src/jalview/io/VamsasAppDatastore.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer
   3  * Copyright (C) 2005 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
  20 package jalview.io;
  21
  22 import jalview.bin.Cache;
  23 import jalview.datamodel.AlignmentAnnotation;
  24 import jalview.datamodel.AlignmentI;
  25 import jalview.datamodel.AlignmentView;
  26 import jalview.datamodel.DBRefEntry;
  27 import jalview.datamodel.GraphLine;
  28 import jalview.datamodel.SequenceFeature;
  29 import jalview.datamodel.SequenceI;
  30 import jalview.gui.AlignFrame;
  31 import jalview.gui.AlignViewport;
  32 import jalview.gui.Desktop;
  33 import jalview.gui.TreePanel;
  34 import jalview.io.vamsas.DatastoreItem;
  35 import jalview.io.vamsas.Rangetype;
  36
  37 import java.util.Enumeration;
  38 import java.util.HashMap;
  39 import java.util.Hashtable;
  40 import java.util.IdentityHashMap;
  41 import java.util.Vector;
  42
  43 import uk.ac.vamsas.client.*;
  44 import uk.ac.vamsas.objects.core.*;
  45
  46 /*
  47  *
  48  * static {
  49  * org.exolab.castor.util.LocalConfiguration.getInstance().getProperties().setProperty(
  50  * "org.exolab.castor.serializer", "org.apache.xml.serialize.XMLSerilazizer"); }
  51  *
  52  */
  53
  54 public class VamsasAppDatastore
  55 {
  56   /**
  57    * Type used for general jalview generated annotation added to vamsas document
  58    */
  59   public static final String JALVIEW_ANNOTATION_ROW = "JalviewAnnotation";
  60
  61   /**
  62    * AlignmentAnnotation property to indicate that values should not be interpolated
  63    */
  64   public static final String DISCRETE_ANNOTATION = "discrete";
  65   /**
  66    * continuous property - optional to specify that annotation should be represented
  67    * as a continous graph line
  68    */
  69   private static final String CONTINUOUS_ANNOTATION = "continuous";
  70
  71   private static final String THRESHOLD = "threshold";
  72
  73
  74   Entry provEntry = null;
  75
  76   IClientDocument cdoc;
  77
  78   Hashtable vobj2jv;
  79
  80   IdentityHashMap jv2vobj;
  81
  82   Hashtable alignRDHash;
  83
  84   public VamsasAppDatastore(IClientDocument cdoc, Hashtable vobj2jv,
  85           IdentityHashMap jv2vobj, Entry provEntry, Hashtable alignRDHash)
  86   {
  87     this.cdoc = cdoc;
  88     this.vobj2jv = vobj2jv;
  89     this.jv2vobj = jv2vobj;
  90     this.provEntry = provEntry;
  91     this.alignRDHash = alignRDHash;
  92   }
  93
  94   /**
  95    * @return the Vobject bound to Jalview datamodel object
  96    */
  97   protected Vobject getjv2vObj(Object jvobj)
  98   {
  99     if (jv2vobj.containsKey(jvobj))
 100     {
 101       return cdoc.getObject((VorbaId) jv2vobj.get(jvobj));
 102     }
 103     if (Cache.log.isDebugEnabled())
 104     {
 105       Cache.log.debug("Returning null VorbaID binding for jalview object "
 106               + jvobj);
 107     }
 108     return null;
 109   }
 110
 111   /**
 112    *
 113    * @param vobj
 114    * @return Jalview datamodel object bound to the vamsas document object
 115    */
 116   protected Object getvObj2jv(uk.ac.vamsas.client.Vobject vobj)
 117   {
 118     VorbaId id = vobj.getVorbaId();
 119     if (id == null)
 120     {
 121       id = cdoc.registerObject(vobj);
 122       Cache.log
 123               .debug("Registering new object and returning null for getvObj2jv");
 124       return null;
 125     }
 126     if (vobj2jv.containsKey(vobj.getVorbaId()))
 127     {
 128       return vobj2jv.get(vobj.getVorbaId());
 129     }
 130     return null;
 131   }
 132
 133   protected void bindjvvobj(Object jvobj, uk.ac.vamsas.client.Vobject vobj)
 134   {
 135     VorbaId id = vobj.getVorbaId();
 136     if (id == null)
 137     {
 138       id = cdoc.registerObject(vobj);
 139       if (id == null || vobj.getVorbaId() == null
 140               || cdoc.getObject(id) != vobj)
 141       {
 142         Cache.log.error("Failed to get id for "
 143                 + (vobj.isRegisterable() ? "registerable"
 144                         : "unregisterable") + " object " + vobj);
 145       }
 146     }
 147
 148     if (vobj2jv.containsKey(vobj.getVorbaId())
 149             && !((VorbaId) vobj2jv.get(vobj.getVorbaId())).equals(jvobj))
 150     {
 151       Cache.log.debug(
 152               "Warning? Overwriting existing vamsas id binding for "
 153                       + vobj.getVorbaId(), new Exception(
 154                       "Overwriting vamsas id binding."));
 155     }
 156     else if (jv2vobj.containsKey(jvobj)
 157             && !((VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
 158     {
 159       Cache.log.debug(
 160               "Warning? Overwriting existing jalview object binding for "
 161                       + jvobj, new Exception(
 162                       "Overwriting jalview object binding."));
 163     }
 164     /*
 165      * Cache.log.error("Attempt to make conflicting object binding! "+vobj+" id "
 166      * +vobj.getVorbaId()+" already bound to "+getvObj2jv(vobj)+" and "+jvobj+"
 167      * already bound to "+getjv2vObj(jvobj),new Exception("Excessive call to
 168      * bindjvvobj")); }
 169      */
 170     // we just update the hash's regardless!
 171     Cache.log.debug("Binding " + vobj.getVorbaId() + " to " + jvobj);
 172     vobj2jv.put(vobj.getVorbaId(), jvobj);
 173     // JBPNote - better implementing a hybrid invertible hash.
 174     jv2vobj.put(jvobj, vobj.getVorbaId());
 175   }
 176
 177   /**
 178    * put the alignment viewed by AlignViewport into cdoc.
 179    *
 180    * @param av
 181    *          alignViewport to be stored
 182    * @param aFtitle
 183    *          title for alignment
 184    */
 185   public void storeVAMSAS(AlignViewport av, String aFtitle)
 186   {
 187     try
 188     {
 189       jalview.datamodel.AlignmentI jal = av.getAlignment();
 190       boolean nw = false;
 191       VAMSAS root = null; // will be resolved based on Dataset Parent.
 192       // /////////////////////////////////////////
 193       // SAVE THE DATASET
 194       DataSet dataset = null;
 195       if (jal.getDataset() == null)
 196       {
 197         Cache.log.warn("Creating new dataset for an alignment.");
 198         jal.setDataset(null);
 199       }
 200       dataset = (DataSet) getjv2vObj(jal.getDataset());
 201       if (dataset == null)
 202       {
 203         // it might be that one of the dataset sequences does actually have a
 204         // binding, so search for it indirectly.
 205         jalview.datamodel.SequenceI[] jdatset = jal.getDataset()
 206                 .getSequencesArray();
 207         for (int i = 0; i < jdatset.length; i++)
 208         {
 209           Vobject vbound = getjv2vObj(jdatset[i]);
 210           if (vbound != null)
 211           {
 212             if (vbound instanceof uk.ac.vamsas.objects.core.Sequence)
 213             {
 214               if (dataset == null)
 215               {
 216                 dataset = (DataSet) vbound.getV_parent();
 217               }
 218               else
 219               {
 220                 if (dataset != vbound.getV_parent())
 221                 {
 222                   throw new Error(
 223                           "IMPLEMENTATION ERROR: Cannot map an alignment of sequences from datasets into the vamsas document.");
 224                   // This occurs because the dataset for the alignment we are
 225                   // trying to
 226                 }
 227               }
 228             }
 229           }
 230         }
 231       }
 232
 233       if (dataset == null)
 234       {
 235         // we create a new dataset on the default vamsas root.
 236         root = cdoc.getVamsasRoots()[0]; // default vamsas root for modifying.
 237         dataset = new DataSet();
 238         root.addDataSet(dataset);
 239         bindjvvobj(jal.getDataset(), dataset);
 240         dataset.setProvenance(dummyProvenance());
 241         // dataset.getProvenance().addEntry(provEntry);
 242         nw = true;
 243       }
 244       else
 245       {
 246         root = (VAMSAS) dataset.getV_parent();
 247       }
 248       // update dataset
 249       Sequence sequence;
 250       DbRef dbref;
 251       // set new dataset and alignment sequences based on alignment Nucleotide
 252       // flag.
 253       // this *will* break when alignment contains both nucleotide and amino
 254       // acid sequences.
 255       String dict = jal.isNucleotide() ? uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA
 256               : uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA;
 257       Vector dssmods = new Vector();
 258       for (int i = 0; i < jal.getHeight(); i++)
 259       {
 260         SequenceI sq = jal.getSequenceAt(i).getDatasetSequence(); // only insert
 261         // referenced
 262         // sequences
 263         // to dataset.
 264         sequence = (Sequence) getjv2vObj(sq);
 265         if (sequence == null)
 266         {
 267           sequence = new Sequence();
 268           bindjvvobj(sq, sequence);
 269           sq.setVamsasId(sequence.getVorbaId().getId());
 270           sequence.setSequence(sq.getSequenceAsString());
 271           sequence.setDictionary(dict);
 272           sequence.setName(sq.getName());
 273           sequence.setStart(sq.getStart());
 274           sequence.setEnd(sq.getEnd());
 275           sequence.setDescription(sq.getDescription());
 276           dataset.addSequence(sequence);
 277           dssmods.addElement(dssmods);
 278         }
 279         else
 280         {
 281           boolean dsmod = false;
 282           // verify and update principal attributes.
 283           if (sq.getDescription()!=null && (sequence.getDescription()==null || !sequence.getDescription().equals(sq.getDescription())))
 284           {
 285             sequence.setDescription(sq.getDescription());
 286             dsmod = true;
 287           }
 288           if (sequence.getSequence()==null || !sequence.getSequence().equals(sq.getSequenceAsString()))
 289           {
 290             if (sequence.getStart()!=sq.getStart() || sequence.getEnd()!=sq.getEnd())
 291             {
 292               // update modified sequence.
