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         groups[i].setShowUnconserved(sg.getShowunconserved());
 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.setShowUnconserved(av.getShowUnconserved());
1026     view.setWrapAlignment(av.getWrapAlignment());
1027     view.setTextCol1(av.textColour.getRGB());
1028     view.setTextCol2(av.textColour2.getRGB());
1029     view.setTextColThreshold(av.thresholdTextColour);
1030
1031     if (av.featuresDisplayed != null)
1032     {
1033       jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
1034
1035       String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
1036
1037       Vector settingsAdded = new Vector();
1038       for (int ro = 0; ro < renderOrder.length; ro++)
1039       {
1040         Setting setting = new Setting();
1041         setting.setType(renderOrder[ro]);
1042         setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
1043                 .getColour(renderOrder[ro]).getRGB());
1044
1045         setting.setDisplay(av.featuresDisplayed
1046                 .containsKey(renderOrder[ro]));
1047         float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
1048                 renderOrder[ro]);
1049         if (rorder > -1)
1050         {
1051           setting.setOrder(rorder);
1052         }
1053         fs.addSetting(setting);
1054         settingsAdded.addElement(renderOrder[ro]);
1055       }
1056
1057       // Make sure we save none displayed feature settings
1058       Enumeration en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
1059               .keys();
1060       while (en.hasMoreElements())
1061       {
1062         String key = en.nextElement().toString();
1063         if (settingsAdded.contains(key))
1064         {
1065           continue;
1066         }
1067
1068         Setting setting = new Setting();
1069         setting.setType(key);
1070         setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
1071                 .getColour(key).getRGB());
1072
1073         setting.setDisplay(false);
1074         float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
1075                 key);
1076         if (rorder > -1)
1077         {
1078           setting.setOrder(rorder);
1079         }
1080         fs.addSetting(setting);
1081         settingsAdded.addElement(key);
1082       }
1083       en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keys();
1084       Vector groupsAdded = new Vector();
1085       while (en.hasMoreElements())
1086       {
1087         String grp = en.nextElement().toString();
1088         if (groupsAdded.contains(grp))
1089         {
1090           continue;
1091         }
1092         Group g = new Group();
1093         g.setName(grp);
1094         g
1095                 .setDisplay(((Boolean) ap.seqPanel.seqCanvas
1096                         .getFeatureRenderer().featureGroups.get(grp))
1097                         .booleanValue());
1098         fs.addGroup(g);
1099         groupsAdded.addElement(grp);
1100       }
1101       jms.setFeatureSettings(fs);
1102
1103     }
1104
1105     if (av.hasHiddenColumns)
1106     {
1107       for (int c = 0; c < av.getColumnSelection().getHiddenColumns().size(); c++)
1108       {
1109         int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
1110                 .elementAt(c);
1111         HiddenColumns hc = new HiddenColumns();
1112         hc.setStart(region[0]);
1113         hc.setEnd(region[1]);
1114         view.addHiddenColumns(hc);
1115       }
1116     }
1117
1118     jms.addViewport(view);
1119
1120     object.setJalviewModelSequence(jms);
1121     object.getVamsasModel().addSequenceSet(vamsasSet);
1122
1123     if (jout != null && fileName != null)
1124     {
1125       // We may not want to write the object to disk,
1126       // eg we can copy the alignViewport to a new view object
1127       // using save and then load
1128       try
1129       {
1130         JarEntry entry = new JarEntry(fileName);
1131         jout.putNextEntry(entry);
1132         PrintWriter pout = new PrintWriter(new OutputStreamWriter(jout,
1133                 "UTF-8"));
1134         org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller(
1135                 pout);
1136         marshaller.marshal(object);
1137         pout.flush();
1138         jout.closeEntry();
1139       } catch (Exception ex)
1140       {
1141         // TODO: raise error in GUI if marshalling failed.
1142         ex.printStackTrace();
1143       }
1144     }
1145     return object;
1146   }
1147
1148   /**
1149    * External mapping between jalview objects and objects yielding a valid and
1150    * unique object ID string. This is null for normal Jalview project IO, but
1151    * non-null when a jalview project is being read or written as part of a
1152    * vamsas session.
1153    */
1154   IdentityHashMap jv2vobj = null;
1155
1156   /**
1157    * Construct a unique ID for jvobj using either existing bindings or if none
1158    * exist, the result of the hashcode call for the object.
1159    *
1160    * @param jvobj
1161    *                jalview data object
1162    * @return unique ID for referring to jvobj
1163    */
1164   private String makeHashCode(Object jvobj, String altCode)
1165   {
1166     if (jv2vobj != null)
1167     {
1168       Object id = jv2vobj.get(jvobj);
1169       if (id != null)
1170       {
1171         return id.toString();
1172       }
1173       // check string ID mappings
1174       if (jvids2vobj != null && jvobj instanceof String)
1175       {
1176         id = jvids2vobj.get(jvobj);
1177       }
1178       if (id != null)
1179       {
1180         return id.toString();
1181       }
1182       // give up and warn that something has gone wrong
1183       warn("Cannot find ID for object in external mapping : " + jvobj);
1184     }
1185     return altCode;
1186   }
1187
1188   /**
1189    * return local jalview object mapped to ID, if it exists
1190    *
1191    * @param idcode
1192    *                (may be null)
1193    * @return null or object bound to idcode
1194    */
1195   private Object retrieveExistingObj(String idcode)
1196   {
1197     if (idcode != null && vobj2jv != null)
1198     {
1199       return vobj2jv.get(idcode);
1200     }
1201     return null;
1202   }
1203
1204   /**
1205    * binding from ID strings from external mapping table to jalview data model
1206    * objects.
1207    */
1208   private Hashtable vobj2jv;
1209
1210   private Sequence createVamsasSequence(String id, SequenceI jds)
1211   {
1212     return createVamsasSequence(true, id, jds, null);
1213   }
1214
1215   private Sequence createVamsasSequence(boolean recurse, String id,
1216           SequenceI jds, SequenceI parentseq)
1217   {
1218     Sequence vamsasSeq = new Sequence();
1219     vamsasSeq.setId(id);
1220     vamsasSeq.setName(jds.getName());
1221     vamsasSeq.setSequence(jds.getSequenceAsString());
1222     vamsasSeq.setDescription(jds.getDescription());
1223     jalview.datamodel.DBRefEntry[] dbrefs = null;
1224     if (jds.getDatasetSequence() != null)
1225     {
1226       vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
1227       if (jds.getDatasetSequence().getDBRef() != null)
1228       {
1229         dbrefs = jds.getDatasetSequence().getDBRef();
1230       }
1231     }
1232     else
1233     {
1234       vamsasSeq.setDsseqid(id); // so we can tell which sequences really are
1235       // dataset sequences only
1236       dbrefs = jds.getDBRef();
1237     }
1238     if (dbrefs != null)
1239     {
1240       for (int d = 0; d < dbrefs.length; d++)
1241       {
1242         DBRef dbref = new DBRef();
1243         dbref.setSource(dbrefs[d].getSource());
1244         dbref.setVersion(dbrefs[d].getVersion());
1245         dbref.setAccessionId(dbrefs[d].getAccessionId());
1246         if (dbrefs[d].hasMap())
1247         {
1248           Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
1249                   jds, recurse);
1250           dbref.setMapping(mp);
1251         }
1252         vamsasSeq.addDBRef(dbref);
1253       }
1254     }
1255     return vamsasSeq;
1256   }
1257
1258   private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
1259           SequenceI parentseq, SequenceI jds, boolean recurse)
1260   {
1261     Mapping mp = null;
1262     if (jmp.getMap() != null)
1263     {
1264       mp = new Mapping();
1265
1266       jalview.util.MapList mlst = jmp.getMap();
1267       int r[] = mlst.getFromRanges();
1268       for (int s = 0; s < r.length; s += 2)
1269       {
1270         MapListFrom mfrom = new MapListFrom();
1271         mfrom.setStart(r[s]);
1272         mfrom.setEnd(r[s + 1]);
1273         mp.addMapListFrom(mfrom);
1274       }
1275       r = mlst.getToRanges();
1276       for (int s = 0; s < r.length; s += 2)
1277       {
1278         MapListTo mto = new MapListTo();
1279         mto.setStart(r[s]);
1280         mto.setEnd(r[s + 1]);
1281         mp.addMapListTo(mto);
1282       }
1283       mp.setMapFromUnit(mlst.getFromRatio());
1284       mp.setMapToUnit(mlst.getToRatio());
1285       if (jmp.getTo() != null)
1286       {
1287         MappingChoice mpc = new MappingChoice();
1288         if (recurse
1289                 && (parentseq != jmp.getTo() || parentseq
1290                         .getDatasetSequence() != jmp.getTo()))
1291         {
1292           mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo()),
1293                   jmp.getTo(), jds));
1294         }
1295         else
1296         {
1297           String jmpid = "";
1298           SequenceI ps = null;
1299           if (parentseq != jmp.getTo()
1300                   && parentseq.getDatasetSequence() != jmp.getTo())
1301           {
1302             // chaining dbref rather than a handshaking one
1303             jmpid = seqHash(ps = jmp.getTo());
1304           }
1305           else
1306           {
1307             jmpid = seqHash(ps = parentseq);
1308           }
1309           mpc.setDseqFor(jmpid);
