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      * This maintains a list of viewports, the key being the
 826      * seqSetId. Important to set historyItem and redoList
 827      * for multiple views
 828      */
 829     Hashtable viewportsAdded;
 830
 831     /**
 832      * DOCUMENT ME!
 833      *
 834      * @param file DOCUMENT ME!
 835      */
 836     public AlignFrame LoadJalviewAlign(final String file)
 837     {
 838         jalview.gui.AlignFrame af = null;
 839
 840         seqRefIds = new Hashtable();
 841         viewportsAdded = new Hashtable();
 842
 843         Vector gatherToThisFrame= new Vector();
 844
 845         try
 846         {
 847             //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
 848             URL url = null;
 849
 850             if (file.startsWith("http://"))
 851             {
 852                 url = new URL(file);
 853             }
 854
 855             JarInputStream jin = null;
 856             JarEntry jarentry = null;
 857             int entryCount = 1;
 858
 859             do
 860             {
 861                 if (url != null)
 862                 {
 863                     jin = new JarInputStream(url.openStream());
 864                 }
 865                 else
 866                 {
 867                     jin = new JarInputStream(new FileInputStream(file));
 868                 }
 869
 870                 for (int i = 0; i < entryCount; i++)
 871                 {
 872                     jarentry = jin.getNextJarEntry();
 873                 }
 874
 875                 if (jarentry != null && jarentry.getName().endsWith(".xml"))
 876                 {
 877                     InputStreamReader in = new InputStreamReader(jin, "UTF-8");
 878                     JalviewModel object = new JalviewModel();
 879
 880                     Unmarshaller unmar = new Unmarshaller(object);
 881                     unmar.setValidation(false);
 882                     object = (JalviewModel) unmar.unmarshal( in );
 883
 884                     af = LoadFromObject(object, file);
 885                     if(af.viewport.gatherViewsHere)
 886                     {
 887                       gatherToThisFrame.add(af);
 888                     }
 889                     entryCount++;
 890                 }
 891                 else if (jarentry != null)
 892                 {
 893                   //Some other file here.
 894                   entryCount++;
 895                 }
 896             }
 897             while (jarentry != null);
 898         }
 899         catch(java.net.UnknownHostException ex)
 900         {
 901           ex.printStackTrace();
 902           System.err.println("Couldn't locate Jalview XML file : " +
 903               ex + "\n");
 904
 905           javax.swing.SwingUtilities.invokeLater(new Runnable()
 906           {
 907             public void run()
 908             {
 909               JOptionPane.showInternalMessageDialog(Desktop.desktop,
 910                   "Couldn't locate " + file,
 911                   "URL not found",
 912                   JOptionPane.WARNING_MESSAGE);
 913             }
 914           });
 915         }
 916         catch (Exception ex)
 917         {
 918           //Is Version 1 Jar file?
 919           af =  new Jalview2XML_V1().LoadJalviewAlign(file);
 920
 921           if(af!=null)
 922           {
 923             System.out.println("Successfully loaded archive file");
 924             return af;
 925           }
 926
 927             System.err.println("Exception whilst loading jalview XML file : " +
 928                 ex + "\n");
 929             javax.swing.SwingUtilities.invokeLater(new Runnable()
 930             {
 931               public void run()
 932               {
 933
 934                 JOptionPane.showInternalMessageDialog(Desktop.desktop,
 935                     "Error loading  " + file,
 936                     "Error loading Jalview file",
 937                     JOptionPane.WARNING_MESSAGE);
 938               }});
 939         }
 940
 941         if (Desktop.instance != null)
 942           Desktop.instance.stopLoading();
 943
 944         for (int i = 0; i < gatherToThisFrame.size(); i++)
 945         {
 946           Desktop.instance.gatherViews(
 947               (AlignFrame) gatherToThisFrame.elementAt(i));
 948         }
 949
 950         return af;
 951     }
 952
 953     String loadPDBFile(String file, String pdbId)
 954     {
 955       try
 956       {
 957         JarInputStream jin = null;
 958
 959         if (file.startsWith("http://"))
 960         {
 961           jin = new JarInputStream(new URL(file).openStream());
 962         }
 963         else
 964         {
 965           jin = new JarInputStream(new FileInputStream(file));
 966         }
 967
 968         JarEntry entry = null;
