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.setShowConservation(av.showConservation);
 649         view.setShowFullId(av.getShowJVSuffix());
 650         view.setShowIdentity(av.showIdentity);
 651         view.setShowQuality(av.showQuality);
 652         view.setShowSequenceFeatures(av.showSequenceFeatures);
 653         view.setShowText(av.getShowText());
 654         view.setWrapAlignment(av.getWrapAlignment());
 655
 656         if(av.featuresDisplayed!=null)
 657         {
 658           jalview.schemabinding.version2.FeatureSettings fs
 659               = new jalview.schemabinding.version2.FeatureSettings();
 660
 661           String [] renderOrder =
 662               ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
 663
 664           Vector settingsAdded = new Vector();
 665           for(int ro=0; ro<renderOrder.length; ro++)
 666           {
 667             Setting setting = new Setting();
 668             setting.setType(renderOrder[ro]);
 669             setting.setColour(
 670                 ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).getRGB()
 671                 );
 672
 673             setting.setDisplay(
 674                 av.featuresDisplayed.containsKey(renderOrder[ro])
 675                 );
 676
 677             fs.addSetting(setting);
 678             settingsAdded.addElement(renderOrder[ro]);
 679           }
 680
 681           //Make sure we save none displayed feature settings
 682           Enumeration en =
 683               ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
 684           while(en.hasMoreElements())
 685           {
 686             String key = en.nextElement().toString();
 687             if(settingsAdded.contains(key))
 688               continue;
 689
 690             Setting setting = new Setting();
 691             setting.setType(key);
 692             setting.setColour(
 693                 ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()
 694                 );
 695
 696             setting.setDisplay(false);
 697
 698             fs.addSetting(setting);
 699             settingsAdded.addElement(key);
 700           }
 701
 702           jms.setFeatureSettings(fs);
 703
 704         }
 705
 706         if(av.hasHiddenColumns)
 707         {
 708           for(int c=0; c<av.getColumnSelection().getHiddenColumns().size(); c++)
 709           {
 710             int [] region = (int[]) av.getColumnSelection().getHiddenColumns().elementAt(c);
 711             HiddenColumns hc = new HiddenColumns();
 712             hc.setStart(region[0]);
 713             hc.setEnd(region[1]);
 714             view.addHiddenColumns(hc);
 715           }
 716         }
 717
 718         jms.addViewport(view);
 719
 720
 721         object.setJalviewModelSequence(jms);
 722         object.getVamsasModel().addSequenceSet(vamsasSet);
 723
 724         try
 725         {
 726             if (!fileName.endsWith(".xml"))
 727             {
 728                 fileName = fileName + ".xml";
 729             }
 730
 731             JarEntry entry = new JarEntry(fileName);
 732             jout.putNextEntry(entry);
 733
 734             object.marshal(out);
 735         }
 736         catch (Exception ex)
 737         {
 738             ex.printStackTrace();
 739         }
 740     }
 741
 742     String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
 743         Vector userColours, JalviewModelSequence jms)
 744     {
 745         String id = null;
 746         jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
 747
 748         if (!userColours.contains(ucs))
 749         {
 750             userColours.add(ucs);
 751
 752             java.awt.Color[] colours = ucs.getColours();
 753             jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
 754             jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
 755
 756             for (int i = 0; i < colours.length; i++)
 757             {
 758                 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
 759                 col.setName(ResidueProperties.aa[i]);
 760                 col.setRGB(jalview.util.Format.getHexString(colours[i]));
 761                 jbucs.addColour(col);
 762             }
 763             if(ucs.getLowerCaseColours()!=null)
 764             {
 765               colours = ucs.getLowerCaseColours();
 766               for (int i = 0; i < colours.length; i++)
 767              {
 768                  jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
 769                  col.setName(ResidueProperties.aa[i].toLowerCase());
 770                  col.setRGB(jalview.util.Format.getHexString(colours[i]));