 293               sequence.setSequence(sq.getSequenceAsString());
 294               sequence.setStart(sq.getStart());
 295               sequence.setEnd(sq.getEnd());
 296               dsmod = true;
 297             }
 298           }
 299           if (!dict.equals(sequence.getDictionary()))
 300           {
 301             sequence.setDictionary(dict);
 302             dsmod = true;
 303           }
 304           if (!sequence.getName().equals(sq.getName()))
 305           {
 306             sequence.setName(sq.getName());
 307             dsmod = true;
 308           }
 309           if (dsmod)
 310           {
 311             dssmods.addElement(sequence);
 312           }
 313         }
 314         // add or update any new features/references on dataset sequence
 315         if (sq.getSequenceFeatures() != null)
 316         {
 317           int sfSize = sq.getSequenceFeatures().length;
 318
 319           for (int sf = 0; sf < sfSize; sf++)
 320           {
 321             // TODO: update/modifiable synchronizer
 322             jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) sq
 323                     .getSequenceFeatures()[sf];
 324
 325             DataSetAnnotations dsa = (DataSetAnnotations) getjv2vObj(feature);
 326             if (dsa == null)
 327             {
 328               dsa = (DataSetAnnotations) getDSAnnotationFromJalview(
 329                       new DataSetAnnotations(), feature);
 330               if (dsa.getProvenance() == null)
 331               {
 332                 dsa.setProvenance(new Provenance());
 333               }
 334               addProvenance(dsa.getProvenance(), "created"); // JBPNote - need
 335               // to update
 336               dsa.addSeqRef(sequence); // we have just created this annotation
 337                                         // - so safe to use this
 338               bindjvvobj(feature, dsa);
 339               dataset.addDataSetAnnotations(dsa);
 340             }
 341             else
 342             {
 343               // todo: verify and update dataset annotations for sequence
 344               System.out.println("update dataset sequence annotations.");
 345             }
 346           }
 347         }
 348
 349         if (sq.getDBRef() != null)
 350         {
 351           DBRefEntry[] entries = sq.getDBRef();
 352           jalview.datamodel.DBRefEntry dbentry;
 353           for (int db = 0; db < entries.length; db++)
 354           {
 355             Rangetype dbr = new jalview.io.vamsas.Dbref(this,
 356                     dbentry = entries[db], sq, sequence);
 357           }
 358
 359         }
 360       }
 361       if (dssmods.size()>0)
 362       {
 363         if (!nw)
 364         {
 365           Entry pentry = this.addProvenance(dataset.getProvenance(), "updated sequences");
 366           // pentry.addInput(vInput); could write in which sequences were modified.
 367           dssmods.removeAllElements();
 368         }
 369       }
 370       // dataset.setProvenance(getVamsasProvenance(jal.getDataset().getProvenance()));
 371       // ////////////////////////////////////////////
 372       if (!av.getAlignment().isAligned())
 373         return; // TODO: trees could be written - but for the moment we just skip
 374       // ////////////////////////////////////////////
 375       // Save the Alignments
 376
 377       Alignment alignment = (Alignment) getjv2vObj(av.getSequenceSetId()); // this is so we can get
 378                                                         // the alignviewport
 379                                                         // back
 380       if (alignment == null)
 381       {
 382         alignment = new Alignment();
 383         bindjvvobj(av.getSequenceSetId(), alignment);
 384         if (alignment.getProvenance() == null)
 385         {
 386           alignment.setProvenance(new Provenance());
 387         }
 388         addProvenance(alignment.getProvenance(), "added"); // TODO: insert some
 389         // sensible source
 390         // here
 391         dataset.addAlignment(alignment);
 392         {
 393           Property title = new Property();
 394           title.setName("title");
 395           title.setType("string");
 396           title.setContent(aFtitle);
 397           alignment.addProperty(title);
 398         }
 399         alignment.setGapChar(String.valueOf(av.getGapCharacter()));
 400         for (int i = 0; i < jal.getHeight(); i++)
 401         {
 402           syncToAlignmentSequence(jal.getSequenceAt(i), alignment);
 403         }
 404         alignRDHash.put(av.getSequenceSetId(),av.getUndoRedoHash());
 405       }
 406       else
 407       {
 408         boolean alismod = av.isUndoRedoHashModified((long[]) alignRDHash.get(av.getSequenceSetId()));
 409         // todo: verify and update mutable alignment props.
 410         // TODO: Use isLocked methods
 411         if (alignment.getModifiable() == null || alignment.getModifiable().length()==0)
 412         {
 413           boolean modified = false;
 414           for (int i = 0; i < jal.getHeight(); i++)
 415           {
 416             modified |= syncToAlignmentSequence(jal.getSequenceAt(i), alignment);
 417           }
 418           if (modified)
 419           {
 420             if (alismod)
 421             {
 422               // info in the undo
 423               addProvenance(alignment.getProvenance(), "Edited"); // TODO: insert something sensible here again
 424                       }
 425             else {
 426               // info in the undo
 427               addProvenance(alignment.getProvenance(), "Attributes Edited"); // TODO: insert something sensible here again
 428             }
 429           }
 430           System.out.println("update alignment in document.");
 431         }
 432         else
 433         {
 434           System.out
 435                   .println("update edited alignment to new alignment in document.");
 436         }
 437       }
 438       // ////////////////////////////////////////////
 439       // SAVE Alignment Sequence Features
 440       for (int i = 0, iSize = alignment.getAlignmentSequenceCount(); i < iSize; i++)
 441       {
 442         AlignmentSequence valseq;
 443         SequenceI alseq = (SequenceI) getvObj2jv(valseq = alignment
 444                 .getAlignmentSequence(i));
 445         if (alseq != null && alseq.getSequenceFeatures() != null)
 446         {
 447           /*
 448            * We do not put local Alignment Sequence Features into the vamsas
 449            * document yet.
 450            *
 451            *
 452            * jalview.datamodel.SequenceFeature[] features = alseq
 453            * .getSequenceFeatures(); for (int f = 0; f < features.length; f++) {
 454            * if (features[f] != null) { AlignmentSequenceAnnotation valseqf = (
 455            * AlignmentSequenceAnnotation) getjv2vObj(features[i]); if (valseqf ==
 456            * null) {
 457            *
 458            * valseqf = (AlignmentSequenceAnnotation) getDSAnnotationFromJalview(
 459            * new AlignmentSequenceAnnotation(), features[i]);
 460            * valseqf.setGraph(false);
 461            * valseqf.addProperty(newProperty("jalview:feature","boolean","true"));
 462            * if (valseqf.getProvenance() == null) { valseqf.setProvenance(new
 463            * Provenance()); } addProvenance(valseqf.getProvenance(), "created"); //
 464            * JBPNote - // need to // update bindjvvobj(features[i], valseqf);
 465            * valseq.addAlignmentSequenceAnnotation(valseqf); } }
 466            *  }
 467            */
 468         }
 469       }
 470
 471       // ////////////////////////////////////////////
 472       // SAVE ANNOTATIONS
 473       if (jal.getAlignmentAnnotation() != null)
 474       {
 475         jalview.datamodel.AlignmentAnnotation[] aa = jal
 476                 .getAlignmentAnnotation();
 477         java.util.HashMap AlSeqMaps = new HashMap(); // stores int maps from
 478         // alignment columns to
 479         // sequence positions.
 480         for (int i = 0; i < aa.length; i++)
 481         {
 482           if (aa[i] == null || isJalviewOnly(aa[i]))
 483           {
 484             continue;
 485           }
 486           if (aa[i].sequenceRef != null)
 487           {
 488             // Deal with sequence associated annotation
 489             Vobject sref = getjv2vObj(aa[i].sequenceRef);
 490             if (sref instanceof uk.ac.vamsas.objects.core.AlignmentSequence)
 491             {
 492               saveAlignmentSequenceAnnotation(AlSeqMaps,
 493                       (AlignmentSequence) sref, aa[i]);
 494             }
 495             else
 496             {
 497               // first find the alignment sequence to associate this with.
 498               SequenceI jvalsq = null;
 499               Enumeration jval = av.getAlignment().getSequences()
 500                       .elements();
 501               while (jval.hasMoreElements())
 502               {
 503                 jvalsq = (SequenceI) jval.nextElement();
 504                 // saveDatasetSequenceAnnotation(AlSeqMaps,(uk.ac.vamsas.objects.core.Sequence)
 505                 // sref, aa[i]);
 506                 if (jvalsq.getDatasetSequence() == aa[i].sequenceRef)
 507                 {
 508                   Vobject alsref = getjv2vObj(jvalsq);
 509                   saveAlignmentSequenceAnnotation(AlSeqMaps,
 510                           (AlignmentSequence) alsref, aa[i]);
 511                   break;
 512                 }
 513                 ;
 514               }
 515             }
 516           }
 517           else
 518           {
 519             // add Alignment Annotation
 520             uk.ac.vamsas.objects.core.AlignmentAnnotation an = (uk.ac.vamsas.objects.core.AlignmentAnnotation) getjv2vObj(aa[i]);
 521             if (an == null)
 522             {
 523               an = new uk.ac.vamsas.objects.core.AlignmentAnnotation();
 524               an.setType(JALVIEW_ANNOTATION_ROW);
 525               an.setDescription(aa[i].description);
 526               alignment.addAlignmentAnnotation(an);
 527               Seg vSeg = new Seg(); // TODO: refactor to have a default
 528                                     // rangeAnnotationType initer/updater that
 529                                     // takes a set of int ranges.
 530               vSeg.setStart(1);
 531               vSeg.setInclusive(true);
 532               vSeg.setEnd(jal.getWidth());
 533               an.addSeg(vSeg);
 534               if (aa[i].graph > 0)
 535               {
 536                 an.setGraph(true); // aa[i].graph);
 537               }
 538               an.setLabel(aa[i].label);
 539               an.setProvenance(dummyProvenance());
 540               if (aa[i].graph != AlignmentAnnotation.NO_GRAPH)
 541               {
 542                 an.setGroup(Integer.toString(aa[i].graphGroup)); // // JBPNote
 543                                                                   // -
 544                 // originally we
 545                 // were going to
 546                 // store
 547                 // graphGroup in
 548                 // the Jalview
 549                 // specific
 550                 // bits.
 551                 an.setGraph(true);
 552               }
 553               else
 554               {
 555                 an.setGraph(false);
 556               }
 557               AnnotationElement ae;
 558
 559               for (int a = 0; a < aa[i].annotations.length; a++)
 560               {
 561                 if ((aa[i] == null) || (aa[i].annotations[a] == null))
 562                 {
 563                   continue;
 564                 }
 565
 566                 ae = new AnnotationElement();
 567                 ae.setDescription(aa[i].annotations[a].description);
 568                 ae.addGlyph(new Glyph());
 569                 ae.getGlyph(0).setContent(
 570                         aa[i].annotations[a].displayCharacter); // assume
 571                 // jax-b
 572                 // takes
 573                 // care
 574                 // of
 575                 // utf8
 576                 // translation
 577                 ae.addValue(aa[i].annotations[a].value);
 578                 ae.setPosition(a + 1);
 579                 if (aa[i].annotations[a].secondaryStructure != ' ')
 580                 {
 581                   Glyph ss = new Glyph();
 582                   ss
 583                           .setDict(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
 584                   ss
 585                           .setContent(String
 586                                   .valueOf(aa[i].annotations[a].secondaryStructure));
 587                   ae.addGlyph(ss);
 588                 }
 589                 an.addAnnotationElement(ae);
 590               }
 591               if (aa[i].editable)
 592               {
 593                 // an.addProperty(newProperty("jalview:editable", null,
 594                 // "true"));
 595                 // an.setModifiable(""); // TODO: This is not the way the
 596                 // modifiable flag is supposed to be used.
