src/jalview/io/JSONFile.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
   3  * Copyright (C) 2015 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.JalviewBioJsColorSchemeMapper;
  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.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   public JSONFile()
  97   {
  98     super();
  99   }
 100
 101   public JSONFile(FileParse source) throws IOException
 102   {
 103     super(source);
 104   }
 105
 106   public JSONFile(String inFile, String type) throws IOException
 107   {
 108     super(inFile, type);
 109   }
 110
 111   @Override
 112   public void parse() throws IOException
 113   {
 114     parse(getReader());
 115
 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           @Override
 164           public boolean isCancelled()
 165           {
 166             return false;
 167           }
 168         };
 169       }
 170
 171       int count = 0;
 172       for (SequenceI seq : seqs)
 173       {
 174         StringBuilder name = new StringBuilder();
 175         name.append(seq.getName()).append("/").append(seq.getStart())
 176                 .append("-").append(seq.getEnd());
 177         SequencePojo jsonSeqPojo = new SequencePojo();
 178         jsonSeqPojo.setId(String.valueOf(seq.hashCode()));
 179         jsonSeqPojo.setOrder(++count);
 180         jsonSeqPojo.setEnd(seq.getEnd());
 181         jsonSeqPojo.setStart(seq.getStart());
 182         jsonSeqPojo.setName(name.toString());
 183         jsonSeqPojo.setSeq(seq.getSequenceAsString());
 184         jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
 185       }
 186       jsonAlignmentPojo.setGlobalColorScheme(globalColorScheme);
 187       jsonAlignmentPojo.getAppSettings().put("application", application);
 188       jsonAlignmentPojo.getAppSettings().put("version", version);
 189       jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
 190       jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
 191               String.valueOf(showSeqFeatures));
 192
 193       String[] hiddenSections = getHiddenSections();
 194       if (hiddenSections != null)
 195       {
 196         if (hiddenSections[0] != null
 197                 && exportSettings.isExportHiddenColumns())
 198         {
 199           jsonAlignmentPojo.getAppSettings().put("hiddenCols",
 200                   String.valueOf(hiddenSections[0]));
 201         }
 202         if (hiddenSections[1] != null
 203                 && exportSettings.isExportHiddenSequences())
 204         {
 205           jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
 206                   String.valueOf(hiddenSections[1]));
 207         }
 208       }
 209
 210       if (exportSettings.isExportAnnotations())
 211       {
 212         jsonAlignmentPojo
 213                 .setAlignAnnotation(annotationToJsonPojo(annotations));
 214       }
 215
 216       if (exportSettings.isExportFeatures())
 217       {
 218         jsonAlignmentPojo
 219                 .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
 220       }
 221
 222       if (exportSettings.isExportGroups() && seqGroups != null
 223               && seqGroups.size() > 0)
 224       {
 225         for (SequenceGroup seqGrp : seqGroups)
 226         {
 227           SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
 228           seqGrpPojo.setGroupName(seqGrp.getName());
 229           seqGrpPojo.setColourScheme(ColourSchemeProperty
 230                   .getColourName(seqGrp.cs));
 231           seqGrpPojo.setColourText(seqGrp.getColourText());
 232           seqGrpPojo.setDescription(seqGrp.getDescription());
 233           seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
 234           seqGrpPojo.setDisplayText(seqGrp.getDisplayText());
 235           seqGrpPojo.setEndRes(seqGrp.getEndRes());
 236           seqGrpPojo.setStartRes(seqGrp.getStartRes());
 237           seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
 238           for (SequenceI seq : seqGrp.getSequences())
 239           {
 240             seqGrpPojo.getSequenceRefs()
 241                     .add(String.valueOf(seq.hashCode()));
 242           }
 243           jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
 244         }
 245       }
 246       org.json.JSONObject generatedJSon = new org.json.JSONObject(
 247               jsonAlignmentPojo);
 248       jsonOutput = generatedJSon.toString();
 249       return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
 250               "xEnd");
 251     } catch (Exception e)
 252     {
 253       e.printStackTrace();
 254     }
 255     return jsonOutput;
 256   }
 257
 258   public String[] getHiddenSections()
 259   {
 260     String[] hiddenSections = new String[2];
