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.FeatureSettingsModelI;
  30 import jalview.api.FeaturesDisplayedI;
  31 import jalview.bin.BuildDetails;
  32 import jalview.datamodel.AlignmentAnnotation;
  33 import jalview.datamodel.AlignmentI;
  34 import jalview.datamodel.Annotation;
  35 import jalview.datamodel.HiddenColumns;
  36 import jalview.datamodel.HiddenSequences;
  37 import jalview.datamodel.Sequence;
  38 import jalview.datamodel.SequenceFeature;
  39 import jalview.datamodel.SequenceGroup;
  40 import jalview.datamodel.SequenceI;
  41 import jalview.json.binding.biojson.v1.AlignmentAnnotationPojo;
  42 import jalview.json.binding.biojson.v1.AlignmentPojo;
  43 import jalview.json.binding.biojson.v1.AnnotationDisplaySettingPojo;
  44 import jalview.json.binding.biojson.v1.AnnotationPojo;
  45 import jalview.json.binding.biojson.v1.ColourSchemeMapper;
  46 import jalview.json.binding.biojson.v1.SequenceFeaturesPojo;
  47 import jalview.json.binding.biojson.v1.SequenceGrpPojo;
  48 import jalview.json.binding.biojson.v1.SequencePojo;
  49 import jalview.renderer.seqfeatures.FeatureColourFinder;
  50 import jalview.schemes.ColourSchemeProperty;
  51 import jalview.schemes.JalviewColourScheme;
  52 import jalview.schemes.ResidueColourScheme;
  53 import jalview.util.ColorUtils;
  54 import jalview.util.Format;
  55 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
  56
  57 import java.awt.Color;
  58 import java.io.IOException;
  59 import java.io.Reader;
  60 import java.util.ArrayList;
  61 import java.util.Hashtable;
  62 import java.util.Iterator;
  63 import java.util.List;
  64 import java.util.Vector;
  65
  66 import org.json.simple.JSONArray;
  67 import org.json.simple.JSONObject;
  68 import org.json.simple.parser.JSONParser;
  69
  70 public class JSONFile extends AlignFile implements ComplexAlignFile
  71 {
  72   private static String version = new BuildDetails().getVersion();
  73
  74   private String webstartUrl = "http://www.jalview.org/services/launchApp";
  75
  76   private String application = "Jalview";
  77
  78   private String globalColourScheme;
  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 HiddenColumns hiddenColumns;
  89
  90   private List<String> hiddenSeqRefs;
  91
  92   private ArrayList<SequenceI> hiddenSequences;
  93
  94   private final static String TCOFFEE_SCORE = "TCoffeeScore";
  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, DataSourceType sourceType)
 107           throws IOException
 108   {
 109     super(inFile, sourceType);
 110   }
 111
 112   @Override
 113   public void parse() throws IOException
 114   {
 115     parse(getReader());
 116
 117   }
 118
 119   @Override
 120   public String print(SequenceI[] sqs, boolean jvsuffix)
 121   {
 122     String jsonOutput = null;
 123     try
 124     {
 125       AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
 126       AlignExportSettingI exportSettings = getExportSettings();
 127
 128       // if no export settings were supplied use the following with all values
 129       // defaulting to true
 130       if (exportSettings == null)
 131       {
 132         exportSettings = new AlignExportSettingI()
 133         {
 134           @Override
 135           public boolean isExportHiddenSequences()
 136           {
 137             return true;
 138           }
 139
 140           @Override
 141           public boolean isExportHiddenColumns()
 142           {
 143             return true;
 144           }
 145
 146           @Override
 147           public boolean isExportGroups()
 148           {
 149             return true;
 150           }
 151
 152           @Override
 153           public boolean isExportFeatures()
 154           {
 155             return true;
 156           }
 157
 158           @Override
 159           public boolean isExportAnnotations()
 160           {
 161             return true;
 162           }
 163
 164           @Override
 165           public boolean isCancelled()
 166           {
 167             return false;
 168           }
 169         };
 170       }
 171
 172       int count = 0;
 173       for (SequenceI seq : sqs)
 174       {
 175         StringBuilder name = new StringBuilder();
 176         name.append(seq.getName()).append("/").append(seq.getStart())
 177                 .append("-").append(seq.getEnd());
 178         SequencePojo jsonSeqPojo = new SequencePojo();
 179         jsonSeqPojo.setId(String.valueOf(seq.hashCode()));
 180         jsonSeqPojo.setOrder(++count);
 181         jsonSeqPojo.setEnd(seq.getEnd());
