src/jalview/io/JSONFile.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21
  22 package jalview.io;
  23
  24 import jalview.api.AlignExportSettingI;
  25 import jalview.api.AlignViewportI;
  26 import jalview.api.AlignmentViewPanel;
  27 import jalview.api.ComplexAlignFile;
  28 import jalview.api.FeatureRenderer;
  29 import jalview.api.FeatureSettingsModelI;
  30 import jalview.api.FeaturesDisplayedI;
  31 import jalview.bin.BuildDetails;
  32 import jalview.datamodel.AlignmentAnnotation;
  33 import jalview.datamodel.AlignmentI;
  34 import jalview.datamodel.Annotation;
  35 import jalview.datamodel.ColumnSelection;
  36 import jalview.datamodel.HiddenSequences;
  37 import jalview.datamodel.Sequence;
  38 import jalview.datamodel.SequenceFeature;
  39 import jalview.datamodel.SequenceGroup;
  40 import jalview.datamodel.SequenceI;
  41 import jalview.json.binding.biojson.v1.AlignmentAnnotationPojo;
  42 import jalview.json.binding.biojson.v1.AlignmentPojo;
  43 import jalview.json.binding.biojson.v1.AnnotationDisplaySettingPojo;
  44 import jalview.json.binding.biojson.v1.AnnotationPojo;
  45 import jalview.json.binding.biojson.v1.ColourSchemeMapper;
  46 import jalview.json.binding.biojson.v1.SequenceFeaturesPojo;
  47 import jalview.json.binding.biojson.v1.SequenceGrpPojo;
  48 import jalview.json.binding.biojson.v1.SequencePojo;
  49 import jalview.schemes.Colour;
  50 import jalview.schemes.ColourSchemeProperty;
  51 import jalview.schemes.UserColourScheme;
  52 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
  53
  54 import java.awt.Color;
  55 import java.io.IOException;
  56 import java.io.Reader;
  57 import java.util.ArrayList;
  58 import java.util.Hashtable;
  59 import java.util.Iterator;
  60 import java.util.List;
  61 import java.util.Vector;
  62
  63 import org.json.simple.JSONArray;
  64 import org.json.simple.JSONObject;
  65 import org.json.simple.parser.JSONParser;
  66
  67 public class JSONFile extends AlignFile implements ComplexAlignFile
  68 {
  69   private static String version = new BuildDetails().getVersion();
  70
  71   private String webstartUrl = "http://www.jalview.org/services/launchApp";
  72
  73   private String application = "Jalview";
  74
  75   public static final String FILE_EXT = "json";
  76
  77   public static final String FILE_DESC = "JSON";
  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 List<int[]> hiddenColumns;
  90
  91   private ColumnSelection columnSelection;
  92
  93   private List<String> hiddenSeqRefs;
  94
  95   private ArrayList<SequenceI> hiddenSequences;
  96
  97   private final static String TCOFFEE_SCORE = "TCoffeeScore";
  98
  99   public JSONFile()
 100   {
 101     super();
 102   }
 103
 104   public JSONFile(FileParse source) throws IOException
 105   {
 106     super(source);
 107   }
 108
 109   public JSONFile(String inFile, String type) throws IOException
 110   {
 111     super(inFile, type);
 112   }
 113
 114   @Override
 115   public void parse() throws IOException
 116   {
 117     parse(getReader());
 118
 119   }
 120
 121   @Override
 122   public String print()
 123   {
 124     String jsonOutput = null;
 125     try
 126     {
 127       AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
 128       AlignExportSettingI exportSettings = getExportSettings();
 129
 130       // if no export settings were supplied use the following with all values
 131       // defaulting to true
 132       if (exportSettings == null)
 133       {
 134         exportSettings = new AlignExportSettingI()
 135         {
 136           @Override
 137           public boolean isExportHiddenSequences()
 138           {
 139             return true;
 140           }
 141
 142           @Override
 143           public boolean isExportHiddenColumns()
 144           {
 145             return true;
 146           }
 147
 148           @Override
 149           public boolean isExportGroups()
 150           {
 151             return true;
 152           }
 153
 154           @Override
 155           public boolean isExportFeatures()
 156           {
 157             return true;
 158           }
 159
 160           @Override
 161           public boolean isExportAnnotations()
 162           {
 163             return true;
 164           }
 165
 166           @Override
 167           public boolean isCancelled()
 168           {
 169             return false;
 170           }
 171         };
 172       }
 173
 174       int count = 0;
 175       for (SequenceI seq : seqs)
 176       {
 177         StringBuilder name = new StringBuilder();
 178         name.append(seq.getName()).append("/").append(seq.getStart())
 179                 .append("-").append(seq.getEnd());
 180         SequencePojo jsonSeqPojo = new SequencePojo();
