src/jalview/gui/Jalview2XML.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer
   3  * Copyright (C) 2007 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 import java.io.*;
  22 import java.net.*;
  23 import java.util.*;
  24 import java.util.jar.*;
  25
  26 import javax.swing.*;
  27
  28 import org.exolab.castor.xml.*;
  29
  30 import uk.ac.vamsas.objects.utils.MapList;
  31 import jalview.datamodel.Alignment;
  32 import jalview.datamodel.AlignmentI;
  33 import jalview.datamodel.SequenceI;
  34 import jalview.schemabinding.version2.*;
  35 import jalview.schemes.*;
  36 import jalview.structure.StructureSelectionManager;
  37
  38 /**
  39  * Write out the current jalview desktop state
  40  * as a Jalview XML stream.
  41  *
  42  * Note: the vamsas objects referred to here are primitive
  43  * versions of the VAMSAS project schema elements - they are
  44  * not the same and most likely never will be :)
  45  *
  46  * @author $author$
  47  * @version $Revision$
  48  */
  49 public class Jalview2XML
  50 {
  51
  52   Hashtable seqRefIds = null;
  53
  54   Vector frefedSequence = null;
  55
  56   public void resolveFrefedSequences()
  57   {
  58     if (frefedSequence.size() > 0)
  59     {
  60       int r = 0, rSize = frefedSequence.size();
  61       while (r < rSize)
  62       {
  63         Object[] ref = (Object[]) frefedSequence.elementAt(r);
  64         if (ref != null)
  65         {
  66           String sref = (String) ref[0];
  67           if (seqRefIds.containsKey(sref))
  68           {
  69             if (ref[1] instanceof jalview.datamodel.Mapping)
  70             {
  71               SequenceI seq = (SequenceI) seqRefIds.get(sref);
  72               while (seq.getDatasetSequence() != null)
  73               {
  74                 seq = seq.getDatasetSequence();
  75               }
  76               ((jalview.datamodel.Mapping) ref[1]).setTo(seq);
  77             }
  78             else
  79             {
  80               System.err
  81                       .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for "
  82                               + ref[1].getClass() + " type objects.");
  83             }
  84             frefedSequence.remove(r);
  85             rSize--;
  86           }
  87           else
  88           {
  89             r++;
  90           }
  91         }
  92         else
  93         {
  94           frefedSequence.remove(r);
  95           rSize--;
  96         }
  97       }
  98     }
  99   }
 100
 101   /**
 102    * This maintains a list of viewports, the key being the
 103    * seqSetId. Important to set historyItem and redoList
 104    * for multiple views
 105    */
 106   Hashtable viewportsAdded;
 107
 108   Hashtable annotationIds = new Hashtable();
 109
 110   String uniqueSetSuffix = "";
 111
 112   /**
 113    * List of pdbfiles added to Jar
 114    */
 115   Vector pdbfiles = null;
 116
 117   // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
 118   public void SaveState(File statefile)
 119   {
 120     JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 121
 122     if (frames == null)
 123     {
 124       return;
 125     }
 126
 127     try
 128     {
 129       FileOutputStream fos = new FileOutputStream(statefile);
 130       JarOutputStream jout = new JarOutputStream(fos);
 131
 132       //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
 133       ////////////////////////////////////////////////////
 134       PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
 135               "UTF-8"));
 136
 137       Vector shortNames = new Vector();
 138
 139       //REVERSE ORDER
 140       for (int i = frames.length - 1; i > -1; i--)
 141       {
 142         if (frames[i] instanceof AlignFrame)
 143         {
 144           AlignFrame af = (AlignFrame) frames[i];
 145
 146           String shortName = af.getTitle();
 147
 148           if (shortName.indexOf(File.separatorChar) > -1)
 149           {
 150             shortName = shortName.substring(shortName
 151                     .lastIndexOf(File.separatorChar) + 1);
 152           }
 153
 154           int count = 1;
 155
 156           while (shortNames.contains(shortName))
 157           {
 158             if (shortName.endsWith("_" + (count - 1)))
 159             {
 160               shortName = shortName
 161                       .substring(0, shortName.lastIndexOf("_"));
 162             }
 163
 164             shortName = shortName.concat("_" + count);
 165             count++;
 166           }
 167
 168           shortNames.addElement(shortName);
 169
 170           if (!shortName.endsWith(".xml"))
 171           {
 172             shortName = shortName + ".xml";
 173           }
 174
 175           int ap, apSize = af.alignPanels.size();
 176           for (ap = 0; ap < apSize; ap++)
 177           {
 178             AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
 179                     .elementAt(ap);
 180
 181             SaveState(apanel, apSize == 1 ? shortName : ap + shortName,
 182                     jout, out);
 183           }
 184         }
 185       }
 186
 187       out.close();
 188       jout.close();
 189     } catch (Exception ex)
 190     {
 191       //TODO: inform user of the problem - they need to know if their data was not saved !
 192       ex.printStackTrace();
 193     }
 194   }
 195
 196   // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
 197   public boolean SaveAlignment(AlignFrame af, String jarFile,
 198           String fileName)
 199   {
 200     try
 201     {
 202       int ap, apSize = af.alignPanels.size();
 203       FileOutputStream fos = new FileOutputStream(jarFile);
 204       JarOutputStream jout = new JarOutputStream(fos);
 205       PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
 206               "UTF-8"));
 207       for (ap = 0; ap < apSize; ap++)
 208       {
 209         AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
 210                 .elementAt(ap);
 211
 212         SaveState(apanel, apSize == 1 ? fileName : fileName + ap, jout, out);
 213       }
 214
 215       out.close();
 216       jout.close();
 217       return true;
 218     } catch (Exception ex)
 219     {
 220       ex.printStackTrace();
 221       return false;
 222     }
 223   }
 224
 225   /**
 226    * DOCUMENT ME!
 227    *
 228    * @param af DOCUMENT ME!
 229    * @param timeStamp DOCUMENT ME!
 230    * @param fileName DOCUMENT ME!
 231    * @param jout DOCUMENT ME!
 232    * @param out DOCUMENT ME!
 233    */
 234   public JalviewModel SaveState(AlignmentPanel ap, String fileName,
 235           JarOutputStream jout, PrintWriter out)
 236   {
 237     if (seqRefIds == null)
 238     {
 239       seqRefIds = new Hashtable();
 240     }
 241
 242     Vector userColours = new Vector();
 243
 244     AlignViewport av = ap.av;
 245
 246     JalviewModel object = new JalviewModel();
 247     object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
 248
 249     object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
 250     object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
 251
 252     jalview.datamodel.AlignmentI jal = av.alignment;
 253
 254     if (av.hasHiddenRows)
 255     {
 256       jal = jal.getHiddenSequences().getFullAlignment();
 257     }
 258
 259     SequenceSet vamsasSet = new SequenceSet();
 260     Sequence vamsasSeq;
 261     JalviewModelSequence jms = new JalviewModelSequence();
 262
 263     vamsasSet.setGapChar(jal.getGapCharacter() + "");
 264
 265     if (jal.getDataset() != null)
 266     {
 267       // dataset id is the dataset's hashcode
 268       vamsasSet.setDatasetId(jal.getDataset().hashCode() + "");
 269     }
 270     if (jal.getProperties() != null)
 271     {
 272       Enumeration en = jal.getProperties().keys();
 273       while (en.hasMoreElements())
 274       {
 275         String key = en.nextElement().toString();
 276         SequenceSetProperties ssp = new SequenceSetProperties();
 277         ssp.setKey(key);
 278         ssp.setValue(jal.getProperties().get(key).toString());
 279         vamsasSet.addSequenceSetProperties(ssp);
 280       }
 281     }
 282
 283     JSeq jseq;
 284
 285     //SAVE SEQUENCES
 286     int id = 0;
 287     jalview.datamodel.SequenceI jds;
 288     for (int i = 0; i < jal.getHeight(); i++)
 289     {
 290       jds = jal.getSequenceAt(i);
 291       id = jds.hashCode();
 292
 293       if (seqRefIds.get(id + "") != null)
 294       {
 295
 296       }
 297       else
 298       {
 299         vamsasSeq = createVamsasSequence(id, jds);
 300         vamsasSet.addSequence(vamsasSeq);
 301         seqRefIds.put(id + "", jal.getSequenceAt(i));
 302       }
 303
 304       jseq = new JSeq();
 305       jseq.setStart(jds.getStart());
 306       jseq.setEnd(jds.getEnd());
 307       jseq.setColour(av.getSequenceColour(jds).getRGB());
 308
 309       jseq.setId(id);
 310
 311       if (av.hasHiddenRows)
 312       {
 313         jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
 314
 315         if (av.hiddenRepSequences != null
 316                 && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
 317         {
 318           jalview.datamodel.SequenceI[] reps = ((jalview.datamodel.SequenceGroup) av.hiddenRepSequences
 319                   .get(jal.getSequenceAt(i))).getSequencesInOrder(jal);
 320
 321           for (int h = 0; h < reps.length; h++)
 322           {
 323             if (reps[h] != jal.getSequenceAt(i))
 324             {
 325               jseq.addHiddenSequences(jal.findIndex(reps[h]));
 326             }
 327           }
 328         }
 329       }
 330
 331       if (jds.getDatasetSequence().getSequenceFeatures() != null)
 332       {
 333         jalview.datamodel.SequenceFeature[] sf = jds.getDatasetSequence()
 334                 .getSequenceFeatures();
 335         int index = 0;
 336         while (index < sf.length)
 337         {
 338           Features features = new Features();
 339
 340           features.setBegin(sf[index].getBegin());
 341           features.setEnd(sf[index].getEnd());
 342           features.setDescription(sf[index].getDescription());
 343           features.setType(sf[index].getType());
 344           features.setFeatureGroup(sf[index].getFeatureGroup());
 345           features.setScore(sf[index].getScore());
 346           if (sf[index].links != null)
 347           {
 348             for (int l = 0; l < sf[index].links.size(); l++)
 349             {
 350               OtherData keyValue = new OtherData();
 351               keyValue.setKey("LINK_" + l);
 352               keyValue.setValue(sf[index].links.elementAt(l).toString());
 353               features.addOtherData(keyValue);
 354             }
 355           }
 356           if (sf[index].otherDetails != null)
 357           {
 358             String key;
 359             Enumeration keys = sf[index].otherDetails.keys();
 360             while (keys.hasMoreElements())
 361             {
 362               key = keys.nextElement().toString();
 363               OtherData keyValue = new OtherData();
 364               keyValue.setKey(key);
 365               keyValue.setValue(sf[index].otherDetails.get(key).toString());
 366               features.addOtherData(keyValue);
 367             }
 368           }
 369
 370           jseq.addFeatures(features);
 371           index++;
 372         }
 373       }
 374
 375       if (jds.getDatasetSequence().getPDBId() != null)
 376       {
 377         Enumeration en = jds.getDatasetSequence().getPDBId().elements();
 378         while (en.hasMoreElements())
 379         {
 380           Pdbids pdb = new Pdbids();
 381           jalview.datamodel.PDBEntry entry = (jalview.datamodel.PDBEntry) en
 382                   .nextElement();
 383
 384           pdb.setId(entry.getId());
 385           pdb.setType(entry.getType());
 386
 387           AppJmol jmol;
 388           //This must have been loaded, is it still visible?