 182         jsonSeqPojo.setStart(seq.getStart());
 183         jsonSeqPojo.setName(name.toString());
 184         jsonSeqPojo.setSeq(seq.getSequenceAsString());
 185         jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
 186       }
 187       jsonAlignmentPojo.setGlobalColorScheme(globalColourScheme);
 188       jsonAlignmentPojo.getAppSettings().put("application", application);
 189       jsonAlignmentPojo.getAppSettings().put("version", version);
 190       jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
 191       jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
 192               String.valueOf(showSeqFeatures));
 193
 194       String[] hiddenSections = getHiddenSections();
 195       if (hiddenSections != null)
 196       {
 197         if (hiddenSections[0] != null
 198                 && exportSettings.isExportHiddenColumns())
 199         {
 200           jsonAlignmentPojo.getAppSettings().put("hiddenCols",
 201                   String.valueOf(hiddenSections[0]));
 202         }
 203         if (hiddenSections[1] != null
 204                 && exportSettings.isExportHiddenSequences())
 205         {
 206           jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
 207                   String.valueOf(hiddenSections[1]));
 208         }
 209       }
 210
 211       if (exportSettings.isExportAnnotations())
 212       {
 213         jsonAlignmentPojo
 214                 .setAlignAnnotation(annotationToJsonPojo(annotations));
 215       }
 216       else
 217       {
 218         // These color schemes require annotation, disable them if annotations
 219         // are not exported
 220         if (globalColourScheme
 221                 .equalsIgnoreCase(JalviewColourScheme.RNAHelices.toString())
 222                 || globalColourScheme
 223                         .equalsIgnoreCase(JalviewColourScheme.TCoffee
 224                                 .toString()))
 225         {
 226           jsonAlignmentPojo.setGlobalColorScheme(ResidueColourScheme.NONE);
 227         }
 228       }
 229
 230       if (exportSettings.isExportFeatures())
 231       {
 232         jsonAlignmentPojo.setSeqFeatures(sequenceFeatureToJsonPojo(sqs));
 233       }
 234
 235       if (exportSettings.isExportGroups() && seqGroups != null
 236               && seqGroups.size() > 0)
 237       {
 238         for (SequenceGroup seqGrp : seqGroups)
 239         {
 240           SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
 241           seqGrpPojo.setGroupName(seqGrp.getName());
 242           seqGrpPojo.setColourScheme(ColourSchemeProperty
 243                   .getColourName(seqGrp.getColourScheme()));
 244           seqGrpPojo.setColourText(seqGrp.getColourText());
 245           seqGrpPojo.setDescription(seqGrp.getDescription());
 246           seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
 247           seqGrpPojo.setDisplayText(seqGrp.getDisplayText());
 248           seqGrpPojo.setEndRes(seqGrp.getEndRes());
 249           seqGrpPojo.setStartRes(seqGrp.getStartRes());
 250           seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
 251           for (SequenceI seq : seqGrp.getSequences())
 252           {
 253             seqGrpPojo.getSequenceRefs()
 254                     .add(String.valueOf(seq.hashCode()));
 255           }
 256           jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
 257         }
 258       }
 259       org.json.JSONObject generatedJSon = new org.json.JSONObject(
 260               jsonAlignmentPojo);
 261       jsonOutput = generatedJSon.toString();
 262       return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
 263               "xEnd");
 264     } catch (Exception e)
 265     {
 266       e.printStackTrace();
 267     }
 268     return jsonOutput;
 269   }
 270
 271   public String[] getHiddenSections()
 272   {
 273     String[] hiddenSections = new String[2];
 274     if (getViewport() == null)
 275     {
 276       return null;
 277     }
 278
 279     // hidden column business
 280     if (getViewport().hasHiddenColumns())
 281     {
 282       List<int[]> hiddenCols = getViewport().getAlignment()
 283               .getHiddenColumns()
 284               .getHiddenRegions();
 285       StringBuilder hiddenColsBuilder = new StringBuilder();
 286       for (int[] range : hiddenCols)
 287       {
 288         hiddenColsBuilder.append(";").append(range[0]).append("-")
 289                 .append(range[1]);
 290       }
 291
 292       hiddenColsBuilder.deleteCharAt(0);
 293       hiddenSections[0] = hiddenColsBuilder.toString();
 294     }
