src/jalview/gui/Jalview2XML.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
   3  * Copyright (C) 2008 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.awt.Rectangle;
  22 import java.io.*;
  23 import java.net.*;
  24 import java.util.*;
  25 import java.util.jar.*;
  26
  27 import javax.swing.*;
  28
  29 import org.exolab.castor.xml.*;
  30
  31 import uk.ac.vamsas.objects.utils.MapList;
  32 import jalview.bin.Cache;
  33 import jalview.datamodel.Alignment;
  34 import jalview.datamodel.AlignmentI;
  35 import jalview.datamodel.SequenceI;
  36 import jalview.schemabinding.version2.*;
  37 import jalview.schemes.*;
  38 import jalview.structure.StructureSelectionManager;
  39 import jalview.util.jarInputStreamProvider;
  40
  41 /**
  42  * Write out the current jalview desktop state as a Jalview XML stream.
  43  *
  44  * Note: the vamsas objects referred to here are primitive versions of the
  45  * VAMSAS project schema elements - they are not the same and most likely never
  46  * will be :)
  47  *
  48  * @author $author$
  49  * @version $Revision$
  50  */
  51 public class Jalview2XML
  52 {
  53   /**
  54    * create/return unique hash string for sq
  55    *
  56    * @param sq
  57    * @return new or existing unique string for sq
  58    */
  59   String seqHash(SequenceI sq)
  60   {
  61     if (seqsToIds == null)
  62     {
  63       initSeqRefs();
  64     }
  65     if (seqsToIds.containsKey(sq))
  66     {
  67       return (String) seqsToIds.get(sq);
  68     }
  69     else
  70     {
  71       // create sequential key
  72       String key = "sq" + (seqsToIds.size() + 1);
  73       key = makeHashCode(sq, key); // check we don't have an external reference
  74       // for it already.
  75       seqsToIds.put(sq, key);
  76       return key;
  77     }
  78   }
  79
  80   void clearSeqRefs()
  81   {
  82     if (_cleartables)
  83     {
  84       if (seqRefIds != null)
  85       {
  86         seqRefIds.clear();
  87       }
  88       if (seqsToIds != null)
  89       {
  90         seqsToIds.clear();
  91       }
  92       // seqRefIds = null;
  93       // seqsToIds = null;
  94     }
  95     else
  96     {
  97       // do nothing
  98       warn("clearSeqRefs called when _cleartables was not set. Doing nothing.");
  99       // seqRefIds = new Hashtable();
 100       // seqsToIds = new IdentityHashMap();
 101     }
 102   }
 103
 104   void initSeqRefs()
 105   {
 106     if (seqsToIds == null)
 107     {
 108       seqsToIds = new IdentityHashMap();
 109     }
 110     if (seqRefIds == null)
 111     {
 112       seqRefIds = new Hashtable();
 113     }
 114   }
 115
 116   /**
 117    * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps
 118    * of sequence objects are created.
 119    */
 120   java.util.IdentityHashMap seqsToIds = null;
 121
 122   /**
 123    * jalview XML Sequence ID to jalview sequence object reference (both dataset
 124    * and alignment sequences. Populated as XML reps of sequence objects are
 125    * created.)
 126    */
 127   java.util.Hashtable seqRefIds = null; // key->SequenceI resolution
 128
 129   Vector frefedSequence = null;
 130
 131   boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
 132
 133   public Jalview2XML()
 134   {
 135   }
 136
 137   public Jalview2XML(boolean raiseGUI)
 138   {
 139     this.raiseGUI = raiseGUI;
 140   }
 141
 142   public void resolveFrefedSequences()
 143   {
 144     if (frefedSequence.size() > 0)
 145     {
 146       int r = 0, rSize = frefedSequence.size();
 147       while (r < rSize)
 148       {
 149         Object[] ref = (Object[]) frefedSequence.elementAt(r);
 150         if (ref != null)
 151         {
 152           String sref = (String) ref[0];
 153           if (seqRefIds.containsKey(sref))
 154           {
 155             if (ref[1] instanceof jalview.datamodel.Mapping)
 156             {
 157               SequenceI seq = (SequenceI) seqRefIds.get(sref);
 158               while (seq.getDatasetSequence() != null)
 159               {
 160                 seq = seq.getDatasetSequence();
 161               }
 162               ((jalview.datamodel.Mapping) ref[1]).setTo(seq);
 163             }
 164             else
 165             {
 166               if (ref[1] instanceof jalview.datamodel.AlignedCodonFrame)
 167               {
 168                 SequenceI seq = (SequenceI) seqRefIds.get(sref);
 169                 while (seq.getDatasetSequence() != null)
 170                 {
 171                   seq = seq.getDatasetSequence();
 172                 }
 173                 if (ref[2] != null
 174                         && ref[2] instanceof jalview.datamodel.Mapping)
 175                 {
 176                   jalview.datamodel.Mapping mp = (jalview.datamodel.Mapping) ref[2];
 177                   ((jalview.datamodel.AlignedCodonFrame) ref[1]).addMap(
 178                           seq, mp.getTo(), mp.getMap());
 179                 }
 180                 else
 181                 {
 182                   System.err
 183                           .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for AlcodonFrames involving "
 184                                   + ref[2].getClass() + " type objects.");
 185                 }
 186               }
 187               else
 188               {
 189                 System.err
 190                         .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for "
 191                                 + ref[1].getClass() + " type objects.");
 192               }
 193             }
 194             frefedSequence.remove(r);
 195             rSize--;
 196           }
 197           else
 198           {
 199             System.err
 200                     .println("IMPLEMENTATION WARNING: Unresolved forward reference for hash string "
 201                             + ref[0]
 202                             + " with objecttype "
 203                             + ref[1].getClass());
 204             r++;
 205           }
 206         }
 207         else
 208         {
 209           // empty reference
 210           frefedSequence.remove(r);
 211           rSize--;
 212         }
 213       }
 214     }
 215   }
 216
 217   /**
 218    * This maintains a list of viewports, the key being the seqSetId. Important
 219    * to set historyItem and redoList for multiple views
 220    */
 221   Hashtable viewportsAdded;
 222
 223   Hashtable annotationIds = new Hashtable();
 224
 225   String uniqueSetSuffix = "";
 226
 227   /**
 228    * List of pdbfiles added to Jar
 229    */
 230   Vector pdbfiles = null;
 231
 232   // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
 233   public void SaveState(File statefile)
 234   {
 235     try
 236     {
 237       FileOutputStream fos = new FileOutputStream(statefile);
 238       JarOutputStream jout = new JarOutputStream(fos);
 239       SaveState(jout);
 240
 241     } catch (Exception e)
 242     {
 243       // TODO: inform user of the problem - they need to know if their data was
 244       // not saved !
 245       if (errorMessage == null)
 246       {
 247         errorMessage = "Couldn't write Jalview Archive to output file '"
 248                 + statefile + "' - See console error log for details";
 249       }
 250       else
 251       {
 252         errorMessage += "(output file was '" + statefile + "')";
 253       }
 254       e.printStackTrace();
 255     }
 256     reportErrors();
 257   }
 258
 259   /**
 260    * Writes a jalview project archive to the given Jar output stream.
 261    *
 262    * @param jout
 263    */
 264   public void SaveState(JarOutputStream jout)
 265   {
 266     JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 267
 268     if (frames == null)
 269     {
 270       return;
 271     }
 272
 273     try
 274     {
 275
 276       // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
 277       // //////////////////////////////////////////////////
 278       // NOTE ALSO new PrintWriter must be used for each new JarEntry
 279       PrintWriter out = null;
 280
 281       Vector shortNames = new Vector();
 282
 283       // REVERSE ORDER
 284       for (int i = frames.length - 1; i > -1; i--)
 285       {
 286         if (frames[i] instanceof AlignFrame)
 287         {
 288           AlignFrame af = (AlignFrame) frames[i];
 289           // skip ?
 290           if (skipList != null
 291                   && skipList.containsKey(af.getViewport()
 292                           .getSequenceSetId()))
 293           {
 294             continue;
 295           }
 296
 297           String shortName = af.getTitle();
 298
 299           if (shortName.indexOf(File.separatorChar) > -1)
 300           {
 301             shortName = shortName.substring(shortName
 302                     .lastIndexOf(File.separatorChar) + 1);
 303           }
 304
 305           int count = 1;
 306
 307           while (shortNames.contains(shortName))
 308           {
 309             if (shortName.endsWith("_" + (count - 1)))
 310             {
 311               shortName = shortName
 312                       .substring(0, shortName.lastIndexOf("_"));
 313             }
 314
 315             shortName = shortName.concat("_" + count);
 316             count++;
 317           }
 318
 319           shortNames.addElement(shortName);
 320
 321           if (!shortName.endsWith(".xml"))
 322           {
 323             shortName = shortName + ".xml";
 324           }
 325
 326           int ap, apSize = af.alignPanels.size();
 327           for (ap = 0; ap < apSize; ap++)
 328           {
 329             AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
 330                     .elementAt(ap);
 331             String fileName = apSize == 1 ? shortName : ap + shortName;
 332             if (!fileName.endsWith(".xml"))
 333             {
 334               fileName = fileName + ".xml";
 335             }
 336
 337             SaveState(apanel, fileName, jout);
 338           }
 339         }
 340       }
 341       try
 342       {
 343         jout.flush();
 344       } catch (Exception foo)
 345       {
 346       }
 347       ;
 348       jout.close();
 349     } catch (Exception ex)
 350     {
 351       // TODO: inform user of the problem - they need to know if their data was
 352       // not saved !
 353       if (errorMessage == null)
 354       {
 355         errorMessage = "Couldn't write Jalview Archive - see error output for details";
 356       }
 357       ex.printStackTrace();
 358     }
 359   }
 360
 361   // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
 362   public boolean SaveAlignment(AlignFrame af, String jarFile,
 363           String fileName)
 364   {
 365     try
 366     {
 367       int ap, apSize = af.alignPanels.size();
 368       FileOutputStream fos = new FileOutputStream(jarFile);
 369       JarOutputStream jout = new JarOutputStream(fos);
 370       for (ap = 0; ap < apSize; ap++)
 371       {
 372         AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
 373                 .elementAt(ap);
 374         String jfileName = apSize == 1 ? fileName : fileName + ap;
 375         if (!jfileName.endsWith(".xml"))
 376         {
 377           jfileName = jfileName + ".xml";
 378         }
 379         SaveState(apanel, jfileName, jout);
 380       }
 381
 382       try
 383       {
 384         jout.flush();
 385       } catch (Exception foo)
 386       {
 387       }
 388       ;
 389       jout.close();
 390       return true;
 391     } catch (Exception ex)
 392     {
 393       errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details";
 394       ex.printStackTrace();
 395       return false;
 396     }
 397   }
 398
 399   /**
 400    * create a JalviewModel from an algnment view and marshall it to a
 401    * JarOutputStream
 402    *
 403    * @param ap
 404    *                panel to create jalview model for
 405    * @param fileName
 406    *                name of alignment panel written to output stream
 407    * @param jout
 408    *                jar output stream
 409    * @param out
 410    *                jar entry name
 411    */
 412   public JalviewModel SaveState(AlignmentPanel ap, String fileName,
 413           JarOutputStream jout)
 414   {
 415     initSeqRefs();
 416
 417     Vector userColours = new Vector();
 418
 419     AlignViewport av = ap.av;
 420
 421     JalviewModel object = new JalviewModel();
 422     object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
 423
 424     object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
 425     object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
 426
 427     jalview.datamodel.AlignmentI jal = av.alignment;
 428
 429     if (av.hasHiddenRows)
 430     {
 431       jal = jal.getHiddenSequences().getFullAlignment();
 432     }
 433
 434     SequenceSet vamsasSet = new SequenceSet();
 435     Sequence vamsasSeq;
 436     JalviewModelSequence jms = new JalviewModelSequence();
 437
 438     vamsasSet.setGapChar(jal.getGapCharacter() + "");
 439
 440     if (jal.getDataset() != null)
 441     {
 442       // dataset id is the dataset's hashcode
 443       vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset()));
 444     }
 445     if (jal.getProperties() != null)
 446     {
 447       Enumeration en = jal.getProperties().keys();
 448       while (en.hasMoreElements())
 449       {
 450         String key = en.nextElement().toString();
 451         SequenceSetProperties ssp = new SequenceSetProperties();
 452         ssp.setKey(key);
 453         ssp.setValue(jal.getProperties().get(key).toString());
 454         vamsasSet.addSequenceSetProperties(ssp);
 455       }
 456     }
 457
 458     JSeq jseq;
 459
 460     // SAVE SEQUENCES
 461     String id = "";
 462     jalview.datamodel.SequenceI jds;
 463     for (int i = 0; i < jal.getHeight(); i++)
 464     {
 465       jds = jal.getSequenceAt(i);
 466       id = seqHash(jds);
 467
 468       if (seqRefIds.get(id) != null)
 469       {
 470         // This happens for two reasons: 1. multiple views are being serialised.
