src/jalview/io/JSONFile.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21
  22 package jalview.io;
  23
  24 import jalview.api.AlignExportSettingI;
  25 import jalview.api.AlignViewportI;
  26 import jalview.api.AlignmentViewPanel;
  27 import jalview.api.ComplexAlignFile;
  28 import jalview.api.FeatureRenderer;
  29 import jalview.api.FeatureSettingsModelI;
  30 import jalview.api.FeaturesDisplayedI;
  31 import jalview.bin.BuildDetails;
  32 import jalview.datamodel.AlignmentAnnotation;
  33 import jalview.datamodel.AlignmentI;
  34 import jalview.datamodel.Annotation;
  35 import jalview.datamodel.ColumnSelection;
  36 import jalview.datamodel.HiddenSequences;
  37 import jalview.datamodel.Sequence;
  38 import jalview.datamodel.SequenceFeature;
  39 import jalview.datamodel.SequenceGroup;
  40 import jalview.datamodel.SequenceI;
  41 import jalview.json.binding.biojson.v1.AlignmentAnnotationPojo;
  42 import jalview.json.binding.biojson.v1.AlignmentPojo;
  43 import jalview.json.binding.biojson.v1.AnnotationDisplaySettingPojo;
  44 import jalview.json.binding.biojson.v1.AnnotationPojo;
  45 import jalview.json.binding.biojson.v1.ColourSchemeMapper;
  46 import jalview.json.binding.biojson.v1.SequenceFeaturesPojo;
  47 import jalview.json.binding.biojson.v1.SequenceGrpPojo;
  48 import jalview.json.binding.biojson.v1.SequencePojo;
  49 import jalview.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 List<int[]> hiddenColumns;
  88
  89   private ColumnSelection columnSelection;
  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       AlignExportSettingI 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 AlignExportSettingI()
 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
 224                         .equalsIgnoreCase(JalviewColourScheme.TCoffee
 225                                 .toString()))
 226         {
 227           jsonAlignmentPojo.setGlobalColorScheme(ResidueColourScheme.NONE);
 228         }
 229       }
 230
 231       if (exportSettings.isExportFeatures())
 232       {
 233         jsonAlignmentPojo
 234                 .setSeqFeatures(sequenceFeatureToJsonPojo(sqs, fr));
 235       }
 236
 237       if (exportSettings.isExportGroups() && seqGroups != null
 238               && seqGroups.size() > 0)
 239       {
 240         for (SequenceGroup seqGrp : seqGroups)
 241         {
 242           SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
 243           seqGrpPojo.setGroupName(seqGrp.getName());
 244           seqGrpPojo.setColourScheme(ColourSchemeProperty
 245                   .getColourName(seqGrp.getColourScheme()));
 246           seqGrpPojo.setColourText(seqGrp.getColourText());
 247           seqGrpPojo.setDescription(seqGrp.getDescription());
 248           seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
 249           seqGrpPojo.setDisplayText(seqGrp.getDisplayText());
 250           seqGrpPojo.setEndRes(seqGrp.getEndRes());
 251           seqGrpPojo.setStartRes(seqGrp.getStartRes());
 252           seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
 253           for (SequenceI seq : seqGrp.getSequences())
 254           {
 255             seqGrpPojo.getSequenceRefs()
 256                     .add(String.valueOf(seq.hashCode()));
 257           }
 258           jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
 259         }
 260       }
 261       org.json.JSONObject generatedJSon = new org.json.JSONObject(
 262               jsonAlignmentPojo);
 263       jsonOutput = generatedJSon.toString();
 264       return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
 265               "xEnd");
 266     } catch (Exception e)
 267     {
 268       e.printStackTrace();
 269     }
 270     return jsonOutput;
 271   }
 272
 273   public String[] getHiddenSections()
 274   {
 275     String[] hiddenSections = new String[2];
 276     if (getViewport() == null)
 277     {
 278       return null;
 279     }
 280
 281     // hidden column business
 282     if (getViewport().hasHiddenColumns())
 283     {
 284       List<int[]> hiddenCols = getViewport().getColumnSelection()
 285               .getHiddenColumns();
 286       StringBuilder hiddenColsBuilder = new StringBuilder();
 287       for (int[] range : hiddenCols)
 288       {
 289         hiddenColsBuilder.append(";").append(range[0]).append("-")
 290                 .append(range[1]);
 291       }
 292
 293       hiddenColsBuilder.deleteCharAt(0);
 294       hiddenSections[0] = hiddenColsBuilder.toString();
 295     }
 296
 297     // hidden rows/seqs business
