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.AlignExportSettingBeanI;
  33 import jalview.datamodel.AlignmentAnnotation;
  34 import jalview.datamodel.AlignmentI;
  35 import jalview.datamodel.Annotation;
  36 import jalview.datamodel.HiddenColumns;
  37 import jalview.datamodel.HiddenSequences;
  38 import jalview.datamodel.Sequence;
  39 import jalview.datamodel.SequenceFeature;
  40 import jalview.datamodel.SequenceGroup;
  41 import jalview.datamodel.SequenceI;
  42 import jalview.json.binding.biojson.v1.AlignmentAnnotationPojo;
  43 import jalview.json.binding.biojson.v1.AlignmentPojo;
  44 import jalview.json.binding.biojson.v1.AnnotationDisplaySettingPojo;
  45 import jalview.json.binding.biojson.v1.AnnotationPojo;
  46 import jalview.json.binding.biojson.v1.ColourSchemeMapper;
  47 import jalview.json.binding.biojson.v1.SequenceFeaturesPojo;
  48 import jalview.json.binding.biojson.v1.SequenceGrpPojo;
  49 import jalview.json.binding.biojson.v1.SequencePojo;
  50 import jalview.renderer.seqfeatures.FeatureColourFinder;
  51 import jalview.schemes.ColourSchemeProperty;
  52 import jalview.schemes.JalviewColourScheme;
  53 import jalview.schemes.ResidueColourScheme;
  54 import jalview.util.ColorUtils;
  55 import jalview.util.Format;
  56 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
  57
  58 import java.awt.Color;
  59 import java.io.IOException;
  60 import java.io.Reader;
  61 import java.util.ArrayList;
  62 import java.util.Hashtable;
  63 import java.util.Iterator;
  64 import java.util.List;
  65 import java.util.Vector;
  66
  67 import org.json.simple.JSONArray;
  68 import org.json.simple.JSONObject;
  69 import org.json.simple.parser.JSONParser;
  70
  71 public class JSONFile extends AlignFile implements ComplexAlignFile
  72 {
  73   private static String version = new BuildDetails().getVersion();
  74
  75   private String webstartUrl = "http://www.jalview.org/services/launchApp";
  76
  77   private String application = "Jalview";
  78
  79   private String globalColourScheme;
  80
  81   private boolean showSeqFeatures;
  82
  83   private Hashtable<String, Sequence> seqMap;
  84
  85   private FeaturesDisplayedI displayedFeatures;
  86
  87   private FeatureRenderer fr;
  88
  89   private HiddenColumns hiddenColumns;
  90
  91   private List<String> hiddenSeqRefs;
  92
  93   private ArrayList<SequenceI> hiddenSequences;
  94
  95   private final static String TCOFFEE_SCORE = "TCoffeeScore";
  96
  97   public JSONFile()
  98   {
  99     super();
 100   }
 101
 102   public JSONFile(FileParse source) throws IOException
 103   {
 104     super(source);
 105   }
 106
 107   public JSONFile(String inFile, DataSourceType sourceType)
 108           throws IOException
 109   {
 110     super(inFile, sourceType);
 111   }
 112
 113   @Override
 114   public void parse() throws IOException
 115   {
 116     parse(getReader());
 117
 118   }
 119
 120   @Override
 121   public String print(SequenceI[] sqs, boolean jvsuffix)
 122   {
 123     String jsonOutput = null;
 124     try
 125     {
 126       AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
 127       AlignExportSettingBeanI exportSettings = getExportSettings();
 128
 129       // if no export settings were supplied use the following with all values
 130       // defaulting to true
 131       if (exportSettings == null)
 132       {
 133         exportSettings = new AlignExportSettingBeanI()
 134         {
 135           @Override
 136           public boolean isExportHiddenSequences()
 137           {
 138             return true;
 139           }
 140
 141           @Override
 142           public boolean isExportHiddenColumns()
 143           {
 144             return true;
 145           }
 146
 147           @Override
 148           public boolean isExportGroups()
 149           {
 150             return true;
 151           }
 152
 153           @Override
 154           public boolean isExportFeatures()
 155           {
 156             return true;
 157           }
 158
 159           @Override
 160           public boolean isExportAnnotations()
 161           {
 162             return true;
 163           }
 164
 165           @Override
 166           public boolean isCancelled()
