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.JalviewColourScheme;
  51 import jalview.schemes.ResidueColourScheme;
  52 import jalview.util.ColorUtils;
  53 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
  54
  55 import java.awt.Color;
  56 import java.io.IOException;
  57 import java.io.Reader;
  58 import java.util.ArrayList;
  59 import java.util.Hashtable;
  60 import java.util.Iterator;
  61 import java.util.List;
  62 import java.util.Vector;
  63
  64 import org.json.simple.JSONArray;
  65 import org.json.simple.JSONObject;
  66 import org.json.simple.parser.JSONParser;
  67
  68 public class JSONFile extends AlignFile implements ComplexAlignFile
  69 {
  70   private static String version = new BuildDetails().getVersion();
  71
  72   private String webstartUrl = "http://www.jalview.org/services/launchApp";
  73
  74   private String application = "Jalview";
  75
  76   private String globalColourScheme;
  77
  78   private boolean showSeqFeatures;
  79
  80   private Hashtable<String, Sequence> seqMap;
  81
  82   private FeaturesDisplayedI displayedFeatures;
  83
  84   private FeatureRenderer fr;
  85
  86   private HiddenColumns hiddenColumns;
  87
  88   private List<String> hiddenSeqRefs;
  89
  90   private ArrayList<SequenceI> hiddenSequences;
  91
  92   private final static String TCOFFEE_SCORE = "TCoffeeScore";
  93
  94   public JSONFile()
  95   {
  96     super();
  97   }
  98
  99   public JSONFile(FileParse source) throws IOException
 100   {
 101     super(source);
 102   }
 103
 104   public JSONFile(String inFile, DataSourceType sourceType)
 105           throws IOException
 106   {
 107     super(inFile, sourceType);
 108   }
 109
 110   @Override
 111   public void parse() throws IOException
 112   {
 113     parse(getReader());
 114
 115   }
 116
 117   @Override
 118   public String print(SequenceI[] sqs, boolean jvsuffix)
 119   {
 120     String jsonOutput = null;
 121     try
 122     {
 123       AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
 124       AlignExportSettingI exportSettings = getExportSettings();
 125
 126       // if no export settings were supplied use the following with all values
 127       // defaulting to true
 128       if (exportSettings == null)
 129       {
 130         exportSettings = new AlignExportSettingI()
 131         {
 132           @Override
 133           public boolean isExportHiddenSequences()
 134           {
 135             return true;
 136           }
 137
 138           @Override
 139           public boolean isExportHiddenColumns()
 140           {
 141             return true;
 142           }
 143
 144           @Override
 145           public boolean isExportGroups()
 146           {
 147             return true;
 148           }
 149
 150           @Override
 151           public boolean isExportFeatures()
 152           {
 153             return true;
 154           }
 155
 156           @Override
 157           public boolean isExportAnnotations()
 158           {
 159             return true;
 160           }
 161
 162           @Override
 163           public boolean isCancelled()
 164           {
 165             return false;
 166           }
 167         };
 168       }
 169
 170       int count = 0;
 171       for (SequenceI seq : sqs)
 172       {
 173         StringBuilder name = new StringBuilder();
 174         name.append(seq.getName()).append("/").append(seq.getStart())
 175                 .append("-").append(seq.getEnd());
 176         SequencePojo jsonSeqPojo = new SequencePojo();
 177         jsonSeqPojo.setId(String.valueOf(seq.hashCode()));
 178         jsonSeqPojo.setOrder(++count);
 179         jsonSeqPojo.setEnd(seq.getEnd());
 180         jsonSeqPojo.setStart(seq.getStart());
 181         jsonSeqPojo.setName(name.toString());
 182         jsonSeqPojo.setSeq(seq.getSequenceAsString());
 183         jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
 184       }
 185       jsonAlignmentPojo.setGlobalColorScheme(globalColourScheme);
 186       jsonAlignmentPojo.getAppSettings().put("application", application);
 187       jsonAlignmentPojo.getAppSettings().put("version", version);
 188       jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
