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 ALIGNMENT WINDOWS TO SAME JARFILE
  52     public void SaveState(File statefile)
  53     {
  54         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
  55
  56         if (frames == null)
  57         {
  58             return;
  59         }
  60
  61         try
  62         {
  63             FileOutputStream fos = new FileOutputStream(statefile);
  64             JarOutputStream jout = new JarOutputStream(fos);
  65
  66             //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
  67             ////////////////////////////////////////////////////
  68             PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
  69                         "UTF-8"));
  70
  71             Vector shortNames = new Vector();
  72
  73             //REVERSE ORDER
  74             for (int i = frames.length - 1; i > -1; i--)
  75             {
  76                 if (frames[i] instanceof AlignFrame)
  77                 {
  78                     AlignFrame af = (AlignFrame) frames[i];
  79
  80                     String shortName = af.getTitle();
  81
  82                     if (shortName.indexOf(File.separatorChar) > -1)
  83                     {
  84                         shortName = shortName.substring(shortName.lastIndexOf(
  85                                     File.separatorChar) + 1);
  86                     }
  87
  88                     int count = 1;
  89
  90                     while (shortNames.contains(shortName))
  91                     {
  92                         if (shortName.endsWith("_" + (count - 1)))
  93                         {
  94                             shortName = shortName.substring(0,
  95                                     shortName.lastIndexOf("_"));
  96                         }
  97
  98                         shortName = shortName.concat("_" + count);
  99                         count++;
 100                     }
 101
 102                     shortNames.addElement(shortName);
 103
 104                     if (!shortName.endsWith(".xml"))
 105                     {
 106                         shortName = shortName + ".xml";
 107                     }
 108
 109                     int ap, apSize= af.alignPanels.size();
 110                     for (ap = 0; ap < apSize; ap++)
 111                     {
 112                       AlignmentPanel apanel = (AlignmentPanel) af.alignPanels.
 113                           elementAt(ap);
 114
 115                       if (apanel.av.explodedPosition == null)
 116                         apanel.av.explodedPosition = af.getBounds();
 117
 118                       SaveState(apanel,
 119                                 apSize == 1 ? shortName : ap+shortName,
 120                                 jout, out);
 121                     }
 122                 }
 123             }
 124
 125             out.close();
 126             jout.close();
 127         }
 128         catch (Exception ex)
 129         {
 130             ex.printStackTrace();
 131         }
 132     }
 133
 134     // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
 135     public void SaveAlignment(AlignFrame af, String jarFile,
 136         String fileName)
 137     {
 138         try
 139         {
 140           int ap, apSize= af.alignPanels.size();
 141           FileOutputStream fos = new FileOutputStream(jarFile);
 142           JarOutputStream jout = new JarOutputStream(fos);
 143           PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
 144                 "UTF-8"));
 145           for( ap=0; ap<apSize; ap++)
 146           {
 147             AlignmentPanel apanel = (AlignmentPanel)af.alignPanels.elementAt(ap);
 148
 149             if (apanel.av.explodedPosition == null)
 150               apanel.av.explodedPosition = af.getBounds();
 151
 152             SaveState(apanel,
 153                       apSize==1?fileName:fileName+ap,
 154                       jout, out);
 155           }
 156
 157           out.close();
 158           jout.close();
 159         }
 160         catch (Exception ex)
 161         {
 162           ex.printStackTrace();
 163         }
 164     }
 165
 166     /**
 167      * DOCUMENT ME!
 168      *
 169      * @param af DOCUMENT ME!
 170      * @param timeStamp DOCUMENT ME!
 171      * @param fileName DOCUMENT ME!
 172      * @param jout DOCUMENT ME!
 173      * @param out DOCUMENT ME!
 174      */
 175     public void SaveState(AlignmentPanel ap,
 176                           String fileName,
 177                           JarOutputStream jout,
 178                           PrintWriter out)
 179     {
 180       if (seqRefIds == null)
 181         seqRefIds = new Hashtable();
 182
 183         Vector userColours = new Vector();
 184
 185         AlignViewport av = ap.av;
 186
 187         JalviewModel object = new JalviewModel();
 188         object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
 189
 190         object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
 191         object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
 192
 193         jalview.datamodel.AlignmentI jal = av.alignment;
 194
 195         if(av.hasHiddenRows)
 196         {
 197           jal = jal.getHiddenSequences().getFullAlignment();
 198         }
 199
 200         SequenceSet vamsasSet = new SequenceSet();
 201         Sequence vamsasSeq;
 202         JalviewModelSequence jms = new JalviewModelSequence();
 203
 204         vamsasSet.setGapChar(jal.getGapCharacter() + "");
 205
 206         JSeq jseq;
 207         Vector pdbfiles = null;
 208
 209         //SAVE SEQUENCES
 210         int id = 0;
 211         for (int i = 0; i < jal.getHeight(); i++)
 212         {
 213             id = jal.getSequenceAt(i).hashCode();
 214
 215             if(seqRefIds.get(id+"")!=null)
 216             {
 217
 218             }
 219             else
 220             {
 221               vamsasSeq = new Sequence();
 222               vamsasSeq.setId(id + "");
 223               vamsasSeq.setName(jal.getSequenceAt(i).getName());
 224               vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());
 225               vamsasSeq.setDescription(jal.getSequenceAt(i).getDescription());
 226
 227               if (jal.getSequenceAt(i).getDatasetSequence().getDBRef() != null)
 228               {
 229                 jalview.datamodel.DBRefEntry[] dbrefs =
 230                     jal.getSequenceAt(i).getDatasetSequence().getDBRef();
 231
 232                 for (int d = 0; d < dbrefs.length; d++)
 233                 {
 234                   DBRef dbref = new DBRef();
 235                   dbref.setSource(dbrefs[d].getSource());
 236                   dbref.setVersion(dbrefs[d].getVersion());
 237                   dbref.setAccessionId(dbrefs[d].getAccessionId());
 238                   vamsasSeq.addDBRef(dbref);
 239                 }
 240               }
 241
 242               vamsasSet.addSequence(vamsasSeq);
 243               seqRefIds.put(id+"", vamsasSeq);
 244             }
 245
 246             jseq = new JSeq();
 247             jseq.setStart(jal.getSequenceAt(i).getStart());
 248             jseq.setEnd(jal.getSequenceAt(i).getEnd());
 249             jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());
 250
 251             jseq.setId(id);
 252
 253             if (av.hasHiddenRows)
 254             {
 255               jseq.setHidden(av.alignment.getHiddenSequences().isHidden(