1310           if (!seqRefIds.containsKey(mpc.getDseqFor()))
1311           {
1312             jalview.bin.Cache.log.debug("creatign new DseqFor ID");
1313             seqRefIds.put(mpc.getDseqFor(), ps);
1314           }
1315           else
1316           {
1317             jalview.bin.Cache.log.debug("reusing DseqFor ID");
1318           }
1319         }
1320         mp.setMappingChoice(mpc);
1321       }
1322     }
1323     return mp;
1324   }
1325
1326   String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
1327           Vector userColours, JalviewModelSequence jms)
1328   {
1329     String id = null;
1330     jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
1331
1332     if (!userColours.contains(ucs))
1333     {
1334       userColours.add(ucs);
1335
1336       java.awt.Color[] colours = ucs.getColours();
1337       jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
1338       jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
1339
1340       for (int i = 0; i < colours.length; i++)
1341       {
1342         jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
1343         col.setName(ResidueProperties.aa[i]);
1344         col.setRGB(jalview.util.Format.getHexString(colours[i]));
1345         jbucs.addColour(col);
1346       }
1347       if (ucs.getLowerCaseColours() != null)
1348       {
1349         colours = ucs.getLowerCaseColours();
1350         for (int i = 0; i < colours.length; i++)
1351         {
1352           jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
1353           col.setName(ResidueProperties.aa[i].toLowerCase());
1354           col.setRGB(jalview.util.Format.getHexString(colours[i]));
1355           jbucs.addColour(col);
1356         }
1357       }
1358
1359       id = "ucs" + userColours.indexOf(ucs);
1360       uc.setId(id);
1361       uc.setUserColourScheme(jbucs);
1362       jms.addUserColours(uc);
1363     }
1364
1365     return id;
1366   }
1367
1368   jalview.schemes.UserColourScheme GetUserColourScheme(
1369           JalviewModelSequence jms, String id)
1370   {
1371     UserColours[] uc = jms.getUserColours();
1372     UserColours colours = null;
1373
1374     for (int i = 0; i < uc.length; i++)
1375     {
1376       if (uc[i].getId().equals(id))
1377       {
1378         colours = uc[i];
1379
1380         break;
1381       }
1382     }
1383
1384     java.awt.Color[] newColours = new java.awt.Color[24];
1385
1386     for (int i = 0; i < 24; i++)
1387     {
1388       newColours[i] = new java.awt.Color(Integer.parseInt(colours
1389               .getUserColourScheme().getColour(i).getRGB(), 16));
1390     }
1391
1392     jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
1393             newColours);
1394
1395     if (colours.getUserColourScheme().getColourCount() > 24)
1396     {
1397       newColours = new java.awt.Color[23];
1398       for (int i = 0; i < 23; i++)
1399       {
1400         newColours[i] = new java.awt.Color(Integer.parseInt(colours
1401                 .getUserColourScheme().getColour(i + 24).getRGB(), 16));
1402       }
1403       ucs.setLowerCaseColours(newColours);
1404     }
1405
1406     return ucs;
1407   }
1408
1409   /**
1410    * contains last error message (if any) encountered by XML loader.
1411    */
1412   String errorMessage = null;
1413
1414   /**
1415    * flag to control whether the Jalview2XML_V1 parser should be deferred to if
1416    * exceptions are raised during project XML parsing
1417    */
1418   public boolean attemptversion1parse = true;
1419
1420   /**
1421    * Load a jalview project archive from a jar file
1422    *
1423    * @param file -
1424    *                HTTP URL or filename
1425    */
1426   public AlignFrame LoadJalviewAlign(final String file)
1427   {
1428
1429     jalview.gui.AlignFrame af = null;
1430
1431     try
1432     {
1433       // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
1434       // Workaround is to make sure caller implements the JarInputStreamProvider
1435       // interface
1436       // so we can re-open the jar input stream for each entry.
1437
1438       jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
1439       af = LoadJalviewAlign(jprovider);
1440     } catch (MalformedURLException e)
1441     {
1442       errorMessage = "Invalid URL format for '" + file + "'";
1443       reportErrors();
1444     }
1445     return af;
1446   }
1447
1448   private jarInputStreamProvider createjarInputStreamProvider(
1449           final String file) throws MalformedURLException
1450   {
1451     URL url = null;
1452     errorMessage = null;
1453     uniqueSetSuffix = null;
1454     seqRefIds = null;
1455     viewportsAdded = null;
1456     frefedSequence = null;
1457
1458     if (file.startsWith("http://"))
1459     {
1460       url = new URL(file);
1461     }
1462     final URL _url = url;
1463     return new jarInputStreamProvider()
1464     {
1465
1466       public JarInputStream getJarInputStream() throws IOException
1467       {
1468         if (_url != null)
1469         {
1470           return new JarInputStream(_url.openStream());
1471         }
1472         else
1473         {
1474           return new JarInputStream(new FileInputStream(file));
1475         }
1476       }
1477
1478       public String getFilename()
1479       {
1480         return file;
1481       }
1482     };
1483   }
1484
1485   /**
1486    * Recover jalview session from a jalview project archive. Caller may
1487    * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
1488    * themselves. Any null fields will be initialised with default values,
1489    * non-null fields are left alone.
1490    *
1491    * @param jprovider
1492    * @return
1493    */
1494   public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
1495   {
1496     errorMessage = null;
1497     if (uniqueSetSuffix == null)
1498     {
1499       uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
1500     }
1501     if (seqRefIds == null)
1502     {
1503       seqRefIds = new Hashtable();
1504     }
1505     if (viewportsAdded == null)
1506     {
1507       viewportsAdded = new Hashtable();
1508     }
1509     if (frefedSequence == null)
1510     {
1511       frefedSequence = new Vector();
1512     }
1513
1514     jalview.gui.AlignFrame af = null;
1515     Hashtable gatherToThisFrame = new Hashtable();
1516     final String file = jprovider.getFilename();
1517     try
1518     {
1519       JarInputStream jin = null;
1520       JarEntry jarentry = null;
1521       int entryCount = 1;
1522
1523       do
1524       {
1525         jin = jprovider.getJarInputStream();
1526         for (int i = 0; i < entryCount; i++)
1527         {
1528           jarentry = jin.getNextJarEntry();
1529         }
1530
1531         if (jarentry != null && jarentry.getName().endsWith(".xml"))
1532         {
1533           InputStreamReader in = new InputStreamReader(jin, "UTF-8");
1534           JalviewModel object = new JalviewModel();
1535
1536           Unmarshaller unmar = new Unmarshaller(object);
1537           unmar.setValidation(false);
1538           object = (JalviewModel) unmar.unmarshal(in);
1539           if (true) // !skipViewport(object))
1540           {
1541             af = LoadFromObject(object, file, true, jprovider);
1542             if (af.viewport.gatherViewsHere)
1543             {
1544               gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
1545             }
1546           }
1547           entryCount++;
1548         }
1549         else if (jarentry != null)
1550         {
1551           // Some other file here.
1552           entryCount++;
1553         }
1554       } while (jarentry != null);
1555       resolveFrefedSequences();
1556     } catch (java.io.FileNotFoundException ex)
1557     {
1558       ex.printStackTrace();
1559       errorMessage = "Couldn't locate Jalview XML file : " + file;
1560       System.err.println("Exception whilst loading jalview XML file : "
1561               + ex + "\n");
1562     } catch (java.net.UnknownHostException ex)
1563     {
1564       ex.printStackTrace();
1565       errorMessage = "Couldn't locate Jalview XML file : " + file;
1566       System.err.println("Exception whilst loading jalview XML file : "
1567               + ex + "\n");
1568     } catch (Exception ex)
1569     {
1570       System.err.println("Parsing as Jalview Version 2 file failed.");
1571       ex.printStackTrace(System.err);
1572       if (attemptversion1parse)
1573       {
1574         // Is Version 1 Jar file?
1575         try
1576         {
1577           af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(jprovider);
1578         } catch (Exception ex2)
1579         {
1580           System.err.println("Exception whilst loading as jalviewXMLV1:");
1581           ex2.printStackTrace();
1582           af = null;
1583         }
1584       }
1585       if (Desktop.instance != null)
1586       {
1587         Desktop.instance.stopLoading();
1588       }
1589       if (af != null)
1590       {
1591         System.out.println("Successfully loaded archive file");
1592         return af;
1593       }
1594       ex.printStackTrace();
1595
1596       System.err.println("Exception whilst loading jalview XML file : "
1597               + ex + "\n");
1598     } catch (OutOfMemoryError e)
1599     {
1600       new jalview.gui.OOMWarning("loading jalview XML file", e,
1601               Desktop.instance);
1602     }
1603
1604     if (Desktop.instance != null)
1605     {
1606       Desktop.instance.stopLoading();
1607     }
1608
1609     Enumeration en = gatherToThisFrame.elements();
1610     while (en.hasMoreElements())
1611     {
1612       Desktop.instance.gatherViews((AlignFrame) en.nextElement());
1613     }
1614     if (errorMessage != null)
1615     {
1616       reportErrors();
1617     }
1618     return af;
1619   }
1620
1621   /**
1622    * check errorMessage for a valid error message and raise an error box in the
1623    * GUI or write the current errorMessage to stderr and then clear the error
1624    * state.
