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.viewmodel.seqfeatures.FeaturesDisplayed;
  55
  56 import java.awt.Color;
  57 import java.io.IOException;
  58 import java.io.Reader;
  59 import java.util.ArrayList;
  60 import java.util.Hashtable;
  61 import java.util.Iterator;
  62 import java.util.List;
  63 import java.util.Vector;
  64
  65 import org.json.simple.JSONArray;
  66 import org.json.simple.JSONObject;
  67 import org.json.simple.parser.JSONParser;
  68
  69 public class JSONFile extends AlignFile implements ComplexAlignFile
  70 {
  71   private static String version = new BuildDetails().getVersion();
  72
  73   private String webstartUrl = "http://www.jalview.org/services/launchApp";
  74
  75   private String application = "Jalview";
  76
  77   private String globalColourScheme;
  78
  79   private boolean showSeqFeatures;
  80
  81   private Hashtable<String, Sequence> seqMap;
  82
  83   private FeaturesDisplayedI displayedFeatures;
  84
  85   private FeatureRenderer fr;
  86
  87   private HiddenColumns hiddenColumns;
  88
  89   private List<String> hiddenSeqRefs;
  90
  91   private ArrayList<SequenceI> hiddenSequences;
  92
  93   private final static String TCOFFEE_SCORE = "TCoffeeScore";
  94
  95   public JSONFile()
  96   {
  97     super();
  98   }
  99
 100   public JSONFile(FileParse source) throws IOException
 101   {
 102     super(source);
 103   }
 104
 105   public JSONFile(String inFile, DataSourceType sourceType)
 106           throws IOException
 107   {
 108     super(inFile, sourceType);
 109   }
 110
 111   @Override
 112   public void parse() throws IOException
 113   {
 114     parse(getReader());
 115
 116   }
 117
 118   @Override
 119   public String print(SequenceI[] sqs, boolean jvsuffix)
 120   {
 121     String jsonOutput = null;
 122     try
 123     {
 124       AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
 125       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(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       hiddenSections[0] = getViewport().getAlignment().getHiddenColumns()
 283               .regionsToString(";", "-");
 284     }
 285
 286     // hidden rows/seqs business
 287     HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
 288             .getHiddenSequences();
 289     if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
 290     {
 291       return hiddenSections;
 292     }
 293
 294     SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
 295     StringBuilder hiddenSeqsBuilder = new StringBuilder();
 296     for (SequenceI hiddenSeq : hiddenSeqs)
 297     {
 298       if (hiddenSeq != null)
 299       {
 300         hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
 301       }
 302     }
 303     if (hiddenSeqsBuilder.length() > 0)
 304     {
 305       hiddenSeqsBuilder.deleteCharAt(0);
 306     }
 307     hiddenSections[1] = hiddenSeqsBuilder.toString();
 308
 309     return hiddenSections;
 310   }
 311
 312   public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
 313           SequenceI[] sqs, FeatureRenderer fr)
 314   {
 315     displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
 316     List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<>();
 317     if (sqs == null)
 318     {
 319       return sequenceFeaturesPojo;
 320     }
 321
 322     FeatureColourFinder finder = new FeatureColourFinder(fr);
 323
 324     for (SequenceI seq : sqs)
 325     {
 326       SequenceI dataSetSequence = seq.getDatasetSequence();
 327       SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
 328               : seq.getDatasetSequence().getSequenceFeatures();
 329
 330       seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
 331               : seqFeatures;
 332       if (seqFeatures == null)
 333       {
 334         continue;
 335       }
 336
 337       for (SequenceFeature sf : seqFeatures)
 338       {
 339         if (displayedFeatures != null
 340                 && displayedFeatures.isVisible(sf.getType()))
 341         {
 342           SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
 343                   String.valueOf(seq.hashCode()));
 344
 345           String featureColour = (fr == null) ? null : jalview.util.Format
 346                   .getHexString(finder.findFeatureColour(Color.white, seq,
 347                           seq.findIndex(sf.getBegin())));
 348           jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
 349           jsonFeature.setXend(seq.findIndex(sf.getEnd()));
 350           jsonFeature.setType(sf.getType());
 351           jsonFeature.setDescription(sf.getDescription());
 352           jsonFeature.setLinks(sf.links);
 353           jsonFeature.setOtherDetails(sf.otherDetails);
 354           jsonFeature.setScore(sf.getScore());
 355           jsonFeature.setFillColor(featureColour);
 356           jsonFeature.setFeatureGroup(sf.getFeatureGroup());
 357           sequenceFeaturesPojo.add(jsonFeature);
 358         }
 359       }
