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 java.io.*;
  25
  26 import java.net.*;
  27
  28 import java.util.*;
  29
  30 import java.util.jar.*;
  31
  32 import javax.swing.*;
  33
  34 import org.exolab.castor.xml.*;
  35
  36 import jalview.schemabinding.version2.*;
  37
  38
  39
  40
  41 /**
  42  * DOCUMENT ME!
  43  *
  44  * @author $author$
  45  * @version $Revision$
  46  */
  47 public class Jalview2XML
  48 {
  49
  50   Hashtable seqRefIds;
  51
  52   /**
  53    * This maintains a list of viewports, the key being the
  54    * seqSetId. Important to set historyItem and redoList
  55    * for multiple views
  56    */
  57   Hashtable viewportsAdded;
  58
  59   String uniqueSetSuffix = "";
  60
  61
  62     // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
  63     public void SaveState(File statefile)
  64     {
  65         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
  66
  67         if (frames == null)
  68         {
  69             return;
  70         }
  71
  72         try
  73         {
  74             FileOutputStream fos = new FileOutputStream(statefile);
  75             JarOutputStream jout = new JarOutputStream(fos);
  76
  77             //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
  78             ////////////////////////////////////////////////////
  79             PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
  80                         "UTF-8"));
  81
  82             Vector shortNames = new Vector();
  83
  84             //REVERSE ORDER
  85             for (int i = frames.length - 1; i > -1; i--)
  86             {
  87                 if (frames[i] instanceof AlignFrame)
  88                 {
  89                     AlignFrame af = (AlignFrame) frames[i];
  90
  91                     String shortName = af.getTitle();
  92
  93                     if (shortName.indexOf(File.separatorChar) > -1)
  94                     {
  95                         shortName = shortName.substring(shortName.lastIndexOf(
  96                                     File.separatorChar) + 1);
  97                     }
  98
  99                     int count = 1;
 100
 101                     while (shortNames.contains(shortName))
 102                     {
 103                         if (shortName.endsWith("_" + (count - 1)))
 104                         {
 105                             shortName = shortName.substring(0,
 106                                     shortName.lastIndexOf("_"));
 107                         }
 108
 109                         shortName = shortName.concat("_" + count);
 110                         count++;
 111                     }
 112
 113                     shortNames.addElement(shortName);
 114
 115                     if (!shortName.endsWith(".xml"))
 116                     {
 117                         shortName = shortName + ".xml";
 118                     }
 119
 120                     int ap, apSize= af.alignPanels.size();
 121                     for (ap = 0; ap < apSize; ap++)
 122                     {
 123                       AlignmentPanel apanel = (AlignmentPanel) af.alignPanels.
 124                           elementAt(ap);
 125
 126                       SaveState(apanel,
 127                                 apSize == 1 ? shortName : ap+shortName,
 128                                 jout, out);
 129                     }
 130                 }
 131             }
 132
 133             out.close();
 134             jout.close();
 135         }
 136         catch (Exception ex)
 137         {
 138             ex.printStackTrace();
 139         }
 140     }
 141
 142     // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
 143     public boolean SaveAlignment(AlignFrame af, String jarFile,
 144         String fileName)
 145     {
 146         try
 147         {
 148           int ap, apSize= af.alignPanels.size();
 149           FileOutputStream fos = new FileOutputStream(jarFile);
 150           JarOutputStream jout = new JarOutputStream(fos);
 151           PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
 152                 "UTF-8"));
 153           for( ap=0; ap<apSize; ap++)
 154           {
 155             AlignmentPanel apanel = (AlignmentPanel)af.alignPanels.elementAt(ap);
 156
 157             SaveState(apanel,
 158                       apSize==1?fileName:fileName+ap,
 159                       jout, out);
 160           }
 161
 162           out.close();
 163           jout.close();
 164           return true;
 165         }
 166         catch (Exception ex)
 167         {
 168           ex.printStackTrace();
 169           return false;
 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.getSequenceAsString());
 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(av.hiddenRepSequences!=null
 267               && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
 268               {
 269                 jalview.datamodel.SequenceI[] reps =
 270                     ( (jalview.datamodel.SequenceGroup)
 271                      av.hiddenRepSequences.get(
 272                          jal.getSequenceAt(i))).getSequencesInOrder(jal);
 273
 274                 for(int h=0; h<reps.length; h++)
 275                 {
 276                   if (reps[h] != jal.getSequenceAt(i))
 277                     jseq.addHiddenSequences(
 278                         jal.findIndex(reps[h])
 279                         );
 280                 }
 281               }
 282             }
 283
 284
 285             if(jds.getDatasetSequence().getSequenceFeatures()!=null)
 286             {
 287               jalview.datamodel.SequenceFeature[] sf
 288                   = jds.getDatasetSequence().getSequenceFeatures();
 289               int index = 0;
 290               while(index < sf.length)
 291               {
 292                 Features features = new Features();
 293
 294                 features.setBegin(sf[index].getBegin());
 295                 features.setEnd(sf[index].getEnd());
 296                 features.setDescription(sf[index].getDescription());
 297                 features.setType(sf[index].getType());
 298                 features.setFeatureGroup(sf[index].getFeatureGroup());
 299                 features.setScore(sf[index].getScore());
 300                 if(sf[index].links!=null)
 301                 {
 302                   for(int l=0; l<sf[index].links.size(); l++)
 303                   {
 304                     OtherData keyValue = new OtherData();
 305                     keyValue.setKey("LINK_"+l);
 306                     keyValue.setValue(sf[index].links.elementAt(l).toString());
 307                     features.addOtherData(keyValue);
 308                   }
 309                 }
 310                 if(sf[index].otherDetails!=null)
 311                 {
 312                   String key;
 313                   Enumeration keys = sf[index].otherDetails.keys();
 314                   while(keys.hasMoreElements())
 315                   {
 316                     key = keys.nextElement().toString();
 317                     OtherData keyValue = new OtherData();
 318                     keyValue.setKey( key );
 319                     keyValue.setValue(
 320                         sf[index].otherDetails.get(key).toString());
 321                     features.addOtherData(keyValue);
 322                   }
 323                 }
 324
 325                 jseq.addFeatures(features);
 326                 index ++;
 327               }
 328             }
 329
 330             if(jds.getDatasetSequence().getPDBId()!=null)
 331             {
 332               Enumeration en = jds.getDatasetSequence().getPDBId().elements();
 333               while(en.hasMoreElements())
 334               {
 335                 Pdbids pdb = new Pdbids();
 336                 jalview.datamodel.PDBEntry entry
 337                    = (jalview.datamodel.PDBEntry)en.nextElement();
 338
 339                 pdb.setId(entry.getId());
 340                 pdb.setType(entry.getType());
 341
 342
 343                 if(entry.getFile()!=null)
 344                 {
 345                   pdb.setFile(entry.getFile());
