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.Alignment;
  32 import jalview.datamodel.AlignmentAnnotation;
  33 import jalview.datamodel.AlignmentI;
  34 import jalview.datamodel.Annotation;
  35 import jalview.datamodel.ColumnSelection;
  36 import jalview.datamodel.HiddenSequences;
  37 import jalview.datamodel.Sequence;
  38 import jalview.datamodel.SequenceFeature;
  39 import jalview.datamodel.SequenceGroup;
  40 import jalview.datamodel.SequenceI;
  41 import jalview.json.binding.biojson.v1.AlignmentAnnotationPojo;
  42 import jalview.json.binding.biojson.v1.AlignmentPojo;
  43 import jalview.json.binding.biojson.v1.AnnotationPojo;
  44 import jalview.json.binding.biojson.v1.ColourSchemeMapper;
  45 import jalview.json.binding.biojson.v1.SequenceFeaturesPojo;
  46 import jalview.json.binding.biojson.v1.SequenceGrpPojo;
  47 import jalview.json.binding.biojson.v1.SequencePojo;
  48 import jalview.schemes.ColourSchemeI;
  49 import jalview.schemes.ColourSchemeProperty;
  50 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
  51
  52 import java.awt.Color;
  53 import java.io.IOException;
  54 import java.io.Reader;
  55 import java.util.ArrayList;
  56 import java.util.Hashtable;
  57 import java.util.Iterator;
  58 import java.util.List;
  59 import java.util.Vector;
  60
  61 import org.json.simple.JSONArray;
  62 import org.json.simple.JSONObject;
  63 import org.json.simple.parser.JSONParser;
  64
  65 public class JSONFile extends AlignFile implements ComplexAlignFile
  66 {
  67   private ColourSchemeI colourScheme;
  68
  69   private static String version = new BuildDetails().getVersion();
  70
  71   private String webstartUrl = "http://www.jalview.org/services/launchApp";
  72
  73   private String application = "Jalview";
  74
  75   public static final String FILE_EXT = "json";
  76
  77   public static final String FILE_DESC = "JSON";
  78
  79   private String globalColorScheme;
  80
  81   private boolean showSeqFeatures;
  82
  83   private Hashtable<String, Sequence> seqMap;
  84
  85   private FeaturesDisplayedI displayedFeatures;
  86
  87   private FeatureRenderer fr;
  88
  89   private List<int[]> hiddenColumns;
  90
  91   private ColumnSelection columnSelection;
  92
  93   private List<String> hiddenSeqRefs;
  94
  95   private ArrayList<SequenceI> hiddenSequences;
  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
 119   @Override
 120   public String print()
 121   {
 122     String jsonOutput = null;
 123     try
 124     {
 125       AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
 126       AlignExportSettingI exportSettings = getExportSettings();
 127
 128       // if no export settings were supplied use the following with all values
 129       // defaulting to true
 130       if (exportSettings == null)
 131       {
 132         exportSettings = new AlignExportSettingI()
 133         {
 134           @Override
 135           public boolean isExportHiddenSequences()
 136           {
 137             return true;
 138           }
 139
 140           @Override
 141           public boolean isExportHiddenColumns()
 142           {
 143             return true;
 144           }
 145
 146           @Override
 147           public boolean isExportGroups()
 148           {
 149             return true;
 150           }
 151
 152           @Override
 153           public boolean isExportFeatures()
 154           {
 155             return true;
 156           }
 157
 158           @Override
 159           public boolean isExportAnnotations()
 160           {
 161             return true;
 162           }
 163
 164           @Override
 165           public boolean isCancelled()
 166           {
 167             return false;
 168           }
 169         };
 170       }
 171
 172       int count = 0;
 173       for (SequenceI seq : seqs)
 174       {
 175         StringBuilder name = new StringBuilder();
 176         name.append(seq.getName()).append("/").append(seq.getStart())
 177                 .append("-").append(seq.getEnd());
 178         SequencePojo jsonSeqPojo = new SequencePojo();
 179         jsonSeqPojo.setId(String.valueOf(seq.hashCode()));
 180         jsonSeqPojo.setOrder(++count);
 181         jsonSeqPojo.setEnd(seq.getEnd());
 182         jsonSeqPojo.setStart(seq.getStart());
 183         jsonSeqPojo.setName(name.toString());
 184         jsonSeqPojo.setSeq(seq.getSequenceAsString());
 185         jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
 186       }
 187       jsonAlignmentPojo.setGlobalColorScheme(globalColorScheme);
 188       jsonAlignmentPojo.getAppSettings().put("application", application);
 189       jsonAlignmentPojo.getAppSettings().put("version", version);
 190       jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
 191       jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
 192               String.valueOf(showSeqFeatures));