 771                  jbucs.addColour(col);
 772              }
 773             }
 774
 775             id = "ucs" + userColours.indexOf(ucs);
 776             uc.setId(id);
 777             uc.setUserColourScheme(jbucs);
 778             jms.addUserColours(uc);
 779         }
 780
 781         return id;
 782     }
 783
 784    jalview.schemes.UserColourScheme GetUserColourScheme(
 785         JalviewModelSequence jms, String id)
 786     {
 787         UserColours[] uc = jms.getUserColours();
 788         UserColours colours = null;
 789
 790         for (int i = 0; i < uc.length; i++)
 791         {
 792             if (uc[i].getId().equals(id))
 793             {
 794                 colours = uc[i];
 795
 796                 break;
 797             }
 798         }
 799
 800         java.awt.Color[] newColours = new java.awt.Color[24];
 801
 802         for (int i = 0; i < 24; i++)
 803         {
 804             newColours[i] = new java.awt.Color(Integer.parseInt(
 805                         colours.getUserColourScheme().getColour(i).getRGB(), 16));
 806         }
 807
 808         jalview.schemes.UserColourScheme ucs =
 809             new jalview.schemes.UserColourScheme(newColours);
 810
 811         if (colours.getUserColourScheme().getColourCount() > 24)
 812         {
 813           newColours = new java.awt.Color[23];
 814           for (int i = 0; i < 23; i++)
 815           {
 816             newColours[i] = new java.awt.Color(Integer.parseInt(
 817                 colours.getUserColourScheme().getColour(i+24).getRGB(), 16));
 818           }
 819           ucs.setLowerCaseColours(newColours);
 820         }
 821
 822         return ucs;
 823     }
 824
 825     Hashtable seqRefIds;
 826
 827     /**
 828      * DOCUMENT ME!
 829      *
 830      * @param file DOCUMENT ME!
 831      */
 832     public AlignFrame LoadJalviewAlign(final String file)
 833     {
 834         jalview.gui.AlignFrame af = null;
 835
 836         seqRefIds = new Hashtable();
 837         Vector gatherToThisFrame= new Vector();
 838
 839         try
 840         {
 841             //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
 842             URL url = null;
 843
 844             if (file.startsWith("http://"))
 845             {
 846                 url = new URL(file);
 847             }
 848
 849             JarInputStream jin = null;
 850             JarEntry jarentry = null;
 851             int entryCount = 1;
 852
 853             do
 854             {
 855                 if (url != null)
 856                 {
 857                     jin = new JarInputStream(url.openStream());
 858                 }
 859                 else
 860                 {
 861                     jin = new JarInputStream(new FileInputStream(file));
 862                 }
 863
 864                 for (int i = 0; i < entryCount; i++)
 865                 {
 866                     jarentry = jin.getNextJarEntry();
 867                 }
 868
 869                 if (jarentry != null && jarentry.getName().endsWith(".xml"))
 870                 {
 871                     InputStreamReader in = new InputStreamReader(jin, "UTF-8");
 872                     JalviewModel object = new JalviewModel();
 873
 874                     Unmarshaller unmar = new Unmarshaller(object);
 875                     unmar.setValidation(false);
 876                     object = (JalviewModel) unmar.unmarshal( in );
 877
 878                     af = LoadFromObject(object, file);
 879                     if(af.viewport.gatherViewsHere)
 880                     {
 881                       gatherToThisFrame.add(af);
 882                     }
 883                     entryCount++;
 884                 }
 885                 else if (jarentry != null)
 886                 {
 887                   //Some other file here.
 888                   entryCount++;
 889                 }
 890             }
 891             while (jarentry != null);
 892         }
 893         catch(java.net.UnknownHostException ex)
 894         {
 895           ex.printStackTrace();
 896           System.err.println("Couldn't locate Jalview XML file : " +
 897               ex + "\n");
 898
 899           javax.swing.SwingUtilities.invokeLater(new Runnable()
 900           {
 901             public void run()
 902             {
 903               JOptionPane.showInternalMessageDialog(Desktop.desktop,
 904                   "Couldn't locate " + file,
 905                   "URL not found",
 906                   JOptionPane.WARNING_MESSAGE);
 907             }
 908           });
 909         }
 910         catch (Exception ex)
 911         {
 912           //Is Version 1 Jar file?
