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.v1.AlignmentAnnotationPojo;
  41 import jalview.json.binding.v1.AlignmentPojo;
  42 import jalview.json.binding.v1.AlignmentPojo.JalviewBioJsColorSchemeMapper;
  43 import jalview.json.binding.v1.AnnotationPojo;
  44 import jalview.json.binding.v1.SequenceFeaturesPojo;
  45 import jalview.json.binding.v1.SequenceGrpPojo;
  46 import jalview.json.binding.v1.SequencePojo;
  47 import jalview.schemes.ColourSchemeI;
  48 import jalview.schemes.ColourSchemeProperty;
  49 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
  50
  51 import java.awt.Color;
  52 import java.io.IOException;
  53 import java.io.Reader;
  54 import java.util.ArrayList;
  55 import java.util.Hashtable;
  56 import java.util.Iterator;
  57 import java.util.List;
  58 import java.util.Vector;
  59
  60 import org.json.simple.JSONArray;
  61 import org.json.simple.JSONObject;
  62 import org.json.simple.parser.JSONParser;
  63
  64 public class JSONFile extends AlignFile implements ComplexAlignFile
  65 {
  66   private ColourSchemeI colourScheme;
  67
  68   private static String version = new BuildDetails().getVersion();
  69
  70   private String webstartUrl = "http://www.jalview.org/services/launchApp";
  71
  72   private String application = "Jalview";
  73
  74   public static final String FILE_EXT = "json";
  75
  76   public static final String FILE_DESC = "JSON";
  77
  78   private String globalColorScheme;
  79
  80   private boolean showSeqFeatures;
  81
  82   private Hashtable<String, Sequence> seqMap;
  83
  84   private FeaturesDisplayedI displayedFeatures;
  85
  86   private FeatureRenderer fr;
  87
  88   private List<int[]> hiddenColumns;
  89
  90   private ColumnSelection columnSelection;
  91
  92   private List<String> hiddenSeqRefs;
  93
  94   private ArrayList<SequenceI> hiddenSequences;
  95
  96
  97   public JSONFile()
  98   {
  99     super();
 100   }
 101
 102   public JSONFile(FileParse source) throws IOException
 103   {
 104     super(source);
 105   }
 106
 107   public JSONFile(String inFile, String type) throws IOException
 108   {
 109     super(inFile, type);
 110   }
 111
 112   @Override
 113   public void parse() throws IOException
 114   {
 115     parse(getReader());
 116
 117   }
 118   @Override
 119   public String print()
 120   {
 121     String jsonOutput = null;
 122     try
 123     {
 124       AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
 125       AlignExportSettingI exportSettings = getExportSettings();
 126
 127       // if no export settings were supplied use the following with all values
 128       // defaulting to true
 129       if (exportSettings == null)
 130       {
 131         exportSettings = new AlignExportSettingI()
 132         {
 133           @Override
 134           public boolean isExportHiddenSequences()
 135           {
 136             return true;
 137           }
 138
 139           @Override
 140           public boolean isExportHiddenColumns()
 141           {
 142             return true;
 143           }
 144
 145           @Override
 146           public boolean isExportGroups()
 147           {
 148             return true;
 149           }
 150
 151           @Override
 152           public boolean isExportFeatures()
 153           {
 154             return true;
 155           }
 156
 157           @Override
 158           public boolean isExportAnnotations()
 159           {
 160             return true;
 161           }
 162         };
 163       }
 164
 165       int count = 0;
 166       for (SequenceI seq : seqs)
 167       {
 168         StringBuilder name = new StringBuilder();
 169         name.append(seq.getName()).append("/").append(seq.getStart())
 170                 .append("-").append(seq.getEnd());
 171         SequencePojo jsonSeqPojo = new SequencePojo();
 172         jsonSeqPojo.setId(String.valueOf(seq.hashCode()));
 173         jsonSeqPojo.setOrder(++count);
 174         jsonSeqPojo.setEnd(seq.getEnd());
 175         jsonSeqPojo.setStart(seq.getStart());
 176         jsonSeqPojo.setName(name.toString());
 177         jsonSeqPojo.setSeq(seq.getSequenceAsString());
 178         jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
 179       }
 180       jsonAlignmentPojo.setGlobalColorScheme(globalColorScheme);
 181       jsonAlignmentPojo.getAppSettings().put("application", application);
