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.getSequenceRefs()
 238                     .add(String.valueOf(seq.hashCode()));
 239           }
 240           jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
 241         }
 242       }
 243       org.json.JSONObject generatedJSon = new org.json.JSONObject(
 244               jsonAlignmentPojo);
 245       jsonOutput = generatedJSon.toString();
 246       return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
 247               "xEnd");
 248     } catch (Exception e)
 249     {
 250       e.printStackTrace();
 251     }
 252     return jsonOutput;
 253   }
 254
 255   public String[] getHiddenSections()
 256   {
 257     String[] hiddenSections = new String[2];
 258     if (getViewport() == null)
 259     {
 260       return null;
 261     }
 262
 263     // hidden column business
 264     if (getViewport().hasHiddenColumns())
 265     {
 266       List<int[]> hiddenCols = getViewport().getColumnSelection()
 267               .getHiddenColumns();
 268       StringBuilder hiddenColsBuilder = new StringBuilder();
 269       for (int[] range : hiddenCols)
 270       {
 271         hiddenColsBuilder.append(";").append(range[0]).append("-")
 272                 .append(range[1]);
 273       }
 274
 275       hiddenColsBuilder.deleteCharAt(0);
 276       hiddenSections[0] = hiddenColsBuilder.toString();
 277     }
 278
 279     // hidden rows/seqs business
 280     HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
 281             .getHiddenSequences();
 282     if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
 283     {
 284       return hiddenSections;
 285     }
 286
 287     SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
 288     StringBuilder hiddenSeqsBuilder = new StringBuilder();
 289     for (SequenceI hiddenSeq : hiddenSeqs)
 290     {
 291       if (hiddenSeq != null)
 292       {
 293         hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
 294       }
 295     }
 296     if (hiddenSeqsBuilder.length() > 0)
 297     {
 298       hiddenSeqsBuilder.deleteCharAt(0);
 299     }
 300     hiddenSections[1] = hiddenSeqsBuilder.toString();
 301
 302     return hiddenSections;
 303   }
 304
 305   public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
 306           List<SequenceI> seqs, FeatureRenderer fr)
 307   {
 308     displayedFeatures = (fr == null) ? null : fr
 309             .getFeaturesDisplayed();
 310     List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
 311     for (SequenceI seq : seqs)
 312     {
 313       SequenceI dataSetSequence = seq.getDatasetSequence();
 314       SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
 315               : seq.getDatasetSequence().getSequenceFeatures();
 316
 317       seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
 318               : seqFeatures;
 319       if (seqFeatures == null)
 320       {
 321         continue;
 322       }
 323
 324       for (SequenceFeature sf : seqFeatures)
 325       {
 326         if (displayedFeatures != null
 327                 && displayedFeatures.isVisible(sf.getType()))
 328         {
 329           SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
 330                   String.valueOf(seq.hashCode()));
 331
 332           String featureColour = (fr == null) ? null : jalview.util.Format
 333                   .getHexString(fr
 334                   .findFeatureColour(Color.white, seq,
 335                           seq.findIndex(sf.getBegin())));
 336           jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
 337           jsonFeature.setXend(seq.findIndex(sf.getEnd()));
 338           jsonFeature.setType(sf.getType());
 339           jsonFeature.setDescription(sf.getDescription());
 340           jsonFeature.setLinks(sf.links);
 341           jsonFeature.setOtherDetails(sf.otherDetails);
 342           jsonFeature.setScore(sf.getScore());
 343           jsonFeature.setFillColor(featureColour);
 344           jsonFeature.setFeatureGroup(sf.getFeatureGroup());
 345           sequenceFeaturesPojo.add(jsonFeature);
 346         }
 347       }
 348     }
 349     return sequenceFeaturesPojo;
 350   }
 351
 352   public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
 353           Vector<AlignmentAnnotation> annotations)
 354   {
 355     List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
 356     if (annotations == null)
 357     {
 358       return jsonAnnotations;
 359     }
 360     for (AlignmentAnnotation annot : annotations)
 361     {
 362       AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
 363       alignAnnotPojo.setDescription(annot.description);
 364       alignAnnotPojo.setLabel(annot.label);
