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