 181         jsonSeqPojo.setId(String.valueOf(seq.hashCode()));
 182         jsonSeqPojo.setOrder(++count);
 183         jsonSeqPojo.setEnd(seq.getEnd());
 184         jsonSeqPojo.setStart(seq.getStart());
 185         jsonSeqPojo.setName(name.toString());
 186         jsonSeqPojo.setSeq(seq.getSequenceAsString());
 187         jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
 188       }
 189       jsonAlignmentPojo.setGlobalColorScheme(globalColourScheme);
 190       jsonAlignmentPojo.getAppSettings().put("application", application);
 191       jsonAlignmentPojo.getAppSettings().put("version", version);
 192       jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
 193       jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
 194               String.valueOf(showSeqFeatures));
 195
 196       String[] hiddenSections = getHiddenSections();
 197       if (hiddenSections != null)
 198       {
 199         if (hiddenSections[0] != null
 200                 && exportSettings.isExportHiddenColumns())
 201         {
 202           jsonAlignmentPojo.getAppSettings().put("hiddenCols",
 203                   String.valueOf(hiddenSections[0]));
 204         }
 205         if (hiddenSections[1] != null
 206                 && exportSettings.isExportHiddenSequences())
 207         {
 208           jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
 209                   String.valueOf(hiddenSections[1]));
 210         }
 211       }
 212
 213       if (exportSettings.isExportAnnotations())
 214       {
 215         jsonAlignmentPojo
 216                 .setAlignAnnotation(annotationToJsonPojo(annotations));
 217       }
 218       else
 219       {
 220         // These color schemes require annotation, disable them if annotations
 221         // are not exported
 222         if (globalColourScheme.equalsIgnoreCase("RNA Helices")
 223                 || globalColourScheme.equalsIgnoreCase("T-COFFEE SCORES"))
 224         {
 225           jsonAlignmentPojo.setGlobalColorScheme("None");
 226         }
 227       }
 228
 229       if (exportSettings.isExportFeatures())
 230       {
 231         jsonAlignmentPojo
 232                 .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, 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.cs));
 244           seqGrpPojo.setColourText(seqGrp.getColourText());
 245           seqGrpPojo.setDescription(seqGrp.getDescription());
 246           seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
 247           seqGrpPojo.setDisplayText(seqGrp.getDisplayText());
 248           seqGrpPojo.setEndRes(seqGrp.getEndRes());
 249           seqGrpPojo.setStartRes(seqGrp.getStartRes());
 250           seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
 251           for (SequenceI seq : seqGrp.getSequences())
 252           {
 253             seqGrpPojo.getSequenceRefs()
 254                     .add(String.valueOf(seq.hashCode()));
 255           }
 256           jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
 257         }
 258       }
 259       org.json.JSONObject generatedJSon = new org.json.JSONObject(
 260               jsonAlignmentPojo);
 261       jsonOutput = generatedJSon.toString();
 262       return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
 263               "xEnd");
 264     } catch (Exception e)
 265     {
 266       e.printStackTrace();
 267     }
 268     return jsonOutput;
 269   }
 270
 271   public String[] getHiddenSections()
 272   {
 273     String[] hiddenSections = new String[2];
 274     if (getViewport() == null)
 275     {
 276       return null;
 277     }
 278
 279     // hidden column business
 280     if (getViewport().hasHiddenColumns())
 281     {
 282       List<int[]> hiddenCols = getViewport().getColumnSelection()
 283               .getHiddenColumns();
 284       StringBuilder hiddenColsBuilder = new StringBuilder();
 285       for (int[] range : hiddenCols)
 286       {
 287         hiddenColsBuilder.append(";").append(range[0]).append("-")
 288                 .append(range[1]);
 289       }
 290
 291       hiddenColsBuilder.deleteCharAt(0);
 292       hiddenSections[0] = hiddenColsBuilder.toString();
 293     }
 294
 295     // hidden rows/seqs business
 296     HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
 297             .getHiddenSequences();
 298     if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
 299     {
 300       return hiddenSections;
 301     }
 302
 303     SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
 304     StringBuilder hiddenSeqsBuilder = new StringBuilder();
 305     for (SequenceI hiddenSeq : hiddenSeqs)
 306     {
 307       if (hiddenSeq != null)
 308       {
 309         hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
 310       }
 311     }
 312     if (hiddenSeqsBuilder.length() > 0)
 313     {