 365       for (Annotation annotation : annot.annotations)
 366       {
 367         AnnotationPojo annotationPojo = new AnnotationPojo();
 368         if (annotation != null)
 369         {
 370           annotationPojo.setDescription(annotation.description);
 371           annotationPojo.setValue(annotation.value);
 372           annotationPojo
 373                   .setSecondaryStructure(annotation.secondaryStructure);
 374           annotationPojo.setDisplayCharacter(annotation.displayCharacter);
 375           alignAnnotPojo.getAnnotations().add(annotationPojo);
 376         }
 377         else
 378         {
 379           alignAnnotPojo.getAnnotations().add(annotationPojo);
 380         }
 381       }
 382       jsonAnnotations.add(alignAnnotPojo);
 383     }
 384     return jsonAnnotations;
 385   }
 386
 387   @SuppressWarnings("unchecked")
 388   public JSONFile parse(Reader jsonAlignmentString)
 389   {
 390     try
 391     {
 392       JSONParser jsonParser = new JSONParser();
 393       JSONObject alignmentJsonObj = (JSONObject) jsonParser
 394               .parse(jsonAlignmentString);
 395       JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
 396       JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
 397               .get("alignAnnotation");
 398       JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
 399               .get("seqFeatures");
 400       JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
 401               .get("seqGroups");
 402       JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
 403               .get("appSettings");
 404
 405       if (jvSettingsJsonObj != null)
 406       {
 407         String jsColourScheme = (String) jvSettingsJsonObj
 408                 .get("globalColorScheme");
 409         Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
 410                 "showSeqFeatures").toString());
 411         setColourScheme(getJalviewColorScheme(jsColourScheme));
 412         setShowSeqFeatures(showFeatures);
 413         parseHiddenSeqRefsAsList(jvSettingsJsonObj);
 414         parseHiddenCols(jvSettingsJsonObj);
 415       }
 416
 417       hiddenSequences = new ArrayList<SequenceI>();
 418       seqMap = new Hashtable<String, Sequence>();
 419       for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
 420               .hasNext();)
 421       {
 422         JSONObject sequence = sequenceIter.next();
 423         String sequcenceString = sequence.get("seq").toString();
 424         String sequenceName = sequence.get("name").toString();
 425         String seqUniqueId = sequence.get("id").toString();
 426         int start = Integer.valueOf(sequence.get("start").toString());
 427         int end = Integer.valueOf(sequence.get("end").toString());
 428         Sequence seq = new Sequence(sequenceName, sequcenceString, start,
 429                 end);
 430         if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
 431         {
 432           hiddenSequences.add(seq);
 433         }
 434         seqs.add(seq);
 435         seqMap.put(seqUniqueId, seq);
 436       }
 437       parseFeatures(jsonSeqArray);
 438
 439       for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
 440               .hasNext();)
 441       {
 442         JSONObject seqGrpObj = seqGrpIter.next();
 443         String grpName = seqGrpObj.get("groupName").toString();
 444         String colourScheme = seqGrpObj.get("colourScheme").toString();
 445         String description = (seqGrpObj.get("description") == null) ? null
 446                 : seqGrpObj.get("description").toString();
 447         boolean displayBoxes = Boolean.valueOf(seqGrpObj
 448                 .get("displayBoxes").toString());
 449         boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
 450                 .toString());
 451         boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
 452                 .toString());
 453         boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
 454                 "showNonconserved").toString());
 455         int startRes = Integer
 456                 .valueOf(seqGrpObj.get("startRes").toString());
 457         int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
 458         JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
 459
 460         ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
 461         if (sequenceRefs.size() > 0)
 462         {
 463           Iterator<String> seqHashIter = sequenceRefs.iterator();
 464           while (seqHashIter.hasNext())
 465           {
 466             String seqHash = seqHashIter.next();
 467             Sequence sequence = seqMap.get(seqHash);
 468             if (sequence != null)
