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       }
 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.isExportHiddenColumns())
 192         {
 193           jsonAlignmentPojo.getAppSettings().put("hiddenCols",
 194                   String.valueOf(hiddenSections[0]));
 195         }
 196         if (hiddenSections[1] != null
 197                 && exportSettings.isExportHiddenSequences())
 198         {
 199           jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
 200                   String.valueOf(hiddenSections[1]));
 201         }
 202       }
 203
 204       if (exportSettings.isExportAnnotations())
 205       {
 206         jsonAlignmentPojo
 207                 .setAlignAnnotation(annotationToJsonPojo(annotations));
 208       }
 209
 210       if (exportSettings.isExportFeatures())
 211       {
 212         jsonAlignmentPojo
 213                 .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
 214       }
 215
 216       if (exportSettings.isExportGroups() && seqGroups != null
 217               && seqGroups.size() > 0)
 218       {
 219         for (SequenceGroup seqGrp : seqGroups)
 220         {
 221           SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
 222           seqGrpPojo.setGroupName(seqGrp.getName());
 223           seqGrpPojo.setColourScheme(ColourSchemeProperty
 224                   .getColourName(seqGrp.cs));
 225           seqGrpPojo.setColourText(seqGrp.getColourText());
 226           seqGrpPojo.setDescription(seqGrp.getDescription());
 227           seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
 228           seqGrpPojo.setDisplayText(seqGrp.getDisplayText());
 229           seqGrpPojo.setEndRes(seqGrp.getEndRes());
 230           seqGrpPojo.setStartRes(seqGrp.getStartRes());
 231           seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
 232           for (SequenceI seq : seqGrp.getSequences())
 233           {
 234             seqGrpPojo.getSequenceRefs()
 235                     .add(String.valueOf(seq.hashCode()));
 236           }
 237           jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
 238         }
 239       }
 240       org.json.JSONObject generatedJSon = new org.json.JSONObject(
 241               jsonAlignmentPojo);
 242       jsonOutput = generatedJSon.toString();
 243       return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
 244               "xEnd");
 245     } catch (Exception e)
 246     {
 247       e.printStackTrace();
 248     }
 249     return jsonOutput;
 250   }
 251
 252   public String[] getHiddenSections()
 253   {
 254     String[] hiddenSections = new String[2];
 255     if (getViewport() == null)
 256     {
 257       return null;
 258     }
 259
 260     // hidden column business
 261     if (getViewport().hasHiddenColumns())
 262     {
 263       List<int[]> hiddenCols = getViewport().getColumnSelection()
 264               .getHiddenColumns();
 265       StringBuilder hiddenColsBuilder = new StringBuilder();
 266       for (int[] range : hiddenCols)
 267       {
 268         hiddenColsBuilder.append(";").append(range[0]).append("-")
 269                 .append(range[1]);
 270       }
 271
 272       hiddenColsBuilder.deleteCharAt(0);
 273       hiddenSections[0] = hiddenColsBuilder.toString();
 274     }
 275
 276     // hidden rows/seqs business
 277     HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
 278             .getHiddenSequences();
 279     if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
 280     {
 281       return hiddenSections;
 282     }
 283
 284     SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
 285     StringBuilder hiddenSeqsBuilder = new StringBuilder();
 286     for (SequenceI hiddenSeq : hiddenSeqs)
 287     {
 288       if (hiddenSeq != null)
 289       {
 290         hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
 291       }
 292     }
 293     if (hiddenSeqsBuilder.length() > 0)
 294     {
 295       hiddenSeqsBuilder.deleteCharAt(0);
 296     }
 297     hiddenSections[1] = hiddenSeqsBuilder.toString();
 298
 299     return hiddenSections;
 300   }
 301
 302   public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
 303           List<SequenceI> seqs, FeatureRenderer fr)
 304   {
 305     displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
 306     List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
 307     for (SequenceI seq : seqs)
 308     {
 309       SequenceI dataSetSequence = seq.getDatasetSequence();
 310       SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
