src/jalview/io/JSONFile.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21
  22 package jalview.io;
  23
  24 import jalview.api.AlignExportSettingI;
  25 import jalview.api.AlignViewportI;
  26 import jalview.api.AlignmentViewPanel;
  27 import jalview.api.ComplexAlignFile;
  28 import jalview.api.FeatureRenderer;
  29 import jalview.api.FeaturesDisplayedI;
  30 import jalview.bin.BuildDetails;
  31 import jalview.datamodel.AlignmentAnnotation;
  32 import jalview.datamodel.AlignmentI;
  33 import jalview.datamodel.Annotation;
  34 import jalview.datamodel.ColumnSelection;
  35 import jalview.datamodel.HiddenSequences;
  36 import jalview.datamodel.Sequence;
  37 import jalview.datamodel.SequenceFeature;
  38 import jalview.datamodel.SequenceGroup;
  39 import jalview.datamodel.SequenceI;
  40 import jalview.json.binding.biojson.v1.AlignmentAnnotationPojo;
  41 import jalview.json.binding.biojson.v1.AlignmentPojo;
  42 import jalview.json.binding.biojson.v1.AnnotationPojo;
  43 import jalview.json.binding.biojson.v1.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
 507             char ss = annot.get("secondaryStructure") == null ? ' ' : annot
 508                     .get("secondaryStructure").toString().charAt(0);
 509             String displayChar = annot.get("displayCharacter") == null ? ""
 510                     : annot.get("displayCharacter").toString();
 511
 512             annotations[count] = new Annotation(displayChar, desc, ss, val);
 513           }
 514           ++count;
 515         }
 516
 517         AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
 518                 .get("label").toString(), alAnnot.get("description")
 519                 .toString(), annotations);
 520         this.annotations.add(alignAnnot);
 521       }
 522
 523     } catch (Exception e)
 524     {
 525       e.printStackTrace();
 526     }
 527     return this;
 528   }
 529
 530   public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
 531   {
 532     hiddenSeqRefs = new ArrayList<String>();
 533     String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
 534     if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
 535     {
 536       String[] seqRefs = hiddenSeqs.split(";");
 537       for (String seqRef : seqRefs)
 538       {
 539         hiddenSeqRefs.add(seqRef);
 540       }
 541     }
 542   }
 543
 544   public void parseHiddenCols(JSONObject jvSettingsJson)
 545   {
 546     String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
 547     if (hiddenCols != null && !hiddenCols.isEmpty())
 548     {
 549       columnSelection = new ColumnSelection();
 550       String[] rangeStrings = hiddenCols.split(";");
 551       for (String rangeString : rangeStrings)
 552       {
 553         String[] range = rangeString.split("-");
 554         columnSelection.hideColumns(Integer.valueOf(range[0]),
 555                 Integer.valueOf(range[1]));
 556       }
 557     }
 558   }
 559
 560   @SuppressWarnings("unchecked")
 561   private void parseFeatures(JSONArray jsonSeqFeatures)
 562   {
 563     if (jsonSeqFeatures != null)
 564     {
 565       displayedFeatures = new FeaturesDisplayed();
 566       for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
 567               .hasNext();)
 568       {
 569         JSONObject jsonFeature = seqFeatureItr.next();
 570         Long begin = (Long) jsonFeature.get("xStart");
 571         Long end = (Long) jsonFeature.get("xEnd");
 572         String type = (String) jsonFeature.get("type");
 573         String featureGrp = (String) jsonFeature.get("featureGroup");
 574         String descripiton = (String) jsonFeature.get("description");
 575         String seqRef = (String) jsonFeature.get("sequenceRef");
 576         Float score = Float.valueOf(jsonFeature.get("score").toString());
 577
 578         Sequence seq = seqMap.get(seqRef);
 579         SequenceFeature sequenceFeature = new SequenceFeature();
 580         JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
 581         if (linksJsonArray != null && linksJsonArray.size() > 0)
 582         {
 583           Iterator<String> linkList = linksJsonArray.iterator();
 584           while (linkList.hasNext())
 585           {
 586             String link = linkList.next();
 587             sequenceFeature.addLink(link);
 588           }
 589         }
 590         sequenceFeature.setFeatureGroup(featureGrp);
 591         sequenceFeature.setScore(score);
 592         sequenceFeature.setDescription(descripiton);
 593         sequenceFeature.setType(type);
 594         sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
 595         sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
 596         seq.addSequenceFeature(sequenceFeature);
 597         displayedFeatures.setVisible(type);
 598       }
 599     }
 600   }
 601
 602   public static ColourSchemeI getJalviewColorScheme(
 603           String bioJsColourSchemeName)