 261     if (getViewport() == null)
 262     {
 263       return null;
 264     }
 265
 266     // hidden column business
 267     if (getViewport().hasHiddenColumns())
 268     {
 269       List<int[]> hiddenCols = getViewport().getColumnSelection()
 270               .getHiddenColumns();
 271       StringBuilder hiddenColsBuilder = new StringBuilder();
 272       for (int[] range : hiddenCols)
 273       {
 274         hiddenColsBuilder.append(";").append(range[0]).append("-")
 275                 .append(range[1]);
 276       }
 277
 278       hiddenColsBuilder.deleteCharAt(0);
 279       hiddenSections[0] = hiddenColsBuilder.toString();
 280     }
 281
 282     // hidden rows/seqs business
 283     HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
 284             .getHiddenSequences();
 285     if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
 286     {
 287       return hiddenSections;
 288     }
 289
 290     SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
 291     StringBuilder hiddenSeqsBuilder = new StringBuilder();
 292     for (SequenceI hiddenSeq : hiddenSeqs)
 293     {
 294       if (hiddenSeq != null)
 295       {
 296         hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
 297       }
 298     }
 299     if (hiddenSeqsBuilder.length() > 0)
 300     {
 301       hiddenSeqsBuilder.deleteCharAt(0);
 302     }
 303     hiddenSections[1] = hiddenSeqsBuilder.toString();
 304
 305     return hiddenSections;
 306   }
 307
 308   public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
 309           List<SequenceI> seqs, FeatureRenderer fr)
 310   {
 311     displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
 312     List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
 313     for (SequenceI seq : seqs)
 314     {
 315       SequenceI dataSetSequence = seq.getDatasetSequence();
 316       SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
 317               : seq.getDatasetSequence().getSequenceFeatures();
 318
 319       seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
 320               : seqFeatures;
 321       if (seqFeatures == null)
 322       {
 323         continue;
 324       }
 325
 326       for (SequenceFeature sf : seqFeatures)
 327       {
 328         if (displayedFeatures != null
 329                 && displayedFeatures.isVisible(sf.getType()))
 330         {
 331           SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
 332                   String.valueOf(seq.hashCode()));
 333
 334           String featureColour = (fr == null) ? null : jalview.util.Format
 335                   .getHexString(fr.findFeatureColour(Color.white, seq,
 336                           seq.findIndex(sf.getBegin())));
 337           jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
 338           jsonFeature.setXend(seq.findIndex(sf.getEnd()));
 339           jsonFeature.setType(sf.getType());
 340           jsonFeature.setDescription(sf.getDescription());
 341           jsonFeature.setLinks(sf.links);
 342           jsonFeature.setOtherDetails(sf.otherDetails);
 343           jsonFeature.setScore(sf.getScore());
 344           jsonFeature.setFillColor(featureColour);
 345           jsonFeature.setFeatureGroup(sf.getFeatureGroup());
 346           sequenceFeaturesPojo.add(jsonFeature);
 347         }
 348       }
 349     }
 350     return sequenceFeaturesPojo;
 351   }
 352
 353   public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
 354           Vector<AlignmentAnnotation> annotations)
 355   {
 356     List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
 357     if (annotations == null)
 358     {
 359       return jsonAnnotations;
 360     }
 361     for (AlignmentAnnotation annot : annotations)
 362     {
 363       AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
 364       alignAnnotPojo.setDescription(annot.description);
 365       alignAnnotPojo.setLabel(annot.label);
 366       for (Annotation annotation : annot.annotations)
 367       {
 368         AnnotationPojo annotationPojo = new AnnotationPojo();
 369         if (annotation != null)
 370         {
 371           annotationPojo.setDescription(annotation.description);
 372           annotationPojo.setValue(annotation.value);
 373           annotationPojo
 374                   .setSecondaryStructure(annotation.secondaryStructure);
 375           annotationPojo.setDisplayCharacter(annotation.displayCharacter);
 376           alignAnnotPojo.getAnnotations().add(annotationPojo);
 377         }
 378         else
 379         {
 380           alignAnnotPojo.getAnnotations().add(annotationPojo);
 381         }
 382       }
 383       jsonAnnotations.add(alignAnnotPojo);
 384     }
 385     return jsonAnnotations;
 386   }
 387
 388   @SuppressWarnings("unchecked")