 182       jsonAlignmentPojo.getAppSettings().put("version", version);
 183       jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
 184       jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
 185               String.valueOf(showSeqFeatures));
 186
 187       String[] hiddenSections = getHiddenSections();
 188       if (hiddenSections != null)
 189       {
 190         if (hiddenSections[0] != null
 191                 && exportSettings
 192                         .isExportHiddenColumns())
 193         {
 194           jsonAlignmentPojo.getAppSettings().put("hiddenCols",
 195                   String.valueOf(hiddenSections[0]));
 196         }
 197         if (hiddenSections[1] != null
 198                 && exportSettings
 199                         .isExportHiddenSequences())
 200         {
 201           jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
 202                   String.valueOf(hiddenSections[1]));
 203         }
 204       }
 205
 206       if (exportSettings.isExportAnnotations())
 207       {
 208         jsonAlignmentPojo
 209                 .setAlignAnnotation(annotationToJsonPojo(annotations));
 210       }
 211
 212       if (exportSettings.isExportFeatures())
 213       {
 214         jsonAlignmentPojo
 215                 .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
 216       }
 217
 218       if (exportSettings.isExportGroups()
 219               && seqGroups != null
 220               && seqGroups.size() > 0)
 221       {
 222         for (SequenceGroup seqGrp : seqGroups)
 223         {
 224           SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
 225           seqGrpPojo.setGroupName(seqGrp.getName());
 226           seqGrpPojo.setColourScheme(ColourSchemeProperty
 227                   .getColourName(seqGrp.cs));
 228           seqGrpPojo.setColourText(seqGrp.getColourText());
 229           seqGrpPojo.setDescription(seqGrp.getDescription());
 230           seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
 231           seqGrpPojo.setDisplayText(seqGrp.getDisplayText());
 232           seqGrpPojo.setEndRes(seqGrp.getEndRes());
 233           seqGrpPojo.setStartRes(seqGrp.getStartRes());
 234           seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
 235           for (SequenceI seq : seqGrp.getSequences())
 236           {
 237             seqGrpPojo.getSeqsHash().add(String.valueOf(seq.hashCode()));
 238           }
 239           jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
 240         }
 241       }
 242       org.json.JSONObject generatedJSon = new org.json.JSONObject(
 243               jsonAlignmentPojo);
 244       jsonOutput = generatedJSon.toString();
 245       return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
 246               "xEnd");
 247     } catch (Exception e)
 248     {
 249       e.printStackTrace();
 250     }
 251     return jsonOutput;
 252   }
 253
 254   public String[] getHiddenSections()
 255   {
 256     String[] hiddenSections = new String[2];
 257     if (getViewport() == null)
 258     {
 259       return null;
 260     }
 261
 262     // hidden column business
 263     if (getViewport().hasHiddenColumns())
 264     {
 265       List<int[]> hiddenCols = getViewport().getColumnSelection()
 266               .getHiddenColumns();
 267       StringBuilder hiddenColsBuilder = new StringBuilder();
 268       for (int[] range : hiddenCols)
 269       {
 270         hiddenColsBuilder.append(";").append(range[0]).append("-")
 271                 .append(range[1]);
 272       }
 273
 274       hiddenColsBuilder.deleteCharAt(0);
 275       hiddenSections[0] = hiddenColsBuilder.toString();
 276     }
 277
 278     // hidden rows/seqs business
 279     HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
 280             .getHiddenSequences();
 281     if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
 282     {
 283       return hiddenSections;
 284     }
 285
 286     SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
 287     StringBuilder hiddenSeqsBuilder = new StringBuilder();
 288     for (SequenceI hiddenSeq : hiddenSeqs)
 289     {
 290       if (hiddenSeq != null)
 291       {
 292         hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
 293       }
 294     }
 295     if (hiddenSeqsBuilder.length() > 0)
 296     {