 311               : seq.getDatasetSequence().getSequenceFeatures();
 312
 313       seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
 314               : seqFeatures;
 315       if (seqFeatures == null)
 316       {
 317         continue;
 318       }
 319
 320       for (SequenceFeature sf : seqFeatures)
 321       {
 322         if (displayedFeatures != null
 323                 && displayedFeatures.isVisible(sf.getType()))
 324         {
 325           SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
 326                   String.valueOf(seq.hashCode()));
 327
 328           String featureColour = (fr == null) ? null : jalview.util.Format
 329                   .getHexString(fr.findFeatureColour(Color.white, seq,
 330                           seq.findIndex(sf.getBegin())));
 331           jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
 332           jsonFeature.setXend(seq.findIndex(sf.getEnd()));
 333           jsonFeature.setType(sf.getType());
 334           jsonFeature.setDescription(sf.getDescription());
 335           jsonFeature.setLinks(sf.links);
 336           jsonFeature.setOtherDetails(sf.otherDetails);
 337           jsonFeature.setScore(sf.getScore());
 338           jsonFeature.setFillColor(featureColour);
 339           jsonFeature.setFeatureGroup(sf.getFeatureGroup());
 340           sequenceFeaturesPojo.add(jsonFeature);
 341         }
 342       }
 343     }
 344     return sequenceFeaturesPojo;
 345   }
 346
 347   public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
 348           Vector<AlignmentAnnotation> annotations)
 349   {
 350     List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
 351     if (annotations == null)
 352     {
 353       return jsonAnnotations;
 354     }
 355     for (AlignmentAnnotation annot : annotations)
 356     {
 357       AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
 358       alignAnnotPojo.setDescription(annot.description);
 359       alignAnnotPojo.setLabel(annot.label);
 360       for (Annotation annotation : annot.annotations)
 361       {
 362         AnnotationPojo annotationPojo = new AnnotationPojo();
 363         if (annotation != null)
 364         {
 365           annotationPojo.setDescription(annotation.description);
 366           annotationPojo.setValue(annotation.value);
 367           annotationPojo
 368                   .setSecondaryStructure(annotation.secondaryStructure);
 369           annotationPojo.setDisplayCharacter(annotation.displayCharacter);
 370           alignAnnotPojo.getAnnotations().add(annotationPojo);
 371         }
 372         else
 373         {
 374           alignAnnotPojo.getAnnotations().add(annotationPojo);
 375         }
 376       }
 377       jsonAnnotations.add(alignAnnotPojo);
 378     }
 379     return jsonAnnotations;
 380   }
 381
 382   @SuppressWarnings("unchecked")
 383   public JSONFile parse(Reader jsonAlignmentString)
 384   {
 385     try
 386     {
 387       JSONParser jsonParser = new JSONParser();
 388       JSONObject alignmentJsonObj = (JSONObject) jsonParser
 389               .parse(jsonAlignmentString);
 390       JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
 391       JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
 392               .get("alignAnnotation");
 393       JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
 394               .get("seqFeatures");
 395       JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
 396               .get("seqGroups");
 397       JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
 398               .get("appSettings");
 399
 400       if (jvSettingsJsonObj != null)
 401       {
 402         String jsColourScheme = (String) jvSettingsJsonObj
 403                 .get("globalColorScheme");
 404         Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
 405                 "showSeqFeatures").toString());
 406         setColourScheme(getJalviewColorScheme(jsColourScheme));
 407         setShowSeqFeatures(showFeatures);
 408         parseHiddenSeqRefsAsList(jvSettingsJsonObj);
 409         parseHiddenCols(jvSettingsJsonObj);
 410       }
 411
 412       hiddenSequences = new ArrayList<SequenceI>();
 413       seqMap = new Hashtable<String, Sequence>();
 414       for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
 415               .hasNext();)
 416       {
 417         JSONObject sequence = sequenceIter.next();
 418         String sequcenceString = sequence.get("seq").toString();
 419         String sequenceName = sequence.get("name").toString();