 167           {
 168             return false;
 169           }
 170         };
 171       }
 172
 173       int count = 0;
 174       for (SequenceI seq : sqs)
 175       {
 176         StringBuilder name = new StringBuilder();
 177         name.append(seq.getName()).append("/").append(seq.getStart())
 178                 .append("-").append(seq.getEnd());
 179         SequencePojo jsonSeqPojo = new SequencePojo();
 180         jsonSeqPojo.setId(String.valueOf(seq.hashCode()));
 181         jsonSeqPojo.setOrder(++count);
 182         jsonSeqPojo.setEnd(seq.getEnd());
 183         jsonSeqPojo.setStart(seq.getStart());
 184         jsonSeqPojo.setName(name.toString());
 185         jsonSeqPojo.setSeq(seq.getSequenceAsString());
 186         jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
 187       }
 188       jsonAlignmentPojo.setGlobalColorScheme(globalColourScheme);
 189       jsonAlignmentPojo.getAppSettings().put("application", application);
 190       jsonAlignmentPojo.getAppSettings().put("version", version);
 191       jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
 192       jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
 193               String.valueOf(showSeqFeatures));
 194
 195       String[] hiddenSections = getHiddenSections();
 196       if (hiddenSections != null)
 197       {
 198         if (hiddenSections[0] != null
 199                 && exportSettings.isExportHiddenColumns())
 200         {
 201           jsonAlignmentPojo.getAppSettings().put("hiddenCols",
 202                   String.valueOf(hiddenSections[0]));
 203         }
 204         if (hiddenSections[1] != null
 205                 && exportSettings.isExportHiddenSequences())
 206         {
 207           jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
 208                   String.valueOf(hiddenSections[1]));
 209         }
 210       }
 211
 212       if (exportSettings.isExportAnnotations())
 213       {
 214         jsonAlignmentPojo
 215                 .setAlignAnnotation(annotationToJsonPojo(annotations));
 216       }
 217       else
 218       {
 219         // These color schemes require annotation, disable them if annotations
 220         // are not exported
 221         if (globalColourScheme
 222                 .equalsIgnoreCase(JalviewColourScheme.RNAHelices.toString())
 223                 || globalColourScheme.equalsIgnoreCase(
 224                         JalviewColourScheme.TCoffee.toString()))
 225         {
 226           jsonAlignmentPojo.setGlobalColorScheme(ResidueColourScheme.NONE);
 227         }
 228       }
 229
 230       if (exportSettings.isExportFeatures())
 231       {
 232         jsonAlignmentPojo.setSeqFeatures(sequenceFeatureToJsonPojo(sqs));
 233       }
 234
 235       if (exportSettings.isExportGroups() && seqGroups != null
 236               && seqGroups.size() > 0)
 237       {
 238         for (SequenceGroup seqGrp : seqGroups)
 239         {
 240           SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
 241           seqGrpPojo.setGroupName(seqGrp.getName());
 242           seqGrpPojo.setColourScheme(ColourSchemeProperty
 243                   .getColourName(seqGrp.getColourScheme()));
 244           seqGrpPojo.setColourText(seqGrp.getColourText());
 245           seqGrpPojo.setDescription(seqGrp.getDescription());
 246           seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
 247           seqGrpPojo.setDisplayText(seqGrp.getDisplayText());
 248           seqGrpPojo.setEndRes(seqGrp.getEndRes());
 249           seqGrpPojo.setStartRes(seqGrp.getStartRes());
 250           seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
 251           for (SequenceI seq : seqGrp.getSequences())
 252           {
 253             seqGrpPojo.getSequenceRefs()
 254                     .add(String.valueOf(seq.hashCode()));
 255           }
 256           jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
 257         }
 258       }
 259       org.json.JSONObject generatedJSon = new org.json.JSONObject(
 260               jsonAlignmentPojo);
 261       jsonOutput = generatedJSon.toString();
 262       return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
 263               "xEnd");
 264     } catch (Exception e)
