1192         AlignFrame af = new AlignFrame(al);
1193
1194         if(hiddenSeqs!=null)
1195         {
1196           for(int s=0; s<JSEQ.length; s++)
1197           {
1198             for(int r=0; r<JSEQ[s].getHiddenSequencesCount(); r++)
1199             {
1200               al.getSequenceAt(s).addHiddenSequence(
1201                   al.getSequenceAt( JSEQ[s].getHiddenSequences(r)  )
1202                   );
1203             }
1204           }
1205
1206           jalview.datamodel.SequenceI [] hseqs = new
1207               jalview.datamodel.SequenceI[hiddenSeqs.size()];
1208
1209           for(int s=0; s<hiddenSeqs.size(); s++)
1210             hseqs[s] = (jalview.datamodel.SequenceI)hiddenSeqs.elementAt(s);
1211
1212           af.viewport.hideSequence( hseqs );
1213
1214         }
1215
1216
1217         if(hideConsensus || hideQuality || hideConservation)
1218         {
1219           int hSize = al.getAlignmentAnnotation().length;
1220           for (int h = 0; h < hSize; h++)
1221           {
1222             if (
1223                 (hideConsensus &&
1224                  al.getAlignmentAnnotation()[h].label.equals("Consensus"))
1225                 ||
1226                 (hideQuality &&
1227                  al.getAlignmentAnnotation()[h].label.equals("Quality"))
1228                 ||
1229                 (hideConservation &&
1230                  al.getAlignmentAnnotation()[h].label.equals("Conservation")))
1231             {
1232               al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
1233               hSize--;
1234               h--;
1235             }
1236           }
1237           af.alignPanel.adjustAnnotationHeight();
1238         }
1239
1240         af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
1241             view.getHeight());
1242         af.viewport.setStartRes(view.getStartRes());
1243         af.viewport.setStartSeq(view.getStartSeq());
1244         af.viewport.setShowAnnotation(view.getShowAnnotation());
1245         af.viewport.showConservation = view.getShowConservation();
1246         af.viewport.showQuality = view.getShowQuality();
1247         af.viewport.showIdentity = view.getShowIdentity();
1248         af.viewport.setAbovePIDThreshold(view.getPidSelected());
1249         af.abovePIDThreshold.setSelected(view.getPidSelected());
1250         af.viewport.setColourText(view.getShowColourText());
1251         af.colourTextMenuItem.setSelected(view.getShowColourText());
1252         af.viewport.setConservationSelected(view.getConservationSelected());
1253         af.conservationMenuItem.setSelected(view.getConservationSelected());
1254
1255         af.viewport.setShowJVSuffix(view.getShowFullId());
1256         af.seqLimits.setSelected(view.getShowFullId());
1257
1258         af.viewport.setFont(new java.awt.Font(view.getFontName(),
1259                 view.getFontStyle(), view.getFontSize()));
1260         af.alignPanel.fontChanged();
1261
1262         af.viewport.setRenderGaps(view.getRenderGaps());
1263         af.renderGapsMenuItem.setSelected(view.getRenderGaps());
1264
1265         af.viewport.setWrapAlignment(view.getWrapAlignment());
1266         af.wrapMenuItem.setSelected(view.getWrapAlignment());
1267
1268         af.alignPanel.setWrapAlignment(view.getWrapAlignment());
1269
1270         af.annotationPanelMenuItem.setState(view.getShowAnnotation());
1271         af.viewport.setShowAnnotation(view.getShowAnnotation());
1272         af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
1273
1274         af.viewport.setShowBoxes(view.getShowBoxes());
1275         af.viewBoxesMenuItem.setSelected(view.getShowBoxes());
1276         af.viewport.setShowText(view.getShowText());
1277         af.viewTextMenuItem.setSelected(view.getShowText());
1278
1279         ColourSchemeI cs = null;
1280
1281         if (view.getBgColour() != null)
1282         {
1283             if (view.getBgColour().startsWith("ucs"))
1284             {
1285                 cs = GetUserColourScheme(jms, view.getBgColour());
1286             }
1287             else if(view.getBgColour().startsWith("Annotation"))
1288             {
1289               //int find annotation
1290               for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
1291               {
1292                 if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
1293                     equals(view.getAnnotationColours().getAnnotation()))
1294                 {
1295                   if (af.viewport.alignment.getAlignmentAnnotation()[i].
1296                       getThreshold() == null)
1297                   {
1298                     af.viewport.alignment.getAlignmentAnnotation()[i].
1299                         setThreshold(
1300                             new jalview.datamodel.GraphLine(
1301                                 view.getAnnotationColours().getThreshold(),
1302                                 "Threshold", java.awt.Color.black)
1303
1304                         );
1305                   }
1306
1307
1308                   if (view.getAnnotationColours().getColourScheme().equals(
1309                       "None"))
1310                   {
1311                     cs = new AnnotationColourGradient(
1312                         af.viewport.alignment.getAlignmentAnnotation()[i],
1313                         new java.awt.Color(view.getAnnotationColours().
1314                                            getMinColour()),
1315                         new java.awt.Color(view.getAnnotationColours().
1316                                            getMaxColour()),
1317                         view.getAnnotationColours().getAboveThreshold());
1318                   }
1319                   else if (view.getAnnotationColours().getColourScheme().