 913           af =  new Jalview2XML_V1().LoadJalviewAlign(file);
 914
 915           if(af!=null)
 916           {
 917             System.out.println("Successfully loaded archive file");
 918             return af;
 919           }
 920
 921             System.err.println("Exception whilst loading jalview XML file : " +
 922                 ex + "\n");
 923             javax.swing.SwingUtilities.invokeLater(new Runnable()
 924             {
 925               public void run()
 926               {
 927
 928                 JOptionPane.showInternalMessageDialog(Desktop.desktop,
 929                     "Error loading  " + file,
 930                     "Error loading Jalview file",
 931                     JOptionPane.WARNING_MESSAGE);
 932               }});
 933         }
 934
 935         if (Desktop.instance != null)
 936           Desktop.instance.stopLoading();
 937
 938         for (int i = 0; i < gatherToThisFrame.size(); i++)
 939         {
 940           Desktop.instance.gatherViews(
 941               (AlignFrame) gatherToThisFrame.elementAt(i));
 942         }
 943
 944         return af;
 945     }
 946
 947     String loadPDBFile(String file, String pdbId)
 948     {
 949       try
 950       {
 951         JarInputStream jin = null;
 952
 953         if (file.startsWith("http://"))
 954         {
 955           jin = new JarInputStream(new URL(file).openStream());
 956         }
 957         else
 958         {
 959           jin = new JarInputStream(new FileInputStream(file));
 960         }
 961
 962         JarEntry entry = null;
 963         do
 964         {
 965           entry = jin.getNextJarEntry();
 966         }
 967         while (!entry.getName().equals(pdbId));
 968
 969         BufferedReader in = new BufferedReader(new InputStreamReader(jin));
 970         File outFile = File.createTempFile("jalview_pdb", ".txt");
 971         outFile.deleteOnExit();
 972         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
 973         String data;
 974
 975         while ( (data = in.readLine()) != null)
 976         {
 977           out.println(data);
 978         }
 979         out.close();
 980         return outFile.getAbsolutePath();
 981
 982       }
 983       catch (Exception ex)
 984       {
 985         ex.printStackTrace();
 986       }
 987
 988       return null;
 989     }
 990
 991
 992     AlignFrame LoadFromObject(JalviewModel object, String file)
 993     {
 994         SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
 995         Sequence[] vamsasSeq = vamsasSet.getSequence();
 996
 997         JalviewModelSequence jms = object.getJalviewModelSequence();
 998
 999         Viewport[] views = jms.getViewport();
1000         Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
1001
1002         //////////////////////////////////
1003         //LOAD SEQUENCES
1004
1005         Vector hiddenSeqs = null;
1006         jalview.datamodel.Sequence jseq;
1007
1008         ArrayList tmpseqs = new ArrayList();
1009
1010
1011         boolean multipleView = false;
1012
1013         JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
1014         for (int i = 0; i < JSEQ.length; i++)
1015         {
1016           String seqId = JSEQ[i].getId() + "";
1017
1018           if (seqRefIds.get(seqId) != null)
1019           {
1020             tmpseqs.add( (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1021             multipleView = true;
1022           }
1023           else
1024           {
1025             jseq = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
1026                 vamsasSeq[i].getSequence());
1027             jseq.setDescription(vamsasSeq[i].getDescription());
1028             jseq.setStart(JSEQ[i].getStart());
1029             jseq.setEnd(JSEQ[i].getEnd());
1030             jseq.setColor(new java.awt.Color(JSEQ[i].getColour()));
1031             seqRefIds.put(vamsasSeq[i].getId(), jseq);
1032             tmpseqs.add( jseq );
1033           }
1034
1035
1036           if (JSEQ[i].getHidden())
1037           {
1038             if (hiddenSeqs == null)
1039               hiddenSeqs = new Vector();
1040
1041
1042             hiddenSeqs.addElement(
1043                 (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1044           }
1045
1046         }
1047
1048         ///SequenceFeatures are added to the DatasetSequence,