1625    */
1626   protected void reportErrors()
1627   {
1628     reportErrors(false);
1629   }
1630
1631   protected void reportErrors(final boolean saving)
1632   {
1633     if (errorMessage != null)
1634     {
1635       final String finalErrorMessage = errorMessage;
1636       if (raiseGUI)
1637       {
1638         javax.swing.SwingUtilities.invokeLater(new Runnable()
1639         {
1640           public void run()
1641           {
1642             JOptionPane.showInternalMessageDialog(Desktop.desktop,
1643                     finalErrorMessage, "Error "
1644                             + (saving ? "saving" : "loading")
1645                             + " Jalview file", JOptionPane.WARNING_MESSAGE);
1646           }
1647         });
1648       }
1649       else
1650       {
1651         System.err.println("Problem loading Jalview file: " + errorMessage);
1652       }
1653     }
1654     errorMessage = null;
1655   }
1656
1657   Hashtable alreadyLoadedPDB;
1658
1659   /**
1660    * when set, local views will be updated from view stored in JalviewXML
1661    * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
1662    * sync if this is set to true.
1663    */
1664   private boolean updateLocalViews = false;
1665
1666   String loadPDBFile(jarInputStreamProvider jprovider, String pdbId)
1667   {
1668     if (alreadyLoadedPDB == null)
1669       alreadyLoadedPDB = new Hashtable();
1670
1671     if (alreadyLoadedPDB.containsKey(pdbId))
1672       return alreadyLoadedPDB.get(pdbId).toString();
1673
1674     try
1675     {
1676       JarInputStream jin = jprovider.getJarInputStream();
1677       /*
1678        * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
1679        * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
1680        * FileInputStream(jprovider)); }
1681        */
1682
1683       JarEntry entry = null;
1684       do
1685       {
1686         entry = jin.getNextJarEntry();
1687       } while (entry != null && !entry.getName().equals(pdbId));
1688       if (entry != null)
1689       {
1690         BufferedReader in = new BufferedReader(new InputStreamReader(jin));
1691         File outFile = File.createTempFile("jalview_pdb", ".txt");
1692         outFile.deleteOnExit();
1693         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
1694         String data;
1695
1696         while ((data = in.readLine()) != null)
1697         {
1698           out.println(data);
1699         }
1700         try
1701         {
1702           out.flush();
1703         } catch (Exception foo)
1704         {
1705         }
1706         ;
1707         out.close();
1708
1709         alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath());
1710         return outFile.getAbsolutePath();
1711       }
1712       else
1713       {
1714         warn("Couldn't find PDB file entry in Jalview Jar for " + pdbId);
1715       }
1716     } catch (Exception ex)
1717     {
1718       ex.printStackTrace();
1719     }
1720
1721     return null;
1722   }
1723
1724   /**
1725    * Load alignment frame from jalview XML DOM object
1726    *
1727    * @param object
1728    *                DOM
1729    * @param file
1730    *                filename source string
1731    * @param loadTreesAndStructures
1732    *                when false only create Viewport
1733    * @param jprovider
1734    *                data source provider
1735    * @return alignment frame created from view stored in DOM
1736    */
1737   AlignFrame LoadFromObject(JalviewModel object, String file,
1738           boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
1739   {
1740     SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
1741     Sequence[] vamsasSeq = vamsasSet.getSequence();
1742
1743     JalviewModelSequence jms = object.getJalviewModelSequence();
1744
1745     Viewport view = jms.getViewport(0);
1746     // ////////////////////////////////
1747     // LOAD SEQUENCES
1748
1749     Vector hiddenSeqs = null;
1750     jalview.datamodel.Sequence jseq;
1751
1752     ArrayList tmpseqs = new ArrayList();
1753
1754     boolean multipleView = false;
1755
1756     JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
1757     int vi = 0; // counter in vamsasSeq array
1758     for (int i = 0; i < JSEQ.length; i++)
1759     {
1760       String seqId = JSEQ[i].getId();
1761
1762       if (seqRefIds.get(seqId) != null)
1763       {
1764         tmpseqs.add((jalview.datamodel.Sequence) seqRefIds.get(seqId));
1765         multipleView = true;
1766       }
1767       else
1768       {
1769         jseq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
1770                 vamsasSeq[vi].getSequence());
1771         jseq.setDescription(vamsasSeq[vi].getDescription());
1772         jseq.setStart(JSEQ[i].getStart());
1773         jseq.setEnd(JSEQ[i].getEnd());
1774         jseq.setVamsasId(uniqueSetSuffix + seqId);
1775         seqRefIds.put(vamsasSeq[vi].getId(), jseq);
1776         tmpseqs.add(jseq);
1777         vi++;
1778       }
1779
1780       if (JSEQ[i].getHidden())
1781       {
1782         if (hiddenSeqs == null)
1783         {
1784           hiddenSeqs = new Vector();
1785         }
1786
1787         hiddenSeqs.addElement((jalview.datamodel.Sequence) seqRefIds
1788                 .get(seqId));
1789       }
1790
1791     }
1792
1793     // /
1794     // Create the alignment object from the sequence set
1795     // ///////////////////////////////
1796     jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[tmpseqs
1797             .size()];
1798
1799     tmpseqs.toArray(orderedSeqs);
1800
1801     jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(
1802             orderedSeqs);
1803
1804     // / Add the alignment properties
1805     for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
1806     {
1807       SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
1808       al.setProperty(ssp.getKey(), ssp.getValue());
1809     }
1810
1811     // /
1812     // SequenceFeatures are added to the DatasetSequence,
1813     // so we must create or recover the dataset before loading features
1814     // ///////////////////////////////
1815     if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
1816     {
1817       // older jalview projects do not have a dataset id.
1818       al.setDataset(null);
1819     }
1820     else
1821     {
1822       recoverDatasetFor(vamsasSet, al);
1823     }
1824     // ///////////////////////////////
1825
1826     Hashtable pdbloaded = new Hashtable();
1827     if (!multipleView)
1828     {
1829       // load sequence features, database references and any associated PDB
1830       // structures for the alignment
1831       for (int i = 0; i < vamsasSeq.length; i++)
1832       {
1833         if (JSEQ[i].getFeaturesCount() > 0)
1834         {
1835           Features[] features = JSEQ[i].getFeatures();
1836           for (int f = 0; f < features.length; f++)
1837           {
1838             jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
1839                     features[f].getType(), features[f].getDescription(),
1840                     features[f].getStatus(), features[f].getBegin(),
1841                     features[f].getEnd(), features[f].getFeatureGroup());
1842
1843             sf.setScore(features[f].getScore());
1844             for (int od = 0; od < features[f].getOtherDataCount(); od++)
1845             {
1846               OtherData keyValue = features[f].getOtherData(od);
1847               if (keyValue.getKey().startsWith("LINK"))
1848               {
1849                 sf.addLink(keyValue.getValue());
1850               }
1851               else
1852               {
1853                 sf.setValue(keyValue.getKey(), keyValue.getValue());
1854               }
1855
1856             }
1857
1858             al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1859           }
1860         }
1861         if (vamsasSeq[i].getDBRefCount() > 0)
1862         {
1863           addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]);
1864         }
1865         if (JSEQ[i].getPdbidsCount() > 0)
1866         {
1867           Pdbids[] ids = JSEQ[i].getPdbids();
1868           for (int p = 0; p < ids.length; p++)
1869           {
1870             jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
1871             entry.setId(ids[p].getId());
1872             entry.setType(ids[p].getType());
1873             if (ids[p].getFile() != null)
1874             {
1875               if (!pdbloaded.containsKey(ids[p].getFile()))
1876               {
1877                 entry.setFile(loadPDBFile(jprovider, ids[p].getId()));
1878               }
1879               else
1880               {
1881                 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1882               }
1883             }
1884
1885             al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1886           }
1887         }
1888       }
1889     } // end !multipleview
1890
1891     // ///////////////////////////////
1892     // LOAD SEQUENCE MAPPINGS
1893
1894     if (vamsasSet.getAlcodonFrameCount() > 0)
1895     {
1896       // TODO Potentially this should only be done once for all views of an
1897       // alignment
1898       AlcodonFrame[] alc = vamsasSet.getAlcodonFrame();
1899       for (int i = 0; i < alc.length; i++)
1900       {
1901         jalview.datamodel.AlignedCodonFrame cf = new jalview.datamodel.AlignedCodonFrame(
1902                 alc[i].getAlcodonCount());
1903         if (alc[i].getAlcodonCount() > 0)
1904         {
1905           Alcodon[] alcods = alc[i].getAlcodon();
1906           for (int p = 0; p < cf.codons.length; p++)
1907           {
1908             if (alcods[p].hasPos1() && alcods[p].hasPos2() && alcods[p].hasPos3())
1909             {
1910               // translated codons require three valid positions
1911               cf.codons[p] = new int[3];
1912               cf.codons[p][0] = (int) alcods[p].getPos1();
1913               cf.codons[p][1] = (int) alcods[p].getPos2();
1914               cf.codons[p][2] = (int) alcods[p].getPos3();
1915             } else {
1916               cf.codons[p] = null;
1917             }
1918           }
1919         }
1920         if (alc[i].getAlcodMapCount() > 0)
1921         {
1922           AlcodMap[] maps = alc[i].getAlcodMap();
1923           for (int m = 0; m < maps.length; m++)
1924           {
1925             SequenceI dnaseq = (SequenceI) seqRefIds
1926                     .get(maps[m].getDnasq());
1927             // Load Mapping
1928             jalview.datamodel.Mapping mapping = null;
1929             // attach to dna sequence reference.