 471         // 2. the hashCode has collided with another sequence's code. This DOES
 472         // HAPPEN! (PF00072.15.stk does this)
 473         // JBPNote: Uncomment to debug writing out of files that do not read
 474         // back in due to ArrayOutOfBoundExceptions.
 475         // System.err.println("vamsasSeq backref: "+id+"");
 476         // System.err.println(jds.getName()+"
 477         // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
 478         // System.err.println("Hashcode: "+seqHash(jds));
 479         // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
 480         // System.err.println(rsq.getName()+"
 481         // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
 482         // System.err.println("Hashcode: "+seqHash(rsq));
 483       }
 484       else
 485       {
 486         vamsasSeq = createVamsasSequence(id, jds);
 487         vamsasSet.addSequence(vamsasSeq);
 488         seqRefIds.put(id, jds);
 489       }
 490
 491       jseq = new JSeq();
 492       jseq.setStart(jds.getStart());
 493       jseq.setEnd(jds.getEnd());
 494       jseq.setColour(av.getSequenceColour(jds).getRGB());
 495
 496       jseq.setId(id); // jseq id should be a string not a number
 497
 498       if (av.hasHiddenRows)
 499       {
 500         jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
 501
 502         if (av.hiddenRepSequences != null
 503                 && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
 504         {
 505           jalview.datamodel.SequenceI[] reps = ((jalview.datamodel.SequenceGroup) av.hiddenRepSequences
 506                   .get(jal.getSequenceAt(i))).getSequencesInOrder(jal);
 507
 508           for (int h = 0; h < reps.length; h++)
 509           {
 510             if (reps[h] != jal.getSequenceAt(i))
 511             {
 512               jseq.addHiddenSequences(jal.findIndex(reps[h]));
 513             }
 514           }
 515         }
 516       }
 517
 518       if (jds.getDatasetSequence().getSequenceFeatures() != null)
 519       {
 520         jalview.datamodel.SequenceFeature[] sf = jds.getDatasetSequence()
 521                 .getSequenceFeatures();
 522         int index = 0;
 523         while (index < sf.length)
 524         {
 525           Features features = new Features();
 526
 527           features.setBegin(sf[index].getBegin());
 528           features.setEnd(sf[index].getEnd());
 529           features.setDescription(sf[index].getDescription());
 530           features.setType(sf[index].getType());
 531           features.setFeatureGroup(sf[index].getFeatureGroup());
 532           features.setScore(sf[index].getScore());
 533           if (sf[index].links != null)
 534           {
 535             for (int l = 0; l < sf[index].links.size(); l++)
 536             {
 537               OtherData keyValue = new OtherData();
 538               keyValue.setKey("LINK_" + l);
 539               keyValue.setValue(sf[index].links.elementAt(l).toString());
 540               features.addOtherData(keyValue);
 541             }
 542           }
 543           if (sf[index].otherDetails != null)
 544           {
 545             String key;
 546             Enumeration keys = sf[index].otherDetails.keys();
 547             while (keys.hasMoreElements())
 548             {
 549               key = keys.nextElement().toString();
 550               OtherData keyValue = new OtherData();
 551               keyValue.setKey(key);
 552               keyValue.setValue(sf[index].otherDetails.get(key).toString());
 553               features.addOtherData(keyValue);
 554             }
 555           }
 556
 557           jseq.addFeatures(features);
 558           index++;
 559         }
 560       }
 561
 562       if (jds.getDatasetSequence().getPDBId() != null)
 563       {
 564         Enumeration en = jds.getDatasetSequence().getPDBId().elements();
 565         while (en.hasMoreElements())
 566         {
 567           Pdbids pdb = new Pdbids();
 568           jalview.datamodel.PDBEntry entry = (jalview.datamodel.PDBEntry) en
 569                   .nextElement();
 570
 571           pdb.setId(entry.getId());
 572           pdb.setType(entry.getType());
 573
 574           AppJmol jmol;
 575           // This must have been loaded, is it still visible?
 576           JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 577           for (int f = frames.length - 1; f > -1; f--)
 578           {
 579             if (frames[f] instanceof AppJmol)
 580             {
 581               jmol = (AppJmol) frames[f];
 582               if (!jmol.pdbentry.getId().equals(entry.getId())
 583                       && !(entry.getId().length()>4
 584                               && entry.getId().startsWith(jmol.pdbentry.getId())))
 585                 continue;
 586
 587               StructureState state = new StructureState();
 588               state.setVisible(true);
 589               state.setXpos(jmol.getX());
 590               state.setYpos(jmol.getY());
 591               state.setWidth(jmol.getWidth());
 592               state.setHeight(jmol.getHeight());
 593               state.setViewId(jmol.getViewId());
 594               String statestring = jmol.viewer.getStateInfo();
 595               if (state != null)
 596               {
 597                 state.setContent(statestring.replaceAll("\n", ""));
 598               }
 599               for (int s = 0; s < jmol.sequence.length; s++)
 600               {
 601                 if (jal.findIndex(jmol.sequence[s]) > -1)
 602                 {
 603                   pdb.addStructureState(state);
 604                 }
 605               }
 606             }
 607           }
 608
 609           if (entry.getFile() != null)
 610           {
 611             pdb.setFile(entry.getFile());
 612             if (pdbfiles == null)
 613             {
 614               pdbfiles = new Vector();
 615             }
 616
 617             if (!pdbfiles.contains(entry.getId()))
 618             {
 619               pdbfiles.addElement(entry.getId());
 620               try
 621               {
 622                 File file = new File(entry.getFile());
 623                 if (file.exists() && jout != null)
 624                 {
 625                   byte[] data = new byte[(int) file.length()];
 626                   jout.putNextEntry(new JarEntry(entry.getId()));
 627                   DataInputStream dis = new DataInputStream(
 628                           new FileInputStream(file));
 629                   dis.readFully(data);
 630
 631                   DataOutputStream dout = new DataOutputStream(jout);
 632                   dout.write(data, 0, data.length);
 633                   dout.flush();
 634                   jout.closeEntry();
 635                 }
 636               } catch (Exception ex)
 637               {
 638                 ex.printStackTrace();
 639               }
 640
 641             }
 642           }
 643
 644           if (entry.getProperty() != null)
 645           {
 646             PdbentryItem item = new PdbentryItem();
 647             Hashtable properties = entry.getProperty();
 648             Enumeration en2 = properties.keys();
 649             while (en2.hasMoreElements())
 650             {
 651               Property prop = new Property();
 652               String key = en2.nextElement().toString();
 653               prop.setName(key);
 654               prop.setValue(properties.get(key).toString());
 655               item.addProperty(prop);
 656             }
 657             pdb.addPdbentryItem(item);
 658           }
 659
 660           jseq.addPdbids(pdb);
 661         }
 662       }
 663
 664       jms.addJSeq(jseq);
 665     }
 666
 667     if (av.hasHiddenRows)
 668     {
 669       jal = av.alignment;
 670     }
 671     // SAVE MAPPINGS
 672     if (jal.getCodonFrames() != null && jal.getCodonFrames().length > 0)
 673     {
 674       jalview.datamodel.AlignedCodonFrame[] jac = jal.getCodonFrames();
 675       for (int i = 0; i < jac.length; i++)
 676       {
 677         AlcodonFrame alc = new AlcodonFrame();
 678         vamsasSet.addAlcodonFrame(alc);
 679         for (int p = 0; p < jac[i].aaWidth; p++)
 680         {
 681           Alcodon cmap = new Alcodon();
 682           if (jac[i].codons[p]!=null)
 683           {
 684             // Null codons indicate a gapped column in the translated peptide alignment.
 685             cmap.setPos1(jac[i].codons[p][0]);
 686             cmap.setPos2(jac[i].codons[p][1]);
 687             cmap.setPos3(jac[i].codons[p][2]);
 688           }
 689           alc.addAlcodon(cmap);
 690         }
 691         if (jac[i].getProtMappings() != null
 692                 && jac[i].getProtMappings().length > 0)
 693         {
 694           SequenceI[] dnas = jac[i].getdnaSeqs();
 695           jalview.datamodel.Mapping[] pmaps = jac[i].getProtMappings();
 696           for (int m = 0; m < pmaps.length; m++)
 697           {
 698             AlcodMap alcmap = new AlcodMap();
 699             alcmap.setDnasq(seqHash(dnas[m]));
 700             alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
 701                     false));
 702             alc.addAlcodMap(alcmap);
 703           }
 704         }
 705       }
 706     }
 707
 708     // SAVE TREES
 709     // /////////////////////////////////
 710     if (av.currentTree != null)
 711     {
 712       // FIND ANY ASSOCIATED TREES
 713       // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
 714       if (Desktop.desktop != null)
 715       {
 716         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 717
 718         for (int t = 0; t < frames.length; t++)
 719         {
 720           if (frames[t] instanceof TreePanel)
 721           {
 722             TreePanel tp = (TreePanel) frames[t];
 723
 724             if (tp.treeCanvas.av.alignment == jal)
 725             {
 726               Tree tree = new Tree();
 727               tree.setTitle(tp.getTitle());
 728               tree.setCurrentTree((av.currentTree == tp.getTree()));
 729               tree.setNewick(tp.getTree().toString());
 730               tree.setThreshold(tp.treeCanvas.threshold);
 731
 732               tree.setFitToWindow(tp.fitToWindow.getState());
 733               tree.setFontName(tp.getTreeFont().getName());
 734               tree.setFontSize(tp.getTreeFont().getSize());
 735               tree.setFontStyle(tp.getTreeFont().getStyle());
 736               tree.setMarkUnlinked(tp.placeholdersMenu.getState());
 737
 738               tree.setShowBootstrap(tp.bootstrapMenu.getState());
 739               tree.setShowDistances(tp.distanceMenu.getState());
 740
 741               tree.setHeight(tp.getHeight());
 742               tree.setWidth(tp.getWidth());
 743               tree.setXpos(tp.getX());
 744               tree.setYpos(tp.getY());
 745               tree.setId(makeHashCode(tp, null));
 746               jms.addTree(tree);
 747             }
 748           }
 749         }
 750       }
 751     }
 752
 753     // SAVE ANNOTATIONS
 754     if (jal.getAlignmentAnnotation() != null)
 755     {
 756       jalview.datamodel.AlignmentAnnotation[] aa = jal
 757               .getAlignmentAnnotation();
 758
 759       for (int i = 0; i < aa.length; i++)
 760       {
 761         Annotation an = new Annotation();
 762
 763         if (aa[i].annotationId != null)
 764         {
 765           annotationIds.put(aa[i].annotationId, aa[i]);
 766         }
 767
 768         an.setId(aa[i].annotationId);
 769
 770         if (aa[i] == av.quality || aa[i] == av.conservation
 771                 || aa[i] == av.consensus)
 772         {
 773           an.setLabel(aa[i].label);
 774           an.setGraph(true);
 775           vamsasSet.addAnnotation(an);
 776           continue;
 777         }
 778
 779         an.setVisible(aa[i].visible);
 780
 781         an.setDescription(aa[i].description);
 782
 783         if (aa[i].sequenceRef != null)
 784         {
 785           // TODO later annotation sequenceRef should be the XML ID of the
 786           // sequence rather than its display name
 787           an.setSequenceRef(aa[i].sequenceRef.getName());
 788         }
 789
 790         if (aa[i].graph > 0)
 791         {
 792           an.setGraph(true);
 793           an.setGraphType(aa[i].graph);
 794           an.setGraphGroup(aa[i].graphGroup);
 795           if (aa[i].getThreshold() != null)
 796           {
 797             ThresholdLine line = new ThresholdLine();
 798             line.setLabel(aa[i].getThreshold().label);
 799             line.setValue(aa[i].getThreshold().value);
 800             line.setColour(aa[i].getThreshold().colour.getRGB());
 801             an.setThresholdLine(line);
 802           }
 803         }
 804         else
 805         {
 806           an.setGraph(false);
 807         }
 808
 809         an.setLabel(aa[i].label);
 810         if (aa[i].hasScore())
 811         {
 812           an.setScore(aa[i].getScore());
 813         }
 814         AnnotationElement ae;
 815         if (aa[i].annotations != null)
 816         {
 817           an.setScoreOnly(false);
 818           for (int a = 0; a < aa[i].annotations.length; a++)
 819           {
 820             if ((aa[i] == null) || (aa[i].annotations[a] == null))
 821             {
 822               continue;
 823             }
 824
 825             ae = new AnnotationElement();
 826             if (aa[i].annotations[a].description != null)
 827               ae.setDescription(aa[i].annotations[a].description);