 969         do
 970         {
 971           entry = jin.getNextJarEntry();
 972         }
 973         while (!entry.getName().equals(pdbId));
 974
 975         BufferedReader in = new BufferedReader(new InputStreamReader(jin));
 976         File outFile = File.createTempFile("jalview_pdb", ".txt");
 977         outFile.deleteOnExit();
 978         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
 979         String data;
 980
 981         while ( (data = in.readLine()) != null)
 982         {
 983           out.println(data);
 984         }
 985         out.close();
 986         return outFile.getAbsolutePath();
 987
 988       }
 989       catch (Exception ex)
 990       {
 991         ex.printStackTrace();
 992       }
 993
 994       return null;
 995     }
 996
 997
 998     AlignFrame LoadFromObject(JalviewModel object, String file)
 999     {
1000         SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
1001         Sequence[] vamsasSeq = vamsasSet.getSequence();
1002
1003         JalviewModelSequence jms = object.getJalviewModelSequence();
1004
1005         Viewport view = jms.getViewport(0);
1006
1007         //////////////////////////////////
1008         //LOAD SEQUENCES
1009
1010         Vector hiddenSeqs = null;
1011         jalview.datamodel.Sequence jseq;
1012
1013         ArrayList tmpseqs = new ArrayList();
1014
1015
1016         boolean multipleView = false;
1017
1018         JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
1019         for (int i = 0; i < JSEQ.length; i++)
1020         {
1021           String seqId = JSEQ[i].getId() + "";
1022
1023           if (seqRefIds.get(seqId) != null)
1024           {
1025             tmpseqs.add( (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1026             multipleView = true;
1027           }
1028           else
1029           {
1030             jseq = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
1031                 vamsasSeq[i].getSequence());
1032             jseq.setDescription(vamsasSeq[i].getDescription());
1033             jseq.setStart(JSEQ[i].getStart());
1034             jseq.setEnd(JSEQ[i].getEnd());
1035             jseq.setColor(new java.awt.Color(JSEQ[i].getColour()));
1036             seqRefIds.put(vamsasSeq[i].getId(), jseq);
1037             tmpseqs.add( jseq );
1038           }
1039
1040
1041           if (JSEQ[i].getHidden())
1042           {
1043             if (hiddenSeqs == null)
1044               hiddenSeqs = new Vector();
1045
1046
1047             hiddenSeqs.addElement(
1048                 (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1049           }
1050
1051         }
1052
1053         ///SequenceFeatures are added to the DatasetSequence,
1054         // so we must create the dataset before loading features
1055         /////////////////////////////////
1056
1057
1058       jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[
1059           tmpseqs.size()];
1060
1061        tmpseqs.toArray(orderedSeqs) ;
1062
1063
1064         jalview.datamodel.Alignment al =
1065             new jalview.datamodel.Alignment(orderedSeqs);
1066
1067         al.setDataset(null);
1068         /////////////////////////////////
1069
1070
1071         Hashtable pdbloaded = new Hashtable();
1072         if(!multipleView)
1073         {
1074           for (int i = 0; i < vamsasSeq.length; i++)
1075           {
1076             if (JSEQ[i].getFeaturesCount() > 0)
1077             {
1078               Features[] features = JSEQ[i].getFeatures();
1079               for (int f = 0; f < features.length; f++)
1080               {
1081                 jalview.datamodel.SequenceFeature sf
1082                     = new jalview.datamodel.SequenceFeature(features[f].getType(),
1083                     features[f].getDescription(), features[f].getStatus(),
1084                     features[f].getBegin(), features[f].getEnd(),
1085                     features[f].getFeatureGroup());
1086
1087                 sf.setScore(features[f].getScore());
1088                 for (int od = 0; od < features[f].getOtherDataCount(); od++)
1089                 {
1090                   OtherData keyValue = features[f].getOtherData(od);
1091                   if (keyValue.getKey().startsWith("LINK"))
1092                     sf.addLink(keyValue.getValue());
1093                   else
1094                     sf.setValue(keyValue.getKey(), keyValue.getValue());
1095
1096                 }
1097
1098                 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1099               }
1100             }
1101             if (JSEQ[i].getPdbidsCount() > 0)
1102             {
1103               Pdbids[] ids = JSEQ[i].getPdbids();
1104               for (int p = 0; p < ids.length; p++)
1105               {
1106                 jalview.datamodel.PDBEntry entry = new jalview.datamodel.
