src/jalview/gui/Jalview2XML.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
   3  * Copyright (C) 2009 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           String matchedFile=null;
 578           for (int f = frames.length - 1; f > -1; f--)
 579           {
 580             if (frames[f] instanceof AppJmol)
 581             {
 582               jmol = (AppJmol) frames[f];
 583               if (!jmol.pdbentry.getId().equals(entry.getId())
 584                       && !(entry.getId().length()>4
 585                               && entry.getId().toLowerCase().startsWith(jmol.pdbentry.getId().toLowerCase())))
 586                 continue;
 587               matchedFile = jmol.pdbentry.getFile(); // record the file so we can get at it if the ID match is ambiguous (e.g. 1QIP==1qipA)
 588               StructureState state = new StructureState();
 589               state.setVisible(true);
 590               state.setXpos(jmol.getX());
 591               state.setYpos(jmol.getY());
 592               state.setWidth(jmol.getWidth());
 593               state.setHeight(jmol.getHeight());
 594               state.setViewId(jmol.getViewId());
 595               String statestring = jmol.viewer.getStateInfo();
 596               if (state != null)
 597               {
 598                 state.setContent(statestring.replaceAll("\n", ""));
 599               }
 600               for (int s = 0; s < jmol.sequence.length; s++)
 601               {
 602                 if (jal.findIndex(jmol.sequence[s]) > -1)
 603                 {
 604                   pdb.addStructureState(state);
 605                 }
 606               }
 607             }
 608           }
 609
 610           if (matchedFile!=null || entry.getFile() != null )
 611           {
 612             if (entry.getFile()!=null)
 613             {
 614               // use entry's file
 615               matchedFile = entry.getFile();
 616             }
 617             pdb.setFile(matchedFile); // entry.getFile());
 618             if (pdbfiles == null)
 619             {
 620               pdbfiles = new Vector();
 621             }
 622
 623             if (!pdbfiles.contains(entry.getId()))
 624             {
 625               pdbfiles.addElement(entry.getId());
 626               try
 627               {
 628                 File file = new File(matchedFile);
 629                 if (file.exists() && jout != null)
 630                 {
 631                   byte[] data = new byte[(int) file.length()];
 632                   jout.putNextEntry(new JarEntry(entry.getId()));
 633                   DataInputStream dis = new DataInputStream(
 634                           new FileInputStream(file));
 635                   dis.readFully(data);
 636
 637                   DataOutputStream dout = new DataOutputStream(jout);
 638                   dout.write(data, 0, data.length);
 639                   dout.flush();
 640                   jout.closeEntry();
 641                 }
 642               } catch (Exception ex)
 643               {
 644                 ex.printStackTrace();
 645               }
 646
 647             }
 648           }
 649
 650           if (entry.getProperty() != null)
 651           {
 652             PdbentryItem item = new PdbentryItem();
 653             Hashtable properties = entry.getProperty();
 654             Enumeration en2 = properties.keys();
 655             while (en2.hasMoreElements())
 656             {
 657               Property prop = new Property();
 658               String key = en2.nextElement().toString();
 659               prop.setName(key);
 660               prop.setValue(properties.get(key).toString());
 661               item.addProperty(prop);
 662             }
 663             pdb.addPdbentryItem(item);
 664           }
 665
 666           jseq.addPdbids(pdb);
 667         }
 668       }
 669
 670       jms.addJSeq(jseq);
 671     }
 672
 673     if (av.hasHiddenRows)
 674     {
 675       jal = av.alignment;
 676     }
 677     // SAVE MAPPINGS
 678     if (jal.getCodonFrames() != null && jal.getCodonFrames().length > 0)
 679     {
 680       jalview.datamodel.AlignedCodonFrame[] jac = jal.getCodonFrames();
 681       for (int i = 0; i < jac.length; i++)
 682       {
 683         AlcodonFrame alc = new AlcodonFrame();
 684         vamsasSet.addAlcodonFrame(alc);
 685         for (int p = 0; p < jac[i].aaWidth; p++)
 686         {
 687           Alcodon cmap = new Alcodon();
 688           if (jac[i].codons[p]!=null)
 689           {
 690             // Null codons indicate a gapped column in the translated peptide alignment.
 691             cmap.setPos1(jac[i].codons[p][0]);
 692             cmap.setPos2(jac[i].codons[p][1]);
 693             cmap.setPos3(jac[i].codons[p][2]);
 694           }
 695           alc.addAlcodon(cmap);
 696         }
 697         if (jac[i].getProtMappings() != null
 698                 && jac[i].getProtMappings().length > 0)
 699         {
 700           SequenceI[] dnas = jac[i].getdnaSeqs();
 701           jalview.datamodel.Mapping[] pmaps = jac[i].getProtMappings();
 702           for (int m = 0; m < pmaps.length; m++)
 703           {
 704             AlcodMap alcmap = new AlcodMap();
 705             alcmap.setDnasq(seqHash(dnas[m]));
 706             alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
 707                     false));
 708             alc.addAlcodMap(alcmap);
 709           }
 710         }
 711       }
 712     }
 713
 714     // SAVE TREES
 715     // /////////////////////////////////
 716     if (av.currentTree != null)
 717     {
 718       // FIND ANY ASSOCIATED TREES
 719       // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
 720       if (Desktop.desktop != null)
 721       {
 722         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 723
 724         for (int t = 0; t < frames.length; t++)
 725         {
 726           if (frames[t] instanceof TreePanel)
 727           {
 728             TreePanel tp = (TreePanel) frames[t];
 729
 730             if (tp.treeCanvas.av.alignment == jal)
 731             {
 732               Tree tree = new Tree();
 733               tree.setTitle(tp.getTitle());
 734               tree.setCurrentTree((av.currentTree == tp.getTree()));
 735               tree.setNewick(tp.getTree().toString());
 736               tree.setThreshold(tp.treeCanvas.threshold);
 737
 738               tree.setFitToWindow(tp.fitToWindow.getState());
 739               tree.setFontName(tp.getTreeFont().getName());
 740               tree.setFontSize(tp.getTreeFont().getSize());
 741               tree.setFontStyle(tp.getTreeFont().getStyle());
 742               tree.setMarkUnlinked(tp.placeholdersMenu.getState());
 743
 744               tree.setShowBootstrap(tp.bootstrapMenu.getState());
 745               tree.setShowDistances(tp.distanceMenu.getState());
 746
 747               tree.setHeight(tp.getHeight());
 748               tree.setWidth(tp.getWidth());
 749               tree.setXpos(tp.getX());
 750               tree.setYpos(tp.getY());
 751               tree.setId(makeHashCode(tp, null));
 752               jms.addTree(tree);
 753             }
 754           }
 755         }
 756       }
 757     }
 758
 759     // SAVE ANNOTATIONS
 760     if (jal.getAlignmentAnnotation() != null)
 761     {
 762       jalview.datamodel.AlignmentAnnotation[] aa = jal
 763               .getAlignmentAnnotation();
 764
 765       for (int i = 0; i < aa.length; i++)
 766       {
 767         Annotation an = new Annotation();
 768
 769         if (aa[i].annotationId != null)
 770         {
 771           annotationIds.put(aa[i].annotationId, aa[i]);
 772         }
 773
 774         an.setId(aa[i].annotationId);
 775
 776         if (aa[i] == av.quality || aa[i] == av.conservation
 777                 || aa[i] == av.consensus)
 778         {
 779           an.setLabel(aa[i].label);
 780           an.setGraph(true);
 781           vamsasSet.addAnnotation(an);
 782           continue;
 783         }
 784
 785         an.setVisible(aa[i].visible);
 786
 787         an.setDescription(aa[i].description);
 788
 789         if (aa[i].sequenceRef != null)
 790         {
 791           // TODO later annotation sequenceRef should be the XML ID of the
 792           // sequence rather than its display name
 793           an.setSequenceRef(aa[i].sequenceRef.getName());
 794         }
 795
 796         if (aa[i].graph > 0)
 797         {
 798           an.setGraph(true);
 799           an.setGraphType(aa[i].graph);
 800           an.setGraphGroup(aa[i].graphGroup);
 801           if (aa[i].getThreshold() != null)
 802           {
 803             ThresholdLine line = new ThresholdLine();
 804             line.setLabel(aa[i].getThreshold().label);
 805             line.setValue(aa[i].getThreshold().value);
 806             line.setColour(aa[i].getThreshold().colour.getRGB());
 807             an.setThresholdLine(line);
 808           }
 809         }
 810         else
 811         {
 812           an.setGraph(false);
 813         }
 814
 815         an.setLabel(aa[i].label);
 816         if (aa[i].hasScore())
 817         {
 818           an.setScore(aa[i].getScore());
 819         }
 820         AnnotationElement ae;
 821         if (aa[i].annotations != null)
 822         {
 823           an.setScoreOnly(false);
 824           for (int a = 0; a < aa[i].annotations.length; a++)
 825           {
 826             if ((aa[i] == null) || (aa[i].annotations[a] == null))
 827             {
 828               continue;
 829             }
 830
 831             ae = new AnnotationElement();
 832             if (aa[i].annotations[a].description != null)
 833               ae.setDescription(aa[i].annotations[a].description);
 834             if (aa[i].annotations[a].displayCharacter != null)
 835               ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
 836
 837             if (!Float.isNaN(aa[i].annotations[a].value))
 838               ae.setValue(aa[i].annotations[a].value);
 839
 840             ae.setPosition(a);
 841             if (aa[i].annotations[a].secondaryStructure != ' '
 842                     && aa[i].annotations[a].secondaryStructure != '\0')
 843               ae
 844                       .setSecondaryStructure(aa[i].annotations[a].secondaryStructure
 845                               + "");
 846
 847             if (aa[i].annotations[a].colour != null
 848                     && aa[i].annotations[a].colour != java.awt.Color.black)
 849             {
 850               ae.setColour(aa[i].annotations[a].colour.getRGB());
 851             }
 852
 853             an.addAnnotationElement(ae);
 854           }
 855         }
 856         else
 857         {
 858           an.setScoreOnly(true);
 859         }
 860         vamsasSet.addAnnotation(an);
 861       }
 862     }
 863
 864     // SAVE GROUPS
 865     if (jal.getGroups() != null)
 866     {
 867       JGroup[] groups = new JGroup[jal.getGroups().size()];
 868
 869       for (int i = 0; i < groups.length; i++)
 870       {
 871         groups[i] = new JGroup();
 872
 873         jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal
 874                 .getGroups().elementAt(i);
 875         groups[i].setStart(sg.getStartRes());
 876         groups[i].setEnd(sg.getEndRes());
 877         groups[i].setName(sg.getName()); // TODO later sequence group should
 878         // specify IDs of sequences, not just
 879         // names
 880         if (sg.cs != null)
 881         {
 882           if (sg.cs.conservationApplied())
 883           {
 884             groups[i].setConsThreshold(sg.cs.getConservationInc());
 885
 886             if (sg.cs instanceof jalview.schemes.UserColourScheme)