 256                   jal.getSequenceAt(i)));
 257
 258               if(jal.getSequenceAt(i).getHiddenSequences()!=null)
 259               {
 260                 jalview.datamodel.SequenceI [] reps =
 261                     jal.getSequenceAt(i).getHiddenSequences().getSequencesInOrder(jal);
 262
 263                 for(int h=0; h<reps.length; h++)
 264                 {
 265                   jseq.addHiddenSequences(
 266                       jal.findIndex(reps[h])
 267                       );
 268                 }
 269               }
 270             }
 271
 272
 273             if(jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures()!=null)
 274             {
 275               jalview.datamodel.SequenceFeature[] sf
 276                   = jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
 277               int index = 0;
 278               while(index < sf.length)
 279               {
 280                 Features features = new Features();
 281
 282                 features.setBegin(sf[index].getBegin());
 283                 features.setEnd(sf[index].getEnd());
 284                 features.setDescription(sf[index].getDescription());
 285                 features.setType(sf[index].getType());
 286                 features.setFeatureGroup(sf[index].getFeatureGroup());
 287                 features.setScore(sf[index].getScore());
 288                 if(sf[index].links!=null)
 289                 {
 290                   for(int l=0; l<sf[index].links.size(); l++)
 291                   {
 292                     OtherData keyValue = new OtherData();
 293                     keyValue.setKey("LINK_"+l);
 294                     keyValue.setValue(sf[index].links.elementAt(l).toString());
 295                     features.addOtherData(keyValue);
 296                   }
 297                 }
 298                 if(sf[index].otherDetails!=null)
 299                 {
 300                   String key;
 301                   Enumeration keys = sf[index].otherDetails.keys();
 302                   while(keys.hasMoreElements())
 303                   {
 304                     key = keys.nextElement().toString();
 305                     OtherData keyValue = new OtherData();
 306                     keyValue.setKey( key );
 307                     keyValue.setValue(
 308                         sf[index].otherDetails.get(key).toString());
 309                     features.addOtherData(keyValue);
 310                   }
 311                 }
 312
 313                 jseq.addFeatures(features);
 314                 index ++;
 315               }
 316             }
 317
 318             if(jal.getSequenceAt(i).getDatasetSequence().getPDBId()!=null)
 319             {
 320               Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getPDBId().elements();
 321               while(en.hasMoreElements())
 322               {
 323                 Pdbids pdb = new Pdbids();
 324                 jalview.datamodel.PDBEntry entry
 325                    = (jalview.datamodel.PDBEntry)en.nextElement();
 326
 327                 pdb.setId(entry.getId());
 328                 pdb.setType(entry.getType());
 329
 330                 if(entry.getFile()!=null)
 331                 {
 332                   if(pdbfiles==null)
 333                     pdbfiles = new Vector();
 334
 335
 336                   if(!pdbfiles.contains(entry.getId()))
 337                   {
 338                     pdbfiles.addElement(entry.getId());
 339                     try
 340                     {
 341                       File file = new File(entry.getFile());
 342                       if(file.exists())
 343                       {
 344                         byte[] data = new byte[ (int) file.length()];
 345                         jout.putNextEntry(new JarEntry(entry.getId()));
 346                         DataInputStream dis = new DataInputStream(new
 347                             FileInputStream(file));
 348                         dis.readFully(data);
 349
 350                         DataOutputStream dout = new DataOutputStream(jout);
 351                         dout.write(data, 0, data.length);
 352                         jout.closeEntry();
 353                       }
 354                     }
 355                     catch (Exception ex)
 356                     {
 357                       ex.printStackTrace();
 358                     }
 359                   }
 360                 }
 361
 362
 363                 if(entry.getProperty()!=null)
 364                 {
 365                   PdbentryItem item = new PdbentryItem();
 366                   Hashtable properties = entry.getProperty();
 367                   Enumeration en2 = properties.keys();
 368                   while(en2.hasMoreElements())
 369                   {
 370                     Property prop = new Property();
 371                     String key = en2.nextElement().toString();
 372                     prop.setName(key);
 373                     prop.setValue( properties.get(key).toString() );
 374                     item.addProperty(prop);
 375                   }
 376                   pdb.addPdbentryItem(item);
 377                 }
 378
 379                 jseq.addPdbids(pdb);
 380               }
 381             }
 382
 383             jms.addJSeq(jseq);
 384         }
 385
 386         if(av.hasHiddenRows)
 387           jal = av.alignment;
 388
 389
 390         //SAVE TREES
 391         ///////////////////////////////////
 392         if (av.currentTree != null)
 393         {
 394           // FIND ANY ASSOCIATED TREES
 395           // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
 396           if (Desktop.desktop != null)
 397           {
 398             JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 399
 400             for (int t = 0; t < frames.length; t++)
 401             {
 402               if (frames[t] instanceof TreePanel)
 403               {
 404                 TreePanel tp = (TreePanel) frames[t];
 405
 406                 if (tp.treeCanvas.av.alignment == jal)
 407                 {
 408                   Tree tree = new Tree();
 409                   tree.setTitle(tp.getTitle());
 410                   tree.setCurrentTree( (av.currentTree == tp.getTree()));
 411                   tree.setNewick(tp.getTree().toString());
 412                   tree.setThreshold(tp.treeCanvas.threshold);
 413
 414                   tree.setFitToWindow(tp.fitToWindow.getState());
 415                   tree.setFontName(tp.getTreeFont().getName());
 416                   tree.setFontSize(tp.getTreeFont().getSize());
 417                   tree.setFontStyle(tp.getTreeFont().getStyle());
 418                   tree.setMarkUnlinked(tp.placeholdersMenu.getState());
 419
 420                   tree.setShowBootstrap(tp.bootstrapMenu.getState());
 421                   tree.setShowDistances(tp.distanceMenu.getState());
 422
 423                   tree.setHeight(tp.getHeight());
 424                   tree.setWidth(tp.getWidth());
 425                   tree.setXpos(tp.getX());
 426                   tree.setYpos(tp.getY());
 427
 428                   jms.addTree(tree);
 429                 }
 430               }
 431             }
 432           }
 433         }
 434
 435         //SAVE ANNOTATIONS
 436         if (jal.getAlignmentAnnotation() != null)
 437         {
 438             jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
 439
