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 java.awt.Color;
  25 import java.io.IOException;
  26 import java.util.ArrayList;
  27 import java.util.Hashtable;
  28 import java.util.Iterator;
  29 import java.util.List;
  30 import java.util.Vector;
  31
  32 import org.json.simple.JSONArray;
  33 import org.json.simple.JSONObject;
  34 import org.json.simple.parser.JSONParser;
  35
  36 import jalview.api.AlignViewportI;
  37 import jalview.api.ComplexAlignFile;
  38 import jalview.api.FeatureRenderer;
  39 import jalview.api.FeaturesDisplayedI;
  40 import jalview.datamodel.AlignmentAnnotation;
  41 import jalview.datamodel.Annotation;
  42 import jalview.datamodel.ColumnSelection;
  43 import jalview.datamodel.HiddenSequences;
  44 import jalview.datamodel.Sequence;
  45 import jalview.datamodel.SequenceFeature;
  46 import jalview.datamodel.SequenceGroup;
  47 import jalview.datamodel.SequenceI;
  48 import jalview.json.binding.v1.AlignmentAnnotationPojo;
  49 import jalview.json.binding.v1.AlignmentPojo;
  50 import jalview.json.binding.v1.AlignmentPojo.JalviewBioJsColorSchemeMapper;
  51 import jalview.json.binding.v1.AnnotationPojo;
  52 import jalview.json.binding.v1.SequenceFeaturesPojo;
  53 import jalview.json.binding.v1.SequenceGrpPojo;
  54 import jalview.json.binding.v1.SequencePojo;
  55 import jalview.schemes.ColourSchemeI;
  56 import jalview.schemes.ColourSchemeProperty;
  57
  58 public class JSONFile extends AlignFile implements ComplexAlignFile
  59 {
  60   private ColourSchemeI colourScheme;
  61
  62   private String version = "2.9";
  63
  64   private String webstartUrl = "www.jalview.org/services/launchApp";
  65
  66   private String application = "Jalview";
  67
  68   public static final String FILE_EXT = "json";
  69
  70   public static final String FILE_DESC = "JSON";
  71
  72   private String globalColorScheme;
  73
  74   private boolean showSeqFeatures;
  75
  76   private Hashtable<String, Sequence> seqMap;
  77
  78   private FeaturesDisplayedI displayedFeatures;
  79
  80   private FeatureRenderer fr;
  81
  82   private List<int[]> hiddenColumns;
  83
  84   private ColumnSelection columnSelection;
  85
  86   private List<String> hiddenSeqRefs;
  87
  88   private ArrayList<SequenceI> hiddenSequences;
  89
  90   public JSONFile()
  91   {
  92     super();
  93   }
  94
  95   public JSONFile(FileParse source) throws IOException
  96   {
  97     super(source);
  98   }
  99
 100   public JSONFile(String inFile, String type) throws IOException
 101   {
 102     super(inFile, type);
 103   }
 104
 105   @Override
 106   public void parse() throws IOException
 107   {
 108     StringBuilder jsonStringBuilder = new StringBuilder();
 109     String currentLine;
 110     while ((currentLine = nextLine()) != null)
 111     {
 112       jsonStringBuilder.append(currentLine);
 113     }
 114     parse(jsonStringBuilder.toString());
 115
 116   }
 117
 118   @Override
 119   public String print()
 120   {
 121     String jsonOutput = null;
 122     try
 123     {
 124       AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
 125       if (getViewport() != null)
 126       {
 127         globalColorScheme = ColourSchemeProperty
 128                 .getColourName(getViewport()
 129                 .getGlobalColourScheme());
 130         setDisplayedFeatures(getViewport().getFeaturesDisplayed());
 131         showSeqFeatures = getViewport().isShowSequenceFeatures();
 132         fr = getViewport().getFeatureRenderer();
 133       }
 134
 135       int count = 0;
 136       for (SequenceI seq : seqs)
 137       {
 138         StringBuilder name = new StringBuilder();
 139         name.append(seq.getName()).append("/").append(seq.getStart())
 140                 .append("-").append(seq.getEnd());
 141         SequencePojo jsonSeqPojo = new SequencePojo();
 142         jsonSeqPojo.setId(String.valueOf(seq.hashCode()));
 143         jsonSeqPojo.setOrder(++count);
 144         jsonSeqPojo.setEnd(seq.getEnd());
 145         jsonSeqPojo.setStart(seq.getStart());
 146         jsonSeqPojo.setName(name.toString());
 147         jsonSeqPojo.setSeq(seq.getSequenceAsString());
 148         jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
 149       }
 150
 151       jsonAlignmentPojo.setGlobalColorScheme(globalColorScheme);