1930             if (maps[m].getMapping() != null)
1931             {
1932               mapping = addMapping(maps[m].getMapping());
1933             }
1934             if (dnaseq != null)
1935             {
1936               cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
1937             }
1938             else
1939             {
1940               // defer to later
1941               frefedSequence.add(new Object[]
1942               { maps[m].getDnasq(), cf, mapping });
1943             }
1944           }
1945         }
1946         al.addCodonFrame(cf);
1947       }
1948
1949     }
1950
1951     // ////////////////////////////////
1952     // LOAD ANNOTATIONS
1953     boolean hideQuality = true, hideConservation = true, hideConsensus = true;
1954
1955     if (vamsasSet.getAnnotationCount() > 0)
1956     {
1957       Annotation[] an = vamsasSet.getAnnotation();
1958
1959       for (int i = 0; i < an.length; i++)
1960       {
1961         // set visibility for automatic annotation for this view
1962         if (an[i].getLabel().equals("Quality"))
1963         {
1964           hideQuality = false;
1965           continue;
1966         }
1967         else if (an[i].getLabel().equals("Conservation"))
1968         {
1969           hideConservation = false;
1970           continue;
1971         }
1972         else if (an[i].getLabel().equals("Consensus"))
1973         {
1974           hideConsensus = false;
1975           continue;
1976         }
1977         // set visiblity for other annotation in this view
1978         if (an[i].getId() != null
1979                 && annotationIds.containsKey(an[i].getId()))
1980         {
1981           jalview.datamodel.AlignmentAnnotation jda = (jalview.datamodel.AlignmentAnnotation) annotationIds
1982                   .get(an[i].getId());
1983           // in principle Visible should always be true for annotation displayed
1984           // in multiple views
1985           if (an[i].hasVisible())
1986             jda.visible = an[i].getVisible();
1987
1988           al.addAnnotation(jda);
1989
1990           continue;
1991         }
1992         // Construct new annotation from model.
1993         AnnotationElement[] ae = an[i].getAnnotationElement();
1994         jalview.datamodel.Annotation[] anot = null;
1995
1996         if (!an[i].getScoreOnly())
1997         {
1998           anot = new jalview.datamodel.Annotation[al.getWidth()];
1999
2000           for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
2001           {
2002             if (ae[aa].getPosition() >= anot.length)
2003               continue;
2004
2005             anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
2006
2007             ae[aa].getDisplayCharacter(), ae[aa].getDescription(), (ae[aa]
2008                     .getSecondaryStructure() == null || ae[aa]
2009                     .getSecondaryStructure().length() == 0) ? ' ' : ae[aa]
2010                     .getSecondaryStructure().charAt(0), ae[aa].getValue()
2011
2012             );
2013             // JBPNote: Consider verifying dataflow for IO of secondary
2014             // structure annotation read from Stockholm files
2015             // this was added to try to ensure that
2016             // if (anot[ae[aa].getPosition()].secondaryStructure>' ')
2017             // {
2018             // anot[ae[aa].getPosition()].displayCharacter = "";
2019             // }
2020             anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa]
2021                     .getColour());
2022           }
2023         }
2024         jalview.datamodel.AlignmentAnnotation jaa = null;
2025
2026         if (an[i].getGraph())
2027         {
2028           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
2029                   an[i].getDescription(), anot, 0, 0, an[i].getGraphType());
2030
2031           jaa.graphGroup = an[i].getGraphGroup();
2032
2033           if (an[i].getThresholdLine() != null)
2034           {
2035             jaa.setThreshold(new jalview.datamodel.GraphLine(an[i]
2036                     .getThresholdLine().getValue(), an[i]
2037                     .getThresholdLine().getLabel(), new java.awt.Color(
2038                     an[i].getThresholdLine().getColour())));
2039
2040           }
2041
2042         }
2043         else
2044         {
2045           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
2046                   an[i].getDescription(), anot);
2047         }
2048         // register new annotation
2049         if (an[i].getId() != null)
2050         {
2051           annotationIds.put(an[i].getId(), jaa);
2052           jaa.annotationId = an[i].getId();
2053         }
2054         // recover sequence association
2055         if (an[i].getSequenceRef() != null)
2056         {
2057           if (al.findName(an[i].getSequenceRef()) != null)
2058           {
2059             jaa.createSequenceMapping(al.findName(an[i].getSequenceRef()),
2060                     1, true);
2061             al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
2062           }
2063         }
2064         if (an[i].hasScore())
2065         {
2066           jaa.setScore(an[i].getScore());
2067         }
2068
2069         if (an[i].hasVisible())
2070           jaa.visible = an[i].getVisible();
2071
2072         al.addAnnotation(jaa);
2073       }
2074     }
2075
2076     // ///////////////////////
2077     // LOAD GROUPS
2078     // Create alignment markup and styles for this view
2079     if (jms.getJGroupCount() > 0)
2080     {
2081       JGroup[] groups = jms.getJGroup();
2082
2083       for (int i = 0; i < groups.length; i++)
2084       {
2085         ColourSchemeI cs = null;
2086
2087         if (groups[i].getColour() != null)
2088         {
2089           if (groups[i].getColour().startsWith("ucs"))
2090           {
2091             cs = GetUserColourScheme(jms, groups[i].getColour());
2092           }
2093           else
2094           {
2095             cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
2096           }
2097
2098           if (cs != null)
2099           {
2100             cs.setThreshold(groups[i].getPidThreshold(), true);
2101           }
2102         }
2103
2104         Vector seqs = new Vector();
2105
2106         for (int s = 0; s < groups[i].getSeqCount(); s++)
2107         {
2108           String seqId = groups[i].getSeq(s) + "";
2109           jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI) seqRefIds
2110                   .get(seqId);
2111
2112           if (ts != null)
2113           {
2114             seqs.addElement(ts);
2115           }
2116         }
2117
2118         if (seqs.size() < 1)
2119         {
2120           continue;
2121         }
2122
2123         jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
2124                 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
2125                 groups[i].getDisplayText(), groups[i].getColourText(),
2126                 groups[i].getStart(), groups[i].getEnd());
2127
2128         sg
2129                 .setOutlineColour(new java.awt.Color(groups[i]
2130                         .getOutlineColour()));
2131
2132         sg.textColour = new java.awt.Color(groups[i].getTextCol1());
2133         sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
2134         sg.setShowunconserved(groups[i].hasShowUnconserved() ? groups[i].isShowUnconserved() : false);
2135         sg.thresholdTextColour = groups[i].getTextColThreshold();
2136
2137         if (groups[i].getConsThreshold() != 0)
2138         {
2139           jalview.analysis.Conservation c = new jalview.analysis.Conservation(
2140                   "All", ResidueProperties.propHash, 3, sg
2141                           .getSequences(null), 0, sg.getWidth() - 1);
2142           c.calculate();
2143           c.verdict(false, 25);
2144           sg.cs.setConservation(c);
2145         }
2146
2147         al.addGroup(sg);
2148       }
2149     }
2150
2151     // ///////////////////////////////
2152     // LOAD VIEWPORT
2153
2154     // If we just load in the same jar file again, the sequenceSetId
2155     // will be the same, and we end up with multiple references
2156     // to the same sequenceSet. We must modify this id on load
2157     // so that each load of the file gives a unique id
2158     String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
2159     String viewId = (view.getId() == null ? null : view.getId()
2160             + uniqueSetSuffix);
2161     AlignFrame af = null;
2162     AlignViewport av = null;
2163     // now check to see if we really need to create a new viewport.
2164     if (multipleView && viewportsAdded.size() == 0)
2165     {
2166       // We recovered an alignment for which a viewport already exists.
2167       // TODO: fix up any settings necessary for overlaying stored state onto
2168       // state recovered from another document. (may not be necessary).
2169       // we may need a binding from a viewport in memory to one recovered from
2170       // XML.
2171       // and then recover its containing af to allow the settings to be applied.
