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
  52   Hashtable seqRefIds;
  53
  54   /**
  55    * This maintains a list of viewports, the key being the
  56    * seqSetId. Important to set historyItem and redoList
  57    * for multiple views
  58    */
  59   Hashtable viewportsAdded;
  60
  61   String uniqueSetSuffix = "";
  62
  63
  64     // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
  65     public void SaveState(File statefile)
  66     {
  67         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
  68
  69         if (frames == null)
  70         {
  71             return;
  72         }
  73
  74         try
  75         {
  76             FileOutputStream fos = new FileOutputStream(statefile);
  77             JarOutputStream jout = new JarOutputStream(fos);
  78
  79             //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
  80             ////////////////////////////////////////////////////
  81             PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
  82                         "UTF-8"));
  83
  84             Vector shortNames = new Vector();
  85
  86             //REVERSE ORDER
  87             for (int i = frames.length - 1; i > -1; i--)
  88             {
  89                 if (frames[i] instanceof AlignFrame)
  90                 {
  91                     AlignFrame af = (AlignFrame) frames[i];
  92
  93                     String shortName = af.getTitle();
  94
  95                     if (shortName.indexOf(File.separatorChar) > -1)
  96                     {
  97                         shortName = shortName.substring(shortName.lastIndexOf(
  98                                     File.separatorChar) + 1);
  99                     }
 100
 101                     int count = 1;
 102
 103                     while (shortNames.contains(shortName))
 104                     {
 105                         if (shortName.endsWith("_" + (count - 1)))
 106                         {
 107                             shortName = shortName.substring(0,
 108                                     shortName.lastIndexOf("_"));
 109                         }
 110
 111                         shortName = shortName.concat("_" + count);
 112                         count++;
 113                     }
 114
 115                     shortNames.addElement(shortName);
 116
 117                     if (!shortName.endsWith(".xml"))
 118                     {
 119                         shortName = shortName + ".xml";
 120                     }
 121
 122                     int ap, apSize= af.alignPanels.size();
 123                     for (ap = 0; ap < apSize; ap++)
 124                     {
 125                       AlignmentPanel apanel = (AlignmentPanel) af.alignPanels.
 126                           elementAt(ap);
 127
 128                       SaveState(apanel,
 129                                 apSize == 1 ? shortName : ap+shortName,
 130                                 jout, out);
 131                     }
 132                 }
 133             }
 134
 135             out.close();
 136             jout.close();
 137         }
 138         catch (Exception ex)
 139         {
 140             ex.printStackTrace();
 141         }
 142     }
 143
 144     // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
 145     public void SaveAlignment(AlignFrame af, String jarFile,
 146         String fileName)
 147     {
 148         try
 149         {
 150           int ap, apSize= af.alignPanels.size();
 151           FileOutputStream fos = new FileOutputStream(jarFile);
 152           JarOutputStream jout = new JarOutputStream(fos);
 153           PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
 154                 "UTF-8"));
 155           for( ap=0; ap<apSize; ap++)
 156           {
 157             AlignmentPanel apanel = (AlignmentPanel)af.alignPanels.elementAt(ap);
 158
 159             SaveState(apanel,
 160                       apSize==1?fileName:fileName+ap,
 161                       jout, out);
 162           }
 163
 164           out.close();
 165           jout.close();
 166         }
 167         catch (Exception ex)
 168         {
 169           ex.printStackTrace();
 170         }
 171     }
 172
 173     /**
 174      * DOCUMENT ME!
 175      *
 176      * @param af DOCUMENT ME!
 177      * @param timeStamp DOCUMENT ME!
 178      * @param fileName DOCUMENT ME!
 179      * @param jout DOCUMENT ME!
 180      * @param out DOCUMENT ME!
 181      */
 182     public JalviewModel SaveState(AlignmentPanel ap,
 183                           String fileName,
 184                           JarOutputStream jout,
 185                           PrintWriter out)
 186     {
 187       if (seqRefIds == null)
 188         seqRefIds = new Hashtable();
 189
 190         Vector userColours = new Vector();
 191
 192         AlignViewport av = ap.av;
 193
 194         JalviewModel object = new JalviewModel();
 195         object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
 196
 197         object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
 198         object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
 199
 200         jalview.datamodel.AlignmentI jal = av.alignment;
 201
 202         if(av.hasHiddenRows)
 203         {
 204           jal = jal.getHiddenSequences().getFullAlignment();
 205         }
 206
 207         SequenceSet vamsasSet = new SequenceSet();
 208         Sequence vamsasSeq;
 209         JalviewModelSequence jms = new JalviewModelSequence();
 210
 211         vamsasSet.setGapChar(jal.getGapCharacter() + "");
 212
 213         JSeq jseq;
 214         Vector pdbfiles = null;
 215
 216         //SAVE SEQUENCES
 217         int id = 0;
 218         jalview.datamodel.SequenceI jds;
 219         for (int i = 0; i < jal.getHeight(); i++)
 220         {
 221             jds = jal.getSequenceAt(i);
 222             id = jds.hashCode();
 223
 224             if(seqRefIds.get(id+"")!=null)
 225             {
 226
 227             }
 228             else
 229             {
 230               vamsasSeq = new Sequence();
 231               vamsasSeq.setId(id + "");
 232               vamsasSeq.setName(jds.getName());
 233               vamsasSeq.setSequence(jds.getSequence());
 234               vamsasSeq.setDescription(jds.getDescription());
 235
 236               if (jds.getDatasetSequence().getDBRef() != null)
 237               {
 238                 jalview.datamodel.DBRefEntry[] dbrefs =
 239                     jds.getDatasetSequence().getDBRef();
 240
 241                 for (int d = 0; d < dbrefs.length; d++)
 242                 {
 243                   DBRef dbref = new DBRef();
 244                   dbref.setSource(dbrefs[d].getSource());
 245                   dbref.setVersion(dbrefs[d].getVersion());
 246                   dbref.setAccessionId(dbrefs[d].getAccessionId());
 247                   vamsasSeq.addDBRef(dbref);
 248                 }
 249               }
 250
 251               vamsasSet.addSequence(vamsasSeq);
 252               seqRefIds.put(id+"", jal.getSequenceAt(i));
 253             }
 254
 255             jseq = new JSeq();
 256             jseq.setStart(jds.getStart());
 257             jseq.setEnd(jds.getEnd());
 258             jseq.setColour( av.getSequenceColour(jds).getRGB());
 259
 260             jseq.setId(id);
 261
 262             if (av.hasHiddenRows)
 263             {
 264               jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
 265
 266               if(jal.getSequenceAt(i).getHiddenSequences()!=null)
 267               {
 268                 jalview.datamodel.SequenceI [] reps =
 269                     jal.getSequenceAt(i).getHiddenSequences().getSequencesInOrder(jal);