1049         // so we must create the dataset before loading features
1050         /////////////////////////////////
1051
1052
1053       jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[
1054           tmpseqs.size()];
1055
1056        tmpseqs.toArray(orderedSeqs) ;
1057
1058
1059         jalview.datamodel.Alignment al =
1060             new jalview.datamodel.Alignment(orderedSeqs);
1061
1062         al.setDataset(null);
1063         /////////////////////////////////
1064
1065
1066         Hashtable pdbloaded = new Hashtable();
1067         if(!multipleView)
1068         {
1069           for (int i = 0; i < vamsasSeq.length; i++)
1070           {
1071             if (JSEQ[i].getFeaturesCount() > 0)
1072             {
1073               Features[] features = JSEQ[i].getFeatures();
1074               for (int f = 0; f < features.length; f++)
1075               {
1076                 jalview.datamodel.SequenceFeature sf
1077                     = new jalview.datamodel.SequenceFeature(features[f].getType(),
1078                     features[f].getDescription(), features[f].getStatus(),
1079                     features[f].getBegin(), features[f].getEnd(),
1080                     features[f].getFeatureGroup());
1081
1082                 sf.setScore(features[f].getScore());
1083                 for (int od = 0; od < features[f].getOtherDataCount(); od++)
1084                 {
1085                   OtherData keyValue = features[f].getOtherData(od);
1086                   if (keyValue.getKey().startsWith("LINK"))
1087                     sf.addLink(keyValue.getValue());
1088                   else
1089                     sf.setValue(keyValue.getKey(), keyValue.getValue());
1090
1091                 }
1092
1093                 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1094               }
1095             }
1096             if (JSEQ[i].getPdbidsCount() > 0)
1097             {
1098               Pdbids[] ids = JSEQ[i].getPdbids();
1099               for (int p = 0; p < ids.length; p++)
1100               {
1101                 jalview.datamodel.PDBEntry entry = new jalview.datamodel.
1102                     PDBEntry();
1103                 entry.setId(ids[p].getId());
1104                 entry.setType(ids[p].getType());
1105                 if (ids[p].getFile() != null)
1106                 {
1107                   if (!pdbloaded.containsKey(ids[p].getFile()))
1108                   {
1109                     String tmppdb = loadPDBFile(file, ids[p].getId());
1110                     entry.setFile(tmppdb);
1111                     pdbloaded.put(ids[p].getId(), tmppdb);
1112                   }
1113                   else
1114                     entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1115                 }
1116
1117                 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1118               }
1119             }
1120             if (vamsasSeq[i].getDBRefCount() > 0)
1121             {
1122               for (int d = 0; d < vamsasSeq[i].getDBRefCount(); d++)
1123               {
1124                 jalview.datamodel.DBRefEntry entry =
1125                     new jalview.datamodel.DBRefEntry(
1126                         vamsasSeq[i].getDBRef(d).getSource(),
1127                         vamsasSeq[i].getDBRef(d).getVersion(),
1128                         vamsasSeq[i].getDBRef(d).getAccessionId()
1129                     );
1130                 al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);
1131               }
1132
1133             }
1134           }
1135         }
1136
1137
1138          /////////////////////////////////
1139         //////////////////////////////////
1140         //LOAD ANNOTATIONS
1141         boolean hideQuality = true,
1142             hideConservation = true,
1143             hideConsensus = true;
1144
1145         if (vamsasSet.getAnnotationCount()>0)
1146         {
1147             Annotation[] an = vamsasSet.getAnnotation();
1148
1149             for (int i = 0; i < an.length; i++)
1150             {
1151                if (an[i].getLabel().equals("Quality"))
1152                 {
1153                  hideQuality = false;
1154                  continue;
1155                 }
1156                else if(an[i].getLabel().equals("Conservation"))
1157                {
1158                  hideConservation = false;
1159                  continue;