 314       hiddenSeqsBuilder.deleteCharAt(0);
 315     }
 316     hiddenSections[1] = hiddenSeqsBuilder.toString();
 317
 318     return hiddenSections;
 319   }
 320
 321   public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
 322           List<SequenceI> seqs, FeatureRenderer fr)
 323   {
 324     displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
 325     List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
 326     for (SequenceI seq : seqs)
 327     {
 328       SequenceI dataSetSequence = seq.getDatasetSequence();
 329       SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
 330               : seq.getDatasetSequence().getSequenceFeatures();
 331
 332       seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
 333               : seqFeatures;
 334       if (seqFeatures == null)
 335       {
 336         continue;
 337       }
 338
 339       for (SequenceFeature sf : seqFeatures)
 340       {
 341         if (displayedFeatures != null
 342                 && displayedFeatures.isVisible(sf.getType()))
 343         {
 344           SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
 345                   String.valueOf(seq.hashCode()));
 346
 347           String featureColour = (fr == null) ? null : jalview.util.Format
 348                   .getHexString(fr.findFeatureColour(Colour.white, seq,
 349                           seq.findIndex(sf.getBegin())));
 350           jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
 351           jsonFeature.setXend(seq.findIndex(sf.getEnd()));
 352           jsonFeature.setType(sf.getType());
 353           jsonFeature.setDescription(sf.getDescription());
 354           jsonFeature.setLinks(sf.links);
 355           jsonFeature.setOtherDetails(sf.otherDetails);
 356           jsonFeature.setScore(sf.getScore());
 357           jsonFeature.setFillColor(featureColour);
 358           jsonFeature.setFeatureGroup(sf.getFeatureGroup());
 359           sequenceFeaturesPojo.add(jsonFeature);
 360         }
 361       }
 362     }
 363     return sequenceFeaturesPojo;
 364   }
 365
 366   public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
 367           Vector<AlignmentAnnotation> annotations)
 368   {
 369     List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
 370     if (annotations == null)
 371     {
 372       return jsonAnnotations;
 373     }
 374     for (AlignmentAnnotation annot : annotations)
 375     {
 376       AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
 377       alignAnnotPojo.setDescription(annot.description);
 378       alignAnnotPojo.setLabel(annot.label);
 379       if (!Double.isNaN(annot.score))
 380       {
 381         alignAnnotPojo.setScore(annot.score);
 382       }
 383       alignAnnotPojo.setCalcId(annot.getCalcId());
 384       alignAnnotPojo.setGraphType(annot.graph);
 385
 386       AnnotationDisplaySettingPojo annotSetting = new AnnotationDisplaySettingPojo();
 387       annotSetting.setBelowAlignment(annot.belowAlignment);
 388       annotSetting.setCentreColLabels(annot.centreColLabels);
 389       annotSetting.setScaleColLabel(annot.scaleColLabel);
 390       annotSetting.setShowAllColLabels(annot.showAllColLabels);
 391       annotSetting.setVisible(annot.visible);
 392       annotSetting.setHasIcon(annot.hasIcons);
 393       alignAnnotPojo.setAnnotationSettings(annotSetting);
 394       SequenceI refSeq = annot.sequenceRef;
 395       if (refSeq != null)
 396       {
 397         alignAnnotPojo.setSequenceRef(String.valueOf(refSeq.hashCode()));
 398       }
 399       for (Annotation annotation : annot.annotations)
 400       {
 401         AnnotationPojo annotationPojo = new AnnotationPojo();
 402         if (annotation != null)
 403         {
 404           annotationPojo.setDescription(annotation.description);
 405           annotationPojo.setValue(annotation.value);
 406           annotationPojo
 407                   .setSecondaryStructure(annotation.secondaryStructure);
 408           String displayChar = annotation.displayCharacter == null ? null
 409                   : annotation.displayCharacter;
 410           // System.out.println("--------------------->[" + displayChar + "]");
 411           annotationPojo.setDisplayCharacter(displayChar);
 412           if (annotation.colour != null)
 413           {
 414             annotationPojo.setColour(jalview.util.Format
 415                     .getHexString(annotation.colour));
 416           }
 417           alignAnnotPojo.getAnnotations().add(annotationPojo);
 418         }
 419         else
 420         {
 421           if (annot.getCalcId() != null
 422                   && annot.getCalcId().equalsIgnoreCase(TCOFFEE_SCORE))
 423           {
 424             // do nothing
 425           }
 426           else
 427           {
