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.AlignExportSettingI;
  25 import jalview.api.AlignViewportI;
  26 import jalview.api.AlignmentViewPanel;
  27 import jalview.api.ComplexAlignFile;
  28 import jalview.api.FeatureRenderer;
  29 import jalview.api.FeaturesDisplayedI;
  30 import jalview.bin.BuildDetails;
  31 import jalview.datamodel.AlignmentAnnotation;
  32 import jalview.datamodel.AlignmentI;
  33 import jalview.datamodel.Annotation;
  34 import jalview.datamodel.ColumnSelection;
  35 import jalview.datamodel.HiddenSequences;
  36 import jalview.datamodel.Sequence;
  37 import jalview.datamodel.SequenceFeature;
  38 import jalview.datamodel.SequenceGroup;
  39 import jalview.datamodel.SequenceI;
  40 import jalview.json.binding.biojson.v1.AlignmentAnnotationPojo;
  41 import jalview.json.binding.biojson.v1.AlignmentPojo;
  42 import jalview.json.binding.biojson.v1.AnnotationPojo;
  43 import jalview.json.binding.biojson.v1.ColourSchemeMapper;
  44 import jalview.json.binding.biojson.v1.SequenceFeaturesPojo;
  45 import jalview.json.binding.biojson.v1.SequenceGrpPojo;
  46 import jalview.json.binding.biojson.v1.SequencePojo;
  47 import jalview.schemes.ColourSchemeProperty;
  48 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
  49
  50 import java.awt.Color;
  51 import java.io.IOException;
  52 import java.io.Reader;
  53 import java.util.ArrayList;
  54 import java.util.Hashtable;
  55 import java.util.Iterator;
  56 import java.util.List;
  57 import java.util.Vector;
  58
  59 import org.json.simple.JSONArray;
  60 import org.json.simple.JSONObject;
  61 import org.json.simple.parser.JSONParser;
  62
  63 public class JSONFile extends AlignFile implements ComplexAlignFile
  64 {
  65   private static String version = new BuildDetails().getVersion();
  66
  67   private String webstartUrl = "http://www.jalview.org/services/launchApp";
  68
  69   private String application = "Jalview";
  70
  71   public static final String FILE_EXT = "json";
  72
  73   public static final String FILE_DESC = "JSON";
  74
  75   private String globalColourScheme;
  76
  77   private boolean showSeqFeatures;
  78
  79   private Hashtable<String, Sequence> seqMap;
  80
  81   private FeaturesDisplayedI displayedFeatures;
  82
  83   private FeatureRenderer fr;
  84
  85   private List<int[]> hiddenColumns;
  86
  87   private ColumnSelection columnSelection;
  88
  89   private List<String> hiddenSeqRefs;
  90
  91   private ArrayList<SequenceI> hiddenSequences;
  92
  93   public JSONFile()
  94   {
  95     super();
  96   }
  97
  98   public JSONFile(FileParse source) throws IOException
  99   {
 100     super(source);
 101   }
 102
 103   public JSONFile(String inFile, String type) throws IOException
 104   {
 105     super(inFile, type);
 106   }
 107
 108   @Override
 109   public void parse() throws IOException
 110   {
 111     parse(getReader());
 112
 113   }
 114
 115   @Override
 116   public String print()
 117   {
 118     String jsonOutput = null;
 119     try
 120     {
 121       AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
 122       AlignExportSettingI exportSettings = getExportSettings();
 123
 124       // if no export settings were supplied use the following with all values
 125       // defaulting to true
 126       if (exportSettings == null)
 127       {
 128         exportSettings = new AlignExportSettingI()
 129         {
 130           @Override
 131           public boolean isExportHiddenSequences()
 132           {
 133             return true;
 134           }
 135
 136           @Override
 137           public boolean isExportHiddenColumns()
 138           {
 139             return true;
 140           }
 141
 142           @Override
 143           public boolean isExportGroups()
 144           {
 145             return true;
 146           }
 147
 148           @Override
 149           public boolean isExportFeatures()
 150           {
 151             return true;
 152           }
 153
 154           @Override
 155           public boolean isExportAnnotations()
 156           {
 157             return true;
 158           }
 159
 160           @Override
 161           public boolean isCancelled()
 162           {
 163             return false;
 164           }
 165         };
 166       }
 167
 168       int count = 0;
 169       for (SequenceI seq : seqs)
 170       {
 171         StringBuilder name = new StringBuilder();