 360     }
 361     return sequenceFeaturesPojo;
 362   }
 363
 364   public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
 365           Vector<AlignmentAnnotation> annotations)
 366   {
 367     List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<>();
 368     if (annotations == null)
 369     {
 370       return jsonAnnotations;
 371     }
 372     for (AlignmentAnnotation annot : annotations)
 373     {
 374       AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
 375       alignAnnotPojo.setDescription(annot.description);
 376       alignAnnotPojo.setLabel(annot.label);
 377       if (!Double.isNaN(annot.score))
 378       {
 379         alignAnnotPojo.setScore(annot.score);
 380       }
 381       alignAnnotPojo.setCalcId(annot.getCalcId());
 382       alignAnnotPojo.setGraphType(annot.graph);
 383
 384       AnnotationDisplaySettingPojo annotSetting = new AnnotationDisplaySettingPojo();
 385       annotSetting.setBelowAlignment(annot.belowAlignment);
 386       annotSetting.setCentreColLabels(annot.centreColLabels);
 387       annotSetting.setScaleColLabel(annot.scaleColLabel);
 388       annotSetting.setShowAllColLabels(annot.showAllColLabels);
 389       annotSetting.setVisible(annot.visible);
 390       annotSetting.setHasIcon(annot.hasIcons);
 391       alignAnnotPojo.setAnnotationSettings(annotSetting);
 392       SequenceI refSeq = annot.sequenceRef;
 393       if (refSeq != null)
 394       {
 395         alignAnnotPojo.setSequenceRef(String.valueOf(refSeq.hashCode()));
 396       }
 397       for (Annotation annotation : annot.annotations)
 398       {
 399         AnnotationPojo annotationPojo = new AnnotationPojo();
 400         if (annotation != null)
 401         {
 402           annotationPojo.setDescription(annotation.description);
 403           annotationPojo.setValue(annotation.value);
 404           annotationPojo
 405                   .setSecondaryStructure(annotation.secondaryStructure);
 406           String displayChar = annotation.displayCharacter == null ? null
 407                   : annotation.displayCharacter;
 408           // System.out.println("--------------------->[" + displayChar + "]");
 409           annotationPojo.setDisplayCharacter(displayChar);
 410           if (annotation.colour != null)
 411           {
 412             annotationPojo.setColour(jalview.util.Format
 413                     .getHexString(annotation.colour));
 414           }
 415           alignAnnotPojo.getAnnotations().add(annotationPojo);
 416         }
 417         else
 418         {
 419           if (annot.getCalcId() != null
 420                   && annot.getCalcId().equalsIgnoreCase(TCOFFEE_SCORE))
 421           {
 422             // do nothing
 423           }
 424           else
 425           {
 426             alignAnnotPojo.getAnnotations().add(annotationPojo);
 427           }
 428         }
 429       }
 430       jsonAnnotations.add(alignAnnotPojo);
 431     }
 432     return jsonAnnotations;
 433   }
 434
 435   @SuppressWarnings("unchecked")
 436   public JSONFile parse(Reader jsonAlignmentString)
 437   {
 438     try
 439     {
 440       JSONParser jsonParser = new JSONParser();
 441       JSONObject alignmentJsonObj = (JSONObject) jsonParser
 442               .parse(jsonAlignmentString);
 443       JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
 444       JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
 445               .get("alignAnnotation");
 446       JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
 447               .get("seqFeatures");
 448       JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
 449               .get("seqGroups");
 450       JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
 451               .get("appSettings");
 452
 453       if (jvSettingsJsonObj != null)
 454       {
 455         globalColourScheme = (String) jvSettingsJsonObj
 456                 .get("globalColorScheme");
 457         Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
 458                 "showSeqFeatures").toString());
 459         setShowSeqFeatures(showFeatures);
 460         parseHiddenSeqRefsAsList(jvSettingsJsonObj);
 461         parseHiddenCols(jvSettingsJsonObj);
 462       }
 463
 464       hiddenSequences = new ArrayList<>();
 465       seqMap = new Hashtable<>();
 466       for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
 467               .hasNext();)
 468       {
 469         JSONObject sequence = sequenceIter.next();
 470         String sequcenceString = sequence.get("seq").toString();
 471         String sequenceName = sequence.get("name").toString();
 472         String seqUniqueId = sequence.get("id").toString();
 473         int start = Integer.valueOf(sequence.get("start").toString());
 474         int end = Integer.valueOf(sequence.get("end").toString());
 475         Sequence seq = new Sequence(sequenceName, sequcenceString, start,
 476                 end);
 477         if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
