src/jalview/io/JSONFile.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21
  22 package jalview.io;
  23
  24 import jalview.api.AlignViewportI;
  25 import jalview.api.ComplexAlignFile;
  26 import jalview.api.FeatureRenderer;
  27 import jalview.api.FeaturesDisplayedI;
  28 import jalview.datamodel.AlignmentAnnotation;
  29 import jalview.datamodel.Annotation;
  30 import jalview.datamodel.ColumnSelection;
  31 import jalview.datamodel.HiddenSequences;
  32 import jalview.datamodel.Sequence;
  33 import jalview.datamodel.SequenceFeature;
  34 import jalview.datamodel.SequenceGroup;
  35 import jalview.datamodel.SequenceI;
  36 import jalview.json.binding.v1.AlignmentAnnotationPojo;
  37 import jalview.json.binding.v1.AlignmentPojo;
  38 import jalview.json.binding.v1.AlignmentPojo.JalviewBioJsColorSchemeMapper;
  39 import jalview.json.binding.v1.AnnotationPojo;
  40 import jalview.json.binding.v1.SequenceFeaturesPojo;
  41 import jalview.json.binding.v1.SequenceGrpPojo;
  42 import jalview.json.binding.v1.SequencePojo;
  43 import jalview.schemes.ColourSchemeI;
  44 import jalview.schemes.ColourSchemeProperty;
  45
  46 import java.awt.Color;
  47 import java.io.IOException;
  48 import java.io.Reader;
  49 import java.util.ArrayList;
  50 import java.util.Hashtable;
  51 import java.util.Iterator;
  52 import java.util.List;
  53 import java.util.Vector;
  54
  55 import org.json.simple.JSONArray;
  56 import org.json.simple.JSONObject;
  57 import org.json.simple.parser.JSONParser;
  58
  59 public class JSONFile extends AlignFile implements ComplexAlignFile
  60 {
  61   private ColourSchemeI colourScheme;
  62
  63   private String version = "2.9";
  64
  65   private String webstartUrl = "www.jalview.org/services/launchApp";
  66
  67   private String application = "Jalview";
  68
  69   public static final String FILE_EXT = "json";
  70
  71   public static final String FILE_DESC = "JSON";
  72
  73   private String globalColorScheme;
  74
  75   private boolean showSeqFeatures;
  76
  77   private Hashtable<String, Sequence> seqMap;
  78
  79   private FeaturesDisplayedI displayedFeatures;
  80
  81   private FeatureRenderer fr;
  82
  83   private List<int[]> hiddenColumns;
  84
  85   private ColumnSelection columnSelection;
  86
  87   private List<String> hiddenSeqRefs;
  88
  89   private ArrayList<SequenceI> hiddenSequences;
  90
  91   public JSONFile()
  92   {
  93     super();
  94   }
  95
  96   public JSONFile(FileParse source) throws IOException
  97   {
  98     super(source);
  99   }
 100
 101   public JSONFile(String inFile, String type) throws IOException
 102   {
 103     super(inFile, type);
 104   }
 105
 106   @Override
 107   public void parse() throws IOException
 108   {
 109     parse(getReader());
 110
 111   }
 112
 113   @Override
 114   public String print()
 115   {
 116     String jsonOutput = null;
 117     try
 118     {
 119       AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
 120       if (getViewport() != null)
 121       {
 122         globalColorScheme = ColourSchemeProperty
 123                 .getColourName(getViewport()
 124                 .getGlobalColourScheme());
 125         setDisplayedFeatures(getViewport().getFeaturesDisplayed());
 126         showSeqFeatures = getViewport().isShowSequenceFeatures();
 127         fr = getViewport().getFeatureRenderer();
 128       }
 129
 130       int count = 0;
 131       for (SequenceI seq : seqs)
 132       {
 133         StringBuilder name = new StringBuilder();
 134         name.append(seq.getName()).append("/").append(seq.getStart())
 135                 .append("-").append(seq.getEnd());
 136         SequencePojo jsonSeqPojo = new SequencePojo();
 137         jsonSeqPojo.setId(String.valueOf(seq.hashCode()));
 138         jsonSeqPojo.setOrder(++count);
 139         jsonSeqPojo.setEnd(seq.getEnd());
 140         jsonSeqPojo.setStart(seq.getStart());
 141         jsonSeqPojo.setName(name.toString());
 142         jsonSeqPojo.setSeq(seq.getSequenceAsString());
 143         jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
 144       }
 145
 146       jsonAlignmentPojo.setGlobalColorScheme(globalColorScheme);
 147       jsonAlignmentPojo.getAppSettings().put("application", application);
 148       jsonAlignmentPojo.getAppSettings().put("version", version);