 597               }
 598               setAnnotationType(an, aa[i]);
 599
 600               if (aa[i].graph != jalview.datamodel.AlignmentAnnotation.NO_GRAPH)
 601               {
 602                 an.setGraph(true);
 603                 an.setGroup(Integer.toString(aa[i].graphGroup));
 604                 if (aa[i].threshold!=null && aa[i].threshold.displayed)
 605                   an.addProperty(newProperty(THRESHOLD, "float", ""+aa[i].threshold.value));
 606                   if (aa[i].threshold.label!=null)
 607                     an.addProperty(newProperty(THRESHOLD+"Name", "string", ""+aa[i].threshold.label));
 608                 }
 609
 610               }
 611
 612             else
 613             {
 614               if (an.getModifiable() == null) // TODO: USE VAMSAS LIBRARY OBJECT
 615                                               // LOCK METHODS)
 616               {
 617                 // verify annotation - update (perhaps)
 618                 Cache.log
 619                         .info("update alignment sequence annotation. not yet implemented.");
 620               }
 621               else
 622               {
 623                 // verify annotation - update (perhaps)
 624                 Cache.log
 625                         .info("updated alignment sequence annotation added.");
 626               }
 627             }
 628           }
 629         }
 630       }
 631       // /////////////////////////////////////////////////////
 632
 633       // //////////////////////////////////////////////
 634       // /SAVE THE TREES
 635       // /////////////////////////////////
 636       // FIND ANY ASSOCIATED TREES
 637       if (Desktop.desktop != null)
 638       {
 639         javax.swing.JInternalFrame[] frames = Desktop.instance
 640                 .getAllFrames();
 641
 642         for (int t = 0; t < frames.length; t++)
 643         {
 644           if (frames[t] instanceof TreePanel)
 645           {
 646             TreePanel tp = (TreePanel) frames[t];
 647
 648             if (tp.getAlignment() == jal)
 649             {
 650               DatastoreItem vtree = new jalview.io.vamsas.Tree(this, tp,
 651                       jal, alignment);
 652             }
 653           }
 654         }
 655       }
 656       // Store Jalview specific stuff in the Jalview appData
 657       // not implemented in the SimpleDoc interface.
 658     }
 659
 660     catch (Exception ex)
 661     {
 662       ex.printStackTrace();
 663     }
 664
 665   }
 666   /**
 667    *  sync a jalview alignment seuqence into a vamsas alignment
 668    *  assumes all lock transformation/bindings have been sorted out before hand.
 669    *  creates/syncs the vamsas alignment sequence for jvalsq and adds it to the alignment if necessary.
 670    */
 671   private boolean syncToAlignmentSequence(SequenceI jvalsq,
 672           Alignment alignment)
 673   {
 674     boolean modal = false;
 675     // todo: islocked method here
 676     boolean up2doc=false;
 677     AlignmentSequence alseq = (AlignmentSequence) getjv2vObj(jvalsq);
 678     if (alseq==null)
 679     {
 680       alseq = new AlignmentSequence();
 681       up2doc = true;
 682     }
 683     // boolean locked = (alignment.getModifiable()==null || alignment.getModifiable().length()>0);
 684     // TODO: VAMSAS: translate lowercase symbols to annotation ?
 685     if (up2doc || !alseq.getSequence().equals(jvalsq.getSequenceAsString()))
 686     {
 687       alseq.setSequence(jvalsq.getSequenceAsString());
 688       alseq.setStart(jvalsq.getStart());
 689       alseq.setEnd(jvalsq.getEnd());
 690       modal = true;
 691     }
 692     if (up2doc || !alseq.getName().equals(jvalsq.getName()))
 693     {
 694       modal = true;
 695       alseq.setName(jvalsq.getName());
 696     }
 697     if (jvalsq.getDescription()!=null && (alseq.getDescription()==null || !jvalsq.getDescription().equals(alseq.getDescription())))
 698     {
 699       modal = true;
 700       alseq.setDescription(jvalsq.getDescription());
 701     }
 702     if (getjv2vObj(jvalsq.getDatasetSequence()) == null)
 703     {
 704       Cache.log
 705       .warn("Serious Implementation error - Unbound dataset sequence in alignment: "
 706               + jvalsq.getDatasetSequence());
 707     }
 708     alseq.setRefid(getjv2vObj(jvalsq
 709             .getDatasetSequence()));
 710     if (up2doc)
 711     {
 712
 713       alignment.addAlignmentSequence(alseq);
 714       bindjvvobj(jvalsq, alseq);
 715     }
 716     return up2doc || modal;
 717   }
 718   /**
 719    *  locally sync a jalview alignment seuqence from a vamsas alignment
 720    *  assumes all lock transformation/bindings have been sorted out before hand.
 721    *  creates/syncs the jvalsq from the alignment sequence
 722    */
 723   private boolean syncFromAlignmentSequence(AlignmentSequence valseq, char valGapchar, char gapChar, Vector dsseqs)
 724
 725   {
 726     boolean modal = false;
 727     // todo: islocked method here
 728     boolean upFromdoc=false;
 729     jalview.datamodel.SequenceI alseq = (SequenceI) getvObj2jv(valseq);
 730     if (alseq==null)
 731     {
 732       upFromdoc = true;
 733     }
 734     if (alseq != null)
 735     {
 736
 737       // boolean locked = (alignment.getModifiable()==null || alignment.getModifiable().length()>0);
 738       // TODO: VAMSAS: translate lowercase symbols to annotation ?
 739       if (upFromdoc || !valseq.getSequence().equals(alseq.getSequenceAsString()))
 740       {
 741         // this might go *horribly* wrong
 742         alseq.setSequence(new String(valseq.getSequence()).replace(
 743                 valGapchar, gapChar));
 744         alseq.setStart((int) valseq.getStart());
 745         alseq.setEnd((int) valseq.getEnd());
 746         modal = true;
 747       }
 748       if (!valseq.getName().equals(alseq.getName()))
 749       {
 750         modal = true;
 751         alseq.setName(valseq.getName());
 752       }
 753       if (alseq.getDescription()==null
 754               || (valseq.getDescription()==null
 755                       || alseq.getDescription().equals(valseq.getDescription())))
 756       {
 757         alseq.setDescription(valseq.getDescription());
 758         modal = true;
 759       }
 760       if (modal && Cache.log.isDebugEnabled())
 761       {
 762         Cache.log.debug("Updating apparently edited sequence "
 763                 + alseq.getName());
 764       }
 765     }
 766     else
 767     {
 768       alseq = new jalview.datamodel.Sequence(valseq.getName(),
 769               valseq.getSequence().replace(valGapchar, gapChar),
 770               (int) valseq.getStart(), (int) valseq.getEnd());
 771
 772       Vobject datsetseq = (Vobject) valseq.getRefid();
 773       if (datsetseq != null)
 774       {
 775         alseq
 776                 .setDatasetSequence((SequenceI) getvObj2jv(datsetseq)); // exceptions
 777                                                                         // if
 778                                                                         // AlignemntSequence
 779                                                                         // reference
 780                                                                         // isn't
 781                                                                         // a
 782                                                                         // simple
 783                                                                         // SequenceI
 784       }
 785       else
 786       {
 787         Cache.log
 788                 .error("Invalid dataset sequence id (null) for alignment sequence "
 789                         + valseq.getVorbaId());
 790       }
 791       bindjvvobj(alseq, valseq);
 792       alseq.setVamsasId(valseq.getVorbaId().getId());
 793       dsseqs.add(alseq);
 794     }
 795     Vobject datsetseq = (Vobject) valseq.getRefid();
 796     if (datsetseq != null)
 797     {
 798       if (datsetseq != alseq.getDatasetSequence())
 799       {
 800         modal = true;
 801       }
 802       alseq
 803               .setDatasetSequence((SequenceI) getvObj2jv(datsetseq)); // exceptions
 804     }
 805     return upFromdoc || modal;
 806   }
 807
 808   private void initRangeAnnotationType(RangeAnnotation an,
 809           AlignmentAnnotation alan, int[] gapMap)
 810   {
 811     Seg vSeg = new Seg();
 812     vSeg.setStart(1);
 813     vSeg.setInclusive(true);
 814     vSeg.setEnd(gapMap.length);
 815     an.addSeg(vSeg);
 816
 817     // LATER: much of this is verbatim from the alignmentAnnotation
 818     // method below. suggests refactoring to make rangeAnnotation the
 819     // base class
 820     an.setDescription(alan.description);
 821     an.setLabel(alan.label);
 822     an.setGroup(Integer.toString(alan.graphGroup));
 823     // // JBPNote -
 824     // originally we
 825     // were going to
 826     // store
 827     // graphGroup in
 828     // the Jalview
 829     // specific
 830     // bits.
 831     AnnotationElement ae;
 832     for (int a = 0; a < alan.annotations.length; a++)
 833     {
 834       if (alan.annotations[a] == null)
 835       {
 836         continue;
 837       }
 838
 839       ae = new AnnotationElement();
 840       ae.setDescription(alan.annotations[a].description);
 841       ae.addGlyph(new Glyph());
 842       ae.getGlyph(0).setContent(alan.annotations[a].displayCharacter); // assume
 843       // jax-b
 844       // takes
 845       // care
 846       // of
 847       // utf8
 848       // translation
 849       if (alan.graph != jalview.datamodel.AlignmentAnnotation.NO_GRAPH)
 850       {
 851         ae.addValue(alan.annotations[a].value);
 852       }
 853       ae.setPosition(gapMap[a] + 1); // position w.r.t. AlignmentSequence
 854       // symbols
 855       if (alan.annotations[a].secondaryStructure != ' ')
 856       {
 857         // we only write an annotation where it really exists.
 858         Glyph ss = new Glyph();
 859         ss
 860                 .setDict(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
 861         ss.setContent(String
 862                 .valueOf(alan.annotations[a].secondaryStructure));
 863         ae.addGlyph(ss);
 864       }
 865       an.addAnnotationElement(ae);
 866     }
 867
 868   }
 869
 870   private void saveDatasetSequenceAnnotation(HashMap AlSeqMaps,
 871           uk.ac.vamsas.objects.core.Sequence sref, AlignmentAnnotation alan)
 872   {
 873     // {
 874     // uk.ac.vamsas.
 875     // objects.core.AlignmentSequence alsref = (uk.ac.vamsas.