 389   public JSONFile parse(Reader jsonAlignmentString)
 390   {
 391     try
 392     {
 393       JSONParser jsonParser = new JSONParser();
 394       JSONObject alignmentJsonObj = (JSONObject) jsonParser
 395               .parse(jsonAlignmentString);
 396       JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
 397       JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
 398               .get("alignAnnotation");
 399       JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
 400               .get("seqFeatures");
 401       JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
 402               .get("seqGroups");
 403       JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
 404               .get("appSettings");
 405
 406       if (jvSettingsJsonObj != null)
 407       {
 408         String jsColourScheme = (String) jvSettingsJsonObj
 409                 .get("globalColorScheme");
 410         Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
 411                 "showSeqFeatures").toString());
 412         setColourScheme(getJalviewColorScheme(jsColourScheme));
 413         setShowSeqFeatures(showFeatures);
 414         parseHiddenSeqRefsAsList(jvSettingsJsonObj);
 415         parseHiddenCols(jvSettingsJsonObj);
 416       }
 417
 418       hiddenSequences = new ArrayList<SequenceI>();
 419       seqMap = new Hashtable<String, Sequence>();
 420       for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
 421               .hasNext();)
 422       {
 423         JSONObject sequence = sequenceIter.next();
 424         String sequcenceString = sequence.get("seq").toString();
 425         String sequenceName = sequence.get("name").toString();
 426         String seqUniqueId = sequence.get("id").toString();
 427         int start = Integer.valueOf(sequence.get("start").toString());
 428         int end = Integer.valueOf(sequence.get("end").toString());
 429         Sequence seq = new Sequence(sequenceName, sequcenceString, start,
 430                 end);
 431         if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
 432         {
 433           hiddenSequences.add(seq);
 434         }
 435         seqs.add(seq);
 436         seqMap.put(seqUniqueId, seq);
 437       }
 438       parseFeatures(jsonSeqArray);
 439
 440       for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
 441               .hasNext();)
 442       {
 443         JSONObject seqGrpObj = seqGrpIter.next();
 444         String grpName = seqGrpObj.get("groupName").toString();
 445         String colourScheme = seqGrpObj.get("colourScheme").toString();
 446         String description = (seqGrpObj.get("description") == null) ? null
 447                 : seqGrpObj.get("description").toString();
 448         boolean displayBoxes = Boolean.valueOf(seqGrpObj
 449                 .get("displayBoxes").toString());
 450         boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
 451                 .toString());
 452         boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
 453                 .toString());
 454         boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
 455                 "showNonconserved").toString());
 456         int startRes = Integer
 457                 .valueOf(seqGrpObj.get("startRes").toString());
 458         int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
 459         JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
 460
 461         ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
 462         if (sequenceRefs.size() > 0)
 463         {
 464           Iterator<String> seqHashIter = sequenceRefs.iterator();
 465           while (seqHashIter.hasNext())
 466           {
 467             String seqHash = seqHashIter.next();
 468             Sequence sequence = seqMap.get(seqHash);
 469             if (sequence != null)
 470             {
 471               grpSeqs.add(sequence);
 472             }
 473           }
 474         }
 475         ColourSchemeI grpColourScheme = getJalviewColorScheme(colourScheme);
 476         SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName,
 477                 grpColourScheme, displayBoxes, displayText, colourText,
 478                 startRes, endRes);
 479         seqGrp.setShowNonconserved(showNonconserved);
 480         seqGrp.setDescription(description);
 481         this.seqGroups.add(seqGrp);
 482
 483       }
 484
 485       for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
 486               .hasNext();)
 487       {
 488         JSONObject alAnnot = alAnnotIter.next();
 489         JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
 490         Annotation[] annotations = new Annotation[annotJsonArray.size()];
 491         int count = 0;