 295
 296     // hidden rows/seqs business
 297     HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
 298             .getHiddenSequences();
 299     if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
 300     {
 301       return hiddenSections;
 302     }
 303
 304     SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
 305     StringBuilder hiddenSeqsBuilder = new StringBuilder();
 306     for (SequenceI hiddenSeq : hiddenSeqs)
 307     {
 308       if (hiddenSeq != null)
 309       {
 310         hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
 311       }
 312     }
 313     if (hiddenSeqsBuilder.length() > 0)
 314     {
 315       hiddenSeqsBuilder.deleteCharAt(0);
 316     }
 317     hiddenSections[1] = hiddenSeqsBuilder.toString();
 318
 319     return hiddenSections;
 320   }
 321
 322   protected List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
 323           SequenceI[] sqs)
 324   {
 325     displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
 326     List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
 327     if (sqs == null)
 328     {
 329       return sequenceFeaturesPojo;
 330     }
 331
 332     FeatureColourFinder finder = new FeatureColourFinder(fr);
 333
 334     String[] visibleFeatureTypes = displayedFeatures == null ? null
 335             : displayedFeatures.getVisibleFeatures().toArray(
 336                     new String[displayedFeatures.getVisibleFeatureCount()]);
 337
 338     for (SequenceI seq : sqs)
 339     {
 340       /*
 341        * get all features currently visible (and any non-positional features)
 342        */
 343       List<SequenceFeature> seqFeatures = seq.getFeatures().getAllFeatures(
 344               visibleFeatureTypes);
 345       for (SequenceFeature sf : seqFeatures)
 346       {
 347         SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
 348                 String.valueOf(seq.hashCode()));
 349
 350         String featureColour = (fr == null) ? null : Format
 351                 .getHexString(finder.findFeatureColour(Color.white, seq,
 352                         seq.findIndex(sf.getBegin())));
 353         int xStart = sf.getBegin() == 0 ? 0
 354                 : seq.findIndex(sf.getBegin()) - 1;
 355         int xEnd = sf.getEnd() == 0 ? 0 : seq.findIndex(sf.getEnd());
 356         jsonFeature.setXstart(xStart);
 357         jsonFeature.setXend(xEnd);
 358         jsonFeature.setType(sf.getType());
 359         jsonFeature.setDescription(sf.getDescription());
 360         jsonFeature.setLinks(sf.links);
 361         jsonFeature.setOtherDetails(sf.otherDetails);
 362         jsonFeature.setScore(sf.getScore());
 363         jsonFeature.setFillColor(featureColour);
 364         jsonFeature.setFeatureGroup(sf.getFeatureGroup());
 365         sequenceFeaturesPojo.add(jsonFeature);
 366       }
 367     }
 368     return sequenceFeaturesPojo;
 369   }
 370
 371   public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
 372           Vector<AlignmentAnnotation> annotations)
 373   {
 374     List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
 375     if (annotations == null)
 376     {
 377       return jsonAnnotations;
 378     }
 379     for (AlignmentAnnotation annot : annotations)
 380     {
 381       AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
 382       alignAnnotPojo.setDescription(annot.description);
 383       alignAnnotPojo.setLabel(annot.label);
 384       if (!Double.isNaN(annot.score))
 385       {
 386         alignAnnotPojo.setScore(annot.score);
 387       }
 388       alignAnnotPojo.setCalcId(annot.getCalcId());
 389       alignAnnotPojo.setGraphType(annot.graph);
 390
 391       AnnotationDisplaySettingPojo annotSetting = new AnnotationDisplaySettingPojo();
 392       annotSetting.setBelowAlignment(annot.belowAlignment);
 393       annotSetting.setCentreColLabels(annot.centreColLabels);
 394       annotSetting.setScaleColLabel(annot.scaleColLabel);
 395       annotSetting.setShowAllColLabels(annot.showAllColLabels);
 396       annotSetting.setVisible(annot.visible);
 397       annotSetting.setHasIcon(annot.hasIcons);
 398       alignAnnotPojo.setAnnotationSettings(annotSetting);
 399       SequenceI refSeq = annot.sequenceRef;
 400       if (refSeq != null)
 401       {
 402         alignAnnotPojo.setSequenceRef(String.valueOf(refSeq.hashCode()));
 403       }
 404       for (Annotation annotation : annot.annotations)
 405       {
 406         AnnotationPojo annotationPojo = new AnnotationPojo();
 407         if (annotation != null)
 408         {