2172       // TODO: fix for vamsas demo
2173       System.err
2174               .println("About to recover a viewport for existing alignment: Sequence set ID is "
2175                       + uniqueSeqSetId);
2176       Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
2177       if (seqsetobj != null)
2178       {
2179         if (seqsetobj instanceof String)
2180         {
2181           uniqueSeqSetId = (String) seqsetobj;
2182           System.err
2183                   .println("Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
2184                           + uniqueSeqSetId);
2185         }
2186         else
2187         {
2188           System.err
2189                   .println("Warning : Collision between sequence set ID string and existing jalview object mapping.");
2190         }
2191
2192       }
2193     }
2194     AlignmentPanel ap = null;
2195     boolean isnewview = true;
2196     if (viewId != null)
2197     {
2198       // Check to see if this alignment already has a view id == viewId
2199       jalview.gui.AlignmentPanel views[] = Desktop
2200               .getAlignmentPanels(uniqueSeqSetId);
2201       if (views != null && views.length > 0)
2202       {
2203         for (int v = 0; v < views.length; v++)
2204         {
2205           if (views[v].av.getViewId().equalsIgnoreCase(viewId))
2206           {
2207             // recover the existing alignpanel, alignframe, viewport
2208             af = views[v].alignFrame;
2209             av = views[v].av;
2210             ap = views[v];
2211             // TODO: could even skip resetting view settings if we don't want to
2212             // change the local settings from other jalview processes
2213             isnewview = false;
2214           }
2215         }
2216       }
2217     }
2218
2219     if (isnewview)
2220     {
2221       af = loadViewport(file, JSEQ, hiddenSeqs, al, hideConsensus,
2222               hideQuality, hideConservation, jms, view, uniqueSeqSetId,
2223               viewId);
2224       av = af.viewport;
2225       ap = af.alignPanel;
2226     }
2227     // LOAD TREES
2228     // /////////////////////////////////////
2229     if (loadTreesAndStructures && jms.getTreeCount() > 0)
2230     {
2231       try
2232       {
2233         for (int t = 0; t < jms.getTreeCount(); t++)
2234         {
2235
2236           Tree tree = jms.getTree(t);
2237
2238           TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
2239           if (tp == null)
2240           {
2241             tp = af.ShowNewickTree(new jalview.io.NewickFile(tree
2242                     .getNewick()), tree.getTitle(), tree.getWidth(), tree
2243                     .getHeight(), tree.getXpos(), tree.getYpos());
2244             if (tree.getId() != null)
2245             {
2246
2247             }
2248           }
2249           else
2250           {
2251             // update local tree attributes ?
2252             tp.setTitle(tree.getTitle());
2253             tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(), tree
2254                     .getWidth(), tree.getHeight()));
2255             tp.av = av; // af.viewport; // TODO: verify 'associate with all
2256             // views'
2257             // works still
2258             tp.treeCanvas.av = av; // af.viewport;
2259             tp.treeCanvas.ap = ap; // af.alignPanel;
2260
2261           }
2262           if (tp==null)
2263           {
2264             warn("There was a problem recovering stored Newick tree: \n"+tree.getNewick());
2265             continue;
2266           }
2267
2268           tp.fitToWindow.setState(tree.getFitToWindow());
2269           tp.fitToWindow_actionPerformed(null);
2270
2271           if (tree.getFontName() != null)
2272           {
2273             tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
2274                     .getFontStyle(), tree.getFontSize()));
2275           }
2276           else
2277           {
2278             tp.setTreeFont(new java.awt.Font(view.getFontName(), view
2279                     .getFontStyle(), tree.getFontSize()));
2280           }
2281
2282           tp.showPlaceholders(tree.getMarkUnlinked());
2283           tp.showBootstrap(tree.getShowBootstrap());
2284           tp.showDistances(tree.getShowDistances());
2285
2286           tp.treeCanvas.threshold = tree.getThreshold();
2287
2288           if (tree.getCurrentTree())
2289           {
2290             af.viewport.setCurrentTree(tp.getTree());
2291           }
2292         }
2293
2294       } catch (Exception ex)
2295       {
2296         ex.printStackTrace();
2297       }
2298     }
2299
2300     // //LOAD STRUCTURES
2301     if (loadTreesAndStructures)
2302     {
2303       for (int i = 0; i < JSEQ.length; i++)
2304       {
2305         if (JSEQ[i].getPdbidsCount() > 0)
2306         {
2307           Pdbids[] ids = JSEQ[i].getPdbids();
2308           for (int p = 0; p < ids.length; p++)
2309           {
2310             for (int s = 0; s < ids[p].getStructureStateCount(); s++)
2311             {
2312               // check to see if we haven't already created this structure view
2313               String sviewid = (ids[p].getStructureState(s).getViewId() == null) ? null
2314                       : ids[p].getStructureState(s).getViewId()
2315                               + uniqueSetSuffix;
2316               jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
2317               // Originally : ids[p].getFile()
2318               // : TODO: verify external PDB file recovery still works in normal
2319               // jalview project load
2320               jpdb.setFile(loadPDBFile(jprovider, ids[p].getId()));
2321               jpdb.setId(ids[p].getId());
2322
2323               int x = ids[p].getStructureState(s).getXpos();
2324               int y = ids[p].getStructureState(s).getYpos();
2325               int width = ids[p].getStructureState(s).getWidth();
2326               int height = ids[p].getStructureState(s).getHeight();
2327               AppJmol comp = null;
2328               JInternalFrame[] frames = null;
2329               do
2330               {
2331                 try
2332                 {
2333                   frames = Desktop.desktop.getAllFrames();
2334                 } catch (ArrayIndexOutOfBoundsException e)
2335                 {
2336                   // occasional No such child exceptions are thrown here...
2337                   frames = null;
2338                   try
2339                   {
2340                     Thread.sleep(10);
2341                   } catch (Exception f)
2342                   {
2343                   }
2344                   ;
2345                 }
2346               } while (frames == null);
2347               // search for any Jmol windows already open from other
2348               // alignment views that exactly match the stored structure state
2349               for (int f = 0; comp == null && f < frames.length; f++)
2350               {
2351                 if (frames[f] instanceof AppJmol)
2352                 {
2353                   if (sviewid != null
2354                           && ((AppJmol) frames[f]).getViewId().equals(
2355                                   sviewid))
2356                   {
2357                     // post jalview 2.4 schema includes structure view id
2358                     comp = (AppJmol) frames[f];
2359                   }
2360                   else if (frames[f].getX() == x && frames[f].getY() == y
2361                           && frames[f].getHeight() == height
2362                           && frames[f].getWidth() == width)
2363                   {
2364                     comp = (AppJmol) frames[f];
2365                   }
2366                 }
2367               }
2368               Desktop.desktop.getComponentAt(x, y);
2369
2370               String pdbFile = loadPDBFile(jprovider, ids[p].getId());
2371
2372               jalview.datamodel.SequenceI[] seq = new jalview.datamodel.SequenceI[]
2373               { (jalview.datamodel.SequenceI) seqRefIds.get(JSEQ[i].getId()
2374                       + "") };
2375
2376               if (comp == null)
2377               {
2378                 // create a new Jmol window
2379                 String state = ids[p].getStructureState(s).getContent();
2380
2381                 StringBuffer newFileLoc = new StringBuffer(state.substring(
2382                         0, state.indexOf("\"", state.indexOf("load")) + 1));
2383
2384                 newFileLoc.append(jpdb.getFile());
2385                 newFileLoc.append(state.substring(state.indexOf("\"", state
2386                         .indexOf("load \"") + 6)));
2387
2388                 new AppJmol(pdbFile, ids[p].getId(), seq, af.alignPanel,
2389                         newFileLoc.toString(), new java.awt.Rectangle(x, y,
2390                                 width, height), sviewid);
2391
2392               }
2393               else
2394               // if (comp != null)
2395               {
2396                 // NOTE: if the jalview project is part of a shared session then
2397                 // view synchronization should/could be done here.
2398
2399                 // add mapping for this sequence to the already open Jmol
2400                 // instance (if it doesn't already exist)
2401                 // These
2402                 StructureSelectionManager.getStructureSelectionManager()
2403                         .setMapping(seq, null, pdbFile,
2404                                 jalview.io.AppletFormatAdapter.FILE);
2405
2406                 ((AppJmol) comp).addSequence(seq);
2407               }
2408             }
2409           }
2410         }
2411       }
2412     }
2413
2414     return af;
2415   }
2416
2417   AlignFrame loadViewport(String file, JSeq[] JSEQ, Vector hiddenSeqs,
2418           Alignment al, boolean hideConsensus, boolean hideQuality,
2419           boolean hideConservation, JalviewModelSequence jms,
2420           Viewport view, String uniqueSeqSetId, String viewId)
2421   {
2422     AlignFrame af = null;
2423     af = new AlignFrame(al, view.getWidth(), view.getHeight(),
2424             uniqueSeqSetId, viewId);
2425
2426     af.setFileName(file, "Jalview");
2427
2428     for (int i = 0; i < JSEQ.length; i++)
2429     {
2430       af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i),
2431               new java.awt.Color(JSEQ[i].getColour()));
2432     }
2433
2434     af.viewport.gatherViewsHere = view.getGatheredViews();
2435
2436     if (view.getSequenceSetId() != null)
2437     {
2438       jalview.gui.AlignViewport av = (jalview.gui.AlignViewport) viewportsAdded
2439               .get(uniqueSeqSetId);
2440
2441       af.viewport.sequenceSetID = uniqueSeqSetId;
2442       if (av != null)
2443       {
2444         // propagate shared settings to this new view
2445         af.viewport.historyList = av.historyList;
2446         af.viewport.redoList = av.redoList;
2447       }
2448       else
2449       {
2450         viewportsAdded.put(uniqueSeqSetId, af.viewport);
2451       }
2452       // TODO: check if this method can be called repeatedly without
2453       // side-effects if alignpanel already registered.