 492         for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
 493                 .hasNext();)
 494         {
 495           JSONObject annot = annotIter.next();
 496           if (annot == null)
 497           {
 498             annotations[count] = null;
 499           }
 500           else
 501           {
 502             float val = annot.get("value") == null ? null : Float
 503                     .valueOf(annot.get("value").toString());
 504             String desc = annot.get("description") == null ? null : annot
 505                     .get("description").toString();
 506             char ss = annot.get("secondaryStructure") == null
 507                     || annot.get("secondaryStructure").toString()
 508                             .equalsIgnoreCase("u0000") ? ' ' : annot
 509                     .get("secondaryStructure").toString().charAt(0);
 510             String displayChar = annot.get("displayCharacter") == null ? ""
 511                     : annot.get("displayCharacter").toString();
 512
 513             annotations[count] = new Annotation(displayChar, desc, ss, val);
 514           }
 515           ++count;
 516         }
 517
 518         AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
 519                 .get("label").toString(), alAnnot.get("description")
 520                 .toString(), annotations);
 521         this.annotations.add(alignAnnot);
 522       }
 523
 524     } catch (Exception e)
 525     {
 526       e.printStackTrace();
 527     }
 528     return this;
 529   }
 530
 531   public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
 532   {
 533     hiddenSeqRefs = new ArrayList<String>();
 534     String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
 535     if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
 536     {
 537       String[] seqRefs = hiddenSeqs.split(";");
 538       for (String seqRef : seqRefs)
 539       {
 540         hiddenSeqRefs.add(seqRef);
 541       }
 542     }
 543   }
 544
 545   public void parseHiddenCols(JSONObject jvSettingsJson)
 546   {
 547     String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
 548     if (hiddenCols != null && !hiddenCols.isEmpty())
 549     {
 550       columnSelection = new ColumnSelection();
 551       String[] rangeStrings = hiddenCols.split(";");
 552       for (String rangeString : rangeStrings)
 553       {
 554         String[] range = rangeString.split("-");
 555         columnSelection.hideColumns(Integer.valueOf(range[0]),
 556                 Integer.valueOf(range[1]));
 557       }
 558     }
 559   }
 560
 561   @SuppressWarnings("unchecked")
 562   private void parseFeatures(JSONArray jsonSeqFeatures)
 563   {
 564     if (jsonSeqFeatures != null)
 565     {
 566       displayedFeatures = new FeaturesDisplayed();
 567       for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
 568               .hasNext();)
 569       {
 570         JSONObject jsonFeature = seqFeatureItr.next();
 571         Long begin = (Long) jsonFeature.get("xStart");
 572         Long end = (Long) jsonFeature.get("xEnd");
 573         String type = (String) jsonFeature.get("type");
 574         String featureGrp = (String) jsonFeature.get("featureGroup");
 575         String descripiton = (String) jsonFeature.get("description");
 576         String seqRef = (String) jsonFeature.get("sequenceRef");
 577         Float score = Float.valueOf(jsonFeature.get("score").toString());
 578
 579         Sequence seq = seqMap.get(seqRef);
 580         SequenceFeature sequenceFeature = new SequenceFeature();
 581         JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
 582         if (linksJsonArray != null && linksJsonArray.size() > 0)
 583         {
 584           Iterator<String> linkList = linksJsonArray.iterator();
 585           while (linkList.hasNext())
 586           {
 587             String link = linkList.next();
 588             sequenceFeature.addLink(link);
 589           }
 590         }
 591         sequenceFeature.setFeatureGroup(featureGrp);
 592         sequenceFeature.setScore(score);
 593         sequenceFeature.setDescription(descripiton);
 594         sequenceFeature.setType(type);
 595         sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
 596         sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
 597         seq.addSequenceFeature(sequenceFeature);
 598         displayedFeatures.setVisible(type);
 599       }
 600     }
 601   }
 602
 603   public static ColourSchemeI getJalviewColorScheme(
 604           String bioJsColourSchemeName)
 605   {
 606     ColourSchemeI jalviewColor = null;
 607     for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
 608             .values())
 609     {
 610       if (cs.getBioJsName().equalsIgnoreCase(bioJsColourSchemeName)