 420         String seqUniqueId = sequence.get("id").toString();
 421         int start = Integer.valueOf(sequence.get("start").toString());
 422         int end = Integer.valueOf(sequence.get("end").toString());
 423         Sequence seq = new Sequence(sequenceName, sequcenceString, start,
 424                 end);
 425         if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
 426         {
 427           hiddenSequences.add(seq);
 428         }
 429         seqs.add(seq);
 430         seqMap.put(seqUniqueId, seq);
 431       }
 432       parseFeatures(jsonSeqArray);
 433
 434       for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
 435               .hasNext();)
 436       {
 437         JSONObject seqGrpObj = seqGrpIter.next();
 438         String grpName = seqGrpObj.get("groupName").toString();
 439         String colourScheme = seqGrpObj.get("colourScheme").toString();
 440         String description = (seqGrpObj.get("description") == null) ? null
 441                 : seqGrpObj.get("description").toString();
 442         boolean displayBoxes = Boolean.valueOf(seqGrpObj
 443                 .get("displayBoxes").toString());
 444         boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
 445                 .toString());
 446         boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
 447                 .toString());
 448         boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
 449                 "showNonconserved").toString());
 450         int startRes = Integer
 451                 .valueOf(seqGrpObj.get("startRes").toString());
 452         int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
 453         JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
 454
 455         ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
 456         if (sequenceRefs.size() > 0)
 457         {
 458           Iterator<String> seqHashIter = sequenceRefs.iterator();
 459           while (seqHashIter.hasNext())
 460           {
 461             String seqHash = seqHashIter.next();
 462             Sequence sequence = seqMap.get(seqHash);
 463             if (sequence != null)
 464             {
 465               grpSeqs.add(sequence);
 466             }
 467           }
 468         }
 469         ColourSchemeI grpColourScheme = getJalviewColorScheme(colourScheme);
 470         SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName,
 471                 grpColourScheme, displayBoxes, displayText, colourText,
 472                 startRes, endRes);
 473         seqGrp.setShowNonconserved(showNonconserved);
 474         seqGrp.setDescription(description);
 475         this.seqGroups.add(seqGrp);
 476
 477       }
 478
 479       for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
 480               .hasNext();)
 481       {
 482         JSONObject alAnnot = alAnnotIter.next();
 483         JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
 484         Annotation[] annotations = new Annotation[annotJsonArray.size()];
 485         int count = 0;
 486         for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
 487                 .hasNext();)
 488         {
 489           JSONObject annot = annotIter.next();
 490           if (annot == null)
 491           {
 492             annotations[count] = null;
 493           }
 494           else
 495           {
 496             float val = annot.get("value") == null ? null : Float
 497                     .valueOf(annot.get("value").toString());
 498             String desc = annot.get("description") == null ? null : annot
 499                     .get("description").toString();
 500
 501             char ss = annot.get("secondaryStructure") == null ? ' ' : annot
 502                     .get("secondaryStructure").toString().charAt(0);
 503             String displayChar = annot.get("displayCharacter") == null ? ""
 504                     : annot.get("displayCharacter").toString();
 505
 506             annotations[count] = new Annotation(displayChar, desc, ss, val);
 507           }
 508           ++count;
 509         }
 510
 511         AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
 512                 .get("label").toString(), alAnnot.get("description")
 513                 .toString(), annotations);
 514         this.annotations.add(alignAnnot);
 515       }
 516
 517     } catch (Exception e)
 518     {
 519       e.printStackTrace();
 520     }
 521     return this;
 522   }
 523
 524   public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
 525   {