 152       jsonAlignmentPojo.getAppSettings().put("application", application);
 153       jsonAlignmentPojo.getAppSettings().put("version", version);
 154       jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
 155       jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
 156               String.valueOf(showSeqFeatures));
 157
 158       String[] hiddenSections = getHiddenSections();
 159       if (hiddenSections != null)
 160       {
 161         if (hiddenSections[0] != null
 162                 && getViewport().getExportSettings()
 163                         .isExportHiddenColumns())
 164         {
 165           jsonAlignmentPojo.getAppSettings().put("hiddenCols",
 166                   String.valueOf(hiddenSections[0]));
 167         }
 168         if (hiddenSections[1] != null
 169                 && getViewport().getExportSettings()
 170                         .isExportHiddenSequences())
 171         {
 172           jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
 173                   String.valueOf(hiddenSections[1]));
 174         }
 175       }
 176
 177       if (getViewport().getExportSettings().isExportAnnotations())
 178       {
 179         jsonAlignmentPojo
 180                 .setAlignAnnotation(annotationToJsonPojo(annotations));
 181       }
 182
 183       if (getViewport().getExportSettings().isExportFeatures())
 184       {
 185         jsonAlignmentPojo
 186                 .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
 187       }
 188
 189       if (getViewport().getExportSettings().isExportGroups()
 190               && seqGroups != null
 191               && seqGroups.size() > 0)
 192       {
 193         for (SequenceGroup seqGrp : seqGroups)
 194         {
 195           SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
 196           seqGrpPojo.setGroupName(seqGrp.getName());
 197           seqGrpPojo.setColourScheme(ColourSchemeProperty
 198                   .getColourName(seqGrp.cs));
 199           seqGrpPojo.setColourText(seqGrp.getColourText());
 200           seqGrpPojo.setDescription(seqGrp.getDescription());
 201           seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
 202           seqGrpPojo.setDisplayText(seqGrp.getDisplayText());
 203           seqGrpPojo.setEndRes(seqGrp.getEndRes());
 204           seqGrpPojo.setStartRes(seqGrp.getStartRes());
 205           seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
 206           for (SequenceI seq : seqGrp.getSequences())
 207           {
 208             seqGrpPojo.getSeqsHash().add(String.valueOf(seq.hashCode()));
 209           }
 210           jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
 211         }
 212       }
 213       org.json.JSONObject generatedJSon = new org.json.JSONObject(
 214               jsonAlignmentPojo);
 215       jsonOutput = generatedJSon.toString();
 216       return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
 217               "xEnd");
 218     } catch (Exception e)
 219     {
 220       e.printStackTrace();
 221     }
 222     return jsonOutput;
 223   }
 224
 225   public String[] getHiddenSections()
 226   {
 227     String[] hiddenSections = new String[2];
 228     if (getViewport() == null)
 229     {
 230       return null;
 231     }
 232
 233     // hidden column business
 234     if (getViewport().hasHiddenColumns())
 235     {
 236       List<int[]> hiddenCols = getViewport().getColumnSelection()
 237               .getHiddenColumns();
 238       StringBuilder hiddenColsBuilder = new StringBuilder();
 239       for (int[] range : hiddenCols)
 240       {
 241         hiddenColsBuilder.append(";").append(range[0]).append("-")
 242                 .append(range[1]);
 243       }
 244
 245       hiddenColsBuilder.deleteCharAt(0);
 246       hiddenSections[0] = hiddenColsBuilder.toString();
 247     }
 248
 249     // hidden rows/seqs business
 250     HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
 251             .getHiddenSequences();
 252     if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
 253     {
 254       return hiddenSections;
 255     }
 256
 257     SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
 258     StringBuilder hiddenSeqsBuilder = new StringBuilder();
 259     for (SequenceI hiddenSeq : hiddenSeqs)
 260     {
 261       if (hiddenSeq != null)
 262       {
