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