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.AlignExportSettingsI;
  25 import jalview.api.AlignViewportI;
  26 import jalview.api.AlignmentViewPanel;
  27 import jalview.api.ComplexAlignFile;
  28 import jalview.api.FeatureRenderer;
  29 import jalview.api.FeatureSettingsModelI;
  30 import jalview.api.FeaturesDisplayedI;
  31 import jalview.bin.BuildDetails;
  32 import jalview.datamodel.AlignExportSettingsAdapter;
  33 import jalview.datamodel.AlignmentAnnotation;
  34 import jalview.datamodel.AlignmentI;
  35 import jalview.datamodel.Annotation;
  36 import jalview.datamodel.HiddenColumns;
  37 import jalview.datamodel.HiddenSequences;
  38 import jalview.datamodel.Sequence;
  39 import jalview.datamodel.SequenceFeature;
  40 import jalview.datamodel.SequenceGroup;
  41 import jalview.datamodel.SequenceI;
  42 import jalview.json.binding.biojson.v1.AlignmentAnnotationPojo;
  43 import jalview.json.binding.biojson.v1.AlignmentPojo;
  44 import jalview.json.binding.biojson.v1.AnnotationDisplaySettingPojo;
  45 import jalview.json.binding.biojson.v1.AnnotationPojo;
  46 import jalview.json.binding.biojson.v1.ColourSchemeMapper;
  47 import jalview.json.binding.biojson.v1.SequenceFeaturesPojo;
  48 import jalview.json.binding.biojson.v1.SequenceGrpPojo;
  49 import jalview.json.binding.biojson.v1.SequencePojo;
  50 import jalview.renderer.seqfeatures.FeatureColourFinder;
  51 import jalview.schemes.ColourSchemeProperty;
  52 import jalview.schemes.JalviewColourScheme;
  53 import jalview.schemes.ResidueColourScheme;
  54 import jalview.util.ColorUtils;
  55 import jalview.util.Format;
  56 import jalview.util.JSONUtils;
  57 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
  58
  59 import java.awt.Color;
  60 import java.io.IOException;
  61 import java.io.Reader;
  62 import java.util.ArrayList;
  63 import java.util.Hashtable;
  64 import java.util.Iterator;
  65 import java.util.List;
  66 import java.util.Map;
  67 import java.util.Vector;
  68
  69 public class JSONFile extends AlignFile implements ComplexAlignFile
  70 {
  71   private static String version = new BuildDetails().getVersion();
  72
  73   private String webstartUrl = "https://www.jalview.org/services/launchApp";
  74
  75   private String application = "Jalview";
  76
  77   private String globalColourScheme;
  78
  79   private boolean showSeqFeatures;
  80
  81   private Hashtable<String, Sequence> seqMap;
  82
  83   private FeaturesDisplayedI displayedFeatures;
  84
  85   private FeatureRenderer fr;
  86
  87   private HiddenColumns hiddenColumns;
  88
  89   private List<String> hiddenSeqRefs;
  90
  91   private ArrayList<SequenceI> hiddenSequences;
  92
  93   private final static String TCOFFEE_SCORE = "TCoffeeScore";
  94
  95   public JSONFile()
  96   {
  97     super();
  98   }
  99
 100   public JSONFile(FileParse source) throws IOException
 101   {
 102     super(source);
 103   }
 104
 105   public JSONFile(String inFile, DataSourceType sourceType)
 106           throws IOException
 107   {
 108     super(inFile, sourceType);
 109   }
 110
 111   @Override
 112   public void parse() throws IOException
 113   {
 114     parse(getReader());
 115
 116   }
 117
 118   @Override
 119   public String print(SequenceI[] sqs, boolean jvsuffix)
 120   {
 121     String jsonOutput = null;
 122     try
 123     {
 124       AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
 125       AlignExportSettingsI exportSettings = getExportSettings();
 126
 127       /*
 128        * if no export settings were supplied, provide an 'export all' setting
 129        */
 130       if (exportSettings == null)
 131       {
 132         exportSettings = new AlignExportSettingsAdapter(true);
 133       }
 134
 135       int count = 0;
 136       for (SequenceI seq : sqs)
 137       {
 138         StringBuilder name = new StringBuilder();
 139         name.append(seq.getName()).append("/").append(seq.getStart())