 263         hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
 264       }
 265     }
 266     if (hiddenSeqsBuilder.length() > 0)
 267     {
 268       hiddenSeqsBuilder.deleteCharAt(0);
 269     }
 270     hiddenSections[1] = hiddenSeqsBuilder.toString();
 271
 272     return hiddenSections;
 273   }
 274
 275   public static List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
 276           List<SequenceI> seqs, FeatureRenderer fr)
 277   {
 278     FeaturesDisplayedI displayedFeatures = (fr == null) ? null : fr
 279             .getFeaturesDisplayed();
 280     List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
 281     for (SequenceI seq : seqs)
 282     {
 283       SequenceI dataSetSequence = seq.getDatasetSequence();
 284       SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
 285               : seq.getDatasetSequence().getSequenceFeatures();
 286
 287       seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
 288               : seqFeatures;
 289       if (seqFeatures == null)
 290       {
 291         continue;
 292       }
 293
 294       for (SequenceFeature sf : seqFeatures)
 295       {
 296         if (displayedFeatures != null
 297                 && displayedFeatures.isVisible(sf.getType()))
 298         {
 299           SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
 300                   String.valueOf(seq.hashCode()));
 301           String featureColour = (fr == null) ? null : jalview.util.Format
 302                   .getHexString(fr
 303                   .findFeatureColour(Color.white, seq,
 304                           seq.findIndex(sf.getBegin())));
 305           jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
 306           jsonFeature.setXend(seq.findIndex(sf.getEnd()));
 307           jsonFeature.setType(sf.getType());
 308           jsonFeature.setDescription(sf.getDescription());
 309           jsonFeature.setLinks(sf.links);
 310           jsonFeature.setOtherDetails(sf.otherDetails);
 311           jsonFeature.setScore(sf.getScore());
 312           jsonFeature.setFillColor(featureColour);
 313           jsonFeature.setFeatureGroup(sf.getFeatureGroup());
 314           sequenceFeaturesPojo.add(jsonFeature);
 315         }
 316       }
 317     }
 318     return sequenceFeaturesPojo;
 319   }
 320
 321   public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
 322           Vector<AlignmentAnnotation> annotations)
 323   {
 324     List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
 325     if (annotations == null)
 326     {
 327       return jsonAnnotations;
 328     }
 329     for (AlignmentAnnotation annot : annotations)
 330     {
 331       AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
 332       alignAnnotPojo.setDescription(annot.description);
 333       alignAnnotPojo.setLabel(annot.label);
 334       for (Annotation annotation : annot.annotations)
 335       {
 336         AnnotationPojo annotationPojo = new AnnotationPojo();
 337         if (annotation != null)
 338         {
 339           annotationPojo.setDescription(annotation.description);
 340           annotationPojo.setValue(annotation.value);
 341           annotationPojo
 342                   .setSecondaryStructure(annotation.secondaryStructure);
 343           annotationPojo.setDisplayCharacter(annotation.displayCharacter);
 344           alignAnnotPojo.getAnnotations().add(annotationPojo);
 345         }
 346         else
 347         {
 348           alignAnnotPojo.getAnnotations().add(annotationPojo);
 349         }
 350       }
 351       jsonAnnotations.add(alignAnnotPojo);
 352     }
 353     return jsonAnnotations;
 354   }
 355
 356   @SuppressWarnings("unchecked")
 357   public JSONFile parse(String jsonAlignmentString)
 358   {
 359     try
 360     {
 361       JSONParser jsonParser = new JSONParser();
 362       JSONObject alignmentJsonObj = (JSONObject) jsonParser
 363               .parse(jsonAlignmentString);
 364       JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
 365       JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
 366               .get("alignAnnotation");
 367       JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
 368               .get("seqFeatures");
 369       JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
 370               .get("seqGroups");
