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.ColumnSelection;
  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.schemes.JalviewColourScheme;
  50 import jalview.schemes.ResidueColourScheme;
  51 import jalview.util.ColorUtils;
  52 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
  53
  54 import java.awt.Color;
  55 import java.io.IOException;
  56 import java.io.Reader;
  57 import java.util.ArrayList;
  58 import java.util.Hashtable;
  59 import java.util.Iterator;
  60 import java.util.List;
  61 import java.util.Vector;
  62
  63 import org.json.simple.JSONArray;
  64 import org.json.simple.JSONObject;
  65 import org.json.simple.parser.JSONParser;
  66
  67 public class JSONFile extends AlignFile implements ComplexAlignFile
  68 {
  69   private static String version = new BuildDetails().getVersion();
  70
  71   private String webstartUrl = "http://www.jalview.org/services/launchApp";
  72
  73   private String application = "Jalview";
  74
  75   private String globalColourScheme;
  76
  77   private boolean showSeqFeatures;
  78
  79   private Hashtable<String, Sequence> seqMap;
  80
  81   private FeaturesDisplayedI displayedFeatures;
  82
  83   private FeatureRenderer fr;
  84
  85   private List<int[]> hiddenColumns;
  86
  87   private ColumnSelection columnSelection;
  88
  89   private List<String> hiddenSeqRefs;
  90
  91   private ArrayList<SequenceI> hiddenSequences;
  92
  93   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       AlignExportSettingI exportSettings = getExportSettings();
 126
 127       // if no export settings were supplied use the following with all values
 128       // defaulting to true
 129       if (exportSettings == null)
 130       {
 131         exportSettings = new AlignExportSettingI()
 132         {
 133           @Override
 134           public boolean isExportHiddenSequences()
 135           {
 136             return true;
 137           }
 138
 139           @Override
 140           public boolean isExportHiddenColumns()
 141           {
 142             return true;
 143           }
 144
 145           @Override
 146           public boolean isExportGroups()
 147           {
 148             return true;
 149           }
 150
 151           @Override
 152           public boolean isExportFeatures()
 153           {
 154             return true;
 155           }
 156
 157           @Override
 158           public boolean isExportAnnotations()
 159           {
 160             return true;
 161           }
 162
 163           @Override
 164           public boolean isCancelled()
 165           {
 166             return false;
 167           }
 168         };
 169       }
 170
 171       int count = 0;
 172       for (SequenceI seq : sqs)
 173       {
 174         StringBuilder name = new StringBuilder();
 175         name.append(seq.getName()).append("/").append(seq.getStart())
 176                 .append("-").append(seq.getEnd());
 177         SequencePojo jsonSeqPojo = new SequencePojo();
 178         jsonSeqPojo.setId(String.valueOf(seq.hashCode()));
 179         jsonSeqPojo.setOrder(++count);
 180         jsonSeqPojo.setEnd(seq.getEnd());
 181         jsonSeqPojo.setStart(seq.getStart());
 182         jsonSeqPojo.setName(name.toString());
 183         jsonSeqPojo.setSeq(seq.getSequenceAsString());
 184         jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
 185       }
 186       jsonAlignmentPojo.setGlobalColorScheme(globalColourScheme);
 187       jsonAlignmentPojo.getAppSettings().put("application", application);
 188       jsonAlignmentPojo.getAppSettings().put("version", version);
 189       jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
 190       jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
 191               String.valueOf(showSeqFeatures));
 192
 193       String[] hiddenSections = getHiddenSections();
 194       if (hiddenSections != null)
 195       {
 196         if (hiddenSections[0] != null
 197                 && exportSettings.isExportHiddenColumns())
 198         {
 199           jsonAlignmentPojo.getAppSettings().put("hiddenCols",
 200                   String.valueOf(hiddenSections[0]));
 201         }
 202         if (hiddenSections[1] != null
 203                 && exportSettings.isExportHiddenSequences())
 204         {
 205           jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
 206                   String.valueOf(hiddenSections[1]));
 207         }
 208       }
 209
 210       if (exportSettings.isExportAnnotations())
 211       {
 212         jsonAlignmentPojo
 213                 .setAlignAnnotation(annotationToJsonPojo(annotations));
 214       }
 215       else
 216       {
 217         // These color schemes require annotation, disable them if annotations
 218         // are not exported
 219         if (globalColourScheme
 220                 .equalsIgnoreCase(JalviewColourScheme.RNAHelices.toString())
 221                 || globalColourScheme