 428             alignAnnotPojo.getAnnotations().add(annotationPojo);
 429           }
 430         }
 431       }
 432       jsonAnnotations.add(alignAnnotPojo);
 433     }
 434     return jsonAnnotations;
 435   }
 436
 437   @SuppressWarnings("unchecked")
 438   public JSONFile parse(Reader jsonAlignmentString)
 439   {
 440     try
 441     {
 442       JSONParser jsonParser = new JSONParser();
 443       JSONObject alignmentJsonObj = (JSONObject) jsonParser
 444               .parse(jsonAlignmentString);
 445       JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
 446       JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
 447               .get("alignAnnotation");
 448       JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
 449               .get("seqFeatures");
 450       JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
 451               .get("seqGroups");
 452       JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
 453               .get("appSettings");
 454
 455       if (jvSettingsJsonObj != null)
 456       {
 457         globalColourScheme = (String) jvSettingsJsonObj
 458                 .get("globalColorScheme");
 459         Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
 460                 "showSeqFeatures").toString());
 461         setShowSeqFeatures(showFeatures);
 462         parseHiddenSeqRefsAsList(jvSettingsJsonObj);
 463         parseHiddenCols(jvSettingsJsonObj);
 464       }
 465
 466       hiddenSequences = new ArrayList<SequenceI>();
 467       seqMap = new Hashtable<String, Sequence>();
 468       for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
 469               .hasNext();)
 470       {
 471         JSONObject sequence = sequenceIter.next();
 472         String sequcenceString = sequence.get("seq").toString();
 473         String sequenceName = sequence.get("name").toString();
 474         String seqUniqueId = sequence.get("id").toString();
 475         int start = Integer.valueOf(sequence.get("start").toString());
 476         int end = Integer.valueOf(sequence.get("end").toString());
 477         Sequence seq = new Sequence(sequenceName, sequcenceString, start,
 478                 end);
 479         if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
 480         {
 481           hiddenSequences.add(seq);
 482         }
 483         seqs.add(seq);
 484         seqMap.put(seqUniqueId, seq);
 485       }
 486
 487       parseFeatures(jsonSeqArray);
 488
 489       for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
 490               .hasNext();)
 491       {
 492         JSONObject seqGrpObj = seqGrpIter.next();
 493         String grpName = seqGrpObj.get("groupName").toString();
 494         String colourScheme = seqGrpObj.get("colourScheme").toString();
 495         String description = (seqGrpObj.get("description") == null) ? null
 496                 : seqGrpObj.get("description").toString();
 497         boolean displayBoxes = Boolean.valueOf(seqGrpObj
 498                 .get("displayBoxes").toString());
 499         boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
 500                 .toString());
 501         boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
 502                 .toString());
 503         boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
 504                 "showNonconserved").toString());
 505         int startRes = Integer
 506                 .valueOf(seqGrpObj.get("startRes").toString());
 507         int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
 508         JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
 509
 510         ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
 511         if (sequenceRefs.size() > 0)
 512         {
 513           Iterator<String> seqHashIter = sequenceRefs.iterator();
 514           while (seqHashIter.hasNext())
 515           {
 516             String seqHash = seqHashIter.next();
 517             Sequence sequence = seqMap.get(seqHash);
 518             if (sequence != null)
 519             {
 520               grpSeqs.add(sequence);
 521             }
 522           }
 523         }
 524         SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
 525                 displayBoxes, displayText, colourText, startRes, endRes);
 526         seqGrp.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme,
 527                 seqGrp);
 528         seqGrp.setShowNonconserved(showNonconserved);
 529         seqGrp.setDescription(description);
 530         this.seqGroups.add(seqGrp);
 531
 532       }
 533
 534       for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
 535               .hasNext();)
 536       {
 537         JSONObject alAnnot = alAnnotIter.next();
 538         JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