 828             if (aa[i].annotations[a].displayCharacter != null)
 829               ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
 830
 831             if (!Float.isNaN(aa[i].annotations[a].value))
 832               ae.setValue(aa[i].annotations[a].value);
 833
 834             ae.setPosition(a);
 835             if (aa[i].annotations[a].secondaryStructure != ' '
 836                     && aa[i].annotations[a].secondaryStructure != '\0')
 837               ae
 838                       .setSecondaryStructure(aa[i].annotations[a].secondaryStructure
 839                               + "");
 840
 841             if (aa[i].annotations[a].colour != null
 842                     && aa[i].annotations[a].colour != java.awt.Color.black)
 843             {
 844               ae.setColour(aa[i].annotations[a].colour.getRGB());
 845             }
 846
 847             an.addAnnotationElement(ae);
 848           }
 849         }
 850         else
 851         {
 852           an.setScoreOnly(true);
 853         }
 854         vamsasSet.addAnnotation(an);
 855       }
 856     }
 857
 858     // SAVE GROUPS
 859     if (jal.getGroups() != null)
 860     {
 861       JGroup[] groups = new JGroup[jal.getGroups().size()];
 862
 863       for (int i = 0; i < groups.length; i++)
 864       {
 865         groups[i] = new JGroup();
 866
 867         jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal
 868                 .getGroups().elementAt(i);
 869         groups[i].setStart(sg.getStartRes());
 870         groups[i].setEnd(sg.getEndRes());
 871         groups[i].setName(sg.getName()); // TODO later sequence group should
 872         // specify IDs of sequences, not just
 873         // names
 874         if (sg.cs != null)
 875         {
 876           if (sg.cs.conservationApplied())
 877           {
 878             groups[i].setConsThreshold(sg.cs.getConservationInc());
 879
 880             if (sg.cs instanceof jalview.schemes.UserColourScheme)
 881             {
 882               groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
 883                       jms));
 884             }
 885             else
 886             {
 887               groups[i]
 888                       .setColour(ColourSchemeProperty.getColourName(sg.cs));
 889             }
 890           }
 891           else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
 892           {
 893             groups[i]
 894                     .setColour(ColourSchemeProperty
 895                             .getColourName(((jalview.schemes.AnnotationColourGradient) sg.cs)
 896                                     .getBaseColour()));
 897           }
 898           else if (sg.cs instanceof jalview.schemes.UserColourScheme)
 899           {
 900             groups[i]
 901                     .setColour(SetUserColourScheme(sg.cs, userColours, jms));
 902           }
 903           else
 904           {
 905             groups[i].setColour(ColourSchemeProperty.getColourName(sg.cs));
 906           }
 907
 908           groups[i].setPidThreshold(sg.cs.getThreshold());
 909         }
 910
 911         groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
 912         groups[i].setDisplayBoxes(sg.getDisplayBoxes());
 913         groups[i].setDisplayText(sg.getDisplayText());
 914         groups[i].setColourText(sg.getColourText());
 915         groups[i].setTextCol1(sg.textColour.getRGB());
 916         groups[i].setTextCol2(sg.textColour2.getRGB());
 917         groups[i].setTextColThreshold(sg.thresholdTextColour);
 918
 919         for (int s = 0; s < sg.getSize(); s++)
 920         {
 921           jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg
 922                   .getSequenceAt(s);
 923           groups[i].addSeq(seqHash(seq));
 924         }
 925       }
 926
 927       jms.setJGroup(groups);
 928     }
 929
 930     // /////////SAVE VIEWPORT
 931     Viewport view = new Viewport();
 932     view.setTitle(ap.alignFrame.getTitle());
 933     view.setSequenceSetId(makeHashCode(av.getSequenceSetId(), av
 934             .getSequenceSetId()));
 935     view.setId(av.getViewId());
 936     view.setViewName(av.viewName);
 937     view.setGatheredViews(av.gatherViewsHere);
 938
 939     if (ap.av.explodedPosition != null)
 940     {
 941       view.setXpos(av.explodedPosition.x);
 942       view.setYpos(av.explodedPosition.y);
 943       view.setWidth(av.explodedPosition.width);
 944       view.setHeight(av.explodedPosition.height);
 945     }
 946     else
 947     {
 948       view.setXpos(ap.alignFrame.getBounds().x);
 949       view.setYpos(ap.alignFrame.getBounds().y);
 950       view.setWidth(ap.alignFrame.getBounds().width);
 951       view.setHeight(ap.alignFrame.getBounds().height);
 952     }
 953
 954     view.setStartRes(av.startRes);
 955     view.setStartSeq(av.startSeq);
 956
 957     if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
 958     {
 959       view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
 960               userColours, jms));
 961     }
 962     else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
 963     {
 964       jalview.schemes.AnnotationColourGradient acg = (jalview.schemes.AnnotationColourGradient) av
 965               .getGlobalColourScheme();
 966
 967       AnnotationColours ac = new AnnotationColours();
 968       ac.setAboveThreshold(acg.getAboveThreshold());
 969       ac.setThreshold(acg.getAnnotationThreshold());
 970       ac.setAnnotation(acg.getAnnotation());
 971       if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
 972       {
 973         ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
 974                 userColours, jms));
 975       }
 976       else
 977       {
 978         ac.setColourScheme(ColourSchemeProperty.getColourName(acg
 979                 .getBaseColour()));
 980       }
 981
 982       ac.setMaxColour(acg.getMaxColour().getRGB());
 983       ac.setMinColour(acg.getMinColour().getRGB());
 984       view.setAnnotationColours(ac);
 985       view.setBgColour("AnnotationColourGradient");
 986     }
 987     else
 988     {
 989       view.setBgColour(ColourSchemeProperty.getColourName(av
 990               .getGlobalColourScheme()));
 991     }
 992
 993     ColourSchemeI cs = av.getGlobalColourScheme();
 994
 995     if (cs != null)
 996     {
 997       if (cs.conservationApplied())
 998       {
 999         view.setConsThreshold(cs.getConservationInc());
1000         if (cs instanceof jalview.schemes.UserColourScheme)
1001         {
1002           view.setBgColour(SetUserColourScheme(cs, userColours, jms));
1003         }
1004       }
1005
1006       if (cs instanceof ResidueColourScheme)
1007       {
1008         view.setPidThreshold(cs.getThreshold());
1009       }
1010     }
1011
1012     view.setConservationSelected(av.getConservationSelected());
1013     view.setPidSelected(av.getAbovePIDThreshold());
1014     view.setFontName(av.font.getName());
1015     view.setFontSize(av.font.getSize());
1016     view.setFontStyle(av.font.getStyle());
1017     view.setRenderGaps(av.renderGaps);
1018     view.setShowAnnotation(av.getShowAnnotation());
1019     view.setShowBoxes(av.getShowBoxes());
1020     view.setShowColourText(av.getColourText());
1021     view.setShowFullId(av.getShowJVSuffix());
1022     view.setRightAlignIds(av.rightAlignIds);
1023     view.setShowSequenceFeatures(av.showSequenceFeatures);
1024     view.setShowText(av.getShowText());
1025     view.setWrapAlignment(av.getWrapAlignment());
1026     view.setTextCol1(av.textColour.getRGB());
1027     view.setTextCol2(av.textColour2.getRGB());
1028     view.setTextColThreshold(av.thresholdTextColour);
1029
1030     if (av.featuresDisplayed != null)
1031     {
1032       jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
1033
1034       String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
1035
1036       Vector settingsAdded = new Vector();
1037       for (int ro = 0; ro < renderOrder.length; ro++)
1038       {
1039         Setting setting = new Setting();
1040         setting.setType(renderOrder[ro]);
1041         setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
1042                 .getColour(renderOrder[ro]).getRGB());
1043
1044         setting.setDisplay(av.featuresDisplayed
1045                 .containsKey(renderOrder[ro]));
1046         float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
1047                 renderOrder[ro]);
1048         if (rorder > -1)
1049         {
1050           setting.setOrder(rorder);
1051         }
1052         fs.addSetting(setting);
1053         settingsAdded.addElement(renderOrder[ro]);
1054       }
1055
1056       // Make sure we save none displayed feature settings
1057       Enumeration en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
1058               .keys();
1059       while (en.hasMoreElements())
1060       {
1061         String key = en.nextElement().toString();
1062         if (settingsAdded.contains(key))
1063         {
1064           continue;
1065         }
1066
1067         Setting setting = new Setting();
1068         setting.setType(key);
1069         setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
1070                 .getColour(key).getRGB());
1071
1072         setting.setDisplay(false);
1073         float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
1074                 key);
1075         if (rorder > -1)
1076         {
1077           setting.setOrder(rorder);
1078         }
1079         fs.addSetting(setting);
1080         settingsAdded.addElement(key);
1081       }
1082       en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keys();
1083       Vector groupsAdded = new Vector();
1084       while (en.hasMoreElements())
1085       {
1086         String grp = en.nextElement().toString();
1087         if (groupsAdded.contains(grp))
1088         {
1089           continue;
1090         }
1091         Group g = new Group();
1092         g.setName(grp);
1093         g
1094                 .setDisplay(((Boolean) ap.seqPanel.seqCanvas
1095                         .getFeatureRenderer().featureGroups.get(grp))
1096                         .booleanValue());
1097         fs.addGroup(g);
1098         groupsAdded.addElement(grp);
1099       }
1100       jms.setFeatureSettings(fs);
1101
1102     }
1103
1104     if (av.hasHiddenColumns)
1105     {
1106       for (int c = 0; c < av.getColumnSelection().getHiddenColumns().size(); c++)
1107       {
1108         int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
1109                 .elementAt(c);
1110         HiddenColumns hc = new HiddenColumns();
1111         hc.setStart(region[0]);
1112         hc.setEnd(region[1]);
1113         view.addHiddenColumns(hc);
1114       }
1115     }
1116
1117     jms.addViewport(view);
1118
1119     object.setJalviewModelSequence(jms);
1120     object.getVamsasModel().addSequenceSet(vamsasSet);
1121
1122     if (jout != null && fileName != null)
1123     {
1124       // We may not want to write the object to disk,
1125       // eg we can copy the alignViewport to a new view object
1126       // using save and then load
1127       try
1128       {
1129         JarEntry entry = new JarEntry(fileName);
1130         jout.putNextEntry(entry);
1131         PrintWriter pout = new PrintWriter(new OutputStreamWriter(jout,
1132                 "UTF-8"));
1133         org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller(
1134                 pout);
1135         marshaller.marshal(object);
1136         pout.flush();
1137         jout.closeEntry();
1138       } catch (Exception ex)
1139       {
1140         // TODO: raise error in GUI if marshalling failed.
1141         ex.printStackTrace();
1142       }
1143     }
1144     return object;
1145   }
1146
1147   /**
1148    * External mapping between jalview objects and objects yielding a valid and
1149    * unique object ID string. This is null for normal Jalview project IO, but
1150    * non-null when a jalview project is being read or written as part of a
1151    * vamsas session.
1152    */
1153   IdentityHashMap jv2vobj = null;
1154
1155   /**
1156    * Construct a unique ID for jvobj using either existing bindings or if none
1157    * exist, the result of the hashcode call for the object.
1158    *
1159    * @param jvobj
1160    *                jalview data object
1161    * @return unique ID for referring to jvobj
1162    */
1163   private String makeHashCode(Object jvobj, String altCode)
1164   {
1165     if (jv2vobj != null)
1166     {
1167       Object id = jv2vobj.get(jvobj);
1168       if (id != null)
1169       {
1170         return id.toString();
1171       }
1172       // check string ID mappings
1173       if (jvids2vobj != null && jvobj instanceof String)
1174       {
1175         id = jvids2vobj.get(jvobj);
1176       }
1177       if (id != null)
1178       {
1179         return id.toString();
1180       }
1181       // give up and warn that something has gone wrong
1182       warn("Cannot find ID for object in external mapping : " + jvobj);
1183     }
1184     return altCode;
1185   }
1186
1187   /**
1188    * return local jalview object mapped to ID, if it exists
1189    *
1190    * @param idcode
1191    *                (may be null)
1192    * @return null or object bound to idcode
1193    */
1194   private Object retrieveExistingObj(String idcode)
1195   {
1196     if (idcode != null && vobj2jv != null)
1197     {
1198       return vobj2jv.get(idcode);
1199     }
1200     return null;
1201   }
1202
1203   /**
1204    * binding from ID strings from external mapping table to jalview data model
1205    * objects.