 876     // objects.core.AlignmentSequence) sref;
 877     uk.ac.vamsas.objects.core.DataSetAnnotations an = (uk.ac.vamsas.objects.core.DataSetAnnotations) getjv2vObj(alan);
 878     int[] gapMap = getGapMap(AlSeqMaps, alan);
 879     if (an == null)
 880     {
 881       an = new uk.ac.vamsas.objects.core.DataSetAnnotations();
 882       initRangeAnnotationType(an, alan, gapMap);
 883
 884       an.setProvenance(dummyProvenance()); // get provenance as user
 885       // created, or jnet, or
 886       // something else.
 887       setAnnotationType(an, alan);
 888       an.setGroup(Integer.toString(alan.graphGroup)); // // JBPNote -
 889       // originally we
 890       // were going to
 891       // store
 892       // graphGroup in
 893       // the Jalview
 894       // specific
 895       // bits.
 896       if (alan.getThreshold()!=null && alan.getThreshold().displayed)
 897       {
 898         an.addProperty(newProperty(THRESHOLD, "float", ""+alan.getThreshold().value));
 899         if (alan.getThreshold().label!=null)
 900           an.addProperty(newProperty(THRESHOLD+"Name", "string", ""+alan.getThreshold().label));
 901       }
 902       ((DataSet) sref.getV_parent()).addDataSetAnnotations(an);
 903       bindjvvobj(alan, an);
 904     }
 905     else
 906     {
 907       // update reference sequence Annotation
 908       if (an.getModifiable() == null) // TODO: USE VAMSAS LIBRARY OBJECT LOCK
 909                                       // METHODS)
 910       {
 911         // verify existing alignment sequence annotation is up to date
 912         System.out.println("update dataset sequence annotation.");
 913       }
 914       else
 915       {
 916         // verify existing alignment sequence annotation is up to date
 917         System.out
 918                 .println("make new alignment dataset sequence annotation if modification has happened.");
 919       }
 920     }
 921
 922   }
 923
 924   private int[] getGapMap(HashMap AlSeqMaps, AlignmentAnnotation alan)
 925   {
 926     int[] gapMap;
 927     if (AlSeqMaps.containsKey(alan.sequenceRef))
 928     {
 929       gapMap = (int[]) AlSeqMaps.get(alan.sequenceRef);
 930     }
 931     else
 932     {
 933       gapMap = new int[alan.sequenceRef.getLength()];
 934       // map from alignment position to sequence position.
 935       int[] sgapMap = alan.sequenceRef.gapMap();
 936       for (int a = 0; a < sgapMap.length; a++)
 937       {
 938         gapMap[sgapMap[a]] = a;
 939       }
 940     }
 941     return gapMap;
 942   }
 943
 944   private void saveAlignmentSequenceAnnotation(HashMap AlSeqMaps,
 945           AlignmentSequence alsref, AlignmentAnnotation alan)
 946   {
 947     // {
 948     // uk.ac.vamsas.
 949     // objects.core.AlignmentSequence alsref = (uk.ac.vamsas.
 950     // objects.core.AlignmentSequence) sref;
 951     uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation an = (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) getjv2vObj(alan);
 952     int[] gapMap = getGapMap(AlSeqMaps, alan);
 953     if (an == null)
 954     {
 955       an = new uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation();
 956       initRangeAnnotationType(an, alan, gapMap);
 957       /**
 958        * I mean here that we don't actually have a semantic 'type' for the
 959        * annotation (this might be - score, intrinsic property, measurement,
 960        * something extracted from another program, etc)
 961        */
 962       an.setType(JALVIEW_ANNOTATION_ROW); // TODO: better fix
 963                                                           // this rough guess ;)
 964       alsref.addAlignmentSequenceAnnotation(an);
 965       bindjvvobj(alan, an);
 966       // These properties are directly supported by the
 967       // AlignmentSequenceAnnotation type.
 968       setAnnotationType(an, alan);
 969       an.setProvenance(dummyProvenance()); // get provenance as user
 970       // created, or jnet, or
 971       // something else.
 972     }
 973     else
 974     {
 975       // update reference sequence Annotation
 976       if (an.getModifiable() == null) // TODO: USE VAMSAS LIBRARY OBJECT LOCK
 977                                       // METHODS)
 978       {
 979         // verify existing alignment sequence annotation is up to date
 980         System.out.println("update alignment sequence annotation.");
 981       }
 982       else
 983       {
 984         // verify existing alignment sequence annotation is up to date
 985         System.out
 986                 .println("make new alignment sequence annotation if modification has happened.");
 987       }
 988     }
 989   }
 990
 991   /**
 992    * set vamsas annotation object type from jalview annotation
 993    * @param an
 994    * @param alan
 995    */
 996   private void setAnnotationType(RangeAnnotation an, AlignmentAnnotation alan)
 997   {
 998     if (an instanceof AlignmentSequenceAnnotation)
 999     {
1000       if (alan.graph != AlignmentAnnotation.NO_GRAPH)
1001       {
1002         ((AlignmentSequenceAnnotation)an).setGraph(true);
1003       } else
1004       {
1005       ((AlignmentSequenceAnnotation)an).setGraph(false);
1006       }
1007     }
1008     if (an instanceof uk.ac.vamsas.objects.core.AlignmentAnnotation)
1009     {
1010       if (alan.graph != AlignmentAnnotation.NO_GRAPH)
1011       {
1012         ((uk.ac.vamsas.objects.core.AlignmentAnnotation)an).setGraph(true);
1013       } else
1014       {
1015       ((uk.ac.vamsas.objects.core.AlignmentAnnotation)an).setGraph(false);
1016       }
1017     }
1018     switch (alan.graph)
1019     {
1020       case AlignmentAnnotation.BAR_GRAPH:
1021         an.addProperty(newProperty(DISCRETE_ANNOTATION, "boolean","true"));
1022         break;
1023       case AlignmentAnnotation.LINE_GRAPH:
1024         an.addProperty(newProperty(CONTINUOUS_ANNOTATION, "boolean","true"));
1025         break;
1026         default:
1027           // don't add any kind of discrete or continous property info.
1028     }
1029   }
1030
1031   private Property newProperty(String name, String type, String content)
1032   {
1033     Property vProperty = new Property();
1034     vProperty.setName(name);
1035     if (type != null)
1036     {
1037       vProperty.setType(type);
1038     }
1039     else
1040     {
1041       vProperty.setType("String");
1042     }
1043     vProperty.setContent(content);
1044     return vProperty;
1045   }
1046
1047   /**
1048    * correctly create a RangeAnnotation from a jalview sequence feature
1049    *
1050    * @param dsa
1051    *          (typically DataSetAnnotations or AlignmentSequenceAnnotation)
1052    * @param feature
1053    *          (the feature to be mapped from)
1054    * @return
1055    */
1056   private RangeAnnotation getDSAnnotationFromJalview(RangeAnnotation dsa,
1057           SequenceFeature feature)
1058   {
1059     dsa.setType(feature.getType());
1060     Seg vSeg = new Seg();
1061     vSeg.setStart(feature.getBegin());
1062     vSeg.setEnd(feature.getEnd());
1063     vSeg.setInclusive(true);
1064     dsa.addSeg(vSeg);
1065     dsa.setDescription(feature.getDescription());
1066     dsa.setStatus(feature.getStatus());
1067     if (feature.links != null && feature.links.size() > 0)
1068     {
1069       for (int i = 0, iSize = feature.links.size(); i < iSize; i++)
1070       {
1071         String link = (String) feature.links.elementAt(i);
1072         int sep = link.indexOf('|');
1073         if (sep > -1)
1074         {
1075           Link vLink = new Link();
1076           if (sep > 0)
1077           {
1078             vLink.setContent(link.substring(0, sep - 1));
1079           }
1080           else
1081           {
1082             vLink.setContent("");
1083           }
1084           vLink.setHref(link.substring(sep + 1)); // TODO: validate href.
1085           dsa.addLink(vLink);
1086         }
1087       }
1088     }
1089     dsa.setGroup(feature.getFeatureGroup());
1090     return dsa;
1091   }
1092
1093   /**
1094    * get start<end range of segment, adjusting for inclusivity flag and
1095    * polarity.
1096    *
1097    * @param visSeg
1098    * @param ensureDirection
1099    *          when true - always ensure start is less than end.
1100    * @return int[] { start, end, direction} where direction==1 for range running
1101    *         from end to start.
1102    */
1103   private int[] getSegRange(Seg visSeg, boolean ensureDirection)
1104   {
1105     boolean incl = visSeg.getInclusive();
1106     // adjust for inclusive flag.
1107     int pol = (visSeg.getStart() <= visSeg.getEnd()) ? 1 : -1; // polarity of
1108     // region.
1109     int start = visSeg.getStart() + (incl ? 0 : pol);
1110     int end = visSeg.getEnd() + (incl ? 0 : -pol);
1111     if (ensureDirection && pol == -1)
1112     {
1113       // jalview doesn't deal with inverted ranges, yet.
1114       int t = end;
1115       end = start;
1116       start = t;
1117     }
1118     return new int[]
1119     { start, end, pol < 0 ? 1 : 0 };
1120   }
1121
1122   /**
1123    *
1124    * @param annotation
1125    * @return true if annotation is not to be stored in document
1126    */
1127   private boolean isJalviewOnly(AlignmentAnnotation annotation)
1128   {
1129     return annotation.label.equals("Quality")
1130             || annotation.label.equals("Conservation")
1131             || annotation.label.equals("Consensus");
1132   }
1133
1134   /**
1135    * This will return the first AlignFrame viewing AlignViewport av. It will
1136    * break if there are more than one AlignFrames viewing a particular av. This
1137    * also shouldn't be in the io package.