 346                   if(pdbfiles==null)
 347                     pdbfiles = new Vector();
 348
 349                   if(!pdbfiles.contains(entry.getId()))
 350                   {
 351                     pdbfiles.addElement(entry.getId());
 352                     try
 353                     {
 354                       File file = new File(entry.getFile());
 355                       if(file.exists() && jout!=null)
 356                       {
 357                         byte[] data = new byte[ (int) file.length()];
 358                         jout.putNextEntry(new JarEntry(entry.getId()));
 359                         DataInputStream dis = new DataInputStream(new
 360                             FileInputStream(file));
 361                         dis.readFully(data);
 362
 363                         DataOutputStream dout = new DataOutputStream(jout);
 364                         dout.write(data, 0, data.length);
 365                         jout.closeEntry();
 366                       }
 367                     }
 368                     catch (Exception ex)
 369                     {
 370                       ex.printStackTrace();
 371                     }
 372                   }
 373                 }
 374
 375
 376                 if(entry.getProperty()!=null)
 377                 {
 378                   PdbentryItem item = new PdbentryItem();
 379                   Hashtable properties = entry.getProperty();
 380                   Enumeration en2 = properties.keys();
 381                   while(en2.hasMoreElements())
 382                   {
 383                     Property prop = new Property();
 384                     String key = en2.nextElement().toString();
 385                     prop.setName(key);
 386                     prop.setValue( properties.get(key).toString() );
 387                     item.addProperty(prop);
 388                   }
 389                   pdb.addPdbentryItem(item);
 390                 }
 391
 392                 jseq.addPdbids(pdb);
 393               }
 394             }
 395
 396             jms.addJSeq(jseq);
 397         }
 398
 399         if(av.hasHiddenRows)
 400           jal = av.alignment;
 401
 402
 403         //SAVE TREES
 404         ///////////////////////////////////
 405         if (av.currentTree != null)
 406         {
 407           // FIND ANY ASSOCIATED TREES
 408           // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
 409           if (Desktop.desktop != null)
 410           {
 411             JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 412
 413             for (int t = 0; t < frames.length; t++)
 414             {
 415               if (frames[t] instanceof TreePanel)
 416               {
 417                 TreePanel tp = (TreePanel) frames[t];
 418
 419                 if (tp.treeCanvas.av.alignment == jal)
 420                 {
 421                   Tree tree = new Tree();
 422                   tree.setTitle(tp.getTitle());
 423                   tree.setCurrentTree( (av.currentTree == tp.getTree()));
 424                   tree.setNewick(tp.getTree().toString());
 425                   tree.setThreshold(tp.treeCanvas.threshold);
 426
 427                   tree.setFitToWindow(tp.fitToWindow.getState());
 428                   tree.setFontName(tp.getTreeFont().getName());
 429                   tree.setFontSize(tp.getTreeFont().getSize());
 430                   tree.setFontStyle(tp.getTreeFont().getStyle());
 431                   tree.setMarkUnlinked(tp.placeholdersMenu.getState());
 432
 433                   tree.setShowBootstrap(tp.bootstrapMenu.getState());
 434                   tree.setShowDistances(tp.distanceMenu.getState());
 435
 436                   tree.setHeight(tp.getHeight());
 437                   tree.setWidth(tp.getWidth());
 438                   tree.setXpos(tp.getX());
 439                   tree.setYpos(tp.getY());
 440
 441                   jms.addTree(tree);
 442                 }
 443               }
 444             }
 445           }
 446         }
 447
 448         //SAVE ANNOTATIONS
 449         if (jal.getAlignmentAnnotation() != null)
 450         {
 451             jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
 452
 453             for (int i = 0; i < aa.length; i++)
 454             {
 455                 Annotation an = new Annotation();
 456
 457                 if (aa[i].label.equals("Quality") ||
 458                         aa[i].label.equals("Conservation") ||
 459                         aa[i].label.equals("Consensus"))
 460                 {
 461                     an.setLabel(aa[i].label);
 462                     an.setGraph(true);
 463                     vamsasSet.addAnnotation(an);
 464                     continue;
 465                 }
 466
 467
 468                 an.setDescription(aa[i].description);
 469
 470                 if(aa[i].sequenceRef!=null)
 471                  {
 472                    an.setSequenceRef(aa[i].sequenceRef.getName());
 473                  }
 474
 475                 if(aa[i].graph>0)
 476                 {
 477                   an.setGraph(true);
 478                   an.setGraphType(aa[i].graph);
 479                   an.setGraphGroup(aa[i].graphGroup);
 480                   if(aa[i].getThreshold()!=null)
 481                   {
 482                     ThresholdLine line = new ThresholdLine();
 483                     line.setLabel(aa[i].getThreshold().label);
 484                     line.setValue(aa[i].getThreshold().value);
 485                     line.setColour(aa[i].getThreshold().colour.getRGB());
 486                     an.setThresholdLine(line);
 487                   }
 488                 }
 489                 else
 490                   an.setGraph(false);
 491
 492                 an.setLabel(aa[i].label);
 493
 494                 AnnotationElement ae;
 495
 496                 for (int a = 0; a < aa[i].annotations.length; a++)
 497                 {
 498                     if ((aa[i] == null) || (aa[i].annotations[a] == null))
 499                     {
 500                         continue;
 501                     }
 502
 503                     ae = new AnnotationElement();
 504                     ae.setDescription(aa[i].annotations[a].description);
 505                     ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
 506                     ae.setValue(aa[i].annotations[a].value);
 507                     ae.setPosition(a);
 508                     ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
 509                         "");
 510
 511                     if(aa[i].annotations[a].colour!=java.awt.Color.black)
 512                       ae.setColour(aa[i].annotations[a].colour.getRGB());
 513
 514                     an.addAnnotationElement(ae);
 515                 }
 516
 517                 vamsasSet.addAnnotation(an);
 518             }
 519         }
 520
 521         //SAVE GROUPS
 522         if (jal.getGroups() != null)
 523         {
 524             JGroup[] groups = new JGroup[jal.getGroups().size()];
 525
 526             for (int i = 0; i < groups.length; i++)
 527             {
 528                 groups[i] = new JGroup();
 529
 530                 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()
 531                                                                                           .elementAt(i);
 532                 groups[i].setStart(sg.getStartRes());
 533                 groups[i].setEnd(sg.getEndRes());
 534                 groups[i].setName(sg.getName());
 535                 if(sg.cs!=null)
 536                 {
 537                   if (sg.cs.conservationApplied())
 538                   {
 539                     groups[i].setConsThreshold(sg.cs.getConservationInc());
 540
 541                     if (sg.cs instanceof jalview.schemes.UserColourScheme)
 542                     {
 543                       groups[i].setColour(SetUserColourScheme(sg.cs,
 544                           userColours,
 545                           jms));
 546                     }
 547                     else
 548                     {
 549                       groups[i].setColour(ColourSchemeProperty.getColourName(sg.