 189       jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
 190               String.valueOf(showSeqFeatures));
 191
 192       String[] hiddenSections = getHiddenSections();
 193       if (hiddenSections != null)
 194       {
 195         if (hiddenSections[0] != null
 196                 && exportSettings.isExportHiddenColumns())
 197         {
 198           jsonAlignmentPojo.getAppSettings().put("hiddenCols",
 199                   String.valueOf(hiddenSections[0]));
 200         }
 201         if (hiddenSections[1] != null
 202                 && exportSettings.isExportHiddenSequences())
 203         {
 204           jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
 205                   String.valueOf(hiddenSections[1]));
 206         }
 207       }
 208
 209       if (exportSettings.isExportAnnotations())
 210       {
 211         jsonAlignmentPojo
 212                 .setAlignAnnotation(annotationToJsonPojo(annotations));
 213       }
 214       else
 215       {
 216         // These color schemes require annotation, disable them if annotations
 217         // are not exported
 218         if (globalColourScheme
 219                 .equalsIgnoreCase(JalviewColourScheme.RNAHelices.toString())
 220                 || globalColourScheme
 221                         .equalsIgnoreCase(JalviewColourScheme.TCoffee
 222                                 .toString()))
 223         {
 224           jsonAlignmentPojo.setGlobalColorScheme(ResidueColourScheme.NONE);
 225         }
 226       }
 227
 228       if (exportSettings.isExportFeatures())
 229       {
 230         jsonAlignmentPojo
 231                 .setSeqFeatures(sequenceFeatureToJsonPojo(sqs, fr));
 232       }
 233
 234       if (exportSettings.isExportGroups() && seqGroups != null
 235               && seqGroups.size() > 0)
 236       {
 237         for (SequenceGroup seqGrp : seqGroups)
 238         {
 239           SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
 240           seqGrpPojo.setGroupName(seqGrp.getName());
 241           seqGrpPojo.setColourScheme(seqGrp.getColourScheme()
 242                   .getSchemeName());
 243           seqGrpPojo.setColourText(seqGrp.getColourText());
 244           seqGrpPojo.setDescription(seqGrp.getDescription());
 245           seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
 246           seqGrpPojo.setDisplayText(seqGrp.getDisplayText());
 247           seqGrpPojo.setEndRes(seqGrp.getEndRes());
 248           seqGrpPojo.setStartRes(seqGrp.getStartRes());
 249           seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
 250           for (SequenceI seq : seqGrp.getSequences())
 251           {
 252             seqGrpPojo.getSequenceRefs()
 253                     .add(String.valueOf(seq.hashCode()));
 254           }
 255           jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
 256         }
 257       }
 258       org.json.JSONObject generatedJSon = new org.json.JSONObject(
 259               jsonAlignmentPojo);
 260       jsonOutput = generatedJSon.toString();
 261       return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
 262               "xEnd");
 263     } catch (Exception e)
 264     {
 265       e.printStackTrace();
 266     }
 267     return jsonOutput;
 268   }
 269
 270   public String[] getHiddenSections()
 271   {
 272     String[] hiddenSections = new String[2];
 273     if (getViewport() == null)
 274     {
 275       return null;
 276     }
 277
 278     // hidden column business
 279     if (getViewport().hasHiddenColumns())
 280     {
 281       List<int[]> hiddenCols = getViewport().getAlignment()
 282               .getHiddenColumns()
 283               .getListOfCols();
 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     FeatureColourFinder finder = new FeatureColourFinder(fr);
 332
 333     for (SequenceI seq : sqs)
 334     {
 335       SequenceI dataSetSequence = seq.getDatasetSequence();
 336       SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
 337               : seq.getDatasetSequence().getSequenceFeatures();
 338
 339       seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
 340               : seqFeatures;
 341       if (seqFeatures == null)
 342       {