 389           JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 390           for (int f = frames.length - 1; f > -1; f--)
 391           {
 392             if (frames[f] instanceof AppJmol)
 393             {
 394               jmol = (AppJmol) frames[f];
 395               if (!jmol.pdbentry.getId().equals(entry.getId()))
 396                 continue;
 397
 398               StructureState state = new StructureState();
 399               state.setVisible(true);
 400               state.setXpos(jmol.getX());
 401               state.setYpos(jmol.getY());
 402               state.setWidth(jmol.getWidth());
 403               state.setHeight(jmol.getHeight());
 404
 405               String statestring = jmol.viewer.getStateInfo();
 406               if (state != null)
 407               {
 408                 state.setContent(statestring.replaceAll("\n", ""));
 409               }
 410               for (int s = 0; s < jmol.sequence.length; s++)
 411               {
 412                 if (jal.findIndex(jmol.sequence[s]) > -1)
 413                 {
 414                   pdb.addStructureState(state);
 415                 }
 416               }
 417             }
 418           }
 419
 420           if (entry.getFile() != null)
 421           {
 422             pdb.setFile(entry.getFile());
 423             if (pdbfiles == null)
 424             {
 425               pdbfiles = new Vector();
 426             }
 427
 428             if (!pdbfiles.contains(entry.getId()))
 429             {
 430               pdbfiles.addElement(entry.getId());
 431               try
 432               {
 433                 File file = new File(entry.getFile());
 434                 if (file.exists() && jout != null)
 435                 {
 436                   byte[] data = new byte[(int) file.length()];
 437                   jout.putNextEntry(new JarEntry(entry.getId()));
 438                   DataInputStream dis = new DataInputStream(
 439                           new FileInputStream(file));
 440                   dis.readFully(data);
 441
 442                   DataOutputStream dout = new DataOutputStream(jout);
 443                   dout.write(data, 0, data.length);
 444                   jout.closeEntry();
 445                 }
 446               } catch (Exception ex)
 447               {
 448                 ex.printStackTrace();
 449               }
 450
 451             }
 452           }
 453
 454           if (entry.getProperty() != null)
 455           {
 456             PdbentryItem item = new PdbentryItem();
 457             Hashtable properties = entry.getProperty();
 458             Enumeration en2 = properties.keys();
 459             while (en2.hasMoreElements())
 460             {
 461               Property prop = new Property();
 462               String key = en2.nextElement().toString();
 463               prop.setName(key);
 464               prop.setValue(properties.get(key).toString());
 465               item.addProperty(prop);
 466             }
 467             pdb.addPdbentryItem(item);
 468           }
 469
 470           jseq.addPdbids(pdb);
 471         }
 472       }
 473
 474       jms.addJSeq(jseq);
 475     }
 476
 477     if (av.hasHiddenRows)
 478     {
 479       jal = av.alignment;
 480     }
 481     // SAVE MAPPINGS
 482     if (jal.getCodonFrames() != null && jal.getCodonFrames().length > 0)
 483     {
 484       jalview.datamodel.AlignedCodonFrame[] jac = jal.getCodonFrames();
 485       for (int i = 0; i < jac.length; i++)
 486       {
 487         AlcodonFrame alc = new AlcodonFrame();
 488         vamsasSet.addAlcodonFrame(alc);
 489         for (int p = 0; p < jac[i].aaWidth; i++)
 490         {
 491           Alcodon cmap = new Alcodon();
 492           cmap.setPos1(jac[i].codons[p][0]);
 493           cmap.setPos2(jac[i].codons[p][1]);
 494           cmap.setPos3(jac[i].codons[p][2]);
 495           alc.addAlcodon(cmap);
 496         }
 497         if (jac[i].getProtMappings() != null
 498                 && jac[i].getProtMappings().length > 0)
 499         {
 500           SequenceI[] dnas = jac[i].getdnaSeqs();
 501           jalview.datamodel.Mapping[] pmaps = jac[i].getProtMappings();
 502           for (int m = 0; m < pmaps.length; m++)
 503           {
 504             AlcodMap alcmap = new AlcodMap();
 505             alcmap.setDnasq("" + dnas[m].hashCode());
 506             alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
 507                     false));
 508             alc.addAlcodMap(alcmap);
 509           }
 510         }
 511       }
 512     }
 513
 514     //SAVE TREES
 515     ///////////////////////////////////
 516     if (av.currentTree != null)
 517     {
 518       // FIND ANY ASSOCIATED TREES
 519       // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
 520       if (Desktop.desktop != null)
 521       {
 522         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 523
 524         for (int t = 0; t < frames.length; t++)
 525         {
 526           if (frames[t] instanceof TreePanel)
 527           {
 528             TreePanel tp = (TreePanel) frames[t];
 529
 530             if (tp.treeCanvas.av.alignment == jal)
 531             {
 532               Tree tree = new Tree();
 533               tree.setTitle(tp.getTitle());
 534               tree.setCurrentTree((av.currentTree == tp.getTree()));
 535               tree.setNewick(tp.getTree().toString());
 536               tree.setThreshold(tp.treeCanvas.threshold);
 537
 538               tree.setFitToWindow(tp.fitToWindow.getState());
 539               tree.setFontName(tp.getTreeFont().getName());
 540               tree.setFontSize(tp.getTreeFont().getSize());
 541               tree.setFontStyle(tp.getTreeFont().getStyle());
 542               tree.setMarkUnlinked(tp.placeholdersMenu.getState());
 543
 544               tree.setShowBootstrap(tp.bootstrapMenu.getState());
 545               tree.setShowDistances(tp.distanceMenu.getState());
 546
 547               tree.setHeight(tp.getHeight());
 548               tree.setWidth(tp.getWidth());
 549               tree.setXpos(tp.getX());
 550               tree.setYpos(tp.getY());
 551
 552               jms.addTree(tree);
 553             }
 554           }
 555         }
 556       }
 557     }
 558
 559     //SAVE ANNOTATIONS
 560     if (jal.getAlignmentAnnotation() != null)
 561     {
 562       jalview.datamodel.AlignmentAnnotation[] aa = jal
 563               .getAlignmentAnnotation();
 564
 565       for (int i = 0; i < aa.length; i++)
 566       {
 567         Annotation an = new Annotation();
 568
 569         if (aa[i].annotationId != null)
 570         {
 571           annotationIds.put(aa[i].annotationId, aa[i]);
 572         }
 573
 574         an.setId(aa[i].annotationId);
 575
 576         if (aa[i] == av.quality || aa[i] == av.conservation
 577                 || aa[i] == av.consensus)
 578         {
 579           an.setLabel(aa[i].label);
 580           an.setGraph(true);
 581           vamsasSet.addAnnotation(an);
 582           continue;
 583         }
 584
 585         an.setVisible(aa[i].visible);
 586
 587         an.setDescription(aa[i].description);
 588
 589         if (aa[i].sequenceRef != null)
 590         {
 591           an.setSequenceRef(aa[i].sequenceRef.getName());
 592         }
 593
 594         if (aa[i].graph > 0)
 595         {
 596           an.setGraph(true);
 597           an.setGraphType(aa[i].graph);
 598           an.setGraphGroup(aa[i].graphGroup);
 599           if (aa[i].getThreshold() != null)
 600           {
 601             ThresholdLine line = new ThresholdLine();
 602             line.setLabel(aa[i].getThreshold().label);
 603             line.setValue(aa[i].getThreshold().value);
 604             line.setColour(aa[i].getThreshold().colour.getRGB());
 605             an.setThresholdLine(line);
 606           }
 607         }
 608         else
 609         {
 610           an.setGraph(false);
 611         }
 612
 613         an.setLabel(aa[i].label);
 614         if (aa[i].hasScore())
 615         {
 616           an.setScore(aa[i].getScore());
 617         }
 618         AnnotationElement ae;
 619         if (aa[i].annotations != null)
 620         {
 621           an.setScoreOnly(false);
 622           for (int a = 0; a < aa[i].annotations.length; a++)
 623           {
 624             if ((aa[i] == null) || (aa[i].annotations[a] == null))
 625             {
 626               continue;
 627             }
 628
 629             ae = new AnnotationElement();
 630             if (aa[i].annotations[a].description != null)
 631               ae.setDescription(aa[i].annotations[a].description);
 632             if (aa[i].annotations[a].displayCharacter != null)
 633               ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
 634
 635             if (!Float.isNaN(aa[i].annotations[a].value))
 636               ae.setValue(aa[i].annotations[a].value);
 637
 638             ae.setPosition(a);
 639             if (aa[i].annotations[a].secondaryStructure != ' '
 640                     && aa[i].annotations[a].secondaryStructure != '\0')
 641               ae
 642                       .setSecondaryStructure(aa[i].annotations[a].secondaryStructure
 643                               + "");
 644
 645             if (aa[i].annotations[a].colour != null
 646                     && aa[i].annotations[a].colour != java.awt.Color.black)
 647             {
 648               ae.setColour(aa[i].annotations[a].colour.getRGB());
 649             }