2454       PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
2455     }
2456     // apply Hidden regions to view.
2457     if (hiddenSeqs != null)
2458     {
2459       for (int s = 0; s < JSEQ.length; s++)
2460       {
2461         jalview.datamodel.SequenceGroup hidden = new jalview.datamodel.SequenceGroup();
2462
2463         for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
2464         {
2465           hidden.addSequence(al
2466                   .getSequenceAt(JSEQ[s].getHiddenSequences(r)), false);
2467         }
2468         af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
2469       }
2470
2471       jalview.datamodel.SequenceI[] hseqs = new jalview.datamodel.SequenceI[hiddenSeqs
2472               .size()];
2473
2474       for (int s = 0; s < hiddenSeqs.size(); s++)
2475       {
2476         hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
2477       }
2478
2479       af.viewport.hideSequence(hseqs);
2480
2481     }
2482     // set visibility of annotation in view
2483     if ((hideConsensus || hideQuality || hideConservation)
2484             && al.getAlignmentAnnotation() != null)
2485     {
2486       int hSize = al.getAlignmentAnnotation().length;
2487       for (int h = 0; h < hSize; h++)
2488       {
2489         if ((hideConsensus && al.getAlignmentAnnotation()[h].label
2490                 .equals("Consensus"))
2491                 || (hideQuality && al.getAlignmentAnnotation()[h].label
2492                         .equals("Quality"))
2493                 || (hideConservation && al.getAlignmentAnnotation()[h].label
2494                         .equals("Conservation")))
2495         {
2496           al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
2497           hSize--;
2498           h--;
2499         }
2500       }
2501       af.alignPanel.adjustAnnotationHeight();
2502     }
2503     // recover view properties and display parameters
2504     if (view.getViewName() != null)
2505     {
2506       af.viewport.viewName = view.getViewName();
2507       af.setInitialTabVisible();
2508     }
2509     af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view
2510             .getHeight());
2511
2512     af.viewport.setShowAnnotation(view.getShowAnnotation());
2513     af.viewport.setAbovePIDThreshold(view.getPidSelected());
2514
2515     af.viewport.setColourText(view.getShowColourText());
2516
2517     af.viewport.setConservationSelected(view.getConservationSelected());
2518     af.viewport.setShowJVSuffix(view.getShowFullId());
2519     af.viewport.rightAlignIds = view.getRightAlignIds();
2520     af.viewport.setFont(new java.awt.Font(view.getFontName(), view
2521             .getFontStyle(), view.getFontSize()));
2522     af.alignPanel.fontChanged();
2523     af.viewport.setRenderGaps(view.getRenderGaps());
2524     af.viewport.setWrapAlignment(view.getWrapAlignment());
2525     af.alignPanel.setWrapAlignment(view.getWrapAlignment());
2526     af.viewport.setShowAnnotation(view.getShowAnnotation());
2527     af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
2528
2529     af.viewport.setShowBoxes(view.getShowBoxes());
2530
2531     af.viewport.setShowText(view.getShowText());
2532
2533     af.viewport.textColour = new java.awt.Color(view.getTextCol1());
2534     af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
2535     af.viewport.thresholdTextColour = view.getTextColThreshold();
2536     af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view.isShowUnconserved() : false);
2537     af.viewport.setStartRes(view.getStartRes());
2538     af.viewport.setStartSeq(view.getStartSeq());
2539
2540     ColourSchemeI cs = null;
2541     // apply colourschemes
2542     if (view.getBgColour() != null)
2543     {
2544       if (view.getBgColour().startsWith("ucs"))
2545       {
2546         cs = GetUserColourScheme(jms, view.getBgColour());
2547       }
2548       else if (view.getBgColour().startsWith("Annotation"))
2549       {
2550         // int find annotation
2551         for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
2552         {
2553           if (af.viewport.alignment.getAlignmentAnnotation()[i].label
2554                   .equals(view.getAnnotationColours().getAnnotation()))
2555           {
2556             if (af.viewport.alignment.getAlignmentAnnotation()[i]
2557                     .getThreshold() == null)
2558             {
2559               af.viewport.alignment.getAlignmentAnnotation()[i]
2560                       .setThreshold(new jalview.datamodel.GraphLine(view
2561                               .getAnnotationColours().getThreshold(),
2562                               "Threshold", java.awt.Color.black)
2563
2564                       );
2565             }
2566
2567             if (view.getAnnotationColours().getColourScheme()
2568                     .equals("None"))
2569             {
2570               cs = new AnnotationColourGradient(af.viewport.alignment
2571                       .getAlignmentAnnotation()[i], new java.awt.Color(view
2572                       .getAnnotationColours().getMinColour()),
2573                       new java.awt.Color(view.getAnnotationColours()
2574                               .getMaxColour()), view.getAnnotationColours()
2575                               .getAboveThreshold());
2576             }
2577             else if (view.getAnnotationColours().getColourScheme()
2578                     .startsWith("ucs"))
2579             {
2580               cs = new AnnotationColourGradient(af.viewport.alignment
2581                       .getAlignmentAnnotation()[i], GetUserColourScheme(
2582                       jms, view.getAnnotationColours().getColourScheme()),
2583                       view.getAnnotationColours().getAboveThreshold());
2584             }
2585             else
2586             {
2587               cs = new AnnotationColourGradient(af.viewport.alignment
2588                       .getAlignmentAnnotation()[i], ColourSchemeProperty
2589                       .getColour(al, view.getAnnotationColours()
2590                               .getColourScheme()), view
2591                       .getAnnotationColours().getAboveThreshold());
2592             }
2593
2594             // Also use these settings for all the groups
2595             if (al.getGroups() != null)
2596             {
2597               for (int g = 0; g < al.getGroups().size(); g++)
2598               {
2599                 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) al
2600                         .getGroups().elementAt(g);
2601
2602                 if (sg.cs == null)
2603                 {
2604                   continue;
2605                 }
2606
2607                 /*
2608                  * if
2609                  * (view.getAnnotationColours().getColourScheme().equals("None")) {
2610                  * sg.cs = new AnnotationColourGradient(
2611                  * af.viewport.alignment.getAlignmentAnnotation()[i], new
2612                  * java.awt.Color(view.getAnnotationColours(). getMinColour()),
2613                  * new java.awt.Color(view.getAnnotationColours().
2614                  * getMaxColour()),
2615                  * view.getAnnotationColours().getAboveThreshold()); } else
2616                  */
2617                 {
2618                   sg.cs = new AnnotationColourGradient(
2619                           af.viewport.alignment.getAlignmentAnnotation()[i],
2620                           sg.cs, view.getAnnotationColours()
2621                                   .getAboveThreshold());
2622                 }
2623
2624               }
2625             }
2626
2627             break;
2628           }
2629
2630         }
2631       }
2632       else
2633       {
2634         cs = ColourSchemeProperty.getColour(al, view.getBgColour());
2635       }
2636
2637       if (cs != null)
2638       {
2639         cs.setThreshold(view.getPidThreshold(), true);
2640         cs.setConsensus(af.viewport.hconsensus);
2641       }
2642     }
2643
2644     af.viewport.setGlobalColourScheme(cs);
2645     af.viewport.setColourAppliesToAllGroups(false);
2646
2647     if (view.getConservationSelected() && cs != null)
2648     {
2649       cs.setConservationInc(view.getConsThreshold());
2650     }
2651
2652     af.changeColour(cs);
2653
2654     af.viewport.setColourAppliesToAllGroups(true);
2655
2656     if (view.getShowSequenceFeatures())
2657     {
2658       af.viewport.showSequenceFeatures = true;
2659     }
2660     // recover featre settings
2661     if (jms.getFeatureSettings() != null)
2662     {
2663       af.viewport.featuresDisplayed = new Hashtable();
2664       String[] renderOrder = new String[jms.getFeatureSettings()
2665               .getSettingCount()];
2666       for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
2667       {
2668         Setting setting = jms.getFeatureSettings().getSetting(fs);
2669         if (setting.hasMincolour())
2670         {
2671           // TODO: determine how to set data independent bounds for a graduated colour scheme's range.
