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.FeaturesDisplayedI;
  30 import jalview.bin.BuildDetails;
  31 import jalview.datamodel.AlignmentAnnotation;
  32 import jalview.datamodel.AlignmentI;
  33 import jalview.datamodel.Annotation;
  34 import jalview.datamodel.ColumnSelection;
  35 import jalview.datamodel.HiddenSequences;
  36 import jalview.datamodel.Sequence;
  37 import jalview.datamodel.SequenceFeature;
  38 import jalview.datamodel.SequenceGroup;
  39 import jalview.datamodel.SequenceI;
  40 import jalview.json.binding.biojson.v1.AlignmentAnnotationPojo;
  41 import jalview.json.binding.biojson.v1.AlignmentPojo;
  42 import jalview.json.binding.biojson.v1.AnnotationDisplaySettingPojo;
  43 import jalview.json.binding.biojson.v1.AnnotationPojo;
  44 import jalview.json.binding.biojson.v1.ColourSchemeMapper;
  45 import jalview.json.binding.biojson.v1.SequenceFeaturesPojo;
  46 import jalview.json.binding.biojson.v1.SequenceGrpPojo;
  47 import jalview.json.binding.biojson.v1.SequencePojo;
  48 import jalview.schemes.ColourSchemeProperty;
  49 import jalview.schemes.UserColourScheme;
  50 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
  51
  52 import java.awt.Color;
  53 import java.io.IOException;
  54 import java.io.Reader;
  55 import java.util.ArrayList;
  56 import java.util.Hashtable;
  57 import java.util.Iterator;
  58 import java.util.List;
  59 import java.util.Vector;
  60
  61 import org.json.simple.JSONArray;
  62 import org.json.simple.JSONObject;
  63 import org.json.simple.parser.JSONParser;
  64
  65 public class JSONFile extends AlignFile implements ComplexAlignFile
  66 {
  67   private static String version = new BuildDetails().getVersion();
  68
  69   private String webstartUrl = "http://www.jalview.org/services/launchApp";
  70
  71   private String application = "Jalview";
  72
  73   public static final String FILE_EXT = "json";
  74
  75   public static final String FILE_DESC = "JSON";
  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, String type) throws IOException
 108   {
 109     super(inFile, type);
 110   }
 111
 112   @Override
 113   public void parse() throws IOException
 114   {
 115     parse(getReader());
 116
 117   }
 118
 119   @Override
 120   public String print()
 121   {
 122     String jsonOutput = null;
 123     try
 124     {
 125       AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
 126       AlignExportSettingI exportSettings = getExportSettings();
 127
 128       // if no export settings were supplied use the following with all values
 129       // defaulting to true
 130       if (exportSettings == null)
 131       {
 132         exportSettings = new AlignExportSettingI()
 133         {
 134           @Override
 135           public boolean isExportHiddenSequences()
 136           {
 137             return true;
 138           }
 139
 140           @Override
 141           public boolean isExportHiddenColumns()
 142           {
 143             return true;
 144           }
 145
 146           @Override
 147           public boolean isExportGroups()
 148           {
 149             return true;
 150           }
 151
 152           @Override
 153           public boolean isExportFeatures()
 154           {
 155             return true;
 156           }
 157
 158           @Override
 159           public boolean isExportAnnotations()
 160           {
 161             return true;
 162           }
 163
 164           @Override
 165           public boolean isCancelled()
 166           {
 167             return false;
 168           }
 169         };
 170       }
 171
 172       int count = 0;
 173       for (SequenceI seq : seqs)
 174       {
 175         StringBuilder name = new StringBuilder();
 176         name.append(seq.getName()).append("/").append(seq.getStart())
 177                 .append("-").append(seq.getEnd());
 178         SequencePojo jsonSeqPojo = new SequencePojo();
 179         jsonSeqPojo.setId(String.valueOf(seq.hashCode()));
 180         jsonSeqPojo.setOrder(++count);
 181         jsonSeqPojo.setEnd(seq.getEnd());
 182         jsonSeqPojo.setStart(seq.getStart());
 183         jsonSeqPojo.setName(name.toString());
 184         jsonSeqPojo.setSeq(seq.getSequenceAsString());
 185         jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
 186       }
 187       jsonAlignmentPojo.setGlobalColorScheme(globalColourScheme);
 188       jsonAlignmentPojo.getAppSettings().put("application", application);
 189       jsonAlignmentPojo.getAppSettings().put("version", version);
 190       jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
 191       jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