 172         name.append(seq.getName()).append("/").append(seq.getStart())
 173                 .append("-").append(seq.getEnd());
 174         SequencePojo jsonSeqPojo = new SequencePojo();
 175         jsonSeqPojo.setId(String.valueOf(seq.hashCode()));
 176         jsonSeqPojo.setOrder(++count);
 177         jsonSeqPojo.setEnd(seq.getEnd());
 178         jsonSeqPojo.setStart(seq.getStart());
 179         jsonSeqPojo.setName(name.toString());
 180         jsonSeqPojo.setSeq(seq.getSequenceAsString());
 181         jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
 182       }
 183       jsonAlignmentPojo.setGlobalColorScheme(globalColourScheme);
 184       jsonAlignmentPojo.getAppSettings().put("application", application);
 185       jsonAlignmentPojo.getAppSettings().put("version", version);
 186       jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
 187       jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
 188               String.valueOf(showSeqFeatures));
 189
 190       String[] hiddenSections = getHiddenSections();
 191       if (hiddenSections != null)
 192       {
 193         if (hiddenSections[0] != null
 194                 && exportSettings.isExportHiddenColumns())
 195         {
 196           jsonAlignmentPojo.getAppSettings().put("hiddenCols",
 197                   String.valueOf(hiddenSections[0]));
 198         }
 199         if (hiddenSections[1] != null
 200                 && exportSettings.isExportHiddenSequences())
 201         {
 202           jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
 203                   String.valueOf(hiddenSections[1]));
 204         }
 205       }
 206
 207       if (exportSettings.isExportAnnotations())
 208       {
 209         jsonAlignmentPojo
 210                 .setAlignAnnotation(annotationToJsonPojo(annotations));
 211       }
 212       else
 213       {
 214         if (globalColourScheme.equalsIgnoreCase("RNA Helices"))
 215         {
 216           jsonAlignmentPojo.setGlobalColorScheme("None");
 217         }
 218       }
 219
 220       if (exportSettings.isExportFeatures())
 221       {
 222         jsonAlignmentPojo
 223                 .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
 224       }
 225
 226       if (exportSettings.isExportGroups() && seqGroups != null
 227               && seqGroups.size() > 0)
 228       {
 229         for (SequenceGroup seqGrp : seqGroups)
 230         {
 231           SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
 232           seqGrpPojo.setGroupName(seqGrp.getName());
 233           seqGrpPojo.setColourScheme(ColourSchemeProperty
 234                   .getColourName(seqGrp.cs));
 235           seqGrpPojo.setColourText(seqGrp.getColourText());
 236           seqGrpPojo.setDescription(seqGrp.getDescription());
 237           seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
 238           seqGrpPojo.setDisplayText(seqGrp.getDisplayText());
 239           seqGrpPojo.setEndRes(seqGrp.getEndRes());
 240           seqGrpPojo.setStartRes(seqGrp.getStartRes());
 241           seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
 242           for (SequenceI seq : seqGrp.getSequences())
 243           {
 244             seqGrpPojo.getSequenceRefs()
 245                     .add(String.valueOf(seq.hashCode()));
 246           }
 247           jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
 248         }
 249       }
 250       org.json.JSONObject generatedJSon = new org.json.JSONObject(
 251               jsonAlignmentPojo);
 252       jsonOutput = generatedJSon.toString();
 253       return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
 254               "xEnd");
 255     } catch (Exception e)
 256     {
 257       e.printStackTrace();
 258     }
 259     return jsonOutput;
 260   }
 261
 262   public String[] getHiddenSections()
 263   {
 264     String[] hiddenSections = new String[2];
 265     if (getViewport() == null)
 266     {
 267       return null;
 268     }
 269
 270     // hidden column business
 271     if (getViewport().hasHiddenColumns())
 272     {
 273       List<int[]> hiddenCols = getViewport().getColumnSelection()
 274               .getHiddenColumns();
 275       StringBuilder hiddenColsBuilder = new StringBuilder();
 276       for (int[] range : hiddenCols)
 277       {
 278         hiddenColsBuilder.append(";").append(range[0]).append("-")