 550                           cs));
 551                     }
 552                   }
 553                   else if(sg.cs instanceof jalview.schemes.AnnotationColourGradient)
 554                   {
 555                     groups[i].setColour(
 556                         ColourSchemeProperty.getColourName(
 557                       ( (jalview.schemes.AnnotationColourGradient) sg.cs).getBaseColour()));
 558                   }
 559                   else if (sg.cs instanceof jalview.schemes.UserColourScheme)
 560                   {
 561                     groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
 562                         jms));
 563                   }
 564                   else
 565                   {
 566                     groups[i].setColour(ColourSchemeProperty.getColourName(
 567                         sg.cs));
 568                   }
 569
 570                   groups[i].setPidThreshold(sg.cs.getThreshold());
 571                 }
 572
 573                 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
 574                 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
 575                 groups[i].setDisplayText(sg.getDisplayText());
 576                 groups[i].setColourText(sg.getColourText());
 577                 groups[i].setTextCol1(sg.textColour.getRGB());
 578                 groups[i].setTextCol2(sg.textColour2.getRGB());
 579                 groups[i].setTextColThreshold(sg.thresholdTextColour);
 580
 581                 for (int s = 0; s < sg.getSize(); s++)
 582                 {
 583                     jalview.datamodel.Sequence seq =
 584                         (jalview.datamodel.Sequence) sg.getSequenceAt(s);
 585                     groups[i].addSeq(seq.hashCode());
 586                 }
 587             }
 588
 589             jms.setJGroup(groups);
 590         }
 591
 592
 593         ///////////SAVE VIEWPORT
 594         Viewport view = new Viewport();
 595         view.setTitle(ap.alignFrame.getTitle());
 596         view.setSequenceSetId(av.getSequenceSetId());
 597         view.setViewName(av.viewName);
 598         view.setGatheredViews(av.gatherViewsHere);
 599
 600
 601         if (ap.av.explodedPosition != null)
 602         {
 603           view.setXpos(av.explodedPosition.x);
 604           view.setYpos(av.explodedPosition.y);
 605           view.setWidth(av.explodedPosition.width);
 606           view.setHeight(av.explodedPosition.height);
 607         }
 608         else
 609         {
 610           view.setXpos(ap.alignFrame.getBounds().x);
 611           view.setYpos(ap.alignFrame.getBounds().y);
 612           view.setWidth(ap.alignFrame.getBounds().width);
 613           view.setHeight(ap.alignFrame.getBounds().height);
 614         }
 615
 616         view.setStartRes(av.startRes);
 617         view.setStartSeq(av.startSeq);
 618
 619         if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
 620         {
 621             view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
 622                     userColours, jms));
 623         }
 624         else if(av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
 625         {
 626            jalview.schemes.AnnotationColourGradient acg
 627               = (jalview.schemes.AnnotationColourGradient)av.getGlobalColourScheme();
 628
 629             AnnotationColours ac = new AnnotationColours();
 630             ac.setAboveThreshold(acg.getAboveThreshold());
 631             ac.setThreshold(acg.getAnnotationThreshold());
 632             ac.setAnnotation(acg.getAnnotation());
 633             if(acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
 634               ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
 635                     userColours, jms));
 636             else
 637               ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
 638
 639             ac.setMaxColour(acg.getMaxColour().getRGB());
 640             ac.setMinColour(acg.getMinColour().getRGB());
 641             view.setAnnotationColours(ac);
 642             view.setBgColour("AnnotationColourGradient");
 643         }
 644         else
 645         {
 646             view.setBgColour(ColourSchemeProperty.getColourName(
 647                     av.getGlobalColourScheme()));
 648         }
 649
 650         ColourSchemeI cs = av.getGlobalColourScheme();
 651
 652         if(cs!=null)
 653         {
 654           if (cs.conservationApplied())
 655           {
 656             view.setConsThreshold(cs.getConservationInc());
 657             if (cs instanceof jalview.schemes.UserColourScheme)
 658               view.setBgColour(SetUserColourScheme(cs, userColours, jms));
 659           }
 660
 661           if (cs instanceof ResidueColourScheme)
 662           {
 663             view.setPidThreshold(cs.getThreshold());
 664           }
 665         }
 666
 667         view.setConservationSelected(av.getConservationSelected());
 668         view.setPidSelected(av.getAbovePIDThreshold());
 669         view.setFontName(av.font.getName());
 670         view.setFontSize(av.font.getSize());
 671         view.setFontStyle(av.font.getStyle());
 672         view.setRenderGaps(av.renderGaps);
 673         view.setShowAnnotation(av.getShowAnnotation());
 674         view.setShowBoxes(av.getShowBoxes());
 675         view.setShowColourText(av.getColourText());
 676         view.setShowFullId(av.getShowJVSuffix());
 677         view.setRightAlignIds(av.rightAlignIds);
 678         view.setShowSequenceFeatures(av.showSequenceFeatures);
 679         view.setShowText(av.getShowText());
 680         view.setWrapAlignment(av.getWrapAlignment());
 681         view.setTextCol1(av.textColour.getRGB());
 682         view.setTextCol2(av.textColour2.getRGB());
 683         view.setTextColThreshold(av.thresholdTextColour);
 684
 685
 686         if(av.featuresDisplayed!=null)
 687         {
 688           jalview.schemabinding.version2.FeatureSettings fs
 689               = new jalview.schemabinding.version2.FeatureSettings();
 690
 691           String [] renderOrder =
 692               ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
 693
 694           Vector settingsAdded = new Vector();
 695           for(int ro=0; ro<renderOrder.length; ro++)
 696           {
 697             Setting setting = new Setting();
 698             setting.setType(renderOrder[ro]);
 699             setting.setColour(
 700                 ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).getRGB()
 701                 );
 702
 703             setting.setDisplay(
 704                 av.featuresDisplayed.containsKey(renderOrder[ro])
 705                 );
 706
 707             fs.addSetting(setting);
 708             settingsAdded.addElement(renderOrder[ro]);
 709           }
 710
 711           //Make sure we save none displayed feature settings
 712           Enumeration en =
 713               ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
 714           while(en.hasMoreElements())
 715           {
 716             String key = en.nextElement().toString();
 717             if(settingsAdded.contains(key))
