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.ColourSchemeMapper;
  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.ColourSchemeProperty;
  48 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
  49
  50 import java.awt.Color;
  51 import java.io.IOException;
  52 import java.io.Reader;
  53 import java.util.ArrayList;
  54 import java.util.Hashtable;
  55 import java.util.Iterator;
  56 import java.util.List;
  57 import java.util.Vector;
  58
  59 import org.json.simple.JSONArray;
  60 import org.json.simple.JSONObject;
  61 import org.json.simple.parser.JSONParser;
  62
  63 public class JSONFile extends AlignFile implements ComplexAlignFile
  64 {
  65   private static String version = new BuildDetails().getVersion();
  66
  67   private String webstartUrl = "http://www.jalview.org/services/launchApp";
  68
  69   private String application = "Jalview";
  70
  71   public static final String FILE_EXT = "json";
  72
  73   public static final String FILE_DESC = "JSON";
  74
  75   private String globalColourScheme;
  76
  77   private boolean showSeqFeatures;
  78
  79   private Hashtable<String, Sequence> seqMap;
  80
  81   private FeaturesDisplayedI displayedFeatures;
  82
  83   private FeatureRenderer fr;
  84
  85   private List<int[]> hiddenColumns;
  86
  87   private ColumnSelection columnSelection;
  88
  89   private List<String> hiddenSeqRefs;
  90
  91   private ArrayList<SequenceI> hiddenSequences;
  92
  93   public JSONFile()
  94   {
  95     super();
  96   }
  97
  98   public JSONFile(FileParse source) throws IOException
  99   {
 100     super(source);
 101   }
 102
 103   public JSONFile(String inFile, String type) throws IOException
 104   {
 105     super(inFile, type);
 106   }
 107
 108   @Override
 109   public void parse() throws IOException
 110   {
 111     parse(getReader());
 112
 113   }
 114
 115   @Override
 116   public String print()
 117   {
 118     String jsonOutput = null;
 119     try
 120     {
 121       AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
 122       AlignExportSettingI exportSettings = getExportSettings();
 123
 124       // if no export settings were supplied use the following with all values
 125       // defaulting to true
 126       if (exportSettings == null)
 127       {
 128         exportSettings = new AlignExportSettingI()
 129         {
 130           @Override
 131           public boolean isExportHiddenSequences()
 132           {
 133             return true;
 134           }
 135
 136           @Override
 137           public boolean isExportHiddenColumns()
 138           {
 139             return true;
 140           }
 141
 142           @Override
 143           public boolean isExportGroups()
 144           {
 145             return true;
 146           }
 147
 148           @Override
 149           public boolean isExportFeatures()
 150           {
 151             return true;
 152           }
 153
 154           @Override
 155           public boolean isExportAnnotations()
 156           {
 157             return true;
 158           }
 159
 160           @Override
 161           public boolean isCancelled()
 162           {
 163             return false;
 164           }
 165         };
 166       }
 167
 168       int count = 0;
 169       for (SequenceI seq : seqs)
 170       {
 171         StringBuilder name = new StringBuilder();
 172         name.append(seq.getName()).append("/").append(seq.getStart())
 173                 .append("-").append(seq.getEnd());
 174         SequencePojo jsonSeqPojo = new SequencePojo();
 175         jsonSeqPojo.setId(String.valueOf(seq.hashCode()));
 176         jsonSeqPojo.setOrder(++count);
 177         jsonSeqPojo.setEnd(seq.getEnd());
 178         jsonSeqPojo.setStart(seq.getStart());
 179         jsonSeqPojo.setName(name.toString());
 180         jsonSeqPojo.setSeq(seq.getSequenceAsString());
 181         jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
 182       }
 183       jsonAlignmentPojo.setGlobalColorScheme(globalColourScheme);
 184       jsonAlignmentPojo.getAppSettings().put("application", application);
 185       jsonAlignmentPojo.getAppSettings().put("version", version);
 186       jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
 187       jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
 188               String.valueOf(showSeqFeatures));
 189
 190       String[] hiddenSections = getHiddenSections();
 191       if (hiddenSections != null)
 192       {
 193         if (hiddenSections[0] != null
 194                 && exportSettings.isExportHiddenColumns())
 195         {
 196           jsonAlignmentPojo.getAppSettings().put("hiddenCols",
 197                   String.valueOf(hiddenSections[0]));
 198         }
 199         if (hiddenSections[1] != null
 200                 && exportSettings.isExportHiddenSequences())
 201         {
 202           jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
 203                   String.valueOf(hiddenSections[1]));
 204         }
 205       }
 206
 207       if (exportSettings.isExportAnnotations())
 208       {