 409           annotationPojo.setDescription(annotation.description);
 410           annotationPojo.setValue(annotation.value);
 411           annotationPojo
 412                   .setSecondaryStructure(annotation.secondaryStructure);
 413           String displayChar = annotation.displayCharacter == null ? null
 414                   : annotation.displayCharacter;
 415           // System.out.println("--------------------->[" + displayChar + "]");
 416           annotationPojo.setDisplayCharacter(displayChar);
 417           if (annotation.colour != null)
 418           {
 419             annotationPojo.setColour(jalview.util.Format
 420                     .getHexString(annotation.colour));
 421           }
 422           alignAnnotPojo.getAnnotations().add(annotationPojo);
 423         }
 424         else
 425         {
 426           if (annot.getCalcId() != null
 427                   && annot.getCalcId().equalsIgnoreCase(TCOFFEE_SCORE))
 428           {
 429             // do nothing
 430           }
 431           else
 432           {
 433             alignAnnotPojo.getAnnotations().add(annotationPojo);
 434           }
 435         }
 436       }
 437       jsonAnnotations.add(alignAnnotPojo);
 438     }
 439     return jsonAnnotations;
 440   }
 441
 442   @SuppressWarnings("unchecked")
 443   public JSONFile parse(Reader jsonAlignmentString)
 444   {
 445     try
 446     {
 447       JSONParser jsonParser = new JSONParser();
 448       JSONObject alignmentJsonObj = (JSONObject) jsonParser
 449               .parse(jsonAlignmentString);
 450       JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
 451       JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
 452               .get("alignAnnotation");
 453       JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
 454               .get("seqFeatures");
 455       JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
 456               .get("seqGroups");
 457       JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
 458               .get("appSettings");
 459
 460       if (jvSettingsJsonObj != null)
 461       {
 462         globalColourScheme = (String) jvSettingsJsonObj
 463                 .get("globalColorScheme");
 464         Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
 465                 "showSeqFeatures").toString());
 466         setShowSeqFeatures(showFeatures);
 467         parseHiddenSeqRefsAsList(jvSettingsJsonObj);
 468         parseHiddenCols(jvSettingsJsonObj);
 469       }
 470
 471       hiddenSequences = new ArrayList<SequenceI>();
 472       seqMap = new Hashtable<String, Sequence>();
 473       for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
 474               .hasNext();)
 475       {
 476         JSONObject sequence = sequenceIter.next();
 477         String sequcenceString = sequence.get("seq").toString();
 478         String sequenceName = sequence.get("name").toString();
 479         String seqUniqueId = sequence.get("id").toString();
 480         int start = Integer.valueOf(sequence.get("start").toString());
 481         int end = Integer.valueOf(sequence.get("end").toString());
 482         Sequence seq = new Sequence(sequenceName, sequcenceString, start,
 483                 end);
 484         if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
 485         {
 486           hiddenSequences.add(seq);
 487         }
 488         seqs.add(seq);
 489         seqMap.put(seqUniqueId, seq);
 490       }
 491
 492       parseFeatures(jsonSeqArray);
 493
 494       for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
 495               .hasNext();)
 496       {
 497         JSONObject seqGrpObj = seqGrpIter.next();
 498         String grpName = seqGrpObj.get("groupName").toString();
 499         String colourScheme = seqGrpObj.get("colourScheme").toString();
 500         String description = (seqGrpObj.get("description") == null) ? null
 501                 : seqGrpObj.get("description").toString();
 502         boolean displayBoxes = Boolean.valueOf(seqGrpObj
 503                 .get("displayBoxes").toString());
 504         boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
 505                 .toString());
 506         boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
 507                 .toString());
 508         boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
 509                 "showNonconserved").toString());
 510         int startRes = Integer
 511                 .valueOf(seqGrpObj.get("startRes").toString());
 512         int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