1206    */
1207   private Hashtable vobj2jv;
1208
1209   private Sequence createVamsasSequence(String id, SequenceI jds)
1210   {
1211     return createVamsasSequence(true, id, jds, null);
1212   }
1213
1214   private Sequence createVamsasSequence(boolean recurse, String id,
1215           SequenceI jds, SequenceI parentseq)
1216   {
1217     Sequence vamsasSeq = new Sequence();
1218     vamsasSeq.setId(id);
1219     vamsasSeq.setName(jds.getName());
1220     vamsasSeq.setSequence(jds.getSequenceAsString());
1221     vamsasSeq.setDescription(jds.getDescription());
1222     jalview.datamodel.DBRefEntry[] dbrefs = null;
1223     if (jds.getDatasetSequence() != null)
1224     {
1225       vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
1226       if (jds.getDatasetSequence().getDBRef() != null)
1227       {
1228         dbrefs = jds.getDatasetSequence().getDBRef();
1229       }
1230     }
1231     else
1232     {
1233       vamsasSeq.setDsseqid(id); // so we can tell which sequences really are
1234       // dataset sequences only
1235       dbrefs = jds.getDBRef();
1236     }
1237     if (dbrefs != null)
1238     {
1239       for (int d = 0; d < dbrefs.length; d++)
1240       {
1241         DBRef dbref = new DBRef();
1242         dbref.setSource(dbrefs[d].getSource());
1243         dbref.setVersion(dbrefs[d].getVersion());
1244         dbref.setAccessionId(dbrefs[d].getAccessionId());
1245         if (dbrefs[d].hasMap())
1246         {
1247           Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
1248                   jds, recurse);
1249           dbref.setMapping(mp);
1250         }
1251         vamsasSeq.addDBRef(dbref);
1252       }
1253     }
1254     return vamsasSeq;
1255   }
1256
1257   private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
1258           SequenceI parentseq, SequenceI jds, boolean recurse)
1259   {
1260     Mapping mp = null;
1261     if (jmp.getMap() != null)
1262     {
1263       mp = new Mapping();
1264
1265       jalview.util.MapList mlst = jmp.getMap();
1266       int r[] = mlst.getFromRanges();
1267       for (int s = 0; s < r.length; s += 2)
1268       {
1269         MapListFrom mfrom = new MapListFrom();
1270         mfrom.setStart(r[s]);
1271         mfrom.setEnd(r[s + 1]);
1272         mp.addMapListFrom(mfrom);
1273       }
1274       r = mlst.getToRanges();
1275       for (int s = 0; s < r.length; s += 2)
1276       {
1277         MapListTo mto = new MapListTo();
1278         mto.setStart(r[s]);
1279         mto.setEnd(r[s + 1]);
1280         mp.addMapListTo(mto);
1281       }
1282       mp.setMapFromUnit(mlst.getFromRatio());
1283       mp.setMapToUnit(mlst.getToRatio());
1284       if (jmp.getTo() != null)
1285       {
1286         MappingChoice mpc = new MappingChoice();
1287         if (recurse
1288                 && (parentseq != jmp.getTo() || parentseq
1289                         .getDatasetSequence() != jmp.getTo()))
1290         {
1291           mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo()),
1292                   jmp.getTo(), jds));
1293         }
1294         else
1295         {
1296           String jmpid = "";
1297           SequenceI ps = null;
1298           if (parentseq != jmp.getTo()
1299                   && parentseq.getDatasetSequence() != jmp.getTo())
1300           {
1301             // chaining dbref rather than a handshaking one
1302             jmpid = seqHash(ps = jmp.getTo());
1303           }
1304           else
1305           {
1306             jmpid = seqHash(ps = parentseq);
1307           }
1308           mpc.setDseqFor(jmpid);
1309           if (!seqRefIds.containsKey(mpc.getDseqFor()))
1310           {
1311             jalview.bin.Cache.log.debug("creatign new DseqFor ID");
1312             seqRefIds.put(mpc.getDseqFor(), ps);
1313           }
1314           else
1315           {
1316             jalview.bin.Cache.log.debug("reusing DseqFor ID");
1317           }
1318         }
1319         mp.setMappingChoice(mpc);
1320       }
1321     }
1322     return mp;
1323   }
1324
1325   String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
1326           Vector userColours, JalviewModelSequence jms)
1327   {
1328     String id = null;
1329     jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
1330
1331     if (!userColours.contains(ucs))
1332     {
1333       userColours.add(ucs);
1334
1335       java.awt.Color[] colours = ucs.getColours();
1336       jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
1337       jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
1338
1339       for (int i = 0; i < colours.length; i++)
1340       {
1341         jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
1342         col.setName(ResidueProperties.aa[i]);
1343         col.setRGB(jalview.util.Format.getHexString(colours[i]));
1344         jbucs.addColour(col);
1345       }
1346       if (ucs.getLowerCaseColours() != null)
1347       {
1348         colours = ucs.getLowerCaseColours();
1349         for (int i = 0; i < colours.length; i++)
1350         {
1351           jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
1352           col.setName(ResidueProperties.aa[i].toLowerCase());
1353           col.setRGB(jalview.util.Format.getHexString(colours[i]));
1354           jbucs.addColour(col);
1355         }
1356       }
1357
1358       id = "ucs" + userColours.indexOf(ucs);
1359       uc.setId(id);
1360       uc.setUserColourScheme(jbucs);
1361       jms.addUserColours(uc);
1362     }
1363
1364     return id;
1365   }
1366
1367   jalview.schemes.UserColourScheme GetUserColourScheme(
1368           JalviewModelSequence jms, String id)
1369   {
1370     UserColours[] uc = jms.getUserColours();
1371     UserColours colours = null;
1372
1373     for (int i = 0; i < uc.length; i++)
1374     {
1375       if (uc[i].getId().equals(id))
1376       {
1377         colours = uc[i];
1378
1379         break;
1380       }
1381     }
1382
1383     java.awt.Color[] newColours = new java.awt.Color[24];
1384
1385     for (int i = 0; i < 24; i++)
1386     {
1387       newColours[i] = new java.awt.Color(Integer.parseInt(colours
1388               .getUserColourScheme().getColour(i).getRGB(), 16));
1389     }
1390
1391     jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
1392             newColours);
1393
1394     if (colours.getUserColourScheme().getColourCount() > 24)
1395     {
1396       newColours = new java.awt.Color[23];
1397       for (int i = 0; i < 23; i++)
1398       {
1399         newColours[i] = new java.awt.Color(Integer.parseInt(colours
1400                 .getUserColourScheme().getColour(i + 24).getRGB(), 16));
1401       }
1402       ucs.setLowerCaseColours(newColours);
1403     }
1404
1405     return ucs;
1406   }
1407
1408   /**
1409    * contains last error message (if any) encountered by XML loader.
1410    */
1411   String errorMessage = null;
1412
1413   /**
1414    * flag to control whether the Jalview2XML_V1 parser should be deferred to if
1415    * exceptions are raised during project XML parsing
1416    */
1417   public boolean attemptversion1parse = true;
1418
1419   /**
1420    * Load a jalview project archive from a jar file
1421    *
1422    * @param file -
1423    *                HTTP URL or filename
1424    */
1425   public AlignFrame LoadJalviewAlign(final String file)
1426   {
1427
1428     jalview.gui.AlignFrame af = null;
1429
1430     try
1431     {
1432       // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
1433       // Workaround is to make sure caller implements the JarInputStreamProvider
1434       // interface
1435       // so we can re-open the jar input stream for each entry.
1436
1437       jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
1438       af = LoadJalviewAlign(jprovider);
1439     } catch (MalformedURLException e)
1440     {
1441       errorMessage = "Invalid URL format for '" + file + "'";
1442       reportErrors();
1443     }
1444     return af;
1445   }
1446
1447   private jarInputStreamProvider createjarInputStreamProvider(
1448           final String file) throws MalformedURLException
1449   {
1450     URL url = null;
1451     errorMessage = null;
1452     uniqueSetSuffix = null;
1453     seqRefIds = null;
1454     viewportsAdded = null;
1455     frefedSequence = null;
1456
1457     if (file.startsWith("http://"))
1458     {
1459       url = new URL(file);
1460     }
1461     final URL _url = url;
1462     return new jarInputStreamProvider()
1463     {
1464
1465       public JarInputStream getJarInputStream() throws IOException
1466       {
1467         if (_url != null)
1468         {
1469           return new JarInputStream(_url.openStream());
1470         }
1471         else
1472         {
1473           return new JarInputStream(new FileInputStream(file));
1474         }
1475       }
1476
1477       public String getFilename()
1478       {
1479         return file;
1480       }
1481     };
1482   }
1483
1484   /**
1485    * Recover jalview session from a jalview project archive. Caller may
1486    * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
1487    * themselves. Any null fields will be initialised with default values,
1488    * non-null fields are left alone.
1489    *
1490    * @param jprovider
1491    * @return
1492    */
1493   public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
1494   {
1495     errorMessage = null;
1496     if (uniqueSetSuffix == null)
1497     {
1498       uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
1499     }
1500     if (seqRefIds == null)
1501     {
1502       seqRefIds = new Hashtable();
1503     }
1504     if (viewportsAdded == null)
1505     {
1506       viewportsAdded = new Hashtable();
1507     }
1508     if (frefedSequence == null)
1509     {
1510       frefedSequence = new Vector();
1511     }
1512
1513     jalview.gui.AlignFrame af = null;
1514     Hashtable gatherToThisFrame = new Hashtable();
1515     final String file = jprovider.getFilename();
1516     try
1517     {
1518       JarInputStream jin = null;
1519       JarEntry jarentry = null;
1520       int entryCount = 1;
1521
1522       do
1523       {
1524         jin = jprovider.getJarInputStream();
1525         for (int i = 0; i < entryCount; i++)
1526         {
1527           jarentry = jin.getNextJarEntry();
1528         }
1529
1530         if (jarentry != null && jarentry.getName().endsWith(".xml"))
1531         {
1532           InputStreamReader in = new InputStreamReader(jin, "UTF-8");
1533           JalviewModel object = new JalviewModel();
1534
1535           Unmarshaller unmar = new Unmarshaller(object);
1536           unmar.setValidation(false);
1537           object = (JalviewModel) unmar.unmarshal(in);
1538           if (true) // !skipViewport(object))
1539           {
1540             af = LoadFromObject(object, file, true, jprovider);
1541             if (af.viewport.gatherViewsHere)
1542             {
1543               gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
1544             }
1545           }
1546           entryCount++;
1547         }
1548         else if (jarentry != null)
1549         {
1550           // Some other file here.
1551           entryCount++;
1552         }
1553       } while (jarentry != null);
1554       resolveFrefedSequences();
1555     } catch (java.io.FileNotFoundException ex)
1556     {
1557       ex.printStackTrace();
1558       errorMessage = "Couldn't locate Jalview XML file : " + file;
1559       System.err.println("Exception whilst loading jalview XML file : "
1560               + ex + "\n");
1561     } catch (java.net.UnknownHostException ex)
1562     {
1563       ex.printStackTrace();
1564       errorMessage = "Couldn't locate Jalview XML file : " + file;
1565       System.err.println("Exception whilst loading jalview XML file : "
1566               + ex + "\n");
1567     } catch (Exception ex)
1568     {
1569       System.err.println("Parsing as Jalview Version 2 file failed.");
1570       ex.printStackTrace(System.err);
1571       if (attemptversion1parse)
1572       {
1573         // Is Version 1 Jar file?
1574         try
1575         {
1576           af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(jprovider);
1577         } catch (Exception ex2)
1578         {
1579           System.err.println("Exception whilst loading as jalviewXMLV1:");
1580           ex2.printStackTrace();
1581           af = null;
1582         }
1583       }
1584       if (Desktop.instance != null)
1585       {
1586         Desktop.instance.stopLoading();
1587       }
1588       if (af != null)
1589       {
1590         System.out.println("Successfully loaded archive file");
1591         return af;
1592       }
1593       ex.printStackTrace();
1594
1595       System.err.println("Exception whilst loading jalview XML file : "
1596               + ex + "\n");
1597     } catch (OutOfMemoryError e)
1598     {
1599       new jalview.gui.OOMWarning("loading jalview XML file", e,
1600               Desktop.instance);
1601     }
1602
1603     if (Desktop.instance != null)
1604     {
1605       Desktop.instance.stopLoading();
1606     }
1607
1608     Enumeration en = gatherToThisFrame.elements();
1609     while (en.hasMoreElements())
1610     {
1611       Desktop.instance.gatherViews((AlignFrame) en.nextElement());
1612     }
1613     if (errorMessage != null)
1614     {
1615       reportErrors();
1616     }
1617     return af;
1618   }
1619
1620   /**
1621    * check errorMessage for a valid error message and raise an error box in the
1622    * GUI or write the current errorMessage to stderr and then clear the error
1623    * state.
1624    */
1625   protected void reportErrors()
1626   {
1627     reportErrors(false);
1628   }
1629
1630   protected void reportErrors(final boolean saving)
1631   {
1632     if (errorMessage != null)
1633     {
1634       final String finalErrorMessage = errorMessage;
1635       if (raiseGUI)
1636       {
1637         javax.swing.SwingUtilities.invokeLater(new Runnable()
1638         {
1639           public void run()
1640           {
1641             JOptionPane.showInternalMessageDialog(Desktop.desktop,
1642                     finalErrorMessage, "Error "
1643                             + (saving ? "saving" : "loading")
1644                             + " Jalview file", JOptionPane.WARNING_MESSAGE);
1645           }
1646         });
1647       }
1648       else
1649       {
1650         System.err.println("Problem loading Jalview file: " + errorMessage);
1651       }
1652     }
1653     errorMessage = null;
1654   }
1655
1656   Hashtable alreadyLoadedPDB;
1657
1658   /**
1659    * when set, local views will be updated from view stored in JalviewXML
1660    * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
1661    * sync if this is set to true.