 270
 271                 for(int h=0; h<reps.length; h++)
 272                 {
 273                   jseq.addHiddenSequences(
 274                       jal.findIndex(reps[h])
 275                       );
 276                 }
 277               }
 278             }
 279
 280
 281             if(jds.getDatasetSequence().getSequenceFeatures()!=null)
 282             {
 283               jalview.datamodel.SequenceFeature[] sf
 284                   = jds.getDatasetSequence().getSequenceFeatures();
 285               int index = 0;
 286               while(index < sf.length)
 287               {
 288                 Features features = new Features();
 289
 290                 features.setBegin(sf[index].getBegin());
 291                 features.setEnd(sf[index].getEnd());
 292                 features.setDescription(sf[index].getDescription());
 293                 features.setType(sf[index].getType());
 294                 features.setFeatureGroup(sf[index].getFeatureGroup());
 295                 features.setScore(sf[index].getScore());
 296                 if(sf[index].links!=null)
 297                 {
 298                   for(int l=0; l<sf[index].links.size(); l++)
 299                   {
 300                     OtherData keyValue = new OtherData();
 301                     keyValue.setKey("LINK_"+l);
 302                     keyValue.setValue(sf[index].links.elementAt(l).toString());
 303                     features.addOtherData(keyValue);
 304                   }
 305                 }
 306                 if(sf[index].otherDetails!=null)
 307                 {
 308                   String key;
 309                   Enumeration keys = sf[index].otherDetails.keys();
 310                   while(keys.hasMoreElements())
 311                   {
 312                     key = keys.nextElement().toString();
 313                     OtherData keyValue = new OtherData();
 314                     keyValue.setKey( key );
 315                     keyValue.setValue(
 316                         sf[index].otherDetails.get(key).toString());
 317                     features.addOtherData(keyValue);
 318                   }
 319                 }
 320
 321                 jseq.addFeatures(features);
 322                 index ++;
 323               }
 324             }
 325
 326             if(jds.getDatasetSequence().getPDBId()!=null)
 327             {
 328               Enumeration en = jds.getDatasetSequence().getPDBId().elements();
 329               while(en.hasMoreElements())
 330               {
 331                 Pdbids pdb = new Pdbids();
 332                 jalview.datamodel.PDBEntry entry
 333                    = (jalview.datamodel.PDBEntry)en.nextElement();
 334
 335                 pdb.setId(entry.getId());
 336                 pdb.setType(entry.getType());
 337
 338                 if(entry.getFile()!=null)
 339                 {
 340                   if(pdbfiles==null)
 341                     pdbfiles = new Vector();
 342
 343
 344                   if(!pdbfiles.contains(entry.getId()))
 345                   {
 346                     pdbfiles.addElement(entry.getId());
 347                     try
 348                     {
 349                       File file = new File(entry.getFile());
 350                       if(file.exists())
 351                       {
 352                         byte[] data = new byte[ (int) file.length()];
 353                         jout.putNextEntry(new JarEntry(entry.getId()));
 354                         DataInputStream dis = new DataInputStream(new
 355                             FileInputStream(file));
 356                         dis.readFully(data);
 357
 358                         DataOutputStream dout = new DataOutputStream(jout);
 359                         dout.write(data, 0, data.length);
 360                         jout.closeEntry();
 361                       }
 362                     }
 363                     catch (Exception ex)
 364                     {
 365                       ex.printStackTrace();
 366                     }
 367                   }
 368                 }
 369
 370
 371                 if(entry.getProperty()!=null)
 372                 {
 373                   PdbentryItem item = new PdbentryItem();
 374                   Hashtable properties = entry.getProperty();
 375                   Enumeration en2 = properties.keys();
 376                   while(en2.hasMoreElements())
 377                   {
 378                     Property prop = new Property();
 379                     String key = en2.nextElement().toString();
 380                     prop.setName(key);
 381                     prop.setValue( properties.get(key).toString() );
 382                     item.addProperty(prop);
 383                   }
 384                   pdb.addPdbentryItem(item);
 385                 }
 386
 387                 jseq.addPdbids(pdb);
 388               }
 389             }
 390
 391             jms.addJSeq(jseq);
 392         }
 393
 394         if(av.hasHiddenRows)
 395           jal = av.alignment;
 396
 397
 398         //SAVE TREES
 399         ///////////////////////////////////
 400         if (av.currentTree != null)
 401         {
 402           // FIND ANY ASSOCIATED TREES
 403           // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
 404           if (Desktop.desktop != null)
 405           {
 406             JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 407
 408             for (int t = 0; t < frames.length; t++)
 409             {
 410               if (frames[t] instanceof TreePanel)
 411               {
 412                 TreePanel tp = (TreePanel) frames[t];
 413
 414                 if (tp.treeCanvas.av.alignment == jal)
 415                 {
 416                   Tree tree = new Tree();
 417                   tree.setTitle(tp.getTitle());
 418                   tree.setCurrentTree( (av.currentTree == tp.getTree()));
 419                   tree.setNewick(tp.getTree().toString());
 420                   tree.setThreshold(tp.treeCanvas.threshold);
 421
 422                   tree.setFitToWindow(tp.fitToWindow.getState());
 423                   tree.setFontName(tp.getTreeFont().getName());
 424                   tree.setFontSize(tp.getTreeFont().getSize());
 425                   tree.setFontStyle(tp.getTreeFont().getStyle());
 426                   tree.setMarkUnlinked(tp.placeholdersMenu.getState());
 427
 428                   tree.setShowBootstrap(tp.bootstrapMenu.getState());
 429                   tree.setShowDistances(tp.distanceMenu.getState());
 430
 431                   tree.setHeight(tp.getHeight());
 432                   tree.setWidth(tp.getWidth());
 433                   tree.setXpos(tp.getX());
 434                   tree.setYpos(tp.getY());
 435
 436                   jms.addTree(tree);
 437                 }
 438               }
 439             }
 440           }
 441         }
 442
 443         //SAVE ANNOTATIONS
 444         if (jal.getAlignmentAnnotation() != null)
 445         {
 446             jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
 447
 448             for (int i = 0; i < aa.length; i++)
 449             {
 450                 Annotation an = new Annotation();
 451
 452                 if (aa[i].label.equals("Quality") ||
 453                         aa[i].label.equals("Conservation") ||
 454                         aa[i].label.equals("Consensus"))
 455                 {
 456                     an.setLabel(aa[i].label);
 457                     an.setGraph(true);
 458                     vamsasSet.addAnnotation(an);
 459                     continue;
 460                 }
 461
 462
 463                 an.setDescription(aa[i].description);