 513         JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
 514
 515         ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
 516         if (sequenceRefs.size() > 0)
 517         {
 518           Iterator<String> seqHashIter = sequenceRefs.iterator();
 519           while (seqHashIter.hasNext())
 520           {
 521             String seqHash = seqHashIter.next();
 522             Sequence sequence = seqMap.get(seqHash);
 523             if (sequence != null)
 524             {
 525               grpSeqs.add(sequence);
 526             }
 527           }
 528         }
 529         SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
 530                 displayBoxes, displayText, colourText, startRes, endRes);
 531         seqGrp.setColourScheme(ColourSchemeMapper.getJalviewColourScheme(
 532                 colourScheme, seqGrp));
 533         seqGrp.setShowNonconserved(showNonconserved);
 534         seqGrp.setDescription(description);
 535         this.seqGroups.add(seqGrp);
 536
 537       }
 538
 539       for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
 540               .hasNext();)
 541       {
 542         JSONObject alAnnot = alAnnotIter.next();
 543         JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
 544         Annotation[] annotations = new Annotation[annotJsonArray.size()];
 545         int count = 0;
 546         for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
 547                 .hasNext();)
 548         {
 549           JSONObject annot = annotIter.next();
 550           if (annot == null)
 551           {
 552             annotations[count] = null;
 553           }
 554           else
 555           {
 556             float val = annot.get("value") == null ? null : Float
 557                     .valueOf(annot.get("value").toString());
 558             String desc = annot.get("description") == null ? null : annot
 559                     .get("description").toString();
 560             char ss = annot.get("secondaryStructure") == null
 561                     || annot.get("secondaryStructure").toString()
 562                             .equalsIgnoreCase("u0000") ? ' ' : annot
 563                     .get("secondaryStructure").toString().charAt(0);
 564             String displayChar = annot.get("displayCharacter") == null ? ""
 565                     : annot.get("displayCharacter").toString();
 566
 567             annotations[count] = new Annotation(displayChar, desc, ss, val);
 568             if (annot.get("colour") != null)
 569             {
 570               Color color = ColorUtils.parseColourString(annot.get(
 571                       "colour").toString());
 572               annotations[count].colour = color;
 573             }
 574           }
 575           ++count;
 576         }
 577
 578         AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
 579                 .get("label").toString(), alAnnot.get("description")
 580                 .toString(), annotations);
 581         alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0 : Integer
 582                 .valueOf(alAnnot.get("graphType").toString());
 583
 584         JSONObject diplaySettings = (JSONObject) alAnnot
 585                 .get("annotationSettings");
 586         if (diplaySettings != null)
 587         {
 588
 589           alignAnnot.scaleColLabel = (diplaySettings.get("scaleColLabel") == null) ? false
 590                   : Boolean.valueOf(diplaySettings.get("scaleColLabel")
 591                           .toString());
 592           alignAnnot.showAllColLabels = (diplaySettings
 593                   .get("showAllColLabels") == null) ? true : Boolean
 594                   .valueOf(diplaySettings.get("showAllColLabels")
 595                           .toString());
 596           alignAnnot.centreColLabels = (diplaySettings
 597                   .get("centreColLabels") == null) ? true
 598                   : Boolean.valueOf(diplaySettings.get("centreColLabels")
 599                           .toString());
 600           alignAnnot.belowAlignment = (diplaySettings.get("belowAlignment") == null) ? false
 601                   : Boolean.valueOf(diplaySettings.get("belowAlignment")
 602                           .toString());
 603           alignAnnot.visible = (diplaySettings.get("visible") == null) ? true
 604                   : Boolean.valueOf(diplaySettings.get("visible")
 605                           .toString());
 606           alignAnnot.hasIcons = (diplaySettings.get("hasIcon") == null) ? true
 607                   : Boolean.valueOf(diplaySettings.get("hasIcon")