 469             {
 470               grpSeqs.add(sequence);
 471             }
 472           }
 473         }
 474         ColourSchemeI grpColourScheme = getJalviewColorScheme(colourScheme);
 475         SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName,
 476                 grpColourScheme,
 477                 displayBoxes, displayText, colourText, startRes, endRes);
 478         seqGrp.setShowNonconserved(showNonconserved);
 479         seqGrp.setDescription(description);
 480         this.seqGroups.add(seqGrp);
 481
 482       }
 483
 484       for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
 485               .hasNext();)
 486       {
 487         JSONObject alAnnot = alAnnotIter.next();
 488         JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
 489         Annotation[] annotations = new Annotation[annotJsonArray.size()];
 490         int count = 0;
 491         for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
 492                 .hasNext();)
 493         {
 494           JSONObject annot = annotIter.next();
 495           if (annot == null)
 496           {
 497             annotations[count] = null;
 498           }
 499           else
 500           {
 501             float val = annot.get("value") == null ? null : Float
 502                     .valueOf(annot.get("value").toString());
 503             String desc = annot.get("description") == null ? null : annot
 504                     .get("description").toString();
 505
 506             char ss = annot.get("secondaryStructure") == null ? ' '
 507                     : annot.get("secondaryStructure").toString().charAt(0);
 508             String displayChar = annot.get("displayCharacter").toString();
 509
 510             annotations[count] = new Annotation(displayChar, desc, ss, val);
 511           }
 512           ++count;
 513         }
 514
 515         AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
 516                 .get("label").toString(), alAnnot.get("description")
 517                 .toString(), annotations);
 518         this.annotations.add(alignAnnot);
 519       }
 520
 521     } catch (Exception e)
 522     {
 523       e.printStackTrace();
 524     }
 525     return this;
 526   }
 527
 528   public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
 529   {
 530     hiddenSeqRefs = new ArrayList<String>();
 531     String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
 532     if(hiddenSeqs != null && !hiddenSeqs.isEmpty()){
 533       String[] seqRefs = hiddenSeqs.split(";");
 534       for(String seqRef : seqRefs){
 535         hiddenSeqRefs.add(seqRef);
 536       }
 537     }
 538   }
 539
 540   public void parseHiddenCols(JSONObject jvSettingsJson)
 541   {
 542     String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
 543     if(hiddenCols != null && !hiddenCols.isEmpty()){
 544       columnSelection = new ColumnSelection();
 545       String[] rangeStrings = hiddenCols.split(";");
 546       for(String rangeString : rangeStrings){
 547         String[] range = rangeString.split("-");
 548         columnSelection.hideColumns(Integer.valueOf(range[0]),
 549                 Integer.valueOf(range[1]));
 550       }
 551     }
 552   }
 553
 554   @SuppressWarnings("unchecked")
 555   private void parseFeatures(JSONArray jsonSeqFeatures)
 556   {
 557     if (jsonSeqFeatures != null)
 558     {
 559       displayedFeatures = new FeaturesDisplayed();
 560       for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
 561               .hasNext();)
 562       {
 563         JSONObject jsonFeature = seqFeatureItr.next();
 564         Long begin = (Long) jsonFeature.get("xStart");
 565         Long end = (Long) jsonFeature.get("xEnd");
 566         String type = (String) jsonFeature.get("type");
 567         String featureGrp = (String) jsonFeature.get("featureGroup");
 568         String descripiton = (String) jsonFeature.get("description");
 569         String seqRef = (String) jsonFeature.get("sequenceRef");
 570         Float score = Float.valueOf(jsonFeature.get("score").toString());
 571
 572         Sequence seq = seqMap.get(seqRef);
 573         SequenceFeature sequenceFeature = new SequenceFeature();
 574         JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
 575         if (linksJsonArray != null && linksJsonArray.size() > 0)
 576         {
 577           Iterator<String> linkList = linksJsonArray.iterator();
 578           while (linkList.hasNext())
 579           {
 580             String link = linkList.next();
 581             sequenceFeature.addLink(link);
 582           }
 583         }
 584         sequenceFeature.setFeatureGroup(featureGrp);