1662    */
1663   private boolean updateLocalViews = false;
1664
1665   String loadPDBFile(jarInputStreamProvider jprovider, String pdbId)
1666   {
1667     if (alreadyLoadedPDB == null)
1668       alreadyLoadedPDB = new Hashtable();
1669
1670     if (alreadyLoadedPDB.containsKey(pdbId))
1671       return alreadyLoadedPDB.get(pdbId).toString();
1672
1673     try
1674     {
1675       JarInputStream jin = jprovider.getJarInputStream();
1676       /*
1677        * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
1678        * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
1679        * FileInputStream(jprovider)); }
1680        */
1681
1682       JarEntry entry = null;
1683       do
1684       {
1685         entry = jin.getNextJarEntry();
1686       } while (entry != null && !entry.getName().equals(pdbId));
1687       if (entry != null)
1688       {
1689         BufferedReader in = new BufferedReader(new InputStreamReader(jin));
1690         File outFile = File.createTempFile("jalview_pdb", ".txt");
1691         outFile.deleteOnExit();
1692         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
1693         String data;
1694
1695         while ((data = in.readLine()) != null)
1696         {
1697           out.println(data);
1698         }
1699         try
1700         {
1701           out.flush();
1702         } catch (Exception foo)
1703         {
1704         }
1705         ;
1706         out.close();
1707
1708         alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath());
1709         return outFile.getAbsolutePath();
1710       }
1711       else
1712       {
1713         warn("Couldn't find PDB file entry in Jalview Jar for " + pdbId);
1714       }
1715     } catch (Exception ex)
1716     {
1717       ex.printStackTrace();
1718     }
1719
1720     return null;
1721   }
1722
1723   /**
1724    * Load alignment frame from jalview XML DOM object
1725    *
1726    * @param object
1727    *                DOM
1728    * @param file
1729    *                filename source string
1730    * @param loadTreesAndStructures
1731    *                when false only create Viewport
1732    * @param jprovider
1733    *                data source provider
1734    * @return alignment frame created from view stored in DOM
1735    */
1736   AlignFrame LoadFromObject(JalviewModel object, String file,
1737           boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
1738   {
1739     SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
1740     Sequence[] vamsasSeq = vamsasSet.getSequence();
1741
1742     JalviewModelSequence jms = object.getJalviewModelSequence();
1743
1744     Viewport view = jms.getViewport(0);
1745     // ////////////////////////////////
1746     // LOAD SEQUENCES
1747
1748     Vector hiddenSeqs = null;
1749     jalview.datamodel.Sequence jseq;
1750
1751     ArrayList tmpseqs = new ArrayList();
1752
1753     boolean multipleView = false;
1754
1755     JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
1756     int vi = 0; // counter in vamsasSeq array
1757     for (int i = 0; i < JSEQ.length; i++)
1758     {
1759       String seqId = JSEQ[i].getId();
1760
1761       if (seqRefIds.get(seqId) != null)
1762       {
1763         tmpseqs.add((jalview.datamodel.Sequence) seqRefIds.get(seqId));
1764         multipleView = true;
1765       }
1766       else
1767       {
1768         jseq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
1769                 vamsasSeq[vi].getSequence());
1770         jseq.setDescription(vamsasSeq[vi].getDescription());
1771         jseq.setStart(JSEQ[i].getStart());
1772         jseq.setEnd(JSEQ[i].getEnd());
1773         jseq.setVamsasId(uniqueSetSuffix + seqId);
1774         seqRefIds.put(vamsasSeq[vi].getId(), jseq);
1775         tmpseqs.add(jseq);
1776         vi++;
1777       }
1778
1779       if (JSEQ[i].getHidden())
1780       {
1781         if (hiddenSeqs == null)
1782         {
1783           hiddenSeqs = new Vector();
1784         }
1785
1786         hiddenSeqs.addElement((jalview.datamodel.Sequence) seqRefIds
1787                 .get(seqId));
1788       }
1789
1790     }
1791
1792     // /
1793     // Create the alignment object from the sequence set
1794     // ///////////////////////////////
1795     jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[tmpseqs
1796             .size()];
1797
1798     tmpseqs.toArray(orderedSeqs);
1799
1800     jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(
1801             orderedSeqs);
1802
1803     // / Add the alignment properties
1804     for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
1805     {
1806       SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
1807       al.setProperty(ssp.getKey(), ssp.getValue());
1808     }
1809
1810     // /
1811     // SequenceFeatures are added to the DatasetSequence,
1812     // so we must create or recover the dataset before loading features
1813     // ///////////////////////////////
1814     if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
1815     {
1816       // older jalview projects do not have a dataset id.
1817       al.setDataset(null);
1818     }
1819     else
1820     {
1821       recoverDatasetFor(vamsasSet, al);
1822     }
1823     // ///////////////////////////////
1824
1825     Hashtable pdbloaded = new Hashtable();
1826     if (!multipleView)
1827     {
1828       // load sequence features, database references and any associated PDB
1829       // structures for the alignment
1830       for (int i = 0; i < vamsasSeq.length; i++)
1831       {
1832         if (JSEQ[i].getFeaturesCount() > 0)
1833         {
1834           Features[] features = JSEQ[i].getFeatures();
1835           for (int f = 0; f < features.length; f++)
1836           {
1837             jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
1838                     features[f].getType(), features[f].getDescription(),
1839                     features[f].getStatus(), features[f].getBegin(),
1840                     features[f].getEnd(), features[f].getFeatureGroup());
1841
1842             sf.setScore(features[f].getScore());
1843             for (int od = 0; od < features[f].getOtherDataCount(); od++)
1844             {
1845               OtherData keyValue = features[f].getOtherData(od);
1846               if (keyValue.getKey().startsWith("LINK"))
1847               {
1848                 sf.addLink(keyValue.getValue());
1849               }
1850               else
1851               {
1852                 sf.setValue(keyValue.getKey(), keyValue.getValue());
1853               }
1854
1855             }
1856
1857             al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1858           }
1859         }
1860         if (vamsasSeq[i].getDBRefCount() > 0)
1861         {
1862           addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]);
1863         }
1864         if (JSEQ[i].getPdbidsCount() > 0)
1865         {
1866           Pdbids[] ids = JSEQ[i].getPdbids();
1867           for (int p = 0; p < ids.length; p++)
1868           {
1869             jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
1870             entry.setId(ids[p].getId());
1871             entry.setType(ids[p].getType());
1872             if (ids[p].getFile() != null)
1873             {
1874               if (!pdbloaded.containsKey(ids[p].getFile()))
1875               {
1876                 entry.setFile(loadPDBFile(jprovider, ids[p].getId()));
1877               }
1878               else
1879               {
1880                 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1881               }
1882             }
1883
1884             al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1885           }
1886         }
1887       }
1888     } // end !multipleview
1889
1890     // ///////////////////////////////
1891     // LOAD SEQUENCE MAPPINGS
1892
1893     if (vamsasSet.getAlcodonFrameCount() > 0)
1894     {
1895       // TODO Potentially this should only be done once for all views of an
1896       // alignment
1897       AlcodonFrame[] alc = vamsasSet.getAlcodonFrame();
1898       for (int i = 0; i < alc.length; i++)
1899       {
1900         jalview.datamodel.AlignedCodonFrame cf = new jalview.datamodel.AlignedCodonFrame(
1901                 alc[i].getAlcodonCount());
1902         if (alc[i].getAlcodonCount() > 0)
1903         {
1904           Alcodon[] alcods = alc[i].getAlcodon();
1905           for (int p = 0; p < cf.codons.length; p++)
1906           {
1907             if (alcods[p].hasPos1() && alcods[p].hasPos2() && alcods[p].hasPos3())
1908             {
1909               // translated codons require three valid positions
1910               cf.codons[p] = new int[3];
1911               cf.codons[p][0] = (int) alcods[p].getPos1();
1912               cf.codons[p][1] = (int) alcods[p].getPos2();
1913               cf.codons[p][2] = (int) alcods[p].getPos3();
1914             } else {
1915               cf.codons[p] = null;
1916             }
1917           }
1918         }
1919         if (alc[i].getAlcodMapCount() > 0)
1920         {
1921           AlcodMap[] maps = alc[i].getAlcodMap();
1922           for (int m = 0; m < maps.length; m++)
1923           {
1924             SequenceI dnaseq = (SequenceI) seqRefIds
1925                     .get(maps[m].getDnasq());
1926             // Load Mapping
1927             jalview.datamodel.Mapping mapping = null;
1928             // attach to dna sequence reference.
1929             if (maps[m].getMapping() != null)
1930             {
1931               mapping = addMapping(maps[m].getMapping());
1932             }
1933             if (dnaseq != null)
1934             {
1935               cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
1936             }
1937             else
1938             {
1939               // defer to later
1940               frefedSequence.add(new Object[]
1941               { maps[m].getDnasq(), cf, mapping });
1942             }
1943           }
1944         }
1945         al.addCodonFrame(cf);
1946       }
1947
1948     }
1949
1950     // ////////////////////////////////
1951     // LOAD ANNOTATIONS
1952     boolean hideQuality = true, hideConservation = true, hideConsensus = true;
1953
1954     if (vamsasSet.getAnnotationCount() > 0)
1955     {
1956       Annotation[] an = vamsasSet.getAnnotation();
1957
1958       for (int i = 0; i < an.length; i++)
1959       {
1960         // set visibility for automatic annotation for this view
1961         if (an[i].getLabel().equals("Quality"))
1962         {
1963           hideQuality = false;
1964           continue;
1965         }
1966         else if (an[i].getLabel().equals("Conservation"))
1967         {
1968           hideConservation = false;
1969           continue;
1970         }
1971         else if (an[i].getLabel().equals("Consensus"))
1972         {
1973           hideConsensus = false;
1974           continue;
1975         }
1976         // set visiblity for other annotation in this view
1977         if (an[i].getId() != null
1978                 && annotationIds.containsKey(an[i].getId()))
1979         {
1980           jalview.datamodel.AlignmentAnnotation jda = (jalview.datamodel.AlignmentAnnotation) annotationIds
1981                   .get(an[i].getId());
1982           // in principle Visible should always be true for annotation displayed
1983           // in multiple views
1984           if (an[i].hasVisible())
1985             jda.visible = an[i].getVisible();
1986
1987           al.addAnnotation(jda);
1988
1989           continue;
1990         }
1991         // Construct new annotation from model.