2672           GraduatedColor gc = new GraduatedColor(new java.awt.Color(setting.getMincolour()), new java.awt.Color(setting.getColour()),
2673                   0,1);
2674           if (setting.hasThreshold()) {
2675             gc.setThresh(setting.getThreshold());
2676             gc.setThreshType(setting.getThreshstate());
2677           }
2678         } else {
2679           af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
2680                   setting.getType(), new java.awt.Color(setting.getColour()));
2681         }
2682         renderOrder[fs] = setting.getType();
2683         if (setting.hasOrder())
2684           af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
2685                   setting.getType(), setting.getOrder());
2686         else
2687           af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
2688                   setting.getType(),
2689                   fs / jms.getFeatureSettings().getSettingCount());
2690         if (setting.getDisplay())
2691         {
2692           af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
2693                   setting.getColour()));
2694         }
2695       }
2696       af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
2697       Hashtable fgtable;
2698       af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable();
2699       for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
2700       {
2701         Group grp = jms.getFeatureSettings().getGroup(gs);
2702         fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
2703       }
2704     }
2705
2706     if (view.getHiddenColumnsCount() > 0)
2707     {
2708       for (int c = 0; c < view.getHiddenColumnsCount(); c++)
2709       {
2710         af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view
2711                 .getHiddenColumns(c).getEnd() // +1
2712                 );
2713       }
2714     }
2715
2716     af.setMenusFromViewport(af.viewport);
2717     // TODO: we don't need to do this if the viewport is aready visible.
2718     Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view
2719             .getHeight());
2720     return af;
2721   }
2722
2723   Hashtable skipList = null;
2724
2725   /**
2726    * TODO remove this method
2727    *
2728    * @param view
2729    * @return AlignFrame bound to sequenceSetId from view, if one exists. private
2730    *         AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
2731    *         throw new Error("Implementation Error. No skipList defined for this
2732    *         Jalview2XML instance."); } return (AlignFrame)
2733    *         skipList.get(view.getSequenceSetId()); }
2734    */
2735
2736   /**
2737    * Check if the Jalview view contained in object should be skipped or not.
2738    *
2739    * @param object
2740    * @return true if view's sequenceSetId is a key in skipList
2741    */
2742   private boolean skipViewport(JalviewModel object)
2743   {
2744     if (skipList == null)
2745     {
2746       return false;
2747     }
2748     String id;
2749     if (skipList.containsKey(id = object.getJalviewModelSequence()
2750             .getViewport()[0].getSequenceSetId()))
2751     {
2752       if (Cache.log != null && Cache.log.isDebugEnabled())
2753       {
2754         Cache.log.debug("Skipping seuqence set id " + id);
2755       }
2756       return true;
2757     }
2758     return false;
2759   }
2760
2761   public void AddToSkipList(AlignFrame af)
2762   {
2763     if (skipList == null)
2764     {
2765       skipList = new Hashtable();
2766     }
2767     skipList.put(af.getViewport().getSequenceSetId(), af);
2768   }
2769
2770   public void clearSkipList()
2771   {
2772     if (skipList != null)
2773     {
2774       skipList.clear();
2775       skipList = null;
2776     }
2777   }
2778
2779   private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al)
2780   {
2781     jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId());
2782     Vector dseqs = null;
2783     if (ds == null)
2784     {
2785       // create a list of new dataset sequences
2786       dseqs = new Vector();
2787     }
2788     for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
2789     {
2790       Sequence vamsasSeq = vamsasSet.getSequence(i);
2791       ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs);
2792     }
2793     // create a new dataset
2794     if (ds == null)
2795     {
2796       SequenceI[] dsseqs = new SequenceI[dseqs.size()];
2797       dseqs.copyInto(dsseqs);
2798       ds = new jalview.datamodel.Alignment(dsseqs);
2799       addDatasetRef(vamsasSet.getDatasetId(), ds);
2800     }
2801     // set the dataset for the newly imported alignment.
2802     if (al.getDataset() == null)
2803     {
2804       al.setDataset(ds);
2805     }
2806   }
2807
2808   /**
2809    *
2810    * @param vamsasSeq
2811    *                sequence definition to create/merge dataset sequence for
2812    * @param ds
2813    *                dataset alignment
2814    * @param dseqs
2815    *                vector to add new dataset sequence to
2816    */
2817   private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
2818           AlignmentI ds, Vector dseqs)
2819   {
2820     // JBP TODO: Check this is called for AlCodonFrames to support recovery of
2821     // xRef Codon Maps
2822     jalview.datamodel.Sequence sq = (jalview.datamodel.Sequence) seqRefIds
2823             .get(vamsasSeq.getId());
2824     jalview.datamodel.SequenceI dsq = null;
2825     if (sq != null && sq.getDatasetSequence() != null)
2826     {
2827       dsq = (jalview.datamodel.SequenceI) sq.getDatasetSequence();
2828     }
2829
2830     String sqid = vamsasSeq.getDsseqid();
2831     if (dsq == null)
2832     {
2833       // need to create or add a new dataset sequence reference to this sequence
2834       if (sqid != null)
2835       {
2836         dsq = (jalview.datamodel.SequenceI) seqRefIds.get(sqid);
2837       }
2838       // check again
2839       if (dsq == null)
2840       {
2841         // make a new dataset sequence
2842         dsq = sq.createDatasetSequence();
2843         if (sqid == null)
2844         {
2845           // make up a new dataset reference for this sequence
2846           sqid = seqHash(dsq);
2847         }
2848         dsq.setVamsasId(uniqueSetSuffix + sqid);
2849         seqRefIds.put(sqid, dsq);
2850         if (ds == null)
2851         {
2852           if (dseqs != null)
2853           {
2854             dseqs.addElement(dsq);
2855           }
2856         }
2857         else
2858         {
2859           ds.addSequence(dsq);
2860         }
2861       }
2862       else
2863       {
2864         if (sq != dsq)
2865         { // make this dataset sequence sq's dataset sequence
2866           sq.setDatasetSequence(dsq);
2867         }
2868       }
2869     }
2870     // TODO: refactor this as a merge dataset sequence function
2871     // now check that sq (the dataset sequence) sequence really is the union of
2872     // all references to it
2873     // boolean pre = sq.getStart() < dsq.getStart();
2874     // boolean post = sq.getEnd() > dsq.getEnd();
2875     // if (pre || post)
2876     if (sq != dsq)
2877     {
2878       StringBuffer sb = new StringBuffer();
2879       String newres = jalview.analysis.AlignSeq.extractGaps(
2880               jalview.util.Comparison.GapChars, sq.getSequenceAsString());
2881       if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
2882               && newres.length() > dsq.getLength())
2883       {
2884         // Update with the longer sequence.