 265     {
 266       e.printStackTrace();
 267     }
 268     return jsonOutput;
 269   }
 270
 271   public String[] getHiddenSections()
 272   {
 273     String[] hiddenSections = new String[2];
 274     if (getViewport() == null)
 275     {
 276       return null;
 277     }
 278
 279     // hidden column business
 280     if (getViewport().hasHiddenColumns())
 281     {
 282       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   protected List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
 313           SequenceI[] sqs)
 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     String[] visibleFeatureTypes = displayedFeatures == null ? null
 325             : displayedFeatures.getVisibleFeatures().toArray(
 326                     new String[displayedFeatures.getVisibleFeatureCount()]);
 327
 328     for (SequenceI seq : sqs)
 329     {
 330       /*
 331        * get all features currently visible (and any non-positional features)
 332        */
 333       List<SequenceFeature> seqFeatures = seq.getFeatures().getAllFeatures(
 334               visibleFeatureTypes);
 335       for (SequenceFeature sf : seqFeatures)
 336       {
 337         SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
 338                 String.valueOf(seq.hashCode()));
 339
 340         String featureColour = (fr == null) ? null : Format
 341                 .getHexString(finder.findFeatureColour(Color.white, seq,
 342                         seq.findIndex(sf.getBegin())));
 343         int xStart = sf.getBegin() == 0 ? 0
 344                 : seq.findIndex(sf.getBegin()) - 1;
 345         int xEnd = sf.getEnd() == 0 ? 0 : seq.findIndex(sf.getEnd());
 346         jsonFeature.setXstart(xStart);
 347         jsonFeature.setXend(xEnd);
 348         jsonFeature.setType(sf.getType());
 349         jsonFeature.setDescription(sf.getDescription());
 350         jsonFeature.setLinks(sf.links);
 351         jsonFeature.setOtherDetails(sf.otherDetails);
 352         jsonFeature.setScore(sf.getScore());
 353         jsonFeature.setFillColor(featureColour);
 354         jsonFeature.setFeatureGroup(sf.getFeatureGroup());
 355         sequenceFeaturesPojo.add(jsonFeature);
 356       }
 357     }
 358     return sequenceFeaturesPojo;
 359   }
 360
 361   public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
 362           Vector<AlignmentAnnotation> annotations)
 363   {
 364     List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<>();
 365     if (annotations == null)
 366     {
 367       return jsonAnnotations;
 368     }
 369     for (AlignmentAnnotation annot : annotations)
 370     {
 371       AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
 372       alignAnnotPojo.setDescription(annot.description);
 373       alignAnnotPojo.setLabel(annot.label);
 374       if (!Double.isNaN(annot.score))
 375       {
 376         alignAnnotPojo.setScore(annot.score);
 377       }
 378       alignAnnotPojo.setCalcId(annot.getCalcId());
 379       alignAnnotPojo.setGraphType(annot.graph);
 380
 381       AnnotationDisplaySettingPojo annotSetting = new AnnotationDisplaySettingPojo();
 382       annotSetting.setBelowAlignment(annot.belowAlignment);
 383       annotSetting.setCentreColLabels(annot.centreColLabels);
 384       annotSetting.setScaleColLabel(annot.scaleColLabel);
 385       annotSetting.setShowAllColLabels(annot.showAllColLabels);
 386       annotSetting.setVisible(annot.visible);
 387       annotSetting.setHasIcon(annot.hasIcons);
 388       alignAnnotPojo.setAnnotationSettings(annotSetting);
 389       SequenceI refSeq = annot.sequenceRef;
 390       if (refSeq != null)
 391       {
 392         alignAnnotPojo.setSequenceRef(String.valueOf(refSeq.hashCode()));
 393       }
 394       for (Annotation annotation : annot.annotations)
 395       {
 396         AnnotationPojo annotationPojo = new AnnotationPojo();
 397         if (annotation != null)
 398         {
 399           annotationPojo.setDescription(annotation.description);
 400           annotationPojo.setValue(annotation.value);
 401           annotationPojo
 402                   .setSecondaryStructure(annotation.secondaryStructure);
 403           String displayChar = annotation.displayCharacter == null ? null