 279                 .append(range[1]);
 280       }
 281
 282       hiddenColsBuilder.deleteCharAt(0);
 283       hiddenSections[0] = hiddenColsBuilder.toString();
 284     }
 285
 286     // hidden rows/seqs business
 287     HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
 288             .getHiddenSequences();
 289     if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
 290     {
 291       return hiddenSections;
 292     }
 293
 294     SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
 295     StringBuilder hiddenSeqsBuilder = new StringBuilder();
 296     for (SequenceI hiddenSeq : hiddenSeqs)
 297     {
 298       if (hiddenSeq != null)
 299       {
 300         hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
 301       }
 302     }
 303     if (hiddenSeqsBuilder.length() > 0)
 304     {
 305       hiddenSeqsBuilder.deleteCharAt(0);
 306     }
 307     hiddenSections[1] = hiddenSeqsBuilder.toString();
 308
 309     return hiddenSections;
 310   }
 311
 312   public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
 313           List<SequenceI> seqs, FeatureRenderer fr)
 314   {
 315     displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
 316     List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
 317     for (SequenceI seq : seqs)
 318     {
 319       SequenceI dataSetSequence = seq.getDatasetSequence();
 320       SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
 321               : seq.getDatasetSequence().getSequenceFeatures();
 322
 323       seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
 324               : seqFeatures;
 325       if (seqFeatures == null)
 326       {
 327         continue;
 328       }
 329
 330       for (SequenceFeature sf : seqFeatures)
 331       {
 332         if (displayedFeatures != null
 333                 && displayedFeatures.isVisible(sf.getType()))
 334         {
 335           SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
 336                   String.valueOf(seq.hashCode()));
 337
 338           String featureColour = (fr == null) ? null : jalview.util.Format
 339                   .getHexString(fr.findFeatureColour(Color.white, seq,
 340                           seq.findIndex(sf.getBegin())));
 341           jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
 342           jsonFeature.setXend(seq.findIndex(sf.getEnd()));
 343           jsonFeature.setType(sf.getType());
 344           jsonFeature.setDescription(sf.getDescription());
 345           jsonFeature.setLinks(sf.links);
 346           jsonFeature.setOtherDetails(sf.otherDetails);
 347           jsonFeature.setScore(sf.getScore());
 348           jsonFeature.setFillColor(featureColour);
 349           jsonFeature.setFeatureGroup(sf.getFeatureGroup());
 350           sequenceFeaturesPojo.add(jsonFeature);
 351         }
 352       }
 353     }
 354     return sequenceFeaturesPojo;
 355   }
 356
 357   public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
 358           Vector<AlignmentAnnotation> annotations)
 359   {
 360     List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
 361     if (annotations == null)
 362     {
 363       return jsonAnnotations;
 364     }
 365     for (AlignmentAnnotation annot : annotations)
 366     {
 367       AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
 368       alignAnnotPojo.setDescription(annot.description);
 369       alignAnnotPojo.setLabel(annot.label);
 370       for (Annotation annotation : annot.annotations)
 371       {
 372         AnnotationPojo annotationPojo = new AnnotationPojo();
 373         if (annotation != null)
 374         {
 375           annotationPojo.setDescription(annotation.description);
 376           annotationPojo.setValue(annotation.value);
 377           annotationPojo
 378                   .setSecondaryStructure(annotation.secondaryStructure);
 379           annotationPojo.setDisplayCharacter(annotation.displayCharacter);
 380           alignAnnotPojo.getAnnotations().add(annotationPojo);
 381         }
 382         else
 383         {
 384           alignAnnotPojo.getAnnotations().add(annotationPojo);
 385         }
 386       }
 387       jsonAnnotations.add(alignAnnotPojo);
 388     }
 389     return jsonAnnotations;
 390   }
 391
 392   @SuppressWarnings("unchecked")
 393   public JSONFile parse(Reader jsonAlignmentString)
 394   {
 395     try
 396     {
 397       JSONParser jsonParser = new JSONParser();