 297       hiddenSeqsBuilder.deleteCharAt(0);
 298     }
 299     hiddenSections[1] = hiddenSeqsBuilder.toString();
 300
 301     return hiddenSections;
 302   }
 303
 304   public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
 305           List<SequenceI> seqs, FeatureRenderer fr)
 306   {
 307     displayedFeatures = (fr == null) ? null : fr
 308             .getFeaturesDisplayed();
 309     List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
 310     for (SequenceI seq : seqs)
 311     {
 312       SequenceI dataSetSequence = seq.getDatasetSequence();
 313       SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
 314               : seq.getDatasetSequence().getSequenceFeatures();
 315
 316       seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
 317               : seqFeatures;
 318       if (seqFeatures == null)
 319       {
 320         continue;
 321       }
 322
 323       for (SequenceFeature sf : seqFeatures)
 324       {
 325         if (displayedFeatures != null
 326                 && displayedFeatures.isVisible(sf.getType()))
 327         {
 328           SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
 329                   String.valueOf(seq.hashCode()));
 330
 331           String featureColour = (fr == null) ? null : jalview.util.Format
 332                   .getHexString(fr
 333                   .findFeatureColour(Color.white, seq,
 334                           seq.findIndex(sf.getBegin())));
 335           jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
 336           jsonFeature.setXend(seq.findIndex(sf.getEnd()));
 337           jsonFeature.setType(sf.getType());
 338           jsonFeature.setDescription(sf.getDescription());
 339           jsonFeature.setLinks(sf.links);
 340           jsonFeature.setOtherDetails(sf.otherDetails);
 341           jsonFeature.setScore(sf.getScore());
 342           jsonFeature.setFillColor(featureColour);
 343           jsonFeature.setFeatureGroup(sf.getFeatureGroup());
 344           sequenceFeaturesPojo.add(jsonFeature);
 345         }
 346       }
 347     }
 348     return sequenceFeaturesPojo;
 349   }
 350
 351   public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
 352           Vector<AlignmentAnnotation> annotations)
 353   {
 354     List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
 355     if (annotations == null)
 356     {
 357       return jsonAnnotations;
 358     }
 359     for (AlignmentAnnotation annot : annotations)
 360     {
 361       AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
 362       alignAnnotPojo.setDescription(annot.description);
 363       alignAnnotPojo.setLabel(annot.label);
 364       for (Annotation annotation : annot.annotations)
 365       {
 366         AnnotationPojo annotationPojo = new AnnotationPojo();
 367         if (annotation != null)
 368         {
 369           annotationPojo.setDescription(annotation.description);
 370           annotationPojo.setValue(annotation.value);
 371           annotationPojo
 372                   .setSecondaryStructure(annotation.secondaryStructure);
 373           annotationPojo.setDisplayCharacter(annotation.displayCharacter);
 374           alignAnnotPojo.getAnnotations().add(annotationPojo);
 375         }
 376         else
 377         {
 378           alignAnnotPojo.getAnnotations().add(annotationPojo);
 379         }
 380       }
 381       jsonAnnotations.add(alignAnnotPojo);
 382     }
 383     return jsonAnnotations;
 384   }
 385
 386   @SuppressWarnings("unchecked")
 387   public JSONFile parse(Reader jsonAlignmentString)
 388   {
 389     try
 390     {
 391       JSONParser jsonParser = new JSONParser();
 392       JSONObject alignmentJsonObj = (JSONObject) jsonParser
 393               .parse(jsonAlignmentString);
 394       JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
 395       JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
 396               .get("alignAnnotation");
 397       JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
 398               .get("seqFeatures");
 399       JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
 400               .get("seqGroups");
 401       JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
 402               .get("appSettings");
 403
 404       if (jvSettingsJsonObj != null)
 405       {
 406         String jsColourScheme = (String) jvSettingsJsonObj