 718               continue;
 719
 720             Setting setting = new Setting();
 721             setting.setType(key);
 722             setting.setColour(
 723                 ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()
 724                 );
 725
 726             setting.setDisplay(false);
 727
 728             fs.addSetting(setting);
 729             settingsAdded.addElement(key);
 730           }
 731
 732           jms.setFeatureSettings(fs);
 733
 734         }
 735
 736         if(av.hasHiddenColumns)
 737         {
 738           for(int c=0; c<av.getColumnSelection().getHiddenColumns().size(); c++)
 739           {
 740             int [] region = (int[]) av.getColumnSelection().getHiddenColumns().elementAt(c);
 741             HiddenColumns hc = new HiddenColumns();
 742             hc.setStart(region[0]);
 743             hc.setEnd(region[1]);
 744             view.addHiddenColumns(hc);
 745           }
 746         }
 747
 748         jms.addViewport(view);
 749
 750
 751         object.setJalviewModelSequence(jms);
 752         object.getVamsasModel().addSequenceSet(vamsasSet);
 753
 754         if(out!=null)
 755         {
 756           //We may not want to right the object to disk,
 757           //eg we can copy the alignViewport to a new view object
 758           //using save and then load
 759           try
 760           {
 761             if (!fileName.endsWith(".xml"))
 762             {
 763               fileName = fileName + ".xml";
 764             }
 765
 766             JarEntry entry = new JarEntry(fileName);
 767             jout.putNextEntry(entry);
 768
 769             object.marshal(out);
 770           }
 771           catch (Exception ex)
 772           {
 773             ex.printStackTrace();
 774           }
 775         }
 776         return object;
 777     }
 778
 779     String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
 780         Vector userColours, JalviewModelSequence jms)
 781     {
 782         String id = null;
 783         jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
 784
 785         if (!userColours.contains(ucs))
 786         {
 787             userColours.add(ucs);
 788
 789             java.awt.Color[] colours = ucs.getColours();
 790             jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
 791             jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
 792
 793             for (int i = 0; i < colours.length; i++)
 794             {
 795                 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
 796                 col.setName(ResidueProperties.aa[i]);
 797                 col.setRGB(jalview.util.Format.getHexString(colours[i]));
 798                 jbucs.addColour(col);
 799             }
 800             if(ucs.getLowerCaseColours()!=null)
 801             {
 802               colours = ucs.getLowerCaseColours();
 803               for (int i = 0; i < colours.length; i++)
 804              {
 805                  jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
 806                  col.setName(ResidueProperties.aa[i].toLowerCase());
 807                  col.setRGB(jalview.util.Format.getHexString(colours[i]));
 808                  jbucs.addColour(col);
 809              }
 810             }
 811
 812             id = "ucs" + userColours.indexOf(ucs);
 813             uc.setId(id);
 814             uc.setUserColourScheme(jbucs);
 815             jms.addUserColours(uc);
 816         }
 817
 818         return id;
 819     }
 820
 821    jalview.schemes.UserColourScheme GetUserColourScheme(
 822         JalviewModelSequence jms, String id)
 823     {
 824         UserColours[] uc = jms.getUserColours();
 825         UserColours colours = null;
 826
 827         for (int i = 0; i < uc.length; i++)
 828         {
 829             if (uc[i].getId().equals(id))
 830             {
 831                 colours = uc[i];
 832
 833                 break;
 834             }
 835         }
 836
 837         java.awt.Color[] newColours = new java.awt.Color[24];
 838
 839         for (int i = 0; i < 24; i++)
 840         {
 841             newColours[i] = new java.awt.Color(Integer.parseInt(
 842                         colours.getUserColourScheme().getColour(i).getRGB(), 16));
 843         }
 844
 845         jalview.schemes.UserColourScheme ucs =
 846             new jalview.schemes.UserColourScheme(newColours);
 847
 848         if (colours.getUserColourScheme().getColourCount() > 24)
 849         {
 850           newColours = new java.awt.Color[23];
 851           for (int i = 0; i < 23; i++)
 852           {
 853             newColours[i] = new java.awt.Color(Integer.parseInt(
 854                 colours.getUserColourScheme().getColour(i+24).getRGB(), 16));
 855           }
 856           ucs.setLowerCaseColours(newColours);
 857         }
 858
 859         return ucs;
 860     }
 861
 862
 863     /**
 864      * DOCUMENT ME!
 865      *
 866      * @param file DOCUMENT ME!
 867      */
 868     public AlignFrame LoadJalviewAlign(final String file)
 869     {
 870         uniqueSetSuffix = System.currentTimeMillis()%100000 +"";
 871
 872         jalview.gui.AlignFrame af = null;
 873
 874         seqRefIds = new Hashtable();
 875         viewportsAdded = new Hashtable();
 876
 877         Vector gatherToThisFrame= new Vector();
 878
 879         try
 880         {
 881             //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
 882             URL url = null;
 883
 884             if (file.startsWith("http://"))
 885             {
 886                 url = new URL(file);
 887             }
 888
 889             JarInputStream jin = null;
 890             JarEntry jarentry = null;
 891             int entryCount = 1;
 892
 893             do
 894             {
 895                 if (url != null)
 896                 {
 897                     jin = new JarInputStream(url.openStream());
 898                 }
 899                 else
 900                 {
 901                     jin = new JarInputStream(new FileInputStream(file));
 902                 }
 903
 904                 for (int i = 0; i < entryCount; i++)
 905                 {
 906                     jarentry = jin.getNextJarEntry();
 907                 }
 908
 909                 if (jarentry != null && jarentry.getName().endsWith(".xml"))
 910                 {
 911                     InputStreamReader in = new InputStreamReader(jin, "UTF-8");
 912                     JalviewModel object = new JalviewModel();
 913
 914                     Unmarshaller unmar = new Unmarshaller(object);
 915                     unmar.setValidation(false);
 916                     object = (JalviewModel) unmar.unmarshal( in );
 917
 918                     af = LoadFromObject(object, file, true);
 919                     if(af.viewport.gatherViewsHere)
 920                     {
 921                       gatherToThisFrame.add(af);
 922                     }
 923                     entryCount++;
 924                 }
 925                 else if (jarentry != null)
 926                 {
 927                   //Some other file here.
