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