 140                 .append("-").append(seq.getEnd());
 141         SequencePojo jsonSeqPojo = new SequencePojo();
 142         jsonSeqPojo.setId(String.valueOf(seq.hashCode()));
 143         jsonSeqPojo.setOrder(++count);
 144         jsonSeqPojo.setEnd(seq.getEnd());
 145         jsonSeqPojo.setStart(seq.getStart());
 146         jsonSeqPojo.setName(name.toString());
 147         jsonSeqPojo.setSeq(seq.getSequenceAsString());
 148         jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
 149       }
 150       jsonAlignmentPojo.setGlobalColorScheme(globalColourScheme);
 151       jsonAlignmentPojo.getAppSettings().put("application", application);
 152       jsonAlignmentPojo.getAppSettings().put("version", version);
 153       jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
 154       jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
 155               String.valueOf(showSeqFeatures));
 156
 157       String[] hiddenSections = getHiddenSections();
 158       if (hiddenSections != null)
 159       {
 160         if (hiddenSections[0] != null
 161                 && exportSettings.isExportHiddenColumns())
 162         {
 163           jsonAlignmentPojo.getAppSettings().put("hiddenCols",
 164                   String.valueOf(hiddenSections[0]));
 165         }
 166         if (hiddenSections[1] != null
 167                 && exportSettings.isExportHiddenSequences())
 168         {
 169           jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
 170                   String.valueOf(hiddenSections[1]));
 171         }
 172       }
 173
 174       if (exportSettings.isExportAnnotations())
 175       {
 176         jsonAlignmentPojo
 177                 .setAlignAnnotation(annotationToJsonPojo(annotations));
 178       }
 179       else
 180       {
 181         // These color schemes require annotation, disable them if annotations
 182         // are not exported
 183         if (globalColourScheme
 184                 .equalsIgnoreCase(JalviewColourScheme.RNAHelices.toString())
 185                 || globalColourScheme.equalsIgnoreCase(
 186                         JalviewColourScheme.TCoffee.toString()))
 187         {
 188           jsonAlignmentPojo.setGlobalColorScheme(ResidueColourScheme.NONE);
 189         }
 190       }
 191
 192       if (exportSettings.isExportFeatures())
 193       {
 194         jsonAlignmentPojo.setSeqFeatures(sequenceFeatureToJsonPojo(sqs));
 195       }
 196
 197       if (exportSettings.isExportGroups() && seqGroups != null
 198               && seqGroups.size() > 0)
 199       {
 200         for (SequenceGroup seqGrp : seqGroups)
 201         {
 202           SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
 203           seqGrpPojo.setGroupName(seqGrp.getName());
 204           seqGrpPojo.setColourScheme(ColourSchemeProperty
 205                   .getColourName(seqGrp.getColourScheme()));
 206           seqGrpPojo.setColourText(seqGrp.getColourText());
 207           seqGrpPojo.setDescription(seqGrp.getDescription());
 208           seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
 209           seqGrpPojo.setDisplayText(seqGrp.getDisplayText());
 210           seqGrpPojo.setEndRes(seqGrp.getEndRes());
 211           seqGrpPojo.setStartRes(seqGrp.getStartRes());
 212           seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
 213           for (SequenceI seq : seqGrp.getSequences())
 214           {
 215             seqGrpPojo.getSequenceRefs()
 216                     .add(String.valueOf(seq.hashCode()));
 217           }
 218           jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
 219         }
 220       }
 221
 222       jsonOutput = JSONUtils.stringify(jsonAlignmentPojo);
 223       return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
 224               "xEnd");
 225     } catch (Exception e)
 226     {
 227       e.printStackTrace();
 228     }