1992         AnnotationElement[] ae = an[i].getAnnotationElement();
1993         jalview.datamodel.Annotation[] anot = null;
1994
1995         if (!an[i].getScoreOnly())
1996         {
1997           anot = new jalview.datamodel.Annotation[al.getWidth()];
1998
1999           for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
2000           {
2001             if (ae[aa].getPosition() >= anot.length)
2002               continue;
2003
2004             anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
2005
2006             ae[aa].getDisplayCharacter(), ae[aa].getDescription(), (ae[aa]
2007                     .getSecondaryStructure() == null || ae[aa]
2008                     .getSecondaryStructure().length() == 0) ? ' ' : ae[aa]
2009                     .getSecondaryStructure().charAt(0), ae[aa].getValue()
2010
2011             );
2012             // JBPNote: Consider verifying dataflow for IO of secondary
2013             // structure annotation read from Stockholm files
2014             // this was added to try to ensure that
2015             // if (anot[ae[aa].getPosition()].secondaryStructure>' ')
2016             // {
2017             // anot[ae[aa].getPosition()].displayCharacter = "";
2018             // }
2019             anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa]
2020                     .getColour());
2021           }
2022         }
2023         jalview.datamodel.AlignmentAnnotation jaa = null;
2024
2025         if (an[i].getGraph())
2026         {
2027           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
2028                   an[i].getDescription(), anot, 0, 0, an[i].getGraphType());
2029
2030           jaa.graphGroup = an[i].getGraphGroup();
2031
2032           if (an[i].getThresholdLine() != null)
2033           {
2034             jaa.setThreshold(new jalview.datamodel.GraphLine(an[i]
2035                     .getThresholdLine().getValue(), an[i]
2036                     .getThresholdLine().getLabel(), new java.awt.Color(
2037                     an[i].getThresholdLine().getColour())));
2038
2039           }
2040
2041         }
2042         else
2043         {
2044           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
2045                   an[i].getDescription(), anot);
2046         }
2047         // register new annotation
2048         if (an[i].getId() != null)
2049         {
2050           annotationIds.put(an[i].getId(), jaa);
2051           jaa.annotationId = an[i].getId();
2052         }
2053         // recover sequence association
2054         if (an[i].getSequenceRef() != null)
2055         {
2056           if (al.findName(an[i].getSequenceRef()) != null)
2057           {
2058             jaa.createSequenceMapping(al.findName(an[i].getSequenceRef()),
2059                     1, true);
2060             al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
2061           }
2062         }
2063         if (an[i].hasScore())
2064         {
2065           jaa.setScore(an[i].getScore());
2066         }
2067
2068         if (an[i].hasVisible())
2069           jaa.visible = an[i].getVisible();
2070
2071         al.addAnnotation(jaa);
2072       }
2073     }
2074
2075     // ///////////////////////
2076     // LOAD GROUPS
2077     // Create alignment markup and styles for this view
2078     if (jms.getJGroupCount() > 0)
2079     {
2080       JGroup[] groups = jms.getJGroup();
2081
2082       for (int i = 0; i < groups.length; i++)
2083       {
2084         ColourSchemeI cs = null;
2085
2086         if (groups[i].getColour() != null)
2087         {
2088           if (groups[i].getColour().startsWith("ucs"))
2089           {
2090             cs = GetUserColourScheme(jms, groups[i].getColour());
2091           }
2092           else
2093           {
2094             cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
2095           }
2096
2097           if (cs != null)
2098           {
2099             cs.setThreshold(groups[i].getPidThreshold(), true);
2100           }
2101         }
2102
2103         Vector seqs = new Vector();
2104
2105         for (int s = 0; s < groups[i].getSeqCount(); s++)
2106         {
2107           String seqId = groups[i].getSeq(s) + "";
2108           jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI) seqRefIds
2109                   .get(seqId);
2110
2111           if (ts != null)
2112           {
2113             seqs.addElement(ts);
2114           }
2115         }
2116
2117         if (seqs.size() < 1)
2118         {
2119           continue;
2120         }
2121
2122         jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
2123                 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
2124                 groups[i].getDisplayText(), groups[i].getColourText(),
2125                 groups[i].getStart(), groups[i].getEnd());
2126
2127         sg
2128                 .setOutlineColour(new java.awt.Color(groups[i]
2129                         .getOutlineColour()));
2130
2131         sg.textColour = new java.awt.Color(groups[i].getTextCol1());
2132         sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
2133         sg.thresholdTextColour = groups[i].getTextColThreshold();
2134
2135         if (groups[i].getConsThreshold() != 0)
2136         {
2137           jalview.analysis.Conservation c = new jalview.analysis.Conservation(
2138                   "All", ResidueProperties.propHash, 3, sg
2139                           .getSequences(null), 0, sg.getWidth() - 1);
2140           c.calculate();
2141           c.verdict(false, 25);
2142           sg.cs.setConservation(c);
2143         }
2144
2145         al.addGroup(sg);
2146       }
2147     }
2148
2149     // ///////////////////////////////
2150     // LOAD VIEWPORT
2151
2152     // If we just load in the same jar file again, the sequenceSetId
2153     // will be the same, and we end up with multiple references
2154     // to the same sequenceSet. We must modify this id on load
2155     // so that each load of the file gives a unique id
2156     String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
2157     String viewId = (view.getId() == null ? null : view.getId()
2158             + uniqueSetSuffix);
2159     AlignFrame af = null;
2160     AlignViewport av = null;
2161     // now check to see if we really need to create a new viewport.
2162     if (multipleView && viewportsAdded.size() == 0)
2163     {
2164       // We recovered an alignment for which a viewport already exists.
2165       // TODO: fix up any settings necessary for overlaying stored state onto
2166       // state recovered from another document. (may not be necessary).
2167       // we may need a binding from a viewport in memory to one recovered from
2168       // XML.
2169       // and then recover its containing af to allow the settings to be applied.
2170       // TODO: fix for vamsas demo
2171       System.err
2172               .println("About to recover a viewport for existing alignment: Sequence set ID is "
2173                       + uniqueSeqSetId);
2174       Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
2175       if (seqsetobj != null)
2176       {
2177         if (seqsetobj instanceof String)
2178         {
2179           uniqueSeqSetId = (String) seqsetobj;
2180           System.err
2181                   .println("Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
2182                           + uniqueSeqSetId);
2183         }
2184         else
2185         {
2186           System.err
2187                   .println("Warning : Collision between sequence set ID string and existing jalview object mapping.");
2188         }
2189
2190       }
2191     }
2192     AlignmentPanel ap = null;
2193     boolean isnewview = true;
2194     if (viewId != null)
2195     {
2196       // Check to see if this alignment already has a view id == viewId
2197       jalview.gui.AlignmentPanel views[] = Desktop
2198               .getAlignmentPanels(uniqueSeqSetId);
2199       if (views != null && views.length > 0)
2200       {
2201         for (int v = 0; v < views.length; v++)
2202         {
2203           if (views[v].av.getViewId().equalsIgnoreCase(viewId))
2204           {
2205             // recover the existing alignpanel, alignframe, viewport
2206             af = views[v].alignFrame;
2207             av = views[v].av;
2208             ap = views[v];
2209             // TODO: could even skip resetting view settings if we don't want to
2210             // change the local settings from other jalview processes
2211             isnewview = false;
2212           }
2213         }
2214       }
2215     }
2216
2217     if (isnewview)
2218     {
2219       af = loadViewport(file, JSEQ, hiddenSeqs, al, hideConsensus,
2220               hideQuality, hideConservation, jms, view, uniqueSeqSetId,
2221               viewId);
2222       av = af.viewport;
2223       ap = af.alignPanel;
2224     }
2225     // LOAD TREES
2226     // /////////////////////////////////////
2227     if (loadTreesAndStructures && jms.getTreeCount() > 0)
2228     {
2229       try
2230       {
2231         for (int t = 0; t < jms.getTreeCount(); t++)
2232         {
2233
2234           Tree tree = jms.getTree(t);
2235
2236           TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
2237           if (tp == null)
2238           {
2239             tp = af.ShowNewickTree(new jalview.io.NewickFile(tree
2240                     .getNewick()), tree.getTitle(), tree.getWidth(), tree
2241                     .getHeight(), tree.getXpos(), tree.getYpos());
2242             if (tree.getId() != null)
2243             {
2244
2245             }
2246           }
2247           else
2248           {
2249             // update local tree attributes ?
2250             tp.setTitle(tree.getTitle());
2251             tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(), tree
2252                     .getWidth(), tree.getHeight()));
2253             tp.av = av; // af.viewport; // TODO: verify 'associate with all
2254             // views'
2255             // works still
2256             tp.treeCanvas.av = av; // af.viewport;
2257             tp.treeCanvas.ap = ap; // af.alignPanel;
2258
2259           }
2260
2261           tp.fitToWindow.setState(tree.getFitToWindow());
2262           tp.fitToWindow_actionPerformed(null);
2263
2264           if (tree.getFontName() != null)
2265           {
2266             tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
2267                     .getFontStyle(), tree.getFontSize()));
2268           }
2269           else
2270           {
2271             tp.setTreeFont(new java.awt.Font(view.getFontName(), view
2272                     .getFontStyle(), tree.getFontSize()));
2273           }
2274
2275           tp.showPlaceholders(tree.getMarkUnlinked());
2276           tp.showBootstrap(tree.getShowBootstrap());
2277           tp.showDistances(tree.getShowDistances());
2278
2279           tp.treeCanvas.threshold = tree.getThreshold();
2280
2281           if (tree.getCurrentTree())
2282           {
2283             af.viewport.setCurrentTree(tp.getTree());
2284           }
2285         }
2286
2287       } catch (Exception ex)
2288       {
2289         ex.printStackTrace();
2290       }
2291     }
2292
2293     // //LOAD STRUCTURES
2294     if (loadTreesAndStructures)
2295     {
2296       for (int i = 0; i < JSEQ.length; i++)
2297       {
2298         if (JSEQ[i].getPdbidsCount() > 0)
2299         {
2300           Pdbids[] ids = JSEQ[i].getPdbids();
2301           for (int p = 0; p < ids.length; p++)
2302           {
2303             for (int s = 0; s < ids[p].getStructureStateCount(); s++)
2304             {
2305               // check to see if we haven't already created this structure view
2306               String sviewid = (ids[p].getStructureState(s).getViewId() == null) ? null
2307                       : ids[p].getStructureState(s).getViewId()
2308                               + uniqueSetSuffix;
2309               jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
2310               // Originally : ids[p].getFile()
2311               // : TODO: verify external PDB file recovery still works in normal
2312               // jalview project load
2313               jpdb.setFile(loadPDBFile(jprovider, ids[p].getId()));
2314               jpdb.setId(ids[p].getId());
2315
2316               int x = ids[p].getStructureState(s).getXpos();
2317               int y = ids[p].getStructureState(s).getYpos();
2318               int width = ids[p].getStructureState(s).getWidth();
2319               int height = ids[p].getStructureState(s).getHeight();
2320               AppJmol comp = null;
2321               JInternalFrame[] frames = null;
2322               do
2323               {
2324                 try
2325                 {
2326                   frames = Desktop.desktop.getAllFrames();
2327                 } catch (ArrayIndexOutOfBoundsException e)
2328                 {
2329                   // occasional No such child exceptions are thrown here...
2330                   frames = null;
2331                   try
2332                   {
2333                     Thread.sleep(10);
2334                   } catch (Exception f)
2335                   {
2336                   }
2337                   ;
2338                 }
2339               } while (frames == null);
2340               // search for any Jmol windows already open from other
2341               // alignment views that exactly match the stored structure state
2342               for (int f = 0; comp == null && f < frames.length; f++)
2343               {
2344                 if (frames[f] instanceof AppJmol)
2345                 {
2346                   if (sviewid != null
2347                           && ((AppJmol) frames[f]).getViewId().equals(
2348                                   sviewid))
2349                   {
2350                     // post jalview 2.4 schema includes structure view id
2351                     comp = (AppJmol) frames[f];
2352                   }
2353                   else if (frames[f].getX() == x && frames[f].getY() == y
2354                           && frames[f].getHeight() == height
2355                           && frames[f].getWidth() == width)
2356                   {
2357                     comp = (AppJmol) frames[f];
2358                   }
2359                 }
2360               }
2361               Desktop.desktop.getComponentAt(x, y);
2362
2363               String pdbFile = loadPDBFile(jprovider, ids[p].getId());
2364
2365               jalview.datamodel.SequenceI[] seq = new jalview.datamodel.SequenceI[]
2366               { (jalview.datamodel.SequenceI) seqRefIds.get(JSEQ[i].getId()
2367                       + "") };
2368
2369               if (comp == null)
2370               {
2371                 // create a new Jmol window
2372                 String state = ids[p].getStructureState(s).getContent();
2373
2374                 StringBuffer newFileLoc = new StringBuffer(state.substring(
2375                         0, state.indexOf("\"", state.indexOf("load")) + 1));
2376
2377                 newFileLoc.append(jpdb.getFile());
2378                 newFileLoc.append(state.substring(state.indexOf("\"", state
2379                         .indexOf("load \"") + 6)));
2380
2381                 new AppJmol(pdbFile, ids[p].getId(), seq, af.alignPanel,
2382                         newFileLoc.toString(), new java.awt.Rectangle(x, y,
2383                                 width, height), sviewid);
2384
2385               }
2386               else
2387               // if (comp != null)
2388               {
2389                 // NOTE: if the jalview project is part of a shared session then
2390                 // view synchronization should/could be done here.
2391
2392                 // add mapping for this sequence to the already open Jmol
2393                 // instance (if it doesn't already exist)
2394                 // These
2395                 StructureSelectionManager.getStructureSelectionManager()
2396                         .setMapping(seq, null, pdbFile,
2397                                 jalview.io.AppletFormatAdapter.FILE);
2398
2399                 ((AppJmol) comp).addSequence(seq);
2400               }
2401             }
2402           }
2403         }
2404       }
2405     }
2406
2407     return af;
2408   }
2409
2410   AlignFrame loadViewport(String file, JSeq[] JSEQ, Vector hiddenSeqs,
2411           Alignment al, boolean hideConsensus, boolean hideQuality,
2412           boolean hideConservation, JalviewModelSequence jms,
2413           Viewport view, String uniqueSeqSetId, String viewId)
2414   {
2415     AlignFrame af = null;
2416     af = new AlignFrame(al, view.getWidth(), view.getHeight(),
2417             uniqueSeqSetId, viewId);
2418
2419     af.setFileName(file, "Jalview");
2420
2421     for (int i = 0; i < JSEQ.length; i++)
2422     {
2423       af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i),
2424               new java.awt.Color(JSEQ[i].getColour()));
2425     }
2426
2427     af.viewport.gatherViewsHere = view.getGatheredViews();
2428
2429     if (view.getSequenceSetId() != null)
2430     {
2431       jalview.gui.AlignViewport av = (jalview.gui.AlignViewport) viewportsAdded
2432               .get(uniqueSeqSetId);
2433
2434       af.viewport.sequenceSetID = uniqueSeqSetId;
2435       if (av != null)
2436       {
2437         // propagate shared settings to this new view
2438         af.viewport.historyList = av.historyList;
2439         af.viewport.redoList = av.redoList;
2440       }
2441       else
2442       {
2443         viewportsAdded.put(uniqueSeqSetId, af.viewport);
2444       }
2445       // TODO: check if this method can be called repeatedly without
2446       // side-effects if alignpanel already registered.