 887             {
 888               groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
 889                       jms));
 890             }
 891             else
 892             {
 893               groups[i]
 894                       .setColour(ColourSchemeProperty.getColourName(sg.cs));
 895             }
 896           }
 897           else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
 898           {
 899             groups[i]
 900                     .setColour(ColourSchemeProperty
 901                             .getColourName(((jalview.schemes.AnnotationColourGradient) sg.cs)
 902                                     .getBaseColour()));
 903           }
 904           else if (sg.cs instanceof jalview.schemes.UserColourScheme)
 905           {
 906             groups[i]
 907                     .setColour(SetUserColourScheme(sg.cs, userColours, jms));
 908           }
 909           else
 910           {
 911             groups[i].setColour(ColourSchemeProperty.getColourName(sg.cs));
 912           }
 913
 914           groups[i].setPidThreshold(sg.cs.getThreshold());
 915         }
 916
 917         groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
 918         groups[i].setDisplayBoxes(sg.getDisplayBoxes());
 919         groups[i].setDisplayText(sg.getDisplayText());
 920         groups[i].setColourText(sg.getColourText());
 921         groups[i].setTextCol1(sg.textColour.getRGB());
 922         groups[i].setTextCol2(sg.textColour2.getRGB());
 923         groups[i].setTextColThreshold(sg.thresholdTextColour);
 924         groups[i].setShowUnconserved(sg.getShowunconserved());
 925         for (int s = 0; s < sg.getSize(); s++)
 926         {
 927           jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg
 928                   .getSequenceAt(s);
 929           groups[i].addSeq(seqHash(seq));
 930         }
 931       }
 932
 933       jms.setJGroup(groups);
 934     }
 935
 936     // /////////SAVE VIEWPORT
 937     Viewport view = new Viewport();
 938     view.setTitle(ap.alignFrame.getTitle());
 939     view.setSequenceSetId(makeHashCode(av.getSequenceSetId(), av
 940             .getSequenceSetId()));
 941     view.setId(av.getViewId());
 942     view.setViewName(av.viewName);
 943     view.setGatheredViews(av.gatherViewsHere);
 944
 945     if (ap.av.explodedPosition != null)
 946     {
 947       view.setXpos(av.explodedPosition.x);
 948       view.setYpos(av.explodedPosition.y);
 949       view.setWidth(av.explodedPosition.width);
 950       view.setHeight(av.explodedPosition.height);
 951     }
 952     else
 953     {
 954       view.setXpos(ap.alignFrame.getBounds().x);
 955       view.setYpos(ap.alignFrame.getBounds().y);
 956       view.setWidth(ap.alignFrame.getBounds().width);
 957       view.setHeight(ap.alignFrame.getBounds().height);
 958     }
 959
 960     view.setStartRes(av.startRes);
 961     view.setStartSeq(av.startSeq);
 962
 963     if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
 964     {
 965       view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
 966               userColours, jms));
 967     }
 968     else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
 969     {
 970       jalview.schemes.AnnotationColourGradient acg = (jalview.schemes.AnnotationColourGradient) av
 971               .getGlobalColourScheme();
 972
 973       AnnotationColours ac = new AnnotationColours();
 974       ac.setAboveThreshold(acg.getAboveThreshold());
 975       ac.setThreshold(acg.getAnnotationThreshold());
 976       ac.setAnnotation(acg.getAnnotation());
 977       if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
 978       {
 979         ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
 980                 userColours, jms));
 981       }
 982       else
 983       {
 984         ac.setColourScheme(ColourSchemeProperty.getColourName(acg
 985                 .getBaseColour()));
 986       }
 987
 988       ac.setMaxColour(acg.getMaxColour().getRGB());
 989       ac.setMinColour(acg.getMinColour().getRGB());
 990       view.setAnnotationColours(ac);
 991       view.setBgColour("AnnotationColourGradient");
 992     }
 993     else
 994     {
 995       view.setBgColour(ColourSchemeProperty.getColourName(av
 996               .getGlobalColourScheme()));
 997     }
 998
 999     ColourSchemeI cs = av.getGlobalColourScheme();
1000
1001     if (cs != null)
1002     {
1003       if (cs.conservationApplied())
1004       {
1005         view.setConsThreshold(cs.getConservationInc());
1006         if (cs instanceof jalview.schemes.UserColourScheme)
1007         {
1008           view.setBgColour(SetUserColourScheme(cs, userColours, jms));
1009         }
1010       }
1011
1012       if (cs instanceof ResidueColourScheme)
1013       {
1014         view.setPidThreshold(cs.getThreshold());
1015       }
1016     }
1017
1018     view.setConservationSelected(av.getConservationSelected());
1019     view.setPidSelected(av.getAbovePIDThreshold());
1020     view.setFontName(av.font.getName());
1021     view.setFontSize(av.font.getSize());
1022     view.setFontStyle(av.font.getStyle());
1023     view.setRenderGaps(av.renderGaps);
1024     view.setShowAnnotation(av.getShowAnnotation());
1025     view.setShowBoxes(av.getShowBoxes());
1026     view.setShowColourText(av.getColourText());
1027     view.setShowFullId(av.getShowJVSuffix());
1028     view.setRightAlignIds(av.rightAlignIds);
1029     view.setShowSequenceFeatures(av.showSequenceFeatures);
1030     view.setShowText(av.getShowText());
1031     view.setShowUnconserved(av.getShowUnconserved());
1032     view.setWrapAlignment(av.getWrapAlignment());
1033     view.setTextCol1(av.textColour.getRGB());
1034     view.setTextCol2(av.textColour2.getRGB());
1035     view.setTextColThreshold(av.thresholdTextColour);
1036
1037     if (av.featuresDisplayed != null)
1038     {
1039       jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
1040
1041       String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
1042
1043       Vector settingsAdded = new Vector();
1044       for (int ro = 0; ro < renderOrder.length; ro++)
1045       {
1046         Setting setting = new Setting();
1047         setting.setType(renderOrder[ro]);
1048         setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
1049                 .getColour(renderOrder[ro]).getRGB());
1050
1051         setting.setDisplay(av.featuresDisplayed
1052                 .containsKey(renderOrder[ro]));
1053         float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
1054                 renderOrder[ro]);
1055         if (rorder > -1)
1056         {
1057           setting.setOrder(rorder);
1058         }
1059         fs.addSetting(setting);
1060         settingsAdded.addElement(renderOrder[ro]);
1061       }
1062
1063       // Make sure we save none displayed feature settings
1064       Enumeration en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
1065               .keys();
1066       while (en.hasMoreElements())
1067       {
1068         String key = en.nextElement().toString();
1069         if (settingsAdded.contains(key))
1070         {
1071           continue;
1072         }
1073
1074         Setting setting = new Setting();
1075         setting.setType(key);
1076         setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
1077                 .getColour(key).getRGB());
1078
1079         setting.setDisplay(false);
1080         float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
1081                 key);
1082         if (rorder > -1)
1083         {
1084           setting.setOrder(rorder);
1085         }
1086         fs.addSetting(setting);
1087         settingsAdded.addElement(key);
1088       }
1089       en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keys();
1090       Vector groupsAdded = new Vector();
1091       while (en.hasMoreElements())
1092       {
1093         String grp = en.nextElement().toString();
1094         if (groupsAdded.contains(grp))
1095         {
1096           continue;
1097         }
1098         Group g = new Group();
1099         g.setName(grp);
1100         g
1101                 .setDisplay(((Boolean) ap.seqPanel.seqCanvas
1102                         .getFeatureRenderer().featureGroups.get(grp))
1103                         .booleanValue());
1104         fs.addGroup(g);
1105         groupsAdded.addElement(grp);
1106       }
1107       jms.setFeatureSettings(fs);
1108
1109     }
1110
1111     if (av.hasHiddenColumns)
1112     {
1113       for (int c = 0; c < av.getColumnSelection().getHiddenColumns().size(); c++)
1114       {
1115         int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
1116                 .elementAt(c);
1117         HiddenColumns hc = new HiddenColumns();
1118         hc.setStart(region[0]);
1119         hc.setEnd(region[1]);
1120         view.addHiddenColumns(hc);
1121       }
1122     }
1123
1124     jms.addViewport(view);
1125
1126     object.setJalviewModelSequence(jms);
1127     object.getVamsasModel().addSequenceSet(vamsasSet);
1128
1129     if (jout != null && fileName != null)
1130     {
1131       // We may not want to write the object to disk,
1132       // eg we can copy the alignViewport to a new view object
1133       // using save and then load
1134       try
1135       {
1136         JarEntry entry = new JarEntry(fileName);
1137         jout.putNextEntry(entry);
1138         PrintWriter pout = new PrintWriter(new OutputStreamWriter(jout,
1139                 "UTF-8"));
1140         org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller(
1141                 pout);
1142         marshaller.marshal(object);
1143         pout.flush();
1144         jout.closeEntry();
1145       } catch (Exception ex)
1146       {
1147         // TODO: raise error in GUI if marshalling failed.
1148         ex.printStackTrace();
1149       }
1150     }
1151     return object;
1152   }
1153
1154   /**
1155    * External mapping between jalview objects and objects yielding a valid and
1156    * unique object ID string. This is null for normal Jalview project IO, but
1157    * non-null when a jalview project is being read or written as part of a
1158    * vamsas session.
1159    */
1160   IdentityHashMap jv2vobj = null;
1161
1162   /**
1163    * Construct a unique ID for jvobj using either existing bindings or if none
1164    * exist, the result of the hashcode call for the object.
1165    *
1166    * @param jvobj
1167    *                jalview data object
1168    * @return unique ID for referring to jvobj
1169    */
1170   private String makeHashCode(Object jvobj, String altCode)
1171   {
1172     if (jv2vobj != null)
1173     {
1174       Object id = jv2vobj.get(jvobj);
1175       if (id != null)
1176       {
1177         return id.toString();
1178       }
1179       // check string ID mappings
1180       if (jvids2vobj != null && jvobj instanceof String)
1181       {
1182         id = jvids2vobj.get(jvobj);
1183       }
1184       if (id != null)
1185       {
1186         return id.toString();
1187       }
1188       // give up and warn that something has gone wrong
1189       warn("Cannot find ID for object in external mapping : " + jvobj);
1190     }
1191     return altCode;
1192   }
1193
1194   /**
1195    * return local jalview object mapped to ID, if it exists
1196    *
1197    * @param idcode
1198    *                (may be null)
1199    * @return null or object bound to idcode
1200    */
1201   private Object retrieveExistingObj(String idcode)
1202   {
1203     if (idcode != null && vobj2jv != null)
1204     {
1205       return vobj2jv.get(idcode);
1206     }
1207     return null;
1208   }
1209
1210   /**
1211    * binding from ID strings from external mapping table to jalview data model
1212    * objects.