 209         jsonAlignmentPojo
 210                 .setAlignAnnotation(annotationToJsonPojo(annotations));
 211       }
 212
 213       if (exportSettings.isExportFeatures())
 214       {
 215         jsonAlignmentPojo
 216                 .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
 217       }
 218
 219       if (exportSettings.isExportGroups() && 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.getFeaturesDisplayed();
 309     List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
 310     for (SequenceI seq : seqs)
 311     {
 312       SequenceI dataSetSequence = seq.getDatasetSequence();
 313       SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
 314               : seq.getDatasetSequence().getSequenceFeatures();
 315
 316       seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
 317               : seqFeatures;
 318       if (seqFeatures == null)
 319       {
 320         continue;
 321       }
 322
 323       for (SequenceFeature sf : seqFeatures)
 324       {
 325         if (displayedFeatures != null
 326                 && displayedFeatures.isVisible(sf.getType()))
 327         {
 328           SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
 329                   String.valueOf(seq.hashCode()));
 330
 331           String featureColour = (fr == null) ? null : jalview.util.Format
 332                   .getHexString(fr.findFeatureColour(Color.white, seq,
 333                           seq.findIndex(sf.getBegin())));
 334           jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
 335           jsonFeature.setXend(seq.findIndex(sf.getEnd()));
 336           jsonFeature.setType(sf.getType());
 337           jsonFeature.setDescription(sf.getDescription());
 338           jsonFeature.setLinks(sf.links);
 339           jsonFeature.setOtherDetails(sf.otherDetails);
 340           jsonFeature.setScore(sf.getScore());
 341           jsonFeature.setFillColor(featureColour);
 342           jsonFeature.setFeatureGroup(sf.getFeatureGroup());
 343           sequenceFeaturesPojo.add(jsonFeature);
 344         }
 345       }
 346     }
 347     return sequenceFeaturesPojo;
 348   }
 349
 350   public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
 351           Vector<AlignmentAnnotation> annotations)
 352   {
 353     List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
 354     if (annotations == null)
 355     {
 356       return jsonAnnotations;
 357     }
 358     for (AlignmentAnnotation annot : annotations)
 359     {
 360       AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
 361       alignAnnotPojo.setDescription(annot.description);
 362       alignAnnotPojo.setLabel(annot.label);
 363       for (Annotation annotation : annot.annotations)
 364       {
 365         AnnotationPojo annotationPojo = new AnnotationPojo();
 366         if (annotation != null)
 367         {
 368           annotationPojo.setDescription(annotation.description);
 369           annotationPojo.setValue(annotation.value);
 370           annotationPojo
 371                   .setSecondaryStructure(annotation.secondaryStructure);
 372           annotationPojo.setDisplayCharacter(annotation.displayCharacter);
 373           alignAnnotPojo.getAnnotations().add(annotationPojo);
 374         }
 375         else
 376         {
 377           alignAnnotPojo.getAnnotations().add(annotationPojo);
 378         }
 379       }
 380       jsonAnnotations.add(alignAnnotPojo);
 381     }
 382     return jsonAnnotations;
 383   }
 384
 385   @SuppressWarnings("unchecked")
 386   public JSONFile parse(Reader jsonAlignmentString)
 387   {
 388     try
 389     {
 390       JSONParser jsonParser = new JSONParser();
 391       JSONObject alignmentJsonObj = (JSONObject) jsonParser
 392               .parse(jsonAlignmentString);
 393       JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
 394       JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
 395               .get("alignAnnotation");
 396       JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
 397               .get("seqFeatures");
 398       JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
 399               .get("seqGroups");
 400       JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
 401               .get("appSettings");
 402
 403       if (jvSettingsJsonObj != null)
 404       {
 405         globalColourScheme = (String) jvSettingsJsonObj
 406                 .get("globalColorScheme");
 407         Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
 408                 "showSeqFeatures").toString());
 409         setShowSeqFeatures(showFeatures);
 410         parseHiddenSeqRefsAsList(jvSettingsJsonObj);
 411         parseHiddenCols(jvSettingsJsonObj);
 412       }
 413
 414       hiddenSequences = new ArrayList<SequenceI>();
 415       seqMap = new Hashtable<String, Sequence>();
 416       for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
 417               .hasNext();)
 418       {
 419         JSONObject sequence = sequenceIter.next();
 420         String sequcenceString = sequence.get("seq").toString();