 371       JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
 372               .get("appSettings");
 373
 374       if (jvSettingsJsonObj != null)
 375       {
 376         String jsColourScheme = (String) jvSettingsJsonObj
 377                 .get("globalColorScheme");
 378         Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
 379                 "showSeqFeatures").toString());
 380         setColourScheme(getJalviewColorScheme(jsColourScheme));
 381         setShowSeqFeatures(showFeatures);
 382         parseHiddenSeqRefsAsList(jvSettingsJsonObj);
 383         parseHiddenCols(jvSettingsJsonObj);
 384       }
 385
 386       hiddenSequences = new ArrayList<SequenceI>();
 387       seqMap = new Hashtable<String, Sequence>();
 388       for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
 389               .hasNext();)
 390       {
 391         JSONObject sequence = sequenceIter.next();
 392         String sequcenceString = sequence.get("seq").toString();
 393         String sequenceName = sequence.get("name").toString();
 394         String seqUniqueId = sequence.get("id").toString();
 395         int start = Integer.valueOf(sequence.get("start").toString());
 396         int end = Integer.valueOf(sequence.get("end").toString());
 397         Sequence seq = new Sequence(sequenceName, sequcenceString, start,
 398                 end);
 399         if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
 400         {
 401           hiddenSequences.add(seq);
 402         }
 403         seqs.add(seq);
 404         seqMap.put(seqUniqueId, seq);
 405       }
 406       parseFeatures(jsonSeqArray);
 407
 408       for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
 409               .hasNext();)
 410       {
 411         JSONObject seqGrpObj = seqGrpIter.next();
 412         String grpName = seqGrpObj.get("groupName").toString();
 413         String colourScheme = seqGrpObj.get("colourScheme").toString();
 414         String description = (seqGrpObj.get("description") == null) ? null
 415                 : seqGrpObj.get("description").toString();
 416         boolean displayBoxes = Boolean.valueOf(seqGrpObj
 417                 .get("displayBoxes").toString());
 418         boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
 419                 .toString());
 420         boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
 421                 .toString());
 422         boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
 423                 "showNonconserved").toString());
 424         int startRes = Integer
 425                 .valueOf(seqGrpObj.get("startRes").toString());
 426         int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
 427         JSONArray seqsHashArray = (JSONArray) seqGrpObj.get("seqsHash");
 428
 429         ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
 430         if (seqsHashArray.size() > 0)
 431         {
 432           Iterator<String> seqHashIter = seqsHashArray.iterator();
 433           while (seqHashIter.hasNext())
 434           {
 435             String seqHash = seqHashIter.next();
 436             Sequence sequence = seqMap.get(seqHash);
 437             if (sequence != null)
 438             {
 439               grpSeqs.add(sequence);
 440             }
 441           }
 442         }
 443         ColourSchemeI scheme = getJalviewColorScheme(colourScheme);
 444         SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, scheme,
 445                 displayBoxes, displayText, colourText, startRes, endRes);
 446         seqGrp.setShowNonconserved(showNonconserved);
 447         seqGrp.setDescription(description);
 448         this.seqGroups.add(seqGrp);
 449
 450       }
 451
 452       for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
 453               .hasNext();)
 454       {
 455         JSONObject alAnnot = alAnnotIter.next();
 456         JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
 457         Annotation[] annotations = new Annotation[annotJsonArray.size()];
 458         int count = 0;
 459         for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
 460                 .hasNext();)
 461         {
 462           JSONObject annot = annotIter.next();
 463           if (annot == null)
 464           {
 465             annotations[count] = null;
 466           }
 467           else
 468           {