 192               String.valueOf(showSeqFeatures));
 193
 194       String[] hiddenSections = getHiddenSections();
 195       if (hiddenSections != null)
 196       {
 197         if (hiddenSections[0] != null
 198                 && exportSettings.isExportHiddenColumns())
 199         {
 200           jsonAlignmentPojo.getAppSettings().put("hiddenCols",
 201                   String.valueOf(hiddenSections[0]));
 202         }
 203         if (hiddenSections[1] != null
 204                 && exportSettings.isExportHiddenSequences())
 205         {
 206           jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
 207                   String.valueOf(hiddenSections[1]));
 208         }
 209       }
 210
 211       if (exportSettings.isExportAnnotations())
 212       {
 213         jsonAlignmentPojo
 214                 .setAlignAnnotation(annotationToJsonPojo(annotations));
 215       }
 216       else
 217       {
 218         // These color schemes require annotation, disable them if annotations
 219         // are not exported
 220         if (globalColourScheme.equalsIgnoreCase("RNA Helices")
 221                 || globalColourScheme.equalsIgnoreCase("T-COFFEE SCORES"))
 222         {
 223           jsonAlignmentPojo.setGlobalColorScheme("None");
 224         }
 225       }
 226
 227       if (exportSettings.isExportFeatures())
 228       {
 229         jsonAlignmentPojo
 230                 .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
 231       }
 232
 233       if (exportSettings.isExportGroups() && seqGroups != null
 234               && seqGroups.size() > 0)
 235       {
 236         for (SequenceGroup seqGrp : seqGroups)
 237         {
 238           SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
 239           seqGrpPojo.setGroupName(seqGrp.getName());
 240           seqGrpPojo.setColourScheme(ColourSchemeProperty
 241                   .getColourName(seqGrp.cs));
 242           seqGrpPojo.setColourText(seqGrp.getColourText());
 243           seqGrpPojo.setDescription(seqGrp.getDescription());
 244           seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
 245           seqGrpPojo.setDisplayText(seqGrp.getDisplayText());
 246           seqGrpPojo.setEndRes(seqGrp.getEndRes());
 247           seqGrpPojo.setStartRes(seqGrp.getStartRes());
 248           seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
 249           for (SequenceI seq : seqGrp.getSequences())
 250           {
 251             seqGrpPojo.getSequenceRefs()
 252                     .add(String.valueOf(seq.hashCode()));
 253           }
 254           jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
 255         }
 256       }
 257       org.json.JSONObject generatedJSon = new org.json.JSONObject(
 258               jsonAlignmentPojo);
 259       jsonOutput = generatedJSon.toString();
 260       return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
 261               "xEnd");
 262     } catch (Exception e)
 263     {
 264       e.printStackTrace();
 265     }
 266     return jsonOutput;
 267   }
 268
 269   public String[] getHiddenSections()
 270   {
 271     String[] hiddenSections = new String[2];
 272     if (getViewport() == null)
 273     {
 274       return null;
 275     }
 276
 277     // hidden column business
 278     if (getViewport().hasHiddenColumns())
 279     {
 280       List<int[]> hiddenCols = getViewport().getColumnSelection()
 281               .getHiddenColumns();
 282       StringBuilder hiddenColsBuilder = new StringBuilder();
 283       for (int[] range : hiddenCols)
 284       {
 285         hiddenColsBuilder.append(";").append(range[0]).append("-")
 286                 .append(range[1]);
 287       }
 288
 289       hiddenColsBuilder.deleteCharAt(0);
 290       hiddenSections[0] = hiddenColsBuilder.toString();
 291     }
 292
 293     // hidden rows/seqs business
 294     HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
 295             .getHiddenSequences();
 296     if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
 297     {
 298       return hiddenSections;
 299     }
 300
 301     SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
 302     StringBuilder hiddenSeqsBuilder = new StringBuilder();
 303     for (SequenceI hiddenSeq : hiddenSeqs)
 304     {
 305       if (hiddenSeq != null)
 306       {
 307         hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
 308       }
 309     }
 310     if (hiddenSeqsBuilder.length() > 0)
 311     {
 312       hiddenSeqsBuilder.deleteCharAt(0);
 313     }
 314     hiddenSections[1] = hiddenSeqsBuilder.toString();
 315
 316     return hiddenSections;
 317   }
 318
 319   public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