 407                 .get("globalColorScheme");
 408         Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
 409                 "showSeqFeatures").toString());
 410         setColourScheme(getJalviewColorScheme(jsColourScheme));
 411         setShowSeqFeatures(showFeatures);
 412         parseHiddenSeqRefsAsList(jvSettingsJsonObj);
 413         parseHiddenCols(jvSettingsJsonObj);
 414       }
 415
 416       hiddenSequences = new ArrayList<SequenceI>();
 417       seqMap = new Hashtable<String, Sequence>();
 418       for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
 419               .hasNext();)
 420       {
 421         JSONObject sequence = sequenceIter.next();
 422         String sequcenceString = sequence.get("seq").toString();
 423         String sequenceName = sequence.get("name").toString();
 424         String seqUniqueId = sequence.get("id").toString();
 425         int start = Integer.valueOf(sequence.get("start").toString());
 426         int end = Integer.valueOf(sequence.get("end").toString());
 427         Sequence seq = new Sequence(sequenceName, sequcenceString, start,
 428                 end);
 429         if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
 430         {
 431           hiddenSequences.add(seq);
 432         }
 433         seqs.add(seq);
 434         seqMap.put(seqUniqueId, seq);
 435       }
 436       parseFeatures(jsonSeqArray);
 437
 438       for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
 439               .hasNext();)
 440       {
 441         JSONObject seqGrpObj = seqGrpIter.next();
 442         String grpName = seqGrpObj.get("groupName").toString();
 443         String colourScheme = seqGrpObj.get("colourScheme").toString();
 444         String description = (seqGrpObj.get("description") == null) ? null
 445                 : seqGrpObj.get("description").toString();
 446         boolean displayBoxes = Boolean.valueOf(seqGrpObj
 447                 .get("displayBoxes").toString());
 448         boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
 449                 .toString());
 450         boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
 451                 .toString());
 452         boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
 453                 "showNonconserved").toString());
 454         int startRes = Integer
 455                 .valueOf(seqGrpObj.get("startRes").toString());
 456         int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
 457         JSONArray seqsHashArray = (JSONArray) seqGrpObj.get("seqsHash");
 458
 459         ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
 460         if (seqsHashArray.size() > 0)
 461         {
 462           Iterator<String> seqHashIter = seqsHashArray.iterator();
 463           while (seqHashIter.hasNext())
 464           {
 465             String seqHash = seqHashIter.next();
 466             Sequence sequence = seqMap.get(seqHash);
 467             if (sequence != null)
 468             {
 469               grpSeqs.add(sequence);
 470             }
 471           }
 472         }
 473         ColourSchemeI grpColourScheme = getJalviewColorScheme(colourScheme);
 474         SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName,
 475                 grpColourScheme,
 476                 displayBoxes, displayText, colourText, startRes, endRes);
 477         seqGrp.setShowNonconserved(showNonconserved);
 478         seqGrp.setDescription(description);
 479         this.seqGroups.add(seqGrp);
 480
 481       }
 482
 483       for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
 484               .hasNext();)
 485       {
 486         JSONObject alAnnot = alAnnotIter.next();
 487         JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
 488         Annotation[] annotations = new Annotation[annotJsonArray.size()];
 489         int count = 0;
 490         for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
 491                 .hasNext();)
 492         {
 493           JSONObject annot = annotIter.next();
 494           if (annot == null)
 495           {
 496             annotations[count] = null;
 497           }
 498           else
 499           {
 500             float val = annot.get("value") == null ? null : Float
 501                     .valueOf(annot.get("value").toString());