1160                }
1161                else if(an[i].getLabel().equals("Consensus"))
1162                {
1163                  hideConsensus = false;
1164                  continue;
1165                }
1166
1167                 AnnotationElement[] ae = an[i].getAnnotationElement();
1168                 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];
1169
1170                 for (int aa = 0; aa < ae.length; aa++)
1171                 {
1172                     anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),
1173                             ae[aa].getDescription(),
1174                             ae[aa].getSecondaryStructure().length()==0?' ':ae[aa].getSecondaryStructure().charAt(0),
1175                             ae[aa].getValue());
1176                     anot[ae[aa].getPosition()].colour = new java.awt.Color( ae[aa].getColour() );
1177                 }
1178
1179                 jalview.datamodel.AlignmentAnnotation jaa = null;
1180
1181                 if (an[i].getGraph())
1182                 {
1183                   jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1184                       an[i].getDescription(), anot, 0, 0,
1185                       an[i].getGraphType());
1186
1187                   jaa.graphGroup = an[i].getGraphGroup();
1188
1189                   if (an[i].getThresholdLine() != null)
1190                   {
1191                     jaa.setThreshold(new jalview.datamodel.GraphLine(
1192                                   an[i].getThresholdLine().getValue(),
1193                                   an[i].getThresholdLine().getLabel(),
1194                                 new java.awt.Color(an[i].getThresholdLine().getColour()))
1195                              );
1196
1197                   }
1198
1199                 }
1200                 else
1201                 {
1202                     jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1203                             an[i].getDescription(), anot);
1204                 }
1205
1206                 if(an[i].getSequenceRef()!=null)
1207                 {
1208                   jaa.createSequenceMapping(
1209                       al.findName(an[i].getSequenceRef()), 1, true
1210                       );
1211                   al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
1212                 }
1213
1214                 al.addAnnotation(jaa);
1215             }
1216         }
1217
1218
1219         //  af.changeColour() );
1220         /////////////////////////
1221         //LOAD GROUPS
1222         if (jms.getJGroupCount() > 0)
1223         {
1224             JGroup[] groups = jms.getJGroup();
1225
1226             for (int i = 0; i < groups.length; i++)
1227             {
1228                 ColourSchemeI cs = null;
1229
1230                 if (groups[i].getColour() != null)
1231                 {
1232                     if (groups[i].getColour().startsWith("ucs"))
1233                     {
1234                         cs = GetUserColourScheme(jms, groups[i].getColour());
1235                     }
1236                     else
1237                     {
1238                         cs = ColourSchemeProperty.getColour(al,
1239                                 groups[i].getColour());
1240                     }
1241
1242                     if(cs!=null)
1243                       cs.setThreshold(groups[i].getPidThreshold(), true);
1244                 }
1245
1246                 Vector seqs = new Vector();
1247
1248                 for (int s = 0; s < groups[i].getSeqCount(); s++)
1249                 {
1250                     String seqId = groups[i].getSeq(s)+"";
1251                     seqs.addElement((jalview.datamodel.SequenceI) seqRefIds.get(seqId));
1252                 }
1253
1254                 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,
1255                         groups[i].getName(), cs, groups[i].getDisplayBoxes(),
1256                         groups[i].getDisplayText(), groups[i].getColourText(),
1257                         groups[i].getStart(), groups[i].getEnd());
1258
1259                 sg.setOutlineColour(new java.awt.Color(
1260                         groups[i].getOutlineColour()));
1261
1262                 if (groups[i].getConsThreshold() != 0)
1263                 {
1264                     jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