 398       JSONObject alignmentJsonObj = (JSONObject) jsonParser
 399               .parse(jsonAlignmentString);
 400       JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
 401       JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
 402               .get("alignAnnotation");
 403       JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
 404               .get("seqFeatures");
 405       JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
 406               .get("seqGroups");
 407       JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
 408               .get("appSettings");
 409
 410       if (jvSettingsJsonObj != null)
 411       {
 412         globalColourScheme = (String) jvSettingsJsonObj
 413                 .get("globalColorScheme");
 414         Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
 415                 "showSeqFeatures").toString());
 416         setShowSeqFeatures(showFeatures);
 417         parseHiddenSeqRefsAsList(jvSettingsJsonObj);
 418         parseHiddenCols(jvSettingsJsonObj);
 419       }
 420
 421       hiddenSequences = new ArrayList<SequenceI>();
 422       seqMap = new Hashtable<String, Sequence>();
 423       for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
 424               .hasNext();)
 425       {
 426         JSONObject sequence = sequenceIter.next();
 427         String sequcenceString = sequence.get("seq").toString();
 428         String sequenceName = sequence.get("name").toString();
 429         String seqUniqueId = sequence.get("id").toString();
 430         int start = Integer.valueOf(sequence.get("start").toString());
 431         int end = Integer.valueOf(sequence.get("end").toString());
 432         Sequence seq = new Sequence(sequenceName, sequcenceString, start,
 433                 end);
 434         if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
 435         {
 436           hiddenSequences.add(seq);
 437         }
 438         seqs.add(seq);
 439         seqMap.put(seqUniqueId, seq);
 440       }
 441
 442       parseFeatures(jsonSeqArray);
 443
 444       for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
 445               .hasNext();)
 446       {
 447         JSONObject seqGrpObj = seqGrpIter.next();
 448         String grpName = seqGrpObj.get("groupName").toString();
 449         String colourScheme = seqGrpObj.get("colourScheme").toString();
 450         String description = (seqGrpObj.get("description") == null) ? null
 451                 : seqGrpObj.get("description").toString();
 452         boolean displayBoxes = Boolean.valueOf(seqGrpObj
 453                 .get("displayBoxes").toString());
 454         boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
 455                 .toString());
 456         boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
 457                 .toString());
 458         boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
 459                 "showNonconserved").toString());
 460         int startRes = Integer
 461                 .valueOf(seqGrpObj.get("startRes").toString());
 462         int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
 463         JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
 464
 465         ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
 466         if (sequenceRefs.size() > 0)
 467         {
 468           Iterator<String> seqHashIter = sequenceRefs.iterator();
 469           while (seqHashIter.hasNext())
 470           {
 471             String seqHash = seqHashIter.next();
 472             Sequence sequence = seqMap.get(seqHash);
 473             if (sequence != null)
 474             {
 475               grpSeqs.add(sequence);
 476             }
 477           }
 478         }
 479         SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
 480                 displayBoxes, displayText, colourText, startRes, endRes);
 481         seqGrp.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme,
 482                 seqGrp);
 483         seqGrp.setShowNonconserved(showNonconserved);
 484         seqGrp.setDescription(description);
 485         this.seqGroups.add(seqGrp);
 486
 487       }
 488
 489       for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
 490               .hasNext();)
 491       {
 492         JSONObject alAnnot = alAnnotIter.next();
 493         JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