1138    *
1139    * @param av
1140    * @return alignFrame for av
1141    */
1142   public AlignFrame getAlignFrameFor(AlignViewport av)
1143   {
1144     if (Desktop.desktop != null)
1145     {
1146       javax.swing.JInternalFrame[] frames = Desktop.instance.getAllFrames();
1147
1148       for (int t = 0; t < frames.length; t++)
1149       {
1150         if (frames[t] instanceof AlignFrame)
1151         {
1152           if (((AlignFrame) frames[t]).getViewport() == av)
1153           {
1154             return (AlignFrame) frames[t];
1155           }
1156         }
1157       }
1158     }
1159     return null;
1160   }
1161
1162   public void updateToJalview()
1163   {
1164     VAMSAS _roots[] = cdoc.getVamsasRoots();
1165
1166     for (int _root = 0; _root < _roots.length; _root++)
1167     {
1168       VAMSAS root = _roots[_root];
1169       boolean newds = false;
1170       for (int _ds = 0, _nds = root.getDataSetCount(); _ds < _nds; _ds++)
1171       {
1172         // ///////////////////////////////////
1173         // ///LOAD DATASET
1174         DataSet dataset = root.getDataSet(_ds);
1175         int i, iSize = dataset.getSequenceCount();
1176         Vector dsseqs;
1177         jalview.datamodel.Alignment jdataset = (jalview.datamodel.Alignment) getvObj2jv(dataset);
1178         int jremain = 0;
1179         if (jdataset == null)
1180         {
1181           Cache.log.debug("Initialising new jalview dataset fields");
1182           newds = true;
1183           dsseqs = new Vector();
1184         }
1185         else
1186         {
1187           Cache.log.debug("Update jalview dataset from vamsas.");
1188           jremain = jdataset.getHeight();
1189           dsseqs = jdataset.getSequences();
1190         }
1191
1192         // TODO: test sequence merging - we preserve existing non vamsas
1193         // sequences but add in any new vamsas ones, and don't yet update any
1194         // sequence attributes
1195         for (i = 0; i < iSize; i++)
1196         {
1197           Sequence vdseq = dataset.getSequence(i);
1198           jalview.datamodel.SequenceI dsseq = (SequenceI) getvObj2jv(vdseq);
1199           if (dsseq != null)
1200           {
1201             if (!dsseq.getSequenceAsString().equals(vdseq.getSequence()))
1202             {
1203               throw new Error(
1204                       "Broken! - mismatch of dataset sequence: and jalview internal dataset sequence.");
1205             }
1206             jremain--;
1207           }
1208           else
1209           {
1210             dsseq = new jalview.datamodel.Sequence(dataset.getSequence(i)
1211                     .getName(), dataset.getSequence(i).getSequence(),
1212                     (int) dataset.getSequence(i).getStart(), (int) dataset
1213                             .getSequence(i).getEnd());
1214             dsseq.setDescription(dataset.getSequence(i).getDescription());
1215             bindjvvobj(dsseq, dataset.getSequence(i));
1216             dsseq.setVamsasId(dataset.getSequence(i).getVorbaId().getId());
1217             dsseqs.add(dsseq);
1218           }
1219           if (vdseq.getDbRefCount() > 0)
1220           {
1221             DbRef[] dbref = vdseq.getDbRef();
1222             for (int db = 0; db < dbref.length; db++)
1223             {
1224               new jalview.io.vamsas.Dbref(this, dbref[db], vdseq, dsseq);
1225
1226             }
1227           }
1228         }
1229
1230         if (newds)
1231         {
1232           SequenceI[] seqs = new SequenceI[dsseqs.size()];
1233           for (i = 0, iSize = dsseqs.size(); i < iSize; i++)
1234           {
1235             seqs[i] = (SequenceI) dsseqs.elementAt(i);
1236             dsseqs.setElementAt(null, i);
1237           }
1238           jdataset = new jalview.datamodel.Alignment(seqs);
1239           Cache.log.debug("New vamsas dataset imported into jalview.");
1240           bindjvvobj(jdataset, dataset);
1241         }
1242         // ////////
1243         // add any new dataset sequence feature annotations
1244         if (dataset.getDataSetAnnotations() != null)
1245         {
1246           for (int dsa = 0; dsa < dataset.getDataSetAnnotationsCount(); dsa++)
1247           {
1248             DataSetAnnotations dseta = dataset.getDataSetAnnotations(dsa);
1249             // TODO: deal with group annotation on datset sequences.
1250             if (dseta.getSeqRefCount() == 1)
1251             {
1252               SequenceI dsSeq = (SequenceI) getvObj2jv((Vobject) dseta
1253                       .getSeqRef(0)); // TODO: deal with group dataset
1254                                       // annotations
1255               if (dsSeq == null)
1256               {
1257                 jalview.bin.Cache.log
1258                         .warn("Couldn't resolve jalview sequenceI for dataset object reference "
1259                                 + ((Vobject) dataset.getDataSetAnnotations(
1260                                         dsa).getSeqRef(0)).getVorbaId()
1261                                         .getId());
1262               }
1263               else
1264               {
1265                 if (dseta.getAnnotationElementCount() == 0)
1266                 {
1267                   jalview.datamodel.SequenceFeature sf = (jalview.datamodel.SequenceFeature) getvObj2jv(dseta);
1268                   if (sf == null)
1269                   {
1270                     dsSeq
1271                             .addSequenceFeature(sf = getJalviewSeqFeature(dseta));
1272                     bindjvvobj(sf, dseta);
1273                   }
1274                 }
1275                 else
1276                 {
1277                   // TODO: deal with alignmentAnnotation style annotation
1278                   // appearing on dataset sequences.
1279                   // JBPNote: we could just add them to all alignments but
1280                   // that may complicate cross references in the jalview
1281                   // datamodel
1282                   Cache.log
1283                           .warn("Ignoring dataset annotation with annotationElements. Not yet supported in jalview.");
1284                 }
1285               }
1286             }
1287           }
1288         }
1289         if (dataset.getAlignmentCount() > 0)
1290         {
1291           // LOAD ALIGNMENTS from DATASET
1292
1293           for (int al = 0, nal = dataset.getAlignmentCount(); al < nal; al++)
1294           {
1295             uk.ac.vamsas.objects.core.Alignment alignment = dataset
1296                     .getAlignment(al);
1297             AlignViewport av=findViewport(alignment);
1298
1299             jalview.datamodel.AlignmentI jal = null;
1300             if (av != null)
1301             {
1302               jal = av.getAlignment();
1303             }
1304             iSize = alignment.getAlignmentSequenceCount();
1305             boolean newal = (jal == null) ? true : false;
1306             boolean refreshal = false;
1307             Vector newasAnnots = new Vector();
1308             char gapChar = ' '; // default for new alignments read in from the
1309                                 // document
1310             if (jal != null)
1311             {
1312               dsseqs = jal.getSequences(); // for merge/update
1313               gapChar = jal.getGapCharacter();
1314             }
1315             else
1316             {
1317               dsseqs = new Vector();
1318             }
1319             char valGapchar = alignment.getGapChar().charAt(0);
1320             for (i = 0; i < iSize; i++)
1321             {
1322               AlignmentSequence valseq = alignment.getAlignmentSequence(i);
1323               jalview.datamodel.Sequence alseq = (jalview.datamodel.Sequence) getvObj2jv(valseq);
1324               if (syncFromAlignmentSequence(valseq, valGapchar, gapChar, dsseqs) && alseq!=null)
1325               {
1326
1327                 // updated to sequence from the document
1328                 jremain--;
1329                 refreshal = true;
1330               }
1331               if (valseq.getAlignmentSequenceAnnotationCount() > 0)
1332               {
1333                 AlignmentSequenceAnnotation[] vasannot = valseq
1334                         .getAlignmentSequenceAnnotation();
1335                 for (int a = 0; a < vasannot.length; a++)
1336                 {
1337                   jalview.datamodel.AlignmentAnnotation asa = (jalview.datamodel.AlignmentAnnotation) getvObj2jv(vasannot[a]); // TODO:
1338                                                                                                                                 // 1:many
1339                                                                                                                                 // jalview
1340                                                                                                                                 // alignment
1341                                                                                                                                 // sequence
1342                                                                                                                                 // annotations
1343                   if (asa == null)
1344                   {
1345                     int se[] = getBounds(vasannot[a]);
1346                     asa = getjAlignmentAnnotation(jal, vasannot[a]);
1347                     asa.setSequenceRef(alseq);
1348                     asa.createSequenceMapping(alseq, se[0], false); // TODO:
1349                                                                     // verify
1350                                                                     // that
1351                                                                     // positions
1352                                                                     // in
1353                                                                     // alseqAnnotation
1354                                                                     // correspond
1355                                                                     // to
1356                                                                     // ungapped
1357                                                                     // residue
1358                                                                     // positions.
1359                     alseq.addAlignmentAnnotation(asa);
1360                     bindjvvobj(asa, vasannot[a]);
1361                     newasAnnots.add(asa);
1362                   }
1363                   else
1364                   {
1365                     // update existing annotation - can do this in place
1366                     if (vasannot[a].getModifiable() == null) // TODO: USE
1367                                                               // VAMSAS LIBRARY
1368                                                               // OBJECT LOCK
1369                                                               // METHODS)
1370                     {
1371                       Cache.log
1372                               .info("UNIMPLEMENTED: not recovering user modifiable sequence alignment annotation");
1373                       // TODO: should at least replace with new one - otherwise
1374                       // things will break
1375                       // basically do this:
1376                       // int se[] = getBounds(vasannot[a]);
1377                       // asa.update(getjAlignmentAnnotation(jal, vasannot[a]));
1378                       // // update from another annotation object in place.
1379                       // asa.createSequenceMapping(alseq, se[0], false);
1380
1381                     }
1382                   }
1383                 }
1384               }
1385             }
1386             if (jal == null)
1387             {
1388               SequenceI[] seqs = new SequenceI[dsseqs.size()];
1389               for (i = 0, iSize = dsseqs.size(); i < iSize; i++)
1390               {
1391                 seqs[i] = (SequenceI) dsseqs.elementAt(i);
1392                 dsseqs.setElementAt(null, i);
1393               }
1394               jal = new jalview.datamodel.Alignment(seqs);
1395               Cache.log.debug("New vamsas alignment imported into jalview "
1396                       + alignment.getVorbaId().getId());
1397               jal.setDataset(jdataset);
1398             }
1399             if (newasAnnots != null && newasAnnots.size() > 0)
1400             {
1401               // Add the new sequence annotations in to the alignment.
1402               for (int an = 0, anSize = newasAnnots.size(); an < anSize; an++)
1403               {
1404                 jal.addAnnotation((AlignmentAnnotation) newasAnnots
1405                         .elementAt(an));
1406                 // TODO: check if anything has to be done - like calling
1407                 // adjustForAlignment or something.
1408                 newasAnnots.setElementAt(null, an);
1409               }
1410               newasAnnots = null;
1411             }
1412             // //////////////////////////////////////////
1413             // //LOAD ANNOTATIONS FOR THE ALIGNMENT
1414             // ////////////////////////////////////
1415             if (alignment.getAlignmentAnnotationCount() > 0)
1416             {
1417               uk.ac.vamsas.objects.core.AlignmentAnnotation[] an = alignment
1418                       .getAlignmentAnnotation();
1419
1420               for (int j = 0; j < an.length; j++)
1421               {
1422                 jalview.datamodel.AlignmentAnnotation jan = (jalview.datamodel.AlignmentAnnotation) getvObj2jv(an[j]);
1423                 if (jan != null)
1424                 {
1425                   // update or stay the same.
1426                   // TODO: should at least replace with a new one - otherwise
1427                   // things will break
1428                   // basically do this:
1429                   // jan.update(getjAlignmentAnnotation(jal, an[a])); // update
1430                   // from another annotation object in place.