 404                   : annotation.displayCharacter;
 405           // System.out.println("--------------------->[" + displayChar + "]");
 406           annotationPojo.setDisplayCharacter(displayChar);
 407           if (annotation.colour != null)
 408           {
 409             annotationPojo.setColour(
 410                     jalview.util.Format.getHexString(annotation.colour));
 411           }
 412           alignAnnotPojo.getAnnotations().add(annotationPojo);
 413         }
 414         else
 415         {
 416           if (annot.getCalcId() != null
 417                   && annot.getCalcId().equalsIgnoreCase(TCOFFEE_SCORE))
 418           {
 419             // do nothing
 420           }
 421           else
 422           {
 423             alignAnnotPojo.getAnnotations().add(annotationPojo);
 424           }
 425         }
 426       }
 427       jsonAnnotations.add(alignAnnotPojo);
 428     }
 429     return jsonAnnotations;
 430   }
 431
 432   @SuppressWarnings("unchecked")
 433   public JSONFile parse(Reader jsonAlignmentString)
 434   {
 435     try
 436     {
 437       JSONParser jsonParser = new JSONParser();
 438       JSONObject alignmentJsonObj = (JSONObject) jsonParser
 439               .parse(jsonAlignmentString);
 440       JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
 441       JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
 442               .get("alignAnnotation");
 443       JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
 444               .get("seqFeatures");
 445       JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
 446               .get("seqGroups");
 447       JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
 448               .get("appSettings");
 449
 450       if (jvSettingsJsonObj != null)
 451       {
 452         globalColourScheme = (String) jvSettingsJsonObj
 453                 .get("globalColorScheme");
 454         Boolean showFeatures = Boolean.valueOf(
 455                 jvSettingsJsonObj.get("showSeqFeatures").toString());
 456         setShowSeqFeatures(showFeatures);
 457         parseHiddenSeqRefsAsList(jvSettingsJsonObj);
 458         parseHiddenCols(jvSettingsJsonObj);
 459       }
 460
 461       hiddenSequences = new ArrayList<>();
 462       seqMap = new Hashtable<>();
 463       for (Iterator<JSONObject> sequenceIter = seqJsonArray
 464               .iterator(); sequenceIter.hasNext();)
 465       {
 466         JSONObject sequence = sequenceIter.next();
 467         String sequcenceString = sequence.get("seq").toString();
 468         String sequenceName = sequence.get("name").toString();
 469         String seqUniqueId = sequence.get("id").toString();
 470         int start = Integer.valueOf(sequence.get("start").toString());
 471         int end = Integer.valueOf(sequence.get("end").toString());
 472         Sequence seq = new Sequence(sequenceName, sequcenceString, start,
 473                 end);
 474         if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
 475         {
 476           hiddenSequences.add(seq);
 477         }
 478         seqs.add(seq);
 479         seqMap.put(seqUniqueId, seq);
 480       }
 481
 482       parseFeatures(jsonSeqArray);
 483
 484       for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray
 485               .iterator(); seqGrpIter.hasNext();)
 486       {
 487         JSONObject seqGrpObj = seqGrpIter.next();
 488         String grpName = seqGrpObj.get("groupName").toString();
 489         String colourScheme = seqGrpObj.get("colourScheme").toString();
 490         String description = (seqGrpObj.get("description") == null) ? null
 491                 : seqGrpObj.get("description").toString();
 492         boolean displayBoxes = Boolean
 493                 .valueOf(seqGrpObj.get("displayBoxes").toString());
 494         boolean displayText = Boolean
 495                 .valueOf(seqGrpObj.get("displayText").toString());
 496         boolean colourText = Boolean
 497                 .valueOf(seqGrpObj.get("colourText").toString());
 498         boolean showNonconserved = Boolean
 499                 .valueOf(seqGrpObj.get("showNonconserved").toString());
 500         int startRes = Integer
 501                 .valueOf(seqGrpObj.get("startRes").toString());