 650
 651             an.addAnnotationElement(ae);
 652           }
 653         }
 654         else
 655         {
 656           an.setScoreOnly(true);
 657         }
 658         vamsasSet.addAnnotation(an);
 659       }
 660     }
 661
 662     //SAVE GROUPS
 663     if (jal.getGroups() != null)
 664     {
 665       JGroup[] groups = new JGroup[jal.getGroups().size()];
 666
 667       for (int i = 0; i < groups.length; i++)
 668       {
 669         groups[i] = new JGroup();
 670
 671         jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal
 672                 .getGroups().elementAt(i);
 673         groups[i].setStart(sg.getStartRes());
 674         groups[i].setEnd(sg.getEndRes());
 675         groups[i].setName(sg.getName());
 676         if (sg.cs != null)
 677         {
 678           if (sg.cs.conservationApplied())
 679           {
 680             groups[i].setConsThreshold(sg.cs.getConservationInc());
 681
 682             if (sg.cs instanceof jalview.schemes.UserColourScheme)
 683             {
 684               groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
 685                       jms));
 686             }
 687             else
 688             {
 689               groups[i]
 690                       .setColour(ColourSchemeProperty.getColourName(sg.cs));
 691             }
 692           }
 693           else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
 694           {
 695             groups[i]
 696                     .setColour(ColourSchemeProperty
 697                             .getColourName(((jalview.schemes.AnnotationColourGradient) sg.cs)
 698                                     .getBaseColour()));
 699           }
 700           else if (sg.cs instanceof jalview.schemes.UserColourScheme)
 701           {
 702             groups[i]
 703                     .setColour(SetUserColourScheme(sg.cs, userColours, jms));
 704           }
 705           else
 706           {
 707             groups[i].setColour(ColourSchemeProperty.getColourName(sg.cs));
 708           }
 709
 710           groups[i].setPidThreshold(sg.cs.getThreshold());
 711         }
 712
 713         groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
 714         groups[i].setDisplayBoxes(sg.getDisplayBoxes());
 715         groups[i].setDisplayText(sg.getDisplayText());
 716         groups[i].setColourText(sg.getColourText());
 717         groups[i].setTextCol1(sg.textColour.getRGB());
 718         groups[i].setTextCol2(sg.textColour2.getRGB());
 719         groups[i].setTextColThreshold(sg.thresholdTextColour);
 720
 721         for (int s = 0; s < sg.getSize(); s++)
 722         {
 723           jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg
 724                   .getSequenceAt(s);
 725           groups[i].addSeq(seq.hashCode());
 726         }
 727       }
 728
 729       jms.setJGroup(groups);
 730     }
 731
 732     ///////////SAVE VIEWPORT
 733     Viewport view = new Viewport();
 734     view.setTitle(ap.alignFrame.getTitle());
 735     view.setSequenceSetId(av.getSequenceSetId());
 736     view.setViewName(av.viewName);
 737     view.setGatheredViews(av.gatherViewsHere);
 738
 739     if (ap.av.explodedPosition != null)
 740     {
 741       view.setXpos(av.explodedPosition.x);
 742       view.setYpos(av.explodedPosition.y);
 743       view.setWidth(av.explodedPosition.width);
 744       view.setHeight(av.explodedPosition.height);
 745     }
 746     else
 747     {
 748       view.setXpos(ap.alignFrame.getBounds().x);
 749       view.setYpos(ap.alignFrame.getBounds().y);
 750       view.setWidth(ap.alignFrame.getBounds().width);
 751       view.setHeight(ap.alignFrame.getBounds().height);
 752     }
 753
 754     view.setStartRes(av.startRes);
 755     view.setStartSeq(av.startSeq);
 756
 757     if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
 758     {
 759       view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
 760               userColours, jms));
 761     }
 762     else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
 763     {
 764       jalview.schemes.AnnotationColourGradient acg = (jalview.schemes.AnnotationColourGradient) av
 765               .getGlobalColourScheme();
 766
 767       AnnotationColours ac = new AnnotationColours();
 768       ac.setAboveThreshold(acg.getAboveThreshold());
 769       ac.setThreshold(acg.getAnnotationThreshold());
 770       ac.setAnnotation(acg.getAnnotation());
 771       if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
 772       {
 773         ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
 774                 userColours, jms));
 775       }
 776       else
 777       {
 778         ac.setColourScheme(ColourSchemeProperty.getColourName(acg
 779                 .getBaseColour()));
 780       }
 781
 782       ac.setMaxColour(acg.getMaxColour().getRGB());
 783       ac.setMinColour(acg.getMinColour().getRGB());
 784       view.setAnnotationColours(ac);
 785       view.setBgColour("AnnotationColourGradient");
 786     }
 787     else
 788     {
 789       view.setBgColour(ColourSchemeProperty.getColourName(av
 790               .getGlobalColourScheme()));
 791     }
 792
 793     ColourSchemeI cs = av.getGlobalColourScheme();
 794
 795     if (cs != null)
 796     {
 797       if (cs.conservationApplied())
 798       {
 799         view.setConsThreshold(cs.getConservationInc());
 800         if (cs instanceof jalview.schemes.UserColourScheme)
 801         {
 802           view.setBgColour(SetUserColourScheme(cs, userColours, jms));
 803         }
 804       }
 805
 806       if (cs instanceof ResidueColourScheme)
 807       {
 808         view.setPidThreshold(cs.getThreshold());
 809       }
 810     }
 811
 812     view.setConservationSelected(av.getConservationSelected());
 813     view.setPidSelected(av.getAbovePIDThreshold());
 814     view.setFontName(av.font.getName());
 815     view.setFontSize(av.font.getSize());
 816     view.setFontStyle(av.font.getStyle());
 817     view.setRenderGaps(av.renderGaps);
 818     view.setShowAnnotation(av.getShowAnnotation());
 819     view.setShowBoxes(av.getShowBoxes());
 820     view.setShowColourText(av.getColourText());
 821     view.setShowFullId(av.getShowJVSuffix());
 822     view.setRightAlignIds(av.rightAlignIds);
 823     view.setShowSequenceFeatures(av.showSequenceFeatures);
 824     view.setShowText(av.getShowText());
 825     view.setWrapAlignment(av.getWrapAlignment());
 826     view.setTextCol1(av.textColour.getRGB());
 827     view.setTextCol2(av.textColour2.getRGB());
 828     view.setTextColThreshold(av.thresholdTextColour);
 829
 830     if (av.featuresDisplayed != null)
 831     {
 832       jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
 833
 834       String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
 835
 836       Vector settingsAdded = new Vector();
 837       for (int ro = 0; ro < renderOrder.length; ro++)
 838       {
 839         Setting setting = new Setting();
 840         setting.setType(renderOrder[ro]);
 841         setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
 842                 .getColour(renderOrder[ro]).getRGB());
 843
 844         setting.setDisplay(av.featuresDisplayed
 845                 .containsKey(renderOrder[ro]));
 846         float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
 847                 renderOrder[ro]);
 848         if (rorder > -1)
 849         {
 850           setting.setOrder(rorder);
 851         }
 852         fs.addSetting(setting);
 853         settingsAdded.addElement(renderOrder[ro]);
 854       }
 855
 856       //Make sure we save none displayed feature settings
 857       Enumeration en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
 858               .keys();
 859       while (en.hasMoreElements())
 860       {
 861         String key = en.nextElement().toString();
 862         if (settingsAdded.contains(key))
 863         {
 864           continue;
 865         }
 866
 867         Setting setting = new Setting();
 868         setting.setType(key);
 869         setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
 870                 .getColour(key).getRGB());
 871
 872         setting.setDisplay(false);
 873         float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
 874                 key);
 875         if (rorder > -1)
 876         {
 877           setting.setOrder(rorder);
 878         }
 879         fs.addSetting(setting);
 880         settingsAdded.addElement(key);
 881       }
 882       en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keys();
 883       Vector groupsAdded = new Vector();
 884       while (en.hasMoreElements())
 885       {
 886         String grp = en.nextElement().toString();
 887         if (groupsAdded.contains(grp))
 888         {
 889           continue;
 890         }
 891         Group g = new Group();
 892         g.setName(grp);
 893         g
 894                 .setDisplay(((Boolean) ap.seqPanel.seqCanvas
 895                         .getFeatureRenderer().featureGroups.get(grp))
 896                         .booleanValue());
 897         fs.addGroup(g);
 898         groupsAdded.addElement(grp);
 899       }
 900       jms.setFeatureSettings(fs);
 901
 902     }
 903
 904     if (av.hasHiddenColumns)
 905     {
 906       for (int c = 0; c < av.getColumnSelection().getHiddenColumns().size(); c++)
 907       {
 908         int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
 909                 .elementAt(c);