 298     HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
 299             .getHiddenSequences();
 300     if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
 301     {
 302       return hiddenSections;
 303     }
 304
 305     SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
 306     StringBuilder hiddenSeqsBuilder = new StringBuilder();
 307     for (SequenceI hiddenSeq : hiddenSeqs)
 308     {
 309       if (hiddenSeq != null)
 310       {
 311         hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
 312       }
 313     }
 314     if (hiddenSeqsBuilder.length() > 0)
 315     {
 316       hiddenSeqsBuilder.deleteCharAt(0);
 317     }
 318     hiddenSections[1] = hiddenSeqsBuilder.toString();
 319
 320     return hiddenSections;
 321   }
 322
 323   public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
 324           SequenceI[] sqs, FeatureRenderer fr)
 325   {
 326     displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
 327     List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
 328     if (sqs == null)
 329     {
 330       return sequenceFeaturesPojo;
 331     }
 332
 333     FeatureColourFinder finder = new FeatureColourFinder(fr);
 334
 335     for (SequenceI seq : sqs)
 336     {
 337       SequenceI dataSetSequence = seq.getDatasetSequence();
 338       SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
 339               : seq.getDatasetSequence().getSequenceFeatures();
 340
 341       seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
 342               : seqFeatures;
 343       if (seqFeatures == null)
 344       {
 345         continue;
 346       }
 347
 348       for (SequenceFeature sf : seqFeatures)
 349       {
 350         if (displayedFeatures != null
 351                 && displayedFeatures.isVisible(sf.getType()))
 352         {
 353           SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
 354                   String.valueOf(seq.hashCode()));
 355
 356           String featureColour = (fr == null) ? null : jalview.util.Format
 357                   .getHexString(finder.findFeatureColour(Color.white, seq,
 358                           seq.findIndex(sf.getBegin())));
 359           jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
 360           jsonFeature.setXend(seq.findIndex(sf.getEnd()));
 361           jsonFeature.setType(sf.getType());
 362           jsonFeature.setDescription(sf.getDescription());
 363           jsonFeature.setLinks(sf.links);
 364           jsonFeature.setOtherDetails(sf.otherDetails);
 365           jsonFeature.setScore(sf.getScore());
 366           jsonFeature.setFillColor(featureColour);
 367           jsonFeature.setFeatureGroup(sf.getFeatureGroup());
 368           sequenceFeaturesPojo.add(jsonFeature);
 369         }
 370       }
 371     }
 372     return sequenceFeaturesPojo;
 373   }
 374
 375   public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
 376           Vector<AlignmentAnnotation> annotations)
 377   {
 378     List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
 379     if (annotations == null)
 380     {
 381       return jsonAnnotations;
 382     }
 383     for (AlignmentAnnotation annot : annotations)
 384     {
 385       AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
 386       alignAnnotPojo.setDescription(annot.description);
 387       alignAnnotPojo.setLabel(annot.label);
 388       if (!Double.isNaN(annot.score))
 389       {
 390         alignAnnotPojo.setScore(annot.score);
 391       }
 392       alignAnnotPojo.setCalcId(annot.getCalcId());
 393       alignAnnotPojo.setGraphType(annot.graph);
 394
 395       AnnotationDisplaySettingPojo annotSetting = new AnnotationDisplaySettingPojo();
 396       annotSetting.setBelowAlignment(annot.belowAlignment);
 397       annotSetting.setCentreColLabels(annot.centreColLabels);
 398       annotSetting.setScaleColLabel(annot.scaleColLabel);
 399       annotSetting.setShowAllColLabels(annot.showAllColLabels);
 400       annotSetting.setVisible(annot.visible);
 401       annotSetting.setHasIcon(annot.hasIcons);
 402       alignAnnotPojo.setAnnotationSettings(annotSetting);
 403       SequenceI refSeq = annot.sequenceRef;
 404       if (refSeq != null)
 405       {
 406         alignAnnotPojo.setSequenceRef(String.valueOf(refSeq.hashCode()));
 407       }
 408       for (Annotation annotation : annot.annotations)
 409       {
 410         AnnotationPojo annotationPojo = new AnnotationPojo();
 411         if (annotation != null)
 412         {
 413           annotationPojo.setDescription(annotation.description);