 502         int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
 503         JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
 504
 505         ArrayList<SequenceI> grpSeqs = new ArrayList<>();
 506         if (sequenceRefs.size() > 0)
 507         {
 508           Iterator<String> seqHashIter = sequenceRefs.iterator();
 509           while (seqHashIter.hasNext())
 510           {
 511             String seqHash = seqHashIter.next();
 512             Sequence sequence = seqMap.get(seqHash);
 513             if (sequence != null)
 514             {
 515               grpSeqs.add(sequence);
 516             }
 517           }
 518         }
 519         SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
 520                 displayBoxes, displayText, colourText, startRes, endRes);
 521         seqGrp.setColourScheme(ColourSchemeMapper
 522                 .getJalviewColourScheme(colourScheme, seqGrp));
 523         seqGrp.setShowNonconserved(showNonconserved);
 524         seqGrp.setDescription(description);
 525         this.seqGroups.add(seqGrp);
 526
 527       }
 528
 529       for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray
 530               .iterator(); alAnnotIter.hasNext();)
 531       {
 532         JSONObject alAnnot = alAnnotIter.next();
 533         JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
 534         Annotation[] annotations = new Annotation[annotJsonArray.size()];
 535         int count = 0;
 536         for (Iterator<JSONObject> annotIter = annotJsonArray
 537                 .iterator(); annotIter.hasNext();)
 538         {
 539           JSONObject annot = annotIter.next();
 540           if (annot == null)
 541           {
 542             annotations[count] = null;
 543           }
 544           else
 545           {
 546             float val = annot.get("value") == null ? null
 547                     : Float.valueOf(annot.get("value").toString());
 548             String desc = annot.get("description") == null ? null
 549                     : annot.get("description").toString();
 550             char ss = annot.get("secondaryStructure") == null
 551                     || annot.get("secondaryStructure").toString()
 552                             .equalsIgnoreCase("u0000") ? ' '
 553                                     : annot.get("secondaryStructure")
 554                                             .toString().charAt(0);
 555             String displayChar = annot.get("displayCharacter") == null ? ""
 556                     : annot.get("displayCharacter").toString();
 557
 558             annotations[count] = new Annotation(displayChar, desc, ss, val);
 559             if (annot.get("colour") != null)
 560             {
 561               Color color = ColorUtils
 562                       .parseColourString(annot.get("colour").toString());
 563               annotations[count].colour = color;
 564             }
 565           }
 566           ++count;
 567         }
 568
 569         AlignmentAnnotation alignAnnot = new AlignmentAnnotation(
 570                 alAnnot.get("label").toString(),
 571                 alAnnot.get("description").toString(), annotations);
 572         alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0
 573                 : Integer.valueOf(alAnnot.get("graphType").toString());
 574
 575         JSONObject diplaySettings = (JSONObject) alAnnot
 576                 .get("annotationSettings");
 577         if (diplaySettings != null)
 578         {
 579
 580           alignAnnot.scaleColLabel = (diplaySettings
 581                   .get("scaleColLabel") == null) ? false
 582                           : Boolean.valueOf(diplaySettings
 583                                   .get("scaleColLabel").toString());
 584           alignAnnot.showAllColLabels = (diplaySettings
 585                   .get("showAllColLabels") == null) ? true
 586                           : Boolean.valueOf(diplaySettings
 587                                   .get("showAllColLabels").toString());
 588           alignAnnot.centreColLabels = (diplaySettings
 589                   .get("centreColLabels") == null) ? true
 590                           : Boolean.valueOf(diplaySettings