 910         HiddenColumns hc = new HiddenColumns();
 911         hc.setStart(region[0]);
 912         hc.setEnd(region[1]);
 913         view.addHiddenColumns(hc);
 914       }
 915     }
 916
 917     jms.addViewport(view);
 918
 919     object.setJalviewModelSequence(jms);
 920     object.getVamsasModel().addSequenceSet(vamsasSet);
 921
 922     if (out != null)
 923     {
 924       //We may not want to right the object to disk,
 925       //eg we can copy the alignViewport to a new view object
 926       //using save and then load
 927       try
 928       {
 929         if (!fileName.endsWith(".xml"))
 930         {
 931           fileName = fileName + ".xml";
 932         }
 933
 934         JarEntry entry = new JarEntry(fileName);
 935         jout.putNextEntry(entry);
 936
 937         object.marshal(out);
 938       } catch (Exception ex)
 939       {
 940         ex.printStackTrace();
 941       }
 942     }
 943     return object;
 944   }
 945
 946   private Sequence createVamsasSequence(int id, SequenceI jds)
 947   {
 948     return createVamsasSequence(true, id, jds, null);
 949   }
 950
 951   private Sequence createVamsasSequence(boolean recurse, int id,
 952           SequenceI jds, SequenceI parentseq)
 953   {
 954     Sequence vamsasSeq = new Sequence();
 955     vamsasSeq.setId(id + "");
 956     vamsasSeq.setName(jds.getName());
 957     vamsasSeq.setSequence(jds.getSequenceAsString());
 958     vamsasSeq.setDescription(jds.getDescription());
 959     jalview.datamodel.DBRefEntry[] dbrefs = null;
 960     if (jds.getDatasetSequence() != null)
 961     {
 962       vamsasSeq.setDsseqid(jds.getDatasetSequence().hashCode() + "");
 963       if (jds.getDatasetSequence().getDBRef() != null)
 964       {
 965         dbrefs = jds.getDatasetSequence().getDBRef();
 966       }
 967     }
 968     else
 969     {
 970       dbrefs = jds.getDBRef();
 971     }
 972     if (jds.getDBRef() != null)
 973     {
 974       for (int d = 0; d < dbrefs.length; d++)
 975       {
 976         DBRef dbref = new DBRef();
 977         dbref.setSource(dbrefs[d].getSource());
 978         dbref.setVersion(dbrefs[d].getVersion());
 979         dbref.setAccessionId(dbrefs[d].getAccessionId());
 980         if (dbrefs[d].hasMap())
 981         {
 982           Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
 983                   jds, recurse);
 984           dbref.setMapping(mp);
 985         }
 986         vamsasSeq.addDBRef(dbref);
 987       }
 988     }
 989     return vamsasSeq;
 990   }
 991
 992   private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
 993           SequenceI parentseq, SequenceI jds, boolean recurse)
 994   {
 995     Mapping mp = null;
 996     if (jmp.getMap() != null)
 997     {
 998       mp = new Mapping();
 999
1000       jalview.util.MapList mlst = jmp.getMap();
1001       int r[] = mlst.getFromRanges();
1002       for (int s = 0; s < r.length; s += 2)
1003       {
1004         MapListFrom mfrom = new MapListFrom();
1005         mfrom.setStart(r[s]);
1006         mfrom.setEnd(r[s + 1]);
1007         mp.addMapListFrom(mfrom);
1008       }
1009       r = mlst.getToRanges();
1010       for (int s = 0; s < r.length; s += 2)
1011       {
1012         MapListTo mto = new MapListTo();
1013         mto.setStart(r[s]);
1014         mto.setEnd(r[s + 1]);
1015         mp.addMapListTo(mto);
1016       }
1017       mp.setMapFromUnit(mlst.getFromRatio());
1018       mp.setMapToUnit(mlst.getToRatio());
1019       if (jmp.getTo() != null)
1020       {
1021         MappingChoice mpc = new MappingChoice();
1022         if (recurse
1023                 && (parentseq != jmp.getTo() || parentseq
1024                         .getDatasetSequence() != jmp.getTo()))
1025         {
1026           mpc.setSequence(createVamsasSequence(false, jmp.getTo()
1027                   .hashCode(), jmp.getTo(), jds));
1028         }
1029         else
1030         {
1031           long jmpid = 0;
1032           SequenceI ps = null;
1033           if (parentseq != jmp.getTo()
1034                   && parentseq.getDatasetSequence() != jmp.getTo())
1035           {
1036             // chaining dbref rather than a handshaking one
1037             jmpid = (ps = jmp.getTo()).hashCode();
1038           }
1039           else
1040           {
1041             jmpid = (ps = parentseq).hashCode();
1042           }
1043           mpc.setDseqFor("" + jmpid);
1044           if (!seqRefIds.containsKey(mpc.getDseqFor()))
1045           {
1046             jalview.bin.Cache.log.debug("creatign new DseqFor ID");
1047             seqRefIds.put(mpc.getDseqFor(), ps);
1048           }
1049           else
1050           {
1051             jalview.bin.Cache.log.debug("reusing DseqFor ID");
1052           }
1053         }
1054         mp.setMappingChoice(mpc);
1055       }
1056     }
1057     return mp;
1058   }
1059
1060   String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
1061           Vector userColours, JalviewModelSequence jms)
1062   {
1063     String id = null;
1064     jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
1065
1066     if (!userColours.contains(ucs))
1067     {
1068       userColours.add(ucs);
1069
1070       java.awt.Color[] colours = ucs.getColours();
1071       jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
1072       jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
1073
1074       for (int i = 0; i < colours.length; i++)
1075       {
1076         jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
1077         col.setName(ResidueProperties.aa[i]);
1078         col.setRGB(jalview.util.Format.getHexString(colours[i]));
1079         jbucs.addColour(col);
1080       }
1081       if (ucs.getLowerCaseColours() != null)
1082       {
1083         colours = ucs.getLowerCaseColours();
1084         for (int i = 0; i < colours.length; i++)
1085         {
1086           jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
1087           col.setName(ResidueProperties.aa[i].toLowerCase());
1088           col.setRGB(jalview.util.Format.getHexString(colours[i]));
1089           jbucs.addColour(col);
1090         }
1091       }
1092
1093       id = "ucs" + userColours.indexOf(ucs);
1094       uc.setId(id);
1095       uc.setUserColourScheme(jbucs);
1096       jms.addUserColours(uc);
1097     }
1098
1099     return id;
1100   }
1101
1102   jalview.schemes.UserColourScheme GetUserColourScheme(
1103           JalviewModelSequence jms, String id)
1104   {
1105     UserColours[] uc = jms.getUserColours();
1106     UserColours colours = null;
1107
1108     for (int i = 0; i < uc.length; i++)
1109     {
1110       if (uc[i].getId().equals(id))
1111       {
1112         colours = uc[i];
1113
1114         break;
1115       }
1116     }
1117
1118     java.awt.Color[] newColours = new java.awt.Color[24];
1119
1120     for (int i = 0; i < 24; i++)
1121     {
1122       newColours[i] = new java.awt.Color(Integer.parseInt(colours
1123               .getUserColourScheme().getColour(i).getRGB(), 16));
1124     }
1125
1126     jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
1127             newColours);
1128
1129     if (colours.getUserColourScheme().getColourCount() > 24)
1130     {
1131       newColours = new java.awt.Color[23];
1132       for (int i = 0; i < 23; i++)
1133       {
1134         newColours[i] = new java.awt.Color(Integer.parseInt(colours
1135                 .getUserColourScheme().getColour(i + 24).getRGB(), 16));
1136       }
1137       ucs.setLowerCaseColours(newColours);
1138     }
1139
1140     return ucs;
1141   }
1142
1143   /**
1144    * DOCUMENT ME!
1145    *
1146    * @param file DOCUMENT ME!
1147    */
1148   public AlignFrame LoadJalviewAlign(final String file)
1149   {
1150     uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
1151
1152     jalview.gui.AlignFrame af = null;
1153
1154     seqRefIds = new Hashtable();
1155     viewportsAdded = new Hashtable();
1156     frefedSequence = new Vector();
1157     Hashtable gatherToThisFrame = new Hashtable();
1158
1159     String errorMessage = null;
1160
1161     try
1162     {
1163       //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
1164       URL url = null;
1165
1166       if (file.startsWith("http://"))
1167       {
1168         url = new URL(file);
1169       }
1170
1171       JarInputStream jin = null;
1172       JarEntry jarentry = null;
1173       int entryCount = 1;
1174
1175       do
1176       {
1177         if (url != null)
1178         {
1179           jin = new JarInputStream(url.openStream());
1180         }
1181         else
1182         {
1183           jin = new JarInputStream(new FileInputStream(file));
1184         }
1185
1186         for (int i = 0; i < entryCount; i++)
1187         {
1188           jarentry = jin.getNextJarEntry();
1189         }
1190
1191         if (jarentry != null && jarentry.getName().endsWith(".xml"))
1192         {
1193           InputStreamReader in = new InputStreamReader(jin, "UTF-8");
1194           JalviewModel object = new JalviewModel();
1195
1196           Unmarshaller unmar = new Unmarshaller(object);
1197           unmar.setValidation(false);
1198           object = (JalviewModel) unmar.unmarshal(in);
1199
1200           af = LoadFromObject(object, file, true);
1201           if (af.viewport.gatherViewsHere)
1202           {
1203             gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
1204           }
1205           entryCount++;
1206         }
1207         else if (jarentry != null)
1208         {
1209           //Some other file here.