1213    */
1214   private Hashtable vobj2jv;
1215
1216   private Sequence createVamsasSequence(String id, SequenceI jds)
1217   {
1218     return createVamsasSequence(true, id, jds, null);
1219   }
1220
1221   private Sequence createVamsasSequence(boolean recurse, String id,
1222           SequenceI jds, SequenceI parentseq)
1223   {
1224     Sequence vamsasSeq = new Sequence();
1225     vamsasSeq.setId(id);
1226     vamsasSeq.setName(jds.getName());
1227     vamsasSeq.setSequence(jds.getSequenceAsString());
1228     vamsasSeq.setDescription(jds.getDescription());
1229     jalview.datamodel.DBRefEntry[] dbrefs = null;
1230     if (jds.getDatasetSequence() != null)
1231     {
1232       vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
1233       if (jds.getDatasetSequence().getDBRef() != null)
1234       {
1235         dbrefs = jds.getDatasetSequence().getDBRef();
1236       }
1237     }
1238     else
1239     {
1240       vamsasSeq.setDsseqid(id); // so we can tell which sequences really are
1241       // dataset sequences only
1242       dbrefs = jds.getDBRef();
1243     }
1244     if (dbrefs != null)
1245     {
1246       for (int d = 0; d < dbrefs.length; d++)
1247       {
1248         DBRef dbref = new DBRef();
1249         dbref.setSource(dbrefs[d].getSource());
1250         dbref.setVersion(dbrefs[d].getVersion());
1251         dbref.setAccessionId(dbrefs[d].getAccessionId());
1252         if (dbrefs[d].hasMap())
1253         {
1254           Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
1255                   jds, recurse);
1256           dbref.setMapping(mp);
1257         }
1258         vamsasSeq.addDBRef(dbref);
1259       }
1260     }
1261     return vamsasSeq;
1262   }
1263
1264   private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
1265           SequenceI parentseq, SequenceI jds, boolean recurse)
1266   {
1267     Mapping mp = null;
1268     if (jmp.getMap() != null)
1269     {
1270       mp = new Mapping();
1271
1272       jalview.util.MapList mlst = jmp.getMap();
1273       int r[] = mlst.getFromRanges();
1274       for (int s = 0; s < r.length; s += 2)
1275       {
1276         MapListFrom mfrom = new MapListFrom();
1277         mfrom.setStart(r[s]);
1278         mfrom.setEnd(r[s + 1]);
1279         mp.addMapListFrom(mfrom);
1280       }
1281       r = mlst.getToRanges();
1282       for (int s = 0; s < r.length; s += 2)
1283       {
1284         MapListTo mto = new MapListTo();
1285         mto.setStart(r[s]);
1286         mto.setEnd(r[s + 1]);
1287         mp.addMapListTo(mto);
1288       }
1289       mp.setMapFromUnit(mlst.getFromRatio());
1290       mp.setMapToUnit(mlst.getToRatio());
1291       if (jmp.getTo() != null)
1292       {
1293         MappingChoice mpc = new MappingChoice();
1294         if (recurse
1295                 && (parentseq != jmp.getTo() || parentseq
1296                         .getDatasetSequence() != jmp.getTo()))
1297         {
1298           mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo()),
1299                   jmp.getTo(), jds));
1300         }
1301         else
1302         {
1303           String jmpid = "";
1304           SequenceI ps = null;
1305           if (parentseq != jmp.getTo()
1306                   && parentseq.getDatasetSequence() != jmp.getTo())
1307           {
1308             // chaining dbref rather than a handshaking one
1309             jmpid = seqHash(ps = jmp.getTo());
1310           }
1311           else
1312           {
1313             jmpid = seqHash(ps = parentseq);
1314           }
1315           mpc.setDseqFor(jmpid);
1316           if (!seqRefIds.containsKey(mpc.getDseqFor()))
1317           {
1318             jalview.bin.Cache.log.debug("creatign new DseqFor ID");
1319             seqRefIds.put(mpc.getDseqFor(), ps);
1320           }
1321           else
1322           {
1323             jalview.bin.Cache.log.debug("reusing DseqFor ID");
1324           }
1325         }
1326         mp.setMappingChoice(mpc);
1327       }
1328     }
1329     return mp;
1330   }
1331
1332   String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
1333           Vector userColours, JalviewModelSequence jms)
1334   {
1335     String id = null;
1336     jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
1337
1338     if (!userColours.contains(ucs))
1339     {
1340       userColours.add(ucs);
1341
1342       java.awt.Color[] colours = ucs.getColours();
1343       jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
1344       jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
1345
1346       for (int i = 0; i < colours.length; i++)
1347       {
1348         jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
1349         col.setName(ResidueProperties.aa[i]);
1350         col.setRGB(jalview.util.Format.getHexString(colours[i]));
1351         jbucs.addColour(col);
1352       }
1353       if (ucs.getLowerCaseColours() != null)
1354       {
1355         colours = ucs.getLowerCaseColours();
1356         for (int i = 0; i < colours.length; i++)
1357         {
1358           jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
1359           col.setName(ResidueProperties.aa[i].toLowerCase());
1360           col.setRGB(jalview.util.Format.getHexString(colours[i]));
1361           jbucs.addColour(col);
1362         }
1363       }
1364
1365       id = "ucs" + userColours.indexOf(ucs);
1366       uc.setId(id);
1367       uc.setUserColourScheme(jbucs);
1368       jms.addUserColours(uc);
1369     }
1370
1371     return id;
1372   }
1373
1374   jalview.schemes.UserColourScheme GetUserColourScheme(
1375           JalviewModelSequence jms, String id)
1376   {
1377     UserColours[] uc = jms.getUserColours();
1378     UserColours colours = null;
1379
1380     for (int i = 0; i < uc.length; i++)
1381     {
1382       if (uc[i].getId().equals(id))
1383       {
1384         colours = uc[i];
1385
1386         break;
1387       }
1388     }
1389
1390     java.awt.Color[] newColours = new java.awt.Color[24];
1391
1392     for (int i = 0; i < 24; i++)
1393     {
1394       newColours[i] = new java.awt.Color(Integer.parseInt(colours
1395               .getUserColourScheme().getColour(i).getRGB(), 16));
1396     }
1397
1398     jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
1399             newColours);
1400
1401     if (colours.getUserColourScheme().getColourCount() > 24)
1402     {
1403       newColours = new java.awt.Color[23];
1404       for (int i = 0; i < 23; i++)
1405       {
1406         newColours[i] = new java.awt.Color(Integer.parseInt(colours
1407                 .getUserColourScheme().getColour(i + 24).getRGB(), 16));
1408       }
1409       ucs.setLowerCaseColours(newColours);
1410     }
1411
1412     return ucs;
1413   }
1414
1415   /**
1416    * contains last error message (if any) encountered by XML loader.
1417    */
1418   String errorMessage = null;
1419
1420   /**
1421    * flag to control whether the Jalview2XML_V1 parser should be deferred to if
1422    * exceptions are raised during project XML parsing
1423    */
1424   public boolean attemptversion1parse = true;
1425
1426   /**
1427    * Load a jalview project archive from a jar file
1428    *
1429    * @param file -
1430    *                HTTP URL or filename
1431    */
1432   public AlignFrame LoadJalviewAlign(final String file)
1433   {
1434
1435     jalview.gui.AlignFrame af = null;
1436
1437     try
1438     {
1439       // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
1440       // Workaround is to make sure caller implements the JarInputStreamProvider
1441       // interface
1442       // so we can re-open the jar input stream for each entry.
1443
1444       jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
1445       af = LoadJalviewAlign(jprovider);
1446     } catch (MalformedURLException e)
1447     {
1448       errorMessage = "Invalid URL format for '" + file + "'";
1449       reportErrors();
1450     }
1451     return af;
1452   }
1453
1454   private jarInputStreamProvider createjarInputStreamProvider(
1455           final String file) throws MalformedURLException
1456   {
1457     URL url = null;
1458     errorMessage = null;
1459     uniqueSetSuffix = null;
1460     seqRefIds = null;
1461     viewportsAdded = null;
1462     frefedSequence = null;
1463
1464     if (file.startsWith("http://"))
1465     {
1466       url = new URL(file);
1467     }
1468     final URL _url = url;
1469     return new jarInputStreamProvider()
1470     {
1471
1472       public JarInputStream getJarInputStream() throws IOException
1473       {
1474         if (_url != null)
1475         {
1476           return new JarInputStream(_url.openStream());
1477         }
1478         else
1479         {
1480           return new JarInputStream(new FileInputStream(file));
1481         }
1482       }
1483
1484       public String getFilename()
1485       {
1486         return file;
1487       }
1488     };
1489   }
1490
1491   /**
1492    * Recover jalview session from a jalview project archive. Caller may
1493    * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
1494    * themselves. Any null fields will be initialised with default values,
1495    * non-null fields are left alone.
1496    *
1497    * @param jprovider
1498    * @return
1499    */
1500   public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
1501   {
1502     errorMessage = null;
1503     if (uniqueSetSuffix == null)
1504     {
1505       uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
1506     }
1507     if (seqRefIds == null)
1508     {
1509       seqRefIds = new Hashtable();
1510     }
1511     if (viewportsAdded == null)
1512     {
1513       viewportsAdded = new Hashtable();
1514     }
1515     if (frefedSequence == null)
1516     {
1517       frefedSequence = new Vector();
1518     }
1519
1520     jalview.gui.AlignFrame af = null;
1521     Hashtable gatherToThisFrame = new Hashtable();
1522     final String file = jprovider.getFilename();
1523     try
1524     {
1525       JarInputStream jin = null;
1526       JarEntry jarentry = null;
1527       int entryCount = 1;
1528
1529       do
1530       {
1531         jin = jprovider.getJarInputStream();
1532         for (int i = 0; i < entryCount; i++)
1533         {
1534           jarentry = jin.getNextJarEntry();
1535         }
1536
1537         if (jarentry != null && jarentry.getName().endsWith(".xml"))
1538         {
1539           InputStreamReader in = new InputStreamReader(jin, "UTF-8");
1540           JalviewModel object = new JalviewModel();
1541
1542           Unmarshaller unmar = new Unmarshaller(object);
1543           unmar.setValidation(false);
1544           object = (JalviewModel) unmar.unmarshal(in);
1545           if (true) // !skipViewport(object))
1546           {
1547             af = LoadFromObject(object, file, true, jprovider);
1548             if (af.viewport.gatherViewsHere)
1549             {
1550               gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
1551             }
1552           }
1553           entryCount++;
1554         }
1555         else if (jarentry != null)
1556         {
1557           // Some other file here.
1558           entryCount++;
1559         }
1560       } while (jarentry != null);
1561       resolveFrefedSequences();
1562     } catch (java.io.FileNotFoundException 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 (java.net.UnknownHostException ex)
1569     {
1570       ex.printStackTrace();
1571       errorMessage = "Couldn't locate Jalview XML file : " + file;
1572       System.err.println("Exception whilst loading jalview XML file : "
1573               + ex + "\n");
1574     } catch (Exception ex)
1575     {
1576       System.err.println("Parsing as Jalview Version 2 file failed.");
1577       ex.printStackTrace(System.err);
1578       if (attemptversion1parse)
1579       {
1580         // Is Version 1 Jar file?