 222                         .equalsIgnoreCase(JalviewColourScheme.TCoffee
 223                                 .toString()))
 224         {
 225           jsonAlignmentPojo.setGlobalColorScheme(ResidueColourScheme.NONE);
 226         }
 227       }
 228
 229       if (exportSettings.isExportFeatures())
 230       {
 231         jsonAlignmentPojo
 232                 .setSeqFeatures(sequenceFeatureToJsonPojo(sqs, fr));
 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(seqGrp.getColourScheme()
 243                   .getSchemeName());
 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().getColumnSelection()
 283               .getHiddenColumns();
 284       StringBuilder hiddenColsBuilder = new StringBuilder();
 285       for (int[] range : hiddenCols)
 286       {
 287         hiddenColsBuilder.append(";").append(range[0]).append("-")
 288                 .append(range[1]);
 289       }
 290
 291       hiddenColsBuilder.deleteCharAt(0);
 292       hiddenSections[0] = hiddenColsBuilder.toString();
 293     }
 294
 295     // hidden rows/seqs business
 296     HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
 297             .getHiddenSequences();
 298     if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
 299     {
 300       return hiddenSections;
 301     }
 302
 303     SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
 304     StringBuilder hiddenSeqsBuilder = new StringBuilder();
 305     for (SequenceI hiddenSeq : hiddenSeqs)
 306     {
 307       if (hiddenSeq != null)
 308       {
 309         hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
 310       }
 311     }
 312     if (hiddenSeqsBuilder.length() > 0)
 313     {
 314       hiddenSeqsBuilder.deleteCharAt(0);
 315     }
 316     hiddenSections[1] = hiddenSeqsBuilder.toString();
 317
 318     return hiddenSections;
 319   }
 320
 321   public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
 322           SequenceI[] sqs, FeatureRenderer fr)
 323   {
 324     displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
 325     List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
 326     if (sqs == null)
 327     {
 328       return sequenceFeaturesPojo;
 329     }
 330
 331     for (SequenceI seq : sqs)
 332     {
 333       SequenceI dataSetSequence = seq.getDatasetSequence();
 334       SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
 335               : seq.getDatasetSequence().getSequenceFeatures();
 336
 337       seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
 338               : seqFeatures;
 339       if (seqFeatures == null)
 340       {
 341         continue;
 342       }
 343
 344       for (SequenceFeature sf : seqFeatures)
 345       {
 346         if (displayedFeatures != null
 347                 && displayedFeatures.isVisible(sf.getType()))
 348         {
 349           SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
 350                   String.valueOf(seq.hashCode()));
 351
 352           String featureColour = (fr == null) ? null : jalview.util.Format
 353                   .getHexString(fr.findFeatureColour(Color.white, seq,
 354                           seq.findIndex(sf.getBegin())));
 355           jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
 356           jsonFeature.setXend(seq.findIndex(sf.getEnd()));
 357           jsonFeature.setType(sf.getType());
 358           jsonFeature.setDescription(sf.getDescription());
 359           jsonFeature.setLinks(sf.links);
 360           jsonFeature.setOtherDetails(sf.otherDetails);
 361           jsonFeature.setScore(sf.getScore());
 362           jsonFeature.setFillColor(featureColour);
 363           jsonFeature.setFeatureGroup(sf.getFeatureGroup());
 364           sequenceFeaturesPojo.add(jsonFeature);
 365         }
 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       columnSelection = new ColumnSelection();
 667       String[] rangeStrings = hiddenCols.split(";");
 668       for (String rangeString : rangeStrings)
 669       {
 670         String[] range = rangeString.split("-");
 671         columnSelection.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 descripiton = (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         SequenceFeature sequenceFeature = new SequenceFeature();
 697         JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
 698         if (linksJsonArray != null && linksJsonArray.size() > 0)
 699         {
 700           Iterator<String> linkList = linksJsonArray.iterator();
 701           while (linkList.hasNext())
 702           {
 703             String link = linkList.next();
 704             sequenceFeature.addLink(link);
 705           }
 706         }
 707         sequenceFeature.setFeatureGroup(featureGrp);
 708         sequenceFeature.setScore(score);
 709         sequenceFeature.setDescription(descripiton);
 710         sequenceFeature.setType(type);
 711         sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
 712         sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