1210           entryCount++;
1211         }
1212       } while (jarentry != null);
1213       resolveFrefedSequences();
1214     } catch (java.io.FileNotFoundException ex)
1215     {
1216       ex.printStackTrace();
1217       errorMessage = "Couldn't locate Jalview XML file : " + file;
1218       System.err.println("Exception whilst loading jalview XML file : "
1219               + ex + "\n");
1220     } catch (java.net.UnknownHostException ex)
1221     {
1222       ex.printStackTrace();
1223       errorMessage = "Couldn't locate Jalview XML file : " + file;
1224       System.err.println("Exception whilst loading jalview XML file : "
1225               + ex + "\n");
1226     } catch (Exception ex)
1227     {
1228       //Is Version 1 Jar file?
1229       af = new Jalview2XML_V1().LoadJalviewAlign(file);
1230
1231       if (af != null)
1232       {
1233         System.out.println("Successfully loaded archive file");
1234         return af;
1235       }
1236       ex.printStackTrace();
1237
1238       System.err.println("Exception whilst loading jalview XML file : "
1239               + ex + "\n");
1240     }
1241
1242     if (Desktop.instance != null)
1243     {
1244       Desktop.instance.stopLoading();
1245     }
1246
1247     Enumeration en = gatherToThisFrame.elements();
1248     while (en.hasMoreElements())
1249     {
1250       Desktop.instance.gatherViews((AlignFrame) en.nextElement());
1251     }
1252
1253     if (errorMessage != null)
1254     {
1255       final String finalErrorMessage = errorMessage;
1256       javax.swing.SwingUtilities.invokeLater(new Runnable()
1257       {
1258         public void run()
1259         {
1260           JOptionPane.showInternalMessageDialog(Desktop.desktop,
1261                   finalErrorMessage, "Error loading Jalview file",
1262                   JOptionPane.WARNING_MESSAGE);
1263         }
1264       });
1265     }
1266
1267     return af;
1268   }
1269
1270   Hashtable alreadyLoadedPDB;
1271
1272   String loadPDBFile(String file, String pdbId)
1273   {
1274     if (alreadyLoadedPDB == null)
1275       alreadyLoadedPDB = new Hashtable();
1276
1277     if (alreadyLoadedPDB.containsKey(pdbId))
1278       return alreadyLoadedPDB.get(pdbId).toString();
1279
1280     try
1281     {
1282       JarInputStream jin = null;
1283
1284       if (file.startsWith("http://"))
1285       {
1286         jin = new JarInputStream(new URL(file).openStream());
1287       }
1288       else
1289       {
1290         jin = new JarInputStream(new FileInputStream(file));
1291       }
1292
1293       JarEntry entry = null;
1294       do
1295       {
1296         entry = jin.getNextJarEntry();
1297       } while (!entry.getName().equals(pdbId));
1298
1299       BufferedReader in = new BufferedReader(new InputStreamReader(jin));
1300       File outFile = File.createTempFile("jalview_pdb", ".txt");
1301       outFile.deleteOnExit();
1302       PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
1303       String data;
1304
1305       while ((data = in.readLine()) != null)
1306       {
1307         out.println(data);
1308       }
1309       out.close();
1310
1311       alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath());
1312       return outFile.getAbsolutePath();
1313
1314     } catch (Exception ex)
1315     {
1316       ex.printStackTrace();
1317     }
1318
1319     return null;
1320   }
1321
1322   AlignFrame LoadFromObject(JalviewModel object, String file,
1323           boolean loadTreesAndStructures)
1324   {
1325     SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
1326     Sequence[] vamsasSeq = vamsasSet.getSequence();
1327
1328     JalviewModelSequence jms = object.getJalviewModelSequence();
1329
1330     Viewport view = jms.getViewport(0);
1331
1332     //////////////////////////////////
1333     //LOAD SEQUENCES
1334
1335     Vector hiddenSeqs = null;
1336     jalview.datamodel.Sequence jseq;
1337
1338     ArrayList tmpseqs = new ArrayList();
1339
1340     boolean multipleView = false;
1341
1342     JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
1343     for (int i = 0; i < JSEQ.length; i++)
1344     {
1345       String seqId = JSEQ[i].getId() + "";
1346
1347       if (seqRefIds.get(seqId) != null)
1348       {
1349         tmpseqs.add((jalview.datamodel.Sequence) seqRefIds.get(seqId));
1350         multipleView = true;
1351       }
1352       else
1353       {
1354         jseq = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
1355                 vamsasSeq[i].getSequence());
1356         jseq.setDescription(vamsasSeq[i].getDescription());
1357         jseq.setStart(JSEQ[i].getStart());
1358         jseq.setEnd(JSEQ[i].getEnd());
1359         jseq.setVamsasId(uniqueSetSuffix + seqId);
1360         seqRefIds.put(vamsasSeq[i].getId(), jseq);
1361         tmpseqs.add(jseq);
1362       }
1363
1364       if (JSEQ[i].getHidden())
1365       {
1366         if (hiddenSeqs == null)
1367         {
1368           hiddenSeqs = new Vector();
1369         }
1370
1371         hiddenSeqs.addElement((jalview.datamodel.Sequence) seqRefIds
1372                 .get(seqId));
1373       }
1374
1375     }
1376
1377     ///
1378     // Create the alignment object from the sequence set
1379     /////////////////////////////////
1380     jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[tmpseqs
1381             .size()];
1382
1383     tmpseqs.toArray(orderedSeqs);
1384
1385     jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(
1386             orderedSeqs);
1387
1388     /// Add the alignment properties
1389     for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
1390     {
1391       SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
1392       al.setProperty(ssp.getKey(), ssp.getValue());
1393     }
1394
1395     ///
1396     // SequenceFeatures are added to the DatasetSequence,
1397     // so we must create or recover the dataset before loading features
1398     /////////////////////////////////
1399     if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
1400     {
1401       // older jalview projects do not have a dataset id.
1402       al.setDataset(null);
1403     }
1404     else
1405     {
1406       recoverDatasetFor(vamsasSet, al);
1407     }
1408     /////////////////////////////////
1409
1410     Hashtable pdbloaded = new Hashtable();
1411     if (!multipleView)
1412     {
1413       for (int i = 0; i < vamsasSeq.length; i++)
1414       {
1415         if (JSEQ[i].getFeaturesCount() > 0)
1416         {
1417           Features[] features = JSEQ[i].getFeatures();
1418           for (int f = 0; f < features.length; f++)
1419           {
1420             jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
1421                     features[f].getType(), features[f].getDescription(),
1422                     features[f].getStatus(), features[f].getBegin(),
1423                     features[f].getEnd(), features[f].getFeatureGroup());
1424
1425             sf.setScore(features[f].getScore());
1426             for (int od = 0; od < features[f].getOtherDataCount(); od++)
1427             {
1428               OtherData keyValue = features[f].getOtherData(od);
1429               if (keyValue.getKey().startsWith("LINK"))
1430               {
1431                 sf.addLink(keyValue.getValue());
1432               }
1433               else
1434               {
1435                 sf.setValue(keyValue.getKey(), keyValue.getValue());
1436               }
1437
1438             }
1439
1440             al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1441           }
1442         }
1443         if (vamsasSeq[i].getDBRefCount() > 0)
1444         {
1445           addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]);
1446         }
1447         if (JSEQ[i].getPdbidsCount() > 0)
1448         {
1449           Pdbids[] ids = JSEQ[i].getPdbids();
1450           for (int p = 0; p < ids.length; p++)
1451           {
1452             jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
1453             entry.setId(ids[p].getId());
1454             entry.setType(ids[p].getType());
1455             if (ids[p].getFile() != null)
1456             {
1457               if (!pdbloaded.containsKey(ids[p].getFile()))
1458               {
1459                 entry.setFile(loadPDBFile(file, ids[p].getId()));
1460               }
1461               else
1462               {
1463                 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1464               }
1465             }
1466
1467             al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1468           }
1469         }
1470       }
1471     }
1472
1473     /////////////////////////////////
1474     // LOAD SEQUENCE MAPPINGS
1475     if (vamsasSet.getAlcodonFrameCount() > 0)
1476     {
1477       AlcodonFrame[] alc = vamsasSet.getAlcodonFrame();
1478       for (int i = 0; i < alc.length; i++)
1479       {
1480         jalview.datamodel.AlignedCodonFrame cf = new jalview.datamodel.AlignedCodonFrame(
1481                 alc[i].getAlcodonCount());
1482         if (alc[i].getAlcodonCount() > 0)
1483         {
1484           Alcodon[] alcods = alc[i].getAlcodon();
1485           for (int p = 0; p < cf.codons.length; p++)
1486           {
1487             cf.codons[p] = new int[3];
1488             cf.codons[p][0] = (int) alcods[p].getPos1();
1489             cf.codons[p][1] = (int) alcods[p].getPos2();
1490             cf.codons[p][2] = (int) alcods[p].getPos3();
1491           }
1492         }
1493         if (alc[i].getAlcodMapCount() > 0)
1494         {
1495           AlcodMap[] maps = alc[i].getAlcodMap();
1496           for (int m = 0; m < maps.length; m++)
1497           {
1498             SequenceI dnaseq = (SequenceI) seqRefIds
1499                     .get(maps[m].getDnasq());
1500             // Load Mapping
1501             // attach to dna sequence reference.