1107                     PDBEntry();
1108                 entry.setId(ids[p].getId());
1109                 entry.setType(ids[p].getType());
1110                 if (ids[p].getFile() != null)
1111                 {
1112                   if (!pdbloaded.containsKey(ids[p].getFile()))
1113                   {
1114                     String tmppdb = loadPDBFile(file, ids[p].getId());
1115                     entry.setFile(tmppdb);
1116                     pdbloaded.put(ids[p].getId(), tmppdb);
1117                   }
1118                   else
1119                     entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1120                 }
1121
1122                 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1123               }
1124             }
1125             if (vamsasSeq[i].getDBRefCount() > 0)
1126             {
1127               for (int d = 0; d < vamsasSeq[i].getDBRefCount(); d++)
1128               {
1129                 jalview.datamodel.DBRefEntry entry =
1130                     new jalview.datamodel.DBRefEntry(
1131                         vamsasSeq[i].getDBRef(d).getSource(),
1132                         vamsasSeq[i].getDBRef(d).getVersion(),
1133                         vamsasSeq[i].getDBRef(d).getAccessionId()
1134                     );
1135                 al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);
1136               }
1137
1138             }
1139           }
1140         }
1141
1142
1143          /////////////////////////////////
1144         //////////////////////////////////
1145         //LOAD ANNOTATIONS
1146         boolean hideQuality = true,
1147             hideConservation = true,
1148             hideConsensus = true;
1149
1150         if (vamsasSet.getAnnotationCount()>0)
1151         {
1152             Annotation[] an = vamsasSet.getAnnotation();
1153
1154             for (int i = 0; i < an.length; i++)
1155             {
1156                if (an[i].getLabel().equals("Quality"))
1157                 {
1158                  hideQuality = false;
1159                  continue;
1160                 }
1161                else if(an[i].getLabel().equals("Conservation"))
1162                {
1163                  hideConservation = false;
1164                  continue;
1165                }
1166                else if(an[i].getLabel().equals("Consensus"))
1167                {
1168                  hideConsensus = false;
1169                  continue;
1170                }
1171
1172                 AnnotationElement[] ae = an[i].getAnnotationElement();
1173                 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];
1174
1175                 for (int aa = 0; aa < ae.length; aa++)
1176                 {
1177                     anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),
1178                             ae[aa].getDescription(),
1179                             ae[aa].getSecondaryStructure().length()==0?' ':ae[aa].getSecondaryStructure().charAt(0),
1180                             ae[aa].getValue());
1181                     anot[ae[aa].getPosition()].colour = new java.awt.Color( ae[aa].getColour() );
1182                 }
1183
1184                 jalview.datamodel.AlignmentAnnotation jaa = null;
1185
1186                 if (an[i].getGraph())
1187                 {
1188                   jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1189                       an[i].getDescription(), anot, 0, 0,
1190                       an[i].getGraphType());
1191
1192                   jaa.graphGroup = an[i].getGraphGroup();
1193
1194                   if (an[i].getThresholdLine() != null)
1195                   {
1196                     jaa.setThreshold(new jalview.datamodel.GraphLine(
1197                                   an[i].getThresholdLine().getValue(),
1198                                   an[i].getThresholdLine().getLabel(),
1199                                 new java.awt.Color(an[i].getThresholdLine().getColour()))
1200                              );
1201
1202                   }
1203
1204                 }
1205                 else
1206                 {
1207                     jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1208                             an[i].getDescription(), anot);
1209                 }
1210
1211                 if(an[i].getSequenceRef()!=null)
1212                 {
1213                   jaa.createSequenceMapping(
1214                       al.findName(an[i].getSequenceRef()), 1, true
1215                       );
1216                   al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
1217                 }
1218
1219                 al.addAnnotation(jaa);
1220             }
1221         }
1222
1223         /////////////////////////
1224         //LOAD GROUPS
1225         if (jms.getJGroupCount() > 0)
1226         {
1227             JGroup[] groups = jms.getJGroup();
1228
1229             for (int i = 0; i < groups.length; i++)