 928                   entryCount++;
 929                 }
 930             }
 931             while (jarentry != null);
 932         }
 933         catch(java.net.UnknownHostException ex)
 934         {
 935           ex.printStackTrace();
 936           System.err.println("Couldn't locate Jalview XML file : " +
 937               ex + "\n");
 938
 939           javax.swing.SwingUtilities.invokeLater(new Runnable()
 940           {
 941             public void run()
 942             {
 943               JOptionPane.showInternalMessageDialog(Desktop.desktop,
 944                   "Couldn't locate " + file,
 945                   "URL not found",
 946                   JOptionPane.WARNING_MESSAGE);
 947             }
 948           });
 949         }
 950         catch (Exception ex)
 951         {
 952           //Is Version 1 Jar file?
 953           af =  new Jalview2XML_V1().LoadJalviewAlign(file);
 954
 955           if(af!=null)
 956           {
 957             System.out.println("Successfully loaded archive file");
 958             return af;
 959           }
 960
 961             System.err.println("Exception whilst loading jalview XML file : " +
 962                 ex + "\n");
 963             javax.swing.SwingUtilities.invokeLater(new Runnable()
 964             {
 965               public void run()
 966               {
 967
 968                 JOptionPane.showInternalMessageDialog(Desktop.desktop,
 969                     "Error loading  " + file,
 970                     "Error loading Jalview file",
 971                     JOptionPane.WARNING_MESSAGE);
 972               }});
 973         }
 974
 975         if (Desktop.instance != null)
 976           Desktop.instance.stopLoading();
 977
 978         for (int i = 0; i < gatherToThisFrame.size(); i++)
 979         {
 980           Desktop.instance.gatherViews(
 981               (AlignFrame) gatherToThisFrame.elementAt(i));
 982         }
 983
 984         return af;
 985     }
 986
 987     String loadPDBFile(String file, String pdbId)
 988     {
 989       System.out.println(file +" "+pdbId);
 990       try
 991       {
 992         JarInputStream jin = null;
 993
 994         if (file.startsWith("http://"))
 995         {
 996           jin = new JarInputStream(new URL(file).openStream());
 997         }
 998         else
 999         {
1000           jin = new JarInputStream(new FileInputStream(file));
1001         }
1002
1003         JarEntry entry = null;
1004         do
1005         {
1006           entry = jin.getNextJarEntry();
1007         }
1008         while (!entry.getName().equals(pdbId));
1009
1010         BufferedReader in = new BufferedReader(new InputStreamReader(jin));
1011         File outFile = File.createTempFile("jalview_pdb", ".txt");
1012         outFile.deleteOnExit();
1013         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
1014         String data;
1015
1016         while ( (data = in.readLine()) != null)
1017         {
1018           out.println(data);
1019         }
1020         out.close();
1021         return outFile.getAbsolutePath();
1022
1023       }
1024       catch (Exception ex)
1025       {
1026         ex.printStackTrace();
1027       }
1028
1029       return null;
1030     }
1031
1032
1033     AlignFrame LoadFromObject(JalviewModel object,
1034                               String file,
1035                               boolean loadTrees )
1036     {
1037         SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
1038         Sequence[] vamsasSeq = vamsasSet.getSequence();
1039
1040         JalviewModelSequence jms = object.getJalviewModelSequence();
1041
1042         Viewport view = jms.getViewport(0);
1043
1044         //////////////////////////////////
1045         //LOAD SEQUENCES
1046
1047         Vector hiddenSeqs = null;
1048         jalview.datamodel.Sequence jseq;
1049
1050         ArrayList tmpseqs = new ArrayList();
1051
1052         boolean multipleView = false;
1053
1054         JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
1055         for (int i = 0; i < JSEQ.length; i++)
1056         {
1057           String seqId = JSEQ[i].getId() + "";
1058
1059           if (seqRefIds.get(seqId) != null)
1060           {
1061             tmpseqs.add( (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1062             multipleView = true;
1063           }
1064           else
1065           {
1066             jseq = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
1067                 vamsasSeq[i].getSequence());
1068             jseq.setDescription(vamsasSeq[i].getDescription());
1069             jseq.setStart(JSEQ[i].getStart());
1070             jseq.setEnd(JSEQ[i].getEnd());
1071             seqRefIds.put(vamsasSeq[i].getId(), jseq);
1072             tmpseqs.add( jseq );
1073           }
1074
1075
1076
1077           if (JSEQ[i].getHidden())
1078           {
1079             if (hiddenSeqs == null)
1080               hiddenSeqs = new Vector();
1081
1082
1083             hiddenSeqs.addElement(
1084                 (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1085           }
1086
1087         }
1088
1089         ///SequenceFeatures are added to the DatasetSequence,
1090         // so we must create the dataset before loading features
1091         /////////////////////////////////
1092
1093
1094       jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[
1095           tmpseqs.size()];
1096
1097        tmpseqs.toArray(orderedSeqs) ;
1098
1099
1100         jalview.datamodel.Alignment al =
1101             new jalview.datamodel.Alignment(orderedSeqs);
1102
1103         al.setDataset(null);
1104         /////////////////////////////////
1105
1106
1107         Hashtable pdbloaded = new Hashtable();
1108         if(!multipleView)
1109         {
1110           for (int i = 0; i < vamsasSeq.length; i++)
1111           {
1112             if (JSEQ[i].getFeaturesCount() > 0)
1113             {
1114               Features[] features = JSEQ[i].getFeatures();
1115               for (int f = 0; f < features.length; f++)
1116               {
1117                 jalview.datamodel.SequenceFeature sf
1118                     = new jalview.datamodel.SequenceFeature(features[f].getType(),
1119                     features[f].getDescription(), features[f].getStatus(),
1120                     features[f].getBegin(), features[f].getEnd(),
1121                     features[f].getFeatureGroup());
1122
1123                 sf.setScore(features[f].getScore());
1124                 for (int od = 0; od < features[f].getOtherDataCount(); od++)
1125                 {
1126                   OtherData keyValue = features[f].getOtherData(od);
1127                   if (keyValue.getKey().startsWith("LINK"))
1128                     sf.addLink(keyValue.getValue());
1129                   else
1130                     sf.setValue(keyValue.getKey(), keyValue.getValue());
1131
1132                 }
1133
1134                 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1135               }
1136             }
1137             if (JSEQ[i].getPdbidsCount() > 0)
1138             {
1139               Pdbids[] ids = JSEQ[i].getPdbids();
1140               for (int p = 0; p < ids.length; p++)
1141               {
1142                 jalview.datamodel.PDBEntry entry = new jalview.datamodel.