1320                            startsWith("ucs"))
1321                   {
1322                      cs = new AnnotationColourGradient(
1323                          af.viewport.alignment.getAlignmentAnnotation()[i],
1324                          GetUserColourScheme(jms, view.getAnnotationColours().
1325                                                         getColourScheme()),
1326                          view.getAnnotationColours().getAboveThreshold()
1327                          );
1328                    }
1329                    else
1330                    {
1331                      cs = new AnnotationColourGradient(
1332                          af.viewport.alignment.getAlignmentAnnotation()[i],
1333                          ColourSchemeProperty.getColour(al,
1334                          view.getAnnotationColours().getColourScheme()),
1335                          view.getAnnotationColours().getAboveThreshold()
1336                          );
1337                    }
1338
1339                   // Also use these settings for all the groups
1340                   if (al.getGroups() != null)
1341                     for (int g = 0; g < al.getGroups().size(); g++)
1342                     {
1343                       jalview.datamodel.SequenceGroup sg
1344                           = (jalview.datamodel.SequenceGroup)al.getGroups().elementAt(g);
1345
1346                       if(sg.cs == null)
1347                         continue;
1348
1349
1350                   /*    if (view.getAnnotationColours().getColourScheme().equals("None"))
1351                       {
1352                         sg.cs = new AnnotationColourGradient(
1353                             af.viewport.alignment.getAlignmentAnnotation()[i],
1354                             new java.awt.Color(view.getAnnotationColours().
1355                                                getMinColour()),
1356                             new java.awt.Color(view.getAnnotationColours().
1357                                                getMaxColour()),
1358                             view.getAnnotationColours().getAboveThreshold());
1359                       }
1360                       else*/
1361                       {
1362                         sg.cs = new AnnotationColourGradient(
1363                             af.viewport.alignment.getAlignmentAnnotation()[i],
1364                             sg.cs,
1365                             view.getAnnotationColours().getAboveThreshold()
1366                             );
1367                       }
1368
1369                     }
1370
1371
1372                   break;
1373                 }
1374
1375               }
1376             }
1377             else
1378             {
1379                 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
1380             }
1381
1382             if(cs!=null)
1383             {
1384               cs.setThreshold(view.getPidThreshold(), true);
1385               cs.setConsensus(af.viewport.vconsensus);
1386             }
1387         }
1388
1389         af.setColourSelected(view.getBgColour());
1390         af.viewport.setGlobalColourScheme(cs);
1391         af.viewport.setColourAppliesToAllGroups(false);
1392         af.changeColour(cs);
1393         if (view.getConservationSelected() && cs!=null)
1394         {
1395           cs.setConservationInc(view.getConsThreshold());
1396         }
1397
1398         af.viewport.setColourAppliesToAllGroups(true);
1399
1400         if (view.getShowSequenceFeatures())
1401         {
1402            af.viewport.showSequenceFeatures = true;
1403            af.showSeqFeatures.setSelected(true);
1404         }
1405
1406         if(jms.getFeatureSettings()!=null)
1407         {
1408           af.viewport.featuresDisplayed = new Hashtable();
1409           String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];
1410          for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)
1411          {
1412            Setting setting = jms.getFeatureSettings().getSetting(fs);
1413
1414            af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),
1415                new java.awt.Color(setting.getColour()));
1416
1417            renderOrder[fs] = setting.getType();
1418
1419            if(setting.getDisplay())
1420              af.viewport.featuresDisplayed.put(
1421                  setting.getType(), new Integer(setting.getColour()));
1422          }
1423          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
1424         }
1425
1426         if (view.getHiddenColumnsCount() > 0)
1427         {
1428           for (int c = 0; c < view.getHiddenColumnsCount(); c++)
1429           {
1430               af.viewport.hideColumns(
1431                 view.getHiddenColumns(c).getStart(),
1432                 view.getHiddenColumns(c).getEnd() //+1
1433                 );
1434           }
1435         }
1436
1437
1438         Desktop.addInternalFrame(af, view.getTitle(),
1439              view.getWidth(), view.getHeight());
1440
1441         //LOAD TREES
1442         ///////////////////////////////////////
1443         if (jms.getTreeCount() > 0)
1444         {
1445             try
1446             {
1447                 for (int t = 0; t < jms.getTreeCount(); t++)
1448                 {
1449
1450                     Tree tree = jms.getTree(t);
1451
1452                     TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
1453                                 tree.getNewick()), tree.getTitle(),
1454                                 tree.getWidth(), tree.getHeight(),
1455                                 tree.getXpos(), tree.getYpos());
1456
1457                     tp.fitToWindow.setState(tree.getFitToWindow());
1458                     tp.fitToWindow_actionPerformed(null);
1459
1460                     if(tree.getFontName()!=null)
1461                       tp.setTreeFont(new java.awt.Font(tree.getFontName(),
1462                                           tree.getFontStyle(),
1463                                           tree.getFontSize()));
1464                     else
1465                       tp.setTreeFont(new java.awt.Font(view.getFontName(),
1466                                             view.getFontStyle(),
1467                                             tree.getFontSize()));
1468
1469                     tp.showPlaceholders(tree.getMarkUnlinked());
1470                     tp.showBootstrap(tree.getShowBootstrap());
1471                     tp.showDistances(tree.getShowDistances());
1472
1473                     tp.treeCanvas.threshold = tree.getThreshold();
1474
1475                     if (tree.getCurrentTree())
1476                       af.viewport.setCurrentTree(tp.getTree());
1477                 }
1478
1479             }
1480             catch (Exception ex)
1481             {
1482                 ex.printStackTrace();
1483             }
1484
1485         }
1486
1487         return af;
1488     }
1489 }
1490