 604   {
 605     ColourSchemeI jalviewColor = null;
 606     for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
 607             .values())
 608     {
 609       if (cs.getBioJsName().equalsIgnoreCase(bioJsColourSchemeName))
 610       {
 611         jalviewColor = cs.getJvColourScheme();
 612         break;
 613       }
 614     }
 615     return jalviewColor;
 616   }
 617
 618   public String getGlobalColorScheme()
 619   {
 620     return globalColorScheme;
 621   }
 622
 623   public void setGlobalColorScheme(String globalColorScheme)
 624   {
 625     this.globalColorScheme = globalColorScheme;
 626   }
 627
 628   public ColourSchemeI getColourScheme()
 629   {
 630     return colourScheme;
 631   }
 632
 633   public void setColourScheme(ColourSchemeI colourScheme)
 634   {
 635     this.colourScheme = colourScheme;
 636   }
 637
 638   @Override
 639   public FeaturesDisplayedI getDisplayedFeatures()
 640   {
 641     return displayedFeatures;
 642   }
 643
 644   public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
 645   {
 646     this.displayedFeatures = displayedFeatures;
 647   }
 648
 649   public void configureForView(AlignmentViewPanel avpanel)
 650   {
 651     super.configureForView(avpanel);
 652     AlignViewportI viewport = avpanel.getAlignViewport();
 653     AlignmentI alignment = viewport.getAlignment();
 654     AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
 655
 656     seqGroups = alignment.getGroups();
 657     fr = avpanel.cloneFeatureRenderer();
 658
 659     // Add non auto calculated annotation to AlignFile
 660     for (AlignmentAnnotation annot : annots)
 661     {
 662       if (annot != null && !annot.autoCalculated)
 663       {
 664         if (!annot.visible)
 665         {
 666           continue;
 667         }
 668         annotations.add(annot);
 669       }
 670     }
 671     globalColorScheme = ColourSchemeProperty.getColourName(viewport
 672             .getGlobalColourScheme());
 673     setDisplayedFeatures(viewport.getFeaturesDisplayed());
 674     showSeqFeatures = viewport.isShowSequenceFeatures();
 675
 676   }
 677
 678   public boolean isShowSeqFeatures()
 679   {
 680     return showSeqFeatures;
 681   }
 682
 683   public void setShowSeqFeatures(boolean showSeqFeatures)
 684   {
 685     this.showSeqFeatures = showSeqFeatures;
 686   }
 687
 688   public Vector<AlignmentAnnotation> getAnnotations()
 689   {
 690     return annotations;
 691   }
 692
 693   public List<int[]> getHiddenColumns()
 694   {
 695     return hiddenColumns;
 696   }
 697
 698   public ColumnSelection getColumnSelection()
 699   {
 700     return columnSelection;
 701   }
 702
 703   public void setColumnSelection(ColumnSelection columnSelection)
 704   {
 705     this.columnSelection = columnSelection;
 706   }
 707
 708   public SequenceI[] getHiddenSequences()
 709   {
 710     if (hiddenSequences == null || hiddenSequences.isEmpty())
 711     {
 712       return new SequenceI[] {};
 713     }
 714     synchronized (hiddenSequences)
 715     {
 716       return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
 717     }
 718   }
 719
 720   public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
 721   {
 722     this.hiddenSequences = hiddenSequences;
 723   }
 724
 725   public class JSONExportSettings
 726   {
 727     private boolean exportSequence;
 728
 729     private boolean exportSequenceFeatures;
 730
 731     private boolean exportAnnotations;
 732
 733     private boolean exportGroups;
 734
 735     private boolean exportJalviewSettings;
 736
 737     public boolean isExportSequence()
 738     {
 739       return exportSequence;
 740     }
 741
 742     public void setExportSequence(boolean exportSequence)
 743     {
 744       this.exportSequence = exportSequence;
 745     }
 746
 747     public boolean isExportSequenceFeatures()
 748     {
 749       return exportSequenceFeatures;
 750     }
 751
 752     public void setExportSequenceFeatures(boolean exportSequenceFeatures)
 753     {
 754       this.exportSequenceFeatures = exportSequenceFeatures;
 755     }
 756
 757     public boolean isExportAnnotations()
 758     {
 759       return exportAnnotations;
 760     }
 761
 762     public void setExportAnnotations(boolean exportAnnotations)
 763     {
 764       this.exportAnnotations = exportAnnotations;
 765     }
 766
 767     public boolean isExportGroups()
 768     {
 769       return exportGroups;
 770     }
 771
 772     public void setExportGroups(boolean exportGroups)
 773     {
 774       this.exportGroups = exportGroups;
 775     }
 776
 777     public boolean isExportJalviewSettings()
 778     {
 779       return exportJalviewSettings;
 780     }
 781
 782     public void setExportJalviewSettings(boolean exportJalviewSettings)
 783     {
 784       this.exportJalviewSettings = exportJalviewSettings;
 785     }
 786   }
 787 }