 229     return jsonOutput;
 230   }
 231
 232   public String[] getHiddenSections()
 233   {
 234     String[] hiddenSections = new String[2];
 235     if (getViewport() == null)
 236     {
 237       return null;
 238     }
 239
 240     // hidden column business
 241     if (getViewport().hasHiddenColumns())
 242     {
 243       hiddenSections[0] = getViewport().getAlignment().getHiddenColumns()
 244               .regionsToString(";", "-");
 245     }
 246
 247     // hidden rows/seqs business
 248     HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
 249             .getHiddenSequences();
 250     if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
 251     {
 252       return hiddenSections;
 253     }
 254
 255     SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
 256     StringBuilder hiddenSeqsBuilder = new StringBuilder();
 257     for (SequenceI hiddenSeq : hiddenSeqs)
 258     {
 259       if (hiddenSeq != null)
 260       {
 261         hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
 262       }
 263     }
 264     if (hiddenSeqsBuilder.length() > 0)
 265     {
 266       hiddenSeqsBuilder.deleteCharAt(0);
 267     }
 268     hiddenSections[1] = hiddenSeqsBuilder.toString();
 269
 270     return hiddenSections;
 271   }
 272
 273   protected List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
 274           SequenceI[] sqs)
 275   {
 276     displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
 277     List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<>();
 278     if (sqs == null)
 279     {
 280       return sequenceFeaturesPojo;
 281     }
 282
 283     FeatureColourFinder finder = new FeatureColourFinder(fr);
 284
 285     String[] visibleFeatureTypes = displayedFeatures == null ? null
 286             : displayedFeatures.getVisibleFeatures().toArray(
 287                     new String[displayedFeatures.getVisibleFeatureCount()]);
 288
 289     for (SequenceI seq : sqs)
 290     {
 291       /*
 292        * get all features currently visible (and any non-positional features)
 293        */
 294       List<SequenceFeature> seqFeatures = seq.getFeatures().getAllFeatures(
 295               visibleFeatureTypes);
 296       for (SequenceFeature sf : seqFeatures)
 297       {
 298         SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
 299                 String.valueOf(seq.hashCode()));
 300
 301         String featureColour = (fr == null) ? null : Format
 302                 .getHexString(finder.findFeatureColour(Color.white, seq,
 303                         seq.findIndex(sf.getBegin())));
 304         int xStart = sf.getBegin() == 0 ? 0
 305                 : seq.findIndex(sf.getBegin()) - 1;
 306         int xEnd = sf.getEnd() == 0 ? 0 : seq.findIndex(sf.getEnd());
 307         jsonFeature.setXstart(xStart);
 308         jsonFeature.setXend(xEnd);
 309         jsonFeature.setType(sf.getType());
 310         jsonFeature.setDescription(sf.getDescription());
 311         jsonFeature.setLinks(sf.links);
 312         jsonFeature.setOtherDetails(sf.otherDetails);
 313         jsonFeature.setScore(sf.getScore());
 314         jsonFeature.setFillColor(featureColour);
 315         jsonFeature.setFeatureGroup(sf.getFeatureGroup());
 316         sequenceFeaturesPojo.add(jsonFeature);
 317       }
 318     }
 319     return sequenceFeaturesPojo;
 320   }
 321
 322   public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
 323           Vector<AlignmentAnnotation> annotations)
 324   {
 325     List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<>();
 326     if (annotations == null)
 327     {
 328       return jsonAnnotations;
 329     }
 330     for (AlignmentAnnotation annot : annotations)
 331     {
 332       AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
 333       alignAnnotPojo.setDescription(annot.description);
 334       alignAnnotPojo.setLabel(annot.label);
 335       if (!Double.isNaN(annot.score))