 469             float val = annot.get("value") == null ? null : Float
 470                     .valueOf(annot.get("value").toString());
 471             String desc = annot.get("description") == null ? null : annot
 472                     .get("description").toString();
 473
 474             char ss = annot.get("secondaryStructure") == null ? ' '
 475                     : annot.get("secondaryStructure").toString().charAt(0);
 476             String displayChar = annot.get("displayCharacter").toString();
 477
 478             annotations[count] = new Annotation(displayChar, desc, ss, val);
 479           }
 480           ++count;
 481         }
 482
 483         AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
 484                 .get("label").toString(), alAnnot.get("description")
 485                 .toString(), annotations);
 486         this.annotations.add(alignAnnot);
 487       }
 488
 489     } catch (Exception e)
 490     {
 491       e.printStackTrace();
 492     }
 493     return this;
 494   }
 495
 496   public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
 497   {
 498     hiddenSeqRefs = new ArrayList<String>();
 499     String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
 500     if(hiddenSeqs != null && !hiddenSeqs.isEmpty()){
 501       String[] seqRefs = hiddenSeqs.split(";");
 502       for(String seqRef : seqRefs){
 503         hiddenSeqRefs.add(seqRef);
 504       }
 505     }
 506   }
 507
 508   public void parseHiddenCols(JSONObject jvSettingsJson)
 509   {
 510     String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
 511     if(hiddenCols != null && !hiddenCols.isEmpty()){
 512       columnSelection = new ColumnSelection();
 513       String[] rangeStrings = hiddenCols.split(";");
 514       for(String rangeString : rangeStrings){
 515         String[] range = rangeString.split("-");
 516         columnSelection.hideColumns(Integer.valueOf(range[0]),
 517                 Integer.valueOf(range[1]));
 518       }
 519     }
 520   }
 521
 522   @SuppressWarnings("unchecked")
 523   private void parseFeatures(JSONArray jsonSeqFeatures)
 524   {
 525     if (jsonSeqFeatures != null)
 526     {
 527       for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
 528               .hasNext();)
 529       {
 530         JSONObject jsonFeature = seqFeatureItr.next();
 531         Long begin = (Long) jsonFeature.get("xStart");
 532         Long end = (Long) jsonFeature.get("xEnd");
 533         String type = (String) jsonFeature.get("type");
 534         String featureGrp = (String) jsonFeature.get("featureGroup");
 535         String descripiton = (String) jsonFeature.get("description");
 536         String seqRef = (String) jsonFeature.get("sequenceRef");
 537         Float score = Float.valueOf(jsonFeature.get("score").toString());
 538
 539         Sequence seq = seqMap.get(seqRef);
 540         SequenceFeature sequenceFeature = new SequenceFeature();
 541         JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
 542         if (linksJsonArray != null && linksJsonArray.size() > 0)
 543         {
 544           Iterator<String> linkList = linksJsonArray.iterator();
 545           while (linkList.hasNext())
 546           {
 547             String link = linkList.next();
 548             sequenceFeature.addLink(link);
 549           }
 550         }
 551         sequenceFeature.setFeatureGroup(featureGrp);
 552         sequenceFeature.setScore(score);
 553         sequenceFeature.setDescription(descripiton);
 554         sequenceFeature.setType(type);
 555         sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
 556         sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
 557         seq.addSequenceFeature(sequenceFeature);
 558       }
 559     }
 560   }
 561
 562   public static ColourSchemeI getJalviewColorScheme(
 563           String bioJsColourSchemeName)
 564   {
 565     ColourSchemeI jalviewColor = null;
 566     for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
 567             .values())
 568     {
 569       if (cs.getBioJsName().equalsIgnoreCase(bioJsColourSchemeName))
 570       {
 571         jalviewColor = cs.getJvColourScheme();
 572         break;
 573       }
 574     }
 575     return jalviewColor;
 576   }
 577
 578   public String getGlobalColorScheme()
 579   {
 580     return globalColorScheme;