2885         synchronized (dsq)
2886         {
2887           /*
2888            * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
2889            * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
2890            * sb.append(newres.substring(newres.length() - sq.getEnd() -
2891            * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
2892            */
2893           dsq.setSequence(sb.toString());
2894         }
2895         // TODO: merges will never happen if we 'know' we have the real dataset
2896         // sequence - this should be detected when id==dssid
2897         System.err.println("DEBUG Notice:  Merged dataset sequence"); // ("
2898         // + (pre ? "prepended" : "") + " "
2899         // + (post ? "appended" : ""));
2900       }
2901     }
2902   }
2903
2904   java.util.Hashtable datasetIds = null;
2905   java.util.IdentityHashMap dataset2Ids = null;
2906   private Alignment getDatasetFor(String datasetId)
2907   {
2908     if (datasetIds == null)
2909     {
2910       datasetIds = new Hashtable();
2911       return null;
2912     }
2913     if (datasetIds.containsKey(datasetId))
2914     {
2915       return (Alignment) datasetIds.get(datasetId);
2916     }
2917     return null;
2918   }
2919
2920   private void addDatasetRef(String datasetId, Alignment dataset)
2921   {
2922     if (datasetIds == null)
2923     {
2924       datasetIds = new Hashtable();
2925     }
2926     datasetIds.put(datasetId, dataset);
2927   }
2928   /**
2929    * make a new dataset ID for this jalview dataset alignment
2930    * @param dataset
2931    * @return
2932    */
2933   private String getDatasetIdRef(jalview.datamodel.Alignment dataset)
2934   {
2935     if (dataset.getDataset()!=null)
2936     {
2937       warn("Serious issue!  Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
2938     }
2939     String datasetId=makeHashCode(dataset, null);
2940     if (datasetId==null)
2941     {
2942       // make a new datasetId and record it
2943       if (dataset2Ids == null)
2944       {
2945         dataset2Ids = new IdentityHashMap();
2946       } else {
2947         datasetId = (String) dataset2Ids.get(dataset);
2948       }
2949       if (datasetId==null)
2950       {
2951         datasetId = "ds"+dataset2Ids.size()+1;
2952         dataset2Ids.put(dataset,datasetId);
2953       }
2954     }
2955     return datasetId;
2956   }
2957   private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
2958   {
2959     for (int d = 0; d < sequence.getDBRefCount(); d++)
2960     {
2961       DBRef dr = sequence.getDBRef(d);
2962       jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
2963               sequence.getDBRef(d).getSource(), sequence.getDBRef(d)
2964                       .getVersion(), sequence.getDBRef(d).getAccessionId());
2965       if (dr.getMapping() != null)
2966       {
2967         entry.setMap(addMapping(dr.getMapping()));
2968       }
2969       datasetSequence.addDBRef(entry);
2970     }
2971   }
2972
2973   private jalview.datamodel.Mapping addMapping(Mapping m)
2974   {
2975     SequenceI dsto = null;
2976     // Mapping m = dr.getMapping();
2977     int fr[] = new int[m.getMapListFromCount() * 2];
2978     Enumeration f = m.enumerateMapListFrom();
2979     for (int _i = 0; f.hasMoreElements(); _i += 2)
2980     {
2981       MapListFrom mf = (MapListFrom) f.nextElement();
2982       fr[_i] = mf.getStart();
2983       fr[_i + 1] = mf.getEnd();
2984     }
2985     int fto[] = new int[m.getMapListToCount() * 2];
2986     f = m.enumerateMapListTo();
2987     for (int _i = 0; f.hasMoreElements(); _i += 2)
2988     {
2989       MapListTo mf = (MapListTo) f.nextElement();
2990       fto[_i] = mf.getStart();
2991       fto[_i + 1] = mf.getEnd();
2992     }
2993     jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto,
2994             fr, fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit());
2995     if (m.getMappingChoice() != null)
2996     {
2997       MappingChoice mc = m.getMappingChoice();
2998       if (mc.getDseqFor() != null)
2999       {
3000         String dsfor = ""+mc.getDseqFor();
3001         if (seqRefIds.containsKey(dsfor))
3002         {
3003           /**
3004            * recover from hash
3005            */
3006           jmap.setTo((SequenceI) seqRefIds.get(dsfor));
3007         }
3008         else
3009         {
3010           frefedSequence.add(new Object[]
3011           { dsfor, jmap });
3012         }
3013       }
3014       else
3015       {
3016         /**
3017          * local sequence definition
3018          */
3019         Sequence ms = mc.getSequence();
3020         jalview.datamodel.Sequence djs = null;
3021         String sqid = ms.getDsseqid();
3022         if (sqid != null && sqid.length() > 0)
3023         {
3024           /*
3025            * recover dataset sequence
3026            */
3027           djs = (jalview.datamodel.Sequence) seqRefIds.get(sqid);
3028         }
3029         else
3030         {
3031           System.err
3032                   .println("Warning - making up dataset sequence id for DbRef sequence map reference");
3033           sqid = ((Object) ms).toString(); // make up a new hascode for
3034           // undefined dataset sequence hash
3035           // (unlikely to happen)
3036         }
3037
3038         if (djs == null)
3039         {
3040           /**
3041            * make a new dataset sequence and add it to refIds hash
3042            */
3043           djs = new jalview.datamodel.Sequence(ms.getName(), ms
3044                   .getSequence());
3045           djs.setStart(jmap.getMap().getToLowest());
3046           djs.setEnd(jmap.getMap().getToHighest());
3047           djs.setVamsasId(uniqueSetSuffix + sqid);
3048           jmap.setTo(djs);
3049           seqRefIds.put(sqid, djs);
3050
3051         }
3052         jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
3053         addDBRefs(djs, ms);
3054
3055       }
3056     }
3057     return (jmap);
3058
3059   }
3060
3061   public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
3062           boolean keepSeqRefs)
3063   {
3064     initSeqRefs();
3065     jalview.schemabinding.version2.JalviewModel jm = SaveState(ap, null,
3066             null);
3067
3068     if (!keepSeqRefs)
3069     {
3070       clearSeqRefs();
3071       jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
3072     }
3073     else
3074     {
3075       uniqueSetSuffix = "";
3076       jm.getJalviewModelSequence().getViewport(0).setId(null); // we don't overwrite the view we just copied
3077     }
3078     if (this.frefedSequence==null)
3079     {
3080       frefedSequence = new Vector();
3081     }
3082
3083     viewportsAdded = new Hashtable();
3084
3085     AlignFrame af = LoadFromObject(jm, null, false, null);
3086     af.alignPanels.clear();
3087     af.closeMenuItem_actionPerformed(true);
3088
3089     /*
3090      * if(ap.av.alignment.getAlignmentAnnotation()!=null) { for(int i=0; i<ap.av.alignment.getAlignmentAnnotation().length;
3091      * i++) { if(!ap.av.alignment.getAlignmentAnnotation()[i].autoCalculated) {
3092      * af.alignPanel.av.alignment.getAlignmentAnnotation()[i] =
3093      * ap.av.alignment.getAlignmentAnnotation()[i]; } } }
3094      */
3095
3096     return af.alignPanel;
3097   }
3098
3099   /**
3100    * flag indicating if hashtables should be cleared on finalization TODO this
3101    * flag may not be necessary
3102    */
3103   private boolean _cleartables = true;
3104
3105   private Hashtable jvids2vobj;
3106
3107   /*
3108    * (non-Javadoc)
3109    *
3110    * @see java.lang.Object#finalize()
3111    */
3112   protected void finalize() throws Throwable
3113   {
3114     // really make sure we have no buried refs left.
3115     if (_cleartables)
3116     {
3117       clearSeqRefs();
3118     }
3119     this.seqRefIds = null;
3120     this.seqsToIds = null;
3121     super.finalize();
3122   }
3123
3124   private void warn(String msg)
3125   {
3126     warn(msg, null);
3127   }
3128
3129   private void warn(String msg, Exception e)
3130   {
3131     if (Cache.log != null)
3132     {
3133       if (e != null)
3134       {
3135         Cache.log.warn(msg, e);
3136       }
3137       else
3138       {
3139         Cache.log.warn(msg);
3140       }
3141     }
3142     else
3143     {
3144       System.err.println("Warning: " + msg);
3145       if (e != null)
3146       {
3147         e.printStackTrace();
3148       }
3149     }
3150   }
3151
3152   /**
3153    * set the object to ID mapping tables used to write/recover objects and XML
3154    * ID strings for the jalview project. If external tables are provided then
3155    * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
3156    * object goes out of scope. - also populates the datasetIds hashtable with
3157    * alignment objects containing dataset sequences
3158    *
3159    * @param vobj2jv
3160    *                Map from ID strings to jalview datamodel
3161    * @param jv2vobj
3162    *                Map from jalview datamodel to ID strings
3163    *
3164    *
3165    */
3166   public void setObjectMappingTables(Hashtable vobj2jv,
3167           IdentityHashMap jv2vobj)
3168   {
3169     this.jv2vobj = jv2vobj;
3170     this.vobj2jv = vobj2jv;
3171     Iterator ds = jv2vobj.keySet().iterator();
3172     String id;
3173     while (ds.hasNext())
3174     {
3175       Object jvobj = ds.next();
3176       id = jv2vobj.get(jvobj).toString();
3177       if (jvobj instanceof jalview.datamodel.Alignment)
3178       {
3179         if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
3180         {
3181           addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
3182         }
3183       }
3184       else if (jvobj instanceof jalview.datamodel.Sequence)
3185       {
3186         // register sequence object so the XML parser can recover it.
3187         if (seqRefIds == null)
3188         {
3189           seqRefIds = new Hashtable();
3190         }
3191         if (seqsToIds == null)
3192         {
3193           seqsToIds = new IdentityHashMap();
3194         }
3195         seqRefIds.put(jv2vobj.get(jvobj).toString(), jvobj);
3196         seqsToIds.put(jvobj, id);
3197       }
3198       else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
3199       {
3200         if (annotationIds == null)
3201         {
3202           annotationIds = new Hashtable();
3203         }
3204         String anid;
3205         annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvobj);
3206         jalview.datamodel.AlignmentAnnotation jvann = (jalview.datamodel.AlignmentAnnotation) jvobj;
3207         if (jvann.annotationId == null)
3208         {
3209           jvann.annotationId = anid;
3210         }
3211         if (!jvann.annotationId.equals(anid))
3212         {
3213           // TODO verify that this is the correct behaviour
3214           this.warn("Overriding Annotation ID for " + anid
3215                   + " from different id : " + jvann.annotationId);
3216           jvann.annotationId = anid;
3217         }
3218       }
3219       else if (jvobj instanceof String)
3220       {
3221         if (jvids2vobj == null)
3222         {
3223           jvids2vobj = new Hashtable();
3224           jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
3225         }
3226       }
3227       else
3228         Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
3229     }
3230   }
3231
3232   /**
3233    * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
3234    * objects created from the project archive. If string is null (default for
3235    * construction) then suffix will be set automatically.
3236    *
3237    * @param string
3238    */
3239   public void setUniqueSetSuffix(String string)
3240   {
3241     uniqueSetSuffix = string;
3242
3243   }
3244
3245   /**
3246    * uses skipList2 as the skipList for skipping views on sequence sets
3247    * associated with keys in the skipList
3248    *
3249    * @param skipList2
3250    */
3251   public void setSkipList(Hashtable skipList2)
3252   {
3253     skipList = skipList2;
3254   }
3255
3256 }