 336       {
 337         alignAnnotPojo.setScore(annot.score);
 338       }
 339       alignAnnotPojo.setCalcId(annot.getCalcId());
 340       alignAnnotPojo.setGraphType(annot.graph);
 341
 342       AnnotationDisplaySettingPojo annotSetting = new AnnotationDisplaySettingPojo();
 343       annotSetting.setBelowAlignment(annot.belowAlignment);
 344       annotSetting.setCentreColLabels(annot.centreColLabels);
 345       annotSetting.setScaleColLabel(annot.scaleColLabel);
 346       annotSetting.setShowAllColLabels(annot.showAllColLabels);
 347       annotSetting.setVisible(annot.visible);
 348       annotSetting.setHasIcon(annot.hasIcons);
 349       alignAnnotPojo.setAnnotationSettings(annotSetting);
 350       SequenceI refSeq = annot.sequenceRef;
 351       if (refSeq != null)
 352       {
 353         alignAnnotPojo.setSequenceRef(String.valueOf(refSeq.hashCode()));
 354       }
 355       for (Annotation annotation : annot.annotations)
 356       {
 357         AnnotationPojo annotationPojo = new AnnotationPojo();
 358         if (annotation != null)
 359         {
 360           annotationPojo.setDescription(annotation.description);
 361           annotationPojo.setValue(annotation.value);
 362           annotationPojo
 363                   .setSecondaryStructure(annotation.secondaryStructure);
 364           String displayChar = annotation.displayCharacter == null ? null
 365                   : annotation.displayCharacter;
 366           // System.out.println("--------------------->[" + displayChar + "]");
 367           annotationPojo.setDisplayCharacter(displayChar);
 368           if (annotation.colour != null)
 369           {
 370             annotationPojo.setColour(
 371                     jalview.util.Format.getHexString(annotation.colour));
 372           }
 373           alignAnnotPojo.getAnnotations().add(annotationPojo);
 374         }
 375         else
 376         {
 377           if (annot.getCalcId() != null
 378                   && annot.getCalcId().equalsIgnoreCase(TCOFFEE_SCORE))
 379           {
 380             // do nothing
 381           }
 382           else
 383           {
 384             alignAnnotPojo.getAnnotations().add(annotationPojo);
 385           }
 386         }
 387       }
 388       jsonAnnotations.add(alignAnnotPojo);
 389     }
 390     return jsonAnnotations;
 391   }
 392
 393   @SuppressWarnings("unchecked")
 394   public JSONFile parse(Reader jsonAlignmentString)
 395   {
 396     try
 397     {
 398       Map<String, Object> alignmentJsonObj = (Map<String, Object>) JSONUtils.parse(jsonAlignmentString);
 399       List<Object> seqJsonArray = (List<Object>) alignmentJsonObj.get("seqs");
 400       List<Object> alAnnotJsonArray = (List<Object>) alignmentJsonObj
 401               .get("alignAnnotation");
 402       List<Object> jsonSeqArray = (List<Object>) alignmentJsonObj
 403               .get("seqFeatures");
 404       List<Object> seqGrpJsonArray = (List<Object>) alignmentJsonObj
 405               .get("seqGroups");
 406       Map<String, Object> jvSettingsJsonObj = (Map<String, Object>) alignmentJsonObj
 407               .get("appSettings");
 408
 409       if (jvSettingsJsonObj != null)
 410       {
 411         globalColourScheme = (String) jvSettingsJsonObj
 412                 .get("globalColorScheme");
 413         Boolean showFeatures = Boolean.valueOf(
 414                 jvSettingsJsonObj.get("showSeqFeatures").toString());
 415         setShowSeqFeatures(showFeatures);
 416         parseHiddenSeqRefsAsList(jvSettingsJsonObj);
 417         parseHiddenCols(jvSettingsJsonObj);
 418       }
 419
 420       hiddenSequences = new ArrayList<>();
 421       seqMap = new Hashtable<>();
 422       for (Iterator<Object> sequenceIter = seqJsonArray.iterator(); sequenceIter.hasNext();)
 423       {
 424         Map<String, Object> sequence = (Map<String, Object>) sequenceIter.next();