1581         try
1582         {
1583           af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(jprovider);
1584         } catch (Exception ex2)
1585         {
1586           System.err.println("Exception whilst loading as jalviewXMLV1:");
1587           ex2.printStackTrace();
1588           af = null;
1589         }
1590       }
1591       if (Desktop.instance != null)
1592       {
1593         Desktop.instance.stopLoading();
1594       }
1595       if (af != null)
1596       {
1597         System.out.println("Successfully loaded archive file");
1598         return af;
1599       }
1600       ex.printStackTrace();
1601
1602       System.err.println("Exception whilst loading jalview XML file : "
1603               + ex + "\n");
1604     } catch (OutOfMemoryError e)
1605     {
1606       new jalview.gui.OOMWarning("loading jalview XML file", e,
1607               Desktop.instance);
1608     }
1609
1610     if (Desktop.instance != null)
1611     {
1612       Desktop.instance.stopLoading();
1613     }
1614
1615     Enumeration en = gatherToThisFrame.elements();
1616     while (en.hasMoreElements())
1617     {
1618       Desktop.instance.gatherViews((AlignFrame) en.nextElement());
1619     }
1620     if (errorMessage != null)
1621     {
1622       reportErrors();
1623     }
1624     return af;
1625   }
1626
1627   /**
1628    * check errorMessage for a valid error message and raise an error box in the
1629    * GUI or write the current errorMessage to stderr and then clear the error
1630    * state.
1631    */
1632   protected void reportErrors()
1633   {
1634     reportErrors(false);
1635   }
1636
1637   protected void reportErrors(final boolean saving)
1638   {
1639     if (errorMessage != null)
1640     {
1641       final String finalErrorMessage = errorMessage;
1642       if (raiseGUI)
1643       {
1644         javax.swing.SwingUtilities.invokeLater(new Runnable()
1645         {
1646           public void run()
1647           {
1648             JOptionPane.showInternalMessageDialog(Desktop.desktop,
1649                     finalErrorMessage, "Error "
1650                             + (saving ? "saving" : "loading")
1651                             + " Jalview file", JOptionPane.WARNING_MESSAGE);
1652           }
1653         });
1654       }
1655       else
1656       {
1657         System.err.println("Problem loading Jalview file: " + errorMessage);
1658       }
1659     }
1660     errorMessage = null;
1661   }
1662
1663   Hashtable alreadyLoadedPDB;
1664
1665   /**
1666    * when set, local views will be updated from view stored in JalviewXML
1667    * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
1668    * sync if this is set to true.
1669    */
1670   private boolean updateLocalViews = false;
1671
1672   String loadPDBFile(jarInputStreamProvider jprovider, String pdbId)
1673   {
1674     if (alreadyLoadedPDB == null)
1675       alreadyLoadedPDB = new Hashtable();
1676
1677     if (alreadyLoadedPDB.containsKey(pdbId))
1678       return alreadyLoadedPDB.get(pdbId).toString();
1679
1680     try
1681     {
1682       JarInputStream jin = jprovider.getJarInputStream();
1683       /*
1684        * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
1685        * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
1686        * FileInputStream(jprovider)); }
1687        */
1688
1689       JarEntry entry = null;
1690       do
1691       {
1692         entry = jin.getNextJarEntry();
1693       } while (entry != null && !entry.getName().equals(pdbId));
1694       if (entry != null)
1695       {
1696         BufferedReader in = new BufferedReader(new InputStreamReader(jin));
1697         File outFile = File.createTempFile("jalview_pdb", ".txt");
1698         outFile.deleteOnExit();
1699         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
1700         String data;
1701
1702         while ((data = in.readLine()) != null)
1703         {
1704           out.println(data);
1705         }
1706         try
1707         {
1708           out.flush();
1709         } catch (Exception foo)
1710         {
1711         }
1712         ;
1713         out.close();
1714
1715         alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath());
1716         return outFile.getAbsolutePath();
1717       }
1718       else
1719       {
1720         warn("Couldn't find PDB file entry in Jalview Jar for " + pdbId);
1721       }
1722     } catch (Exception ex)
1723     {
1724       ex.printStackTrace();
1725     }
1726
1727     return null;
1728   }
1729
1730   /**
1731    * Load alignment frame from jalview XML DOM object
1732    *
1733    * @param object
1734    *                DOM
1735    * @param file
1736    *                filename source string
1737    * @param loadTreesAndStructures
1738    *                when false only create Viewport
1739    * @param jprovider
1740    *                data source provider
1741    * @return alignment frame created from view stored in DOM
1742    */
1743   AlignFrame LoadFromObject(JalviewModel object, String file,
1744           boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
1745   {
1746     SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
1747     Sequence[] vamsasSeq = vamsasSet.getSequence();
1748
1749     JalviewModelSequence jms = object.getJalviewModelSequence();
1750
1751     Viewport view = jms.getViewport(0);
1752     // ////////////////////////////////
1753     // LOAD SEQUENCES
1754
1755     Vector hiddenSeqs = null;
1756     jalview.datamodel.Sequence jseq;
1757
1758     ArrayList tmpseqs = new ArrayList();
1759
1760     boolean multipleView = false;
1761
1762     JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
1763     int vi = 0; // counter in vamsasSeq array
1764     for (int i = 0; i < JSEQ.length; i++)
1765     {
1766       String seqId = JSEQ[i].getId();
1767
1768       if (seqRefIds.get(seqId) != null)
1769       {
1770         tmpseqs.add((jalview.datamodel.Sequence) seqRefIds.get(seqId));
1771         multipleView = true;
1772       }
1773       else
1774       {
1775         jseq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
1776                 vamsasSeq[vi].getSequence());
1777         jseq.setDescription(vamsasSeq[vi].getDescription());
1778         jseq.setStart(JSEQ[i].getStart());
1779         jseq.setEnd(JSEQ[i].getEnd());
1780         jseq.setVamsasId(uniqueSetSuffix + seqId);
1781         seqRefIds.put(vamsasSeq[vi].getId(), jseq);
1782         tmpseqs.add(jseq);
1783         vi++;
1784       }
1785
1786       if (JSEQ[i].getHidden())
1787       {
1788         if (hiddenSeqs == null)
1789         {
1790           hiddenSeqs = new Vector();
1791         }
1792
1793         hiddenSeqs.addElement((jalview.datamodel.Sequence) seqRefIds
1794                 .get(seqId));
1795       }
1796
1797     }
1798
1799     // /
1800     // Create the alignment object from the sequence set
1801     // ///////////////////////////////
1802     jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[tmpseqs
1803             .size()];
1804
1805     tmpseqs.toArray(orderedSeqs);
1806
1807     jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(
1808             orderedSeqs);
1809
1810     // / Add the alignment properties
1811     for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
1812     {
1813       SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
1814       al.setProperty(ssp.getKey(), ssp.getValue());
1815     }
1816
1817     // /
1818     // SequenceFeatures are added to the DatasetSequence,
1819     // so we must create or recover the dataset before loading features
1820     // ///////////////////////////////
1821     if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
1822     {
1823       // older jalview projects do not have a dataset id.
1824       al.setDataset(null);
1825     }
1826     else
1827     {
1828       recoverDatasetFor(vamsasSet, al);
1829     }
1830     // ///////////////////////////////
1831
1832     Hashtable pdbloaded = new Hashtable();
1833     if (!multipleView)
1834     {
1835       // load sequence features, database references and any associated PDB
1836       // structures for the alignment
1837       for (int i = 0; i < vamsasSeq.length; i++)
1838       {
1839         if (JSEQ[i].getFeaturesCount() > 0)
1840         {
1841           Features[] features = JSEQ[i].getFeatures();
1842           for (int f = 0; f < features.length; f++)
1843           {
1844             jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
1845                     features[f].getType(), features[f].getDescription(),
1846                     features[f].getStatus(), features[f].getBegin(),
1847                     features[f].getEnd(), features[f].getFeatureGroup());
1848
1849             sf.setScore(features[f].getScore());
1850             for (int od = 0; od < features[f].getOtherDataCount(); od++)
1851             {
1852               OtherData keyValue = features[f].getOtherData(od);
1853               if (keyValue.getKey().startsWith("LINK"))
1854               {
1855                 sf.addLink(keyValue.getValue());
1856               }
1857               else
1858               {
1859                 sf.setValue(keyValue.getKey(), keyValue.getValue());
1860               }
1861
1862             }
1863
1864             al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1865           }
1866         }
1867         if (vamsasSeq[i].getDBRefCount() > 0)
1868         {
1869           addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]);
1870         }
1871         if (JSEQ[i].getPdbidsCount() > 0)
1872         {
1873           Pdbids[] ids = JSEQ[i].getPdbids();
1874           for (int p = 0; p < ids.length; p++)
1875           {
1876             jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
1877             entry.setId(ids[p].getId());
1878             entry.setType(ids[p].getType());
1879             if (ids[p].getFile() != null)
1880             {
1881               if (!pdbloaded.containsKey(ids[p].getFile()))
1882               {
1883                 entry.setFile(loadPDBFile(jprovider, ids[p].getId()));
1884               }
1885               else
1886               {
1887                 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1888               }
1889             }
1890
1891             al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1892           }
1893         }
1894       }
1895     } // end !multipleview
1896
1897     // ///////////////////////////////
1898     // LOAD SEQUENCE MAPPINGS
1899
1900     if (vamsasSet.getAlcodonFrameCount() > 0)
1901     {
1902       // TODO Potentially this should only be done once for all views of an
1903       // alignment
1904       AlcodonFrame[] alc = vamsasSet.getAlcodonFrame();
1905       for (int i = 0; i < alc.length; i++)
1906       {
1907         jalview.datamodel.AlignedCodonFrame cf = new jalview.datamodel.AlignedCodonFrame(
1908                 alc[i].getAlcodonCount());
1909         if (alc[i].getAlcodonCount() > 0)
1910         {
1911           Alcodon[] alcods = alc[i].getAlcodon();
1912           for (int p = 0; p < cf.codons.length; p++)
1913           {
1914             if (alcods[p].hasPos1() && alcods[p].hasPos2() && alcods[p].hasPos3())
1915             {
1916               // translated codons require three valid positions
1917               cf.codons[p] = new int[3];
1918               cf.codons[p][0] = (int) alcods[p].getPos1();
1919               cf.codons[p][1] = (int) alcods[p].getPos2();
1920               cf.codons[p][2] = (int) alcods[p].getPos3();
1921             } else {
1922               cf.codons[p] = null;
1923             }
1924           }
1925         }
1926         if (alc[i].getAlcodMapCount() > 0)
1927         {
1928           AlcodMap[] maps = alc[i].getAlcodMap();
1929           for (int m = 0; m < maps.length; m++)
1930           {
1931             SequenceI dnaseq = (SequenceI) seqRefIds
1932                     .get(maps[m].getDnasq());
1933             // Load Mapping
1934             jalview.datamodel.Mapping mapping = null;
1935             // attach to dna sequence reference.