 502             String desc = annot.get("description") == null ? null : annot
 503                     .get("description").toString();
 504
 505             char ss = annot.get("secondaryStructure") == null ? ' '
 506                     : annot.get("secondaryStructure").toString().charAt(0);
 507             String displayChar = annot.get("displayCharacter").toString();
 508
 509             annotations[count] = new Annotation(displayChar, desc, ss, val);
 510           }
 511           ++count;
 512         }
 513
 514         AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
 515                 .get("label").toString(), alAnnot.get("description")
 516                 .toString(), annotations);
 517         this.annotations.add(alignAnnot);
 518       }
 519
 520     } catch (Exception e)
 521     {
 522       e.printStackTrace();
 523     }
 524     return this;
 525   }
 526
 527   public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
 528   {
 529     hiddenSeqRefs = new ArrayList<String>();
 530     String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
 531     if(hiddenSeqs != null && !hiddenSeqs.isEmpty()){
 532       String[] seqRefs = hiddenSeqs.split(";");
 533       for(String seqRef : seqRefs){
 534         hiddenSeqRefs.add(seqRef);
 535       }
 536     }
 537   }
 538
 539   public void parseHiddenCols(JSONObject jvSettingsJson)
 540   {
 541     String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
 542     if(hiddenCols != null && !hiddenCols.isEmpty()){
 543       columnSelection = new ColumnSelection();
 544       String[] rangeStrings = hiddenCols.split(";");
 545       for(String rangeString : rangeStrings){
 546         String[] range = rangeString.split("-");
 547         columnSelection.hideColumns(Integer.valueOf(range[0]),
 548                 Integer.valueOf(range[1]));
 549       }
 550     }
 551   }
 552
 553   @SuppressWarnings("unchecked")
 554   private void parseFeatures(JSONArray jsonSeqFeatures)
 555   {
 556     if (jsonSeqFeatures != null)
 557     {
 558       displayedFeatures = new FeaturesDisplayed();
 559       for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
 560               .hasNext();)
 561       {
 562         JSONObject jsonFeature = seqFeatureItr.next();
 563         Long begin = (Long) jsonFeature.get("xStart");
 564         Long end = (Long) jsonFeature.get("xEnd");
 565         String type = (String) jsonFeature.get("type");
 566         String featureGrp = (String) jsonFeature.get("featureGroup");
 567         String descripiton = (String) jsonFeature.get("description");
 568         String seqRef = (String) jsonFeature.get("sequenceRef");
 569         Float score = Float.valueOf(jsonFeature.get("score").toString());
 570
 571         Sequence seq = seqMap.get(seqRef);
 572         SequenceFeature sequenceFeature = new SequenceFeature();
 573         JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
 574         if (linksJsonArray != null && linksJsonArray.size() > 0)
 575         {
 576           Iterator<String> linkList = linksJsonArray.iterator();
 577           while (linkList.hasNext())
 578           {
 579             String link = linkList.next();
 580             sequenceFeature.addLink(link);
 581           }
 582         }
 583         sequenceFeature.setFeatureGroup(featureGrp);
 584         sequenceFeature.setScore(score);
 585         sequenceFeature.setDescription(descripiton);
 586         sequenceFeature.setType(type);
 587         sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
 588         sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
 589         seq.addSequenceFeature(sequenceFeature);
 590         displayedFeatures.setVisible(type);
 591       }
 592     }
 593   }
 594
 595   public static ColourSchemeI getJalviewColorScheme(
 596           String bioJsColourSchemeName)
 597   {
 598     ColourSchemeI jalviewColor = null;
 599     for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
 600             .values())
 601     {
 602       if (cs.getBioJsName().equalsIgnoreCase(bioJsColourSchemeName))
 603       {
 604         jalviewColor = cs.getJvColourScheme();
 605         break;
 606       }
 607     }
 608     return jalviewColor;
 609   }
 610
 611   public String getGlobalColorScheme()
 612   {
 613     return globalColorScheme;
 614   }
 615
 616   public void setGlobalColorScheme(String globalColorScheme)