 343         continue;
 344       }
 345
 346       for (SequenceFeature sf : seqFeatures)
 347       {
 348         if (displayedFeatures != null
 349                 && displayedFeatures.isVisible(sf.getType()))
 350         {
 351           SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
 352                   String.valueOf(seq.hashCode()));
 353
 354           String featureColour = (fr == null) ? null : jalview.util.Format
 355                   .getHexString(finder.findFeatureColour(Color.white, seq,
 356                           seq.findIndex(sf.getBegin())));
 357           jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
 358           jsonFeature.setXend(seq.findIndex(sf.getEnd()));
 359           jsonFeature.setType(sf.getType());
 360           jsonFeature.setDescription(sf.getDescription());
 361           jsonFeature.setLinks(sf.links);
 362           jsonFeature.setOtherDetails(sf.otherDetails);
 363           jsonFeature.setScore(sf.getScore());
 364           jsonFeature.setFillColor(featureColour);
 365           jsonFeature.setFeatureGroup(sf.getFeatureGroup());
 366           sequenceFeaturesPojo.add(jsonFeature);
 367         }
 368       }
 369     }
 370     return sequenceFeaturesPojo;
 371   }
 372
 373   public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
 374           Vector<AlignmentAnnotation> annotations)
 375   {
 376     List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
 377     if (annotations == null)
 378     {
 379       return jsonAnnotations;
 380     }
 381     for (AlignmentAnnotation annot : annotations)
 382     {
 383       AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
 384       alignAnnotPojo.setDescription(annot.description);
 385       alignAnnotPojo.setLabel(annot.label);
 386       if (!Double.isNaN(annot.score))
 387       {
 388         alignAnnotPojo.setScore(annot.score);
 389       }
 390       alignAnnotPojo.setCalcId(annot.getCalcId());
 391       alignAnnotPojo.setGraphType(annot.graph);
 392
 393       AnnotationDisplaySettingPojo annotSetting = new AnnotationDisplaySettingPojo();
 394       annotSetting.setBelowAlignment(annot.belowAlignment);
 395       annotSetting.setCentreColLabels(annot.centreColLabels);
 396       annotSetting.setScaleColLabel(annot.scaleColLabel);
 397       annotSetting.setShowAllColLabels(annot.showAllColLabels);
 398       annotSetting.setVisible(annot.visible);
 399       annotSetting.setHasIcon(annot.hasIcons);
 400       alignAnnotPojo.setAnnotationSettings(annotSetting);
 401       SequenceI refSeq = annot.sequenceRef;
 402       if (refSeq != null)
 403       {
 404         alignAnnotPojo.setSequenceRef(String.valueOf(refSeq.hashCode()));
 405       }
 406       for (Annotation annotation : annot.annotations)
 407       {
 408         AnnotationPojo annotationPojo = new AnnotationPojo();
 409         if (annotation != null)
 410         {
 411           annotationPojo.setDescription(annotation.description);
 412           annotationPojo.setValue(annotation.value);
 413           annotationPojo
 414                   .setSecondaryStructure(annotation.secondaryStructure);
 415           String displayChar = annotation.displayCharacter == null ? null
 416                   : annotation.displayCharacter;
 417           // System.out.println("--------------------->[" + displayChar + "]");
 418           annotationPojo.setDisplayCharacter(displayChar);
 419           if (annotation.colour != null)
 420           {
 421             annotationPojo.setColour(jalview.util.Format
 422                     .getHexString(annotation.colour));
 423           }
 424           alignAnnotPojo.getAnnotations().add(annotationPojo);
 425         }
 426         else
 427         {
 428           if (annot.getCalcId() != null
 429                   && annot.getCalcId().equalsIgnoreCase(TCOFFEE_SCORE))
 430           {
 431             // do nothing
 432           }
 433           else
 434           {
 435             alignAnnotPojo.getAnnotations().add(annotationPojo);
 436           }
 437         }
 438       }
 439       jsonAnnotations.add(alignAnnotPojo);
 440     }
 441     return jsonAnnotations;
 442   }
 443
 444   @SuppressWarnings("unchecked")