 149       jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
 150       jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
 151               String.valueOf(showSeqFeatures));
 152
 153       String[] hiddenSections = getHiddenSections();
 154       if (hiddenSections != null)
 155       {
 156         if (hiddenSections[0] != null
 157                 && getViewport().getExportSettings()
 158                         .isExportHiddenColumns())
 159         {
 160           jsonAlignmentPojo.getAppSettings().put("hiddenCols",
 161                   String.valueOf(hiddenSections[0]));
 162         }
 163         if (hiddenSections[1] != null
 164                 && getViewport().getExportSettings()
 165                         .isExportHiddenSequences())
 166         {
 167           jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
 168                   String.valueOf(hiddenSections[1]));
 169         }
 170       }
 171
 172       if (getViewport().getExportSettings().isExportAnnotations())
 173       {
 174         jsonAlignmentPojo
 175                 .setAlignAnnotation(annotationToJsonPojo(annotations));
 176       }
 177
 178       if (getViewport().getExportSettings().isExportFeatures())
 179       {
 180         jsonAlignmentPojo
 181                 .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
 182       }
 183
 184       if (getViewport().getExportSettings().isExportGroups()
 185               && seqGroups != null
 186               && seqGroups.size() > 0)
 187       {
 188         for (SequenceGroup seqGrp : seqGroups)
 189         {
 190           SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
 191           seqGrpPojo.setGroupName(seqGrp.getName());
 192           seqGrpPojo.setColourScheme(ColourSchemeProperty
 193                   .getColourName(seqGrp.cs));
 194           seqGrpPojo.setColourText(seqGrp.getColourText());
 195           seqGrpPojo.setDescription(seqGrp.getDescription());
 196           seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
 197           seqGrpPojo.setDisplayText(seqGrp.getDisplayText());
 198           seqGrpPojo.setEndRes(seqGrp.getEndRes());
 199           seqGrpPojo.setStartRes(seqGrp.getStartRes());
 200           seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
 201           for (SequenceI seq : seqGrp.getSequences())
 202           {
 203             seqGrpPojo.getSeqsHash().add(String.valueOf(seq.hashCode()));
 204           }
 205           jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
 206         }
 207       }
 208       org.json.JSONObject generatedJSon = new org.json.JSONObject(
 209               jsonAlignmentPojo);
 210       jsonOutput = generatedJSon.toString();
 211       return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
 212               "xEnd");
 213     } catch (Exception e)
 214     {
 215       e.printStackTrace();
 216     }
 217     return jsonOutput;
 218   }
 219
 220   public String[] getHiddenSections()
 221   {
 222     String[] hiddenSections = new String[2];
 223     if (getViewport() == null)
 224     {
 225       return null;
 226     }
 227
 228     // hidden column business
 229     if (getViewport().hasHiddenColumns())
 230     {
 231       List<int[]> hiddenCols = getViewport().getColumnSelection()
 232               .getHiddenColumns();
 233       StringBuilder hiddenColsBuilder = new StringBuilder();
 234       for (int[] range : hiddenCols)
 235       {
 236         hiddenColsBuilder.append(";").append(range[0]).append("-")
 237                 .append(range[1]);
 238       }
 239
 240       hiddenColsBuilder.deleteCharAt(0);
 241       hiddenSections[0] = hiddenColsBuilder.toString();
 242     }
 243
 244     // hidden rows/seqs business
 245     HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
 246             .getHiddenSequences();
 247     if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
 248     {
 249       return hiddenSections;
 250     }
 251
 252     SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
 253     StringBuilder hiddenSeqsBuilder = new StringBuilder();
 254     for (SequenceI hiddenSeq : hiddenSeqs)
 255     {
 256       if (hiddenSeq != null)
 257       {
 258         hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
 259       }
 260     }