 414           annotationPojo.setValue(annotation.value);
 415           annotationPojo
 416                   .setSecondaryStructure(annotation.secondaryStructure);
 417           String displayChar = annotation.displayCharacter == null ? null
 418                   : annotation.displayCharacter;
 419           // System.out.println("--------------------->[" + displayChar + "]");
 420           annotationPojo.setDisplayCharacter(displayChar);
 421           if (annotation.colour != null)
 422           {
 423             annotationPojo.setColour(jalview.util.Format
 424                     .getHexString(annotation.colour));
 425           }
 426           alignAnnotPojo.getAnnotations().add(annotationPojo);
 427         }
 428         else
 429         {
 430           if (annot.getCalcId() != null
 431                   && annot.getCalcId().equalsIgnoreCase(TCOFFEE_SCORE))
 432           {
 433             // do nothing
 434           }
 435           else
 436           {
 437             alignAnnotPojo.getAnnotations().add(annotationPojo);
 438           }
 439         }
 440       }
 441       jsonAnnotations.add(alignAnnotPojo);
 442     }
 443     return jsonAnnotations;
 444   }
 445
 446   @SuppressWarnings("unchecked")
 447   public JSONFile parse(Reader jsonAlignmentString)
 448   {
 449     try
 450     {
 451       JSONParser jsonParser = new JSONParser();
 452       JSONObject alignmentJsonObj = (JSONObject) jsonParser
 453               .parse(jsonAlignmentString);
 454       JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
 455       JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
 456               .get("alignAnnotation");
 457       JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
 458               .get("seqFeatures");
 459       JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
 460               .get("seqGroups");
 461       JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
 462               .get("appSettings");
 463
 464       if (jvSettingsJsonObj != null)
 465       {
 466         globalColourScheme = (String) jvSettingsJsonObj
 467                 .get("globalColorScheme");
 468         Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
 469                 "showSeqFeatures").toString());
 470         setShowSeqFeatures(showFeatures);
 471         parseHiddenSeqRefsAsList(jvSettingsJsonObj);
 472         parseHiddenCols(jvSettingsJsonObj);
 473       }
 474
 475       hiddenSequences = new ArrayList<SequenceI>();
 476       seqMap = new Hashtable<String, Sequence>();
 477       for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
 478               .hasNext();)
 479       {
 480         JSONObject sequence = sequenceIter.next();
 481         String sequcenceString = sequence.get("seq").toString();
 482         String sequenceName = sequence.get("name").toString();
 483         String seqUniqueId = sequence.get("id").toString();
 484         int start = Integer.valueOf(sequence.get("start").toString());
 485         int end = Integer.valueOf(sequence.get("end").toString());
 486         Sequence seq = new Sequence(sequenceName, sequcenceString, start,
 487                 end);
 488         if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
 489         {
 490           hiddenSequences.add(seq);
 491         }
 492         seqs.add(seq);
 493         seqMap.put(seqUniqueId, seq);
 494       }
 495
 496       parseFeatures(jsonSeqArray);
 497
 498       for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
 499               .hasNext();)
 500       {
 501         JSONObject seqGrpObj = seqGrpIter.next();
 502         String grpName = seqGrpObj.get("groupName").toString();
 503         String colourScheme = seqGrpObj.get("colourScheme").toString();
 504         String description = (seqGrpObj.get("description") == null) ? null
 505                 : seqGrpObj.get("description").toString();
 506         boolean displayBoxes = Boolean.valueOf(seqGrpObj
 507                 .get("displayBoxes").toString());
 508         boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
 509                 .toString());
 510         boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
 511                 .toString());
 512         boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
 513                 "showNonconserved").toString());
 514         int startRes = Integer
 515                 .valueOf(seqGrpObj.get("startRes").toString());
 516         int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