1230             {
1231                 ColourSchemeI cs = null;
1232
1233                 if (groups[i].getColour() != null)
1234                 {
1235                     if (groups[i].getColour().startsWith("ucs"))
1236                     {
1237                         cs = GetUserColourScheme(jms, groups[i].getColour());
1238                     }
1239                     else
1240                     {
1241                         cs = ColourSchemeProperty.getColour(al,
1242                                 groups[i].getColour());
1243                     }
1244
1245                     if(cs!=null)
1246                       cs.setThreshold(groups[i].getPidThreshold(), true);
1247                 }
1248
1249                 Vector seqs = new Vector();
1250
1251                 for (int s = 0; s < groups[i].getSeqCount(); s++)
1252                 {
1253                     String seqId = groups[i].getSeq(s)+"";
1254                     seqs.addElement((jalview.datamodel.SequenceI) seqRefIds.get(seqId));
1255                 }
1256
1257                 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,
1258                         groups[i].getName(), cs, groups[i].getDisplayBoxes(),
1259                         groups[i].getDisplayText(), groups[i].getColourText(),
1260                         groups[i].getStart(), groups[i].getEnd());
1261
1262                 sg.setOutlineColour(new java.awt.Color(
1263                         groups[i].getOutlineColour()));
1264
1265                 if (groups[i].getConsThreshold() != 0)
1266                 {
1267                     jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
1268                             ResidueProperties.propHash, 3, sg.getSequences(false), 0,
1269                             sg.getWidth() - 1);
1270                     c.calculate();
1271                     c.verdict(false, 25);
1272                     sg.cs.setConservation(c);
1273                 }
1274
1275                 al.addGroup(sg);
1276             }
1277         }
1278
1279
1280         /////////////////////////////////
1281         // LOAD VIEWPORT
1282
1283         AlignFrame af = new AlignFrame(al,
1284                                        view.getWidth(),
1285                                        view.getHeight() );
1286
1287         af.viewport.sequenceSetID = view.getSequenceSetId();
1288
1289         af.viewport.gatherViewsHere = view.getGatheredViews();
1290
1291         if (view.getSequenceSetId() != null)
1292         {
1293           jalview.gui.AlignViewport av =
1294               (jalview.gui.AlignViewport)
1295               viewportsAdded.get(view.getSequenceSetId());
1296
1297           if(av!=null)
1298           {
1299             af.viewport.historyList = av.historyList;
1300             af.viewport.redoList = av.redoList;
1301           }
1302           else
1303           {
1304             viewportsAdded.put(view.getSequenceSetId(), af.viewport);
1305           }
1306
1307           PaintRefresher.Register(af.alignPanel, view.getSequenceSetId());
1308         }
1309         if(hiddenSeqs!=null)
1310         {
1311           for(int s=0; s<JSEQ.length; s++)
1312           {
1313             for(int r=0; r<JSEQ[s].getHiddenSequencesCount(); r++)
1314             {
1315               al.getSequenceAt(s).addHiddenSequence(
1316                   al.getSequenceAt( JSEQ[s].getHiddenSequences(r)  )
1317                   );
1318             }
1319           }
1320
1321           jalview.datamodel.SequenceI [] hseqs = new
1322               jalview.datamodel.SequenceI[hiddenSeqs.size()];
1323
1324           for(int s=0; s<hiddenSeqs.size(); s++)
1325             hseqs[s] = (jalview.datamodel.SequenceI)hiddenSeqs.elementAt(s);
1326
1327           af.viewport.hideSequence( hseqs );
1328
1329         }
1330
1331
1332         if((hideConsensus || hideQuality || hideConservation)
1333             && al.getAlignmentAnnotation()!=null)
1334         {
1335           int hSize = al.getAlignmentAnnotation().length;
1336           for (int h = 0; h < hSize; h++)
1337           {
1338             if (
1339                 (hideConsensus &&
1340                  al.getAlignmentAnnotation()[h].label.equals("Consensus"))
1341                 ||
1342                 (hideQuality &&
1343                  al.getAlignmentAnnotation()[h].label.equals("Quality"))
1344                 ||
1345                 (hideConservation &&
1346                  al.getAlignmentAnnotation()[h].label.equals("Conservation")))
1347             {
1348               al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
1349               hSize--;
1350               h--;
1351             }
1352           }
1353           af.alignPanel.adjustAnnotationHeight();
1354         }
1355
1356         af.viewport.viewName = view.getViewName();
1357         af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
1358             view.getHeight());