 581   }
 582
 583   public void setGlobalColorScheme(String globalColorScheme)
 584   {
 585     this.globalColorScheme = globalColorScheme;
 586   }
 587
 588   public ColourSchemeI getColourScheme()
 589   {
 590     return colourScheme;
 591   }
 592
 593   public void setColourScheme(ColourSchemeI colourScheme)
 594   {
 595     this.colourScheme = colourScheme;
 596   }
 597
 598   public FeaturesDisplayedI getDisplayedFeatures()
 599   {
 600     return displayedFeatures;
 601   }
 602
 603   public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
 604   {
 605     this.displayedFeatures = displayedFeatures;
 606   }
 607
 608
 609   public static String getJSONData(AlignViewportI av)
 610   {
 611     JSONFile jsonFile = new JSONFile();
 612     jsonFile.setViewport(av);
 613     jsonFile.seqGroups = av.getAlignment().getGroups();
 614     jsonFile.setDisplayedFeatures(av.getFeaturesDisplayed());
 615
 616     for (SequenceI seq : av.getAlignment().getSequences())
 617     {
 618       jsonFile.seqs.add(seq);
 619     }
 620
 621     // Add non auto calculated annotation to AlignFile
 622     for (AlignmentAnnotation annot : av.getAlignment()
 623             .getAlignmentAnnotation())
 624     {
 625       if (annot != null && !annot.autoCalculated)
 626       {
 627         if (annot.label.equals("PDB.CATempFactor"))
 628         {
 629           continue;
 630         }
 631         jsonFile.annotations.add(annot);
 632       }
 633     }
 634     String jsonString = jsonFile.print();
 635     return jsonString;
 636   }
 637
 638   public boolean isShowSeqFeatures()
 639   {
 640     return showSeqFeatures;
 641   }
 642
 643   public void setShowSeqFeatures(boolean showSeqFeatures)
 644   {
 645     this.showSeqFeatures = showSeqFeatures;
 646   }
 647
 648   public Vector<AlignmentAnnotation> getAnnotations()
 649   {
 650     return annotations;
 651   }
 652
 653   public List<int[]> getHiddenColumns()
 654   {
 655     return hiddenColumns;
 656   }
 657
 658   public ColumnSelection getColumnSelection()
 659   {
 660     return columnSelection;
 661   }
 662
 663   public void setColumnSelection(ColumnSelection columnSelection)
 664   {
 665     this.columnSelection = columnSelection;
 666   }
 667
 668   public SequenceI[] getHiddenSequences()
 669   {
 670     if (hiddenSequences == null || hiddenSequences.isEmpty())
 671     {
 672       return new SequenceI[]
 673       {};
 674     }
 675     synchronized (hiddenSequences)
 676     {
 677       return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
 678     }
 679   }
 680
 681   public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
 682   {
 683     this.hiddenSequences = hiddenSequences;
 684   }
 685
 686   public class JSONExportSettings
 687   {
 688     private boolean exportSequence;
 689
 690     private boolean exportSequenceFeatures;
 691
 692     private boolean exportAnnotations;
 693
 694     private boolean exportGroups;
 695
 696     private boolean exportJalviewSettings;
 697
 698     public boolean isExportSequence()
 699     {
 700       return exportSequence;
 701     }
 702
 703     public void setExportSequence(boolean exportSequence)
 704     {
 705       this.exportSequence = exportSequence;
 706     }
 707
 708     public boolean isExportSequenceFeatures()
 709     {
 710       return exportSequenceFeatures;
 711     }
 712
 713     public void setExportSequenceFeatures(boolean exportSequenceFeatures)
 714     {
 715       this.exportSequenceFeatures = exportSequenceFeatures;
 716     }
 717
 718     public boolean isExportAnnotations()
 719     {
 720       return exportAnnotations;
 721     }
 722
 723     public void setExportAnnotations(boolean exportAnnotations)
 724     {
 725       this.exportAnnotations = exportAnnotations;
 726     }
 727
 728     public boolean isExportGroups()
 729     {
 730       return exportGroups;
 731     }
 732
 733     public void setExportGroups(boolean exportGroups)
 734     {
 735       this.exportGroups = exportGroups;
 736     }
 737
 738     public boolean isExportJalviewSettings()
 739     {
 740       return exportJalviewSettings;
 741     }
 742
 743     public void setExportJalviewSettings(boolean exportJalviewSettings)
 744     {
 745       this.exportJalviewSettings = exportJalviewSettings;
 746     }
 747   }
 748 }