1502             if (dnaseq != null)
1503             {
1504               if (maps[m].getMapping() != null)
1505               {
1506                 jalview.datamodel.Mapping mapping = addMapping(maps[m]
1507                         .getMapping());
1508                 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
1509               }
1510             }
1511           }
1512         }
1513         al.addCodonFrame(cf);
1514       }
1515
1516     }
1517
1518     //////////////////////////////////
1519     //LOAD ANNOTATIONS
1520     boolean hideQuality = true, hideConservation = true, hideConsensus = true;
1521
1522     if (vamsasSet.getAnnotationCount() > 0)
1523     {
1524       Annotation[] an = vamsasSet.getAnnotation();
1525
1526       for (int i = 0; i < an.length; i++)
1527       {
1528         if (an[i].getLabel().equals("Quality"))
1529         {
1530           hideQuality = false;
1531           continue;
1532         }
1533         else if (an[i].getLabel().equals("Conservation"))
1534         {
1535           hideConservation = false;
1536           continue;
1537         }
1538         else if (an[i].getLabel().equals("Consensus"))
1539         {
1540           hideConsensus = false;
1541           continue;
1542         }
1543
1544         if (an[i].getId() != null
1545                 && annotationIds.containsKey(an[i].getId()))
1546         {
1547           jalview.datamodel.AlignmentAnnotation jda = (jalview.datamodel.AlignmentAnnotation) annotationIds
1548                   .get(an[i].getId());
1549           if (an[i].hasVisible())
1550             jda.visible = an[i].getVisible();
1551
1552           al.addAnnotation(jda);
1553
1554           continue;
1555         }
1556
1557         AnnotationElement[] ae = an[i].getAnnotationElement();
1558         jalview.datamodel.Annotation[] anot = null;
1559
1560         if (!an[i].getScoreOnly())
1561         {
1562           anot = new jalview.datamodel.Annotation[al.getWidth()];
1563
1564           for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
1565           {
1566             if (ae[aa].getPosition() >= anot.length)
1567               continue;
1568
1569             anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
1570
1571             ae[aa].getDisplayCharacter(), ae[aa].getDescription(), (ae[aa]
1572                     .getSecondaryStructure() == null || ae[aa]
1573                     .getSecondaryStructure().length() == 0) ? ' ' : ae[aa]
1574                     .getSecondaryStructure().charAt(0), ae[aa].getValue()
1575
1576             );
1577
1578             anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa]
1579                     .getColour());
1580           }
1581         }
1582         jalview.datamodel.AlignmentAnnotation jaa = null;
1583
1584         if (an[i].getGraph())
1585         {
1586           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1587                   an[i].getDescription(), anot, 0, 0, an[i].getGraphType());
1588
1589           jaa.graphGroup = an[i].getGraphGroup();
1590
1591           if (an[i].getThresholdLine() != null)
1592           {
1593             jaa.setThreshold(new jalview.datamodel.GraphLine(an[i]
1594                     .getThresholdLine().getValue(), an[i]
1595                     .getThresholdLine().getLabel(), new java.awt.Color(
1596                     an[i].getThresholdLine().getColour())));
1597
1598           }
1599
1600         }
1601         else
1602         {
1603           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1604                   an[i].getDescription(), anot);
1605         }
1606
1607         if (an[i].getId() != null)
1608         {
1609           annotationIds.put(an[i].getId(), jaa);
1610           jaa.annotationId = an[i].getId();
1611         }
1612
1613         if (an[i].getSequenceRef() != null)
1614         {
1615           if (al.findName(an[i].getSequenceRef()) != null)
1616           {
1617             jaa.createSequenceMapping(al.findName(an[i].getSequenceRef()),
1618                     1, true);
1619             al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
1620           }
1621         }
1622         if (an[i].hasScore())
1623         {
1624           jaa.setScore(an[i].getScore());
1625         }
1626
1627         if (an[i].hasVisible())
1628           jaa.visible = an[i].getVisible();
1629
1630         al.addAnnotation(jaa);
1631       }
1632     }
1633
1634     /////////////////////////
1635     //LOAD GROUPS
1636     if (jms.getJGroupCount() > 0)
1637     {
1638       JGroup[] groups = jms.getJGroup();
1639
1640       for (int i = 0; i < groups.length; i++)
1641       {
1642         ColourSchemeI cs = null;
1643
1644         if (groups[i].getColour() != null)
1645         {
1646           if (groups[i].getColour().startsWith("ucs"))
1647           {
1648             cs = GetUserColourScheme(jms, groups[i].getColour());
1649           }
1650           else
1651           {
1652             cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
1653           }
1654
1655           if (cs != null)
1656           {
1657             cs.setThreshold(groups[i].getPidThreshold(), true);
1658           }
1659         }
1660
1661         Vector seqs = new Vector();
1662
1663         for (int s = 0; s < groups[i].getSeqCount(); s++)
1664         {
1665           String seqId = groups[i].getSeq(s) + "";
1666           jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI) seqRefIds
1667                   .get(seqId);
1668
1669           if (ts != null)
1670           {
1671             seqs.addElement(ts);
1672           }
1673         }
1674
1675         if (seqs.size() < 1)
1676         {
1677           continue;
1678         }
1679
1680         jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
1681                 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
1682                 groups[i].getDisplayText(), groups[i].getColourText(),
1683                 groups[i].getStart(), groups[i].getEnd());
1684
1685         sg
1686                 .setOutlineColour(new java.awt.Color(groups[i]
1687                         .getOutlineColour()));
1688
1689         sg.textColour = new java.awt.Color(groups[i].getTextCol1());
1690         sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
1691         sg.thresholdTextColour = groups[i].getTextColThreshold();
1692
1693         if (groups[i].getConsThreshold() != 0)
1694         {
1695           jalview.analysis.Conservation c = new jalview.analysis.Conservation(
1696                   "All", ResidueProperties.propHash, 3, sg
1697                           .getSequences(null), 0, sg.getWidth() - 1);
1698           c.calculate();
1699           c.verdict(false, 25);
1700           sg.cs.setConservation(c);
1701         }
1702
1703         al.addGroup(sg);
1704       }
1705     }
1706
1707     /////////////////////////////////
1708     // LOAD VIEWPORT
1709
1710     AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
1711
1712     af.setFileName(file, "Jalview");
1713
1714     for (int i = 0; i < JSEQ.length; i++)
1715     {
1716       af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i),
1717               new java.awt.Color(JSEQ[i].getColour()));
1718     }
1719
1720     //If we just load in the same jar file again, the sequenceSetId
1721     //will be the same, and we end up with multiple references
1722     //to the same sequenceSet. We must modify this id on load
1723     //so that each load of the file gives a unique id
1724     String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
1725
1726     af.viewport.gatherViewsHere = view.getGatheredViews();
1727
1728     if (view.getSequenceSetId() != null)
1729     {
1730       jalview.gui.AlignViewport av = (jalview.gui.AlignViewport) viewportsAdded
1731               .get(uniqueSeqSetId);
1732
1733       af.viewport.sequenceSetID = uniqueSeqSetId;
1734       if (av != null)
1735       {
1736
1737         af.viewport.historyList = av.historyList;
1738         af.viewport.redoList = av.redoList;
1739       }
1740       else
1741       {
1742         viewportsAdded.put(uniqueSeqSetId, af.viewport);
1743       }
1744
1745       PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
1746     }
1747     if (hiddenSeqs != null)
1748     {
1749       for (int s = 0; s < JSEQ.length; s++)
1750       {
1751         jalview.datamodel.SequenceGroup hidden = new jalview.datamodel.SequenceGroup();
1752
1753         for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
1754         {
1755           hidden.addSequence(al
1756                   .getSequenceAt(JSEQ[s].getHiddenSequences(r)), false);
1757         }
1758         af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
1759       }
1760
1761       jalview.datamodel.SequenceI[] hseqs = new jalview.datamodel.SequenceI[hiddenSeqs
1762               .size()];
1763
1764       for (int s = 0; s < hiddenSeqs.size(); s++)
1765       {
1766         hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
1767       }
1768
1769       af.viewport.hideSequence(hseqs);
1770
1771     }
1772
1773     if ((hideConsensus || hideQuality || hideConservation)
1774             && al.getAlignmentAnnotation() != null)
1775     {
1776       int hSize = al.getAlignmentAnnotation().length;
1777       for (int h = 0; h < hSize; h++)
1778       {
1779         if ((hideConsensus && al.getAlignmentAnnotation()[h].label
1780                 .equals("Consensus"))
1781                 || (hideQuality && al.getAlignmentAnnotation()[h].label
1782                         .equals("Quality"))
1783                 || (hideConservation && al.getAlignmentAnnotation()[h].label
1784                         .equals("Conservation")))
1785         {
1786           al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
1787           hSize--;
1788           h--;
1789         }
1790       }
1791       af.alignPanel.adjustAnnotationHeight();
1792     }
1793
1794     if (view.getViewName() != null)
1795     {
1796       af.viewport.viewName = view.getViewName();
1797       af.setInitialTabVisible();
1798     }
1799     af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view
1800             .getHeight());
1801
1802     af.viewport.setShowAnnotation(view.getShowAnnotation());
1803     af.viewport.setAbovePIDThreshold(view.getPidSelected());
1804
1805     af.viewport.setColourText(view.getShowColourText());
1806
1807     af.viewport.setConservationSelected(view.getConservationSelected());
1808     af.viewport.setShowJVSuffix(view.getShowFullId());
1809     af.viewport.rightAlignIds = view.getRightAlignIds();
1810     af.viewport.setFont(new java.awt.Font(view.getFontName(), view
1811             .getFontStyle(), view.getFontSize()));
1812     af.alignPanel.fontChanged();
1813     af.viewport.setRenderGaps(view.getRenderGaps());
1814     af.viewport.setWrapAlignment(view.getWrapAlignment());
1815     af.alignPanel.setWrapAlignment(view.getWrapAlignment());
1816     af.viewport.setShowAnnotation(view.getShowAnnotation());
1817     af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
1818
1819     af.viewport.setShowBoxes(view.getShowBoxes());
1820
1821     af.viewport.setShowText(view.getShowText());
1822
1823     af.viewport.textColour = new java.awt.Color(view.getTextCol1());
1824     af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
1825     af.viewport.thresholdTextColour = view.getTextColThreshold();
1826
1827     af.viewport.setStartRes(view.getStartRes());
1828     af.viewport.setStartSeq(view.getStartSeq());
1829
1830     ColourSchemeI cs = null;
1831
1832     if (view.getBgColour() != null)
1833     {
1834       if (view.getBgColour().startsWith("ucs"))
1835       {
1836         cs = GetUserColourScheme(jms, view.getBgColour());
1837       }
1838       else if (view.getBgColour().startsWith("Annotation"))
1839       {
1840         //int find annotation
1841         for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
1842         {
1843           if (af.viewport.alignment.getAlignmentAnnotation()[i].label
1844                   .equals(view.getAnnotationColours().getAnnotation()))
1845           {
1846             if (af.viewport.alignment.getAlignmentAnnotation()[i]
1847                     .getThreshold() == null)
1848             {
1849               af.viewport.alignment.getAlignmentAnnotation()[i]
1850                       .setThreshold(new jalview.datamodel.GraphLine(view
1851                               .getAnnotationColours().getThreshold(),
1852                               "Threshold", java.awt.Color.black)
1853
1854                       );
1855             }
1856
1857             if (view.getAnnotationColours().getColourScheme()
1858                     .equals("None"))
1859             {
1860               cs = new AnnotationColourGradient(af.viewport.alignment
1861                       .getAlignmentAnnotation()[i], new java.awt.Color(view
1862                       .getAnnotationColours().getMinColour()),
1863                       new java.awt.Color(view.getAnnotationColours()
1864                               .getMaxColour()), view.getAnnotationColours()
1865                               .getAboveThreshold());
1866             }
1867             else if (view.getAnnotationColours().getColourScheme()
1868                     .startsWith("ucs"))
1869             {
1870               cs = new AnnotationColourGradient(af.viewport.alignment
1871                       .getAlignmentAnnotation()[i], GetUserColourScheme(
1872                       jms, view.getAnnotationColours().getColourScheme()),
1873                       view.getAnnotationColours().getAboveThreshold());
1874             }
1875             else
1876             {
1877               cs = new AnnotationColourGradient(af.viewport.alignment
1878                       .getAlignmentAnnotation()[i], ColourSchemeProperty
1879                       .getColour(al, view.getAnnotationColours()
1880                               .getColourScheme()), view
1881                       .getAnnotationColours().getAboveThreshold());
1882             }
1883
1884             // Also use these settings for all the groups
1885             if (al.getGroups() != null)
1886             {
1887               for (int g = 0; g < al.getGroups().size(); g++)
1888               {
1889                 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) al
1890                         .getGroups().elementAt(g);
1891
1892                 if (sg.cs == null)
1893                 {
1894                   continue;
1895                 }
1896
1897                 /*    if (view.getAnnotationColours().getColourScheme().equals("None"))
1898                     {
1899                       sg.cs = new AnnotationColourGradient(
1900                           af.viewport.alignment.getAlignmentAnnotation()[i],
1901                           new java.awt.Color(view.getAnnotationColours().