 440             for (int i = 0; i < aa.length; i++)
 441             {
 442                 Annotation an = new Annotation();
 443
 444                 if (aa[i].label.equals("Quality") ||
 445                         aa[i].label.equals("Conservation") ||
 446                         aa[i].label.equals("Consensus"))
 447                 {
 448                     an.setLabel(aa[i].label);
 449                     an.setGraph(true);
 450                     vamsasSet.addAnnotation(an);
 451                     continue;
 452                 }
 453
 454
 455                 an.setDescription(aa[i].description);
 456
 457                 if(aa[i].sequenceRef!=null)
 458                  {
 459                    an.setSequenceRef(aa[i].sequenceRef.getName());
 460                  }
 461
 462                 if(aa[i].graph>0)
 463                 {
 464                   an.setGraph(true);
 465                   an.setGraphType(aa[i].graph);
 466                   an.setGraphGroup(aa[i].graphGroup);
 467                   if(aa[i].getThreshold()!=null)
 468                   {
 469                     ThresholdLine line = new ThresholdLine();
 470                     line.setLabel(aa[i].getThreshold().label);
 471                     line.setValue(aa[i].getThreshold().value);
 472                     line.setColour(aa[i].getThreshold().colour.getRGB());
 473                     an.setThresholdLine(line);
 474                   }
 475                 }
 476                 else
 477                   an.setGraph(false);
 478
 479                 an.setLabel(aa[i].label);
 480
 481                 AnnotationElement ae;
 482
 483                 for (int a = 0; a < aa[i].annotations.length; a++)
 484                 {
 485                     if ((aa[i] == null) || (aa[i].annotations[a] == null))
 486                     {
 487                         continue;
 488                     }
 489
 490                     ae = new AnnotationElement();
 491                     ae.setDescription(aa[i].annotations[a].description);
 492                     ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
 493                     ae.setValue(aa[i].annotations[a].value);
 494                     ae.setPosition(a);
 495                     ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
 496                         "");
 497
 498                     if(aa[i].annotations[a].colour!=java.awt.Color.black)
 499                       ae.setColour(aa[i].annotations[a].colour.getRGB());
 500
 501                     an.addAnnotationElement(ae);
 502                 }
 503
 504                 vamsasSet.addAnnotation(an);
 505             }
 506         }
 507
 508         //SAVE GROUPS
 509         if (jal.getGroups() != null)
 510         {
 511             JGroup[] groups = new JGroup[jal.getGroups().size()];
 512
 513             for (int i = 0; i < groups.length; i++)
 514             {
 515                 groups[i] = new JGroup();
 516
 517                 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()
 518                                                                                           .elementAt(i);
 519                 groups[i].setStart(sg.getStartRes());
 520                 groups[i].setEnd(sg.getEndRes());
 521                 groups[i].setName(sg.getName());
 522                 if(sg.cs!=null)
 523                 {
 524                   if (sg.cs.conservationApplied())
 525                   {
 526                     groups[i].setConsThreshold(sg.cs.getConservationInc());
 527
 528                     if (sg.cs instanceof jalview.schemes.UserColourScheme)
 529                     {
 530                       groups[i].setColour(SetUserColourScheme(sg.cs,
 531                           userColours,
 532                           jms));
 533                     }
 534                     else
 535                     {
 536                       groups[i].setColour(ColourSchemeProperty.getColourName(sg.
 537                           cs));
 538                     }
 539                   }
 540                   else if(sg.cs instanceof jalview.schemes.AnnotationColourGradient)
 541                   {
 542                     groups[i].setColour(
 543                         ColourSchemeProperty.getColourName(
 544                       ( (jalview.schemes.AnnotationColourGradient) sg.cs).getBaseColour()));
 545                   }
 546                   else if (sg.cs instanceof jalview.schemes.UserColourScheme)
 547                   {
 548                     groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
 549                         jms));
 550                   }
 551                   else
 552                   {
 553                     groups[i].setColour(ColourSchemeProperty.getColourName(
 554                         sg.cs));
 555                   }
 556
 557                   groups[i].setPidThreshold(sg.cs.getThreshold());
 558                 }
 559
 560                 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
 561                 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
 562                 groups[i].setDisplayText(sg.getDisplayText());
 563                 groups[i].setColourText(sg.getColourText());
 564
 565                 for (int s = 0; s < sg.getSize(false); s++)
 566                 {
 567                     jalview.datamodel.Sequence seq =
 568                         (jalview.datamodel.Sequence) sg.getSequenceAt(s);
 569                     groups[i].addSeq(seq.hashCode());
 570                 }
 571             }
 572
 573             jms.setJGroup(groups);
 574         }
 575
 576
 577         ///////////SAVE VIEWPORT
 578         Viewport view = new Viewport();
 579         view.setTitle(ap.alignFrame.getTitle());
 580         view.setSequenceSetId(av.getSequenceSetId());
 581         view.setViewName(av.viewName);
 582         view.setGatheredViews(av.gatherViewsHere);
 583
 584         view.setXpos(av.explodedPosition.x);
 585         view.setYpos(av.explodedPosition.y);
 586         view.setWidth(av.explodedPosition.width);
 587         view.setHeight(av.explodedPosition.height);
 588         view.setStartRes(av.startRes);
 589         view.setStartSeq(av.startSeq);
 590
 591         if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
 592         {
 593             view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
 594                     userColours, jms));
 595         }
 596         else if(av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
 597         {
 598            jalview.schemes.AnnotationColourGradient acg
 599               = (jalview.schemes.AnnotationColourGradient)av.getGlobalColourScheme();
 600
 601             AnnotationColours ac = new AnnotationColours();
 602             ac.setAboveThreshold(acg.getAboveThreshold());
 603             ac.setThreshold(acg.getAnnotationThreshold());
 604             ac.setAnnotation(acg.getAnnotation());
 605             if(acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
 606               ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
 607                     userColours, jms));
 608             else
 609               ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
 610
 611             ac.setMaxColour(acg.getMaxColour().getRGB());
 612             ac.setMinColour(acg.getMinColour().getRGB());
 613             view.setAnnotationColours(ac);
 614             view.setBgColour("AnnotationColourGradient");