1265                             ResidueProperties.propHash, 3, sg.getSequences(false), 0,
1266                             sg.getWidth() - 1);
1267                     c.calculate();
1268                     c.verdict(false, 25);
1269                     sg.cs.setConservation(c);
1270                 }
1271
1272                 al.addGroup(sg);
1273             }
1274         }
1275
1276
1277         /////////////////////////////////
1278         // LOAD VIEWPORT
1279
1280         AlignFrame af = new AlignFrame(al,
1281                                        view.getWidth(),
1282                                        view.getHeight() );
1283
1284         af.viewport.sequenceSetID = view.getSequenceSetId();
1285
1286         af.viewport.gatherViewsHere = view.getGatheredViews();
1287
1288         if (view.getSequenceSetId() != null)
1289           PaintRefresher.Register(af.alignPanel, view.getSequenceSetId());
1290
1291         if(hiddenSeqs!=null)
1292         {
1293           for(int s=0; s<JSEQ.length; s++)
1294           {
1295             for(int r=0; r<JSEQ[s].getHiddenSequencesCount(); r++)
1296             {
1297               al.getSequenceAt(s).addHiddenSequence(
1298                   al.getSequenceAt( JSEQ[s].getHiddenSequences(r)  )
1299                   );
1300             }
1301           }
1302
1303           jalview.datamodel.SequenceI [] hseqs = new
1304               jalview.datamodel.SequenceI[hiddenSeqs.size()];
1305
1306           for(int s=0; s<hiddenSeqs.size(); s++)
1307             hseqs[s] = (jalview.datamodel.SequenceI)hiddenSeqs.elementAt(s);
1308
1309           af.viewport.hideSequence( hseqs );
1310
1311         }
1312
1313
1314         if((hideConsensus || hideQuality || hideConservation)
1315             && al.getAlignmentAnnotation()!=null)
1316         {
1317           int hSize = al.getAlignmentAnnotation().length;
1318           for (int h = 0; h < hSize; h++)
1319           {
1320             if (
1321                 (hideConsensus &&
1322                  al.getAlignmentAnnotation()[h].label.equals("Consensus"))
1323                 ||
1324                 (hideQuality &&
1325                  al.getAlignmentAnnotation()[h].label.equals("Quality"))
1326                 ||
1327                 (hideConservation &&
1328                  al.getAlignmentAnnotation()[h].label.equals("Conservation")))
1329             {
1330               al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
1331               hSize--;
1332               h--;
1333             }
1334           }
1335           af.alignPanel.adjustAnnotationHeight();
1336         }
1337
1338         af.viewport.viewName = view.getViewName();
1339         af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
1340             view.getHeight());
1341         af.viewport.setStartRes(view.getStartRes());
1342         af.viewport.setStartSeq(view.getStartSeq());
1343         af.viewport.setShowAnnotation(view.getShowAnnotation());
1344         af.viewport.showConservation = view.getShowConservation();
1345         af.viewport.showQuality = view.getShowQuality();
1346         af.viewport.showIdentity = view.getShowIdentity();
1347         af.viewport.setAbovePIDThreshold(view.getPidSelected());
1348         af.abovePIDThreshold.setSelected(view.getPidSelected());
1349         af.viewport.setColourText(view.getShowColourText());
1350         af.colourTextMenuItem.setSelected(view.getShowColourText());
1351         af.viewport.setConservationSelected(view.getConservationSelected());
1352         af.conservationMenuItem.setSelected(view.getConservationSelected());
1353
1354         af.viewport.setShowJVSuffix(view.getShowFullId());
1355         af.seqLimits.setSelected(view.getShowFullId());
1356
1357         af.viewport.setFont(new java.awt.Font(view.getFontName(),
1358                 view.getFontStyle(), view.getFontSize()));
1359         af.alignPanel.fontChanged();
1360
1361         af.viewport.setRenderGaps(view.getRenderGaps());
1362         af.renderGapsMenuItem.setSelected(view.getRenderGaps());
1363
1364         af.viewport.setWrapAlignment(view.getWrapAlignment());
1365         af.wrapMenuItem.setSelected(view.getWrapAlignment());
1366
1367         af.alignPanel.setWrapAlignment(view.getWrapAlignment());
1368
1369         af.annotationPanelMenuItem.setState(view.getShowAnnotation());