1902                                              getMinColour()),
1903                           new java.awt.Color(view.getAnnotationColours().
1904                                              getMaxColour()),
1905                           view.getAnnotationColours().getAboveThreshold());
1906                     }
1907                     else*/
1908                 {
1909                   sg.cs = new AnnotationColourGradient(
1910                           af.viewport.alignment.getAlignmentAnnotation()[i],
1911                           sg.cs, view.getAnnotationColours()
1912                                   .getAboveThreshold());
1913                 }
1914
1915               }
1916             }
1917
1918             break;
1919           }
1920
1921         }
1922       }
1923       else
1924       {
1925         cs = ColourSchemeProperty.getColour(al, view.getBgColour());
1926       }
1927
1928       if (cs != null)
1929       {
1930         cs.setThreshold(view.getPidThreshold(), true);
1931         cs.setConsensus(af.viewport.hconsensus);
1932       }
1933     }
1934
1935     af.viewport.setGlobalColourScheme(cs);
1936     af.viewport.setColourAppliesToAllGroups(false);
1937
1938     if (view.getConservationSelected() && cs != null)
1939     {
1940       cs.setConservationInc(view.getConsThreshold());
1941     }
1942
1943     af.changeColour(cs);
1944
1945     af.viewport.setColourAppliesToAllGroups(true);
1946
1947     if (view.getShowSequenceFeatures())
1948     {
1949       af.viewport.showSequenceFeatures = true;
1950     }
1951
1952     if (jms.getFeatureSettings() != null)
1953     {
1954       af.viewport.featuresDisplayed = new Hashtable();
1955       String[] renderOrder = new String[jms.getFeatureSettings()
1956               .getSettingCount()];
1957       for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
1958       {
1959         Setting setting = jms.getFeatureSettings().getSetting(fs);
1960
1961         af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
1962                 setting.getType(), new java.awt.Color(setting.getColour()));
1963         renderOrder[fs] = setting.getType();
1964         if (setting.hasOrder())
1965           af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
1966                   setting.getType(), setting.getOrder());
1967         else
1968           af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
1969                   setting.getType(),
1970                   fs / jms.getFeatureSettings().getSettingCount());
1971         if (setting.getDisplay())
1972         {
1973           af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
1974                   setting.getColour()));
1975         }
1976       }
1977       af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
1978       Hashtable fgtable;
1979       af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable();
1980       for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
1981       {
1982         Group grp = jms.getFeatureSettings().getGroup(gs);
1983         fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
1984       }
1985     }
1986
1987     if (view.getHiddenColumnsCount() > 0)
1988     {
1989       for (int c = 0; c < view.getHiddenColumnsCount(); c++)
1990       {
1991         af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view
1992                 .getHiddenColumns(c).getEnd() //+1
1993                 );
1994       }
1995     }
1996
1997     af.setMenusFromViewport(af.viewport);
1998
1999     Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view
2000             .getHeight());
2001
2002     //LOAD TREES
2003     ///////////////////////////////////////
2004     if (loadTreesAndStructures && jms.getTreeCount() > 0)
2005     {
2006       try
2007       {
2008         for (int t = 0; t < jms.getTreeCount(); t++)
2009         {
2010
2011           Tree tree = jms.getTree(t);
2012
2013           TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(tree
2014                   .getNewick()), tree.getTitle(), tree.getWidth(), tree
2015                   .getHeight(), tree.getXpos(), tree.getYpos());
2016
2017           tp.fitToWindow.setState(tree.getFitToWindow());
2018           tp.fitToWindow_actionPerformed(null);
2019
2020           if (tree.getFontName() != null)
2021           {
2022             tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
2023                     .getFontStyle(), tree.getFontSize()));
2024           }
2025           else
2026           {
2027             tp.setTreeFont(new java.awt.Font(view.getFontName(), view
2028                     .getFontStyle(), tree.getFontSize()));
2029           }
2030
2031           tp.showPlaceholders(tree.getMarkUnlinked());
2032           tp.showBootstrap(tree.getShowBootstrap());
2033           tp.showDistances(tree.getShowDistances());
2034
2035           tp.treeCanvas.threshold = tree.getThreshold();
2036
2037           if (tree.getCurrentTree())
2038           {
2039             af.viewport.setCurrentTree(tp.getTree());
2040           }
2041         }
2042
2043       } catch (Exception ex)
2044       {
2045         ex.printStackTrace();
2046       }
2047     }
2048
2049     ////LOAD STRUCTURES
2050     if (loadTreesAndStructures)
2051     {
2052       for (int i = 0; i < JSEQ.length; i++)
2053       {
2054         if (JSEQ[i].getPdbidsCount() > 0)
2055         {
2056           Pdbids[] ids = JSEQ[i].getPdbids();
2057           for (int p = 0; p < ids.length; p++)
2058           {
2059             for (int s = 0; s < ids[p].getStructureStateCount(); s++)
2060             {
2061               jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
2062
2063               jpdb.setFile(loadPDBFile(ids[p].getFile(), ids[p].getId()));
2064               jpdb.setId(ids[p].getId());
2065
2066               int x = ids[p].getStructureState(s).getXpos();
2067               int y = ids[p].getStructureState(s).getYpos();
2068               int width = ids[p].getStructureState(s).getWidth();
2069               int height = ids[p].getStructureState(s).getHeight();
2070
2071               java.awt.Component comp = null;
2072
2073               JInternalFrame[] frames = Desktop.desktop.getAllFrames();
2074               for (int f = 0; f < frames.length; f++)
2075               {
2076                 if (frames[f] instanceof AppJmol)
2077                 {
2078                   if (frames[f].getX() == x && frames[f].getY() == y
2079                           && frames[f].getHeight() == height
2080                           && frames[f].getWidth() == width)
2081                   {
2082                     comp = frames[f];
2083                     break;
2084                   }
2085                 }
2086               }
2087
2088               Desktop.desktop.getComponentAt(x, y);
2089
2090               String pdbFile = loadPDBFile(file, ids[p].getId());
2091
2092               jalview.datamodel.SequenceI[] seq = new jalview.datamodel.SequenceI[]
2093               { (jalview.datamodel.SequenceI) seqRefIds.get(JSEQ[i].getId()
2094                       + "") };
2095
2096               if (comp == null)
2097               {
2098                 String state = ids[p].getStructureState(s).getContent();
2099
2100                 StringBuffer newFileLoc = new StringBuffer(state.substring(
2101                         0, state.indexOf("\"", state.indexOf("load")) + 1));
2102
2103                 newFileLoc.append(jpdb.getFile());
2104                 newFileLoc.append(state.substring(state.indexOf("\"", state
2105                         .indexOf("load \"") + 6)));
2106
2107                 new AppJmol(pdbFile, ids[p].getId(), seq, af.alignPanel,
2108                         newFileLoc.toString(), new java.awt.Rectangle(x, y,
2109                                 width, height));
2110
2111               }
2112               else if (comp != null)
2113               {
2114                 StructureSelectionManager.getStructureSelectionManager()
2115                         .setMapping(seq, null, pdbFile,
2116                                 jalview.io.AppletFormatAdapter.FILE);
2117
2118                 ((AppJmol) comp).addSequence(seq);
2119               }
2120             }
2121           }
2122         }
2123       }
2124     }
2125
2126     return af;
2127   }
2128
2129   private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al)
2130   {
2131     jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId());
2132     Vector dseqs = null;
2133     if (ds == null)
2134     {
2135       // create a list of new dataset sequences
2136       dseqs = new Vector();
2137     }
2138     for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
2139     {
2140       Sequence vamsasSeq = vamsasSet.getSequence(i);
2141       ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs);
2142     }
2143     // create a new dataset
2144     if (ds == null)
2145     {
2146       SequenceI[] dsseqs = new SequenceI[dseqs.size()];
2147       dseqs.copyInto(dsseqs);
2148       ds = new jalview.datamodel.Alignment(dsseqs);
2149       addDatasetRef(vamsasSet.getDatasetId(), ds);
2150     }
2151     // set the dataset for the newly imported alignment.