 615         }
 616         else
 617         {
 618             view.setBgColour(ColourSchemeProperty.getColourName(
 619                     av.getGlobalColourScheme()));
 620         }
 621
 622         ColourSchemeI cs = av.getGlobalColourScheme();
 623
 624         if(cs!=null)
 625         {
 626           if (cs.conservationApplied())
 627           {
 628             view.setConsThreshold(cs.getConservationInc());
 629             if (cs instanceof jalview.schemes.UserColourScheme)
 630               view.setBgColour(SetUserColourScheme(cs, userColours, jms));
 631           }
 632
 633           if (cs instanceof ResidueColourScheme)
 634           {
 635             view.setPidThreshold(cs.getThreshold());
 636           }
 637         }
 638
 639         view.setConservationSelected(av.getConservationSelected());
 640         view.setPidSelected(av.getAbovePIDThreshold());
 641         view.setFontName(av.font.getName());
 642         view.setFontSize(av.font.getSize());
 643         view.setFontStyle(av.font.getStyle());
 644         view.setRenderGaps(av.renderGaps);
 645         view.setShowAnnotation(av.getShowAnnotation());
 646         view.setShowBoxes(av.getShowBoxes());
 647         view.setShowColourText(av.getColourText());
 648         view.setShowFullId(av.getShowJVSuffix());
 649         view.setShowSequenceFeatures(av.showSequenceFeatures);
 650         view.setShowText(av.getShowText());
 651         view.setWrapAlignment(av.getWrapAlignment());
 652
 653         if(av.featuresDisplayed!=null)
 654         {
 655           jalview.schemabinding.version2.FeatureSettings fs
 656               = new jalview.schemabinding.version2.FeatureSettings();
 657
 658           String [] renderOrder =
 659               ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
 660
 661           Vector settingsAdded = new Vector();
 662           for(int ro=0; ro<renderOrder.length; ro++)
 663           {
 664             Setting setting = new Setting();
 665             setting.setType(renderOrder[ro]);
 666             setting.setColour(
 667                 ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).getRGB()
 668                 );
 669
 670             setting.setDisplay(
 671                 av.featuresDisplayed.containsKey(renderOrder[ro])
 672                 );
 673
 674             fs.addSetting(setting);
 675             settingsAdded.addElement(renderOrder[ro]);
 676           }
 677
 678           //Make sure we save none displayed feature settings
 679           Enumeration en =
 680               ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
 681           while(en.hasMoreElements())
 682           {
 683             String key = en.nextElement().toString();
 684             if(settingsAdded.contains(key))
 685               continue;
 686
 687             Setting setting = new Setting();
 688             setting.setType(key);
 689             setting.setColour(
 690                 ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()
 691                 );
 692
 693             setting.setDisplay(false);
 694
 695             fs.addSetting(setting);
 696             settingsAdded.addElement(key);
 697           }
 698
 699           jms.setFeatureSettings(fs);
 700
 701         }
 702
 703         if(av.hasHiddenColumns)
 704         {
 705           for(int c=0; c<av.getColumnSelection().getHiddenColumns().size(); c++)
 706           {
 707             int [] region = (int[]) av.getColumnSelection().getHiddenColumns().elementAt(c);
 708             HiddenColumns hc = new HiddenColumns();
 709             hc.setStart(region[0]);
 710             hc.setEnd(region[1]);
 711             view.addHiddenColumns(hc);
 712           }
 713         }
 714
 715         jms.addViewport(view);
 716
 717
 718         object.setJalviewModelSequence(jms);
 719         object.getVamsasModel().addSequenceSet(vamsasSet);
 720
 721         try
 722         {
 723             if (!fileName.endsWith(".xml"))
 724             {
 725                 fileName = fileName + ".xml";
 726             }
 727
 728             JarEntry entry = new JarEntry(fileName);
 729             jout.putNextEntry(entry);
 730
 731             object.marshal(out);
 732         }
 733         catch (Exception ex)
 734         {
 735             ex.printStackTrace();
 736         }
 737     }
 738
 739     String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
 740         Vector userColours, JalviewModelSequence jms)
 741     {
 742         String id = null;
 743         jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
 744
 745         if (!userColours.contains(ucs))
 746         {
 747             userColours.add(ucs);
 748
 749             java.awt.Color[] colours = ucs.getColours();
 750             jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
 751             jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
 752
 753             for (int i = 0; i < colours.length; i++)
 754             {
 755                 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
 756                 col.setName(ResidueProperties.aa[i]);
 757                 col.setRGB(jalview.util.Format.getHexString(colours[i]));
 758                 jbucs.addColour(col);
 759             }
 760             if(ucs.getLowerCaseColours()!=null)
 761             {
 762               colours = ucs.getLowerCaseColours();
 763               for (int i = 0; i < colours.length; i++)
 764              {
 765                  jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
 766                  col.setName(ResidueProperties.aa[i].toLowerCase());
 767                  col.setRGB(jalview.util.Format.getHexString(colours[i]));
 768                  jbucs.addColour(col);
 769              }
 770             }
 771
 772             id = "ucs" + userColours.indexOf(ucs);
 773             uc.setId(id);
 774             uc.setUserColourScheme(jbucs);
 775             jms.addUserColours(uc);
 776         }
 777
 778         return id;
 779     }
 780
 781    jalview.schemes.UserColourScheme GetUserColourScheme(
 782         JalviewModelSequence jms, String id)
 783     {
 784         UserColours[] uc = jms.getUserColours();
 785         UserColours colours = null;
 786
 787         for (int i = 0; i < uc.length; i++)
 788         {
 789             if (uc[i].getId().equals(id))
 790             {
 791                 colours = uc[i];
 792
 793                 break;
 794             }
 795         }
 796
 797         java.awt.Color[] newColours = new java.awt.Color[24];
 798
 799         for (int i = 0; i < 24; i++)
 800         {
 801             newColours[i] = new java.awt.Color(Integer.parseInt(
 802                         colours.getUserColourScheme().getColour(i).getRGB(), 16));
 803         }
 804
 805         jalview.schemes.UserColourScheme ucs =
 806             new jalview.schemes.UserColourScheme(newColours);
 807
 808         if (colours.getUserColourScheme().getColourCount() > 24)
 809         {
 810           newColours = new java.awt.Color[23];
 811           for (int i = 0; i < 23; i++)
 812           {
 813             newColours[i] = new java.awt.Color(Integer.parseInt(
 814                 colours.getUserColourScheme().getColour(i+24).getRGB(), 16));
 815           }
 816           ucs.setLowerCaseColours(newColours);
 817         }
 818
 819         return ucs;
 820     }
 821
 822     Hashtable seqRefIds;
 823
 824     /**
 825      * DOCUMENT ME!