 445   public JSONFile parse(Reader jsonAlignmentString)
 446   {
 447     try
 448     {
 449       JSONParser jsonParser = new JSONParser();
 450       JSONObject alignmentJsonObj = (JSONObject) jsonParser
 451               .parse(jsonAlignmentString);
 452       JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
 453       JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
 454               .get("alignAnnotation");
 455       JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
 456               .get("seqFeatures");
 457       JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
 458               .get("seqGroups");
 459       JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
 460               .get("appSettings");
 461
 462       if (jvSettingsJsonObj != null)
 463       {
 464         globalColourScheme = (String) jvSettingsJsonObj
 465                 .get("globalColorScheme");
 466         Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
 467                 "showSeqFeatures").toString());
 468         setShowSeqFeatures(showFeatures);
 469         parseHiddenSeqRefsAsList(jvSettingsJsonObj);
 470         parseHiddenCols(jvSettingsJsonObj);
 471       }
 472
 473       hiddenSequences = new ArrayList<SequenceI>();
 474       seqMap = new Hashtable<String, Sequence>();
 475       for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
 476               .hasNext();)
 477       {
 478         JSONObject sequence = sequenceIter.next();
 479         String sequcenceString = sequence.get("seq").toString();
 480         String sequenceName = sequence.get("name").toString();
 481         String seqUniqueId = sequence.get("id").toString();
 482         int start = Integer.valueOf(sequence.get("start").toString());
 483         int end = Integer.valueOf(sequence.get("end").toString());
 484         Sequence seq = new Sequence(sequenceName, sequcenceString, start,
 485                 end);
 486         if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
 487         {
 488           hiddenSequences.add(seq);
 489         }
 490         seqs.add(seq);
 491         seqMap.put(seqUniqueId, seq);
 492       }
 493
 494       parseFeatures(jsonSeqArray);
 495
 496       for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
 497               .hasNext();)
 498       {
 499         JSONObject seqGrpObj = seqGrpIter.next();
 500         String grpName = seqGrpObj.get("groupName").toString();
 501         String colourScheme = seqGrpObj.get("colourScheme").toString();
 502         String description = (seqGrpObj.get("description") == null) ? null
 503                 : seqGrpObj.get("description").toString();
 504         boolean displayBoxes = Boolean.valueOf(seqGrpObj
 505                 .get("displayBoxes").toString());
 506         boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
 507                 .toString());
 508         boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
 509                 .toString());
 510         boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
 511                 "showNonconserved").toString());
 512         int startRes = Integer
 513                 .valueOf(seqGrpObj.get("startRes").toString());
 514         int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
 515         JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
 516
 517         ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
 518         if (sequenceRefs.size() > 0)
 519         {
 520           Iterator<String> seqHashIter = sequenceRefs.iterator();
 521           while (seqHashIter.hasNext())
 522           {
 523             String seqHash = seqHashIter.next();
 524             Sequence sequence = seqMap.get(seqHash);
 525             if (sequence != null)
 526             {
 527               grpSeqs.add(sequence);
 528             }
 529           }
 530         }
 531         SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
 532                 displayBoxes, displayText, colourText, startRes, endRes);
 533         seqGrp.setColourScheme(ColourSchemeMapper.getJalviewColourScheme(
 534                 colourScheme, seqGrp));
 535         seqGrp.setShowNonconserved(showNonconserved);
 536         seqGrp.setDescription(description);