1431
1432                   Cache.log
1433                           .debug("update from vamsas alignment annotation to existing jalview alignment annotation.");
1434                   if (an[j].getModifiable() == null) // TODO: USE VAMSAS
1435                                                       // LIBRARY OBJECT LOCK
1436                                                       // METHODS)
1437                   {
1438                     // TODO: user defined annotation is totally mutable... - so
1439                     // load it up or throw away if locally edited.
1440                     Cache.log
1441                             .info("NOT IMPLEMENTED - Recovering user-modifiable annotation - yet...");
1442                   }
1443                   // TODO: compare annotation element rows
1444                   // TODO: compare props.
1445                 }
1446                 else
1447                 {
1448                   jan = getjAlignmentAnnotation(jal, an[j]);
1449                   jal.addAnnotation(jan);
1450                   bindjvvobj(jan, an[j]);
1451                 }
1452               }
1453             }
1454             AlignFrame alignFrame;
1455             if (av == null)
1456             {
1457               Cache.log.debug("New alignframe for alignment "
1458                       + alignment.getVorbaId());
1459               // ///////////////////////////////
1460               // construct alignment view
1461               alignFrame = new AlignFrame(jal, AlignFrame.DEFAULT_WIDTH,
1462                       AlignFrame.DEFAULT_HEIGHT);
1463               av = alignFrame.getViewport();
1464               String title = alignment.getProvenance().getEntry(
1465                       alignment.getProvenance().getEntryCount() - 1)
1466                       .getAction();
1467               if (alignment.getPropertyCount() > 0)
1468               {
1469                 for (int p = 0, pe = alignment.getPropertyCount(); p < pe; p++)
1470                 {
1471                   if (alignment.getProperty(p).getName().equals(
1472                           "title"))
1473                   {
1474                     title = alignment.getProperty(p).getContent();
1475                   }
1476                 }
1477               }
1478               // TODO: automatically create meaningful title for a vamsas
1479               // alignment using its provenance.
1480               if (Cache.log.isDebugEnabled())
1481               {
1482                 title = title + "("
1483                  + alignment.getVorbaId() + ")";
1484
1485               }
1486               jalview.gui.Desktop.addInternalFrame(alignFrame, title
1487                       ,
1488                       AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
1489               bindjvvobj(av.getSequenceSetId(), alignment);
1490             }
1491             else
1492             {
1493               // find the alignFrame for jal.
1494               // TODO: fix this so we retrieve the alignFrame handing av
1495               // *directly*
1496               alignFrame = getAlignFrameFor(av);
1497               if (refreshal)
1498               {
1499                 av.alignmentChanged(alignFrame.alignPanel);
1500               }
1501             }
1502             // LOAD TREES
1503             // /////////////////////////////////////
1504             if (alignment.getTreeCount() > 0)
1505             {
1506
1507               for (int t = 0; t < alignment.getTreeCount(); t++)
1508               {
1509                 jalview.io.vamsas.Tree vstree = new jalview.io.vamsas.Tree(
1510                         this, alignFrame, alignment.getTree(t));
1511                 TreePanel tp = null;
1512                 if (vstree.isValidTree())
1513                 {
1514                   tp = alignFrame
1515                         .ShowNewickTree(vstree.getNewickTree(), vstree
1516                                 .getTitle(), vstree.getInputData(), 600,
1517                                 500, t * 20 + 50, t * 20 + 50);
1518
1519                 }
1520                 if (tp!=null)
1521                 {
1522                   bindjvvobj(tp, alignment.getTree(t));
1523                   try
1524                   {
1525                     vstree.UpdateSequenceTreeMap(tp);
1526                   } catch (RuntimeException e)
1527                   {
1528                     Cache.log.warn("update of labels failed.",e);
1529                   }
1530                 }
1531                 else
1532                 {
1533                   Cache.log.warn("Cannot create tree for tree "+t+" in document ("+alignment.getTree(t).getVorbaId());
1534                 }
1535
1536               }
1537             }
1538           }
1539         }
1540       }
1541       // we do sequenceMappings last because they span all datasets in a vamsas
1542       // root
1543       for (int _ds = 0, _nds = root.getDataSetCount(); _ds < _nds; _ds++)
1544       {
1545         DataSet dataset = root.getDataSet(_ds);
1546         if (dataset.getSequenceMappingCount() > 0)
1547         {
1548           for (int sm = 0, smCount = dataset.getSequenceMappingCount(); sm < smCount; sm++)
1549           {
1550             Rangetype seqmap = new jalview.io.vamsas.Sequencemapping(this,
1551                     dataset.getSequenceMapping(sm));
1552           }
1553         }
1554       }
1555     }
1556   }
1557
1558   public AlignViewport findViewport(Alignment alignment)
1559   {
1560     AlignViewport av=null;
1561     AlignViewport[] avs = findViewportForSequenceSetId((String)getvObj2jv(alignment));
1562     if (avs!=null)
1563     {
1564       av = avs[0];
1565     }
1566     return av;
1567   }
1568
1569   private AlignViewport[] findViewportForSequenceSetId(String sequenceSetId)
1570   {
1571     Vector viewp = new Vector();
1572     if (Desktop.desktop != null)
1573     {
1574       javax.swing.JInternalFrame[] frames = Desktop.instance.getAllFrames();
1575
1576       for (int t = 0; t < frames.length; t++)
1577       {
1578         if (frames[t] instanceof AlignFrame)
1579         {
1580           if (((AlignFrame) frames[t]).getViewport().getSequenceSetId().equals(sequenceSetId))
1581           {
1582             viewp.addElement(((AlignFrame) frames[t]).getViewport());
1583           }
1584         }
1585       }
1586       if (viewp.size()>0)
1587       {
1588         AlignViewport[] vp = new AlignViewport[viewp.size()];
1589         viewp.copyInto(vp);
1590         return vp;
1591       }
1592     }
1593     return null;
1594   }
1595
1596   // bitfields - should be a template in j1.5
1597   private static int HASSECSTR = 0;
1598
1599   private static int HASVALS = 1;
1600
1601   private static int HASHPHOB = 2;
1602
1603   private static int HASDC = 3;
1604
1605   private static int HASDESCSTR = 4;
1606
1607   private static int HASTWOSTATE = 5; // not used yet.
1608
1609   /**
1610    * parses the AnnotationElements - if they exist - into
1611    * jalview.datamodel.Annotation[] rows Two annotation rows are made if there
1612    * are distinct annotation for both at 'pos' and 'after pos' at any particular
1613    * site.
1614    *
1615    * @param annotation
1616    * @return { boolean[static int constants ], int[ae.length] - map to annotated
1617    *         object frame, jalview.datamodel.Annotation[],
1618    *         jalview.datamodel.Annotation[] (after)}
1619    */
1620   private Object[] parseRangeAnnotation(
1621           uk.ac.vamsas.objects.core.RangeAnnotation annotation)
1622   {
1623     // set these attributes by looking in the annotation to decide what kind of
1624     // alignment annotation rows will be made
1625     // TODO: potentially we might make several annotation rows from one vamsas
1626     // alignment annotation. the jv2Vobj binding mechanism
1627     // may not quite cope with this (without binding an array of annotations to
1628     // a vamsas alignment annotation)
1629     // summary flags saying what we found over the set of annotation rows.
1630     boolean[] AeContent = new boolean[]
1631     { false, false, false, false, false };
1632     int[] rangeMap = getMapping(annotation);
1633     jalview.datamodel.Annotation[][] anot = new jalview.datamodel.Annotation[][]
1634     { new jalview.datamodel.Annotation[rangeMap.length],
1635         new jalview.datamodel.Annotation[rangeMap.length] };
1636     boolean mergeable = true; // false if 'after positions cant be placed on
1637                               // same annotation row as positions.
1638
1639     if (annotation.getAnnotationElementCount() > 0)
1640     {
1641       AnnotationElement ae[] = annotation.getAnnotationElement();
1642       for (int aa = 0; aa < ae.length; aa++)
1643       {
1644         int pos = (int) ae[aa].getPosition() - 1; // pos counts from 1 to
1645                                                   // (|seg.start-seg.end|+1)
1646         if (pos >= 0 && pos < rangeMap.length)
1647         {
1648           int row = ae[aa].getAfter() ? 1 : 0;
1649           if (anot[row][pos] != null)
1650           {
1651             // only time this should happen is if the After flag is set.
1652             Cache.log.debug("Ignoring duplicate annotation site at " + pos);
1653             continue;
1654           }
1655           if (anot[1 - row][pos] != null)
1656           {
1657             mergeable = false;
1658           }
1659           String desc = "";
1660           if (ae[aa].getDescription() != null)
1661           {
1662             desc = ae[aa].getDescription();
1663             if (desc.length() > 0)
1664             {
1665               // have imported valid description string
1666               AeContent[HASDESCSTR] = true;
1667             }
1668           }
1669           String dc = null; // ae[aa].getDisplayCharacter()==null ? "dc" :
1670                             // ae[aa].getDisplayCharacter();
1671           String ss = null; // ae[aa].getSecondaryStructure()==null ? "ss" :
1672                             // ae[aa].getSecondaryStructure();
1673           java.awt.Color colour = null;
1674           if (ae[aa].getGlyphCount() > 0)
1675           {
1676             Glyph[] glyphs = ae[aa].getGlyph();
1677             for (int g = 0; g < glyphs.length; g++)
1678             {
1679               if (glyphs[g]
1680                       .getDict()
1681                       .equals(
1682                               uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE))
1683               {
1684                 ss = glyphs[g].getContent();
1685                 AeContent[HASSECSTR] = true;
1686               }
1687               else if (glyphs[g]
1688                       .getDict()
1689                       .equals(
1690                               uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_HD_HYDRO))
1691               {
1692                 Cache.log.debug("ignoring hydrophobicity glyph marker.");
1693                 AeContent[HASHPHOB] = true;
1694                 char c = (dc = glyphs[g].getContent()).charAt(0);
1695                 // dc may get overwritten - but we still set the colour.
1696                 colour = new java.awt.Color(c == '+' ? 255 : 0,
1697                         c == '.' ? 255 : 0, c == '-' ? 255 : 0);
1698
1699               }
1700               else if (glyphs[g].getDict().equals(
1701                       uk.ac.vamsas.objects.utils.GlyphDictionary.DEFAULT))
1702               {
1703                 dc = glyphs[g].getContent();
1704                 AeContent[HASDC] = true;
1705               }
1706               else
1707               {
1708                 Cache.log.debug("IMPLEMENTATION TODO: Ignoring unknown glyph type "
1709                         + glyphs[g].getDict());
1710               }
1711             }
1712           }
1713           float val = 0;
1714           if (ae[aa].getValueCount() > 0)
1715           {
1716             AeContent[HASVALS] = true;
1717             if (ae[aa].getValueCount() > 1)
1718             {
1719               Cache.log.warn("ignoring additional "
1720                       + (ae[aa].getValueCount() - 1)
1721                       + "values in annotation element.");
1722             }
1723             val = ae[aa].getValue(0);
1724           }
1725           if (colour == null)
1726           {
1727             anot[row][pos] = new jalview.datamodel.Annotation(
1728                     (dc != null) ? dc : "", desc, (ss != null) ? ss
1729                             .charAt(0) : ' ', val);
1730           }
1731           else
1732           {
1733             anot[row][pos] = new jalview.datamodel.Annotation(
1734                     (dc != null) ? dc : "", desc, (ss != null) ? ss
1735                             .charAt(0) : ' ', val, colour);
1736           }
1737         }
1738         else
1739         {
1740           Cache.log.warn("Ignoring out of bound annotation element " + aa
1741                   + " in " + annotation.getVorbaId().getId());
1742         }
1743       }
1744       // decide on how many annotation rows are needed.