 826      *
 827      * @param file DOCUMENT ME!
 828      */
 829     public AlignFrame LoadJalviewAlign(final String file)
 830     {
 831         jalview.gui.AlignFrame af = null;
 832
 833         seqRefIds = new Hashtable();
 834         Vector gatherToThisFrame= new Vector();
 835
 836         try
 837         {
 838             //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
 839             URL url = null;
 840
 841             if (file.startsWith("http://"))
 842             {
 843                 url = new URL(file);
 844             }
 845
 846             JarInputStream jin = null;
 847             JarEntry jarentry = null;
 848             int entryCount = 1;
 849
 850             do
 851             {
 852                 if (url != null)
 853                 {
 854                     jin = new JarInputStream(url.openStream());
 855                 }
 856                 else
 857                 {
 858                     jin = new JarInputStream(new FileInputStream(file));
 859                 }
 860
 861                 for (int i = 0; i < entryCount; i++)
 862                 {
 863                     jarentry = jin.getNextJarEntry();
 864                 }
 865
 866                 if (jarentry != null && jarentry.getName().endsWith(".xml"))
 867                 {
 868                     InputStreamReader in = new InputStreamReader(jin, "UTF-8");
 869                     JalviewModel object = new JalviewModel();
 870
 871                     Unmarshaller unmar = new Unmarshaller(object);
 872                     unmar.setValidation(false);
 873                     object = (JalviewModel) unmar.unmarshal( in );
 874
 875                     af = LoadFromObject(object, file);
 876                     if(af.viewport.gatherViewsHere)
 877                     {
 878                       gatherToThisFrame.add(af);
 879                     }
 880                     entryCount++;
 881                 }
 882                 else if (jarentry != null)
 883                 {
 884                   //Some other file here.
 885                   entryCount++;
 886                 }
 887             }
 888             while (jarentry != null);
 889         }
 890         catch(java.net.UnknownHostException ex)
 891         {
 892           ex.printStackTrace();
 893           System.err.println("Couldn't locate Jalview XML file : " +
 894               ex + "\n");
 895
 896           javax.swing.SwingUtilities.invokeLater(new Runnable()
 897           {
 898             public void run()
 899             {
 900               JOptionPane.showInternalMessageDialog(Desktop.desktop,
 901                   "Couldn't locate " + file,
 902                   "URL not found",
 903                   JOptionPane.WARNING_MESSAGE);
 904             }
 905           });
 906         }
 907         catch (Exception ex)
 908         {
 909           //Is Version 1 Jar file?
 910           af =  new Jalview2XML_V1().LoadJalviewAlign(file);
 911
 912           if(af!=null)
 913           {
 914             System.out.println("Successfully loaded archive file");
 915             return af;
 916           }
 917
 918             System.err.println("Exception whilst loading jalview XML file : " +
 919                 ex + "\n");
 920             javax.swing.SwingUtilities.invokeLater(new Runnable()
 921             {
 922               public void run()
 923               {
 924
 925                 JOptionPane.showInternalMessageDialog(Desktop.desktop,
 926                     "Error loading  " + file,
 927                     "Error loading Jalview file",
 928                     JOptionPane.WARNING_MESSAGE);
 929               }});
 930         }
 931
 932         if (Desktop.instance != null)
 933           Desktop.instance.stopLoading();
 934
 935         for (int i = 0; i < gatherToThisFrame.size(); i++)
 936         {
 937           Desktop.instance.gatherViews(
 938               (AlignFrame) gatherToThisFrame.elementAt(i));
 939         }
 940
 941         return af;
 942     }
 943
 944     String loadPDBFile(String file, String pdbId)
 945     {
 946       try
 947       {
 948         JarInputStream jin = null;
 949
 950         if (file.startsWith("http://"))
 951         {
 952           jin = new JarInputStream(new URL(file).openStream());
 953         }
 954         else
 955         {
 956           jin = new JarInputStream(new FileInputStream(file));
 957         }
 958
 959         JarEntry entry = null;
 960         do
 961         {
 962           entry = jin.getNextJarEntry();
 963         }
 964         while (!entry.getName().equals(pdbId));
 965
 966         BufferedReader in = new BufferedReader(new InputStreamReader(jin));
 967         File outFile = File.createTempFile("jalview_pdb", ".txt");
 968         outFile.deleteOnExit();
 969         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
 970         String data;
 971
 972         while ( (data = in.readLine()) != null)
 973         {
 974           out.println(data);
 975         }
 976         out.close();
 977         return outFile.getAbsolutePath();
 978
 979       }
 980       catch (Exception ex)
 981       {
 982         ex.printStackTrace();
 983       }
 984
 985       return null;
 986     }
 987
 988
 989     AlignFrame LoadFromObject(JalviewModel object, String file)
 990     {
 991         SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
 992         Sequence[] vamsasSeq = vamsasSet.getSequence();
 993
 994         JalviewModelSequence jms = object.getJalviewModelSequence();
 995
 996         Viewport[] views = jms.getViewport();
 997         Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
 998
 999         //////////////////////////////////
1000         //LOAD SEQUENCES
1001
1002         Vector hiddenSeqs = null;
1003         jalview.datamodel.Sequence jseq;
1004
1005         ArrayList tmpseqs = new ArrayList();
1006
1007
1008         boolean multipleView = false;
1009
1010         JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
1011         for (int i = 0; i < JSEQ.length; i++)
1012         {
1013           String seqId = JSEQ[i].getId() + "";
1014
1015           if (seqRefIds.get(seqId) != null)
1016           {
1017             tmpseqs.add( (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1018             multipleView = true;
1019           }
1020           else
1021           {
1022             jseq = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
1023                 vamsasSeq[i].getSequence());
1024             jseq.setDescription(vamsasSeq[i].getDescription());
1025             jseq.setStart(JSEQ[i].getStart());
1026             jseq.setEnd(JSEQ[i].getEnd());
1027             jseq.setColor(new java.awt.Color(JSEQ[i].getColour()));
1028             seqRefIds.put(vamsasSeq[i].getId(), jseq);
1029             tmpseqs.add( jseq );
1030           }
1031
1032
1033           if (JSEQ[i].getHidden())
1034           {
1035             if (hiddenSeqs == null)
1036               hiddenSeqs = new Vector();
1037
1038
1039             hiddenSeqs.addElement(
1040                 (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1041           }
1042
1043         }
1044