 517         JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
 518
 519         ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
 520         if (sequenceRefs.size() > 0)
 521         {
 522           Iterator<String> seqHashIter = sequenceRefs.iterator();
 523           while (seqHashIter.hasNext())
 524           {
 525             String seqHash = seqHashIter.next();
 526             Sequence sequence = seqMap.get(seqHash);
 527             if (sequence != null)
 528             {
 529               grpSeqs.add(sequence);
 530             }
 531           }
 532         }
 533         SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
 534                 displayBoxes, displayText, colourText, startRes, endRes);
 535         seqGrp.setColourScheme(ColourSchemeMapper.getJalviewColourScheme(
 536                 colourScheme, seqGrp));
 537         seqGrp.setShowNonconserved(showNonconserved);
 538         seqGrp.setDescription(description);
 539         this.seqGroups.add(seqGrp);
 540
 541       }
 542
 543       for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
 544               .hasNext();)
 545       {
 546         JSONObject alAnnot = alAnnotIter.next();
 547         JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
 548         Annotation[] annotations = new Annotation[annotJsonArray.size()];
 549         int count = 0;
 550         for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
 551                 .hasNext();)
 552         {
 553           JSONObject annot = annotIter.next();
 554           if (annot == null)
 555           {
 556             annotations[count] = null;
 557           }
 558           else
 559           {
 560             float val = annot.get("value") == null ? null : Float
 561                     .valueOf(annot.get("value").toString());
 562             String desc = annot.get("description") == null ? null : annot
 563                     .get("description").toString();
 564             char ss = annot.get("secondaryStructure") == null
 565                     || annot.get("secondaryStructure").toString()
 566                             .equalsIgnoreCase("u0000") ? ' ' : annot
 567                     .get("secondaryStructure").toString().charAt(0);
 568             String displayChar = annot.get("displayCharacter") == null ? ""
 569                     : annot.get("displayCharacter").toString();
 570
 571             annotations[count] = new Annotation(displayChar, desc, ss, val);
 572             if (annot.get("colour") != null)
 573             {
 574               Color color = ColorUtils.parseColourString(annot.get(
 575                       "colour").toString());
 576               annotations[count].colour = color;
 577             }
 578           }
 579           ++count;
 580         }
 581
 582         AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
 583                 .get("label").toString(), alAnnot.get("description")
 584                 .toString(), annotations);
 585         alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0 : Integer
 586                 .valueOf(alAnnot.get("graphType").toString());
 587
 588         JSONObject diplaySettings = (JSONObject) alAnnot
 589                 .get("annotationSettings");
 590         if (diplaySettings != null)
 591         {
 592
 593           alignAnnot.scaleColLabel = (diplaySettings.get("scaleColLabel") == null) ? false
 594                   : Boolean.valueOf(diplaySettings.get("scaleColLabel")
 595                           .toString());
 596           alignAnnot.showAllColLabels = (diplaySettings
 597                   .get("showAllColLabels") == null) ? true : Boolean
 598                   .valueOf(diplaySettings.get("showAllColLabels")
 599                           .toString());
 600           alignAnnot.centreColLabels = (diplaySettings
 601                   .get("centreColLabels") == null) ? true
 602                   : Boolean.valueOf(diplaySettings.get("centreColLabels")
 603                           .toString());
 604           alignAnnot.belowAlignment = (diplaySettings.get("belowAlignment") == null) ? false
 605                   : Boolean.valueOf(diplaySettings.get("belowAlignment")
 606                           .toString());
 607           alignAnnot.visible = (diplaySettings.get("visible") == null) ? true
 608                   : Boolean.valueOf(diplaySettings.get("visible")
 609                           .toString());
 610           alignAnnot.hasIcons = (diplaySettings.get("hasIcon") == null) ? true
 611                   : Boolean.valueOf(diplaySettings.get("hasIcon")