 421         String sequenceName = sequence.get("name").toString();
 422         String seqUniqueId = sequence.get("id").toString();
 423         int start = Integer.valueOf(sequence.get("start").toString());
 424         int end = Integer.valueOf(sequence.get("end").toString());
 425         Sequence seq = new Sequence(sequenceName, sequcenceString, start,
 426                 end);
 427         if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
 428         {
 429           hiddenSequences.add(seq);
 430         }
 431         seqs.add(seq);
 432         seqMap.put(seqUniqueId, seq);
 433       }
 434
 435
 436       parseFeatures(jsonSeqArray);
 437
 438       for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
 439               .hasNext();)
 440       {
 441         JSONObject seqGrpObj = seqGrpIter.next();
 442         String grpName = seqGrpObj.get("groupName").toString();
 443         String colourScheme = seqGrpObj.get("colourScheme").toString();
 444         String description = (seqGrpObj.get("description") == null) ? null
 445                 : seqGrpObj.get("description").toString();
 446         boolean displayBoxes = Boolean.valueOf(seqGrpObj
 447                 .get("displayBoxes").toString());
 448         boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
 449                 .toString());
 450         boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
 451                 .toString());
 452         boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
 453                 "showNonconserved").toString());
 454         int startRes = Integer
 455                 .valueOf(seqGrpObj.get("startRes").toString());
 456         int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
 457         JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
 458
 459         ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
 460         if (sequenceRefs.size() > 0)
 461         {
 462           Iterator<String> seqHashIter = sequenceRefs.iterator();
 463           while (seqHashIter.hasNext())
 464           {
 465             String seqHash = seqHashIter.next();
 466             Sequence sequence = seqMap.get(seqHash);
 467             if (sequence != null)
 468             {
 469               grpSeqs.add(sequence);
 470             }
 471           }
 472         }
 473         SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
 474                 displayBoxes, displayText, colourText,
 475                 startRes, endRes);
 476         seqGrp.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme,
 477                 seqGrp);
 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             char ss = annot.get("secondaryStructure") == null
 506                     || annot.get("secondaryStructure").toString()
 507                             .equalsIgnoreCase("u0000") ? ' ' : 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     } catch (Exception e)
 523     {
 524       e.printStackTrace();
 525     }
 526     return this;
 527   }
 528
 529   public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
 530   {
 531     hiddenSeqRefs = new ArrayList<String>();
 532     String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
 533     if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
 534     {
 535       String[] seqRefs = hiddenSeqs.split(";");
 536       for (String seqRef : seqRefs)
 537       {
 538         hiddenSeqRefs.add(seqRef);
 539       }
 540     }
 541   }
 542
 543   public void parseHiddenCols(JSONObject jvSettingsJson)
 544   {
 545     String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
 546     if (hiddenCols != null && !hiddenCols.isEmpty())
 547     {
 548       columnSelection = new ColumnSelection();
 549       String[] rangeStrings = hiddenCols.split(";");
 550       for (String rangeString : rangeStrings)
 551       {
 552         String[] range = rangeString.split("-");
 553         columnSelection.hideColumns(Integer.valueOf(range[0]),
 554                 Integer.valueOf(range[1]));
 555       }
 556     }
 557   }
 558
 559   @SuppressWarnings("unchecked")
 560   private void parseFeatures(JSONArray jsonSeqFeatures)
 561   {
 562     if (jsonSeqFeatures != null)
 563     {
 564       displayedFeatures = new FeaturesDisplayed();
 565       for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
 566               .hasNext();)
 567       {
 568         JSONObject jsonFeature = seqFeatureItr.next();
 569         Long begin = (Long) jsonFeature.get("xStart");
 570         Long end = (Long) jsonFeature.get("xEnd");
 571         String type = (String) jsonFeature.get("type");
 572         String featureGrp = (String) jsonFeature.get("featureGroup");
 573         String descripiton = (String) jsonFeature.get("description");
 574         String seqRef = (String) jsonFeature.get("sequenceRef");
 575         Float score = Float.valueOf(jsonFeature.get("score").toString());
 576
 577         Sequence seq = seqMap.get(seqRef);
 578         SequenceFeature sequenceFeature = new SequenceFeature();
 579         JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