1045         ///SequenceFeatures are added to the DatasetSequence,
1046         // so we must create the dataset before loading features
1047         /////////////////////////////////
1048
1049
1050       jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[
1051           tmpseqs.size()];
1052
1053        tmpseqs.toArray(orderedSeqs) ;
1054
1055
1056         jalview.datamodel.Alignment al =
1057             new jalview.datamodel.Alignment(orderedSeqs);
1058
1059         al.setDataset(null);
1060         /////////////////////////////////
1061
1062
1063         Hashtable pdbloaded = new Hashtable();
1064         if(!multipleView)
1065         {
1066           for (int i = 0; i < vamsasSeq.length; i++)
1067           {
1068             if (JSEQ[i].getFeaturesCount() > 0)
1069             {
1070               Features[] features = JSEQ[i].getFeatures();
1071               for (int f = 0; f < features.length; f++)
1072               {
1073                 jalview.datamodel.SequenceFeature sf
1074                     = new jalview.datamodel.SequenceFeature(features[f].getType(),
1075                     features[f].getDescription(), features[f].getStatus(),
1076                     features[f].getBegin(), features[f].getEnd(),
1077                     features[f].getFeatureGroup());
1078
1079                 sf.setScore(features[f].getScore());
1080                 for (int od = 0; od < features[f].getOtherDataCount(); od++)
1081                 {
1082                   OtherData keyValue = features[f].getOtherData(od);
1083                   if (keyValue.getKey().startsWith("LINK"))
1084                     sf.addLink(keyValue.getValue());
1085                   else
1086                     sf.setValue(keyValue.getKey(), keyValue.getValue());
1087
1088                 }
1089
1090                 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1091               }
1092             }
1093             if (JSEQ[i].getPdbidsCount() > 0)
1094             {
1095               Pdbids[] ids = JSEQ[i].getPdbids();
1096               for (int p = 0; p < ids.length; p++)
1097               {
1098                 jalview.datamodel.PDBEntry entry = new jalview.datamodel.
1099                     PDBEntry();
1100                 entry.setId(ids[p].getId());
1101                 entry.setType(ids[p].getType());
1102                 if (ids[p].getFile() != null)
1103                 {
1104                   if (!pdbloaded.containsKey(ids[p].getFile()))
1105                   {
1106                     String tmppdb = loadPDBFile(file, ids[p].getId());
1107                     entry.setFile(tmppdb);
1108                     pdbloaded.put(ids[p].getId(), tmppdb);
1109                   }
1110                   else
1111                     entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1112                 }
1113
1114                 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1115               }
1116             }
1117             if (vamsasSeq[i].getDBRefCount() > 0)
1118             {
1119               for (int d = 0; d < vamsasSeq[i].getDBRefCount(); d++)
1120               {
1121                 jalview.datamodel.DBRefEntry entry =
1122                     new jalview.datamodel.DBRefEntry(
1123                         vamsasSeq[i].getDBRef(d).getSource(),
1124                         vamsasSeq[i].getDBRef(d).getVersion(),
1125                         vamsasSeq[i].getDBRef(d).getAccessionId()
1126                     );
1127                 al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);
1128               }
1129
1130             }
1131           }
1132         }
1133
1134
1135          /////////////////////////////////
1136         //////////////////////////////////
1137         //LOAD ANNOTATIONS
1138         boolean hideQuality = true,
1139             hideConservation = true,
1140             hideConsensus = true;
1141
1142         if (vamsasSet.getAnnotationCount()>0)
1143         {
1144             Annotation[] an = vamsasSet.getAnnotation();
1145
1146             for (int i = 0; i < an.length; i++)
1147             {
1148                if (an[i].getLabel().equals("Quality"))
1149                 {
1150                  hideQuality = false;
1151                  continue;
1152                 }
1153                else if(an[i].getLabel().equals("Conservation"))
1154                {
1155                  hideConservation = false;
1156                  continue;
1157                }
1158                else if(an[i].getLabel().equals("Consensus"))
1159                {
1160                  hideConsensus = false;
1161                  continue;
1162                }
1163
1164                 AnnotationElement[] ae = an[i].getAnnotationElement();
1165                 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];
1166
1167                 for (int aa = 0; aa < ae.length; aa++)
1168                 {
1169                     anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),
1170                             ae[aa].getDescription(),
1171                             ae[aa].getSecondaryStructure().length()==0?' ':ae[aa].getSecondaryStructure().charAt(0),
1172                             ae[aa].getValue());
1173                     anot[ae[aa].getPosition()].colour = new java.awt.Color( ae[aa].getColour() );
1174                 }
1175
1176                 jalview.datamodel.AlignmentAnnotation jaa = null;
1177
1178                 if (an[i].getGraph())
1179                 {
1180                   jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1181                       an[i].getDescription(), anot, 0, 0,
1182                       an[i].getGraphType());
1183
1184                   jaa.graphGroup = an[i].getGraphGroup();
1185
1186                   if (an[i].getThresholdLine() != null)
1187                   {
1188                     jaa.setThreshold(new jalview.datamodel.GraphLine(
1189                                   an[i].getThresholdLine().getValue(),
1190                                   an[i].getThresholdLine().getLabel(),
1191                                 new java.awt.Color(an[i].getThresholdLine().getColour()))
1192                              );
1193
1194                   }
1195
1196                 }
1197                 else
1198                 {
1199                     jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1200                             an[i].getDescription(), anot);
1201                 }
1202
1203                 if(an[i].getSequenceRef()!=null)
1204                 {
1205                   jaa.createSequenceMapping(
1206                       al.findName(an[i].getSequenceRef()), 1, true
1207                       );
1208                   al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
1209                 }
1210
1211                 al.addAnnotation(jaa);
1212             }
1213         }
1214
1215
1216         //  af.changeColour() );
1217         /////////////////////////
1218         //LOAD GROUPS
1219         if (jms.getJGroupCount() > 0)
1220         {
1221             JGroup[] groups = jms.getJGroup();
1222
1223             for (int i = 0; i < groups.length; i++)
1224             {
1225                 ColourSchemeI cs = null;
1226