 464
 465                 if(aa[i].sequenceRef!=null)
 466                  {
 467                    an.setSequenceRef(aa[i].sequenceRef.getName());
 468                  }
 469
 470                 if(aa[i].graph>0)
 471                 {
 472                   an.setGraph(true);
 473                   an.setGraphType(aa[i].graph);
 474                   an.setGraphGroup(aa[i].graphGroup);
 475                   if(aa[i].getThreshold()!=null)
 476                   {
 477                     ThresholdLine line = new ThresholdLine();
 478                     line.setLabel(aa[i].getThreshold().label);
 479                     line.setValue(aa[i].getThreshold().value);
 480                     line.setColour(aa[i].getThreshold().colour.getRGB());
 481                     an.setThresholdLine(line);
 482                   }
 483                 }
 484                 else
 485                   an.setGraph(false);
 486
 487                 an.setLabel(aa[i].label);
 488
 489                 AnnotationElement ae;
 490
 491                 for (int a = 0; a < aa[i].annotations.length; a++)
 492                 {
 493                     if ((aa[i] == null) || (aa[i].annotations[a] == null))
 494                     {
 495                         continue;
 496                     }
 497
 498                     ae = new AnnotationElement();
 499                     ae.setDescription(aa[i].annotations[a].description);
 500                     ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
 501                     ae.setValue(aa[i].annotations[a].value);
 502                     ae.setPosition(a);
 503                     ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
 504                         "");
 505
 506                     if(aa[i].annotations[a].colour!=java.awt.Color.black)
 507                       ae.setColour(aa[i].annotations[a].colour.getRGB());
 508
 509                     an.addAnnotationElement(ae);
 510                 }
 511
 512                 vamsasSet.addAnnotation(an);
 513             }
 514         }
 515
 516         //SAVE GROUPS
 517         if (jal.getGroups() != null)
 518         {
 519             JGroup[] groups = new JGroup[jal.getGroups().size()];
 520
 521             for (int i = 0; i < groups.length; i++)
 522             {
 523                 groups[i] = new JGroup();
 524
 525                 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()
 526                                                                                           .elementAt(i);
 527                 groups[i].setStart(sg.getStartRes());
 528                 groups[i].setEnd(sg.getEndRes());
 529                 groups[i].setName(sg.getName());
 530                 if(sg.cs!=null)
 531                 {
 532                   if (sg.cs.conservationApplied())
 533                   {
 534                     groups[i].setConsThreshold(sg.cs.getConservationInc());
 535
 536                     if (sg.cs instanceof jalview.schemes.UserColourScheme)
 537                     {
 538                       groups[i].setColour(SetUserColourScheme(sg.cs,
 539                           userColours,
 540                           jms));
 541                     }
 542                     else
 543                     {
 544                       groups[i].setColour(ColourSchemeProperty.getColourName(sg.
 545                           cs));
 546                     }
 547                   }
 548                   else if(sg.cs instanceof jalview.schemes.AnnotationColourGradient)
 549                   {
 550                     groups[i].setColour(
 551                         ColourSchemeProperty.getColourName(
 552                       ( (jalview.schemes.AnnotationColourGradient) sg.cs).getBaseColour()));
 553                   }
 554                   else if (sg.cs instanceof jalview.schemes.UserColourScheme)
 555                   {
 556                     groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
 557                         jms));
 558                   }
 559                   else
 560                   {
 561                     groups[i].setColour(ColourSchemeProperty.getColourName(
 562                         sg.cs));
 563                   }
 564
 565                   groups[i].setPidThreshold(sg.cs.getThreshold());
 566                 }
 567
 568                 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
 569                 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
 570                 groups[i].setDisplayText(sg.getDisplayText());
 571                 groups[i].setColourText(sg.getColourText());
 572                 groups[i].setTextCol1(sg.textColour.getRGB());
 573                 groups[i].setTextCol2(sg.textColour2.getRGB());
 574                 groups[i].setTextColThreshold(sg.thresholdTextColour);
 575
 576                 for (int s = 0; s < sg.getSize(false); s++)
 577                 {
 578                     jalview.datamodel.Sequence seq =
 579                         (jalview.datamodel.Sequence) sg.getSequenceAt(s);
 580                     groups[i].addSeq(seq.hashCode());
 581                 }
 582             }
 583
 584             jms.setJGroup(groups);
 585         }
 586
 587
 588         ///////////SAVE VIEWPORT
 589         Viewport view = new Viewport();
 590         view.setTitle(ap.alignFrame.getTitle());
 591         view.setSequenceSetId(av.getSequenceSetId());
 592         view.setViewName(av.viewName);
 593         view.setGatheredViews(av.gatherViewsHere);
 594
 595
 596         if (ap.av.explodedPosition != null)
 597         {
 598           view.setXpos(av.explodedPosition.x);
 599           view.setYpos(av.explodedPosition.y);
 600           view.setWidth(av.explodedPosition.width);
 601           view.setHeight(av.explodedPosition.height);
 602         }
 603         else
 604         {
 605           view.setXpos(ap.alignFrame.getBounds().x);
 606           view.setYpos(ap.alignFrame.getBounds().y);
 607           view.setWidth(ap.alignFrame.getBounds().width);
 608           view.setHeight(ap.alignFrame.getBounds().height);
 609         }
 610
 611         view.setStartRes(av.startRes);
 612         view.setStartSeq(av.startSeq);
 613
 614         if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
 615         {
 616             view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
 617                     userColours, jms));
 618         }
 619         else if(av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
 620         {
 621            jalview.schemes.AnnotationColourGradient acg
 622               = (jalview.schemes.AnnotationColourGradient)av.getGlobalColourScheme();
 623
 624             AnnotationColours ac = new AnnotationColours();
 625             ac.setAboveThreshold(acg.getAboveThreshold());
 626             ac.setThreshold(acg.getAnnotationThreshold());
 627             ac.setAnnotation(acg.getAnnotation());
 628             if(acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
 629               ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
 630                     userColours, jms));
 631             else
 632               ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
 633
 634             ac.setMaxColour(acg.getMaxColour().getRGB());
 635             ac.setMinColour(acg.getMinColour().getRGB());
 636             view.setAnnotationColours(ac);
 637             view.setBgColour("AnnotationColourGradient");
 638         }
 639         else
 640         {
 641             view.setBgColour(ColourSchemeProperty.getColourName(
 642                     av.getGlobalColourScheme()));
 643         }
 644