2447       PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
2448     }
2449     // apply Hidden regions to view.
2450     if (hiddenSeqs != null)
2451     {
2452       for (int s = 0; s < JSEQ.length; s++)
2453       {
2454         jalview.datamodel.SequenceGroup hidden = new jalview.datamodel.SequenceGroup();
2455
2456         for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
2457         {
2458           hidden.addSequence(al
2459                   .getSequenceAt(JSEQ[s].getHiddenSequences(r)), false);
2460         }
2461         af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
2462       }
2463
2464       jalview.datamodel.SequenceI[] hseqs = new jalview.datamodel.SequenceI[hiddenSeqs
2465               .size()];
2466
2467       for (int s = 0; s < hiddenSeqs.size(); s++)
2468       {
2469         hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
2470       }
2471
2472       af.viewport.hideSequence(hseqs);
2473
2474     }
2475     // set visibility of annotation in view
2476     if ((hideConsensus || hideQuality || hideConservation)
2477             && al.getAlignmentAnnotation() != null)
2478     {
2479       int hSize = al.getAlignmentAnnotation().length;
2480       for (int h = 0; h < hSize; h++)
2481       {
2482         if ((hideConsensus && al.getAlignmentAnnotation()[h].label
2483                 .equals("Consensus"))
2484                 || (hideQuality && al.getAlignmentAnnotation()[h].label
2485                         .equals("Quality"))
2486                 || (hideConservation && al.getAlignmentAnnotation()[h].label
2487                         .equals("Conservation")))
2488         {
2489           al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
2490           hSize--;
2491           h--;
2492         }
2493       }
2494       af.alignPanel.adjustAnnotationHeight();
2495     }
2496     // recover view properties and display parameters
2497     if (view.getViewName() != null)
2498     {
2499       af.viewport.viewName = view.getViewName();
2500       af.setInitialTabVisible();
2501     }
2502     af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view
2503             .getHeight());
2504
2505     af.viewport.setShowAnnotation(view.getShowAnnotation());
2506     af.viewport.setAbovePIDThreshold(view.getPidSelected());
2507
2508     af.viewport.setColourText(view.getShowColourText());
2509
2510     af.viewport.setConservationSelected(view.getConservationSelected());
2511     af.viewport.setShowJVSuffix(view.getShowFullId());
2512     af.viewport.rightAlignIds = view.getRightAlignIds();
2513     af.viewport.setFont(new java.awt.Font(view.getFontName(), view
2514             .getFontStyle(), view.getFontSize()));
2515     af.alignPanel.fontChanged();
2516     af.viewport.setRenderGaps(view.getRenderGaps());
2517     af.viewport.setWrapAlignment(view.getWrapAlignment());
2518     af.alignPanel.setWrapAlignment(view.getWrapAlignment());
2519     af.viewport.setShowAnnotation(view.getShowAnnotation());
2520     af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
2521
2522     af.viewport.setShowBoxes(view.getShowBoxes());
2523
2524     af.viewport.setShowText(view.getShowText());
2525
2526     af.viewport.textColour = new java.awt.Color(view.getTextCol1());
2527     af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
2528     af.viewport.thresholdTextColour = view.getTextColThreshold();
2529
2530     af.viewport.setStartRes(view.getStartRes());
2531     af.viewport.setStartSeq(view.getStartSeq());
2532
2533     ColourSchemeI cs = null;
2534     // apply colourschemes
2535     if (view.getBgColour() != null)
2536     {
2537       if (view.getBgColour().startsWith("ucs"))
2538       {
2539         cs = GetUserColourScheme(jms, view.getBgColour());
2540       }
2541       else if (view.getBgColour().startsWith("Annotation"))
2542       {
2543         // int find annotation
2544         for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
2545         {
2546           if (af.viewport.alignment.getAlignmentAnnotation()[i].label
2547                   .equals(view.getAnnotationColours().getAnnotation()))
2548           {
2549             if (af.viewport.alignment.getAlignmentAnnotation()[i]
2550                     .getThreshold() == null)
2551             {
2552               af.viewport.alignment.getAlignmentAnnotation()[i]
2553                       .setThreshold(new jalview.datamodel.GraphLine(view
2554                               .getAnnotationColours().getThreshold(),
2555                               "Threshold", java.awt.Color.black)
2556
2557                       );
2558             }
2559
2560             if (view.getAnnotationColours().getColourScheme()
2561                     .equals("None"))
2562             {
2563               cs = new AnnotationColourGradient(af.viewport.alignment
2564                       .getAlignmentAnnotation()[i], new java.awt.Color(view
2565                       .getAnnotationColours().getMinColour()),
2566                       new java.awt.Color(view.getAnnotationColours()
2567                               .getMaxColour()), view.getAnnotationColours()
2568                               .getAboveThreshold());
2569             }
2570             else if (view.getAnnotationColours().getColourScheme()
2571                     .startsWith("ucs"))
2572             {
2573               cs = new AnnotationColourGradient(af.viewport.alignment
2574                       .getAlignmentAnnotation()[i], GetUserColourScheme(
2575                       jms, view.getAnnotationColours().getColourScheme()),
2576                       view.getAnnotationColours().getAboveThreshold());
2577             }
2578             else
2579             {
2580               cs = new AnnotationColourGradient(af.viewport.alignment
2581                       .getAlignmentAnnotation()[i], ColourSchemeProperty
2582                       .getColour(al, view.getAnnotationColours()
2583                               .getColourScheme()), view
2584                       .getAnnotationColours().getAboveThreshold());
2585             }
2586
2587             // Also use these settings for all the groups
2588             if (al.getGroups() != null)
2589             {
2590               for (int g = 0; g < al.getGroups().size(); g++)
2591               {
2592                 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) al
2593                         .getGroups().elementAt(g);
2594
2595                 if (sg.cs == null)
2596                 {
2597                   continue;
2598                 }
2599
2600                 /*
2601                  * if
2602                  * (view.getAnnotationColours().getColourScheme().equals("None")) {
2603                  * sg.cs = new AnnotationColourGradient(
2604                  * af.viewport.alignment.getAlignmentAnnotation()[i], new
2605                  * java.awt.Color(view.getAnnotationColours(). getMinColour()),
2606                  * new java.awt.Color(view.getAnnotationColours().
2607                  * getMaxColour()),
2608                  * view.getAnnotationColours().getAboveThreshold()); } else
2609                  */
2610                 {
2611                   sg.cs = new AnnotationColourGradient(
2612                           af.viewport.alignment.getAlignmentAnnotation()[i],
2613                           sg.cs, view.getAnnotationColours()
2614                                   .getAboveThreshold());
2615                 }
2616
2617               }
2618             }
2619
2620             break;
2621           }
2622
2623         }
2624       }
2625       else
2626       {
2627         cs = ColourSchemeProperty.getColour(al, view.getBgColour());
2628       }
2629
2630       if (cs != null)
2631       {
2632         cs.setThreshold(view.getPidThreshold(), true);
2633         cs.setConsensus(af.viewport.hconsensus);
2634       }
2635     }
2636
2637     af.viewport.setGlobalColourScheme(cs);
2638     af.viewport.setColourAppliesToAllGroups(false);
2639
2640     if (view.getConservationSelected() && cs != null)
2641     {
2642       cs.setConservationInc(view.getConsThreshold());
2643     }
2644
2645     af.changeColour(cs);
2646
2647     af.viewport.setColourAppliesToAllGroups(true);
2648
2649     if (view.getShowSequenceFeatures())
2650     {
2651       af.viewport.showSequenceFeatures = true;
2652     }
2653     // recover featre settings
2654     if (jms.getFeatureSettings() != null)
2655     {
2656       af.viewport.featuresDisplayed = new Hashtable();
2657       String[] renderOrder = new String[jms.getFeatureSettings()
2658               .getSettingCount()];
2659       for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
2660       {
2661         Setting setting = jms.getFeatureSettings().getSetting(fs);
2662
2663         af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
2664                 setting.getType(), new java.awt.Color(setting.getColour()));
2665         renderOrder[fs] = setting.getType();
2666         if (setting.hasOrder())
2667           af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
2668                   setting.getType(), setting.getOrder());
2669         else
2670           af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
2671                   setting.getType(),
2672                   fs / jms.getFeatureSettings().getSettingCount());
2673         if (setting.getDisplay())
2674         {
2675           af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
2676                   setting.getColour()));
2677         }
2678       }
2679       af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
2680       Hashtable fgtable;
2681       af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable();
2682       for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
2683       {
2684         Group grp = jms.getFeatureSettings().getGroup(gs);
2685         fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
2686       }
2687     }
2688
2689     if (view.getHiddenColumnsCount() > 0)
2690     {
2691       for (int c = 0; c < view.getHiddenColumnsCount(); c++)
2692       {
2693         af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view
2694                 .getHiddenColumns(c).getEnd() // +1
2695                 );
2696       }
2697     }
2698
2699     af.setMenusFromViewport(af.viewport);
2700     // TODO: we don't need to do this if the viewport is aready visible.
2701     Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view
2702             .getHeight());
2703     return af;
2704   }
2705
2706   Hashtable skipList = null;
2707
2708   /**
2709    * TODO remove this method
2710    *
2711    * @param view
2712    * @return AlignFrame bound to sequenceSetId from view, if one exists. private
2713    *         AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
2714    *         throw new Error("Implementation Error. No skipList defined for this
2715    *         Jalview2XML instance."); } return (AlignFrame)
2716    *         skipList.get(view.getSequenceSetId()); }
2717    */
2718
2719   /**
2720    * Check if the Jalview view contained in object should be skipped or not.
2721    *
2722    * @param object
2723    * @return true if view's sequenceSetId is a key in skipList
2724    */
2725   private boolean skipViewport(JalviewModel object)
2726   {
2727     if (skipList == null)
2728     {
2729       return false;
2730     }
2731     String id;
2732     if (skipList.containsKey(id = object.getJalviewModelSequence()
2733             .getViewport()[0].getSequenceSetId()))
2734     {
2735       if (Cache.log != null && Cache.log.isDebugEnabled())
2736       {
2737         Cache.log.debug("Skipping seuqence set id " + id);
2738       }
2739       return true;
2740     }
2741     return false;
2742   }
2743
2744   public void AddToSkipList(AlignFrame af)
2745   {
2746     if (skipList == null)
2747     {
2748       skipList = new Hashtable();
2749     }
2750     skipList.put(af.getViewport().getSequenceSetId(), af);
2751   }
2752
2753   public void clearSkipList()
2754   {
2755     if (skipList != null)
2756     {
2757       skipList.clear();
2758       skipList = null;
2759     }
2760   }
2761
2762   private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al)
2763   {
2764     jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId());
2765     Vector dseqs = null;
2766     if (ds == null)
2767     {
2768       // create a list of new dataset sequences
2769       dseqs = new Vector();
2770     }
2771     for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
2772     {
2773       Sequence vamsasSeq = vamsasSet.getSequence(i);
2774       ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs);
2775     }
2776     // create a new dataset
2777     if (ds == null)
2778     {
2779       SequenceI[] dsseqs = new SequenceI[dseqs.size()];
2780       dseqs.copyInto(dsseqs);
2781       ds = new jalview.datamodel.Alignment(dsseqs);
2782       addDatasetRef(vamsasSet.getDatasetId(), ds);
2783     }
2784     // set the dataset for the newly imported alignment.