 193
 194       String[] hiddenSections = getHiddenSections();
 195       if (hiddenSections != null)
 196       {
 197         if (hiddenSections[0] != null
 198                 && exportSettings.isExportHiddenColumns())
 199         {
 200           jsonAlignmentPojo.getAppSettings().put("hiddenCols",
 201                   String.valueOf(hiddenSections[0]));
 202         }
 203         if (hiddenSections[1] != null
 204                 && exportSettings.isExportHiddenSequences())
 205         {
 206           jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
 207                   String.valueOf(hiddenSections[1]));
 208         }
 209       }
 210
 211       if (exportSettings.isExportAnnotations())
 212       {
 213         jsonAlignmentPojo
 214                 .setAlignAnnotation(annotationToJsonPojo(annotations));
 215       }
 216
 217       if (exportSettings.isExportFeatures())
 218       {
 219         jsonAlignmentPojo
 220                 .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
 221       }
 222
 223       if (exportSettings.isExportGroups() && seqGroups != null
 224               && seqGroups.size() > 0)
 225       {
 226         for (SequenceGroup seqGrp : seqGroups)
 227         {
 228           SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
 229           seqGrpPojo.setGroupName(seqGrp.getName());
 230           seqGrpPojo.setColourScheme(ColourSchemeProperty
 231                   .getColourName(seqGrp.cs));
 232           seqGrpPojo.setColourText(seqGrp.getColourText());
 233           seqGrpPojo.setDescription(seqGrp.getDescription());
 234           seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
 235           seqGrpPojo.setDisplayText(seqGrp.getDisplayText());
 236           seqGrpPojo.setEndRes(seqGrp.getEndRes());
 237           seqGrpPojo.setStartRes(seqGrp.getStartRes());
 238           seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
 239           for (SequenceI seq : seqGrp.getSequences())
 240           {
 241             seqGrpPojo.getSequenceRefs()
 242                     .add(String.valueOf(seq.hashCode()));
 243           }
 244           jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
 245         }
 246       }
 247       org.json.JSONObject generatedJSon = new org.json.JSONObject(
 248               jsonAlignmentPojo);
 249       jsonOutput = generatedJSon.toString();
 250       return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
 251               "xEnd");
 252     } catch (Exception e)
 253     {
 254       e.printStackTrace();
 255     }
 256     return jsonOutput;
 257   }
 258
 259   public String[] getHiddenSections()
 260   {
 261     String[] hiddenSections = new String[2];
 262     if (getViewport() == null)
 263     {
 264       return null;
 265     }
 266
 267     // hidden column business
 268     if (getViewport().hasHiddenColumns())
 269     {
 270       List<int[]> hiddenCols = getViewport().getColumnSelection()
 271               .getHiddenColumns();
 272       StringBuilder hiddenColsBuilder = new StringBuilder();
 273       for (int[] range : hiddenCols)
 274       {
 275         hiddenColsBuilder.append(";").append(range[0]).append("-")
 276                 .append(range[1]);
 277       }
 278
 279       hiddenColsBuilder.deleteCharAt(0);
 280       hiddenSections[0] = hiddenColsBuilder.toString();
 281     }
 282
 283     // hidden rows/seqs business
 284     HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
 285             .getHiddenSequences();
 286     if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
 287     {
 288       return hiddenSections;
 289     }
 290
 291     SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
 292     StringBuilder hiddenSeqsBuilder = new StringBuilder();
 293     for (SequenceI hiddenSeq : hiddenSeqs)
 294     {
 295       if (hiddenSeq != null)
 296       {
 297         hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
 298       }
 299     }
 300     if (hiddenSeqsBuilder.length() > 0)
 301     {
 302       hiddenSeqsBuilder.deleteCharAt(0);
 303     }
 304     hiddenSections[1] = hiddenSeqsBuilder.toString();
 305
 306     return hiddenSections;
 307   }
 308
 309   public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
 310           List<SequenceI> seqs, FeatureRenderer fr)
 311   {
 312     displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
 313     List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
 314     for (SequenceI seq : seqs)
 315     {
 316       SequenceI dataSetSequence = seq.getDatasetSequence();
 317       SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
 318               : seq.getDatasetSequence().getSequenceFeatures();
 319
 320       seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
 321               : seqFeatures;
 322       if (seqFeatures == null)
 323       {
 324         continue;
 325       }