 612                           .toString());
 613
 614         }
 615         if (alAnnot.get("score") != null)
 616         {
 617           alignAnnot.score = Double
 618                   .valueOf(alAnnot.get("score").toString());
 619         }
 620
 621         String calcId = (alAnnot.get("calcId") == null) ? "" : alAnnot.get(
 622                 "calcId").toString();
 623         alignAnnot.setCalcId(calcId);
 624         String seqHash = (alAnnot.get("sequenceRef") != null) ? alAnnot
 625                 .get("sequenceRef").toString() : null;
 626
 627         Sequence sequence = (seqHash != null) ? seqMap.get(seqHash) : null;
 628         if (sequence != null)
 629         {
 630           alignAnnot.sequenceRef = sequence;
 631           sequence.addAlignmentAnnotation(alignAnnot);
 632           if (alignAnnot.label.equalsIgnoreCase("T-COFFEE"))
 633           {
 634             alignAnnot.createSequenceMapping(sequence, sequence.getStart(),
 635                     false);
 636             sequence.addAlignmentAnnotation(alignAnnot);
 637             alignAnnot.adjustForAlignment();
 638           }
 639         }
 640         alignAnnot.validateRangeAndDisplay();
 641         this.annotations.add(alignAnnot);
 642
 643       }
 644     } catch (Exception e)
 645     {
 646       e.printStackTrace();
 647     }
 648     return this;
 649   }
 650
 651   public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
 652   {
 653     hiddenSeqRefs = new ArrayList<String>();
 654     String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
 655     if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
 656     {
 657       String[] seqRefs = hiddenSeqs.split(";");
 658       for (String seqRef : seqRefs)
 659       {
 660         hiddenSeqRefs.add(seqRef);
 661       }
 662     }
 663   }
 664
 665   public void parseHiddenCols(JSONObject jvSettingsJson)
 666   {
 667     String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
 668     if (hiddenCols != null && !hiddenCols.isEmpty())
 669     {
 670       columnSelection = new ColumnSelection();
 671       String[] rangeStrings = hiddenCols.split(";");
 672       for (String rangeString : rangeStrings)
 673       {
 674         String[] range = rangeString.split("-");
 675         columnSelection.hideColumns(Integer.valueOf(range[0]),
 676                 Integer.valueOf(range[1]));
 677       }
 678     }
 679   }
 680
 681   @SuppressWarnings("unchecked")
 682   private void parseFeatures(JSONArray jsonSeqFeatures)
 683   {
 684     if (jsonSeqFeatures != null)
 685     {
 686       displayedFeatures = new FeaturesDisplayed();
 687       for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
 688               .hasNext();)
 689       {
 690         JSONObject jsonFeature = seqFeatureItr.next();
 691         Long begin = (Long) jsonFeature.get("xStart");
 692         Long end = (Long) jsonFeature.get("xEnd");
 693         String type = (String) jsonFeature.get("type");
 694         String featureGrp = (String) jsonFeature.get("featureGroup");
 695         String description = (String) jsonFeature.get("description");
 696         String seqRef = (String) jsonFeature.get("sequenceRef");
 697         Float score = Float.valueOf(jsonFeature.get("score").toString());
 698
 699         Sequence seq = seqMap.get(seqRef);
 700         int featureBegin = seq.findPosition(begin.intValue());
 701         int featureEnd = seq.findPosition(end.intValue()) - 1;
 702
 703         SequenceFeature sequenceFeature = new SequenceFeature(type,
 704                 description, featureBegin, featureEnd, score, featureGrp);
 705
 706         JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
 707         if (linksJsonArray != null && linksJsonArray.size() > 0)
 708         {
 709           Iterator<String> linkList = linksJsonArray.iterator();
 710           while (linkList.hasNext())
 711           {
 712             String link = linkList.next();
 713             sequenceFeature.addLink(link);
 714           }
 715         }
 716
 717         seq.addSequenceFeature(sequenceFeature);
 718         displayedFeatures.setVisible(type);
 719       }
 720     }
 721   }
 722
 723   @Override
 724   public String getGlobalColourScheme()
 725   {
 726     return globalColourScheme;
 727   }
 728
 729   public void setGlobalColorScheme(String globalColourScheme)
 730   {
 731     this.globalColourScheme = globalColourScheme;
 732   }
 733
 734   @Override
 735   public FeaturesDisplayedI getDisplayedFeatures()
 736   {