 539         Annotation[] annotations = new Annotation[annotJsonArray.size()];
 540         int count = 0;
 541         for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
 542                 .hasNext();)
 543         {
 544           JSONObject annot = annotIter.next();
 545           if (annot == null)
 546           {
 547             annotations[count] = null;
 548           }
 549           else
 550           {
 551             float val = annot.get("value") == null ? null : Float
 552                     .valueOf(annot.get("value").toString());
 553             String desc = annot.get("description") == null ? null : annot
 554                     .get("description").toString();
 555             char ss = annot.get("secondaryStructure") == null
 556                     || annot.get("secondaryStructure").toString()
 557                             .equalsIgnoreCase("u0000") ? ' ' : annot
 558                     .get("secondaryStructure").toString().charAt(0);
 559             String displayChar = annot.get("displayCharacter") == null ? ""
 560                     : annot.get("displayCharacter").toString();
 561
 562             annotations[count] = new Annotation(displayChar, desc, ss, val);
 563             if (annot.get("colour") != null)
 564             {
 565               Color color = UserColourScheme.getColourFromString(annot.get(
 566                       "colour").toString());
 567               annotations[count].colour = color;
 568             }
 569           }
 570           ++count;
 571         }
 572
 573         AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
 574                 .get("label").toString(), alAnnot.get("description")
 575                 .toString(), annotations);
 576         alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0 : Integer
 577                 .valueOf(alAnnot.get("graphType").toString());
 578
 579         JSONObject diplaySettings = (JSONObject) alAnnot
 580                 .get("annotationSettings");
 581         if (diplaySettings != null)
 582         {
 583
 584           alignAnnot.scaleColLabel = (diplaySettings.get("scaleColLabel") == null) ? false
 585                   : Boolean.valueOf(diplaySettings.get("scaleColLabel")
 586                           .toString());
 587           alignAnnot.showAllColLabels = (diplaySettings
 588                   .get("showAllColLabels") == null) ? true : Boolean
 589                   .valueOf(diplaySettings.get("showAllColLabels")
 590                           .toString());
 591           alignAnnot.centreColLabels = (diplaySettings
 592                   .get("centreColLabels") == null) ? true
 593                   : Boolean.valueOf(diplaySettings.get("centreColLabels")
 594                           .toString());
 595           alignAnnot.belowAlignment = (diplaySettings.get("belowAlignment") == null) ? false
 596                   : Boolean.valueOf(diplaySettings.get("belowAlignment")
 597                           .toString());
 598           alignAnnot.visible = (diplaySettings.get("visible") == null) ? true
 599                   : Boolean.valueOf(diplaySettings.get("visible")
 600                           .toString());
 601           alignAnnot.hasIcons = (diplaySettings.get("hasIcon") == null) ? true
 602                   : Boolean.valueOf(diplaySettings.get("hasIcon")
 603                           .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) ? "" : alAnnot.get(
 613                 "calcId").toString();
 614         alignAnnot.setCalcId(calcId);
 615         String seqHash = (alAnnot.get("sequenceRef") != null) ? alAnnot
 616                 .get("sequenceRef").toString() : null;
 617
 618         Sequence sequence = (seqHash != null) ? seqMap.get(seqHash) : null;
 619         if (sequence != null)
 620         {
 621           alignAnnot.sequenceRef = sequence;
 622           sequence.addAlignmentAnnotation(alignAnnot);
 623           if (alignAnnot.label.equalsIgnoreCase("T-COFFEE"))
 624           {
 625             alignAnnot.createSequenceMapping(sequence, sequence.getStart(),
 626                     false);
 627             sequence.addAlignmentAnnotation(alignAnnot);
 628             alignAnnot.adjustForAlignment();
 629           }
 630         }
 631         alignAnnot.validateRangeAndDisplay();
 632         this.annotations.add(alignAnnot);
 633
 634       }
 635     } catch (Exception e)
 636     {
 637       e.printStackTrace();
 638     }
 639     return this;
 640   }
 641
 642   public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
 643   {
 644     hiddenSeqRefs = new ArrayList<String>();
 645     String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
 646     if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
 647     {
 648       String[] seqRefs = hiddenSeqs.split(";");