2785     if (al.getDataset() == null)
2786     {
2787       al.setDataset(ds);
2788     }
2789   }
2790
2791   /**
2792    *
2793    * @param vamsasSeq
2794    *                sequence definition to create/merge dataset sequence for
2795    * @param ds
2796    *                dataset alignment
2797    * @param dseqs
2798    *                vector to add new dataset sequence to
2799    */
2800   private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
2801           AlignmentI ds, Vector dseqs)
2802   {
2803     // JBP TODO: Check this is called for AlCodonFrames to support recovery of
2804     // xRef Codon Maps
2805     jalview.datamodel.Sequence sq = (jalview.datamodel.Sequence) seqRefIds
2806             .get(vamsasSeq.getId());
2807     jalview.datamodel.SequenceI dsq = null;
2808     if (sq != null && sq.getDatasetSequence() != null)
2809     {
2810       dsq = (jalview.datamodel.SequenceI) sq.getDatasetSequence();
2811     }
2812
2813     String sqid = vamsasSeq.getDsseqid();
2814     if (dsq == null)
2815     {
2816       // need to create or add a new dataset sequence reference to this sequence
2817       if (sqid != null)
2818       {
2819         dsq = (jalview.datamodel.SequenceI) seqRefIds.get(sqid);
2820       }
2821       // check again
2822       if (dsq == null)
2823       {
2824         // make a new dataset sequence
2825         dsq = sq.createDatasetSequence();
2826         if (sqid == null)
2827         {
2828           // make up a new dataset reference for this sequence
2829           sqid = seqHash(dsq);
2830         }
2831         dsq.setVamsasId(uniqueSetSuffix + sqid);
2832         seqRefIds.put(sqid, dsq);
2833         if (ds == null)
2834         {
2835           if (dseqs != null)
2836           {
2837             dseqs.addElement(dsq);
2838           }
2839         }
2840         else
2841         {
2842           ds.addSequence(dsq);
2843         }
2844       }
2845       else
2846       {
2847         if (sq != dsq)
2848         { // make this dataset sequence sq's dataset sequence
2849           sq.setDatasetSequence(dsq);
2850         }
2851       }
2852     }
2853     // TODO: refactor this as a merge dataset sequence function
2854     // now check that sq (the dataset sequence) sequence really is the union of
2855     // all references to it
2856     // boolean pre = sq.getStart() < dsq.getStart();
2857     // boolean post = sq.getEnd() > dsq.getEnd();
2858     // if (pre || post)
2859     if (sq != dsq)
2860     {
2861       StringBuffer sb = new StringBuffer();
2862       String newres = jalview.analysis.AlignSeq.extractGaps(
2863               jalview.util.Comparison.GapChars, sq.getSequenceAsString());
2864       if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
2865               && newres.length() > dsq.getLength())
2866       {
2867         // Update with the longer sequence.
2868         synchronized (dsq)
2869         {
2870           /*
2871            * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
2872            * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
2873            * sb.append(newres.substring(newres.length() - sq.getEnd() -
2874            * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
2875            */
2876           dsq.setSequence(sb.toString());
2877         }
2878         // TODO: merges will never happen if we 'know' we have the real dataset
2879         // sequence - this should be detected when id==dssid
2880         System.err.println("DEBUG Notice:  Merged dataset sequence"); // ("
2881         // + (pre ? "prepended" : "") + " "
2882         // + (post ? "appended" : ""));
2883       }
2884     }
2885   }
2886
2887   java.util.Hashtable datasetIds = null;
2888   java.util.IdentityHashMap dataset2Ids = null;
2889   private Alignment getDatasetFor(String datasetId)
2890   {
2891     if (datasetIds == null)
2892     {
2893       datasetIds = new Hashtable();
2894       return null;
2895     }
2896     if (datasetIds.containsKey(datasetId))
2897     {
2898       return (Alignment) datasetIds.get(datasetId);
2899     }
2900     return null;
2901   }
2902
2903   private void addDatasetRef(String datasetId, Alignment dataset)
2904   {
2905     if (datasetIds == null)
2906     {
2907       datasetIds = new Hashtable();
2908     }
2909     datasetIds.put(datasetId, dataset);
2910   }
2911   /**
2912    * make a new dataset ID for this jalview dataset alignment
2913    * @param dataset
2914    * @return
2915    */
2916   private String getDatasetIdRef(jalview.datamodel.Alignment dataset)
2917   {
2918     if (dataset.getDataset()!=null)
2919     {
2920       warn("Serious issue!  Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
2921     }
2922     String datasetId=makeHashCode(dataset, null);
2923     if (datasetId==null)
2924     {
2925       // make a new datasetId and record it
2926       if (dataset2Ids == null)
2927       {
2928         dataset2Ids = new IdentityHashMap();
2929       } else {
2930         datasetId = (String) dataset2Ids.get(dataset);
2931       }
2932       if (datasetId==null)
2933       {
2934         datasetId = "ds"+dataset2Ids.size()+1;
2935         dataset2Ids.put(dataset,datasetId);
2936       }
2937     }
2938     return datasetId;
2939   }
2940   private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
2941   {
2942     for (int d = 0; d < sequence.getDBRefCount(); d++)
2943     {
2944       DBRef dr = sequence.getDBRef(d);
2945       jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
2946               sequence.getDBRef(d).getSource(), sequence.getDBRef(d)
2947                       .getVersion(), sequence.getDBRef(d).getAccessionId());
2948       if (dr.getMapping() != null)
2949       {
2950         entry.setMap(addMapping(dr.getMapping()));
2951       }
2952       datasetSequence.addDBRef(entry);
2953     }
2954   }
2955
2956   private jalview.datamodel.Mapping addMapping(Mapping m)
2957   {
2958     SequenceI dsto = null;
2959     // Mapping m = dr.getMapping();
2960     int fr[] = new int[m.getMapListFromCount() * 2];
2961     Enumeration f = m.enumerateMapListFrom();
2962     for (int _i = 0; f.hasMoreElements(); _i += 2)
2963     {
2964       MapListFrom mf = (MapListFrom) f.nextElement();
2965       fr[_i] = mf.getStart();
2966       fr[_i + 1] = mf.getEnd();
2967     }
2968     int fto[] = new int[m.getMapListToCount() * 2];
2969     f = m.enumerateMapListTo();
2970     for (int _i = 0; f.hasMoreElements(); _i += 2)
2971     {
2972       MapListTo mf = (MapListTo) f.nextElement();
2973       fto[_i] = mf.getStart();
2974       fto[_i + 1] = mf.getEnd();
2975     }
2976     jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto,
2977             fr, fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit());
2978     if (m.getMappingChoice() != null)
2979     {
2980       MappingChoice mc = m.getMappingChoice();
2981       if (mc.getDseqFor() != null)
2982       {
2983         String dsfor = ""+mc.getDseqFor();
2984         if (seqRefIds.containsKey(dsfor))
2985         {
2986           /**
2987            * recover from hash
2988            */
2989           jmap.setTo((SequenceI) seqRefIds.get(dsfor));
2990         }
2991         else
2992         {
2993           frefedSequence.add(new Object[]
2994           { dsfor, jmap });
2995         }
2996       }
2997       else
2998       {
2999         /**
3000          * local sequence definition
3001          */
3002         Sequence ms = mc.getSequence();
3003         jalview.datamodel.Sequence djs = null;
3004         String sqid = ms.getDsseqid();
3005         if (sqid != null && sqid.length() > 0)
3006         {
3007           /*
3008            * recover dataset sequence
3009            */
3010           djs = (jalview.datamodel.Sequence) seqRefIds.get(sqid);
3011         }
3012         else
3013         {
3014           System.err
3015                   .println("Warning - making up dataset sequence id for DbRef sequence map reference");
3016           sqid = ((Object) ms).toString(); // make up a new hascode for
3017           // undefined dataset sequence hash
3018           // (unlikely to happen)
3019         }
3020
3021         if (djs == null)
3022         {
3023           /**
3024            * make a new dataset sequence and add it to refIds hash
3025            */
3026           djs = new jalview.datamodel.Sequence(ms.getName(), ms
3027                   .getSequence());
3028           djs.setStart(jmap.getMap().getToLowest());
3029           djs.setEnd(jmap.getMap().getToHighest());
3030           djs.setVamsasId(uniqueSetSuffix + sqid);
3031           jmap.setTo(djs);
3032           seqRefIds.put(sqid, djs);
3033
3034         }
3035         jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
3036         addDBRefs(djs, ms);
3037
3038       }
3039     }
3040     return (jmap);
3041
3042   }
3043
3044   public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
3045           boolean keepSeqRefs)
3046   {
3047     initSeqRefs();
3048     jalview.schemabinding.version2.JalviewModel jm = SaveState(ap, null,
3049             null);
3050
3051     if (!keepSeqRefs)
3052     {
3053       clearSeqRefs();
3054       jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
3055     }
3056     else
3057     {
3058       uniqueSetSuffix = "";
3059       jm.getJalviewModelSequence().getViewport(0).setId(null); // we don't overwrite the view we just copied
3060     }
3061     if (this.frefedSequence==null)
3062     {
3063       frefedSequence = new Vector();
3064     }
3065
3066     viewportsAdded = new Hashtable();
3067
3068     AlignFrame af = LoadFromObject(jm, null, false, null);
3069     af.alignPanels.clear();
3070     af.closeMenuItem_actionPerformed(true);
3071
3072     /*
3073      * if(ap.av.alignment.getAlignmentAnnotation()!=null) { for(int i=0; i<ap.av.alignment.getAlignmentAnnotation().length;
3074      * i++) { if(!ap.av.alignment.getAlignmentAnnotation()[i].autoCalculated) {
3075      * af.alignPanel.av.alignment.getAlignmentAnnotation()[i] =
3076      * ap.av.alignment.getAlignmentAnnotation()[i]; } } }
3077      */
3078
3079     return af.alignPanel;
3080   }
3081
3082   /**
3083    * flag indicating if hashtables should be cleared on finalization TODO this
3084    * flag may not be necessary
3085    */
3086   private boolean _cleartables = true;
3087
3088   private Hashtable jvids2vobj;
3089
3090   /*
3091    * (non-Javadoc)
3092    *
3093    * @see java.lang.Object#finalize()
3094    */
3095   protected void finalize() throws Throwable
3096   {
3097     // really make sure we have no buried refs left.
3098     if (_cleartables)
3099     {
3100       clearSeqRefs();
3101     }
3102     this.seqRefIds = null;
3103     this.seqsToIds = null;
3104     super.finalize();
3105   }
3106
3107   private void warn(String msg)
3108   {
3109     warn(msg, null);
3110   }
3111
3112   private void warn(String msg, Exception e)
3113   {
3114     if (Cache.log != null)
3115     {
3116       if (e != null)
3117       {
3118         Cache.log.warn(msg, e);
3119       }
3120       else
3121       {
3122         Cache.log.warn(msg);
3123       }
3124     }
3125     else
3126     {
3127       System.err.println("Warning: " + msg);
3128       if (e != null)
3129       {
3130         e.printStackTrace();
3131       }
3132     }
3133   }
3134
3135   /**
3136    * set the object to ID mapping tables used to write/recover objects and XML
3137    * ID strings for the jalview project. If external tables are provided then
3138    * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
3139    * object goes out of scope. - also populates the datasetIds hashtable with
3140    * alignment objects containing dataset sequences
3141    *
3142    * @param vobj2jv
3143    *                Map from ID strings to jalview datamodel
3144    * @param jv2vobj
3145    *                Map from jalview datamodel to ID strings
3146    *
3147    *
3148    */
3149   public void setObjectMappingTables(Hashtable vobj2jv,
3150           IdentityHashMap jv2vobj)
3151   {
3152     this.jv2vobj = jv2vobj;
3153     this.vobj2jv = vobj2jv;
3154     Iterator ds = jv2vobj.keySet().iterator();
3155     String id;
3156     while (ds.hasNext())
3157     {
3158       Object jvobj = ds.next();
3159       id = jv2vobj.get(jvobj).toString();
3160       if (jvobj instanceof jalview.datamodel.Alignment)
3161       {
3162         if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
3163         {
3164           addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
3165         }
3166       }
3167       else if (jvobj instanceof jalview.datamodel.Sequence)
3168       {
3169         // register sequence object so the XML parser can recover it.
3170         if (seqRefIds == null)
3171         {
3172           seqRefIds = new Hashtable();
3173         }
3174         if (seqsToIds == null)
3175         {
3176           seqsToIds = new IdentityHashMap();
3177         }
3178         seqRefIds.put(jv2vobj.get(jvobj).toString(), jvobj);
3179         seqsToIds.put(jvobj, id);
3180       }
3181       else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
3182       {
3183         if (annotationIds == null)
3184         {
3185           annotationIds = new Hashtable();
3186         }
3187         String anid;
3188         annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvobj);
3189         jalview.datamodel.AlignmentAnnotation jvann = (jalview.datamodel.AlignmentAnnotation) jvobj;
3190         if (jvann.annotationId == null)
3191         {
3192           jvann.annotationId = anid;
3193         }
3194         if (!jvann.annotationId.equals(anid))
3195         {
3196           // TODO verify that this is the correct behaviour
3197           this.warn("Overriding Annotation ID for " + anid
3198                   + " from different id : " + jvann.annotationId);
3199           jvann.annotationId = anid;
3200         }
3201       }
3202       else if (jvobj instanceof String)
3203       {
3204         if (jvids2vobj == null)
3205         {
3206           jvids2vobj = new Hashtable();
3207           jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
3208         }
3209       }
3210       else
3211         Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
3212     }
3213   }
3214
3215   /**
3216    * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
3217    * objects created from the project archive. If string is null (default for
3218    * construction) then suffix will be set automatically.
3219    *
3220    * @param string
3221    */
3222   public void setUniqueSetSuffix(String string)
3223   {
3224     uniqueSetSuffix = string;
3225
3226   }
3227
3228   /**
3229    * uses skipList2 as the skipList for skipping views on sequence sets
3230    * associated with keys in the skipList
3231    *
3232    * @param skipList2
3233    */
3234   public void setSkipList(Hashtable skipList2)
3235   {
3236     skipList = skipList2;
3237   }
3238
3239 }