1143                     PDBEntry();
1144                 entry.setId(ids[p].getId());
1145                 entry.setType(ids[p].getType());
1146                 if (ids[p].getFile() != null)
1147                 {
1148                   if (!pdbloaded.containsKey(ids[p].getFile()))
1149                   {
1150                     String tmppdb = loadPDBFile(file, ids[p].getId());
1151                     entry.setFile(tmppdb);
1152                     pdbloaded.put(ids[p].getId(), tmppdb);
1153                   }
1154                   else
1155                     entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1156                 }
1157
1158                 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1159               }
1160             }
1161             if (vamsasSeq[i].getDBRefCount() > 0)
1162             {
1163               for (int d = 0; d < vamsasSeq[i].getDBRefCount(); d++)
1164               {
1165                 jalview.datamodel.DBRefEntry entry =
1166                     new jalview.datamodel.DBRefEntry(
1167                         vamsasSeq[i].getDBRef(d).getSource(),
1168                         vamsasSeq[i].getDBRef(d).getVersion(),
1169                         vamsasSeq[i].getDBRef(d).getAccessionId()
1170                     );
1171                 al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);
1172               }
1173
1174             }
1175           }
1176         }
1177
1178
1179          /////////////////////////////////
1180         //////////////////////////////////
1181         //LOAD ANNOTATIONS
1182         boolean hideQuality = true,
1183             hideConservation = true,
1184             hideConsensus = true;
1185
1186         if (vamsasSet.getAnnotationCount()>0)
1187         {
1188             Annotation[] an = vamsasSet.getAnnotation();
1189
1190             for (int i = 0; i < an.length; i++)
1191             {
1192                if (an[i].getLabel().equals("Quality"))
1193                 {
1194                  hideQuality = false;
1195                  continue;
1196                 }
1197                else if(an[i].getLabel().equals("Conservation"))
1198                {
1199                  hideConservation = false;
1200                  continue;
1201                }
1202                else if(an[i].getLabel().equals("Consensus"))
1203                {
1204                  hideConsensus = false;
1205                  continue;
1206                }
1207
1208                 AnnotationElement[] ae = an[i].getAnnotationElement();
1209                 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];
1210
1211                 for (int aa = 0; aa < ae.length; aa++)
1212                 {
1213                     anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),
1214                             ae[aa].getDescription(),
1215                             ae[aa].getSecondaryStructure().length()==0?' ':ae[aa].getSecondaryStructure().charAt(0),
1216                             ae[aa].getValue());
1217                     anot[ae[aa].getPosition()].colour = new java.awt.Color( ae[aa].getColour() );
1218                 }
1219
1220                 jalview.datamodel.AlignmentAnnotation jaa = null;
1221
1222                 if (an[i].getGraph())
1223                 {
1224                   jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1225                       an[i].getDescription(), anot, 0, 0,
1226                       an[i].getGraphType());
1227
1228                   jaa.graphGroup = an[i].getGraphGroup();
1229
1230                   if (an[i].getThresholdLine() != null)
1231                   {
1232                     jaa.setThreshold(new jalview.datamodel.GraphLine(
1233                                   an[i].getThresholdLine().getValue(),
1234                                   an[i].getThresholdLine().getLabel(),
1235                                 new java.awt.Color(an[i].getThresholdLine().getColour()))
1236                              );
1237
1238                   }
1239
1240                 }
1241                 else
1242                 {
1243                     jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1244                             an[i].getDescription(), anot);
1245                 }
1246
1247                 if(an[i].getSequenceRef()!=null)
1248                 {
1249                   jaa.createSequenceMapping(
1250                       al.findName(an[i].getSequenceRef()), 1, true
1251                       );
1252                   al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
1253                 }
1254
1255                 al.addAnnotation(jaa);
1256             }
1257         }
1258
1259         /////////////////////////
1260         //LOAD GROUPS
1261         if (jms.getJGroupCount() > 0)
1262         {
1263             JGroup[] groups = jms.getJGroup();
1264
1265             for (int i = 0; i < groups.length; i++)
1266             {
1267                 ColourSchemeI cs = null;
1268
1269                 if (groups[i].getColour() != null)
1270                 {
1271                     if (groups[i].getColour().startsWith("ucs"))
1272                     {
1273                         cs = GetUserColourScheme(jms, groups[i].getColour());
1274                     }
1275                     else
1276                     {
1277                         cs = ColourSchemeProperty.getColour(al,
1278                                 groups[i].getColour());
1279                     }
1280
1281                     if(cs!=null)
1282                       cs.setThreshold(groups[i].getPidThreshold(), true);
1283                 }
1284
1285                 Vector seqs = new Vector();
1286
1287                 for (int s = 0; s < groups[i].getSeqCount(); s++)
1288                 {
1289                     String seqId = groups[i].getSeq(s)+"";
1290                     seqs.addElement((jalview.datamodel.SequenceI) seqRefIds.get(seqId));
1291                 }
1292
1293                 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,
1294                         groups[i].getName(), cs, groups[i].getDisplayBoxes(),
1295                         groups[i].getDisplayText(), groups[i].getColourText(),
1296                         groups[i].getStart(), groups[i].getEnd());
1297
1298                 sg.setOutlineColour(new java.awt.Color(
1299                         groups[i].getOutlineColour()));
1300
1301                 sg.textColour = new java.awt.Color(groups[i].getTextCol1());
1302                 sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
1303                 sg.thresholdTextColour = groups[i].getTextColThreshold();
1304
1305                 if (groups[i].getConsThreshold() != 0)
1306                 {
1307                     jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
1308                             ResidueProperties.propHash, 3, sg.getSequences(null), 0,
1309                             sg.getWidth() - 1);
1310                     c.calculate();
1311                     c.verdict(false, 25);
1312                     sg.cs.setConservation(c);