 591                                   .get("centreColLabels").toString());
 592           alignAnnot.belowAlignment = (diplaySettings
 593                   .get("belowAlignment") == null) ? false
 594                           : Boolean.valueOf(diplaySettings
 595                                   .get("belowAlignment").toString());
 596           alignAnnot.visible = (diplaySettings.get("visible") == null)
 597                   ? true
 598                   : Boolean.valueOf(
 599                           diplaySettings.get("visible").toString());
 600           alignAnnot.hasIcons = (diplaySettings.get("hasIcon") == null)
 601                   ? true
 602                   : Boolean.valueOf(
 603                           diplaySettings.get("hasIcon").toString());
 604
 605         }
 606         if (alAnnot.get("score") != null)
 607         {
 608           alignAnnot.score = Double
 609                   .valueOf(alAnnot.get("score").toString());
 610         }
 611
 612         String calcId = (alAnnot.get("calcId") == null) ? ""
 613                 : alAnnot.get("calcId").toString();
 614         alignAnnot.setCalcId(calcId);
 615         String seqHash = (alAnnot.get("sequenceRef") != null)
 616                 ? alAnnot.get("sequenceRef").toString()
 617                 : null;
 618
 619         Sequence sequence = (seqHash != null) ? seqMap.get(seqHash) : null;
 620         if (sequence != null)
 621         {
 622           alignAnnot.sequenceRef = sequence;
 623           sequence.addAlignmentAnnotation(alignAnnot);
 624           if (alignAnnot.label.equalsIgnoreCase("T-COFFEE"))
 625           {
 626             alignAnnot.createSequenceMapping(sequence, sequence.getStart(),
 627                     false);
 628             sequence.addAlignmentAnnotation(alignAnnot);
 629             alignAnnot.adjustForAlignment();
 630           }
 631         }
 632         alignAnnot.validateRangeAndDisplay();
 633         this.annotations.add(alignAnnot);
 634
 635       }
 636     } catch (Exception e)
 637     {
 638       e.printStackTrace();
 639     }
 640     return this;
 641   }
 642
 643   public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
 644   {
 645     hiddenSeqRefs = new ArrayList<>();
 646     String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
 647     if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
 648     {
 649       String[] seqRefs = hiddenSeqs.split(";");
 650       for (String seqRef : seqRefs)
 651       {
 652         hiddenSeqRefs.add(seqRef);
 653       }
 654     }
 655   }
 656
 657   public void parseHiddenCols(JSONObject jvSettingsJson)
 658   {
 659     String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
 660     if (hiddenCols != null && !hiddenCols.isEmpty())
 661     {
 662       hiddenColumns = new HiddenColumns();
 663       String[] rangeStrings = hiddenCols.split(";");
 664       for (String rangeString : rangeStrings)
 665       {
 666         String[] range = rangeString.split("-");
 667         hiddenColumns.hideColumns(Integer.valueOf(range[0]),
 668                 Integer.valueOf(range[1]));
 669       }
 670     }
 671   }
 672
 673   @SuppressWarnings("unchecked")
 674   private void parseFeatures(JSONArray jsonSeqFeatures)
 675   {
 676     if (jsonSeqFeatures != null)
 677     {
 678       displayedFeatures = new FeaturesDisplayed();
 679       for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures
 680               .iterator(); seqFeatureItr.hasNext();)
 681       {
 682         JSONObject jsonFeature = seqFeatureItr.next();
 683         Long begin = (Long) jsonFeature.get("xStart");
 684         Long end = (Long) jsonFeature.get("xEnd");
 685         String type = (String) jsonFeature.get("type");
 686         String featureGrp = (String) jsonFeature.get("featureGroup");
 687         String description = (String) jsonFeature.get("description");
 688         String seqRef = (String) jsonFeature.get("sequenceRef");
 689         Float score = Float.valueOf(jsonFeature.get("score").toString());
 690
 691         Sequence seq = seqMap.get(seqRef);
 692
 693         /*
 694          * begin/end of 0 is for a non-positional feature
 695          */
 696         int featureBegin = begin.intValue() == 0 ? 0 : seq