1936             if (maps[m].getMapping() != null)
1937             {
1938               mapping = addMapping(maps[m].getMapping());
1939             }
1940             if (dnaseq != null)
1941             {
1942               cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
1943             }
1944             else
1945             {
1946               // defer to later
1947               frefedSequence.add(new Object[]
1948               { maps[m].getDnasq(), cf, mapping });
1949             }
1950           }
1951         }
1952         al.addCodonFrame(cf);
1953       }
1954
1955     }
1956
1957     // ////////////////////////////////
1958     // LOAD ANNOTATIONS
1959     boolean hideQuality = true, hideConservation = true, hideConsensus = true;
1960
1961     if (vamsasSet.getAnnotationCount() > 0)
1962     {
1963       Annotation[] an = vamsasSet.getAnnotation();
1964
1965       for (int i = 0; i < an.length; i++)
1966       {
1967         // set visibility for automatic annotation for this view
1968         if (an[i].getLabel().equals("Quality"))
1969         {
1970           hideQuality = false;
1971           continue;
1972         }
1973         else if (an[i].getLabel().equals("Conservation"))
1974         {
1975           hideConservation = false;
1976           continue;
1977         }
1978         else if (an[i].getLabel().equals("Consensus"))
1979         {
1980           hideConsensus = false;
1981           continue;
1982         }
1983         // set visiblity for other annotation in this view
1984         if (an[i].getId() != null
1985                 && annotationIds.containsKey(an[i].getId()))
1986         {
1987           jalview.datamodel.AlignmentAnnotation jda = (jalview.datamodel.AlignmentAnnotation) annotationIds
1988                   .get(an[i].getId());
1989           // in principle Visible should always be true for annotation displayed
1990           // in multiple views
1991           if (an[i].hasVisible())
1992             jda.visible = an[i].getVisible();
1993
1994           al.addAnnotation(jda);
1995
1996           continue;
1997         }
1998         // Construct new annotation from model.
1999         AnnotationElement[] ae = an[i].getAnnotationElement();
2000         jalview.datamodel.Annotation[] anot = null;
2001
2002         if (!an[i].getScoreOnly())
2003         {
2004           anot = new jalview.datamodel.Annotation[al.getWidth()];
2005
2006           for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
2007           {
2008             if (ae[aa].getPosition() >= anot.length)
2009               continue;
2010
2011             anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
2012
2013             ae[aa].getDisplayCharacter(), ae[aa].getDescription(), (ae[aa]
2014                     .getSecondaryStructure() == null || ae[aa]
2015                     .getSecondaryStructure().length() == 0) ? ' ' : ae[aa]
2016                     .getSecondaryStructure().charAt(0), ae[aa].getValue()
2017
2018             );
2019             // JBPNote: Consider verifying dataflow for IO of secondary
2020             // structure annotation read from Stockholm files
2021             // this was added to try to ensure that
2022             // if (anot[ae[aa].getPosition()].secondaryStructure>' ')
2023             // {
2024             // anot[ae[aa].getPosition()].displayCharacter = "";
2025             // }
2026             anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa]
2027                     .getColour());
2028           }
2029         }
2030         jalview.datamodel.AlignmentAnnotation jaa = null;
2031
2032         if (an[i].getGraph())
2033         {
2034           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
2035                   an[i].getDescription(), anot, 0, 0, an[i].getGraphType());
2036
2037           jaa.graphGroup = an[i].getGraphGroup();
2038
2039           if (an[i].getThresholdLine() != null)
2040           {
2041             jaa.setThreshold(new jalview.datamodel.GraphLine(an[i]
2042                     .getThresholdLine().getValue(), an[i]
2043                     .getThresholdLine().getLabel(), new java.awt.Color(
2044                     an[i].getThresholdLine().getColour())));
2045
2046           }
2047
2048         }
2049         else
2050         {
2051           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
2052                   an[i].getDescription(), anot);
2053         }
2054         // register new annotation
2055         if (an[i].getId() != null)
2056         {
2057           annotationIds.put(an[i].getId(), jaa);
2058           jaa.annotationId = an[i].getId();
2059         }
2060         // recover sequence association
2061         if (an[i].getSequenceRef() != null)
2062         {
2063           if (al.findName(an[i].getSequenceRef()) != null)
2064           {
2065             jaa.createSequenceMapping(al.findName(an[i].getSequenceRef()),
2066                     1, true);
2067             al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
2068           }
2069         }
2070         if (an[i].hasScore())
2071         {
2072           jaa.setScore(an[i].getScore());
2073         }
2074
2075         if (an[i].hasVisible())
2076           jaa.visible = an[i].getVisible();
2077
2078         al.addAnnotation(jaa);
2079       }
2080     }
2081
2082     // ///////////////////////
2083     // LOAD GROUPS
2084     // Create alignment markup and styles for this view
2085     if (jms.getJGroupCount() > 0)
2086     {
2087       JGroup[] groups = jms.getJGroup();
2088
2089       for (int i = 0; i < groups.length; i++)
2090       {
2091         ColourSchemeI cs = null;
2092
2093         if (groups[i].getColour() != null)
2094         {
2095           if (groups[i].getColour().startsWith("ucs"))
2096           {
2097             cs = GetUserColourScheme(jms, groups[i].getColour());
2098           }
2099           else
2100           {
2101             cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
2102           }
2103
2104           if (cs != null)
2105           {
2106             cs.setThreshold(groups[i].getPidThreshold(), true);
2107           }
2108         }
2109
2110         Vector seqs = new Vector();
2111
2112         for (int s = 0; s < groups[i].getSeqCount(); s++)
2113         {
2114           String seqId = groups[i].getSeq(s) + "";
2115           jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI) seqRefIds
2116                   .get(seqId);
2117
2118           if (ts != null)
2119           {
2120             seqs.addElement(ts);
2121           }
2122         }
2123
2124         if (seqs.size() < 1)
2125         {
2126           continue;
2127         }
2128
2129         jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
2130                 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
2131                 groups[i].getDisplayText(), groups[i].getColourText(),
2132                 groups[i].getStart(), groups[i].getEnd());
2133
2134         sg
2135                 .setOutlineColour(new java.awt.Color(groups[i]
2136                         .getOutlineColour()));
2137
2138         sg.textColour = new java.awt.Color(groups[i].getTextCol1());
2139         sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
2140         sg.setShowunconserved(groups[i].hasShowUnconserved() ? groups[i].isShowUnconserved() : false);
2141         sg.thresholdTextColour = groups[i].getTextColThreshold();
2142
2143         if (groups[i].getConsThreshold() != 0)
2144         {
2145           jalview.analysis.Conservation c = new jalview.analysis.Conservation(
2146                   "All", ResidueProperties.propHash, 3, sg
2147                           .getSequences(null), 0, sg.getWidth() - 1);
2148           c.calculate();
2149           c.verdict(false, 25);
2150           sg.cs.setConservation(c);
2151         }
2152
2153         al.addGroup(sg);
2154       }
2155     }
2156
2157     // ///////////////////////////////
2158     // LOAD VIEWPORT
2159
2160     // If we just load in the same jar file again, the sequenceSetId
2161     // will be the same, and we end up with multiple references
2162     // to the same sequenceSet. We must modify this id on load
2163     // so that each load of the file gives a unique id
2164     String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
2165     String viewId = (view.getId() == null ? null : view.getId()
2166             + uniqueSetSuffix);
2167     AlignFrame af = null;
2168     AlignViewport av = null;
2169     // now check to see if we really need to create a new viewport.
2170     if (multipleView && viewportsAdded.size() == 0)
2171     {
2172       // We recovered an alignment for which a viewport already exists.
2173       // TODO: fix up any settings necessary for overlaying stored state onto
2174       // state recovered from another document. (may not be necessary).
2175       // we may need a binding from a viewport in memory to one recovered from
2176       // XML.
2177       // and then recover its containing af to allow the settings to be applied.
2178       // TODO: fix for vamsas demo
2179       System.err
2180               .println("About to recover a viewport for existing alignment: Sequence set ID is "
2181                       + uniqueSeqSetId);
2182       Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
2183       if (seqsetobj != null)
2184       {
2185         if (seqsetobj instanceof String)
2186         {
2187           uniqueSeqSetId = (String) seqsetobj;
2188           System.err
2189                   .println("Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
2190                           + uniqueSeqSetId);
2191         }
2192         else
2193         {
2194           System.err
2195                   .println("Warning : Collision between sequence set ID string and existing jalview object mapping.");
2196         }
2197
2198       }
2199     }
2200     AlignmentPanel ap = null;
2201     boolean isnewview = true;
2202     if (viewId != null)
2203     {
2204       // Check to see if this alignment already has a view id == viewId
2205       jalview.gui.AlignmentPanel views[] = Desktop
2206               .getAlignmentPanels(uniqueSeqSetId);
2207       if (views != null && views.length > 0)
2208       {
2209         for (int v = 0; v < views.length; v++)
2210         {
2211           if (views[v].av.getViewId().equalsIgnoreCase(viewId))
2212           {
2213             // recover the existing alignpanel, alignframe, viewport
2214             af = views[v].alignFrame;
2215             av = views[v].av;
2216             ap = views[v];
2217             // TODO: could even skip resetting view settings if we don't want to
2218             // change the local settings from other jalview processes
2219             isnewview = false;
2220           }
2221         }
2222       }
2223     }
2224
2225     if (isnewview)
2226     {
2227       af = loadViewport(file, JSEQ, hiddenSeqs, al, hideConsensus,
2228               hideQuality, hideConservation, jms, view, uniqueSeqSetId,
2229               viewId);
2230       av = af.viewport;
2231       ap = af.alignPanel;
2232     }
2233     // LOAD TREES
2234     // /////////////////////////////////////
2235     if (loadTreesAndStructures && jms.getTreeCount() > 0)
2236     {
2237       try
2238       {
2239         for (int t = 0; t < jms.getTreeCount(); t++)
2240         {
2241
2242           Tree tree = jms.getTree(t);
2243
2244           TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
2245           if (tp == null)
2246           {
2247             tp = af.ShowNewickTree(new jalview.io.NewickFile(tree
2248                     .getNewick()), tree.getTitle(), tree.getWidth(), tree
2249                     .getHeight(), tree.getXpos(), tree.getYpos());
2250             if (tree.getId() != null)
2251             {
2252               // perhaps bind the tree id to something ?
2253             }
2254           }
2255           else
2256           {
2257             // update local tree attributes ?