 649       for (String seqRef : seqRefs)
 650       {
 651         hiddenSeqRefs.add(seqRef);
 652       }
 653     }
 654   }
 655
 656   public void parseHiddenCols(JSONObject jvSettingsJson)
 657   {
 658     String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
 659     if (hiddenCols != null && !hiddenCols.isEmpty())
 660     {
 661       columnSelection = new ColumnSelection();
 662       String[] rangeStrings = hiddenCols.split(";");
 663       for (String rangeString : rangeStrings)
 664       {
 665         String[] range = rangeString.split("-");
 666         columnSelection.hideColumns(Integer.valueOf(range[0]),
 667                 Integer.valueOf(range[1]));
 668       }
 669     }
 670   }
 671
 672   @SuppressWarnings("unchecked")
 673   private void parseFeatures(JSONArray jsonSeqFeatures)
 674   {
 675     if (jsonSeqFeatures != null)
 676     {
 677       displayedFeatures = new FeaturesDisplayed();
 678       for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
 679               .hasNext();)
 680       {
 681         JSONObject jsonFeature = seqFeatureItr.next();
 682         Long begin = (Long) jsonFeature.get("xStart");
 683         Long end = (Long) jsonFeature.get("xEnd");
 684         String type = (String) jsonFeature.get("type");
 685         String featureGrp = (String) jsonFeature.get("featureGroup");
 686         String descripiton = (String) jsonFeature.get("description");
 687         String seqRef = (String) jsonFeature.get("sequenceRef");
 688         Float score = Float.valueOf(jsonFeature.get("score").toString());
 689
 690         Sequence seq = seqMap.get(seqRef);
 691         SequenceFeature sequenceFeature = new SequenceFeature();
 692         JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
 693         if (linksJsonArray != null && linksJsonArray.size() > 0)
 694         {
 695           Iterator<String> linkList = linksJsonArray.iterator();
 696           while (linkList.hasNext())
 697           {
 698             String link = linkList.next();
 699             sequenceFeature.addLink(link);
 700           }
 701         }
 702         sequenceFeature.setFeatureGroup(featureGrp);
 703         sequenceFeature.setScore(score);
 704         sequenceFeature.setDescription(descripiton);
 705         sequenceFeature.setType(type);
 706         sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
 707         sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
 708         seq.addSequenceFeature(sequenceFeature);
 709         displayedFeatures.setVisible(type);
 710       }
 711     }
 712   }
 713
 714   @Override
 715   public String getGlobalColourScheme()
 716   {
 717     return globalColourScheme;
 718   }
 719
 720   public void setGlobalColorScheme(String globalColourScheme)
 721   {
 722     this.globalColourScheme = globalColourScheme;
 723   }
 724
 725   @Override
 726   public FeaturesDisplayedI getDisplayedFeatures()
 727   {
 728     return displayedFeatures;
 729   }
 730
 731   public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
 732   {
 733     this.displayedFeatures = displayedFeatures;
 734   }
 735
 736   @Override
 737   public void configureForView(AlignmentViewPanel avpanel)
 738   {
 739     super.configureForView(avpanel);
 740     AlignViewportI viewport = avpanel.getAlignViewport();
 741     AlignmentI alignment = viewport.getAlignment();
 742     AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
 743
 744     seqGroups = alignment.getGroups();
 745     fr = avpanel.cloneFeatureRenderer();
 746
 747     // Add non auto calculated annotation to AlignFile
 748     for (AlignmentAnnotation annot : annots)
 749     {
 750       if (annot != null && !annot.autoCalculated)
 751       {
 752         annotations.add(annot);
 753       }
 754     }
 755     globalColourScheme = ColourSchemeProperty.getColourName(viewport
 756             .getGlobalColourScheme());
 757     setDisplayedFeatures(viewport.getFeaturesDisplayed());
 758     showSeqFeatures = viewport.isShowSequenceFeatures();
 759
 760   }
 761
 762   @Override
 763   public boolean isShowSeqFeatures()
 764   {
 765     return showSeqFeatures;
 766   }
 767
 768   public void setShowSeqFeatures(boolean showSeqFeatures)
 769   {
 770     this.showSeqFeatures = showSeqFeatures;
 771   }
 772
 773   public Vector<AlignmentAnnotation> getAnnotations()
 774   {
 775     return annotations;
 776   }
 777
 778   public List<int[]> getHiddenColumns()
 779   {
 780     return hiddenColumns;
 781   }
 782
 783   @Override
 784   public ColumnSelection getColumnSelection()
 785   {
 786     return columnSelection;
 787   }
 788
 789   public void setColumnSelection(ColumnSelection columnSelection)
 790   {
 791     this.columnSelection = columnSelection;
 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 }