 425         String sequcenceString = sequence.get("seq").toString();
 426         String sequenceName = sequence.get("name").toString();
 427         String seqUniqueId = sequence.get("id").toString();
 428         int start = Integer.valueOf(sequence.get("start").toString());
 429         int end = Integer.valueOf(sequence.get("end").toString());
 430         Sequence seq = new Sequence(sequenceName, sequcenceString, start,
 431                 end);
 432         if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
 433         {
 434           hiddenSequences.add(seq);
 435         }
 436         seqs.add(seq);
 437         seqMap.put(seqUniqueId, seq);
 438       }
 439
 440       parseFeatures(jsonSeqArray);
 441
 442       for (Iterator<Object> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter.hasNext();)
 443       {
 444         Map<String, Object> seqGrpObj = (Map<String, Object>)seqGrpIter.next();
 445         String grpName = seqGrpObj.get("groupName").toString();
 446         String colourScheme = seqGrpObj.get("colourScheme").toString();
 447         String description = (seqGrpObj.get("description") == null) ? null
 448                 : seqGrpObj.get("description").toString();
 449         boolean displayBoxes = Boolean
 450                 .valueOf(seqGrpObj.get("displayBoxes").toString());
 451         boolean displayText = Boolean
 452                 .valueOf(seqGrpObj.get("displayText").toString());
 453         boolean colourText = Boolean
 454                 .valueOf(seqGrpObj.get("colourText").toString());
 455         boolean showNonconserved = Boolean
 456                 .valueOf(seqGrpObj.get("showNonconserved").toString());
 457         int startRes = Integer
 458                 .valueOf(seqGrpObj.get("startRes").toString());
 459         int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
 460         List<Object> sequenceRefs = (List<Object>) seqGrpObj.get("sequenceRefs");
 461
 462         ArrayList<SequenceI> grpSeqs = new ArrayList<>();
 463         if (sequenceRefs.size() > 0)
 464         {
 465           Iterator<Object> seqHashIter = sequenceRefs.iterator();
 466           while (seqHashIter.hasNext())
 467           {
 468             Sequence sequence = seqMap.get(seqHashIter.next());
 469             if (sequence != null)
 470             {
 471               grpSeqs.add(sequence);
 472             }
 473           }
 474         }
 475         SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
 476                 displayBoxes, displayText, colourText, startRes, endRes);
 477         seqGrp.setColourScheme(ColourSchemeMapper
 478                 .getJalviewColourScheme(colourScheme, seqGrp));
 479         seqGrp.setShowNonconserved(showNonconserved);
 480         seqGrp.setDescription(description);
 481         this.seqGroups.add(seqGrp);
 482
 483       }
 484
 485       for (Iterator<Object> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter.hasNext();)
 486       {
 487         Map<String, Object> alAnnot = (Map<String, Object>) alAnnotIter.next();
 488         List<Object> annotJsonArray = (List<Object>) alAnnot.get("annotations");
 489         Annotation[] annotations = new Annotation[annotJsonArray.size()];
 490         int count = 0;
 491         for (Iterator<Object> annotIter = annotJsonArray.iterator(); annotIter.hasNext();)
 492         {
 493           Map<String, Object> annot = (Map<String, Object>) annotIter.next();
 494           if (annot == null)
 495           {
 496             annotations[count] = null;
 497           }
 498           else
 499           {
 500             float val = annot.get("value") == null ? null
 501                     : Float.valueOf(annot.get("value").toString());
 502             String desc = annot.get("description") == null ? null
 503                     : annot.get("description").toString();
 504             char ss = annot.get("secondaryStructure") == null