 537         this.seqGroups.add(seqGrp);
 538
 539       }
 540
 541       for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
 542               .hasNext();)
 543       {
 544         JSONObject alAnnot = alAnnotIter.next();
 545         JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
 546         Annotation[] annotations = new Annotation[annotJsonArray.size()];
 547         int count = 0;
 548         for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
 549                 .hasNext();)
 550         {
 551           JSONObject annot = annotIter.next();
 552           if (annot == null)
 553           {
 554             annotations[count] = null;
 555           }
 556           else
 557           {
 558             float val = annot.get("value") == null ? null : Float
 559                     .valueOf(annot.get("value").toString());
 560             String desc = annot.get("description") == null ? null : annot
 561                     .get("description").toString();
 562             char ss = annot.get("secondaryStructure") == null
 563                     || annot.get("secondaryStructure").toString()
 564                             .equalsIgnoreCase("u0000") ? ' ' : annot
 565                     .get("secondaryStructure").toString().charAt(0);
 566             String displayChar = annot.get("displayCharacter") == null ? ""
 567                     : annot.get("displayCharacter").toString();
 568
 569             annotations[count] = new Annotation(displayChar, desc, ss, val);
 570             if (annot.get("colour") != null)
 571             {
 572               Color color = ColorUtils.parseColourString(annot.get(
 573                       "colour").toString());
 574               annotations[count].colour = color;
 575             }
 576           }
 577           ++count;
 578         }
 579
 580         AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
 581                 .get("label").toString(), alAnnot.get("description")
 582                 .toString(), annotations);
 583         alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0 : Integer
 584                 .valueOf(alAnnot.get("graphType").toString());
 585
 586         JSONObject diplaySettings = (JSONObject) alAnnot
 587                 .get("annotationSettings");
 588         if (diplaySettings != null)
 589         {
 590
 591           alignAnnot.scaleColLabel = (diplaySettings.get("scaleColLabel") == null) ? false
 592                   : Boolean.valueOf(diplaySettings.get("scaleColLabel")
 593                           .toString());
 594           alignAnnot.showAllColLabels = (diplaySettings
 595                   .get("showAllColLabels") == null) ? true : Boolean
 596                   .valueOf(diplaySettings.get("showAllColLabels")
 597                           .toString());
 598           alignAnnot.centreColLabels = (diplaySettings
 599                   .get("centreColLabels") == null) ? true
 600                   : Boolean.valueOf(diplaySettings.get("centreColLabels")
 601                           .toString());
 602           alignAnnot.belowAlignment = (diplaySettings.get("belowAlignment") == null) ? false
 603                   : Boolean.valueOf(diplaySettings.get("belowAlignment")
 604                           .toString());
 605           alignAnnot.visible = (diplaySettings.get("visible") == null) ? true
 606                   : Boolean.valueOf(diplaySettings.get("visible")
 607                           .toString());
 608           alignAnnot.hasIcons = (diplaySettings.get("hasIcon") == null) ? true
 609                   : Boolean.valueOf(diplaySettings.get("hasIcon")
 610                           .toString());
 611
 612         }
 613         if (alAnnot.get("score") != null)
 614         {
 615           alignAnnot.score = Double
 616                   .valueOf(alAnnot.get("score").toString());
 617         }
 618
 619         String calcId = (alAnnot.get("calcId") == null) ? "" : alAnnot.get(
 620                 "calcId").toString();
 621         alignAnnot.setCalcId(calcId);
 622         String seqHash = (alAnnot.get("sequenceRef") != null) ? alAnnot
 623                 .get("sequenceRef").toString() : null;
 624