 617   {
 618     this.globalColorScheme = globalColorScheme;
 619   }
 620
 621   public ColourSchemeI getColourScheme()
 622   {
 623     return colourScheme;
 624   }
 625
 626   public void setColourScheme(ColourSchemeI colourScheme)
 627   {
 628     this.colourScheme = colourScheme;
 629   }
 630
 631   @Override
 632   public FeaturesDisplayedI getDisplayedFeatures()
 633   {
 634     return displayedFeatures;
 635   }
 636
 637   public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
 638   {
 639     this.displayedFeatures = displayedFeatures;
 640   }
 641
 642
 643   public void configureForView(AlignmentViewPanel avpanel)
 644   {
 645     super.configureForView(avpanel);
 646     AlignViewportI viewport = avpanel.getAlignViewport();
 647     AlignmentI alignment = viewport.getAlignment();
 648     AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
 649
 650     seqGroups = alignment.getGroups();
 651     fr = avpanel.cloneFeatureRenderer();
 652
 653     // Add non auto calculated annotation to AlignFile
 654     for (AlignmentAnnotation annot : annots)
 655     {
 656       if (annot != null && !annot.autoCalculated)
 657       {
 658         if (!annot.visible)
 659         {
 660           continue;
 661         }
 662         annotations.add(annot);
 663       }
 664     }
 665     globalColorScheme = ColourSchemeProperty.getColourName(viewport
 666             .getGlobalColourScheme());
 667     setDisplayedFeatures(viewport.getFeaturesDisplayed());
 668     showSeqFeatures = viewport.isShowSequenceFeatures();
 669
 670   }
 671
 672   public boolean isShowSeqFeatures()
 673   {
 674     return showSeqFeatures;
 675   }
 676
 677   public void setShowSeqFeatures(boolean showSeqFeatures)
 678   {
 679     this.showSeqFeatures = showSeqFeatures;
 680   }
 681
 682   public Vector<AlignmentAnnotation> getAnnotations()
 683   {
 684     return annotations;
 685   }
 686
 687   public List<int[]> getHiddenColumns()
 688   {
 689     return hiddenColumns;
 690   }
 691
 692   public ColumnSelection getColumnSelection()
 693   {
 694     return columnSelection;
 695   }
 696
 697   public void setColumnSelection(ColumnSelection columnSelection)
 698   {
 699     this.columnSelection = columnSelection;
 700   }
 701
 702   public SequenceI[] getHiddenSequences()
 703   {
 704     if (hiddenSequences == null || hiddenSequences.isEmpty())
 705     {
 706       return new SequenceI[]
 707       {};
 708     }
 709     synchronized (hiddenSequences)
 710     {
 711       return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
 712     }
 713   }
 714
 715   public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
 716   {
 717     this.hiddenSequences = hiddenSequences;
 718   }
 719
 720   public class JSONExportSettings
 721   {
 722     private boolean exportSequence;
 723
 724     private boolean exportSequenceFeatures;
 725
 726     private boolean exportAnnotations;
 727
 728     private boolean exportGroups;
 729
 730     private boolean exportJalviewSettings;
 731
 732     public boolean isExportSequence()
 733     {
 734       return exportSequence;
 735     }
 736
 737     public void setExportSequence(boolean exportSequence)
 738     {
 739       this.exportSequence = exportSequence;
 740     }
 741
 742     public boolean isExportSequenceFeatures()
 743     {
 744       return exportSequenceFeatures;
 745     }
 746
 747     public void setExportSequenceFeatures(boolean exportSequenceFeatures)
 748     {
 749       this.exportSequenceFeatures = exportSequenceFeatures;
 750     }
 751
 752     public boolean isExportAnnotations()
 753     {
 754       return exportAnnotations;
 755     }
 756
 757     public void setExportAnnotations(boolean exportAnnotations)
 758     {
 759       this.exportAnnotations = exportAnnotations;
 760     }
 761
 762     public boolean isExportGroups()
 763     {
 764       return exportGroups;
 765     }
 766
 767     public void setExportGroups(boolean exportGroups)
 768     {
 769       this.exportGroups = exportGroups;
 770     }
 771
 772     public boolean isExportJalviewSettings()
 773     {
 774       return exportJalviewSettings;
 775     }
 776
 777     public void setExportJalviewSettings(boolean exportJalviewSettings)
 778     {
 779       this.exportJalviewSettings = exportJalviewSettings;
 780     }
 781   }
 782 }