 494         Annotation[] annotations = new Annotation[annotJsonArray.size()];
 495         int count = 0;
 496         for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
 497                 .hasNext();)
 498         {
 499           JSONObject annot = annotIter.next();
 500           if (annot == null)
 501           {
 502             annotations[count] = null;
 503           }
 504           else
 505           {
 506             float val = annot.get("value") == null ? null : Float
 507                     .valueOf(annot.get("value").toString());
 508             String desc = annot.get("description") == null ? null : annot
 509                     .get("description").toString();
 510             char ss = annot.get("secondaryStructure") == null
 511                     || annot.get("secondaryStructure").toString()
 512                             .equalsIgnoreCase("u0000") ? ' ' : annot
 513                     .get("secondaryStructure").toString().charAt(0);
 514             String displayChar = annot.get("displayCharacter") == null ? ""
 515                     : annot.get("displayCharacter").toString();
 516
 517             annotations[count] = new Annotation(displayChar, desc, ss, val);
 518           }
 519           ++count;
 520         }
 521
 522         AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
 523                 .get("label").toString(), alAnnot.get("description")
 524                 .toString(), annotations);
 525         this.annotations.add(alignAnnot);
 526       }
 527     } catch (Exception e)
 528     {
 529       e.printStackTrace();
 530     }
 531     return this;
 532   }
 533
 534   public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
 535   {
 536     hiddenSeqRefs = new ArrayList<String>();
 537     String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
 538     if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
 539     {
 540       String[] seqRefs = hiddenSeqs.split(";");
 541       for (String seqRef : seqRefs)
 542       {
 543         hiddenSeqRefs.add(seqRef);
 544       }
 545     }
 546   }
 547
 548   public void parseHiddenCols(JSONObject jvSettingsJson)
 549   {
 550     String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
 551     if (hiddenCols != null && !hiddenCols.isEmpty())
 552     {
 553       columnSelection = new ColumnSelection();
 554       String[] rangeStrings = hiddenCols.split(";");
 555       for (String rangeString : rangeStrings)
 556       {
 557         String[] range = rangeString.split("-");
 558         columnSelection.hideColumns(Integer.valueOf(range[0]),
 559                 Integer.valueOf(range[1]));
 560       }
 561     }
 562   }
 563
 564   @SuppressWarnings("unchecked")
 565   private void parseFeatures(JSONArray jsonSeqFeatures)
 566   {
 567     if (jsonSeqFeatures != null)
 568     {
 569       displayedFeatures = new FeaturesDisplayed();
 570       for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
 571               .hasNext();)
 572       {
 573         JSONObject jsonFeature = seqFeatureItr.next();
 574         Long begin = (Long) jsonFeature.get("xStart");
 575         Long end = (Long) jsonFeature.get("xEnd");
 576         String type = (String) jsonFeature.get("type");
 577         String featureGrp = (String) jsonFeature.get("featureGroup");
 578         String descripiton = (String) jsonFeature.get("description");
 579         String seqRef = (String) jsonFeature.get("sequenceRef");
 580         Float score = Float.valueOf(jsonFeature.get("score").toString());
 581
 582         Sequence seq = seqMap.get(seqRef);
 583         SequenceFeature sequenceFeature = new SequenceFeature();
 584         JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
 585         if (linksJsonArray != null && linksJsonArray.size() > 0)
 586         {
 587           Iterator<String> linkList = linksJsonArray.iterator();
 588           while (linkList.hasNext())
 589           {
 590             String link = linkList.next();
 591             sequenceFeature.addLink(link);
 592           }
 593         }
 594         sequenceFeature.setFeatureGroup(featureGrp);
 595         sequenceFeature.setScore(score);
 596         sequenceFeature.setDescription(descripiton);
 597         sequenceFeature.setType(type);
 598         sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
 599         sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