 697                 .findPosition(begin.intValue());
 698         int featureEnd = end.intValue() == 0 ? 0 : seq.findPosition(end
 699                 .intValue()) - 1;
 700
 701         SequenceFeature sequenceFeature = new SequenceFeature(type,
 702                 description, featureBegin, featureEnd, score, featureGrp);
 703
 704         JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
 705         if (linksJsonArray != null && linksJsonArray.size() > 0)
 706         {
 707           Iterator<String> linkList = linksJsonArray.iterator();
 708           while (linkList.hasNext())
 709           {
 710             String link = linkList.next();
 711             sequenceFeature.addLink(link);
 712           }
 713         }
 714
 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 = ColourSchemeProperty
 770             .getColourName(viewport.getGlobalColourScheme());
 771     setDisplayedFeatures(viewport.getFeaturesDisplayed());
 772     showSeqFeatures = viewport.isShowSequenceFeatures();
 773
 774   }
 775
 776   @Override
 777   public boolean isShowSeqFeatures()
 778   {
 779     return showSeqFeatures;
 780   }
 781
 782   public void setShowSeqFeatures(boolean showSeqFeatures)
 783   {
 784     this.showSeqFeatures = showSeqFeatures;
 785   }
 786
 787   public Vector<AlignmentAnnotation> getAnnotations()
 788   {
 789     return annotations;
 790   }
 791
 792   @Override
 793   public HiddenColumns getHiddenColumns()
 794   {
 795     return hiddenColumns;
 796   }
 797
 798   public void setHiddenColumns(HiddenColumns hidden)
 799   {
 800     this.hiddenColumns = hidden;
 801   }
 802
 803   @Override
 804   public SequenceI[] getHiddenSequences()
 805   {
 806     if (hiddenSequences == null || hiddenSequences.isEmpty())
 807     {
 808       return new SequenceI[] {};
 809     }
 810     synchronized (hiddenSequences)
 811     {
 812       return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
 813     }
 814   }
 815
 816   public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
 817   {
 818     this.hiddenSequences = hiddenSequences;
 819   }
 820
 821   public class JSONExportSettings
 822   {
 823     private boolean exportSequence;
 824
 825     private boolean exportSequenceFeatures;
 826
 827     private boolean exportAnnotations;
 828
 829     private boolean exportGroups;
 830
 831     private boolean exportJalviewSettings;
 832
 833     public boolean isExportSequence()
 834     {
 835       return exportSequence;
 836     }
 837
 838     public void setExportSequence(boolean exportSequence)
 839     {
 840       this.exportSequence = exportSequence;
 841     }
 842
 843     public boolean isExportSequenceFeatures()
 844     {
 845       return exportSequenceFeatures;
 846     }
 847
 848     public void setExportSequenceFeatures(boolean exportSequenceFeatures)
 849     {
 850       this.exportSequenceFeatures = exportSequenceFeatures;
 851     }
 852
 853     public boolean isExportAnnotations()
 854     {
 855       return exportAnnotations;
 856     }
 857
 858     public void setExportAnnotations(boolean exportAnnotations)
 859     {
 860       this.exportAnnotations = exportAnnotations;
 861     }
 862
 863     public boolean isExportGroups()
 864     {
 865       return exportGroups;
 866     }
 867
 868     public void setExportGroups(boolean exportGroups)
 869     {
 870       this.exportGroups = exportGroups;
 871     }
 872
 873     public boolean isExportJalviewSettings()
 874     {
 875       return exportJalviewSettings;
 876     }
 877
 878     public void setExportJalviewSettings(boolean exportJalviewSettings)
 879     {
 880       this.exportJalviewSettings = exportJalviewSettings;
 881     }
 882   }
 883
 884   /**
 885    * Returns a descriptor for suitable feature display settings with
 886    * <ul>
 887    * <li>ResNums or insertions features visible</li>
 888    * <li>insertions features coloured red</li>
 889    * <li>ResNum features coloured by label</li>
 890    * <li>Insertions displayed above (on top of) ResNums</li>
 891    * </ul>
 892    */
 893   @Override
 894   public FeatureSettingsModelI getFeatureColourScheme()
 895   {
 896     return new PDBFeatureSettings();
 897   }
 898 }