 645         ColourSchemeI cs = av.getGlobalColourScheme();
 646
 647         if(cs!=null)
 648         {
 649           if (cs.conservationApplied())
 650           {
 651             view.setConsThreshold(cs.getConservationInc());
 652             if (cs instanceof jalview.schemes.UserColourScheme)
 653               view.setBgColour(SetUserColourScheme(cs, userColours, jms));
 654           }
 655
 656           if (cs instanceof ResidueColourScheme)
 657           {
 658             view.setPidThreshold(cs.getThreshold());
 659           }
 660         }
 661
 662         view.setConservationSelected(av.getConservationSelected());
 663         view.setPidSelected(av.getAbovePIDThreshold());
 664         view.setFontName(av.font.getName());
 665         view.setFontSize(av.font.getSize());
 666         view.setFontStyle(av.font.getStyle());
 667         view.setRenderGaps(av.renderGaps);
 668         view.setShowAnnotation(av.getShowAnnotation());
 669         view.setShowBoxes(av.getShowBoxes());
 670         view.setShowColourText(av.getColourText());
 671         view.setShowFullId(av.getShowJVSuffix());
 672         view.setShowSequenceFeatures(av.showSequenceFeatures);
 673         view.setShowText(av.getShowText());
 674         view.setWrapAlignment(av.getWrapAlignment());
 675         view.setTextCol1(av.textColour.getRGB());
 676         view.setTextCol2(av.textColour2.getRGB());
 677         view.setTextColThreshold(av.thresholdTextColour);
 678
 679
 680         if(av.featuresDisplayed!=null)
 681         {
 682           jalview.schemabinding.version2.FeatureSettings fs
 683               = new jalview.schemabinding.version2.FeatureSettings();
 684
 685           String [] renderOrder =
 686               ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
 687
 688           Vector settingsAdded = new Vector();
 689           for(int ro=0; ro<renderOrder.length; ro++)
 690           {
 691             Setting setting = new Setting();
 692             setting.setType(renderOrder[ro]);
 693             setting.setColour(
 694                 ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).getRGB()
 695                 );
 696
 697             setting.setDisplay(
 698                 av.featuresDisplayed.containsKey(renderOrder[ro])
 699                 );
 700
 701             fs.addSetting(setting);
 702             settingsAdded.addElement(renderOrder[ro]);
 703           }
 704
 705           //Make sure we save none displayed feature settings
 706           Enumeration en =
 707               ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
 708           while(en.hasMoreElements())
 709           {
 710             String key = en.nextElement().toString();
 711             if(settingsAdded.contains(key))
 712               continue;
 713
 714             Setting setting = new Setting();
 715             setting.setType(key);
 716             setting.setColour(
 717                 ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()
 718                 );
 719
 720             setting.setDisplay(false);
 721
 722             fs.addSetting(setting);
 723             settingsAdded.addElement(key);
 724           }
 725
 726           jms.setFeatureSettings(fs);
 727
 728         }
 729
 730         if(av.hasHiddenColumns)
 731         {
 732           for(int c=0; c<av.getColumnSelection().getHiddenColumns().size(); c++)
 733           {
 734             int [] region = (int[]) av.getColumnSelection().getHiddenColumns().elementAt(c);
 735             HiddenColumns hc = new HiddenColumns();
 736             hc.setStart(region[0]);
 737             hc.setEnd(region[1]);
 738             view.addHiddenColumns(hc);
 739           }
 740         }
 741
 742         jms.addViewport(view);
 743
 744
 745         object.setJalviewModelSequence(jms);
 746         object.getVamsasModel().addSequenceSet(vamsasSet);
 747
 748         if(out!=null)
 749         {
 750           //We may not want to right the object to disk,
 751           //eg we can copy the alignViewport to a new view object
 752           //using save and then load
 753           try
 754           {
 755             if (!fileName.endsWith(".xml"))
 756             {
 757               fileName = fileName + ".xml";
 758             }
 759
 760             JarEntry entry = new JarEntry(fileName);
 761             jout.putNextEntry(entry);
 762
 763             object.marshal(out);
 764           }
 765           catch (Exception ex)
 766           {
 767             ex.printStackTrace();
 768           }
 769         }
 770         return object;
 771     }
 772
 773     String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
 774         Vector userColours, JalviewModelSequence jms)
 775     {
 776         String id = null;
 777         jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
 778
 779         if (!userColours.contains(ucs))
 780         {
 781             userColours.add(ucs);
 782
 783             java.awt.Color[] colours = ucs.getColours();
 784             jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
 785             jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
 786
 787             for (int i = 0; i < colours.length; i++)
 788             {
 789                 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
 790                 col.setName(ResidueProperties.aa[i]);
 791                 col.setRGB(jalview.util.Format.getHexString(colours[i]));
 792                 jbucs.addColour(col);
 793             }
 794             if(ucs.getLowerCaseColours()!=null)
 795             {
 796               colours = ucs.getLowerCaseColours();
 797               for (int i = 0; i < colours.length; i++)
 798              {
 799                  jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
 800                  col.setName(ResidueProperties.aa[i].toLowerCase());
 801                  col.setRGB(jalview.util.Format.getHexString(colours[i]));
 802                  jbucs.addColour(col);
 803              }
 804             }
 805
 806             id = "ucs" + userColours.indexOf(ucs);
 807             uc.setId(id);
 808             uc.setUserColourScheme(jbucs);
 809             jms.addUserColours(uc);
 810         }
 811
 812         return id;
 813     }
 814
 815    jalview.schemes.UserColourScheme GetUserColourScheme(
 816         JalviewModelSequence jms, String id)
 817     {
 818         UserColours[] uc = jms.getUserColours();
 819         UserColours colours = null;
 820
 821         for (int i = 0; i < uc.length; i++)
 822         {
 823             if (uc[i].getId().equals(id))
 824             {
 825                 colours = uc[i];
 826
 827                 break;
 828             }
 829         }
 830
 831         java.awt.Color[] newColours = new java.awt.Color[24];
 832
 833         for (int i = 0; i < 24; i++)
 834         {
 835             newColours[i] = new java.awt.Color(Integer.parseInt(
 836                         colours.getUserColourScheme().getColour(i).getRGB(), 16));
 837         }
 838
 839         jalview.schemes.UserColourScheme ucs =
 840             new jalview.schemes.UserColourScheme(newColours);
 841
 842         if (colours.getUserColourScheme().getColourCount() > 24)
 843         {
 844           newColours = new java.awt.Color[23];
 845           for (int i = 0; i < 23; i++)
 846           {
 847             newColours[i] = new java.awt.Color(Integer.parseInt(
 848                 colours.getUserColourScheme().getColour(i+24).getRGB(), 16));
 849           }
 850           ucs.setLowerCaseColours(newColours);
 851         }
 852
 853         return ucs;
 854     }
 855
 856
 857     /**
 858      * DOCUMENT ME!
 859      *
 860      * @param file DOCUMENT ME!