 478         {
 479           hiddenSequences.add(seq);
 480         }
 481         seqs.add(seq);
 482         seqMap.put(seqUniqueId, seq);
 483       }
 484
 485       parseFeatures(jsonSeqArray);
 486
 487       for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
 488               .hasNext();)
 489       {
 490         JSONObject seqGrpObj = seqGrpIter.next();
 491         String grpName = seqGrpObj.get("groupName").toString();
 492         String colourScheme = seqGrpObj.get("colourScheme").toString();
 493         String description = (seqGrpObj.get("description") == null) ? null
 494                 : seqGrpObj.get("description").toString();
 495         boolean displayBoxes = Boolean.valueOf(seqGrpObj
 496                 .get("displayBoxes").toString());
 497         boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
 498                 .toString());
 499         boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
 500                 .toString());
 501         boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
 502                 "showNonconserved").toString());
 503         int startRes = Integer
 504                 .valueOf(seqGrpObj.get("startRes").toString());
 505         int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
 506         JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
 507
 508         ArrayList<SequenceI> grpSeqs = new ArrayList<>();
 509         if (sequenceRefs.size() > 0)
 510         {
 511           Iterator<String> seqHashIter = sequenceRefs.iterator();
 512           while (seqHashIter.hasNext())
 513           {
 514             String seqHash = seqHashIter.next();
 515             Sequence sequence = seqMap.get(seqHash);
 516             if (sequence != null)
 517             {
 518               grpSeqs.add(sequence);
 519             }
 520           }
 521         }
 522         SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
 523                 displayBoxes, displayText, colourText, startRes, endRes);
 524         seqGrp.setColourScheme(ColourSchemeMapper.getJalviewColourScheme(
 525                 colourScheme, seqGrp));
 526         seqGrp.setShowNonconserved(showNonconserved);
 527         seqGrp.setDescription(description);
 528         this.seqGroups.add(seqGrp);
 529
 530       }
 531
 532       for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
 533               .hasNext();)
 534       {
 535         JSONObject alAnnot = alAnnotIter.next();
 536         JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
 537         Annotation[] annotations = new Annotation[annotJsonArray.size()];
 538         int count = 0;
 539         for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
 540                 .hasNext();)
 541         {
 542           JSONObject annot = annotIter.next();
 543           if (annot == null)
 544           {
 545             annotations[count] = null;
 546           }
 547           else
 548           {
 549             float val = annot.get("value") == null ? null : Float
 550                     .valueOf(annot.get("value").toString());
 551             String desc = annot.get("description") == null ? null : annot
 552                     .get("description").toString();
 553             char ss = annot.get("secondaryStructure") == null
 554                     || annot.get("secondaryStructure").toString()
 555                             .equalsIgnoreCase("u0000") ? ' ' : annot
 556                     .get("secondaryStructure").toString().charAt(0);
 557             String displayChar = annot.get("displayCharacter") == null ? ""
 558                     : annot.get("displayCharacter").toString();
 559
 560             annotations[count] = new Annotation(displayChar, desc, ss, val);
 561             if (annot.get("colour") != null)
 562             {
 563               Color color = ColorUtils.parseColourString(annot.get(
 564                       "colour").toString());
 565               annotations[count].colour = color;
 566             }
 567           }
 568           ++count;
 569         }
 570
 571         AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
 572                 .get("label").toString(), alAnnot.get("description")
 573                 .toString(), annotations);
 574         alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0 : Integer
 575                 .valueOf(alAnnot.get("graphType").toString());
 576
 577         JSONObject diplaySettings = (JSONObject) alAnnot
 578                 .get("annotationSettings");
 579         if (diplaySettings != null)
 580         {
 581
 582           alignAnnot.scaleColLabel = (diplaySettings.get("scaleColLabel") == null) ? false
 583                   : Boolean.valueOf(diplaySettings.get("scaleColLabel")
 584                           .toString());
 585           alignAnnot.showAllColLabels = (diplaySettings
 586                   .get("showAllColLabels") == null) ? true : Boolean