1745       if (mergeable)
1746       {
1747         for (int i = 0; i < anot[0].length; i++)
1748         {
1749           if (anot[1][i] != null)
1750           {
1751             anot[0][i] = anot[1][i];
1752             anot[0][i].description = anot[0][i].description + " (after)";
1753             AeContent[HASDESCSTR] = true; // we have valid description string
1754                                           // data
1755             anot[1][i] = null;
1756           }
1757         }
1758         anot[1] = null;
1759       }
1760       else
1761       {
1762         for (int i = 0; i < anot[0].length; i++)
1763         {
1764           anot[1][i].description = anot[1][i].description + " (after)";
1765         }
1766       }
1767       return new Object[]
1768       { AeContent, rangeMap, anot[0], anot[1] };
1769     }
1770     else
1771     {
1772       // no annotations to parse. Just return an empty annotationElement[]
1773       // array.
1774       return new Object[]
1775       { AeContent, rangeMap, anot[0], anot[1] };
1776     }
1777     // return null;
1778   }
1779
1780   /**
1781    * @param jal
1782    *          the jalview alignment to which the annotation will be attached
1783    *          (ideally - freshly updated from corresponding vamsas alignment)
1784    * @param annotation
1785    * @return unbound jalview alignment annotation object.
1786    */
1787   private jalview.datamodel.AlignmentAnnotation getjAlignmentAnnotation(
1788           jalview.datamodel.AlignmentI jal,
1789           uk.ac.vamsas.objects.core.RangeAnnotation annotation)
1790   {
1791     if (annotation == null)
1792     {
1793       return null;
1794     }
1795     // boolean
1796     // hasSequenceRef=annotation.getClass().equals(uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation.class);
1797     // boolean hasProvenance=hasSequenceRef ||
1798     // (annotation.getClass().equals(uk.ac.vamsas.objects.core.AlignmentAnnotation.class));
1799     /*
1800      * int se[] = getBounds(annotation); if (se==null) se=new int[]
1801      * {0,jal.getWidth()-1};
1802      */
1803     Object[] parsedRangeAnnotation = parseRangeAnnotation(annotation);
1804     String a_label = annotation.getLabel();
1805     String a_descr = annotation.getDescription();
1806     GraphLine gl=null;
1807     int type=0;
1808     boolean interp=true; // cleared if annotation is DISCRETE
1809     // set type and other attributes from properties
1810     if (annotation.getPropertyCount() > 0)
1811     {
1812       // look for special jalview properties
1813       uk.ac.vamsas.objects.core.Property[] props = annotation
1814               .getProperty();
1815       for (int p = 0; p < props.length; p++)
1816       {
1817         if (props[p].getName().equalsIgnoreCase(DISCRETE_ANNOTATION))
1818         {
1819           type = AlignmentAnnotation.BAR_GRAPH;
1820           interp=false;
1821         } else if
1822          (props[p].getName().equalsIgnoreCase(CONTINUOUS_ANNOTATION)) {
1823           type = AlignmentAnnotation.LINE_GRAPH;
1824         } else if
1825         (props[p].getName().equalsIgnoreCase(THRESHOLD))
1826         {
1827           Float val=null;
1828           try {
1829             val = new Float(props[p].getContent());
1830           }catch (Exception e)
1831           {
1832             Cache.log.warn("Failed to parse threshold property");
1833           }
1834           if (val!=null)
1835           if (gl==null)
1836           {
1837             gl = new GraphLine(val.floatValue(), "", java.awt.Color.black);
1838           } else
1839           {
1840             gl.value = val.floatValue();
1841           }
1842         }
1843         else if (props[p].getName().equalsIgnoreCase(THRESHOLD+"Name"))
1844         {
1845           if (gl==null)
1846             gl = new GraphLine(0, "", java.awt.Color.black);
1847           gl.label = props[p].getContent();
1848         }
1849       }
1850     }
1851     jalview.datamodel.AlignmentAnnotation jan = null;
1852     if (a_label == null || a_label.length() == 0)
1853     {
1854       a_label = annotation.getType();
1855       if (a_label.length() == 0)
1856       {
1857         a_label = "Unamed annotation";
1858       }
1859     }
1860     if (a_descr == null || a_descr.length() == 0)
1861     {
1862       a_descr = "Annotation of type '" + annotation.getType() + "'";
1863     }
1864     if (parsedRangeAnnotation == null)
1865     {
1866       Cache.log
1867               .debug("Inserting empty annotation row elements for a whole-alignment annotation.");
1868     }
1869     else
1870     {
1871       if (parsedRangeAnnotation[3] != null)
1872       {
1873         Cache.log.warn("Ignoring 'After' annotation row in "
1874                 + annotation.getVorbaId());
1875       }
1876       jalview.datamodel.Annotation[] arow = (jalview.datamodel.Annotation[]) parsedRangeAnnotation[2];
1877       boolean[] has = (boolean[]) parsedRangeAnnotation[0];
1878       // VAMSAS: getGraph is only on derived annotation for alignments - in this
1879       // way its 'odd' - there is already an existing TODO about removing this
1880       // flag as being redundant
1881       /*
1882        * if
1883        * ((annotation.getClass().equals(uk.ac.vamsas.objects.core.AlignmentAnnotation.class) &&
1884        * ((uk.ac.vamsas.objects.core.AlignmentAnnotation)annotation).getGraph()) ||
1885        * (hasSequenceRef=true &&
1886        * ((uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation)annotation).getGraph())) {
1887        */
1888       if (has[HASVALS])
1889       {
1890         if (type==0)
1891         {
1892           type = jalview.datamodel.AlignmentAnnotation.BAR_GRAPH; // default type of value annotation
1893           if (has[HASHPHOB])
1894           {
1895             // no hints - so we ensure HPHOB display is like this.
1896             type = jalview.datamodel.AlignmentAnnotation.BAR_GRAPH;
1897           }
1898         }
1899         // make bounds and automatic description strings for jalview user's
1900         // benefit (these shouldn't be written back to vamsas document)
1901         boolean first = true;
1902         float min = 0, max = 1;
1903         int lastval = 0;
1904         for (int i = 0; i < arow.length; i++)
1905         {
1906           if (arow[i] != null)
1907           {
1908             if (i - lastval > 1 && interp)
1909             {
1910               // do some interpolation *between* points
1911               if (arow[lastval] != null)
1912               {
1913                 float interval = arow[i].value - arow[lastval].value;
1914                 interval /= i - lastval;
1915                 float base = arow[lastval].value;
1916                 for (int ip = lastval + 1, np = 0; ip < i; np++, ip++)
1917                 {
1918                   arow[ip] = new jalview.datamodel.Annotation("", "", ' ',
1919                           interval * np + base);
1920                   // NB - Interpolated points don't get a tooltip and
1921                   // description.
1922                 }
1923               }
1924             }
1925             lastval = i;
1926             // check range - shouldn't we have a min and max property in the
1927             // annotation object ?
1928             if (first)
1929             {
1930               min = max = arow[i].value;
1931               first = false;
1932             }
1933             else
1934             {
1935               if (arow[i].value < min)
1936               {
1937                 min = arow[i].value;
1938               }
1939               else if (arow[i].value > max)
1940               {
1941                 max = arow[i].value;
1942               }
1943             }
1944             // make tooltip and display char value
1945             if (!has[HASDESCSTR])
1946             {
1947               arow[i].description = arow[i].value + "";
1948             }
1949             if (!has[HASDC])
1950             {
1951               if (!interp)
1952                 {
1953                 if (arow[i].description!=null && arow[i].description.length()<3)
1954                 {
1955                   // copy over the description as the display char.
1956                   arow[i].displayCharacter = new String(arow[i].description);
1957                 }
1958                 } else
1959                 {
1960                   // mark the position as a point used for the interpolation.
1961                 arow[i].displayCharacter = arow[i].value + "";
1962                 }
1963             }
1964           }
1965         }
1966         jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr,
1967                 arow, min, max, type);
1968       }
1969       else
1970       {
1971         if (annotation.getAnnotationElementCount()==0)
1972         {
1973           // empty annotation array
1974           // TODO: alignment 'features' compare rangeType spec to alignment width - if it is not complete, then mark regions on the annotation row.
1975         }
1976         jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr,
1977                 arow);
1978         jan.setThreshold(null);
1979       }
1980       if (annotation.getLinkCount() > 0)
1981       {
1982         Cache.log.warn("Ignoring " + annotation.getLinkCount()
1983                 + "links added to AlignmentAnnotation.");
1984       }
1985       if (annotation.getModifiable() == null || annotation.getModifiable().length()==0) // TODO: USE VAMSAS LIBRARY OBJECT
1986                                               // LOCK METHODS)
1987       {
1988         jan.editable = true;
1989       }
1990       try
1991       {
1992         if (annotation.getGroup() != null
1993                 && annotation.getGroup().length() > 0)
1994         {
1995           jan.graphGroup = Integer.parseInt(annotation.getGroup()); // TODO: group similarly named annotation together ?
1996         }
1997       } catch (Exception e)
1998       {
1999         Cache.log
2000                 .info("UNIMPLEMENTED : Couldn't parse non-integer group value for setting graphGroup correctly.");
2001       }
2002       return jan;
2003
2004     }
2005
2006     return null;
2007   }
2008
2009   private SequenceFeature getJalviewSeqFeature(RangeAnnotation dseta)
2010   {
2011     int[] se = getBounds(dseta);
2012     SequenceFeature sf = new jalview.datamodel.SequenceFeature(dseta
2013             .getType(), dseta.getDescription(), dseta.getStatus(), se[0],
2014             se[1], dseta.getGroup());
2015     if (dseta.getLinkCount() > 0)
2016     {
2017       Link[] links = dseta.getLink();
2018       for (int i = 0; i < links.length; i++)
2019       {
2020         sf.addLink(links[i].getContent() + "|" + links[i].getHref());
2021       }
2022     }
2023     return sf;
2024   }
2025
2026   /**
2027    * get real bounds of a RangeType's specification. start and end are an
2028    * inclusive range within which all segments and positions lie. TODO: refactor
2029    * to vamsas utils
2030    *
2031    * @param dseta
2032    * @return int[] { start, end}
2033    */
2034   private int[] getBounds(RangeType dseta)
2035   {
2036     if (dseta != null)
2037     {
2038       int[] se = null;
2039       if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
2040       {
2041         throw new Error(
2042                 "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
2043       }
2044       if (dseta.getSegCount() > 0)
2045       {
2046         se = getSegRange(dseta.getSeg(0), true);
2047         for (int s = 1, sSize = dseta.getSegCount(); s < sSize; s++)
2048         {
2049           int nse[] = getSegRange(dseta.getSeg(s), true);
2050           if (se[0] > nse[0])
2051           {
2052             se[0] = nse[0];
2053           }
2054           if (se[1] < nse[1])
2055           {
2056             se[1] = nse[1];
2057           }
2058         }
2059       }
2060       if (dseta.getPosCount() > 0)
2061       {
2062         // could do a polarity for pos range too. and pass back indication of
2063         // discontinuities.