 861      */
 862     public AlignFrame LoadJalviewAlign(final String file)
 863     {
 864         uniqueSetSuffix = System.currentTimeMillis()%100000 +"";
 865
 866         jalview.gui.AlignFrame af = null;
 867
 868         seqRefIds = new Hashtable();
 869         viewportsAdded = new Hashtable();
 870
 871         Vector gatherToThisFrame= new Vector();
 872
 873         try
 874         {
 875             //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
 876             URL url = null;
 877
 878             if (file.startsWith("http://"))
 879             {
 880                 url = new URL(file);
 881             }
 882
 883             JarInputStream jin = null;
 884             JarEntry jarentry = null;
 885             int entryCount = 1;
 886
 887             do
 888             {
 889                 if (url != null)
 890                 {
 891                     jin = new JarInputStream(url.openStream());
 892                 }
 893                 else
 894                 {
 895                     jin = new JarInputStream(new FileInputStream(file));
 896                 }
 897
 898                 for (int i = 0; i < entryCount; i++)
 899                 {
 900                     jarentry = jin.getNextJarEntry();
 901                 }
 902
 903                 if (jarentry != null && jarentry.getName().endsWith(".xml"))
 904                 {
 905                     InputStreamReader in = new InputStreamReader(jin, "UTF-8");
 906                     JalviewModel object = new JalviewModel();
 907
 908                     Unmarshaller unmar = new Unmarshaller(object);
 909                     unmar.setValidation(false);
 910                     object = (JalviewModel) unmar.unmarshal( in );
 911
 912                     af = LoadFromObject(object, file, true);
 913                     if(af.viewport.gatherViewsHere)
 914                     {
 915                       gatherToThisFrame.add(af);
 916                     }
 917                     entryCount++;
 918                 }
 919                 else if (jarentry != null)
 920                 {
 921                   //Some other file here.
 922                   entryCount++;
 923                 }
 924             }
 925             while (jarentry != null);
 926         }
 927         catch(java.net.UnknownHostException ex)
 928         {
 929           ex.printStackTrace();
 930           System.err.println("Couldn't locate Jalview XML file : " +
 931               ex + "\n");
 932
 933           javax.swing.SwingUtilities.invokeLater(new Runnable()
 934           {
 935             public void run()
 936             {
 937               JOptionPane.showInternalMessageDialog(Desktop.desktop,
 938                   "Couldn't locate " + file,
 939                   "URL not found",
 940                   JOptionPane.WARNING_MESSAGE);
 941             }
 942           });
 943         }
 944         catch (Exception ex)
 945         {
 946           //Is Version 1 Jar file?
 947           af =  new Jalview2XML_V1().LoadJalviewAlign(file);
 948
 949           if(af!=null)
 950           {
 951             System.out.println("Successfully loaded archive file");
 952             return af;
 953           }
 954
 955             System.err.println("Exception whilst loading jalview XML file : " +
 956                 ex + "\n");
 957             javax.swing.SwingUtilities.invokeLater(new Runnable()
 958             {
 959               public void run()
 960               {
 961
 962                 JOptionPane.showInternalMessageDialog(Desktop.desktop,
 963                     "Error loading  " + file,
 964                     "Error loading Jalview file",
 965                     JOptionPane.WARNING_MESSAGE);
 966               }});
 967         }
 968
 969         if (Desktop.instance != null)
 970           Desktop.instance.stopLoading();
 971
 972         for (int i = 0; i < gatherToThisFrame.size(); i++)
 973         {
 974           Desktop.instance.gatherViews(
 975               (AlignFrame) gatherToThisFrame.elementAt(i));
 976         }
 977
 978         return af;
 979     }
 980
 981     String loadPDBFile(String file, String pdbId)
 982     {
 983       try
 984       {
 985         JarInputStream jin = null;
 986
 987         if (file.startsWith("http://"))
 988         {
 989           jin = new JarInputStream(new URL(file).openStream());
 990         }
 991         else
 992         {
 993           jin = new JarInputStream(new FileInputStream(file));
 994         }
 995
 996         JarEntry entry = null;
 997         do
 998         {
 999           entry = jin.getNextJarEntry();
1000         }
1001         while (!entry.getName().equals(pdbId));
1002
1003         BufferedReader in = new BufferedReader(new InputStreamReader(jin));
1004         File outFile = File.createTempFile("jalview_pdb", ".txt");
1005         outFile.deleteOnExit();
1006         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
1007         String data;
1008
1009         while ( (data = in.readLine()) != null)
1010         {
1011           out.println(data);
1012         }
1013         out.close();
1014         return outFile.getAbsolutePath();
1015
1016       }
1017       catch (Exception ex)
1018       {
1019         ex.printStackTrace();
1020       }
1021
1022       return null;
1023     }
1024
1025
1026     AlignFrame LoadFromObject(JalviewModel object,
1027                               String file,
1028                               boolean loadTrees )
1029     {
1030         SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
1031         Sequence[] vamsasSeq = vamsasSet.getSequence();
1032
1033         JalviewModelSequence jms = object.getJalviewModelSequence();
1034
1035         Viewport view = jms.getViewport(0);
1036
1037         //////////////////////////////////
1038         //LOAD SEQUENCES
1039
1040         Vector hiddenSeqs = null;
1041         jalview.datamodel.Sequence jseq;
1042
1043         ArrayList tmpseqs = new ArrayList();
1044
1045         boolean multipleView = false;
1046
1047         JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
1048         for (int i = 0; i < JSEQ.length; i++)
1049         {
1050           String seqId = JSEQ[i].getId() + "";
1051
1052           if (seqRefIds.get(seqId) != null)
1053           {
1054             tmpseqs.add( (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1055             multipleView = true;
1056           }
1057           else
1058           {
1059             jseq = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
1060                 vamsasSeq[i].getSequence());
1061             jseq.setDescription(vamsasSeq[i].getDescription());
1062             jseq.setStart(JSEQ[i].getStart());
1063             jseq.setEnd(JSEQ[i].getEnd());
1064             seqRefIds.put(vamsasSeq[i].getId(), jseq);
1065             tmpseqs.add( jseq );
1066           }
1067
1068
1069
1070           if (JSEQ[i].getHidden())
1071           {
1072             if (hiddenSeqs == null)
1073               hiddenSeqs = new Vector();
1074
1075
1076             hiddenSeqs.addElement(
1077                 (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1078           }
1079
1080         }
1081
1082         ///SequenceFeatures are added to the DatasetSequence,
1083         // so we must create the dataset before loading features
1084         /////////////////////////////////
1085
1086
1087       jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[
1088           tmpseqs.size()];
1089
1090        tmpseqs.toArray(orderedSeqs) ;
1091
1092
1093         jalview.datamodel.Alignment al =
1094             new jalview.datamodel.Alignment(orderedSeqs);
1095
1096         al.setDataset(null);
1097         /////////////////////////////////
1098
1099
1100         Hashtable pdbloaded = new Hashtable();
1101         if(!multipleView)
1102         {
1103           for (int i = 0; i < vamsasSeq.length; i++)
1104           {
1105             if (JSEQ[i].getFeaturesCount() > 0)
1106             {
1107               Features[] features = JSEQ[i].getFeatures();
1108               for (int f = 0; f < features.length; f++)
1109               {
1110                 jalview.datamodel.SequenceFeature sf
1111                     = new jalview.datamodel.SequenceFeature(features[f].getType(),
1112                     features[f].getDescription(), features[f].getStatus(),
1113                     features[f].getBegin(), features[f].getEnd(),
1114                     features[f].getFeatureGroup());
1115
1116                 sf.setScore(features[f].getScore());
1117                 for (int od = 0; od < features[f].getOtherDataCount(); od++)
1118                 {
1119                   OtherData keyValue = features[f].getOtherData(od);
1120                   if (keyValue.getKey().startsWith("LINK"))
1121                     sf.addLink(keyValue.getValue());
1122                   else
1123                     sf.setValue(keyValue.getKey(), keyValue.getValue());
1124
1125                 }
1126
1127                 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1128               }
1129             }
1130             if (JSEQ[i].getPdbidsCount() > 0)
1131             {
1132               Pdbids[] ids = JSEQ[i].getPdbids();
1133               for (int p = 0; p < ids.length; p++)
1134               {
1135                 jalview.datamodel.PDBEntry entry = new jalview.datamodel.