 608                           .toString());
 609
 610         }
 611         if (alAnnot.get("score") != null)
 612         {
 613           alignAnnot.score = Double
 614                   .valueOf(alAnnot.get("score").toString());
 615         }
 616
 617         String calcId = (alAnnot.get("calcId") == null) ? "" : alAnnot.get(
 618                 "calcId").toString();
 619         alignAnnot.setCalcId(calcId);
 620         String seqHash = (alAnnot.get("sequenceRef") != null) ? alAnnot
 621                 .get("sequenceRef").toString() : null;
 622
 623         Sequence sequence = (seqHash != null) ? seqMap.get(seqHash) : null;
 624         if (sequence != null)
 625         {
 626           alignAnnot.sequenceRef = sequence;
 627           sequence.addAlignmentAnnotation(alignAnnot);
 628           if (alignAnnot.label.equalsIgnoreCase("T-COFFEE"))
 629           {
 630             alignAnnot.createSequenceMapping(sequence, sequence.getStart(),
 631                     false);
 632             sequence.addAlignmentAnnotation(alignAnnot);
 633             alignAnnot.adjustForAlignment();
 634           }
 635         }
 636         alignAnnot.validateRangeAndDisplay();
 637         this.annotations.add(alignAnnot);
 638
 639       }
 640     } catch (Exception e)
 641     {
 642       e.printStackTrace();
 643     }
 644     return this;
 645   }
 646
 647   public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
 648   {
 649     hiddenSeqRefs = new ArrayList<String>();
 650     String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
 651     if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
 652     {
 653       String[] seqRefs = hiddenSeqs.split(";");
 654       for (String seqRef : seqRefs)
 655       {
 656         hiddenSeqRefs.add(seqRef);
 657       }
 658     }
 659   }
 660
 661   public void parseHiddenCols(JSONObject jvSettingsJson)
 662   {
 663     String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
 664     if (hiddenCols != null && !hiddenCols.isEmpty())
 665     {
 666       hiddenColumns = new HiddenColumns();
 667       String[] rangeStrings = hiddenCols.split(";");
 668       for (String rangeString : rangeStrings)
 669       {
 670         String[] range = rangeString.split("-");
 671         hiddenColumns.hideColumns(Integer.valueOf(range[0]),
 672                 Integer.valueOf(range[1]));
 673       }
 674     }
 675   }
 676
 677   @SuppressWarnings("unchecked")
 678   private void parseFeatures(JSONArray jsonSeqFeatures)
 679   {
 680     if (jsonSeqFeatures != null)
 681     {
 682       displayedFeatures = new FeaturesDisplayed();
 683       for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
 684               .hasNext();)
 685       {
 686         JSONObject jsonFeature = seqFeatureItr.next();
 687         Long begin = (Long) jsonFeature.get("xStart");
 688         Long end = (Long) jsonFeature.get("xEnd");
 689         String type = (String) jsonFeature.get("type");
 690         String featureGrp = (String) jsonFeature.get("featureGroup");
 691         String description = (String) jsonFeature.get("description");
 692         String seqRef = (String) jsonFeature.get("sequenceRef");
 693         Float score = Float.valueOf(jsonFeature.get("score").toString());
 694
 695         Sequence seq = seqMap.get(seqRef);
 696
 697         /*
 698          * begin/end of 0 is for a non-positional feature
 699          */
 700         int featureBegin = begin.intValue() == 0 ? 0 : seq
 701                 .findPosition(begin.intValue());
 702         int featureEnd = end.intValue() == 0 ? 0 : seq.findPosition(end
 703                 .intValue()) - 1;
 704
 705         SequenceFeature sequenceFeature = new SequenceFeature(type,
 706                 description, featureBegin, featureEnd, score, featureGrp);
 707
 708         JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
 709         if (linksJsonArray != null && linksJsonArray.size() > 0)
 710         {
 711           Iterator<String> linkList = linksJsonArray.iterator();
 712           while (linkList.hasNext())
 713           {
 714             String link = linkList.next();
 715             sequenceFeature.addLink(link);
 716           }
 717         }
 718
 719         seq.addSequenceFeature(sequenceFeature);
 720         displayedFeatures.setVisible(type);
 721       }
 722     }
 723   }
 724
 725   @Override
 726   public String getGlobalColourScheme()
 727   {
 728     return globalColourScheme;
 729   }
 730
 731   public void setGlobalColorScheme(String globalColourScheme)
 732   {