 326
 327       for (SequenceFeature sf : seqFeatures)
 328       {
 329         if (displayedFeatures != null
 330                 && displayedFeatures.isVisible(sf.getType()))
 331         {
 332           SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
 333                   String.valueOf(seq.hashCode()));
 334
 335           String featureColour = (fr == null) ? null : jalview.util.Format
 336                   .getHexString(fr.findFeatureColour(Color.white, seq,
 337                           seq.findIndex(sf.getBegin())));
 338           jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
 339           jsonFeature.setXend(seq.findIndex(sf.getEnd()));
 340           jsonFeature.setType(sf.getType());
 341           jsonFeature.setDescription(sf.getDescription());
 342           jsonFeature.setLinks(sf.links);
 343           jsonFeature.setOtherDetails(sf.otherDetails);
 344           jsonFeature.setScore(sf.getScore());
 345           jsonFeature.setFillColor(featureColour);
 346           jsonFeature.setFeatureGroup(sf.getFeatureGroup());
 347           sequenceFeaturesPojo.add(jsonFeature);
 348         }
 349       }
 350     }
 351     return sequenceFeaturesPojo;
 352   }
 353
 354   public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
 355           Vector<AlignmentAnnotation> annotations)
 356   {
 357     List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
 358     if (annotations == null)
 359     {
 360       return jsonAnnotations;
 361     }
 362     for (AlignmentAnnotation annot : annotations)
 363     {
 364       AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
 365       alignAnnotPojo.setDescription(annot.description);
 366       alignAnnotPojo.setLabel(annot.label);
 367       for (Annotation annotation : annot.annotations)
 368       {
 369         AnnotationPojo annotationPojo = new AnnotationPojo();
 370         if (annotation != null)
 371         {
 372           annotationPojo.setDescription(annotation.description);
 373           annotationPojo.setValue(annotation.value);
 374           annotationPojo
 375                   .setSecondaryStructure(annotation.secondaryStructure);
 376           annotationPojo.setDisplayCharacter(annotation.displayCharacter);
 377           alignAnnotPojo.getAnnotations().add(annotationPojo);
 378         }
 379         else
 380         {
 381           alignAnnotPojo.getAnnotations().add(annotationPojo);
 382         }
 383       }
 384       jsonAnnotations.add(alignAnnotPojo);
 385     }
 386     return jsonAnnotations;
 387   }
 388
 389   @SuppressWarnings("unchecked")
 390   public JSONFile parse(Reader jsonAlignmentString)
 391   {
 392     String jsColourScheme = null;
 393     try
 394     {
 395       JSONParser jsonParser = new JSONParser();
 396       JSONObject alignmentJsonObj = (JSONObject) jsonParser
 397               .parse(jsonAlignmentString);
 398       JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
 399       JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
 400               .get("alignAnnotation");
 401       JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
 402               .get("seqFeatures");
 403       JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
 404               .get("seqGroups");
 405       JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
 406               .get("appSettings");
 407
 408       if (jvSettingsJsonObj != null)
 409       {
 410         jsColourScheme = (String) jvSettingsJsonObj
 411                 .get("globalColorScheme");
 412         Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
 413                 "showSeqFeatures").toString());
 414         setShowSeqFeatures(showFeatures);
 415         parseHiddenSeqRefsAsList(jvSettingsJsonObj);
 416         parseHiddenCols(jvSettingsJsonObj);
 417       }
 418
 419       hiddenSequences = new ArrayList<SequenceI>();
 420       seqMap = new Hashtable<String, Sequence>();
 421       for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
 422               .hasNext();)
 423       {
 424         JSONObject sequence = sequenceIter.next();
 425         String sequcenceString = sequence.get("seq").toString();
 426         String sequenceName = sequence.get("name").toString();
 427         String seqUniqueId = sequence.get("id").toString();
 428         int start = Integer.valueOf(sequence.get("start").toString());
 429         int end = Integer.valueOf(sequence.get("end").toString());
 430         Sequence seq = new Sequence(sequenceName, sequcenceString, start,
 431                 end);
 432         if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
 433         {
 434           hiddenSequences.add(seq);
 435         }
 436         seqs.add(seq);
 437         seqMap.put(seqUniqueId, seq);
 438       }
 439
 440       if (jsColourScheme != null)
 441       {