1313                 }
1314
1315                 al.addGroup(sg);
1316             }
1317         }
1318
1319
1320         /////////////////////////////////
1321         // LOAD VIEWPORT
1322
1323         AlignFrame af = new AlignFrame(al,
1324                                        view.getWidth(),
1325                                        view.getHeight() );
1326
1327         af.setFileName(file, "Jalview");
1328
1329         for (int i = 0; i < JSEQ.length; i++)
1330         {
1331           af.viewport.setSequenceColour(
1332               af.viewport.alignment.getSequenceAt(i),
1333               new java.awt.Color(
1334                   JSEQ[i].getColour()));
1335         }
1336
1337         //If we just load in the same jar file again, the sequenceSetId
1338         //will be the same, and we end up with multiple references
1339         //to the same sequenceSet. We must modify this id on load
1340         //so that each load of the file gives a unique id
1341         String uniqueSeqSetId =  view.getSequenceSetId()+uniqueSetSuffix;
1342
1343         af.viewport.gatherViewsHere = view.getGatheredViews();
1344
1345         if (view.getSequenceSetId() != null)
1346         {
1347           jalview.gui.AlignViewport av =
1348               (jalview.gui.AlignViewport)
1349               viewportsAdded.get(uniqueSeqSetId);
1350
1351           af.viewport.sequenceSetID = uniqueSeqSetId;
1352           if(av!=null)
1353           {
1354
1355             af.viewport.historyList = av.historyList;
1356             af.viewport.redoList = av.redoList;
1357           }
1358           else
1359           {
1360             viewportsAdded.put(uniqueSeqSetId, af.viewport);
1361           }
1362
1363           PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
1364         }
1365         if(hiddenSeqs!=null)
1366         {
1367           for(int s=0; s<JSEQ.length; s++)
1368           {
1369             jalview.datamodel.SequenceGroup hidden =
1370                 new jalview.datamodel.SequenceGroup();
1371
1372             for(int r=0; r<JSEQ[s].getHiddenSequencesCount(); r++)
1373             {
1374               hidden.addSequence(
1375                   al.getSequenceAt(JSEQ[s].getHiddenSequences(r))
1376                   , false
1377                   );
1378             }
1379             af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
1380           }
1381
1382           jalview.datamodel.SequenceI [] hseqs = new
1383               jalview.datamodel.SequenceI[hiddenSeqs.size()];
1384
1385           for(int s=0; s<hiddenSeqs.size(); s++)
1386             hseqs[s] = (jalview.datamodel.SequenceI)hiddenSeqs.elementAt(s);
1387
1388           af.viewport.hideSequence( hseqs );
1389
1390         }
1391
1392
1393         if((hideConsensus || hideQuality || hideConservation)
1394             && al.getAlignmentAnnotation()!=null)
1395         {
1396           int hSize = al.getAlignmentAnnotation().length;
1397           for (int h = 0; h < hSize; h++)
1398           {
1399             if (
1400                 (hideConsensus &&
1401                  al.getAlignmentAnnotation()[h].label.equals("Consensus"))
1402                 ||
1403                 (hideQuality &&
1404                  al.getAlignmentAnnotation()[h].label.equals("Quality"))
1405                 ||
1406                 (hideConservation &&
1407                  al.getAlignmentAnnotation()[h].label.equals("Conservation")))
1408             {
1409               al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
1410               hSize--;
1411               h--;
1412             }
1413           }
1414           af.alignPanel.adjustAnnotationHeight();
1415         }
1416
1417         if(view.getViewName()!=null)
1418         {
1419           af.viewport.viewName = view.getViewName();
1420           af.setInitialTabVisible();
1421         }
1422         af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
1423             view.getHeight());
1424
1425         af.viewport.setShowAnnotation(view.getShowAnnotation());
1426         af.viewport.setAbovePIDThreshold(view.getPidSelected());
1427
1428         af.viewport.setColourText(view.getShowColourText());
1429
1430         af.viewport.setConservationSelected(view.getConservationSelected());
1431         af.viewport.setShowJVSuffix(view.getShowFullId());
1432         af.viewport.rightAlignIds=view.getRightAlignIds();
1433         af.viewport.setFont(new java.awt.Font(view.getFontName(),
1434                 view.getFontStyle(), view.getFontSize()));
1435         af.alignPanel.fontChanged();
1436         af.viewport.setRenderGaps(view.getRenderGaps());
1437         af.viewport.setWrapAlignment(view.getWrapAlignment());
1438         af.alignPanel.setWrapAlignment(view.getWrapAlignment());
1439         af.viewport.setShowAnnotation(view.getShowAnnotation());
1440         af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
1441
1442         af.viewport.setShowBoxes(view.getShowBoxes());
1443
1444         af.viewport.setShowText(view.getShowText());
1445
1446         af.viewport.textColour = new java.awt.Color(view.getTextCol1());
1447         af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
1448         af.viewport.thresholdTextColour = view.getTextColThreshold();
1449
1450         af.viewport.setStartRes(view.getStartRes());
1451         af.viewport.setStartSeq(view.getStartSeq());
1452
1453         ColourSchemeI cs = null;
1454
1455         if (view.getBgColour() != null)
1456         {
1457             if (view.getBgColour().startsWith("ucs"))
1458             {
1459                 cs = GetUserColourScheme(jms, view.getBgColour());
1460             }
1461             else if(view.getBgColour().startsWith("Annotation"))
1462             {
1463               //int find annotation
1464               for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
1465               {
1466                 if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
1467                     equals(view.getAnnotationColours().getAnnotation()))
1468                 {
1469                   if (af.viewport.alignment.getAlignmentAnnotation()[i].
1470                       getThreshold() == null)
1471                   {
1472                     af.viewport.alignment.getAlignmentAnnotation()[i].
1473                         setThreshold(
1474                             new jalview.datamodel.GraphLine(
1475                                 view.getAnnotationColours().getThreshold(),
1476                                 "Threshold", java.awt.Color.black)
1477
1478                         );
1479                   }
1480
1481
1482                   if (view.getAnnotationColours().getColourScheme().equals(
1483                       "None"))
1484                   {
1485                     cs = new AnnotationColourGradient(
1486                         af.viewport.alignment.getAlignmentAnnotation()[i],
1487                         new java.awt.Color(view.getAnnotationColours().
1488                                            getMinColour()),
1489                         new java.awt.Color(view.getAnnotationColours().