 733     this.globalColourScheme = globalColourScheme;
 734   }
 735
 736   @Override
 737   public FeaturesDisplayedI getDisplayedFeatures()
 738   {
 739     return displayedFeatures;
 740   }
 741
 742   public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
 743   {
 744     this.displayedFeatures = displayedFeatures;
 745   }
 746
 747   @Override
 748   public void configureForView(AlignmentViewPanel avpanel)
 749   {
 750     if (avpanel == null)
 751     {
 752       return;
 753     }
 754     super.configureForView(avpanel);
 755     AlignViewportI viewport = avpanel.getAlignViewport();
 756     AlignmentI alignment = viewport.getAlignment();
 757     AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
 758
 759     seqGroups = alignment.getGroups();
 760     fr = avpanel.cloneFeatureRenderer();
 761
 762     // Add non auto calculated annotation to AlignFile
 763     if (annots != null)
 764     {
 765       for (AlignmentAnnotation annot : annots)
 766       {
 767         if (annot != null && !annot.autoCalculated)
 768         {
 769           annotations.add(annot);
 770         }
 771       }
 772     }
 773     globalColourScheme = ColourSchemeProperty.getColourName(viewport
 774             .getGlobalColourScheme());
 775     setDisplayedFeatures(viewport.getFeaturesDisplayed());
 776     showSeqFeatures = viewport.isShowSequenceFeatures();
 777
 778   }
 779
 780   @Override
 781   public boolean isShowSeqFeatures()
 782   {
 783     return showSeqFeatures;
 784   }
 785
 786   public void setShowSeqFeatures(boolean showSeqFeatures)
 787   {
 788     this.showSeqFeatures = showSeqFeatures;
 789   }
 790
 791   public Vector<AlignmentAnnotation> getAnnotations()
 792   {
 793     return annotations;
 794   }
 795
 796   @Override
 797   public HiddenColumns getHiddenColumns()
 798   {
 799     return hiddenColumns;
 800   }
 801
 802   public void setHiddenColumns(HiddenColumns hidden)
 803   {
 804     this.hiddenColumns = hidden;
 805   }
 806
 807   @Override
 808   public SequenceI[] getHiddenSequences()
 809   {
 810     if (hiddenSequences == null || hiddenSequences.isEmpty())
 811     {
 812       return new SequenceI[] {};
 813     }
 814     synchronized (hiddenSequences)
 815     {
 816       return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
 817     }
 818   }
 819
 820   public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
 821   {
 822     this.hiddenSequences = hiddenSequences;
 823   }
 824
 825   public class JSONExportSettings
 826   {
 827     private boolean exportSequence;
 828
 829     private boolean exportSequenceFeatures;
 830
 831     private boolean exportAnnotations;
 832
 833     private boolean exportGroups;
 834
 835     private boolean exportJalviewSettings;
 836
 837     public boolean isExportSequence()
 838     {
 839       return exportSequence;
 840     }
 841
 842     public void setExportSequence(boolean exportSequence)
 843     {
 844       this.exportSequence = exportSequence;
 845     }
 846
 847     public boolean isExportSequenceFeatures()
 848     {
 849       return exportSequenceFeatures;
 850     }
 851
 852     public void setExportSequenceFeatures(boolean exportSequenceFeatures)
 853     {
 854       this.exportSequenceFeatures = exportSequenceFeatures;
 855     }
 856
 857     public boolean isExportAnnotations()
 858     {
 859       return exportAnnotations;
 860     }
 861
 862     public void setExportAnnotations(boolean exportAnnotations)
 863     {
 864       this.exportAnnotations = exportAnnotations;
 865     }
 866
 867     public boolean isExportGroups()
 868     {
 869       return exportGroups;
 870     }
 871
 872     public void setExportGroups(boolean exportGroups)
 873     {
 874       this.exportGroups = exportGroups;
 875     }
 876
 877     public boolean isExportJalviewSettings()
 878     {
 879       return exportJalviewSettings;
 880     }
 881
 882     public void setExportJalviewSettings(boolean exportJalviewSettings)
 883     {
 884       this.exportJalviewSettings = exportJalviewSettings;
 885     }
 886   }
 887
 888   /**
 889    * Returns a descriptor for suitable feature display settings with
 890    * <ul>
 891    * <li>ResNums or insertions features visible</li>
 892    * <li>insertions features coloured red</li>
 893    * <li>ResNum features coloured by label</li>
 894    * <li>Insertions displayed above (on top of) ResNums</li>
 895    * </ul>
 896    */
 897   @Override
 898   public FeatureSettingsModelI getFeatureColourScheme()
 899   {
 900     return new PDBFeatureSettings();
 901   }
 902 }