1136                     PDBEntry();
1137                 entry.setId(ids[p].getId());
1138                 entry.setType(ids[p].getType());
1139                 if (ids[p].getFile() != null)
1140                 {
1141                   if (!pdbloaded.containsKey(ids[p].getFile()))
1142                   {
1143                     String tmppdb = loadPDBFile(file, ids[p].getId());
1144                     entry.setFile(tmppdb);
1145                     pdbloaded.put(ids[p].getId(), tmppdb);
1146                   }
1147                   else
1148                     entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1149                 }
1150
1151                 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1152               }
1153             }
1154             if (vamsasSeq[i].getDBRefCount() > 0)
1155             {
1156               for (int d = 0; d < vamsasSeq[i].getDBRefCount(); d++)
1157               {
1158                 jalview.datamodel.DBRefEntry entry =
1159                     new jalview.datamodel.DBRefEntry(
1160                         vamsasSeq[i].getDBRef(d).getSource(),
1161                         vamsasSeq[i].getDBRef(d).getVersion(),
1162                         vamsasSeq[i].getDBRef(d).getAccessionId()
1163                     );
1164                 al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);
1165               }
1166
1167             }
1168           }
1169         }
1170
1171
1172          /////////////////////////////////
1173         //////////////////////////////////
1174         //LOAD ANNOTATIONS
1175         boolean hideQuality = true,
1176             hideConservation = true,
1177             hideConsensus = true;
1178
1179         if (vamsasSet.getAnnotationCount()>0)
1180         {
1181             Annotation[] an = vamsasSet.getAnnotation();
1182
1183             for (int i = 0; i < an.length; i++)
1184             {
1185                if (an[i].getLabel().equals("Quality"))
1186                 {
1187                  hideQuality = false;
1188                  continue;
1189                 }
1190                else if(an[i].getLabel().equals("Conservation"))
1191                {
1192                  hideConservation = false;
1193                  continue;
1194                }
1195                else if(an[i].getLabel().equals("Consensus"))
1196                {
1197                  hideConsensus = false;
1198                  continue;
1199                }
1200
1201                 AnnotationElement[] ae = an[i].getAnnotationElement();
1202                 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];
1203
1204                 for (int aa = 0; aa < ae.length; aa++)
1205                 {
1206                     anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),
1207                             ae[aa].getDescription(),
1208                             ae[aa].getSecondaryStructure().length()==0?' ':ae[aa].getSecondaryStructure().charAt(0),
1209                             ae[aa].getValue());
1210                     anot[ae[aa].getPosition()].colour = new java.awt.Color( ae[aa].getColour() );
1211                 }
1212
1213                 jalview.datamodel.AlignmentAnnotation jaa = null;
1214
1215                 if (an[i].getGraph())
1216                 {
1217                   jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1218                       an[i].getDescription(), anot, 0, 0,
1219                       an[i].getGraphType());
1220
1221                   jaa.graphGroup = an[i].getGraphGroup();
1222
1223                   if (an[i].getThresholdLine() != null)
1224                   {
1225                     jaa.setThreshold(new jalview.datamodel.GraphLine(
1226                                   an[i].getThresholdLine().getValue(),
1227                                   an[i].getThresholdLine().getLabel(),
1228                                 new java.awt.Color(an[i].getThresholdLine().getColour()))
1229                              );
1230
1231                   }
1232
1233                 }
1234                 else
1235                 {
1236                     jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1237                             an[i].getDescription(), anot);
1238                 }
1239
1240                 if(an[i].getSequenceRef()!=null)
1241                 {
1242                   jaa.createSequenceMapping(
1243                       al.findName(an[i].getSequenceRef()), 1, true
1244                       );
1245                   al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
1246                 }
1247
1248                 al.addAnnotation(jaa);
1249             }
1250         }
1251
1252         /////////////////////////
1253         //LOAD GROUPS
1254         if (jms.getJGroupCount() > 0)
1255         {
1256             JGroup[] groups = jms.getJGroup();
1257
1258             for (int i = 0; i < groups.length; i++)
1259             {
1260                 ColourSchemeI cs = null;
1261
1262                 if (groups[i].getColour() != null)
1263                 {
1264                     if (groups[i].getColour().startsWith("ucs"))
1265                     {
1266                         cs = GetUserColourScheme(jms, groups[i].getColour());
1267                     }
1268                     else
1269                     {
1270                         cs = ColourSchemeProperty.getColour(al,
1271                                 groups[i].getColour());
1272                     }
1273
1274                     if(cs!=null)
1275                       cs.setThreshold(groups[i].getPidThreshold(), true);
1276                 }
1277
1278                 Vector seqs = new Vector();
1279
1280                 for (int s = 0; s < groups[i].getSeqCount(); s++)
1281                 {
1282                     String seqId = groups[i].getSeq(s)+"";
1283                     seqs.addElement((jalview.datamodel.SequenceI) seqRefIds.get(seqId));
1284                 }
1285
1286                 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,
1287                         groups[i].getName(), cs, groups[i].getDisplayBoxes(),
1288                         groups[i].getDisplayText(), groups[i].getColourText(),
1289                         groups[i].getStart(), groups[i].getEnd());
1290
1291                 sg.setOutlineColour(new java.awt.Color(
1292                         groups[i].getOutlineColour()));
1293
1294                 sg.textColour = new java.awt.Color(groups[i].getTextCol1());
1295                 sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
1296                 sg.thresholdTextColour = groups[i].getTextColThreshold();
1297
1298                 if (groups[i].getConsThreshold() != 0)
1299                 {
1300                     jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