 587                   .valueOf(diplaySettings.get("showAllColLabels")
 588                           .toString());
 589           alignAnnot.centreColLabels = (diplaySettings
 590                   .get("centreColLabels") == null) ? true
 591                   : Boolean.valueOf(diplaySettings.get("centreColLabels")
 592                           .toString());
 593           alignAnnot.belowAlignment = (diplaySettings.get("belowAlignment") == null) ? false
 594                   : Boolean.valueOf(diplaySettings.get("belowAlignment")
 595                           .toString());
 596           alignAnnot.visible = (diplaySettings.get("visible") == null) ? true
 597                   : Boolean.valueOf(diplaySettings.get("visible")
 598                           .toString());
 599           alignAnnot.hasIcons = (diplaySettings.get("hasIcon") == null) ? true
 600                   : Boolean.valueOf(diplaySettings.get("hasIcon")
 601                           .toString());
 602
 603         }
 604         if (alAnnot.get("score") != null)
 605         {
 606           alignAnnot.score = Double
 607                   .valueOf(alAnnot.get("score").toString());
 608         }
 609
 610         String calcId = (alAnnot.get("calcId") == null) ? "" : alAnnot.get(
 611                 "calcId").toString();
 612         alignAnnot.setCalcId(calcId);
 613         String seqHash = (alAnnot.get("sequenceRef") != null) ? alAnnot
 614                 .get("sequenceRef").toString() : null;
 615
 616         Sequence sequence = (seqHash != null) ? seqMap.get(seqHash) : null;
 617         if (sequence != null)
 618         {
 619           alignAnnot.sequenceRef = sequence;
 620           sequence.addAlignmentAnnotation(alignAnnot);
 621           if (alignAnnot.label.equalsIgnoreCase("T-COFFEE"))
 622           {
 623             alignAnnot.createSequenceMapping(sequence, sequence.getStart(),
 624                     false);
 625             sequence.addAlignmentAnnotation(alignAnnot);
 626             alignAnnot.adjustForAlignment();
 627           }
 628         }
 629         alignAnnot.validateRangeAndDisplay();
 630         this.annotations.add(alignAnnot);
 631
 632       }
 633     } catch (Exception e)
 634     {
 635       e.printStackTrace();
 636     }
 637     return this;
 638   }
 639
 640   public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
 641   {
 642     hiddenSeqRefs = new ArrayList<>();
 643     String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
 644     if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
 645     {
 646       String[] seqRefs = hiddenSeqs.split(";");
 647       for (String seqRef : seqRefs)
 648       {
 649         hiddenSeqRefs.add(seqRef);
 650       }
 651     }
 652   }
 653
 654   public void parseHiddenCols(JSONObject jvSettingsJson)
 655   {
 656     String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
 657     if (hiddenCols != null && !hiddenCols.isEmpty())
 658     {
 659       hiddenColumns = new HiddenColumns();
 660       String[] rangeStrings = hiddenCols.split(";");
 661       for (String rangeString : rangeStrings)
 662       {
 663         String[] range = rangeString.split("-");
 664         hiddenColumns.hideColumns(Integer.valueOf(range[0]),
 665                 Integer.valueOf(range[1]));
 666       }
 667     }
 668   }
 669
 670   @SuppressWarnings("unchecked")
 671   private void parseFeatures(JSONArray jsonSeqFeatures)
 672   {
 673     if (jsonSeqFeatures != null)
 674     {
 675       displayedFeatures = new FeaturesDisplayed();
 676       for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
 677               .hasNext();)
 678       {
 679         JSONObject jsonFeature = seqFeatureItr.next();
 680         Long begin = (Long) jsonFeature.get("xStart");
 681         Long end = (Long) jsonFeature.get("xEnd");
 682         String type = (String) jsonFeature.get("type");
 683         String featureGrp = (String) jsonFeature.get("featureGroup");
 684         String descripiton = (String) jsonFeature.get("description");
 685         String seqRef = (String) jsonFeature.get("sequenceRef");
 686         Float score = Float.valueOf(jsonFeature.get("score").toString());
 687
 688         Sequence seq = seqMap.get(seqRef);
 689         SequenceFeature sequenceFeature = new SequenceFeature();
 690         JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
 691         if (linksJsonArray != null && linksJsonArray.size() > 0)
 692         {
 693           Iterator<String> linkList = linksJsonArray.iterator();
 694           while (linkList.hasNext())
 695           {
 696             String link = linkList.next();
 697             sequenceFeature.addLink(link);
 698           }
 699         }
 700         sequenceFeature.setFeatureGroup(featureGrp);
 701         sequenceFeature.setScore(score);
 702         sequenceFeature.setDescription(descripiton);
 703         sequenceFeature.setType(type);
 704         sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