 625         Sequence sequence = (seqHash != null) ? seqMap.get(seqHash) : null;
 626         if (sequence != null)
 627         {
 628           alignAnnot.sequenceRef = sequence;
 629           sequence.addAlignmentAnnotation(alignAnnot);
 630           if (alignAnnot.label.equalsIgnoreCase("T-COFFEE"))
 631           {
 632             alignAnnot.createSequenceMapping(sequence, sequence.getStart(),
 633                     false);
 634             sequence.addAlignmentAnnotation(alignAnnot);
 635             alignAnnot.adjustForAlignment();
 636           }
 637         }
 638         alignAnnot.validateRangeAndDisplay();
 639         this.annotations.add(alignAnnot);
 640
 641       }
 642     } catch (Exception e)
 643     {
 644       e.printStackTrace();
 645     }
 646     return this;
 647   }
 648
 649   public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
 650   {
 651     hiddenSeqRefs = new ArrayList<String>();
 652     String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
 653     if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
 654     {
 655       String[] seqRefs = hiddenSeqs.split(";");
 656       for (String seqRef : seqRefs)
 657       {
 658         hiddenSeqRefs.add(seqRef);
 659       }
 660     }
 661   }
 662
 663   public void parseHiddenCols(JSONObject jvSettingsJson)
 664   {
 665     String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
 666     if (hiddenCols != null && !hiddenCols.isEmpty())
 667     {
 668       hiddenColumns = new HiddenColumns();
 669       String[] rangeStrings = hiddenCols.split(";");
 670       for (String rangeString : rangeStrings)
 671       {
 672         String[] range = rangeString.split("-");
 673         hiddenColumns.hideColumns(Integer.valueOf(range[0]),
 674                 Integer.valueOf(range[1]));
 675       }
 676     }
 677   }
 678
 679   @SuppressWarnings("unchecked")
 680   private void parseFeatures(JSONArray jsonSeqFeatures)
 681   {
 682     if (jsonSeqFeatures != null)
 683     {
 684       displayedFeatures = new FeaturesDisplayed();
 685       for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
 686               .hasNext();)
 687       {
 688         JSONObject jsonFeature = seqFeatureItr.next();
 689         Long begin = (Long) jsonFeature.get("xStart");
 690         Long end = (Long) jsonFeature.get("xEnd");
 691         String type = (String) jsonFeature.get("type");
 692         String featureGrp = (String) jsonFeature.get("featureGroup");
 693         String descripiton = (String) jsonFeature.get("description");
 694         String seqRef = (String) jsonFeature.get("sequenceRef");
 695         Float score = Float.valueOf(jsonFeature.get("score").toString());
 696
 697         Sequence seq = seqMap.get(seqRef);
 698         SequenceFeature sequenceFeature = new SequenceFeature();
 699         JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
 700         if (linksJsonArray != null && linksJsonArray.size() > 0)
 701         {
 702           Iterator<String> linkList = linksJsonArray.iterator();
 703           while (linkList.hasNext())
 704           {
 705             String link = linkList.next();
 706             sequenceFeature.addLink(link);
 707           }
 708         }
 709         sequenceFeature.setFeatureGroup(featureGrp);
 710         sequenceFeature.setScore(score);
 711         sequenceFeature.setDescription(descripiton);
 712         sequenceFeature.setType(type);
 713         sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
 714         sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
 715         seq.addSequenceFeature(sequenceFeature);
 716         displayedFeatures.setVisible(type);
 717       }
 718     }
 719   }
 720
 721   @Override
 722   public String getGlobalColourScheme()
 723   {
 724     return globalColourScheme;
 725   }
 726
 727   public void setGlobalColorScheme(String globalColourScheme)
 728   {
 729     this.globalColourScheme = globalColourScheme;
 730   }
 731
 732   @Override
 733   public FeaturesDisplayedI getDisplayedFeatures()
 734   {
 735     return displayedFeatures;
 736   }
 737
 738   public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
 739   {
 740     this.displayedFeatures = displayedFeatures;