1301                             ResidueProperties.propHash, 3, sg.getSequences(false), 0,
1302                             sg.getWidth() - 1);
1303                     c.calculate();
1304                     c.verdict(false, 25);
1305                     sg.cs.setConservation(c);
1306                 }
1307
1308                 al.addGroup(sg);
1309             }
1310         }
1311
1312
1313         /////////////////////////////////
1314         // LOAD VIEWPORT
1315
1316         AlignFrame af = new AlignFrame(al,
1317                                        view.getWidth(),
1318                                        view.getHeight() );
1319
1320         af.setFileName(file, "Jalview");
1321
1322         for (int i = 0; i < JSEQ.length; i++)
1323         {
1324           af.viewport.setSequenceColour(
1325               af.viewport.alignment.getSequenceAt(i),
1326               new java.awt.Color(
1327                   JSEQ[i].getColour()));
1328         }
1329
1330         //If we just load in the same jar file again, the sequenceSetId
1331         //will be the same, and we end up with multiple references
1332         //to the same sequenceSet. We must modify this id on load
1333         //so that each load of the file gives a unique id
1334         String uniqueSeqSetId =  view.getSequenceSetId()+uniqueSetSuffix;
1335
1336         af.viewport.gatherViewsHere = view.getGatheredViews();
1337
1338         if (view.getSequenceSetId() != null)
1339         {
1340           jalview.gui.AlignViewport av =
1341               (jalview.gui.AlignViewport)
1342               viewportsAdded.get(uniqueSeqSetId);
1343
1344           af.viewport.sequenceSetID = uniqueSeqSetId;
1345           if(av!=null)
1346           {
1347
1348             af.viewport.historyList = av.historyList;
1349             af.viewport.redoList = av.redoList;
1350           }
1351           else
1352           {
1353             viewportsAdded.put(uniqueSeqSetId, af.viewport);
1354           }
1355
1356           PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
1357         }
1358         if(hiddenSeqs!=null)
1359         {
1360           for(int s=0; s<JSEQ.length; s++)
1361           {
1362             for(int r=0; r<JSEQ[s].getHiddenSequencesCount(); r++)
1363             {
1364               al.getSequenceAt(s).addHiddenSequence(
1365                   al.getSequenceAt( JSEQ[s].getHiddenSequences(r)  )
1366                   );
1367             }
1368           }
1369
1370           jalview.datamodel.SequenceI [] hseqs = new
1371               jalview.datamodel.SequenceI[hiddenSeqs.size()];
1372
1373           for(int s=0; s<hiddenSeqs.size(); s++)
1374             hseqs[s] = (jalview.datamodel.SequenceI)hiddenSeqs.elementAt(s);
1375
1376           af.viewport.hideSequence( hseqs );
1377
1378         }
1379
1380
1381         if((hideConsensus || hideQuality || hideConservation)
1382             && al.getAlignmentAnnotation()!=null)
1383         {
1384           int hSize = al.getAlignmentAnnotation().length;
1385           for (int h = 0; h < hSize; h++)
1386           {
1387             if (
1388                 (hideConsensus &&
1389                  al.getAlignmentAnnotation()[h].label.equals("Consensus"))
1390                 ||
1391                 (hideQuality &&
1392                  al.getAlignmentAnnotation()[h].label.equals("Quality"))
1393                 ||
1394                 (hideConservation &&
1395                  al.getAlignmentAnnotation()[h].label.equals("Conservation")))
1396             {
1397               al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
1398               hSize--;
1399               h--;
1400             }
1401           }
1402           af.alignPanel.adjustAnnotationHeight();
1403         }
1404
1405         af.viewport.viewName = view.getViewName();
1406         af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
1407             view.getHeight());
1408         af.viewport.setStartRes(view.getStartRes());
1409         af.viewport.setStartSeq(view.getStartSeq());
1410         af.viewport.setShowAnnotation(view.getShowAnnotation());
1411         af.viewport.setAbovePIDThreshold(view.getPidSelected());
1412
1413         af.viewport.setColourText(view.getShowColourText());
1414
1415         af.viewport.setConservationSelected(view.getConservationSelected());
1416         af.viewport.setShowJVSuffix(view.getShowFullId());
1417         af.viewport.setFont(new java.awt.Font(view.getFontName(),
1418                 view.getFontStyle(), view.getFontSize()));
1419         af.alignPanel.fontChanged();
1420         af.viewport.setRenderGaps(view.getRenderGaps());
1421         af.viewport.setWrapAlignment(view.getWrapAlignment());
1422         af.alignPanel.setWrapAlignment(view.getWrapAlignment());
1423         af.viewport.setShowAnnotation(view.getShowAnnotation());
1424         af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
1425
1426         af.viewport.setShowBoxes(view.getShowBoxes());
1427
1428         af.viewport.setShowText(view.getShowText());
1429
1430         af.viewport.textColour = new java.awt.Color(view.getTextCol1());
1431         af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
1432         af.viewport.thresholdTextColour = view.getTextColThreshold();
1433
1434
1435         ColourSchemeI cs = null;
1436
1437         if (view.getBgColour() != null)
1438         {
1439             if (view.getBgColour().startsWith("ucs"))
1440             {
1441                 cs = GetUserColourScheme(jms, view.getBgColour());
1442             }
1443             else if(view.getBgColour().startsWith("Annotation"))
1444             {
1445               //int find annotation
1446               for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
1447               {
1448                 if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
1449                     equals(view.getAnnotationColours().getAnnotation()))
1450                 {
1451                   if (af.viewport.alignment.getAlignmentAnnotation()[i].
1452                       getThreshold() == null)
1453                   {
1454                     af.viewport.alignment.getAlignmentAnnotation()[i].
1455                         setThreshold(
1456                             new jalview.datamodel.GraphLine(
1457                                 view.getAnnotationColours().getThreshold(),
1458                                 "Threshold", java.awt.Color.black)
1459
1460                         );
1461                   }
1462
1463
1464                   if (view.getAnnotationColours().getColourScheme().equals(
1465                       "None"))
1466                   {
1467                     cs = new AnnotationColourGradient(
1468                         af.viewport.alignment.getAlignmentAnnotation()[i],
1469                         new java.awt.Color(view.getAnnotationColours().