 261     if (hiddenSeqsBuilder.length() > 0)
 262     {
 263       hiddenSeqsBuilder.deleteCharAt(0);
 264     }
 265     hiddenSections[1] = hiddenSeqsBuilder.toString();
 266
 267     return hiddenSections;
 268   }
 269
 270   public static List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
 271           List<SequenceI> seqs, FeatureRenderer fr)
 272   {
 273     FeaturesDisplayedI displayedFeatures = (fr == null) ? null : fr
 274             .getFeaturesDisplayed();
 275     List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
 276     for (SequenceI seq : seqs)
 277     {
 278       SequenceI dataSetSequence = seq.getDatasetSequence();
 279       SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
 280               : seq.getDatasetSequence().getSequenceFeatures();
 281
 282       seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
 283               : seqFeatures;
 284       if (seqFeatures == null)
 285       {
 286         continue;
 287       }
 288
 289       for (SequenceFeature sf : seqFeatures)
 290       {
 291         if (displayedFeatures != null
 292                 && displayedFeatures.isVisible(sf.getType()))
 293         {
 294           SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
 295                   String.valueOf(seq.hashCode()));
 296           String featureColour = (fr == null) ? null : jalview.util.Format
 297                   .getHexString(fr
 298                   .findFeatureColour(Color.white, seq,
 299                           seq.findIndex(sf.getBegin())));
 300           jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
 301           jsonFeature.setXend(seq.findIndex(sf.getEnd()));
 302           jsonFeature.setType(sf.getType());
 303           jsonFeature.setDescription(sf.getDescription());
 304           jsonFeature.setLinks(sf.links);
 305           jsonFeature.setOtherDetails(sf.otherDetails);
 306           jsonFeature.setScore(sf.getScore());
 307           jsonFeature.setFillColor(featureColour);
 308           jsonFeature.setFeatureGroup(sf.getFeatureGroup());
 309           sequenceFeaturesPojo.add(jsonFeature);
 310         }
 311       }
 312     }
 313     return sequenceFeaturesPojo;
 314   }
 315
 316   public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
 317           Vector<AlignmentAnnotation> annotations)
 318   {
 319     List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
 320     if (annotations == null)
 321     {
 322       return jsonAnnotations;
 323     }
 324     for (AlignmentAnnotation annot : annotations)
 325     {
 326       AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
 327       alignAnnotPojo.setDescription(annot.description);
 328       alignAnnotPojo.setLabel(annot.label);
 329       for (Annotation annotation : annot.annotations)
 330       {
 331         AnnotationPojo annotationPojo = new AnnotationPojo();
 332         if (annotation != null)
 333         {
 334           annotationPojo.setDescription(annotation.description);
 335           annotationPojo.setValue(annotation.value);
 336           annotationPojo
 337                   .setSecondaryStructure(annotation.secondaryStructure);
 338           annotationPojo.setDisplayCharacter(annotation.displayCharacter);
 339           alignAnnotPojo.getAnnotations().add(annotationPojo);
 340         }
 341         else
 342         {
 343           alignAnnotPojo.getAnnotations().add(annotationPojo);
 344         }
 345       }
 346       jsonAnnotations.add(alignAnnotPojo);
 347     }
 348     return jsonAnnotations;
 349   }
 350
 351   @SuppressWarnings("unchecked")
 352   public JSONFile parse(Reader jsonAlignmentString)
 353   {
 354     try
 355     {
 356       JSONParser jsonParser = new JSONParser();
 357       JSONObject alignmentJsonObj = (JSONObject) jsonParser
 358               .parse(jsonAlignmentString);
 359       JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
 360       JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
 361               .get("alignAnnotation");
 362       JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
 363               .get("seqFeatures");
 364       JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
 365               .get("seqGroups");
 366       JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
 367               .get("appSettings");