1370         af.viewport.setShowAnnotation(view.getShowAnnotation());
1371         af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
1372
1373         af.viewport.setShowBoxes(view.getShowBoxes());
1374         af.viewBoxesMenuItem.setSelected(view.getShowBoxes());
1375         af.viewport.setShowText(view.getShowText());
1376         af.viewTextMenuItem.setSelected(view.getShowText());
1377
1378         ColourSchemeI cs = null;
1379
1380         if (view.getBgColour() != null)
1381         {
1382             if (view.getBgColour().startsWith("ucs"))
1383             {
1384                 cs = GetUserColourScheme(jms, view.getBgColour());
1385             }
1386             else if(view.getBgColour().startsWith("Annotation"))
1387             {
1388               //int find annotation
1389               for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
1390               {
1391                 if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
1392                     equals(view.getAnnotationColours().getAnnotation()))
1393                 {
1394                   if (af.viewport.alignment.getAlignmentAnnotation()[i].
1395                       getThreshold() == null)
1396                   {
1397                     af.viewport.alignment.getAlignmentAnnotation()[i].
1398                         setThreshold(
1399                             new jalview.datamodel.GraphLine(
1400                                 view.getAnnotationColours().getThreshold(),
1401                                 "Threshold", java.awt.Color.black)
1402
1403                         );
1404                   }
1405
1406
1407                   if (view.getAnnotationColours().getColourScheme().equals(
1408                       "None"))
1409                   {
1410                     cs = new AnnotationColourGradient(
1411                         af.viewport.alignment.getAlignmentAnnotation()[i],
1412                         new java.awt.Color(view.getAnnotationColours().
1413                                            getMinColour()),
1414                         new java.awt.Color(view.getAnnotationColours().
1415                                            getMaxColour()),
1416                         view.getAnnotationColours().getAboveThreshold());
1417                   }
1418                   else if (view.getAnnotationColours().getColourScheme().
1419                            startsWith("ucs"))
1420                   {
1421                      cs = new AnnotationColourGradient(
1422                          af.viewport.alignment.getAlignmentAnnotation()[i],
1423                          GetUserColourScheme(jms, view.getAnnotationColours().
1424                                                         getColourScheme()),
1425                          view.getAnnotationColours().getAboveThreshold()
1426                          );
1427                    }
1428                    else
1429                    {
1430                      cs = new AnnotationColourGradient(
1431                          af.viewport.alignment.getAlignmentAnnotation()[i],
1432                          ColourSchemeProperty.getColour(al,
1433                          view.getAnnotationColours().getColourScheme()),
1434                          view.getAnnotationColours().getAboveThreshold()
1435                          );
1436                    }
1437
1438                   // Also use these settings for all the groups
1439                   if (al.getGroups() != null)
1440                     for (int g = 0; g < al.getGroups().size(); g++)
1441                     {
1442                       jalview.datamodel.SequenceGroup sg
1443                           = (jalview.datamodel.SequenceGroup)al.getGroups().elementAt(g);
1444
1445                       if(sg.cs == null)
1446                         continue;
1447
1448
1449                   /*    if (view.getAnnotationColours().getColourScheme().equals("None"))
1450                       {
1451                         sg.cs = new AnnotationColourGradient(
1452                             af.viewport.alignment.getAlignmentAnnotation()[i],
1453                             new java.awt.Color(view.getAnnotationColours().
1454                                                getMinColour()),
1455                             new java.awt.Color(view.getAnnotationColours().