2258             // TODO: should check if tp has been manipulated by user - if so its settings shouldn't be modified
2259             tp.setTitle(tree.getTitle());
2260             tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(), tree
2261                     .getWidth(), tree.getHeight()));
2262             tp.av = av; // af.viewport; // TODO: verify 'associate with all
2263             // views'
2264             // works still
2265             tp.treeCanvas.av = av; // af.viewport;
2266             tp.treeCanvas.ap = ap; // af.alignPanel;
2267
2268           }
2269           if (tp==null)
2270           {
2271             warn("There was a problem recovering stored Newick tree: \n"+tree.getNewick());
2272             continue;
2273           }
2274
2275           tp.fitToWindow.setState(tree.getFitToWindow());
2276           tp.fitToWindow_actionPerformed(null);
2277
2278           if (tree.getFontName() != null)
2279           {
2280             tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
2281                     .getFontStyle(), tree.getFontSize()));
2282           }
2283           else
2284           {
2285             tp.setTreeFont(new java.awt.Font(view.getFontName(), view
2286                     .getFontStyle(), tree.getFontSize()));
2287           }
2288
2289           tp.showPlaceholders(tree.getMarkUnlinked());
2290           tp.showBootstrap(tree.getShowBootstrap());
2291           tp.showDistances(tree.getShowDistances());
2292
2293           tp.treeCanvas.threshold = tree.getThreshold();
2294
2295           if (tree.getCurrentTree())
2296           {
2297             af.viewport.setCurrentTree(tp.getTree());
2298           }
2299         }
2300
2301       } catch (Exception ex)
2302       {
2303         ex.printStackTrace();
2304       }
2305     }
2306
2307     // //LOAD STRUCTURES
2308     if (loadTreesAndStructures)
2309     {
2310       for (int i = 0; i < JSEQ.length; i++)
2311       {
2312         if (JSEQ[i].getPdbidsCount() > 0)
2313         {
2314           Pdbids[] ids = JSEQ[i].getPdbids();
2315           for (int p = 0; p < ids.length; p++)
2316           {
2317             for (int s = 0; s < ids[p].getStructureStateCount(); s++)
2318             {
2319               // check to see if we haven't already created this structure view
2320               String sviewid = (ids[p].getStructureState(s).getViewId() == null) ? null
2321                       : ids[p].getStructureState(s).getViewId()
2322                               + uniqueSetSuffix;
2323               jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
2324               // Originally : ids[p].getFile()
2325               // : TODO: verify external PDB file recovery still works in normal
2326               // jalview project load
2327               jpdb.setFile(loadPDBFile(jprovider, ids[p].getId()));
2328               jpdb.setId(ids[p].getId());
2329
2330               int x = ids[p].getStructureState(s).getXpos();
2331               int y = ids[p].getStructureState(s).getYpos();
2332               int width = ids[p].getStructureState(s).getWidth();
2333               int height = ids[p].getStructureState(s).getHeight();
2334               AppJmol comp = null;
2335               JInternalFrame[] frames = null;
2336               do
2337               {
2338                 try
2339                 {
2340                   frames = Desktop.desktop.getAllFrames();
2341                 } catch (ArrayIndexOutOfBoundsException e)
2342                 {
2343                   // occasional No such child exceptions are thrown here...
2344                   frames = null;
2345                   try
2346                   {
2347                     Thread.sleep(10);
2348                   } catch (Exception f)
2349                   {
2350                   }
2351                   ;
2352                 }
2353               } while (frames == null);
2354               // search for any Jmol windows already open from other
2355               // alignment views that exactly match the stored structure state
2356               for (int f = 0; comp == null && f < frames.length; f++)
2357               {
2358                 if (frames[f] instanceof AppJmol)
2359                 {
2360                   if (sviewid != null
2361                           && ((AppJmol) frames[f]).getViewId().equals(
2362                                   sviewid))
2363                   {
2364                     // post jalview 2.4 schema includes structure view id
2365                     comp = (AppJmol) frames[f];
2366                   }
2367                   else if (frames[f].getX() == x && frames[f].getY() == y
2368                           && frames[f].getHeight() == height
2369                           && frames[f].getWidth() == width)
2370                   {
2371                     comp = (AppJmol) frames[f];
2372                   }
2373                 }
2374               }
2375               // Probably don't need to do this anymore...
2376               // Desktop.desktop.getComponentAt(x, y);
2377               // TODO: NOW: check that this recovers the PDB file correctly.
2378               String pdbFile = loadPDBFile(jprovider, ids[p].getId());
2379
2380               jalview.datamodel.SequenceI[] seq = new jalview.datamodel.SequenceI[]
2381               { (jalview.datamodel.SequenceI) seqRefIds.get(JSEQ[i].getId()
2382                       + "") };
2383
2384               if (comp == null)
2385               {
2386                 // create a new Jmol window
2387                 String state = ids[p].getStructureState(s).getContent();
2388                 StringBuffer newFileLoc=null;
2389                 if (state.indexOf("load")>-1) {
2390                 newFileLoc = new StringBuffer(state.substring(
2391                         0, state.indexOf("\"", state.indexOf("load")) + 1));
2392
2393                 newFileLoc.append(jpdb.getFile());
2394                 newFileLoc.append(state.substring(state.indexOf("\"", state
2395                         .indexOf("load \"") + 6)));
2396                 } else {
2397                   System.err.println("Ignoring incomplete Jmol state for PDB "+ids[p].getId());
2398
2399                   newFileLoc = new StringBuffer(state);
2400                   newFileLoc.append("; load \"");
2401                   newFileLoc.append(jpdb.getFile());
2402                   newFileLoc.append("\";");
2403                 }
2404
2405                 if (newFileLoc!=null) {
2406                   new AppJmol(pdbFile, ids[p].getId(), seq, af.alignPanel,
2407                           newFileLoc.toString(), new java.awt.Rectangle(x, y,
2408                                 width, height), sviewid);
2409                 }
2410
2411               }
2412               else
2413               // if (comp != null)
2414               {
2415                 // NOTE: if the jalview project is part of a shared session then
2416                 // view synchronization should/could be done here.
2417
2418                 // add mapping for this sequence to the already open Jmol
2419                 // instance (if it doesn't already exist)
2420                 // These
2421                 StructureSelectionManager.getStructureSelectionManager()
2422                         .setMapping(seq, null, pdbFile,
2423                                 jalview.io.AppletFormatAdapter.FILE);
2424
2425                 ((AppJmol) comp).addSequence(seq);
2426               }
2427             }
2428           }
2429         }
2430       }
2431     }
2432
2433     return af;
2434   }
2435
2436   AlignFrame loadViewport(String file, JSeq[] JSEQ, Vector hiddenSeqs,
2437           Alignment al, boolean hideConsensus, boolean hideQuality,
2438           boolean hideConservation, JalviewModelSequence jms,
2439           Viewport view, String uniqueSeqSetId, String viewId)
2440   {
2441     AlignFrame af = null;
2442     af = new AlignFrame(al, view.getWidth(), view.getHeight(),
2443             uniqueSeqSetId, viewId);
2444
2445     af.setFileName(file, "Jalview");
2446
2447     for (int i = 0; i < JSEQ.length; i++)
2448     {
2449       af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i),
2450               new java.awt.Color(JSEQ[i].getColour()));
2451     }
2452
2453     af.viewport.gatherViewsHere = view.getGatheredViews();
2454
2455     if (view.getSequenceSetId() != null)
2456     {
2457       jalview.gui.AlignViewport av = (jalview.gui.AlignViewport) viewportsAdded
2458               .get(uniqueSeqSetId);
2459
2460       af.viewport.sequenceSetID = uniqueSeqSetId;
2461       if (av != null)
2462       {
2463         // propagate shared settings to this new view
2464         af.viewport.historyList = av.historyList;
2465         af.viewport.redoList = av.redoList;
2466       }
2467       else
2468       {
2469         viewportsAdded.put(uniqueSeqSetId, af.viewport);
2470       }
2471       // TODO: check if this method can be called repeatedly without
2472       // side-effects if alignpanel already registered.
2473       PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
2474     }
2475     // apply Hidden regions to view.
2476     if (hiddenSeqs != null)
2477     {
2478       for (int s = 0; s < JSEQ.length; s++)
2479       {
2480         jalview.datamodel.SequenceGroup hidden = new jalview.datamodel.SequenceGroup();
2481
2482         for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
2483         {
2484           hidden.addSequence(al
2485                   .getSequenceAt(JSEQ[s].getHiddenSequences(r)), false);
2486         }
2487         af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
2488       }
2489
2490       jalview.datamodel.SequenceI[] hseqs = new jalview.datamodel.SequenceI[hiddenSeqs
2491               .size()];
2492
2493       for (int s = 0; s < hiddenSeqs.size(); s++)
2494       {
2495         hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
2496       }
2497
2498       af.viewport.hideSequence(hseqs);
2499
2500     }
2501     // set visibility of annotation in view
2502     if ((hideConsensus || hideQuality || hideConservation)
2503             && al.getAlignmentAnnotation() != null)
2504     {
2505       int hSize = al.getAlignmentAnnotation().length;
2506       for (int h = 0; h < hSize; h++)
2507       {
2508         if ((hideConsensus && al.getAlignmentAnnotation()[h].label
2509                 .equals("Consensus"))
2510                 || (hideQuality && al.getAlignmentAnnotation()[h].label
2511                         .equals("Quality"))
2512                 || (hideConservation && al.getAlignmentAnnotation()[h].label
2513                         .equals("Conservation")))
2514         {
2515           al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
2516           hSize--;
2517           h--;
2518         }
2519       }
2520       af.alignPanel.adjustAnnotationHeight();
2521     }
2522     // recover view properties and display parameters
2523     if (view.getViewName() != null)
2524     {
2525       af.viewport.viewName = view.getViewName();
2526       af.setInitialTabVisible();
2527     }
2528     af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view
2529             .getHeight());
2530
2531     af.viewport.setShowAnnotation(view.getShowAnnotation());
2532     af.viewport.setAbovePIDThreshold(view.getPidSelected());
2533
2534     af.viewport.setColourText(view.getShowColourText());
2535
2536     af.viewport.setConservationSelected(view.getConservationSelected());
2537     af.viewport.setShowJVSuffix(view.getShowFullId());
2538     af.viewport.rightAlignIds = view.getRightAlignIds();
2539     af.viewport.setFont(new java.awt.Font(view.getFontName(), view
2540             .getFontStyle(), view.getFontSize()));
2541     af.alignPanel.fontChanged();
2542     af.viewport.setRenderGaps(view.getRenderGaps());
2543     af.viewport.setWrapAlignment(view.getWrapAlignment());
2544     af.alignPanel.setWrapAlignment(view.getWrapAlignment());
2545     af.viewport.setShowAnnotation(view.getShowAnnotation());
2546     af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
2547
2548     af.viewport.setShowBoxes(view.getShowBoxes());
2549
2550     af.viewport.setShowText(view.getShowText());
2551
2552     af.viewport.textColour = new java.awt.Color(view.getTextCol1());
2553     af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
2554     af.viewport.thresholdTextColour = view.getTextColThreshold();
2555     af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view.isShowUnconserved() : false);
2556     af.viewport.setStartRes(view.getStartRes());
2557     af.viewport.setStartSeq(view.getStartSeq());
2558
2559     ColourSchemeI cs = null;
2560     // apply colourschemes
2561     if (view.getBgColour() != null)
2562     {
2563       if (view.getBgColour().startsWith("ucs"))
2564       {
2565         cs = GetUserColourScheme(jms, view.getBgColour());
2566       }
2567       else if (view.getBgColour().startsWith("Annotation"))
2568       {
2569         // int find annotation
2570         for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
2571         {
2572           if (af.viewport.alignment.getAlignmentAnnotation()[i].label
2573                   .equals(view.getAnnotationColours().getAnnotation()))
2574           {
2575             if (af.viewport.alignment.getAlignmentAnnotation()[i]
2576                     .getThreshold() == null)
2577             {
2578               af.viewport.alignment.getAlignmentAnnotation()[i]
2579                       .setThreshold(new jalview.datamodel.GraphLine(view
2580                               .getAnnotationColours().getThreshold(),
2581                               "Threshold", java.awt.Color.black)
2582
2583                       );
2584             }
2585
2586             if (view.getAnnotationColours().getColourScheme()
2587                     .equals("None"))
2588             {
2589               cs = new AnnotationColourGradient(af.viewport.alignment
2590                       .getAlignmentAnnotation()[i], new java.awt.Color(view
2591                       .getAnnotationColours().getMinColour()),
2592                       new java.awt.Color(view.getAnnotationColours()
2593                               .getMaxColour()), view.getAnnotationColours()
2594                               .getAboveThreshold());
2595             }
2596             else if (view.getAnnotationColours().getColourScheme()
2597                     .startsWith("ucs"))
2598             {
2599               cs = new AnnotationColourGradient(af.viewport.alignment
2600                       .getAlignmentAnnotation()[i], GetUserColourScheme(
2601                       jms, view.getAnnotationColours().getColourScheme()),
2602                       view.getAnnotationColours().getAboveThreshold());
2603             }
2604             else
2605             {
2606               cs = new AnnotationColourGradient(af.viewport.alignment
2607                       .getAlignmentAnnotation()[i], ColourSchemeProperty
2608                       .getColour(al, view.getAnnotationColours()
2609                               .getColourScheme()), view
2610                       .getAnnotationColours().getAboveThreshold());
2611             }
2612
2613             // Also use these settings for all the groups
2614             if (al.getGroups() != null)
2615             {
2616               for (int g = 0; g < al.getGroups().size(); g++)
2617               {
2618                 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) al
2619                         .getGroups().elementAt(g);
2620
2621                 if (sg.cs == null)
2622                 {
2623                   continue;
2624                 }
2625
2626                 /*
2627                  * if
2628                  * (view.getAnnotationColours().getColourScheme().equals("None")) {
2629                  * sg.cs = new AnnotationColourGradient(
2630                  * af.viewport.alignment.getAlignmentAnnotation()[i], new
2631                  * java.awt.Color(view.getAnnotationColours(). getMinColour()),
2632                  * new java.awt.Color(view.getAnnotationColours().