 505                     || annot.get("secondaryStructure").toString()
 506                             .equalsIgnoreCase("u0000") ? ' '
 507                                     : annot.get("secondaryStructure")
 508                                             .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             if (annot.get("colour") != null)
 514             {
 515               Color color = ColorUtils
 516                       .parseColourString(annot.get("colour").toString());
 517               annotations[count].colour = color;
 518             }
 519           }
 520           ++count;
 521         }
 522
 523         AlignmentAnnotation alignAnnot = new AlignmentAnnotation(
 524                 alAnnot.get("label").toString(),
 525                 alAnnot.get("description").toString(), annotations);
 526         alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0
 527                 : Integer.valueOf(alAnnot.get("graphType").toString());
 528
 529         Map<String, Object> diplaySettings = (Map<String, Object>) alAnnot
 530                 .get("annotationSettings");
 531         if (diplaySettings != null)
 532         {
 533
 534           alignAnnot.scaleColLabel = (diplaySettings
 535                   .get("scaleColLabel") == null) ? false
 536                           : Boolean.valueOf(diplaySettings
 537                                   .get("scaleColLabel").toString());
 538           alignAnnot.showAllColLabels = (diplaySettings
 539                   .get("showAllColLabels") == null) ? true
 540                           : Boolean.valueOf(diplaySettings
 541                                   .get("showAllColLabels").toString());
 542           alignAnnot.centreColLabels = (diplaySettings
 543                   .get("centreColLabels") == null) ? true
 544                           : Boolean.valueOf(diplaySettings
 545                                   .get("centreColLabels").toString());
 546           alignAnnot.belowAlignment = (diplaySettings
 547                   .get("belowAlignment") == null) ? false
 548                           : Boolean.valueOf(diplaySettings
 549                                   .get("belowAlignment").toString());
 550           alignAnnot.visible = (diplaySettings.get("visible") == null)
 551                   ? true
 552                   : Boolean.valueOf(
 553                           diplaySettings.get("visible").toString());
 554           alignAnnot.hasIcons = (diplaySettings.get("hasIcon") == null)
 555                   ? true
 556                   : Boolean.valueOf(
 557                           diplaySettings.get("hasIcon").toString());
 558
 559         }
 560         if (alAnnot.get("score") != null)
 561         {
 562           alignAnnot.score = Double
 563                   .valueOf(alAnnot.get("score").toString());
 564         }
 565
 566         String calcId = (alAnnot.get("calcId") == null) ? ""
 567                 : alAnnot.get("calcId").toString();
 568         alignAnnot.setCalcId(calcId);
 569         String seqHash = (alAnnot.get("sequenceRef") != null)
 570                 ? alAnnot.get("sequenceRef").toString()
 571                 : null;
 572
 573         Sequence sequence = (seqHash != null) ? seqMap.get(seqHash) : null;
 574         if (sequence != null)
 575         {
 576           alignAnnot.sequenceRef = sequence;
 577           sequence.addAlignmentAnnotation(alignAnnot);
 578           if (alignAnnot.label.equalsIgnoreCase("T-COFFEE"))
 579           {
 580             alignAnnot.createSequenceMapping(sequence, sequence.getStart(),
 581                     false);
 582             sequence.addAlignmentAnnotation(alignAnnot);
 583             alignAnnot.adjustForAlignment();
 584           }
 585         }
 586         alignAnnot.validateRangeAndDisplay();
 587         this.annotations.add(alignAnnot);
 588
 589       }
 590     } catch (Exception e)
 591     {