1470                                            getMinColour()),
1471                         new java.awt.Color(view.getAnnotationColours().
1472                                            getMaxColour()),
1473                         view.getAnnotationColours().getAboveThreshold());
1474                   }
1475                   else if (view.getAnnotationColours().getColourScheme().
1476                            startsWith("ucs"))
1477                   {
1478                      cs = new AnnotationColourGradient(
1479                          af.viewport.alignment.getAlignmentAnnotation()[i],
1480                          GetUserColourScheme(jms, view.getAnnotationColours().
1481                                                         getColourScheme()),
1482                          view.getAnnotationColours().getAboveThreshold()
1483                          );
1484                    }
1485                    else
1486                    {
1487                      cs = new AnnotationColourGradient(
1488                          af.viewport.alignment.getAlignmentAnnotation()[i],
1489                          ColourSchemeProperty.getColour(al,
1490                          view.getAnnotationColours().getColourScheme()),
1491                          view.getAnnotationColours().getAboveThreshold()
1492                          );
1493                    }
1494
1495                   // Also use these settings for all the groups
1496                   if (al.getGroups() != null)
1497                     for (int g = 0; g < al.getGroups().size(); g++)
1498                     {
1499                       jalview.datamodel.SequenceGroup sg
1500                           = (jalview.datamodel.SequenceGroup)al.getGroups().elementAt(g);
1501
1502                       if(sg.cs == null)
1503                         continue;
1504
1505
1506                   /*    if (view.getAnnotationColours().getColourScheme().equals("None"))
1507                       {
1508                         sg.cs = new AnnotationColourGradient(
1509                             af.viewport.alignment.getAlignmentAnnotation()[i],
1510                             new java.awt.Color(view.getAnnotationColours().
1511                                                getMinColour()),
1512                             new java.awt.Color(view.getAnnotationColours().
1513                                                getMaxColour()),
1514                             view.getAnnotationColours().getAboveThreshold());
1515                       }
1516                       else*/
1517                       {
1518                         sg.cs = new AnnotationColourGradient(
1519                             af.viewport.alignment.getAlignmentAnnotation()[i],
1520                             sg.cs,
1521                             view.getAnnotationColours().getAboveThreshold()
1522                             );
1523                       }
1524
1525                     }
1526
1527
1528                   break;
1529                 }
1530
1531               }
1532             }
1533             else
1534             {
1535                 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
1536             }
1537
1538             if(cs!=null)
1539             {
1540               cs.setThreshold(view.getPidThreshold(), true);
1541               cs.setConsensus(af.viewport.hconsensus);
1542             }
1543         }
1544
1545
1546         af.viewport.setGlobalColourScheme(cs);
1547         af.viewport.setColourAppliesToAllGroups(false);
1548
1549         if (view.getConservationSelected() && cs!=null)
1550         {
1551           cs.setConservationInc(view.getConsThreshold());
1552         }
1553
1554         af.changeColour(cs);
1555
1556         af.viewport.setColourAppliesToAllGroups(true);
1557
1558
1559
1560         if (view.getShowSequenceFeatures())
1561         {
1562            af.viewport.showSequenceFeatures = true;
1563         }
1564
1565         if(jms.getFeatureSettings()!=null)
1566         {
1567           af.viewport.featuresDisplayed = new Hashtable();
1568           String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];
1569          for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)
1570          {
1571            Setting setting = jms.getFeatureSettings().getSetting(fs);
1572
1573            af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),
1574                new java.awt.Color(setting.getColour()));
1575
1576            renderOrder[fs] = setting.getType();
1577
1578            if(setting.getDisplay())
1579              af.viewport.featuresDisplayed.put(
1580                  setting.getType(), new Integer(setting.getColour()));
1581          }
1582          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
1583         }
1584
1585         if (view.getHiddenColumnsCount() > 0)
1586         {
1587           for (int c = 0; c < view.getHiddenColumnsCount(); c++)
1588           {
1589               af.viewport.hideColumns(
1590                 view.getHiddenColumns(c).getStart(),
1591                 view.getHiddenColumns(c).getEnd() //+1
1592                 );
1593           }
1594         }
1595
1596         af.setMenusFromViewport(af.viewport);
1597
1598
1599         Desktop.addInternalFrame(af, view.getTitle(),
1600              view.getWidth(), view.getHeight());
1601
1602         //LOAD TREES
1603         ///////////////////////////////////////
1604         if (loadTrees && jms.getTreeCount() > 0)
1605         {
1606             try
1607             {
1608                 for (int t = 0; t < jms.getTreeCount(); t++)
1609                 {
1610
1611                     Tree tree = jms.getTree(t);
1612
1613                     TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
1614                                 tree.getNewick()), tree.getTitle(),
1615                                 tree.getWidth(), tree.getHeight(),
1616                                 tree.getXpos(), tree.getYpos());
1617
1618                     tp.fitToWindow.setState(tree.getFitToWindow());
1619                     tp.fitToWindow_actionPerformed(null);
1620
1621                     if(tree.getFontName()!=null)
1622                       tp.setTreeFont(new java.awt.Font(tree.getFontName(),
1623                                           tree.getFontStyle(),
1624                                           tree.getFontSize()));
1625                     else
1626                       tp.setTreeFont(new java.awt.Font(view.getFontName(),
1627                                             view.getFontStyle(),
1628                                             tree.getFontSize()));
1629
1630                     tp.showPlaceholders(tree.getMarkUnlinked());
1631                     tp.showBootstrap(tree.getShowBootstrap());
1632                     tp.showDistances(tree.getShowDistances());
1633
1634                     tp.treeCanvas.threshold = tree.getThreshold();
1635
1636                     if (tree.getCurrentTree())
1637                       af.viewport.setCurrentTree(tp.getTree());
1638                 }
1639
1640             }
1641             catch (Exception ex)
1642             {
1643                 ex.printStackTrace();
1644             }
1645
1646         }
1647
1648         return af;
1649     }
1650
1651     public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap, boolean keepSeqRefs )
1652     {
1653       jalview.schemabinding.version2.JalviewModel jm
1654           = SaveState(ap, null, null, null);
1655
1656       if (!keepSeqRefs)
1657       {
1658         seqRefIds.clear();
1659         jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
1660       }
1661       else
1662         uniqueSetSuffix = "";
1663
1664       viewportsAdded = new Hashtable();
1665
1666       AlignFrame af = LoadFromObject(jm, null, false);
1667       af.alignPanels.clear();
1668       af.closeMenuItem_actionPerformed(true);
1669
1670       return af.alignPanel;
1671     }
1672 }
1673