 741   }
 742
 743   @Override
 744   public void configureForView(AlignmentViewPanel avpanel)
 745   {
 746     if (avpanel == null)
 747     {
 748       return;
 749     }
 750     super.configureForView(avpanel);
 751     AlignViewportI viewport = avpanel.getAlignViewport();
 752     AlignmentI alignment = viewport.getAlignment();
 753     AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
 754
 755     seqGroups = alignment.getGroups();
 756     fr = avpanel.cloneFeatureRenderer();
 757
 758     // Add non auto calculated annotation to AlignFile
 759     if (annots != null)
 760     {
 761       for (AlignmentAnnotation annot : annots)
 762       {
 763         if (annot != null && !annot.autoCalculated)
 764         {
 765           annotations.add(annot);
 766         }
 767       }
 768     }
 769     globalColourScheme = viewport.getGlobalColourScheme().getSchemeName();
 770     setDisplayedFeatures(viewport.getFeaturesDisplayed());
 771     showSeqFeatures = viewport.isShowSequenceFeatures();
 772
 773   }
 774
 775   @Override
 776   public boolean isShowSeqFeatures()
 777   {
 778     return showSeqFeatures;
 779   }
 780
 781   public void setShowSeqFeatures(boolean showSeqFeatures)
 782   {
 783     this.showSeqFeatures = showSeqFeatures;
 784   }
 785
 786   public Vector<AlignmentAnnotation> getAnnotations()
 787   {
 788     return annotations;
 789   }
 790
 791   @Override
 792   public HiddenColumns getHiddenColumns()
 793   {
 794     return hiddenColumns;
 795   }
 796
 797   public void setHiddenColumns(HiddenColumns hidden)
 798   {
 799     this.hiddenColumns = hidden;
 800   }
 801
 802   @Override
 803   public SequenceI[] getHiddenSequences()
 804   {
 805     if (hiddenSequences == null || hiddenSequences.isEmpty())
 806     {
 807       return new SequenceI[] {};
 808     }
 809     synchronized (hiddenSequences)
 810     {
 811       return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
 812     }
 813   }
 814
 815   public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
 816   {
 817     this.hiddenSequences = hiddenSequences;
 818   }
 819
 820   public class JSONExportSettings
 821   {
 822     private boolean exportSequence;
 823
 824     private boolean exportSequenceFeatures;
 825
 826     private boolean exportAnnotations;
 827
 828     private boolean exportGroups;
 829
 830     private boolean exportJalviewSettings;
 831
 832     public boolean isExportSequence()
 833     {
 834       return exportSequence;
 835     }
 836
 837     public void setExportSequence(boolean exportSequence)
 838     {
 839       this.exportSequence = exportSequence;
 840     }
 841
 842     public boolean isExportSequenceFeatures()
 843     {
 844       return exportSequenceFeatures;
 845     }
 846
 847     public void setExportSequenceFeatures(boolean exportSequenceFeatures)
 848     {
 849       this.exportSequenceFeatures = exportSequenceFeatures;
 850     }
 851
 852     public boolean isExportAnnotations()
 853     {
 854       return exportAnnotations;
 855     }
 856
 857     public void setExportAnnotations(boolean exportAnnotations)
 858     {
 859       this.exportAnnotations = exportAnnotations;
 860     }
 861
 862     public boolean isExportGroups()
 863     {
 864       return exportGroups;
 865     }
 866
 867     public void setExportGroups(boolean exportGroups)
 868     {
 869       this.exportGroups = exportGroups;
 870     }
 871
 872     public boolean isExportJalviewSettings()
 873     {
 874       return exportJalviewSettings;
 875     }
 876
 877     public void setExportJalviewSettings(boolean exportJalviewSettings)
 878     {
 879       this.exportJalviewSettings = exportJalviewSettings;
 880     }
 881   }
 882
 883   /**
 884    * Returns a descriptor for suitable feature display settings with
 885    * <ul>
 886    * <li>ResNums or insertions features visible</li>
 887    * <li>insertions features coloured red</li>
 888    * <li>ResNum features coloured by label</li>
 889    * <li>Insertions displayed above (on top of) ResNums</li>
 890    * </ul>
 891    */
 892   @Override
 893   public FeatureSettingsModelI getFeatureColourScheme()
 894   {
 895     return new PDBFeatureSettings();
 896   }
 897 }