 592       e.printStackTrace();
 593     }
 594     return this;
 595   }
 596
 597   public void parseHiddenSeqRefsAsList(Map<String, Object> jvSettingsJson)
 598   {
 599     hiddenSeqRefs = new ArrayList<>();
 600     String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
 601     if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
 602     {
 603       String[] seqRefs = hiddenSeqs.split(";");
 604       for (int i = 0, n = seqRefs.length; i < n; i++)
 605       {
 606         hiddenSeqRefs.add(seqRefs[i]);
 607       }
 608     }
 609   }
 610
 611   public void parseHiddenCols(Map<String, Object> jvSettingsJson)
 612   {
 613     String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
 614     if (hiddenCols != null && !hiddenCols.isEmpty())
 615     {
 616       hiddenColumns = new HiddenColumns();
 617       String[] rangeStrings = hiddenCols.split(";");
 618       for (int i = 0, n = rangeStrings.length; i < n; i++)
 619       {
 620         String[] range = rangeStrings[i].split("-");
 621         hiddenColumns.hideColumns(Integer.valueOf(range[0]),
 622                 Integer.valueOf(range[1]));
 623       }
 624     }
 625   }
 626
 627   @SuppressWarnings("unchecked")
 628   private void parseFeatures(List<Object> jsonSeqFeatures)
 629   {
 630     if (jsonSeqFeatures != null)
 631     {
 632       displayedFeatures = new FeaturesDisplayed();
 633       for (Object o : jsonSeqFeatures)
 634       {
 635         Map<String, Object> jsonFeature = (Map<String, Object>) o;
 636         Long begin = (Long) jsonFeature.get("xStart");
 637         Long end = (Long) jsonFeature.get("xEnd");
 638         String type = (String) jsonFeature.get("type");
 639         String featureGrp = (String) jsonFeature.get("featureGroup");
 640         String description = (String) jsonFeature.get("description");
 641         String seqRef = (String) jsonFeature.get("sequenceRef");
 642         Float score = Float.valueOf(jsonFeature.get("score").toString());
 643
 644         Sequence seq = seqMap.get(seqRef);
 645
 646         /*
 647          * begin/end of 0 is for a non-positional feature
 648          */
 649         int featureBegin = begin.intValue() == 0 ? 0 : seq
 650                 .findPosition(begin.intValue());
 651         int featureEnd = end.intValue() == 0 ? 0 : seq.findPosition(end
 652                 .intValue()) - 1;
 653
 654         SequenceFeature sequenceFeature = new SequenceFeature(type,
 655                 description, featureBegin, featureEnd, score, featureGrp);
 656
 657         List<Object> linksJsonArray = (List<Object>) jsonFeature.get("links");
 658         if (linksJsonArray != null && linksJsonArray.size() > 0)
 659         {
 660           Iterator<Object> linkList = linksJsonArray.iterator();
 661           while (linkList.hasNext())
 662           {
 663             sequenceFeature.addLink((String) linkList.next());
 664           }
 665         }
 666
 667         seq.addSequenceFeature(sequenceFeature);
 668         displayedFeatures.setVisible(type);
 669       }
 670     }
 671   }
 672
 673   @Override
 674   public String getGlobalColourScheme()
 675   {
 676     return globalColourScheme;
 677   }
 678
 679   public void setGlobalColorScheme(String globalColourScheme)
 680   {
 681     this.globalColourScheme = globalColourScheme;
 682   }
 683
 684   @Override
 685   public FeaturesDisplayedI getDisplayedFeatures()
 686   {
 687     return displayedFeatures;
 688   }
 689
 690   public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
 691   {
 692     this.displayedFeatures = displayedFeatures;
 693   }
 694
 695   @Override
 696   public void configureForView(AlignmentViewPanel avpanel)
 697   {
 698     if (avpanel == null)
 699     {
 700       return;
 701     }
 702     super.configureForView(avpanel);
 703     AlignViewportI viewport = avpanel.getAlignViewport();
 704     AlignmentI alignment = viewport.getAlignment();