 368
 369       if (jvSettingsJsonObj != null)
 370       {
 371         String jsColourScheme = (String) jvSettingsJsonObj
 372                 .get("globalColorScheme");
 373         Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
 374                 "showSeqFeatures").toString());
 375         setColourScheme(getJalviewColorScheme(jsColourScheme));
 376         setShowSeqFeatures(showFeatures);
 377         parseHiddenSeqRefsAsList(jvSettingsJsonObj);
 378         parseHiddenCols(jvSettingsJsonObj);
 379       }
 380
 381       hiddenSequences = new ArrayList<SequenceI>();
 382       seqMap = new Hashtable<String, Sequence>();
 383       for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
 384               .hasNext();)
 385       {
 386         JSONObject sequence = sequenceIter.next();
 387         String sequcenceString = sequence.get("seq").toString();
 388         String sequenceName = sequence.get("name").toString();
 389         String seqUniqueId = sequence.get("id").toString();
 390         int start = Integer.valueOf(sequence.get("start").toString());
 391         int end = Integer.valueOf(sequence.get("end").toString());
 392         Sequence seq = new Sequence(sequenceName, sequcenceString, start,
 393                 end);
 394         if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
 395         {
 396           hiddenSequences.add(seq);
 397         }
 398         seqs.add(seq);
 399         seqMap.put(seqUniqueId, seq);
 400       }
 401       parseFeatures(jsonSeqArray);
 402
 403       for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
 404               .hasNext();)
 405       {
 406         JSONObject seqGrpObj = seqGrpIter.next();
 407         String grpName = seqGrpObj.get("groupName").toString();
 408         String colourScheme = seqGrpObj.get("colourScheme").toString();
 409         String description = (seqGrpObj.get("description") == null) ? null
 410                 : seqGrpObj.get("description").toString();
 411         boolean displayBoxes = Boolean.valueOf(seqGrpObj
 412                 .get("displayBoxes").toString());
 413         boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
 414                 .toString());
 415         boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
 416                 .toString());
 417         boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
 418                 "showNonconserved").toString());
 419         int startRes = Integer
 420                 .valueOf(seqGrpObj.get("startRes").toString());
 421         int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
 422         JSONArray seqsHashArray = (JSONArray) seqGrpObj.get("seqsHash");
 423
 424         ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
 425         if (seqsHashArray.size() > 0)
 426         {
 427           Iterator<String> seqHashIter = seqsHashArray.iterator();
 428           while (seqHashIter.hasNext())
 429           {
 430             String seqHash = seqHashIter.next();
 431             Sequence sequence = seqMap.get(seqHash);
 432             if (sequence != null)
 433             {
 434               grpSeqs.add(sequence);
 435             }
 436           }
 437         }
 438         ColourSchemeI scheme = getJalviewColorScheme(colourScheme);
 439         SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, scheme,
 440                 displayBoxes, displayText, colourText, startRes, endRes);
 441         seqGrp.setShowNonconserved(showNonconserved);
 442         seqGrp.setDescription(description);
 443         this.seqGroups.add(seqGrp);
 444
 445       }
 446
 447       for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
 448               .hasNext();)
 449       {
 450         JSONObject alAnnot = alAnnotIter.next();
 451         JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
 452         Annotation[] annotations = new Annotation[annotJsonArray.size()];
 453         int count = 0;
 454         for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
 455                 .hasNext();)
 456         {
 457           JSONObject annot = annotIter.next();
 458           if (annot == null)
 459           {
 460             annotations[count] = null;
 461           }
 462           else
 463           {
 464             float val = annot.get("value") == null ? null : Float