 713         seq.addSequenceFeature(sequenceFeature);
 714         displayedFeatures.setVisible(type);
 715       }
 716     }
 717   }
 718
 719   @Override
 720   public String getGlobalColourScheme()
 721   {
 722     return globalColourScheme;
 723   }
 724
 725   public void setGlobalColorScheme(String globalColourScheme)
 726   {
 727     this.globalColourScheme = globalColourScheme;
 728   }
 729
 730   @Override
 731   public FeaturesDisplayedI getDisplayedFeatures()
 732   {
 733     return displayedFeatures;
 734   }
 735
 736   public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
 737   {
 738     this.displayedFeatures = displayedFeatures;
 739   }
 740
 741   @Override
 742   public void configureForView(AlignmentViewPanel avpanel)
 743   {
 744     if (avpanel == null)
 745     {
 746       return;
 747     }
 748     super.configureForView(avpanel);
 749     AlignViewportI viewport = avpanel.getAlignViewport();
 750     AlignmentI alignment = viewport.getAlignment();
 751     AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
 752
 753     seqGroups = alignment.getGroups();
 754     fr = avpanel.cloneFeatureRenderer();
 755
 756     // Add non auto calculated annotation to AlignFile
 757     if (annots != null)
 758     {
 759       for (AlignmentAnnotation annot : annots)
 760       {
 761         if (annot != null && !annot.autoCalculated)
 762         {
 763           annotations.add(annot);
 764         }
 765       }
 766     }
 767     globalColourScheme = viewport.getGlobalColourScheme().getSchemeName();
 768     setDisplayedFeatures(viewport.getFeaturesDisplayed());
 769     showSeqFeatures = viewport.isShowSequenceFeatures();
 770
 771   }
 772
 773   @Override
 774   public boolean isShowSeqFeatures()
 775   {
 776     return showSeqFeatures;
 777   }
 778
 779   public void setShowSeqFeatures(boolean showSeqFeatures)
 780   {
 781     this.showSeqFeatures = showSeqFeatures;
 782   }
 783
 784   public Vector<AlignmentAnnotation> getAnnotations()
 785   {
 786     return annotations;
 787   }
 788
 789   public List<int[]> getHiddenColumns()
 790   {
 791     return hiddenColumns;
 792   }
 793
 794   @Override
 795   public ColumnSelection getColumnSelection()
 796   {
 797     return columnSelection;
 798   }
 799
 800   public void setColumnSelection(ColumnSelection columnSelection)
 801   {
 802     this.columnSelection = columnSelection;
 803   }
 804
 805   @Override
 806   public SequenceI[] getHiddenSequences()
 807   {
 808     if (hiddenSequences == null || hiddenSequences.isEmpty())
 809     {
 810       return new SequenceI[] {};
 811     }
 812     synchronized (hiddenSequences)
 813     {
 814       return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
 815     }
 816   }
 817
 818   public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
 819   {
 820     this.hiddenSequences = hiddenSequences;
 821   }
 822
 823   public class JSONExportSettings
 824   {
 825     private boolean exportSequence;
 826
 827     private boolean exportSequenceFeatures;
 828
 829     private boolean exportAnnotations;
 830
 831     private boolean exportGroups;
 832
 833     private boolean exportJalviewSettings;
 834
 835     public boolean isExportSequence()
 836     {
 837       return exportSequence;
 838     }
 839
 840     public void setExportSequence(boolean exportSequence)
 841     {
 842       this.exportSequence = exportSequence;
 843     }
 844
 845     public boolean isExportSequenceFeatures()
 846     {
 847       return exportSequenceFeatures;
 848     }
 849
 850     public void setExportSequenceFeatures(boolean exportSequenceFeatures)
 851     {
 852       this.exportSequenceFeatures = exportSequenceFeatures;
 853     }
 854
 855     public boolean isExportAnnotations()
 856     {
 857       return exportAnnotations;
 858     }
 859
 860     public void setExportAnnotations(boolean exportAnnotations)
 861     {
 862       this.exportAnnotations = exportAnnotations;
 863     }
 864
 865     public boolean isExportGroups()
 866     {
 867       return exportGroups;
 868     }
 869
 870     public void setExportGroups(boolean exportGroups)
 871     {
 872       this.exportGroups = exportGroups;
 873     }
 874
 875     public boolean isExportJalviewSettings()
 876     {
 877       return exportJalviewSettings;
 878     }
 879
 880     public void setExportJalviewSettings(boolean exportJalviewSettings)
 881     {
 882       this.exportJalviewSettings = exportJalviewSettings;
 883     }
 884   }
 885
 886   /**
 887    * Returns a descriptor for suitable feature display settings with
 888    * <ul>
 889    * <li>ResNums or insertions features visible</li>
 890    * <li>insertions features coloured red</li>
 891    * <li>ResNum features coloured by label</li>
 892    * <li>Insertions displayed above (on top of) ResNums</li>
 893    * </ul>
 894    */
 895   @Override
 896   public FeatureSettingsModelI getFeatureColourScheme()
 897   {
 898     return new PDBFeatureSettings();
 899   }
 900 }