2152     if (al.getDataset() == null)
2153     {
2154       al.setDataset(ds);
2155     }
2156   }
2157
2158
2159   /**
2160    *
2161    * @param vamsasSeq sequence definition to create/merge dataset sequence for
2162    * @param ds dataset alignment
2163    * @param dseqs vector to add new dataset sequence to
2164    */
2165   private void ensureJalviewDatasetSequence(Sequence vamsasSeq, AlignmentI ds, Vector dseqs)
2166   {
2167     jalview.datamodel.Sequence sq = (jalview.datamodel.Sequence) seqRefIds.get(vamsasSeq.getId());
2168     jalview.datamodel.SequenceI dsq = null;
2169     if (sq!=null && sq.getDatasetSequence()!=null)
2170     {
2171       dsq = (jalview.datamodel.SequenceI) sq.getDatasetSequence();
2172     }
2173
2174     String sqid = vamsasSeq.getDsseqid();
2175     if (dsq==null)
2176     {
2177       // need to create or add a new dataset sequence reference to this sequence
2178       if (sqid != null)
2179       {
2180         dsq = (jalview.datamodel.SequenceI) seqRefIds.get(sqid);
2181       }
2182       // check again
2183       if (dsq == null)
2184       {
2185         // make a new dataset sequence
2186         dsq = sq.createDatasetSequence();
2187         if (sqid == null)
2188         {
2189           // make up a new dataset reference for this sequence
2190           sqid = "" + dsq.hashCode();
2191         }
2192         dsq.setVamsasId(uniqueSetSuffix + sqid);
2193         seqRefIds.put(sqid, dsq);
2194         if (ds == null)
2195         {
2196           if (dseqs!=null)
2197           {
2198             dseqs.addElement(dsq);
2199           }
2200         }
2201         else
2202         {
2203           ds.addSequence(dsq);
2204         }
2205       } else {
2206         // make this dataset sequence sq's dataset sequence
2207         sq.setDatasetSequence(dsq);
2208       }
2209     }
2210     // TODO: refactor this as a merge dataset sequence function
2211     // now check that sq (the dataset sequence) sequence really is the union of all references to it
2212     boolean pre = sq.getStart() < dsq.getStart();
2213     boolean post = sq.getEnd() > dsq.getEnd();
2214     if (pre || post)
2215     {
2216       StringBuffer sb = new StringBuffer();
2217       String newres = jalview.analysis.AlignSeq.extractGaps(
2218               jalview.util.Comparison.GapChars, sq.getSequenceAsString());
2219       synchronized (dsq)
2220       {
2221         sb.append(dsq.getSequence());
2222         if (pre)
2223         {
2224           sb.insert(0, newres
2225                   .substring(0, dsq.getStart() - sq.getStart()));
2226           dsq.setStart(sq.getStart());
2227         }
2228         if (post)
2229         {
2230           sb.append(newres.substring(newres.length() - sq.getEnd()
2231                   - dsq.getEnd()));
2232           dsq.setEnd(sq.getEnd());
2233         }
2234         dsq.setSequence(sb.toString());
2235       }
2236       System.err
2237               .println("DEBUG Notice:  Merged dataset sequence ("
2238                       + (pre ? "prepended" : "") + " "
2239                       + (post ? "appended" : ""));
2240     }
2241   }
2242
2243   java.util.Hashtable datasetIds = null;
2244
2245   private Alignment getDatasetFor(String datasetId)
2246   {
2247     if (datasetIds == null)
2248     {
2249       datasetIds = new Hashtable();
2250       return null;
2251     }
2252     if (datasetIds.containsKey(datasetId))
2253     {
2254       return (Alignment) datasetIds.get(datasetId);
2255     }
2256     return null;
2257   }
2258
2259   private void addDatasetRef(String datasetId, Alignment dataset)
2260   {
2261     if (datasetIds == null)
2262     {
2263       datasetIds = new Hashtable();
2264     }
2265     datasetIds.put(datasetId, dataset);
2266   }
2267
2268   private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
2269   {
2270     for (int d = 0; d < sequence.getDBRefCount(); d++)
2271     {
2272       DBRef dr = sequence.getDBRef(d);
2273       jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
2274               sequence.getDBRef(d).getSource(), sequence.getDBRef(d)
2275                       .getVersion(), sequence.getDBRef(d).getAccessionId());
2276       if (dr.getMapping() != null)
2277       {
2278         entry.setMap(addMapping(dr.getMapping()));
2279       }
2280       datasetSequence.addDBRef(entry);
2281     }
2282   }
2283
2284   private jalview.datamodel.Mapping addMapping(Mapping m)
2285   {
2286     SequenceI dsto = null;
2287     // Mapping m = dr.getMapping();
2288     int fr[] = new int[m.getMapListFromCount() * 2];
2289     Enumeration f = m.enumerateMapListFrom();
2290     for (int _i = 0; f.hasMoreElements(); _i += 2)
2291     {
2292       MapListFrom mf = (MapListFrom) f.nextElement();
2293       fr[_i] = mf.getStart();
2294       fr[_i + 1] = mf.getEnd();
2295     }
2296     int fto[] = new int[m.getMapListToCount() * 2];
2297     f = m.enumerateMapListTo();
2298     for (int _i = 0; f.hasMoreElements(); _i += 2)
2299     {
2300       MapListTo mf = (MapListTo) f.nextElement();
2301       fto[_i] = mf.getStart();
2302       fto[_i + 1] = mf.getEnd();
2303     }
2304     jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto,
2305             fr, fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit());
2306     if (m.getMappingChoice() != null)
2307     {
2308       MappingChoice mc = m.getMappingChoice();
2309       if (mc.getDseqFor() != null)
2310       {
2311         if (seqRefIds.containsKey(mc.getDseqFor()))
2312         {
2313           /**
2314            * recover from hash
2315            */
2316           jmap.setTo((SequenceI) seqRefIds.get(mc.getDseqFor()));
2317         }
2318         else
2319         {
2320           frefedSequence.add(new Object[]
2321           { mc.getDseqFor(), jmap });
2322         }
2323       }
2324       else
2325       {
2326         /**
2327          * local sequence definition
2328          */
2329         Sequence ms = mc.getSequence();
2330         jalview.datamodel.Sequence djs=null;
2331         String sqid = ms.getDsseqid();
2332         if (sqid!=null && sqid.length()>0)
2333         {
2334           /*
2335            * recover dataset sequence
2336            */
2337           djs = (jalview.datamodel.Sequence) seqRefIds.get(sqid);
2338         } else {
2339           System.err.println("Warning - making up dataset sequence id for DbRef sequence map reference");
2340           sqid = ""+ms.hashCode(); // make up a new hascode for undefined dataset sequence hash (unlikely to happen)
2341         }
2342
2343         if (djs==null) {
2344           /**
2345            * make a new dataset sequence and add it to refIds hash
2346            */
2347           djs = new jalview.datamodel.Sequence(ms
2348                 .getName(), ms.getSequence());
2349           djs.setStart(jmap.getMap().getToLowest());
2350           djs.setEnd(jmap.getMap().getToHighest());
2351           djs.setVamsasId(uniqueSetSuffix + sqid);
2352           jmap.setTo(djs);
2353           seqRefIds.put(sqid, djs);
2354
2355         }
2356         jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
2357         addDBRefs(djs, ms);
2358
2359       }
2360     }
2361     return (jmap);
2362
2363   }
2364
2365   public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
2366           boolean keepSeqRefs)
2367   {
2368     jalview.schemabinding.version2.JalviewModel jm = SaveState(ap, null,
2369             null, null);
2370
2371     if (!keepSeqRefs)
2372     {
2373       seqRefIds.clear();
2374       jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
2375     }
2376     else
2377     {
2378       uniqueSetSuffix = "";
2379     }
2380
2381     viewportsAdded = new Hashtable();
2382
2383     AlignFrame af = LoadFromObject(jm, null, false);
2384     af.alignPanels.clear();
2385     af.closeMenuItem_actionPerformed(true);
2386
2387     /*  if(ap.av.alignment.getAlignmentAnnotation()!=null)
2388       {
2389         for(int i=0; i<ap.av.alignment.getAlignmentAnnotation().length; i++)
2390         {
2391           if(!ap.av.alignment.getAlignmentAnnotation()[i].autoCalculated)
2392           {
2393             af.alignPanel.av.alignment.getAlignmentAnnotation()[i] =
2394                 ap.av.alignment.getAlignmentAnnotation()[i];
2395           }
2396         }
2397       }   */
2398
2399     return af.alignPanel;
2400   }
2401 }