2633                  * getMaxColour()),
2634                  * view.getAnnotationColours().getAboveThreshold()); } else
2635                  */
2636                 {
2637                   sg.cs = new AnnotationColourGradient(
2638                           af.viewport.alignment.getAlignmentAnnotation()[i],
2639                           sg.cs, view.getAnnotationColours()
2640                                   .getAboveThreshold());
2641                 }
2642
2643               }
2644             }
2645
2646             break;
2647           }
2648
2649         }
2650       }
2651       else
2652       {
2653         cs = ColourSchemeProperty.getColour(al, view.getBgColour());
2654       }
2655
2656       if (cs != null)
2657       {
2658         cs.setThreshold(view.getPidThreshold(), true);
2659         cs.setConsensus(af.viewport.hconsensus);
2660       }
2661     }
2662
2663     af.viewport.setGlobalColourScheme(cs);
2664     af.viewport.setColourAppliesToAllGroups(false);
2665
2666     if (view.getConservationSelected() && cs != null)
2667     {
2668       cs.setConservationInc(view.getConsThreshold());
2669     }
2670
2671     af.changeColour(cs);
2672
2673     af.viewport.setColourAppliesToAllGroups(true);
2674
2675     if (view.getShowSequenceFeatures())
2676     {
2677       af.viewport.showSequenceFeatures = true;
2678     }
2679     // recover featre settings
2680     if (jms.getFeatureSettings() != null)
2681     {
2682       af.viewport.featuresDisplayed = new Hashtable();
2683       String[] renderOrder = new String[jms.getFeatureSettings()
2684               .getSettingCount()];
2685       for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
2686       {
2687         Setting setting = jms.getFeatureSettings().getSetting(fs);
2688         if (setting.hasMincolour())
2689         {
2690           // TODO: determine how to set data independent bounds for a graduated colour scheme's range.
2691           GraduatedColor gc = new GraduatedColor(new java.awt.Color(setting.getMincolour()), new java.awt.Color(setting.getColour()),
2692                   0,1);
2693           if (setting.hasThreshold()) {
2694             gc.setThresh(setting.getThreshold());
2695             gc.setThreshType(setting.getThreshstate());
2696           }
2697         } else {
2698           af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
2699                   setting.getType(), new java.awt.Color(setting.getColour()));
2700         }
2701         renderOrder[fs] = setting.getType();
2702         if (setting.hasOrder())
2703           af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
2704                   setting.getType(), setting.getOrder());
2705         else
2706           af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
2707                   setting.getType(),
2708                   fs / jms.getFeatureSettings().getSettingCount());
2709         if (setting.getDisplay())
2710         {
2711           af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
2712                   setting.getColour()));
2713         }
2714       }
2715       af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
2716       Hashtable fgtable;
2717       af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable();
2718       for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
2719       {
2720         Group grp = jms.getFeatureSettings().getGroup(gs);
2721         fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
2722       }
2723     }
2724
2725     if (view.getHiddenColumnsCount() > 0)
2726     {
2727       for (int c = 0; c < view.getHiddenColumnsCount(); c++)
2728       {
2729         af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view
2730                 .getHiddenColumns(c).getEnd() // +1
2731                 );
2732       }
2733     }
2734
2735     af.setMenusFromViewport(af.viewport);
2736     // TODO: we don't need to do this if the viewport is aready visible.
2737     Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view
2738             .getHeight());
2739     return af;
2740   }
2741
2742   Hashtable skipList = null;
2743
2744   /**
2745    * TODO remove this method
2746    *
2747    * @param view
2748    * @return AlignFrame bound to sequenceSetId from view, if one exists. private
2749    *         AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
2750    *         throw new Error("Implementation Error. No skipList defined for this
2751    *         Jalview2XML instance."); } return (AlignFrame)
2752    *         skipList.get(view.getSequenceSetId()); }
2753    */
2754
2755   /**
2756    * Check if the Jalview view contained in object should be skipped or not.
2757    *
2758    * @param object
2759    * @return true if view's sequenceSetId is a key in skipList
2760    */
2761   private boolean skipViewport(JalviewModel object)
2762   {
2763     if (skipList == null)
2764     {
2765       return false;
2766     }
2767     String id;
2768     if (skipList.containsKey(id = object.getJalviewModelSequence()
2769             .getViewport()[0].getSequenceSetId()))
2770     {
2771       if (Cache.log != null && Cache.log.isDebugEnabled())
2772       {
2773         Cache.log.debug("Skipping seuqence set id " + id);
2774       }
2775       return true;
2776     }
2777     return false;
2778   }
2779
2780   public void AddToSkipList(AlignFrame af)
2781   {
2782     if (skipList == null)
2783     {
2784       skipList = new Hashtable();
2785     }
2786     skipList.put(af.getViewport().getSequenceSetId(), af);
2787   }
2788
2789   public void clearSkipList()
2790   {
2791     if (skipList != null)
2792     {
2793       skipList.clear();
2794       skipList = null;
2795     }
2796   }
2797
2798   private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al)
2799   {
2800     jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId());
2801     Vector dseqs = null;
2802     if (ds == null)
2803     {
2804       // create a list of new dataset sequences
2805       dseqs = new Vector();
2806     }
2807     for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
2808     {
2809       Sequence vamsasSeq = vamsasSet.getSequence(i);
2810       ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs);
2811     }
2812     // create a new dataset
2813     if (ds == null)
2814     {
2815       SequenceI[] dsseqs = new SequenceI[dseqs.size()];
2816       dseqs.copyInto(dsseqs);
2817       ds = new jalview.datamodel.Alignment(dsseqs);
2818       debug("Created new dataset "+vamsasSet.getDatasetId()+" for alignment "+System.identityHashCode(al));
2819       addDatasetRef(vamsasSet.getDatasetId(), ds);
2820     }
2821     // set the dataset for the newly imported alignment.
2822     if (al.getDataset() == null)
2823     {
2824       al.setDataset(ds);
2825     }
2826   }
2827
2828   /**
2829    *
2830    * @param vamsasSeq
2831    *                sequence definition to create/merge dataset sequence for
2832    * @param ds
2833    *                dataset alignment
2834    * @param dseqs
2835    *                vector to add new dataset sequence to
2836    */
2837   private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
2838           AlignmentI ds, Vector dseqs)
2839   {
2840     // JBP TODO: Check this is called for AlCodonFrames to support recovery of
2841     // xRef Codon Maps
2842     jalview.datamodel.Sequence sq = (jalview.datamodel.Sequence) seqRefIds
2843             .get(vamsasSeq.getId());
2844     jalview.datamodel.SequenceI dsq = null;
2845     if (sq != null && sq.getDatasetSequence() != null)
2846     {
2847       dsq = (jalview.datamodel.SequenceI) sq.getDatasetSequence();
2848     }
2849
2850     String sqid = vamsasSeq.getDsseqid();
2851     if (dsq == null)
2852     {
2853       // need to create or add a new dataset sequence reference to this sequence
2854       if (sqid != null)
2855       {
2856         dsq = (jalview.datamodel.SequenceI) seqRefIds.get(sqid);
2857       }
2858       // check again
2859       if (dsq == null)
2860       {
2861         // make a new dataset sequence
2862         dsq = sq.createDatasetSequence();
2863         if (sqid == null)
2864         {
2865           // make up a new dataset reference for this sequence
2866           sqid = seqHash(dsq);
2867         }
2868         dsq.setVamsasId(uniqueSetSuffix + sqid);
2869         seqRefIds.put(sqid, dsq);
2870         if (ds == null)
2871         {
2872           if (dseqs != null)
2873           {
2874             dseqs.addElement(dsq);
2875           }
2876         }
2877         else
2878         {
2879           ds.addSequence(dsq);
2880         }
2881       }
2882       else
2883       {
2884         if (sq != dsq)
2885         { // make this dataset sequence sq's dataset sequence
2886           sq.setDatasetSequence(dsq);
2887         }
2888       }
2889     }
2890     // TODO: refactor this as a merge dataset sequence function
2891     // now check that sq (the dataset sequence) sequence really is the union of
2892     // all references to it
2893     // boolean pre = sq.getStart() < dsq.getStart();
2894     // boolean post = sq.getEnd() > dsq.getEnd();
2895     // if (pre || post)
2896     if (sq != dsq)
2897     {
2898       StringBuffer sb = new StringBuffer();
2899       String newres = jalview.analysis.AlignSeq.extractGaps(
2900               jalview.util.Comparison.GapChars, sq.getSequenceAsString());
2901       if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
2902               && newres.length() > dsq.getLength())
2903       {
2904         // Update with the longer sequence.