 705         sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
 706         seq.addSequenceFeature(sequenceFeature);
 707         displayedFeatures.setVisible(type);
 708       }
 709     }
 710   }
 711
 712   @Override
 713   public String getGlobalColourScheme()
 714   {
 715     return globalColourScheme;
 716   }
 717
 718   public void setGlobalColorScheme(String globalColourScheme)
 719   {
 720     this.globalColourScheme = globalColourScheme;
 721   }
 722
 723   @Override
 724   public FeaturesDisplayedI getDisplayedFeatures()
 725   {
 726     return displayedFeatures;
 727   }
 728
 729   public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
 730   {
 731     this.displayedFeatures = displayedFeatures;
 732   }
 733
 734   @Override
 735   public void configureForView(AlignmentViewPanel avpanel)
 736   {
 737     if (avpanel == null)
 738     {
 739       return;
 740     }
 741     super.configureForView(avpanel);
 742     AlignViewportI viewport = avpanel.getAlignViewport();
 743     AlignmentI alignment = viewport.getAlignment();
 744     AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
 745
 746     seqGroups = alignment.getGroups();
 747     fr = avpanel.cloneFeatureRenderer();
 748
 749     // Add non auto calculated annotation to AlignFile
 750     if (annots != null)
 751     {
 752       for (AlignmentAnnotation annot : annots)
 753       {
 754         if (annot != null && !annot.autoCalculated)
 755         {
 756           annotations.add(annot);
 757         }
 758       }
 759     }
 760     globalColourScheme = ColourSchemeProperty.getColourName(viewport
 761             .getGlobalColourScheme());
 762     setDisplayedFeatures(viewport.getFeaturesDisplayed());
 763     showSeqFeatures = viewport.isShowSequenceFeatures();
 764
 765   }
 766
 767   @Override
 768   public boolean isShowSeqFeatures()
 769   {
 770     return showSeqFeatures;
 771   }
 772
 773   public void setShowSeqFeatures(boolean showSeqFeatures)
 774   {
 775     this.showSeqFeatures = showSeqFeatures;
 776   }
 777
 778   public Vector<AlignmentAnnotation> getAnnotations()
 779   {
 780     return annotations;
 781   }
 782
 783   @Override
 784   public HiddenColumns getHiddenColumns()
 785   {
 786     return hiddenColumns;
 787   }
 788
 789   public void setHiddenColumns(HiddenColumns hidden)
 790   {
 791     this.hiddenColumns = hidden;
 792   }
 793
 794   @Override
 795   public SequenceI[] getHiddenSequences()
 796   {
 797     if (hiddenSequences == null || hiddenSequences.isEmpty())
 798     {
 799       return new SequenceI[] {};
 800     }
 801     synchronized (hiddenSequences)
 802     {
 803       return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
 804     }
 805   }
 806
 807   public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
 808   {
 809     this.hiddenSequences = hiddenSequences;
 810   }
 811
 812   public class JSONExportSettings
 813   {
 814     private boolean exportSequence;
 815
 816     private boolean exportSequenceFeatures;
 817
 818     private boolean exportAnnotations;
 819
 820     private boolean exportGroups;
 821
 822     private boolean exportJalviewSettings;
 823
 824     public boolean isExportSequence()
 825     {
 826       return exportSequence;
 827     }
 828
 829     public void setExportSequence(boolean exportSequence)
 830     {
 831       this.exportSequence = exportSequence;
 832     }
 833
 834     public boolean isExportSequenceFeatures()
 835     {
 836       return exportSequenceFeatures;
 837     }
 838
 839     public void setExportSequenceFeatures(boolean exportSequenceFeatures)
 840     {
 841       this.exportSequenceFeatures = exportSequenceFeatures;
 842     }
 843
 844     public boolean isExportAnnotations()
 845     {
 846       return exportAnnotations;
 847     }
 848
 849     public void setExportAnnotations(boolean exportAnnotations)
 850     {
 851       this.exportAnnotations = exportAnnotations;
 852     }
 853
 854     public boolean isExportGroups()
 855     {
 856       return exportGroups;
 857     }
 858
 859     public void setExportGroups(boolean exportGroups)
 860     {
 861       this.exportGroups = exportGroups;
 862     }
 863
 864     public boolean isExportJalviewSettings()
 865     {
 866       return exportJalviewSettings;
 867     }
 868
 869     public void setExportJalviewSettings(boolean exportJalviewSettings)
 870     {
 871       this.exportJalviewSettings = exportJalviewSettings;
 872     }
 873   }
 874
 875   /**
 876    * Returns a descriptor for suitable feature display settings with
 877    * <ul>
 878    * <li>ResNums or insertions features visible</li>
 879    * <li>insertions features coloured red</li>
 880    * <li>ResNum features coloured by label</li>
 881    * <li>Insertions displayed above (on top of) ResNums</li>
 882    * </ul>
 883    */
 884   @Override
 885   public FeatureSettingsModelI getFeatureColourScheme()
 886   {
 887     return new PDBFeatureSettings();
 888   }
 889 }