1359         af.viewport.setStartRes(view.getStartRes());
1360         af.viewport.setStartSeq(view.getStartSeq());
1361         af.viewport.setShowAnnotation(view.getShowAnnotation());
1362         af.viewport.setAbovePIDThreshold(view.getPidSelected());
1363
1364         af.viewport.setColourText(view.getShowColourText());
1365
1366         af.viewport.setConservationSelected(view.getConservationSelected());
1367         af.viewport.setShowJVSuffix(view.getShowFullId());
1368         af.viewport.setFont(new java.awt.Font(view.getFontName(),
1369                 view.getFontStyle(), view.getFontSize()));
1370         af.alignPanel.fontChanged();
1371         af.viewport.setRenderGaps(view.getRenderGaps());
1372         af.viewport.setWrapAlignment(view.getWrapAlignment());
1373         af.alignPanel.setWrapAlignment(view.getWrapAlignment());
1374         af.viewport.setShowAnnotation(view.getShowAnnotation());
1375         af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
1376
1377         af.viewport.setShowBoxes(view.getShowBoxes());
1378
1379         af.viewport.setShowText(view.getShowText());
1380
1381
1382         ColourSchemeI cs = null;
1383
1384         if (view.getBgColour() != null)
1385         {
1386             if (view.getBgColour().startsWith("ucs"))
1387             {
1388                 cs = GetUserColourScheme(jms, view.getBgColour());
1389             }
1390             else if(view.getBgColour().startsWith("Annotation"))
1391             {
1392               //int find annotation
1393               for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
1394               {
1395                 if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
1396                     equals(view.getAnnotationColours().getAnnotation()))
1397                 {
1398                   if (af.viewport.alignment.getAlignmentAnnotation()[i].
1399                       getThreshold() == null)
1400                   {
1401                     af.viewport.alignment.getAlignmentAnnotation()[i].
1402                         setThreshold(
1403                             new jalview.datamodel.GraphLine(
1404                                 view.getAnnotationColours().getThreshold(),
1405                                 "Threshold", java.awt.Color.black)
1406
1407                         );
1408                   }
1409
1410
1411                   if (view.getAnnotationColours().getColourScheme().equals(
1412                       "None"))
1413                   {
1414                     cs = new AnnotationColourGradient(
1415                         af.viewport.alignment.getAlignmentAnnotation()[i],
1416                         new java.awt.Color(view.getAnnotationColours().
1417                                            getMinColour()),
1418                         new java.awt.Color(view.getAnnotationColours().
1419                                            getMaxColour()),
1420                         view.getAnnotationColours().getAboveThreshold());
1421                   }
1422                   else if (view.getAnnotationColours().getColourScheme().
1423                            startsWith("ucs"))
1424                   {
1425                      cs = new AnnotationColourGradient(
1426                          af.viewport.alignment.getAlignmentAnnotation()[i],
1427                          GetUserColourScheme(jms, view.getAnnotationColours().
1428                                                         getColourScheme()),
1429                          view.getAnnotationColours().getAboveThreshold()
1430                          );
1431                    }
1432                    else
1433                    {
1434                      cs = new AnnotationColourGradient(
1435                          af.viewport.alignment.getAlignmentAnnotation()[i],
1436                          ColourSchemeProperty.getColour(al,
1437                          view.getAnnotationColours().getColourScheme()),
1438                          view.getAnnotationColours().getAboveThreshold()
1439                          );
1440                    }
1441
1442                   // Also use these settings for all the groups
1443                   if (al.getGroups() != null)
1444                     for (int g = 0; g < al.getGroups().size(); g++)
1445                     {
1446                       jalview.datamodel.SequenceGroup sg
1447                           = (jalview.datamodel.SequenceGroup)al.getGroups().elementAt(g);
1448
1449                       if(sg.cs == null)
1450                         continue;
1451
1452
1453                   /*    if (view.getAnnotationColours().getColourScheme().equals("None"))
1454                       {
1455                         sg.cs = new AnnotationColourGradient(
1456                             af.viewport.alignment.getAlignmentAnnotation()[i],
1457                             new java.awt.Color(view.getAnnotationColours().