2905         synchronized (dsq)
2906         {
2907           /*
2908            * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
2909            * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
2910            * sb.append(newres.substring(newres.length() - sq.getEnd() -
2911            * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
2912            */
2913           dsq.setSequence(sb.toString());
2914         }
2915         // TODO: merges will never happen if we 'know' we have the real dataset
2916         // sequence - this should be detected when id==dssid
2917         System.err.println("DEBUG Notice:  Merged dataset sequence"); // ("
2918         // + (pre ? "prepended" : "") + " "
2919         // + (post ? "appended" : ""));
2920       }
2921     }
2922   }
2923
2924   java.util.Hashtable datasetIds = null;
2925   java.util.IdentityHashMap dataset2Ids = null;
2926   private Alignment getDatasetFor(String datasetId)
2927   {
2928     if (datasetIds == null)
2929     {
2930       datasetIds = new Hashtable();
2931       return null;
2932     }
2933     if (datasetIds.containsKey(datasetId))
2934     {
2935       return (Alignment) datasetIds.get(datasetId);
2936     }
2937     return null;
2938   }
2939
2940   private void addDatasetRef(String datasetId, Alignment dataset)
2941   {
2942     if (datasetIds == null)
2943     {
2944       datasetIds = new Hashtable();
2945     }
2946     datasetIds.put(datasetId, dataset);
2947   }
2948   /**
2949    * make a new dataset ID for this jalview dataset alignment
2950    * @param dataset
2951    * @return
2952    */
2953   private String getDatasetIdRef(jalview.datamodel.Alignment dataset)
2954   {
2955     if (dataset.getDataset()!=null)
2956     {
2957       warn("Serious issue!  Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
2958     }
2959     String datasetId=makeHashCode(dataset, null);
2960     if (datasetId==null)
2961     {
2962       // make a new datasetId and record it
2963       if (dataset2Ids == null)
2964       {
2965         dataset2Ids = new IdentityHashMap();
2966       } else {
2967         datasetId = (String) dataset2Ids.get(dataset);
2968       }
2969       if (datasetId==null)
2970       {
2971         datasetId = "ds"+dataset2Ids.size()+1;
2972         dataset2Ids.put(dataset,datasetId);
2973       }
2974     }
2975     return datasetId;
2976   }
2977   private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
2978   {
2979     for (int d = 0; d < sequence.getDBRefCount(); d++)
2980     {
2981       DBRef dr = sequence.getDBRef(d);
2982       jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
2983               sequence.getDBRef(d).getSource(), sequence.getDBRef(d)
2984                       .getVersion(), sequence.getDBRef(d).getAccessionId());
2985       if (dr.getMapping() != null)
2986       {
2987         entry.setMap(addMapping(dr.getMapping()));
2988       }
2989       datasetSequence.addDBRef(entry);
2990     }
2991   }
2992
2993   private jalview.datamodel.Mapping addMapping(Mapping m)
2994   {
2995     SequenceI dsto = null;
2996     // Mapping m = dr.getMapping();
2997     int fr[] = new int[m.getMapListFromCount() * 2];
2998     Enumeration f = m.enumerateMapListFrom();
2999     for (int _i = 0; f.hasMoreElements(); _i += 2)
3000     {
3001       MapListFrom mf = (MapListFrom) f.nextElement();
3002       fr[_i] = mf.getStart();
3003       fr[_i + 1] = mf.getEnd();
3004     }
3005     int fto[] = new int[m.getMapListToCount() * 2];
3006     f = m.enumerateMapListTo();
3007     for (int _i = 0; f.hasMoreElements(); _i += 2)
3008     {
3009       MapListTo mf = (MapListTo) f.nextElement();
3010       fto[_i] = mf.getStart();
3011       fto[_i + 1] = mf.getEnd();
3012     }
3013     jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto,
3014             fr, fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit());
3015     if (m.getMappingChoice() != null)
3016     {
3017       MappingChoice mc = m.getMappingChoice();
3018       if (mc.getDseqFor() != null)
3019       {
3020         String dsfor = ""+mc.getDseqFor();
3021         if (seqRefIds.containsKey(dsfor))
3022         {
3023           /**
3024            * recover from hash
3025            */
3026           jmap.setTo((SequenceI) seqRefIds.get(dsfor));
3027         }
3028         else
3029         {
3030           frefedSequence.add(new Object[]
3031           { dsfor, jmap });
3032         }
3033       }
3034       else
3035       {
3036         /**
3037          * local sequence definition
3038          */
3039         Sequence ms = mc.getSequence();
3040         jalview.datamodel.Sequence djs = null;
3041         String sqid = ms.getDsseqid();
3042         if (sqid != null && sqid.length() > 0)
3043         {
3044           /*
3045            * recover dataset sequence
3046            */
3047           djs = (jalview.datamodel.Sequence) seqRefIds.get(sqid);
3048         }
3049         else
3050         {
3051           System.err
3052                   .println("Warning - making up dataset sequence id for DbRef sequence map reference");
3053           sqid = ((Object) ms).toString(); // make up a new hascode for
3054           // undefined dataset sequence hash
3055           // (unlikely to happen)
3056         }
3057
3058         if (djs == null)
3059         {
3060           /**
3061            * make a new dataset sequence and add it to refIds hash
3062            */
3063           djs = new jalview.datamodel.Sequence(ms.getName(), ms
3064                   .getSequence());
3065           djs.setStart(jmap.getMap().getToLowest());
3066           djs.setEnd(jmap.getMap().getToHighest());
3067           djs.setVamsasId(uniqueSetSuffix + sqid);
3068           jmap.setTo(djs);
3069           seqRefIds.put(sqid, djs);
3070
3071         }
3072         jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
3073         addDBRefs(djs, ms);
3074
3075       }
3076     }
3077     return (jmap);
3078
3079   }
3080
3081   public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
3082           boolean keepSeqRefs)
3083   {
3084     initSeqRefs();
3085     jalview.schemabinding.version2.JalviewModel jm = SaveState(ap, null,
3086             null);
3087
3088     if (!keepSeqRefs)
3089     {
3090       clearSeqRefs();
3091       jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
3092     }
3093     else
3094     {
3095       uniqueSetSuffix = "";
3096       jm.getJalviewModelSequence().getViewport(0).setId(null); // we don't overwrite the view we just copied
3097     }
3098     if (this.frefedSequence==null)
3099     {
3100       frefedSequence = new Vector();
3101     }
3102
3103     viewportsAdded = new Hashtable();
3104
3105     AlignFrame af = LoadFromObject(jm, null, false, null);
3106     af.alignPanels.clear();
3107     af.closeMenuItem_actionPerformed(true);
3108
3109     /*
3110      * if(ap.av.alignment.getAlignmentAnnotation()!=null) { for(int i=0; i<ap.av.alignment.getAlignmentAnnotation().length;
3111      * i++) { if(!ap.av.alignment.getAlignmentAnnotation()[i].autoCalculated) {
3112      * af.alignPanel.av.alignment.getAlignmentAnnotation()[i] =
3113      * ap.av.alignment.getAlignmentAnnotation()[i]; } } }
3114      */
3115
3116     return af.alignPanel;
3117   }
3118
3119   /**
3120    * flag indicating if hashtables should be cleared on finalization TODO this
3121    * flag may not be necessary
3122    */
3123   private boolean _cleartables = true;
3124
3125   private Hashtable jvids2vobj;
3126
3127   /*
3128    * (non-Javadoc)
3129    *
3130    * @see java.lang.Object#finalize()
3131    */
3132   protected void finalize() throws Throwable
3133   {
3134     // really make sure we have no buried refs left.
3135     if (_cleartables)
3136     {
3137       clearSeqRefs();
3138     }
3139     this.seqRefIds = null;
3140     this.seqsToIds = null;
3141     super.finalize();
3142   }
3143
3144   private void warn(String msg)
3145   {
3146     warn(msg, null);
3147   }
3148
3149   private void warn(String msg, Exception e)
3150   {
3151     if (Cache.log != null)
3152     {
3153       if (e != null)
3154       {
3155         Cache.log.warn(msg, e);
3156       }
3157       else
3158       {
3159         Cache.log.warn(msg);
3160       }
3161     }
3162     else
3163     {
3164       System.err.println("Warning: " + msg);
3165       if (e != null)
3166       {
3167         e.printStackTrace();
3168       }
3169     }
3170   }
3171
3172   private void debug(String string)
3173   {
3174     debug(string,null);
3175   }
3176   private void debug(String msg, Exception e)
3177   {
3178     if (Cache.log != null)
3179     {
3180       if (e != null)
3181       {
3182         Cache.log.debug(msg, e);
3183       }
3184       else
3185       {
3186         Cache.log.debug(msg);
3187       }
3188     }
3189     else
3190     {
3191       System.err.println("Warning: " + msg);
3192       if (e != null)
3193       {
3194         e.printStackTrace();
3195       }
3196     }
3197   }
3198
3199   /**
3200    * set the object to ID mapping tables used to write/recover objects and XML
3201    * ID strings for the jalview project. If external tables are provided then
3202    * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
3203    * object goes out of scope. - also populates the datasetIds hashtable with
3204    * alignment objects containing dataset sequences
3205    *
3206    * @param vobj2jv
3207    *                Map from ID strings to jalview datamodel
3208    * @param jv2vobj
3209    *                Map from jalview datamodel to ID strings
3210    *
3211    *
3212    */
3213   public void setObjectMappingTables(Hashtable vobj2jv,
3214           IdentityHashMap jv2vobj)
3215   {
3216     this.jv2vobj = jv2vobj;
3217     this.vobj2jv = vobj2jv;
3218     Iterator ds = jv2vobj.keySet().iterator();
3219     String id;
3220     while (ds.hasNext())
3221     {
3222       Object jvobj = ds.next();
3223       id = jv2vobj.get(jvobj).toString();
3224       if (jvobj instanceof jalview.datamodel.Alignment)
3225       {
3226         if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
3227         {
3228           addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
3229         }
3230       }
3231       else if (jvobj instanceof jalview.datamodel.Sequence)
3232       {
3233         // register sequence object so the XML parser can recover it.
3234         if (seqRefIds == null)
3235         {
3236           seqRefIds = new Hashtable();
3237         }
3238         if (seqsToIds == null)
3239         {
3240           seqsToIds = new IdentityHashMap();
3241         }
3242         seqRefIds.put(jv2vobj.get(jvobj).toString(), jvobj);
3243         seqsToIds.put(jvobj, id);
3244       }
3245       else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
3246       {
3247         if (annotationIds == null)
3248         {
3249           annotationIds = new Hashtable();
3250         }
3251         String anid;
3252         annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvobj);
3253         jalview.datamodel.AlignmentAnnotation jvann = (jalview.datamodel.AlignmentAnnotation) jvobj;
3254         if (jvann.annotationId == null)
3255         {
3256           jvann.annotationId = anid;
3257         }
3258         if (!jvann.annotationId.equals(anid))
3259         {
3260           // TODO verify that this is the correct behaviour
3261           this.warn("Overriding Annotation ID for " + anid
3262                   + " from different id : " + jvann.annotationId);
3263           jvann.annotationId = anid;
3264         }
3265       }
3266       else if (jvobj instanceof String)
3267       {
3268         if (jvids2vobj == null)
3269         {
3270           jvids2vobj = new Hashtable();
3271           jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
3272         }
3273       }
3274       else
3275         Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
3276     }
3277   }
3278
3279   /**
3280    * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
3281    * objects created from the project archive. If string is null (default for
3282    * construction) then suffix will be set automatically.
3283    *
3284    * @param string
3285    */
3286   public void setUniqueSetSuffix(String string)
3287   {
3288     uniqueSetSuffix = string;
3289
3290   }
3291
3292   /**
3293    * uses skipList2 as the skipList for skipping views on sequence sets
3294    * associated with keys in the skipList
3295    *
3296    * @param skipList2
3297    */
3298   public void setSkipList(Hashtable skipList2)
3299   {
3300     skipList = skipList2;
3301   }
3302
3303 }