 465                     .valueOf(annot.get("value").toString());
 466             String desc = annot.get("description") == null ? null : annot
 467                     .get("description").toString();
 468
 469             char ss = annot.get("secondaryStructure") == null ? ' '
 470                     : annot.get("secondaryStructure").toString().charAt(0);
 471             String displayChar = annot.get("displayCharacter").toString();
 472
 473             annotations[count] = new Annotation(displayChar, desc, ss, val);
 474           }
 475           ++count;
 476         }
 477
 478         AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
 479                 .get("label").toString(), alAnnot.get("description")
 480                 .toString(), annotations);
 481         this.annotations.add(alignAnnot);
 482       }
 483
 484     } catch (Exception e)
 485     {
 486       e.printStackTrace();
 487     }
 488     return this;
 489   }
 490
 491   public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
 492   {
 493     hiddenSeqRefs = new ArrayList<String>();
 494     String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
 495     if(hiddenSeqs != null && !hiddenSeqs.isEmpty()){
 496       String[] seqRefs = hiddenSeqs.split(";");
 497       for(String seqRef : seqRefs){
 498         hiddenSeqRefs.add(seqRef);
 499       }
 500     }
 501   }
 502
 503   public void parseHiddenCols(JSONObject jvSettingsJson)
 504   {
 505     String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
 506     if(hiddenCols != null && !hiddenCols.isEmpty()){
 507       columnSelection = new ColumnSelection();
 508       String[] rangeStrings = hiddenCols.split(";");
 509       for(String rangeString : rangeStrings){
 510         String[] range = rangeString.split("-");
 511         columnSelection.hideColumns(Integer.valueOf(range[0]),
 512                 Integer.valueOf(range[1]));
 513       }
 514     }
 515   }
 516
 517   @SuppressWarnings("unchecked")
 518   private void parseFeatures(JSONArray jsonSeqFeatures)
 519   {
 520     if (jsonSeqFeatures != null)
 521     {
 522       for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
 523               .hasNext();)
 524       {
 525         JSONObject jsonFeature = seqFeatureItr.next();
 526         Long begin = (Long) jsonFeature.get("xStart");
 527         Long end = (Long) jsonFeature.get("xEnd");
 528         String type = (String) jsonFeature.get("type");
 529         String featureGrp = (String) jsonFeature.get("featureGroup");
 530         String descripiton = (String) jsonFeature.get("description");
 531         String seqRef = (String) jsonFeature.get("sequenceRef");
 532         Float score = Float.valueOf(jsonFeature.get("score").toString());
 533
 534         Sequence seq = seqMap.get(seqRef);
 535         SequenceFeature sequenceFeature = new SequenceFeature();
 536         JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
 537         if (linksJsonArray != null && linksJsonArray.size() > 0)
 538         {
 539           Iterator<String> linkList = linksJsonArray.iterator();
 540           while (linkList.hasNext())
 541           {
 542             String link = linkList.next();
 543             sequenceFeature.addLink(link);
 544           }
 545         }
 546         sequenceFeature.setFeatureGroup(featureGrp);
 547         sequenceFeature.setScore(score);
 548         sequenceFeature.setDescription(descripiton);
 549         sequenceFeature.setType(type);
 550         sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
 551         sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
 552         seq.addSequenceFeature(sequenceFeature);
 553       }
 554     }
 555   }
 556
 557   public static ColourSchemeI getJalviewColorScheme(
 558           String bioJsColourSchemeName)
 559   {
 560     ColourSchemeI jalviewColor = null;
 561     for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
 562             .values())
 563     {
 564       if (cs.getBioJsName().equalsIgnoreCase(bioJsColourSchemeName))
 565       {
 566         jalviewColor = cs.getJvColourScheme();
 567         break;
 568       }
 569     }
 570     return jalviewColor;
 571   }
 572
 573   public String getGlobalColorScheme()
 574   {
 575     return globalColorScheme;
 576   }
 577