 442         setColourScheme(ColourSchemeMapper.getJalviewColourScheme(
 443                 jsColourScheme,
 444                 new Alignment(seqs.toArray(new SequenceI[0]))));
 445       }
 446       parseFeatures(jsonSeqArray);
 447
 448       for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
 449               .hasNext();)
 450       {
 451         JSONObject seqGrpObj = seqGrpIter.next();
 452         String grpName = seqGrpObj.get("groupName").toString();
 453         String colourScheme = seqGrpObj.get("colourScheme").toString();
 454         String description = (seqGrpObj.get("description") == null) ? null
 455                 : seqGrpObj.get("description").toString();
 456         boolean displayBoxes = Boolean.valueOf(seqGrpObj
 457                 .get("displayBoxes").toString());
 458         boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
 459                 .toString());
 460         boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
 461                 .toString());
 462         boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
 463                 "showNonconserved").toString());
 464         int startRes = Integer
 465                 .valueOf(seqGrpObj.get("startRes").toString());
 466         int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
 467         JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
 468
 469         ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
 470         if (sequenceRefs.size() > 0)
 471         {
 472           Iterator<String> seqHashIter = sequenceRefs.iterator();
 473           while (seqHashIter.hasNext())
 474           {
 475             String seqHash = seqHashIter.next();
 476             Sequence sequence = seqMap.get(seqHash);
 477             if (sequence != null)
 478             {
 479               grpSeqs.add(sequence);
 480             }
 481           }
 482         }
 483         SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
 484                 displayBoxes, displayText, colourText,
 485                 startRes, endRes);
 486         seqGrp.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme,
 487                 seqGrp);
 488         seqGrp.setShowNonconserved(showNonconserved);
 489         seqGrp.setDescription(description);
 490         this.seqGroups.add(seqGrp);
 491
 492       }
 493
 494       for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
 495               .hasNext();)
 496       {
 497         JSONObject alAnnot = alAnnotIter.next();
 498         JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
 499         Annotation[] annotations = new Annotation[annotJsonArray.size()];
 500         int count = 0;
 501         for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
 502                 .hasNext();)
 503         {
 504           JSONObject annot = annotIter.next();
 505           if (annot == null)
 506           {
 507             annotations[count] = null;
 508           }
 509           else
 510           {
 511             float val = annot.get("value") == null ? null : Float
 512                     .valueOf(annot.get("value").toString());
 513             String desc = annot.get("description") == null ? null : annot
 514                     .get("description").toString();
 515             char ss = annot.get("secondaryStructure") == null
 516                     || annot.get("secondaryStructure").toString()
 517                             .equalsIgnoreCase("u0000") ? ' ' : annot
 518                     .get("secondaryStructure").toString().charAt(0);
 519             String displayChar = annot.get("displayCharacter") == null ? ""
 520                     : annot.get("displayCharacter").toString();
 521
 522             annotations[count] = new Annotation(displayChar, desc, ss, val);
 523           }
 524           ++count;
 525         }
 526
 527         AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
 528                 .get("label").toString(), alAnnot.get("description")
 529                 .toString(), annotations);
 530         this.annotations.add(alignAnnot);
 531       }
 532
 533     } catch (Exception e)
 534     {
 535       e.printStackTrace();
 536     }
 537     return this;
 538   }
 539
 540   public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
 541   {
 542     hiddenSeqRefs = new ArrayList<String>();
 543     String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
 544     if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
 545     {
 546       String[] seqRefs = hiddenSeqs.split(";");
 547       for (String seqRef : seqRefs)
 548       {
 549         hiddenSeqRefs.add(seqRef);
 550       }
 551     }
 552   }
 553
 554   public void parseHiddenCols(JSONObject jvSettingsJson)
 555   {
 556     String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
 557     if (hiddenCols != null && !hiddenCols.isEmpty())
 558     {
 559       columnSelection = new ColumnSelection();