 580         if (linksJsonArray != null && linksJsonArray.size() > 0)
 581         {
 582           Iterator<String> linkList = linksJsonArray.iterator();
 583           while (linkList.hasNext())
 584           {
 585             String link = linkList.next();
 586             sequenceFeature.addLink(link);
 587           }
 588         }
 589         sequenceFeature.setFeatureGroup(featureGrp);
 590         sequenceFeature.setScore(score);
 591         sequenceFeature.setDescription(descripiton);
 592         sequenceFeature.setType(type);
 593         sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
 594         sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
 595         seq.addSequenceFeature(sequenceFeature);
 596         displayedFeatures.setVisible(type);
 597       }
 598     }
 599   }
 600
 601   public String getGlobalColourScheme()
 602   {
 603     return globalColourScheme;
 604   }
 605
 606   public void setGlobalColorScheme(String globalColourScheme)
 607   {
 608     this.globalColourScheme = globalColourScheme;
 609   }
 610
 611   @Override
 612   public FeaturesDisplayedI getDisplayedFeatures()
 613   {
 614     return displayedFeatures;
 615   }
 616
 617   public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
 618   {
 619     this.displayedFeatures = displayedFeatures;
 620   }
 621
 622   public void configureForView(AlignmentViewPanel avpanel)
 623   {
 624     super.configureForView(avpanel);
 625     AlignViewportI viewport = avpanel.getAlignViewport();
 626     AlignmentI alignment = viewport.getAlignment();
 627     AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
 628
 629     seqGroups = alignment.getGroups();
 630     fr = avpanel.cloneFeatureRenderer();
 631
 632     // Add non auto calculated annotation to AlignFile
 633     for (AlignmentAnnotation annot : annots)
 634     {
 635       if (annot != null && !annot.autoCalculated)
 636       {
 637         if (!annot.visible)
 638         {
 639           continue;
 640         }
 641         annotations.add(annot);
 642       }
 643     }
 644     globalColourScheme = ColourSchemeProperty.getColourName(viewport
 645             .getGlobalColourScheme());
 646     setDisplayedFeatures(viewport.getFeaturesDisplayed());
 647     showSeqFeatures = viewport.isShowSequenceFeatures();
 648
 649   }
 650
 651   public boolean isShowSeqFeatures()
 652   {
 653     return showSeqFeatures;
 654   }
 655
 656   public void setShowSeqFeatures(boolean showSeqFeatures)
 657   {
 658     this.showSeqFeatures = showSeqFeatures;
 659   }
 660
 661   public Vector<AlignmentAnnotation> getAnnotations()
 662   {
 663     return annotations;
 664   }
 665
 666   public List<int[]> getHiddenColumns()
 667   {
 668     return hiddenColumns;
 669   }
 670
 671   public ColumnSelection getColumnSelection()
 672   {
 673     return columnSelection;
 674   }
 675
 676   public void setColumnSelection(ColumnSelection columnSelection)
 677   {
 678     this.columnSelection = columnSelection;
 679   }
 680
 681   public SequenceI[] getHiddenSequences()
 682   {
 683     if (hiddenSequences == null || hiddenSequences.isEmpty())
 684     {
 685       return new SequenceI[] {};
 686     }
 687     synchronized (hiddenSequences)
 688     {
 689       return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
 690     }
 691   }
 692
 693   public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
 694   {
 695     this.hiddenSequences = hiddenSequences;
 696   }
 697
 698   public class JSONExportSettings
 699   {
 700     private boolean exportSequence;
 701
 702     private boolean exportSequenceFeatures;
 703
 704     private boolean exportAnnotations;
 705
 706     private boolean exportGroups;
 707
 708     private boolean exportJalviewSettings;
 709
 710     public boolean isExportSequence()
 711     {
 712       return exportSequence;
 713     }
 714
 715     public void setExportSequence(boolean exportSequence)
 716     {
 717       this.exportSequence = exportSequence;
 718     }
 719
 720     public boolean isExportSequenceFeatures()
 721     {
 722       return exportSequenceFeatures;
 723     }
 724
 725     public void setExportSequenceFeatures(boolean exportSequenceFeatures)
 726     {
 727       this.exportSequenceFeatures = exportSequenceFeatures;
 728     }
 729
 730     public boolean isExportAnnotations()
 731     {
 732       return exportAnnotations;
 733     }
 734
 735     public void setExportAnnotations(boolean exportAnnotations)
 736     {
 737       this.exportAnnotations = exportAnnotations;
 738     }
 739
 740     public boolean isExportGroups()
 741     {
 742       return exportGroups;
 743     }
 744
 745     public void setExportGroups(boolean exportGroups)
 746     {
 747       this.exportGroups = exportGroups;
 748     }
 749
 750     public boolean isExportJalviewSettings()
 751     {
 752       return exportJalviewSettings;
 753     }
 754
 755     public void setExportJalviewSettings(boolean exportJalviewSettings)
 756     {
 757       this.exportJalviewSettings = exportJalviewSettings;
 758     }
 759   }
 760 }