 578   public void setGlobalColorScheme(String globalColorScheme)
 579   {
 580     this.globalColorScheme = globalColorScheme;
 581   }
 582
 583   public ColourSchemeI getColourScheme()
 584   {
 585     return colourScheme;
 586   }
 587
 588   public void setColourScheme(ColourSchemeI colourScheme)
 589   {
 590     this.colourScheme = colourScheme;
 591   }
 592
 593   public FeaturesDisplayedI getDisplayedFeatures()
 594   {
 595     return displayedFeatures;
 596   }
 597
 598   public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
 599   {
 600     this.displayedFeatures = displayedFeatures;
 601   }
 602
 603
 604   public static String getJSONData(AlignViewportI av)
 605   {
 606     JSONFile jsonFile = new JSONFile();
 607     jsonFile.setViewport(av);
 608     jsonFile.seqGroups = av.getAlignment().getGroups();
 609     jsonFile.setDisplayedFeatures(av.getFeaturesDisplayed());
 610
 611     for (SequenceI seq : av.getAlignment().getSequences())
 612     {
 613       jsonFile.seqs.add(seq);
 614     }
 615
 616     // Add non auto calculated annotation to AlignFile
 617     for (AlignmentAnnotation annot : av.getAlignment()
 618             .getAlignmentAnnotation())
 619     {
 620       if (annot != null && !annot.autoCalculated)
 621       {
 622         if (annot.label.equals("PDB.CATempFactor"))
 623         {
 624           continue;
 625         }
 626         jsonFile.annotations.add(annot);
 627       }
 628     }
 629     String jsonString = jsonFile.print();
 630     return jsonString;
 631   }
 632
 633   public boolean isShowSeqFeatures()
 634   {
 635     return showSeqFeatures;
 636   }
 637
 638   public void setShowSeqFeatures(boolean showSeqFeatures)
 639   {
 640     this.showSeqFeatures = showSeqFeatures;
 641   }
 642
 643   public Vector<AlignmentAnnotation> getAnnotations()
 644   {
 645     return annotations;
 646   }
 647
 648   public List<int[]> getHiddenColumns()
 649   {
 650     return hiddenColumns;
 651   }
 652
 653   public ColumnSelection getColumnSelection()
 654   {
 655     return columnSelection;
 656   }
 657
 658   public void setColumnSelection(ColumnSelection columnSelection)
 659   {
 660     this.columnSelection = columnSelection;
 661   }
 662
 663   public SequenceI[] getHiddenSequences()
 664   {
 665     if (hiddenSequences == null || hiddenSequences.isEmpty())
 666     {
 667       return new SequenceI[]
 668       {};
 669     }
 670     synchronized (hiddenSequences)
 671     {
 672       return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
 673     }
 674   }
 675
 676   public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
 677   {
 678     this.hiddenSequences = hiddenSequences;
 679   }
 680
 681   public class JSONExportSettings
 682   {
 683     private boolean exportSequence;
 684
 685     private boolean exportSequenceFeatures;
 686
 687     private boolean exportAnnotations;
 688
 689     private boolean exportGroups;
 690
 691     private boolean exportJalviewSettings;
 692
 693     public boolean isExportSequence()
 694     {
 695       return exportSequence;
 696     }
 697
 698     public void setExportSequence(boolean exportSequence)
 699     {
 700       this.exportSequence = exportSequence;
 701     }
 702
 703     public boolean isExportSequenceFeatures()
 704     {
 705       return exportSequenceFeatures;
 706     }
 707
 708     public void setExportSequenceFeatures(boolean exportSequenceFeatures)
 709     {
 710       this.exportSequenceFeatures = exportSequenceFeatures;
 711     }
 712
 713     public boolean isExportAnnotations()
 714     {
 715       return exportAnnotations;
 716     }
 717
 718     public void setExportAnnotations(boolean exportAnnotations)
 719     {
 720       this.exportAnnotations = exportAnnotations;
 721     }
 722
 723     public boolean isExportGroups()
 724     {
 725       return exportGroups;
 726     }
 727
 728     public void setExportGroups(boolean exportGroups)
 729     {
 730       this.exportGroups = exportGroups;
 731     }
 732
 733     public boolean isExportJalviewSettings()
 734     {
 735       return exportJalviewSettings;
 736     }
 737
 738     public void setExportJalviewSettings(boolean exportJalviewSettings)
 739     {
 740       this.exportJalviewSettings = exportJalviewSettings;
 741     }
 742   }
 743 }