 611               || cs.getJalviewName()
 612                       .equalsIgnoreCase(bioJsColourSchemeName))
 613       {
 614         jalviewColor = cs.getJvColourScheme();
 615         break;
 616       }
 617     }
 618     return jalviewColor;
 619   }
 620
 621   public String getGlobalColorScheme()
 622   {
 623     return globalColorScheme;
 624   }
 625
 626   public void setGlobalColorScheme(String globalColorScheme)
 627   {
 628     this.globalColorScheme = globalColorScheme;
 629   }
 630
 631   public ColourSchemeI getColourScheme()
 632   {
 633     return colourScheme;
 634   }
 635
 636   public void setColourScheme(ColourSchemeI colourScheme)
 637   {
 638     this.colourScheme = colourScheme;
 639   }
 640
 641   @Override
 642   public FeaturesDisplayedI getDisplayedFeatures()
 643   {
 644     return displayedFeatures;
 645   }
 646
 647   public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
 648   {
 649     this.displayedFeatures = displayedFeatures;
 650   }
 651
 652   public void configureForView(AlignmentViewPanel avpanel)
 653   {
 654     super.configureForView(avpanel);
 655     AlignViewportI viewport = avpanel.getAlignViewport();
 656     AlignmentI alignment = viewport.getAlignment();
 657     AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
 658
 659     seqGroups = alignment.getGroups();
 660     fr = avpanel.cloneFeatureRenderer();
 661
 662     // Add non auto calculated annotation to AlignFile
 663     for (AlignmentAnnotation annot : annots)
 664     {
 665       if (annot != null && !annot.autoCalculated)
 666       {
 667         if (!annot.visible)
 668         {
 669           continue;
 670         }
 671         annotations.add(annot);
 672       }
 673     }
 674     globalColorScheme = ColourSchemeProperty.getColourName(viewport
 675             .getGlobalColourScheme());
 676     setDisplayedFeatures(viewport.getFeaturesDisplayed());
 677     showSeqFeatures = viewport.isShowSequenceFeatures();
 678
 679   }
 680
 681   public boolean isShowSeqFeatures()
 682   {
 683     return showSeqFeatures;
 684   }
 685
 686   public void setShowSeqFeatures(boolean showSeqFeatures)
 687   {
 688     this.showSeqFeatures = showSeqFeatures;
 689   }
 690
 691   public Vector<AlignmentAnnotation> getAnnotations()
 692   {
 693     return annotations;
 694   }
 695
 696   public List<int[]> getHiddenColumns()
 697   {
 698     return hiddenColumns;
 699   }
 700
 701   public ColumnSelection getColumnSelection()
 702   {
 703     return columnSelection;
 704   }
 705
 706   public void setColumnSelection(ColumnSelection columnSelection)
 707   {
 708     this.columnSelection = columnSelection;
 709   }
 710
 711   public SequenceI[] getHiddenSequences()
 712   {
 713     if (hiddenSequences == null || hiddenSequences.isEmpty())
 714     {
 715       return new SequenceI[] {};
 716     }
 717     synchronized (hiddenSequences)
 718     {
 719       return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
 720     }
 721   }
 722
 723   public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
 724   {
 725     this.hiddenSequences = hiddenSequences;
 726   }
 727
 728   public class JSONExportSettings
 729   {
 730     private boolean exportSequence;
 731
 732     private boolean exportSequenceFeatures;
 733
 734     private boolean exportAnnotations;
 735
 736     private boolean exportGroups;
 737
 738     private boolean exportJalviewSettings;
 739
 740     public boolean isExportSequence()
 741     {
 742       return exportSequence;
 743     }
 744
 745     public void setExportSequence(boolean exportSequence)
 746     {
 747       this.exportSequence = exportSequence;
 748     }
 749
 750     public boolean isExportSequenceFeatures()
 751     {
 752       return exportSequenceFeatures;
 753     }
 754
 755     public void setExportSequenceFeatures(boolean exportSequenceFeatures)
 756     {
 757       this.exportSequenceFeatures = exportSequenceFeatures;
 758     }
 759
 760     public boolean isExportAnnotations()
 761     {
 762       return exportAnnotations;
 763     }
 764
 765     public void setExportAnnotations(boolean exportAnnotations)
 766     {
 767       this.exportAnnotations = exportAnnotations;
 768     }
 769
 770     public boolean isExportGroups()
 771     {
 772       return exportGroups;
 773     }
 774
 775     public void setExportGroups(boolean exportGroups)
 776     {
 777       this.exportGroups = exportGroups;
 778     }
 779
 780     public boolean isExportJalviewSettings()
 781     {
 782       return exportJalviewSettings;
 783     }
 784
 785     public void setExportJalviewSettings(boolean exportJalviewSettings)
 786     {
 787       this.exportJalviewSettings = exportJalviewSettings;
 788     }
 789   }
 790 }