1490                                            getMaxColour()),
1491                         view.getAnnotationColours().getAboveThreshold());
1492                   }
1493                   else if (view.getAnnotationColours().getColourScheme().
1494                            startsWith("ucs"))
1495                   {
1496                      cs = new AnnotationColourGradient(
1497                          af.viewport.alignment.getAlignmentAnnotation()[i],
1498                          GetUserColourScheme(jms, view.getAnnotationColours().
1499                                                         getColourScheme()),
1500                          view.getAnnotationColours().getAboveThreshold()
1501                          );
1502                    }
1503                    else
1504                    {
1505                      cs = new AnnotationColourGradient(
1506                          af.viewport.alignment.getAlignmentAnnotation()[i],
1507                          ColourSchemeProperty.getColour(al,
1508                          view.getAnnotationColours().getColourScheme()),
1509                          view.getAnnotationColours().getAboveThreshold()
1510                          );
1511                    }
1512
1513                   // Also use these settings for all the groups
1514                   if (al.getGroups() != null)
1515                     for (int g = 0; g < al.getGroups().size(); g++)
1516                     {
1517                       jalview.datamodel.SequenceGroup sg
1518                           = (jalview.datamodel.SequenceGroup)al.getGroups().elementAt(g);
1519
1520                       if(sg.cs == null)
1521                         continue;
1522
1523
1524                   /*    if (view.getAnnotationColours().getColourScheme().equals("None"))
1525                       {
1526                         sg.cs = new AnnotationColourGradient(
1527                             af.viewport.alignment.getAlignmentAnnotation()[i],
1528                             new java.awt.Color(view.getAnnotationColours().
1529                                                getMinColour()),
1530                             new java.awt.Color(view.getAnnotationColours().
1531                                                getMaxColour()),
1532                             view.getAnnotationColours().getAboveThreshold());
1533                       }
1534                       else*/
1535                       {
1536                         sg.cs = new AnnotationColourGradient(
1537                             af.viewport.alignment.getAlignmentAnnotation()[i],
1538                             sg.cs,
1539                             view.getAnnotationColours().getAboveThreshold()
1540                             );
1541                       }
1542
1543                     }
1544
1545
1546                   break;
1547                 }
1548
1549               }
1550             }
1551             else
1552             {
1553                 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
1554             }
1555
1556             if(cs!=null)
1557             {
1558               cs.setThreshold(view.getPidThreshold(), true);
1559               cs.setConsensus(af.viewport.hconsensus);
1560             }
1561         }
1562
1563
1564         af.viewport.setGlobalColourScheme(cs);
1565         af.viewport.setColourAppliesToAllGroups(false);
1566
1567         if (view.getConservationSelected() && cs!=null)
1568         {
1569           cs.setConservationInc(view.getConsThreshold());
1570         }
1571
1572         af.changeColour(cs);
1573
1574         af.viewport.setColourAppliesToAllGroups(true);
1575
1576
1577
1578         if (view.getShowSequenceFeatures())
1579         {
1580            af.viewport.showSequenceFeatures = true;
1581         }
1582
1583         if(jms.getFeatureSettings()!=null)
1584         {
1585           af.viewport.featuresDisplayed = new Hashtable();
1586           String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];
1587          for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)
1588          {
1589            Setting setting = jms.getFeatureSettings().getSetting(fs);
1590
1591            af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),
1592                new java.awt.Color(setting.getColour()));
1593
1594            renderOrder[fs] = setting.getType();
1595
1596            if(setting.getDisplay())
1597              af.viewport.featuresDisplayed.put(
1598                  setting.getType(), new Integer(setting.getColour()));
1599          }
1600          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
1601         }
1602
1603         if (view.getHiddenColumnsCount() > 0)
1604         {
1605           for (int c = 0; c < view.getHiddenColumnsCount(); c++)
1606           {
1607               af.viewport.hideColumns(
1608                 view.getHiddenColumns(c).getStart(),
1609                 view.getHiddenColumns(c).getEnd() //+1
1610                 );
1611           }
1612         }
1613
1614         af.setMenusFromViewport(af.viewport);
1615
1616
1617         Desktop.addInternalFrame(af, view.getTitle(),
1618              view.getWidth(), view.getHeight());
1619
1620         //LOAD TREES
1621         ///////////////////////////////////////
1622         if (loadTrees && jms.getTreeCount() > 0)
1623         {
1624             try
1625             {
1626                 for (int t = 0; t < jms.getTreeCount(); t++)
1627                 {
1628
1629                     Tree tree = jms.getTree(t);
1630
1631                     TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
1632                                 tree.getNewick()), tree.getTitle(),
1633                                 tree.getWidth(), tree.getHeight(),
1634                                 tree.getXpos(), tree.getYpos());
1635
1636                     tp.fitToWindow.setState(tree.getFitToWindow());
1637                     tp.fitToWindow_actionPerformed(null);
1638
1639                     if(tree.getFontName()!=null)
1640                       tp.setTreeFont(new java.awt.Font(tree.getFontName(),
1641                                           tree.getFontStyle(),
1642                                           tree.getFontSize()));
1643                     else
1644                       tp.setTreeFont(new java.awt.Font(view.getFontName(),
1645                                             view.getFontStyle(),
1646                                             tree.getFontSize()));
1647
1648                     tp.showPlaceholders(tree.getMarkUnlinked());
1649                     tp.showBootstrap(tree.getShowBootstrap());
1650                     tp.showDistances(tree.getShowDistances());
1651
1652                     tp.treeCanvas.threshold = tree.getThreshold();
1653
1654                     if (tree.getCurrentTree())
1655                       af.viewport.setCurrentTree(tp.getTree());
1656                 }
1657
1658             }
1659             catch (Exception ex)
1660             {
1661                 ex.printStackTrace();
1662             }
1663
1664         }
1665
1666         return af;
1667     }
1668
1669     public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap, boolean keepSeqRefs )
1670     {
1671       jalview.schemabinding.version2.JalviewModel jm
1672           = SaveState(ap, null, null, null);
1673
1674       if (!keepSeqRefs)
1675       {
1676         seqRefIds.clear();
1677         jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
1678       }
1679       else
1680         uniqueSetSuffix = "";
1681
1682       viewportsAdded = new Hashtable();
1683
1684       AlignFrame af = LoadFromObject(jm, null, false);
1685       af.alignPanels.clear();
1686       af.closeMenuItem_actionPerformed(true);
1687
1688       return af.alignPanel;
1689     }
1690 }
1691