1227                 if (groups[i].getColour() != null)
1228                 {
1229                     if (groups[i].getColour().startsWith("ucs"))
1230                     {
1231                         cs = GetUserColourScheme(jms, groups[i].getColour());
1232                     }
1233                     else
1234                     {
1235                         cs = ColourSchemeProperty.getColour(al,
1236                                 groups[i].getColour());
1237                     }
1238
1239                     if(cs!=null)
1240                       cs.setThreshold(groups[i].getPidThreshold(), true);
1241                 }
1242
1243                 Vector seqs = new Vector();
1244
1245                 for (int s = 0; s < groups[i].getSeqCount(); s++)
1246                 {
1247                     String seqId = groups[i].getSeq(s)+"";
1248                     seqs.addElement((jalview.datamodel.SequenceI) seqRefIds.get(seqId));
1249                 }
1250
1251                 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,
1252                         groups[i].getName(), cs, groups[i].getDisplayBoxes(),
1253                         groups[i].getDisplayText(), groups[i].getColourText(),
1254                         groups[i].getStart(), groups[i].getEnd());
1255
1256                 sg.setOutlineColour(new java.awt.Color(
1257                         groups[i].getOutlineColour()));
1258
1259                 if (groups[i].getConsThreshold() != 0)
1260                 {
1261                     jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
1262                             ResidueProperties.propHash, 3, sg.getSequences(false), 0,
1263                             sg.getWidth() - 1);
1264                     c.calculate();
1265                     c.verdict(false, 25);
1266                     sg.cs.setConservation(c);
1267                 }
1268
1269                 al.addGroup(sg);
1270             }
1271         }
1272
1273
1274         /////////////////////////////////
1275         // LOAD VIEWPORT
1276
1277         AlignFrame af = new AlignFrame(al,
1278                                        view.getWidth(),
1279                                        view.getHeight() );
1280
1281         af.viewport.sequenceSetID = view.getSequenceSetId();
1282
1283         af.viewport.gatherViewsHere = view.getGatheredViews();
1284
1285         if (view.getSequenceSetId() != null)
1286           PaintRefresher.Register(af.alignPanel, view.getSequenceSetId());
1287
1288         if(hiddenSeqs!=null)
1289         {
1290           for(int s=0; s<JSEQ.length; s++)
1291           {
1292             for(int r=0; r<JSEQ[s].getHiddenSequencesCount(); r++)
1293             {
1294               al.getSequenceAt(s).addHiddenSequence(
1295                   al.getSequenceAt( JSEQ[s].getHiddenSequences(r)  )
1296                   );
1297             }
1298           }
1299
1300           jalview.datamodel.SequenceI [] hseqs = new
1301               jalview.datamodel.SequenceI[hiddenSeqs.size()];
1302
1303           for(int s=0; s<hiddenSeqs.size(); s++)
1304             hseqs[s] = (jalview.datamodel.SequenceI)hiddenSeqs.elementAt(s);
1305
1306           af.viewport.hideSequence( hseqs );
1307
1308         }
1309
1310
1311         if((hideConsensus || hideQuality || hideConservation)
1312             && al.getAlignmentAnnotation()!=null)
1313         {
1314           int hSize = al.getAlignmentAnnotation().length;
1315           for (int h = 0; h < hSize; h++)
1316           {
1317             if (
1318                 (hideConsensus &&
1319                  al.getAlignmentAnnotation()[h].label.equals("Consensus"))
1320                 ||
1321                 (hideQuality &&
1322                  al.getAlignmentAnnotation()[h].label.equals("Quality"))
1323                 ||
1324                 (hideConservation &&
1325                  al.getAlignmentAnnotation()[h].label.equals("Conservation")))
1326             {
1327               al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
1328               hSize--;
1329               h--;
1330             }
1331           }
1332           af.alignPanel.adjustAnnotationHeight();
1333         }
1334
1335         af.viewport.viewName = view.getViewName();
1336         af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
1337             view.getHeight());
1338         af.viewport.setStartRes(view.getStartRes());
1339         af.viewport.setStartSeq(view.getStartSeq());
1340         af.viewport.setShowAnnotation(view.getShowAnnotation());
1341         af.viewport.showConservation = !hideConservation;
1342         af.viewport.showQuality = !hideQuality;
1343         af.viewport.showIdentity = !hideConsensus;
1344
1345         af.viewport.setAbovePIDThreshold(view.getPidSelected());
1346         af.abovePIDThreshold.setSelected(view.getPidSelected());
1347         af.viewport.setColourText(view.getShowColourText());
1348         af.colourTextMenuItem.setSelected(view.getShowColourText());
1349         af.viewport.setConservationSelected(view.getConservationSelected());
1350         af.conservationMenuItem.setSelected(view.getConservationSelected());
1351
1352         af.viewport.setShowJVSuffix(view.getShowFullId());
1353         af.seqLimits.setSelected(view.getShowFullId());
1354
1355         af.viewport.setFont(new java.awt.Font(view.getFontName(),
1356                 view.getFontStyle(), view.getFontSize()));
1357         af.alignPanel.fontChanged();
1358
1359         af.viewport.setRenderGaps(view.getRenderGaps());
1360         af.renderGapsMenuItem.setSelected(view.getRenderGaps());
1361
1362         af.viewport.setWrapAlignment(view.getWrapAlignment());
1363         af.wrapMenuItem.setSelected(view.getWrapAlignment());
1364
1365         af.alignPanel.setWrapAlignment(view.getWrapAlignment());
1366
1367         af.annotationPanelMenuItem.setState(view.getShowAnnotation());
1368         af.viewport.setShowAnnotation(view.getShowAnnotation());
1369         af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
1370
1371         af.viewport.setShowBoxes(view.getShowBoxes());
1372         af.viewBoxesMenuItem.setSelected(view.getShowBoxes());
1373         af.viewport.setShowText(view.getShowText());
1374         af.viewTextMenuItem.setSelected(view.getShowText());
1375
1376         ColourSchemeI cs = null;
1377
1378         if (view.getBgColour() != null)
1379         {
1380             if (view.getBgColour().startsWith("ucs"))
1381             {
1382                 cs = GetUserColourScheme(jms, view.getBgColour());
1383             }
1384             else if(view.getBgColour().startsWith("Annotation"))
1385             {
1386               //int find annotation
1387               for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
1388               {
1389                 if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
1390                     equals(view.getAnnotationColours().getAnnotation()))
1391                 {
1392                   if (af.viewport.alignment.getAlignmentAnnotation()[i].
1393                       getThreshold() == null)
1394                   {
1395                     af.viewport.alignment.getAlignmentAnnotation()[i].