 705     AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
 706
 707     seqGroups = alignment.getGroups();
 708     fr = avpanel.cloneFeatureRenderer();
 709
 710     // Add non auto calculated annotation to AlignFile
 711     if (annots != null)
 712     {
 713       for (AlignmentAnnotation annot : annots)
 714       {
 715         if (annot != null && !annot.autoCalculated)
 716         {
 717           annotations.add(annot);
 718         }
 719       }
 720     }
 721     globalColourScheme = ColourSchemeProperty
 722             .getColourName(viewport.getGlobalColourScheme());
 723     setDisplayedFeatures(viewport.getFeaturesDisplayed());
 724     showSeqFeatures = viewport.isShowSequenceFeatures();
 725
 726   }
 727
 728   @Override
 729   public boolean isShowSeqFeatures()
 730   {
 731     return showSeqFeatures;
 732   }
 733
 734   public void setShowSeqFeatures(boolean showSeqFeatures)
 735   {
 736     this.showSeqFeatures = showSeqFeatures;
 737   }
 738
 739   public Vector<AlignmentAnnotation> getAnnotations()
 740   {
 741     return annotations;
 742   }
 743
 744   @Override
 745   public HiddenColumns getHiddenColumns()
 746   {
 747     return hiddenColumns;
 748   }
 749
 750   public void setHiddenColumns(HiddenColumns hidden)
 751   {
 752     this.hiddenColumns = hidden;
 753   }
 754
 755   @Override
 756   public SequenceI[] getHiddenSequences()
 757   {
 758     if (hiddenSequences == null || hiddenSequences.isEmpty())
 759     {
 760       return new SequenceI[] {};
 761     }
 762     synchronized (hiddenSequences)
 763     {
 764       return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
 765     }
 766   }
 767
 768   public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
 769   {
 770     this.hiddenSequences = hiddenSequences;
 771   }
 772
 773   public class JSONExportSettings
 774   {
 775     private boolean exportSequence;
 776
 777     private boolean exportSequenceFeatures;
 778
 779     private boolean exportAnnotations;
 780
 781     private boolean exportGroups;
 782
 783     private boolean exportJalviewSettings;
 784
 785     public boolean isExportSequence()
 786     {
 787       return exportSequence;
 788     }
 789
 790     public void setExportSequence(boolean exportSequence)
 791     {
 792       this.exportSequence = exportSequence;
 793     }
 794
 795     public boolean isExportSequenceFeatures()
 796     {
 797       return exportSequenceFeatures;
 798     }
 799
 800     public void setExportSequenceFeatures(boolean exportSequenceFeatures)
 801     {
 802       this.exportSequenceFeatures = exportSequenceFeatures;
 803     }
 804
 805     public boolean isExportAnnotations()
 806     {
 807       return exportAnnotations;
 808     }
 809
 810     public void setExportAnnotations(boolean exportAnnotations)
 811     {
 812       this.exportAnnotations = exportAnnotations;
 813     }
 814
 815     public boolean isExportGroups()
 816     {
 817       return exportGroups;
 818     }
 819
 820     public void setExportGroups(boolean exportGroups)
 821     {
 822       this.exportGroups = exportGroups;
 823     }
 824
 825     public boolean isExportJalviewSettings()
 826     {
 827       return exportJalviewSettings;
 828     }
 829
 830     public void setExportJalviewSettings(boolean exportJalviewSettings)
 831     {
 832       this.exportJalviewSettings = exportJalviewSettings;
 833     }
 834   }
 835
 836   /**
 837    * Returns a descriptor for suitable feature display settings with
 838    * <ul>
 839    * <li>ResNums or insertions features visible</li>
 840    * <li>insertions features coloured red</li>
 841    * <li>ResNum features coloured by label</li>
 842    * <li>Insertions displayed above (on top of) ResNums</li>
 843    * </ul>
 844    */
 845   @Override
 846   public FeatureSettingsModelI getFeatureColourScheme()
 847   {
 848     return new PDBFeatureSettings();
 849   }
 850 }