2064         int pos = dseta.getPos(0).getI();
2065         se = new int[]
2066         { pos, pos };
2067         for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
2068         {
2069           pos = dseta.getPos(p).getI();
2070           if (se[0] > pos)
2071           {
2072             se[0] = pos;
2073           }
2074           if (se[1] < pos)
2075           {
2076             se[1] = pos;
2077           }
2078         }
2079       }
2080       return se;
2081     }
2082     return null;
2083   }
2084
2085   /**
2086    * map from a rangeType's internal frame to the referenced object's coordinate
2087    * frame.
2088    *
2089    * @param dseta
2090    * @return int [] { ref(pos)...} for all pos in rangeType's frame.
2091    */
2092   private int[] getMapping(RangeType dseta)
2093   {
2094     Vector posList = new Vector();
2095     if (dseta != null)
2096     {
2097       int[] se = null;
2098       if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
2099       {
2100         throw new Error(
2101                 "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
2102       }
2103       if (dseta.getSegCount() > 0)
2104       {
2105         for (int s = 0, sSize = dseta.getSegCount(); s < sSize; s++)
2106         {
2107           se = getSegRange(dseta.getSeg(s), false);
2108           int se_end = se[1 - se[2]] + (se[2] == 0 ? 1 : -1);
2109           for (int p = se[se[2]]; p != se_end; p += se[2] == 0 ? 1 : -1)
2110           {
2111             posList.add(new Integer(p));
2112           }
2113         }
2114       }
2115       else if (dseta.getPosCount() > 0)
2116       {
2117         int pos = dseta.getPos(0).getI();
2118
2119         for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
2120         {
2121           pos = dseta.getPos(p).getI();
2122           posList.add(new Integer(pos));
2123         }
2124       }
2125     }
2126     if (posList != null && posList.size() > 0)
2127     {
2128       int[] range = new int[posList.size()];
2129       for (int i = 0; i < range.length; i++)
2130       {
2131         range[i] = ((Integer) posList.elementAt(i)).intValue();
2132       }
2133       posList.clear();
2134       return range;
2135     }
2136     return null;
2137   }
2138
2139   /**
2140    *
2141    * @param maprange
2142    *          where the from range is the local mapped range, and the to range
2143    *          is the 'mapped' range in the MapRangeType
2144    * @param default
2145    *          unit for local
2146    * @param default
2147    *          unit for mapped
2148    * @return MapList
2149    */
2150   private jalview.util.MapList parsemapType(MapType maprange, int localu,
2151           int mappedu)
2152   {
2153     jalview.util.MapList ml = null;
2154     int[] localRange = getMapping(maprange.getLocal());
2155     int[] mappedRange = getMapping(maprange.getMapped());
2156     long lu = maprange.getLocal().hasUnit() ? maprange.getLocal().getUnit()
2157             : localu;
2158     long mu = maprange.getMapped().hasUnit() ? maprange.getMapped()
2159             .getUnit() : mappedu;
2160     ml = new jalview.util.MapList(localRange, mappedRange, (int) lu,
2161             (int) mu);
2162     return ml;
2163   }
2164
2165   /**
2166    * initialise a range type object from a set of start/end inclusive intervals
2167    *
2168    * @param mrt
2169    * @param range
2170    */
2171   private void initRangeType(RangeType mrt, int[] range)
2172   {
2173     for (int i = 0; i < range.length; i += 2)
2174     {
2175       Seg vSeg = new Seg();
2176       vSeg.setStart(range[i]);
2177       vSeg.setEnd(range[i + 1]);
2178       mrt.addSeg(vSeg);
2179     }
2180   }
2181
2182   /**
2183    * initialise a MapType object from a MapList object.
2184    *
2185    * @param maprange
2186    * @param ml
2187    * @param setUnits
2188    */
2189   private void initMapType(MapType maprange, jalview.util.MapList ml,
2190           boolean setUnits)
2191   {
2192     maprange.setLocal(new Local());
2193     maprange.setMapped(new Mapped());
2194     initRangeType(maprange.getLocal(), ml.getFromRanges());
2195     initRangeType(maprange.getMapped(), ml.getToRanges());
2196     if (setUnits)
2197     {
2198       maprange.getLocal().setUnit(ml.getFromRatio());
2199       maprange.getLocal().setUnit(ml.getToRatio());
2200     }
2201   }
2202
2203   /*
2204    * not needed now. Provenance getVamsasProvenance(jalview.datamodel.Provenance
2205    * jprov) { jalview.datamodel.ProvenanceEntry[] entries = null; // TODO: fix
2206    * App and Action here. Provenance prov = new Provenance();
2207    * org.exolab.castor.types.Date date = new org.exolab.castor.types.Date( new
2208    * java.util.Date()); Entry provEntry;
2209    *
2210    * if (jprov != null) { entries = jprov.getEntries(); for (int i = 0; i <
2211    * entries.length; i++) { provEntry = new Entry(); try { date = new
2212    * org.exolab.castor.types.Date(entries[i].getDate()); } catch (Exception ex) {
2213    * ex.printStackTrace();
2214    *
2215    * date = new org.exolab.castor.types.Date(entries[i].getDate()); }
2216    * provEntry.setDate(date); provEntry.setUser(entries[i].getUser());
2217    * provEntry.setAction(entries[i].getAction()); prov.addEntry(provEntry); } }
2218    * else { provEntry = new Entry(); provEntry.setDate(date);
2219    * provEntry.setUser(System.getProperty("user.name")); // TODO: ext string
2220    * provEntry.setApp("JVAPP"); // TODO: ext string provEntry.setAction(action);
2221    * prov.addEntry(provEntry); }
2222    *
2223    * return prov; }
2224    */
2225   jalview.datamodel.Provenance getJalviewProvenance(Provenance prov)
2226   {
2227     // TODO: fix App and Action entries and check use of provenance in jalview.
2228     jalview.datamodel.Provenance jprov = new jalview.datamodel.Provenance();
2229     for (int i = 0; i < prov.getEntryCount(); i++)
2230     {
2231       jprov.addEntry(prov.getEntry(i).getUser(), prov.getEntry(i)
2232               .getAction(), prov.getEntry(i).getDate(), prov.getEntry(i)
2233               .getId());
2234     }
2235
2236     return jprov;
2237   }
2238
2239   /**
2240    *
2241    * @return default initial provenance list for a Jalview created vamsas
2242    *         object.
2243    */
2244   Provenance dummyProvenance()
2245   {
2246     return dummyProvenance(null);
2247   }
2248
2249   Entry dummyPEntry(String action)
2250   {
2251     Entry entry = new Entry();
2252     entry.setApp(this.provEntry.getApp());
2253     if (action != null)
2254     {
2255       entry.setAction(action);
2256     }
2257     else
2258     {
2259       entry.setAction("created.");
2260     }
2261     entry.setDate(new java.util.Date());
2262     entry.setUser(this.provEntry.getUser());
2263     return entry;
2264   }
2265
2266   Provenance dummyProvenance(String action)
2267   {
2268     Provenance prov = new Provenance();
2269     prov.addEntry(dummyPEntry(action));
2270     return prov;
2271   }
2272
2273   Entry addProvenance(Provenance p, String action)
2274   {
2275     Entry dentry = dummyPEntry(action);
2276     p.addEntry(dentry);
2277     return dentry;
2278   }
2279
2280   public Entry getProvEntry()
2281   {
2282     return provEntry;
2283   }
2284
2285   public IClientDocument getClientDocument()
2286   {
2287     return cdoc;
2288   }
2289
2290   public IdentityHashMap getJvObjectBinding()
2291   {
2292     return jv2vobj;
2293   }
2294
2295   public Hashtable getVamsasObjectBinding()
2296   {
2297     return vobj2jv;
2298   }
2299
2300   public void storeSequenceMappings(AlignViewport viewport, String title)
2301           throws Exception
2302   {
2303     AlignViewport av = viewport;
2304     try
2305     {
2306       jalview.datamodel.AlignmentI jal = av.getAlignment();
2307       // /////////////////////////////////////////
2308       // SAVE THE DATASET
2309       DataSet dataset = null;
2310       if (jal.getDataset() == null)
2311       {
2312         Cache.log.warn("Creating new dataset for an alignment.");
2313         jal.setDataset(null);
2314       }
2315       dataset = (DataSet) getjv2vObj(jal.getDataset());
2316       // Store any sequence mappings.
2317       if (av.getAlignment().getCodonFrames() != null
2318               && av.getAlignment().getCodonFrames().length > 0)
2319       {
2320         jalview.datamodel.AlignedCodonFrame[] cframes = av.getAlignment()
2321                 .getCodonFrames();
2322         for (int cf = 0; cf < cframes.length; cf++)
2323         {
2324           if (cframes[cf].getdnaSeqs().length > 0)
2325           {
2326             jalview.datamodel.SequenceI[] dmps = cframes[cf].getdnaSeqs();
2327             jalview.datamodel.Mapping[] mps = cframes[cf].getProtMappings();
2328             for (int smp = 0; smp < mps.length; smp++)
2329             {
2330               uk.ac.vamsas.objects.core.SequenceType mfrom = (SequenceType) getjv2vObj(dmps[smp]);
2331               if (mfrom != null)
2332               {
2333                 new jalview.io.vamsas.Sequencemapping(this, mps[smp],
2334                         mfrom, dataset);
2335               }
2336               else
2337               {
2338                 Cache.log
2339                         .warn("NO Vamsas Binding for local sequence! NOT CREATING MAPPING FOR "
2340                                 + dmps[smp].getDisplayId(true)
2341                                 + " to "
2342                                 + mps[smp].getTo().getName());
2343               }
2344             }
2345           }
2346         }
2347       }
2348     } catch (Exception e)
2349     {
2350       throw new Exception("Couldn't store sequence mappings for " + title,
2351               e);
2352     }
2353   }
2354 }