1396                         setThreshold(
1397                             new jalview.datamodel.GraphLine(
1398                                 view.getAnnotationColours().getThreshold(),
1399                                 "Threshold", java.awt.Color.black)
1400
1401                         );
1402                   }
1403
1404
1405                   if (view.getAnnotationColours().getColourScheme().equals(
1406                       "None"))
1407                   {
1408                     cs = new AnnotationColourGradient(
1409                         af.viewport.alignment.getAlignmentAnnotation()[i],
1410                         new java.awt.Color(view.getAnnotationColours().
1411                                            getMinColour()),
1412                         new java.awt.Color(view.getAnnotationColours().
1413                                            getMaxColour()),
1414                         view.getAnnotationColours().getAboveThreshold());
1415                   }
1416                   else if (view.getAnnotationColours().getColourScheme().
1417                            startsWith("ucs"))
1418                   {
1419                      cs = new AnnotationColourGradient(
1420                          af.viewport.alignment.getAlignmentAnnotation()[i],
1421                          GetUserColourScheme(jms, view.getAnnotationColours().
1422                                                         getColourScheme()),
1423                          view.getAnnotationColours().getAboveThreshold()
1424                          );
1425                    }
1426                    else
1427                    {
1428                      cs = new AnnotationColourGradient(
1429                          af.viewport.alignment.getAlignmentAnnotation()[i],
1430                          ColourSchemeProperty.getColour(al,
1431                          view.getAnnotationColours().getColourScheme()),
1432                          view.getAnnotationColours().getAboveThreshold()
1433                          );
1434                    }
1435
1436                   // Also use these settings for all the groups
1437                   if (al.getGroups() != null)
1438                     for (int g = 0; g < al.getGroups().size(); g++)
1439                     {
1440                       jalview.datamodel.SequenceGroup sg
1441                           = (jalview.datamodel.SequenceGroup)al.getGroups().elementAt(g);
1442
1443                       if(sg.cs == null)
1444                         continue;
1445
1446
1447                   /*    if (view.getAnnotationColours().getColourScheme().equals("None"))
1448                       {
1449                         sg.cs = new AnnotationColourGradient(
1450                             af.viewport.alignment.getAlignmentAnnotation()[i],
1451                             new java.awt.Color(view.getAnnotationColours().
1452                                                getMinColour()),
1453                             new java.awt.Color(view.getAnnotationColours().
1454                                                getMaxColour()),
1455                             view.getAnnotationColours().getAboveThreshold());
1456                       }
1457                       else*/
1458                       {
1459                         sg.cs = new AnnotationColourGradient(
1460                             af.viewport.alignment.getAlignmentAnnotation()[i],
1461                             sg.cs,
1462                             view.getAnnotationColours().getAboveThreshold()
1463                             );
1464                       }
1465
1466                     }
1467
1468
1469                   break;
1470                 }
1471
1472               }
1473             }
1474             else
1475             {
1476                 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
1477             }
1478
1479             if(cs!=null)
1480             {
1481               cs.setThreshold(view.getPidThreshold(), true);
1482               cs.setConsensus(af.viewport.hconsensus);
1483             }
1484         }
1485
1486         af.setColourSelected(view.getBgColour());
1487         af.viewport.setGlobalColourScheme(cs);
1488         af.viewport.setColourAppliesToAllGroups(false);
1489         af.changeColour(cs);
1490         if (view.getConservationSelected() && cs!=null)
1491         {
1492           cs.setConservationInc(view.getConsThreshold());
1493         }
1494
1495         af.viewport.setColourAppliesToAllGroups(true);
1496
1497         if (view.getShowSequenceFeatures())
1498         {
1499            af.viewport.showSequenceFeatures = true;
1500            af.showSeqFeatures.setSelected(true);
1501         }
1502
1503         if(jms.getFeatureSettings()!=null)
1504         {
1505           af.viewport.featuresDisplayed = new Hashtable();
1506           String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];
1507          for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)
1508          {
1509            Setting setting = jms.getFeatureSettings().getSetting(fs);
1510
1511            af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),
1512                new java.awt.Color(setting.getColour()));
1513
1514            renderOrder[fs] = setting.getType();
1515
1516            if(setting.getDisplay())
1517              af.viewport.featuresDisplayed.put(
1518                  setting.getType(), new Integer(setting.getColour()));
1519          }
1520          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
1521         }
1522
1523         if (view.getHiddenColumnsCount() > 0)
1524         {
1525           for (int c = 0; c < view.getHiddenColumnsCount(); c++)
1526           {
1527               af.viewport.hideColumns(
1528                 view.getHiddenColumns(c).getStart(),
1529                 view.getHiddenColumns(c).getEnd() //+1
1530                 );
1531           }
1532         }
1533
1534
1535         Desktop.addInternalFrame(af, view.getTitle(),
1536              view.getWidth(), view.getHeight());
1537
1538         //LOAD TREES
1539         ///////////////////////////////////////
1540         if (jms.getTreeCount() > 0)
1541         {
1542             try
1543             {
1544                 for (int t = 0; t < jms.getTreeCount(); t++)
1545                 {
1546
1547                     Tree tree = jms.getTree(t);
1548
1549                     TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
1550                                 tree.getNewick()), tree.getTitle(),
1551                                 tree.getWidth(), tree.getHeight(),
1552                                 tree.getXpos(), tree.getYpos());
1553
1554                     tp.fitToWindow.setState(tree.getFitToWindow());
1555                     tp.fitToWindow_actionPerformed(null);
1556
1557                     if(tree.getFontName()!=null)
1558                       tp.setTreeFont(new java.awt.Font(tree.getFontName(),
1559                                           tree.getFontStyle(),
1560                                           tree.getFontSize()));
1561                     else
1562                       tp.setTreeFont(new java.awt.Font(view.getFontName(),
1563                                             view.getFontStyle(),
1564                                             tree.getFontSize()));
1565
1566                     tp.showPlaceholders(tree.getMarkUnlinked());
1567                     tp.showBootstrap(tree.getShowBootstrap());
1568                     tp.showDistances(tree.getShowDistances());
1569
1570                     tp.treeCanvas.threshold = tree.getThreshold();
1571
1572                     if (tree.getCurrentTree())
1573                       af.viewport.setCurrentTree(tp.getTree());
1574                 }
1575
1576             }
1577             catch (Exception ex)
1578             {
1579                 ex.printStackTrace();
1580             }
1581
1582         }
1583
1584         return af;
1585     }
1586 }
1587