 560       String[] rangeStrings = hiddenCols.split(";");
 561       for (String rangeString : rangeStrings)
 562       {
 563         String[] range = rangeString.split("-");
 564         columnSelection.hideColumns(Integer.valueOf(range[0]),
 565                 Integer.valueOf(range[1]));
 566       }
 567     }
 568   }
 569
 570   @SuppressWarnings("unchecked")
 571   private void parseFeatures(JSONArray jsonSeqFeatures)
 572   {
 573     if (jsonSeqFeatures != null)
 574     {
 575       displayedFeatures = new FeaturesDisplayed();
 576       for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
 577               .hasNext();)
 578       {
 579         JSONObject jsonFeature = seqFeatureItr.next();
 580         Long begin = (Long) jsonFeature.get("xStart");
 581         Long end = (Long) jsonFeature.get("xEnd");
 582         String type = (String) jsonFeature.get("type");
 583         String featureGrp = (String) jsonFeature.get("featureGroup");
 584         String descripiton = (String) jsonFeature.get("description");
 585         String seqRef = (String) jsonFeature.get("sequenceRef");
 586         Float score = Float.valueOf(jsonFeature.get("score").toString());
 587
 588         Sequence seq = seqMap.get(seqRef);
 589         SequenceFeature sequenceFeature = new SequenceFeature();
 590         JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
 591         if (linksJsonArray != null && linksJsonArray.size() > 0)
 592         {
 593           Iterator<String> linkList = linksJsonArray.iterator();
 594           while (linkList.hasNext())
 595           {
 596             String link = linkList.next();
 597             sequenceFeature.addLink(link);
 598           }
 599         }
 600         sequenceFeature.setFeatureGroup(featureGrp);
 601         sequenceFeature.setScore(score);
 602         sequenceFeature.setDescription(descripiton);
 603         sequenceFeature.setType(type);
 604         sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
 605         sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
 606         seq.addSequenceFeature(sequenceFeature);
 607         displayedFeatures.setVisible(type);
 608       }
 609     }
 610   }
 611
 612   public String getGlobalColorScheme()
 613   {
 614     return globalColorScheme;
 615   }
 616
 617   public void setGlobalColorScheme(String globalColorScheme)
 618   {
 619     this.globalColorScheme = globalColorScheme;
 620   }
 621
 622   public ColourSchemeI getColourScheme()
 623   {
 624     return colourScheme;
 625   }
 626
 627   public void setColourScheme(ColourSchemeI colourScheme)
 628   {
 629     this.colourScheme = colourScheme;
 630   }
 631
 632   @Override
 633   public FeaturesDisplayedI getDisplayedFeatures()
 634   {
 635     return displayedFeatures;
 636   }
 637
 638   public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
 639   {
 640     this.displayedFeatures = displayedFeatures;
 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     synchronized (hiddenSequences)
 709     {
 710       return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
 711     }
 712   }
 713
 714   public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
 715   {
 716     this.hiddenSequences = hiddenSequences;
 717   }
 718
 719   public class JSONExportSettings
 720   {
 721     private boolean exportSequence;
 722
 723     private boolean exportSequenceFeatures;
 724
 725     private boolean exportAnnotations;
 726
 727     private boolean exportGroups;
 728
 729     private boolean exportJalviewSettings;
 730
 731     public boolean isExportSequence()
 732     {
 733       return exportSequence;
 734     }
 735
 736     public void setExportSequence(boolean exportSequence)
 737     {
 738       this.exportSequence = exportSequence;
 739     }
 740
 741     public boolean isExportSequenceFeatures()
 742     {
 743       return exportSequenceFeatures;
 744     }
 745
 746     public void setExportSequenceFeatures(boolean exportSequenceFeatures)
 747     {
 748       this.exportSequenceFeatures = exportSequenceFeatures;
 749     }
 750
 751     public boolean isExportAnnotations()
 752     {
 753       return exportAnnotations;
 754     }
 755
 756     public void setExportAnnotations(boolean exportAnnotations)
 757     {
 758       this.exportAnnotations = exportAnnotations;
 759     }
 760
 761     public boolean isExportGroups()
 762     {
 763       return exportGroups;
 764     }
 765
 766     public void setExportGroups(boolean exportGroups)
 767     {
 768       this.exportGroups = exportGroups;
 769     }
 770
 771     public boolean isExportJalviewSettings()
 772     {
 773       return exportJalviewSettings;
 774     }
 775
 776     public void setExportJalviewSettings(boolean exportJalviewSettings)
 777     {
 778       this.exportJalviewSettings = exportJalviewSettings;
 779     }
 780   }
 781 }