 585         sequenceFeature.setScore(score);
 586         sequenceFeature.setDescription(descripiton);
 587         sequenceFeature.setType(type);
 588         sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
 589         sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
 590         seq.addSequenceFeature(sequenceFeature);
 591         displayedFeatures.setVisible(type);
 592       }
 593     }
 594   }
 595
 596   public static ColourSchemeI getJalviewColorScheme(
 597           String bioJsColourSchemeName)
 598   {
 599     ColourSchemeI jalviewColor = null;
 600     for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
 601             .values())
 602     {
 603       if (cs.getBioJsName().equalsIgnoreCase(bioJsColourSchemeName))
 604       {
 605         jalviewColor = cs.getJvColourScheme();
 606         break;
 607       }
 608     }
 609     return jalviewColor;
 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
 644   public void configureForView(AlignmentViewPanel avpanel)
 645   {
 646     super.configureForView(avpanel);
 647     AlignViewportI viewport = avpanel.getAlignViewport();
 648     AlignmentI alignment = viewport.getAlignment();
 649     AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
 650
 651     seqGroups = alignment.getGroups();
 652     fr = avpanel.cloneFeatureRenderer();
 653
 654     // Add non auto calculated annotation to AlignFile
 655     for (AlignmentAnnotation annot : annots)
 656     {
 657       if (annot != null && !annot.autoCalculated)
 658       {
 659         if (!annot.visible)
 660         {
 661           continue;
 662         }
 663         annotations.add(annot);
 664       }
 665     }
 666     globalColorScheme = ColourSchemeProperty.getColourName(viewport
 667             .getGlobalColourScheme());
 668     setDisplayedFeatures(viewport.getFeaturesDisplayed());
 669     showSeqFeatures = viewport.isShowSequenceFeatures();
 670
 671   }
 672
 673   public boolean isShowSeqFeatures()
 674   {
 675     return showSeqFeatures;
 676   }
 677
 678   public void setShowSeqFeatures(boolean showSeqFeatures)
 679   {
 680     this.showSeqFeatures = showSeqFeatures;
 681   }
 682
 683   public Vector<AlignmentAnnotation> getAnnotations()
 684   {
 685     return annotations;
 686   }
 687
 688   public List<int[]> getHiddenColumns()
 689   {
 690     return hiddenColumns;
 691   }
 692
 693   public ColumnSelection getColumnSelection()
 694   {
 695     return columnSelection;
 696   }
 697
 698   public void setColumnSelection(ColumnSelection columnSelection)
 699   {
 700     this.columnSelection = columnSelection;
 701   }
 702
 703   public SequenceI[] getHiddenSequences()
 704   {
 705     if (hiddenSequences == null || hiddenSequences.isEmpty())
 706     {
 707       return new SequenceI[]
 708       {};
 709     }
 710     synchronized (hiddenSequences)
 711     {
 712       return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
 713     }
 714   }
 715
 716   public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
 717   {
 718     this.hiddenSequences = hiddenSequences;
 719   }
 720
 721   public class JSONExportSettings
 722   {
 723     private boolean exportSequence;
 724
 725     private boolean exportSequenceFeatures;
 726
 727     private boolean exportAnnotations;
 728
 729     private boolean exportGroups;
 730
 731     private boolean exportJalviewSettings;
 732
 733     public boolean isExportSequence()
 734     {
 735       return exportSequence;
 736     }
 737
 738     public void setExportSequence(boolean exportSequence)
 739     {
 740       this.exportSequence = exportSequence;
 741     }
 742
 743     public boolean isExportSequenceFeatures()
 744     {
 745       return exportSequenceFeatures;
 746     }
 747
 748     public void setExportSequenceFeatures(boolean exportSequenceFeatures)
 749     {
 750       this.exportSequenceFeatures = exportSequenceFeatures;
 751     }
 752
 753     public boolean isExportAnnotations()
 754     {
 755       return exportAnnotations;
 756     }
 757
 758     public void setExportAnnotations(boolean exportAnnotations)
 759     {
 760       this.exportAnnotations = exportAnnotations;
 761     }
 762
 763     public boolean isExportGroups()
 764     {
 765       return exportGroups;
 766     }
 767
 768     public void setExportGroups(boolean exportGroups)
 769     {
 770       this.exportGroups = exportGroups;
 771     }
 772
 773     public boolean isExportJalviewSettings()
 774     {
 775       return exportJalviewSettings;
 776     }
 777
 778     public void setExportJalviewSettings(boolean exportJalviewSettings)
 779     {
 780       this.exportJalviewSettings = exportJalviewSettings;
 781     }
 782   }
 783 }