1458                                                getMinColour()),
1459                             new java.awt.Color(view.getAnnotationColours().
1460                                                getMaxColour()),
1461                             view.getAnnotationColours().getAboveThreshold());
1462                       }
1463                       else*/
1464                       {
1465                         sg.cs = new AnnotationColourGradient(
1466                             af.viewport.alignment.getAlignmentAnnotation()[i],
1467                             sg.cs,
1468                             view.getAnnotationColours().getAboveThreshold()
1469                             );
1470                       }
1471
1472                     }
1473
1474
1475                   break;
1476                 }
1477
1478               }
1479             }
1480             else
1481             {
1482                 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
1483             }
1484
1485             if(cs!=null)
1486             {
1487               cs.setThreshold(view.getPidThreshold(), true);
1488               cs.setConsensus(af.viewport.hconsensus);
1489             }
1490         }
1491
1492
1493         af.viewport.setGlobalColourScheme(cs);
1494         af.viewport.setColourAppliesToAllGroups(false);
1495
1496         if (view.getConservationSelected() && cs!=null)
1497         {
1498           cs.setConservationInc(view.getConsThreshold());
1499         }
1500
1501         af.changeColour(cs);
1502
1503         af.viewport.setColourAppliesToAllGroups(true);
1504
1505
1506
1507         if (view.getShowSequenceFeatures())
1508         {
1509            af.viewport.showSequenceFeatures = true;
1510         }
1511
1512         if(jms.getFeatureSettings()!=null)
1513         {
1514           af.viewport.featuresDisplayed = new Hashtable();
1515           String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];
1516          for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)
1517          {
1518            Setting setting = jms.getFeatureSettings().getSetting(fs);
1519
1520            af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),
1521                new java.awt.Color(setting.getColour()));
1522
1523            renderOrder[fs] = setting.getType();
1524
1525            if(setting.getDisplay())
1526              af.viewport.featuresDisplayed.put(
1527                  setting.getType(), new Integer(setting.getColour()));
1528          }
1529          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
1530         }
1531
1532         if (view.getHiddenColumnsCount() > 0)
1533         {
1534           for (int c = 0; c < view.getHiddenColumnsCount(); c++)
1535           {
1536               af.viewport.hideColumns(
1537                 view.getHiddenColumns(c).getStart(),
1538                 view.getHiddenColumns(c).getEnd() //+1
1539                 );
1540           }
1541         }
1542
1543         af.setMenusFromViewport(af.viewport);
1544
1545
1546         Desktop.addInternalFrame(af, view.getTitle(),
1547              view.getWidth(), view.getHeight());
1548
1549         //LOAD TREES
1550         ///////////////////////////////////////
1551         if (jms.getTreeCount() > 0)
1552         {
1553             try
1554             {
1555                 for (int t = 0; t < jms.getTreeCount(); t++)
1556                 {
1557
1558                     Tree tree = jms.getTree(t);
1559
1560                     TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
1561                                 tree.getNewick()), tree.getTitle(),
1562                                 tree.getWidth(), tree.getHeight(),
1563                                 tree.getXpos(), tree.getYpos());
1564
1565                     tp.fitToWindow.setState(tree.getFitToWindow());
1566                     tp.fitToWindow_actionPerformed(null);
1567
1568                     if(tree.getFontName()!=null)
1569                       tp.setTreeFont(new java.awt.Font(tree.getFontName(),
1570                                           tree.getFontStyle(),
1571                                           tree.getFontSize()));
1572                     else
1573                       tp.setTreeFont(new java.awt.Font(view.getFontName(),
1574                                             view.getFontStyle(),
1575                                             tree.getFontSize()));
1576
1577                     tp.showPlaceholders(tree.getMarkUnlinked());
1578                     tp.showBootstrap(tree.getShowBootstrap());
1579                     tp.showDistances(tree.getShowDistances());
1580
1581                     tp.treeCanvas.threshold = tree.getThreshold();
1582
1583                     if (tree.getCurrentTree())
1584                       af.viewport.setCurrentTree(tp.getTree());
1585                 }
1586
1587             }
1588             catch (Exception ex)
1589             {
1590                 ex.printStackTrace();
1591             }
1592
1593         }
1594
1595         return af;
1596     }
1597 }
1598