 526     hiddenSeqRefs = new ArrayList<String>();
 527     String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
 528     if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
 529     {
 530       String[] seqRefs = hiddenSeqs.split(";");
 531       for (String seqRef : seqRefs)
 532       {
 533         hiddenSeqRefs.add(seqRef);
 534       }
 535     }
 536   }
 537
 538   public void parseHiddenCols(JSONObject jvSettingsJson)
 539   {
 540     String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
 541     if (hiddenCols != null && !hiddenCols.isEmpty())
 542     {
 543       columnSelection = new ColumnSelection();
 544       String[] rangeStrings = hiddenCols.split(";");
 545       for (String rangeString : rangeStrings)
 546       {
 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   public void configureForView(AlignmentViewPanel avpanel)
 644   {
 645     super.configureForView(avpanel);
 646     AlignViewportI viewport = avpanel.getAlignViewport();
 647     AlignmentI alignment = viewport.getAlignment();
 648     AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
 649
 650     seqGroups = alignment.getGroups();
 651     fr = avpanel.cloneFeatureRenderer();
 652
 653     // Add non auto calculated annotation to AlignFile
 654     for (AlignmentAnnotation annot : annots)
 655     {
 656       if (annot != null && !annot.autoCalculated)
 657       {
 658         if (!annot.visible)
 659         {
 660           continue;
 661         }
 662         annotations.add(annot);
 663       }
 664     }
 665     globalColorScheme = ColourSchemeProperty.getColourName(viewport
 666             .getGlobalColourScheme());
 667     setDisplayedFeatures(viewport.getFeaturesDisplayed());
 668     showSeqFeatures = viewport.isShowSequenceFeatures();
 669
 670   }
 671
 672   public boolean isShowSeqFeatures()
 673   {
 674     return showSeqFeatures;
 675   }
 676
 677   public void setShowSeqFeatures(boolean showSeqFeatures)
 678   {
 679     this.showSeqFeatures = showSeqFeatures;
 680   }
 681
 682   public Vector<AlignmentAnnotation> getAnnotations()
 683   {
 684     return annotations;
 685   }
 686
 687   public List<int[]> getHiddenColumns()
 688   {
 689     return hiddenColumns;
 690   }
 691
 692   public ColumnSelection getColumnSelection()
 693   {
 694     return columnSelection;
 695   }
 696
 697   public void setColumnSelection(ColumnSelection columnSelection)
 698   {
 699     this.columnSelection = columnSelection;
 700   }
 701
 702   public SequenceI[] getHiddenSequences()
 703   {
 704     if (hiddenSequences == null || hiddenSequences.isEmpty())
 705     {
 706       return new SequenceI[] {};
 707     }
 708     synchronized (hiddenSequences)
 709     {
 710       return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
 711     }
 712   }
 713
 714   public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
 715   {
 716     this.hiddenSequences = hiddenSequences;
 717   }
 718
 719   public class JSONExportSettings
 720   {
 721     private boolean exportSequence;
 722
 723     private boolean exportSequenceFeatures;
 724
 725     private boolean exportAnnotations;
 726
 727     private boolean exportGroups;
 728
 729     private boolean exportJalviewSettings;
 730
 731     public boolean isExportSequence()
 732     {
 733       return exportSequence;
 734     }
 735
 736     public void setExportSequence(boolean exportSequence)
 737     {
 738       this.exportSequence = exportSequence;
 739     }
 740
 741     public boolean isExportSequenceFeatures()
 742     {
 743       return exportSequenceFeatures;
 744     }
 745
 746     public void setExportSequenceFeatures(boolean exportSequenceFeatures)
 747     {
 748       this.exportSequenceFeatures = exportSequenceFeatures;
 749     }
 750
 751     public boolean isExportAnnotations()
 752     {
 753       return exportAnnotations;
 754     }
 755
 756     public void setExportAnnotations(boolean exportAnnotations)
 757     {
 758       this.exportAnnotations = exportAnnotations;
 759     }
 760
 761     public boolean isExportGroups()
 762     {
 763       return exportGroups;
 764     }
 765
 766     public void setExportGroups(boolean exportGroups)
 767     {
 768       this.exportGroups = exportGroups;
 769     }
 770
 771     public boolean isExportJalviewSettings()
 772     {
 773       return exportJalviewSettings;
 774     }
 775
 776     public void setExportJalviewSettings(boolean exportJalviewSettings)
 777     {
 778       this.exportJalviewSettings = exportJalviewSettings;
 779     }
 780   }
 781 }