 600         seq.addSequenceFeature(sequenceFeature);
 601         displayedFeatures.setVisible(type);
 602       }
 603     }
 604   }
 605
 606   public String getGlobalColourScheme()
 607   {
 608     return globalColourScheme;
 609   }
 610
 611   public void setGlobalColorScheme(String globalColourScheme)
 612   {
 613     this.globalColourScheme = globalColourScheme;
 614   }
 615
 616   @Override
 617   public FeaturesDisplayedI getDisplayedFeatures()
 618   {
 619     return displayedFeatures;
 620   }
 621
 622   public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
 623   {
 624     this.displayedFeatures = displayedFeatures;
 625   }
 626
 627   public void configureForView(AlignmentViewPanel avpanel)
 628   {
 629     super.configureForView(avpanel);
 630     AlignViewportI viewport = avpanel.getAlignViewport();
 631     AlignmentI alignment = viewport.getAlignment();
 632     AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
 633
 634     seqGroups = alignment.getGroups();
 635     fr = avpanel.cloneFeatureRenderer();
 636
 637     // Add non auto calculated annotation to AlignFile
 638     for (AlignmentAnnotation annot : annots)
 639     {
 640       if (annot != null && !annot.autoCalculated)
 641       {
 642         if (!annot.visible)
 643         {
 644           continue;
 645         }
 646         annotations.add(annot);
 647       }
 648     }
 649     globalColourScheme = ColourSchemeProperty.getColourName(viewport
 650             .getGlobalColourScheme());
 651     setDisplayedFeatures(viewport.getFeaturesDisplayed());
 652     showSeqFeatures = viewport.isShowSequenceFeatures();
 653
 654   }
 655
 656   public boolean isShowSeqFeatures()
 657   {
 658     return showSeqFeatures;
 659   }
 660
 661   public void setShowSeqFeatures(boolean showSeqFeatures)
 662   {
 663     this.showSeqFeatures = showSeqFeatures;
 664   }
 665
 666   public Vector<AlignmentAnnotation> getAnnotations()
 667   {
 668     return annotations;
 669   }
 670
 671   public List<int[]> getHiddenColumns()
 672   {
 673     return hiddenColumns;
 674   }
 675
 676   public ColumnSelection getColumnSelection()
 677   {
 678     return columnSelection;
 679   }
 680
 681   public void setColumnSelection(ColumnSelection columnSelection)
 682   {
 683     this.columnSelection = columnSelection;
 684   }
 685
 686   public SequenceI[] getHiddenSequences()
 687   {
 688     if (hiddenSequences == null || hiddenSequences.isEmpty())
 689     {
 690       return new SequenceI[] {};
 691     }
 692     synchronized (hiddenSequences)
 693     {
 694       return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
 695     }
 696   }
 697
 698   public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
 699   {
 700     this.hiddenSequences = hiddenSequences;
 701   }
 702
 703   public class JSONExportSettings
 704   {
 705     private boolean exportSequence;
 706
 707     private boolean exportSequenceFeatures;
 708
 709     private boolean exportAnnotations;
 710
 711     private boolean exportGroups;
 712
 713     private boolean exportJalviewSettings;
 714
 715     public boolean isExportSequence()
 716     {
 717       return exportSequence;
 718     }
 719
 720     public void setExportSequence(boolean exportSequence)
 721     {
 722       this.exportSequence = exportSequence;
 723     }
 724
 725     public boolean isExportSequenceFeatures()
 726     {
 727       return exportSequenceFeatures;
 728     }
 729
 730     public void setExportSequenceFeatures(boolean exportSequenceFeatures)
 731     {
 732       this.exportSequenceFeatures = exportSequenceFeatures;
 733     }
 734
 735     public boolean isExportAnnotations()
 736     {
 737       return exportAnnotations;
 738     }
 739
 740     public void setExportAnnotations(boolean exportAnnotations)
 741     {
 742       this.exportAnnotations = exportAnnotations;
 743     }
 744
 745     public boolean isExportGroups()
 746     {
 747       return exportGroups;
 748     }
 749
 750     public void setExportGroups(boolean exportGroups)
 751     {
 752       this.exportGroups = exportGroups;
 753     }
 754
 755     public boolean isExportJalviewSettings()
 756     {
 757       return exportJalviewSettings;
 758     }
 759
 760     public void setExportJalviewSettings(boolean exportJalviewSettings)
 761     {
 762       this.exportJalviewSettings = exportJalviewSettings;
 763     }
 764   }
 765 }