 737     return displayedFeatures;
 738   }
 739
 740   public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
 741   {
 742     this.displayedFeatures = displayedFeatures;
 743   }
 744
 745   @Override
 746   public void configureForView(AlignmentViewPanel avpanel)
 747   {
 748     if (avpanel == null)
 749     {
 750       return;
 751     }
 752     super.configureForView(avpanel);
 753     AlignViewportI viewport = avpanel.getAlignViewport();
 754     AlignmentI alignment = viewport.getAlignment();
 755     AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
 756
 757     seqGroups = alignment.getGroups();
 758     fr = avpanel.cloneFeatureRenderer();
 759
 760     // Add non auto calculated annotation to AlignFile
 761     if (annots != null)
 762     {
 763       for (AlignmentAnnotation annot : annots)
 764       {
 765         if (annot != null && !annot.autoCalculated)
 766         {
 767           annotations.add(annot);
 768         }
 769       }
 770     }
 771     globalColourScheme = ColourSchemeProperty.getColourName(viewport
 772             .getGlobalColourScheme());
 773     setDisplayedFeatures(viewport.getFeaturesDisplayed());
 774     showSeqFeatures = viewport.isShowSequenceFeatures();
 775
 776   }
 777
 778   @Override
 779   public boolean isShowSeqFeatures()
 780   {
 781     return showSeqFeatures;
 782   }
 783
 784   public void setShowSeqFeatures(boolean showSeqFeatures)
 785   {
 786     this.showSeqFeatures = showSeqFeatures;
 787   }
 788
 789   public Vector<AlignmentAnnotation> getAnnotations()
 790   {
 791     return annotations;
 792   }
 793
 794   public List<int[]> getHiddenColumns()
 795   {
 796     return hiddenColumns;
 797   }
 798
 799   @Override
 800   public ColumnSelection getColumnSelection()
 801   {
 802     return columnSelection;
 803   }
 804
 805   public void setColumnSelection(ColumnSelection columnSelection)
 806   {
 807     this.columnSelection = columnSelection;
 808   }
 809
 810   @Override
 811   public SequenceI[] getHiddenSequences()
 812   {
 813     if (hiddenSequences == null || hiddenSequences.isEmpty())
 814     {
 815       return new SequenceI[] {};
 816     }
 817     synchronized (hiddenSequences)
 818     {
 819       return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
 820     }
 821   }
 822
 823   public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
 824   {
 825     this.hiddenSequences = hiddenSequences;
 826   }
 827
 828   public class JSONExportSettings
 829   {
 830     private boolean exportSequence;
 831
 832     private boolean exportSequenceFeatures;
 833
 834     private boolean exportAnnotations;
 835
 836     private boolean exportGroups;
 837
 838     private boolean exportJalviewSettings;
 839
 840     public boolean isExportSequence()
 841     {
 842       return exportSequence;
 843     }
 844
 845     public void setExportSequence(boolean exportSequence)
 846     {
 847       this.exportSequence = exportSequence;
 848     }
 849
 850     public boolean isExportSequenceFeatures()
 851     {
 852       return exportSequenceFeatures;
 853     }
 854
 855     public void setExportSequenceFeatures(boolean exportSequenceFeatures)
 856     {
 857       this.exportSequenceFeatures = exportSequenceFeatures;
 858     }
 859
 860     public boolean isExportAnnotations()
 861     {
 862       return exportAnnotations;
 863     }
 864
 865     public void setExportAnnotations(boolean exportAnnotations)
 866     {
 867       this.exportAnnotations = exportAnnotations;
 868     }
 869
 870     public boolean isExportGroups()
 871     {
 872       return exportGroups;
 873     }
 874
 875     public void setExportGroups(boolean exportGroups)
 876     {
 877       this.exportGroups = exportGroups;
 878     }
 879
 880     public boolean isExportJalviewSettings()
 881     {
 882       return exportJalviewSettings;
 883     }
 884
 885     public void setExportJalviewSettings(boolean exportJalviewSettings)
 886     {
 887       this.exportJalviewSettings = exportJalviewSettings;
 888     }
 889   }
 890
 891   /**
 892    * Returns a descriptor for suitable feature display settings with
 893    * <ul>
 894    * <li>ResNums or insertions features visible</li>
 895    * <li>insertions features coloured red</li>
 896    * <li>ResNum features coloured by label</li>
 897    * <li>Insertions displayed above (on top of) ResNums</li>
 898    * </ul>
 899    */
 900   @Override
 901   public FeatureSettingsModelI getFeatureColourScheme()
 902   {
 903     return new PDBFeatureSettings();
 904   }
 905 }