1456                                                getMaxColour()),
1457                             view.getAnnotationColours().getAboveThreshold());
1458                       }
1459                       else*/
1460                       {
1461                         sg.cs = new AnnotationColourGradient(
1462                             af.viewport.alignment.getAlignmentAnnotation()[i],
1463                             sg.cs,
1464                             view.getAnnotationColours().getAboveThreshold()
1465                             );
1466                       }
1467
1468                     }
1469
1470
1471                   break;
1472                 }
1473
1474               }
1475             }
1476             else
1477             {
1478                 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
1479             }
1480
1481             if(cs!=null)
1482             {
1483               cs.setThreshold(view.getPidThreshold(), true);
1484               cs.setConsensus(af.viewport.hconsensus);
1485             }
1486         }
1487
1488         af.setColourSelected(view.getBgColour());
1489         af.viewport.setGlobalColourScheme(cs);
1490         af.viewport.setColourAppliesToAllGroups(false);
1491         af.changeColour(cs);
1492         if (view.getConservationSelected() && cs!=null)
1493         {
1494           cs.setConservationInc(view.getConsThreshold());
1495         }
1496
1497         af.viewport.setColourAppliesToAllGroups(true);
1498
1499         if (view.getShowSequenceFeatures())
1500         {
1501            af.viewport.showSequenceFeatures = true;
1502            af.showSeqFeatures.setSelected(true);
1503         }
1504
1505         if(jms.getFeatureSettings()!=null)
1506         {
1507           af.viewport.featuresDisplayed = new Hashtable();
1508           String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];
1509          for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)
1510          {
1511            Setting setting = jms.getFeatureSettings().getSetting(fs);
1512
1513            af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),
1514                new java.awt.Color(setting.getColour()));
1515
1516            renderOrder[fs] = setting.getType();
1517
1518            if(setting.getDisplay())
1519              af.viewport.featuresDisplayed.put(
1520                  setting.getType(), new Integer(setting.getColour()));
1521          }
1522          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
1523         }
1524
1525         if (view.getHiddenColumnsCount() > 0)
1526         {
1527           for (int c = 0; c < view.getHiddenColumnsCount(); c++)
1528           {
1529               af.viewport.hideColumns(
1530                 view.getHiddenColumns(c).getStart(),
1531                 view.getHiddenColumns(c).getEnd() //+1
1532                 );
1533           }
1534         }
1535
1536
1537         Desktop.addInternalFrame(af, view.getTitle(),
1538              view.getWidth(), view.getHeight());
1539
1540         //LOAD TREES
1541         ///////////////////////////////////////
1542         if (jms.getTreeCount() > 0)
1543         {
1544             try
1545             {
1546                 for (int t = 0; t < jms.getTreeCount(); t++)
1547                 {
1548
1549                     Tree tree = jms.getTree(t);
1550
1551                     TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
1552                                 tree.getNewick()), tree.getTitle(),
1553                                 tree.getWidth(), tree.getHeight(),
1554                                 tree.getXpos(), tree.getYpos());
1555
1556                     tp.fitToWindow.setState(tree.getFitToWindow());
1557                     tp.fitToWindow_actionPerformed(null);
1558
1559                     if(tree.getFontName()!=null)
1560                       tp.setTreeFont(new java.awt.Font(tree.getFontName(),
1561                                           tree.getFontStyle(),
1562                                           tree.getFontSize()));
1563                     else
1564                       tp.setTreeFont(new java.awt.Font(view.getFontName(),
1565                                             view.getFontStyle(),
1566                                             tree.getFontSize()));
1567
1568                     tp.showPlaceholders(tree.getMarkUnlinked());
1569                     tp.showBootstrap(tree.getShowBootstrap());
1570                     tp.showDistances(tree.getShowDistances());
1571
1572                     tp.treeCanvas.threshold = tree.getThreshold();
1573
1574                     if (tree.getCurrentTree())
1575                       af.viewport.setCurrentTree(tp.getTree());
1576                 }
1577
1578             }
1579             catch (Exception ex)
1580             {
1581                 ex.printStackTrace();
1582             }
1583
1584         }
1585
1586         return af;
1587     }
1588 }
1589