 320           List<SequenceI> seqs, FeatureRenderer fr)
 321   {
 322     displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
 323     List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
 324     for (SequenceI seq : seqs)
 325     {
 326       SequenceI dataSetSequence = seq.getDatasetSequence();
 327       SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
 328               : seq.getDatasetSequence().getSequenceFeatures();
 329
 330       seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
 331               : seqFeatures;
 332       if (seqFeatures == null)
 333       {
 334         continue;
 335       }
 336
 337       for (SequenceFeature sf : seqFeatures)
 338       {
 339         if (displayedFeatures != null
 340                 && displayedFeatures.isVisible(sf.getType()))
 341         {
 342           SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
 343                   String.valueOf(seq.hashCode()));
 344
 345           String featureColour = (fr == null) ? null : jalview.util.Format
 346                   .getHexString(fr.findFeatureColour(Color.white, seq,
 347                           seq.findIndex(sf.getBegin())));
 348           jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
 349           jsonFeature.setXend(seq.findIndex(sf.getEnd()));
 350           jsonFeature.setType(sf.getType());
 351           jsonFeature.setDescription(sf.getDescription());
 352           jsonFeature.setLinks(sf.links);
 353           jsonFeature.setOtherDetails(sf.otherDetails);
 354           jsonFeature.setScore(sf.getScore());
 355           jsonFeature.setFillColor(featureColour);
 356           jsonFeature.setFeatureGroup(sf.getFeatureGroup());
 357           sequenceFeaturesPojo.add(jsonFeature);
 358         }
 359       }
 360     }
 361     return sequenceFeaturesPojo;
 362   }
 363
 364   public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
 365           Vector<AlignmentAnnotation> annotations)
 366   {
 367     List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
 368     if (annotations == null)
 369     {
 370       return jsonAnnotations;
 371     }
 372     for (AlignmentAnnotation annot : annotations)
 373     {
 374       AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
 375       alignAnnotPojo.setDescription(annot.description);
 376       alignAnnotPojo.setLabel(annot.label);
 377       if (!Double.isNaN(annot.score))
 378       {
 379         alignAnnotPojo.setScore(annot.score);
 380       }
 381       alignAnnotPojo.setCalcId(annot.getCalcId());
 382       alignAnnotPojo.setGraphType(annot.graph);
 383
 384       AnnotationDisplaySettingPojo annotSetting = new AnnotationDisplaySettingPojo();
 385       annotSetting.setBelowAlignment(annot.belowAlignment);
 386       annotSetting.setCentreColLabels(annot.centreColLabels);
 387       annotSetting.setScaleColLabel(annot.scaleColLabel);
 388       annotSetting.setShowAllColLabels(annot.showAllColLabels);
 389       annotSetting.setVisible(annot.visible);
 390       annotSetting.setHasIcon(annot.hasIcons);
 391       alignAnnotPojo.setAnnotationSettings(annotSetting);
 392       SequenceI refSeq = annot.sequenceRef;
 393       if (refSeq != null)
 394       {
 395         alignAnnotPojo.setSequenceRef(String.valueOf(refSeq.hashCode()));
 396       }
 397       for (Annotation annotation : annot.annotations)
 398       {
 399         AnnotationPojo annotationPojo = new AnnotationPojo();
 400         if (annotation != null)
 401         {
 402           annotationPojo.setDescription(annotation.description);
 403           annotationPojo.setValue(annotation.value);
 404           annotationPojo
 405                   .setSecondaryStructure(annotation.secondaryStructure);
 406           String displayChar = annotation.displayCharacter == null ? null
 407                   : annotation.displayCharacter;
 408           // System.out.println("--------------------->[" + displayChar + "]");
 409           annotationPojo.setDisplayCharacter(displayChar);
 410           if (annotation.colour != null)
 411           {
 412             annotationPojo.setColour(jalview.util.Format
 413                     .getHexString(annotation.colour));
 414           }
 415           alignAnnotPojo.getAnnotations().add(annotationPojo);
 416         }
 417         else
 418         {
 419           if (annot.getCalcId() != null
 420                   && annot.getCalcId().equalsIgnoreCase(TCOFFEE_SCORE))
 421           {
 422             // do nothing
 423           }
 424           else
 425           {
 426             alignAnnotPojo.getAnnotations().add(annotationPojo);
 427           }
 428         }
 429       }
 430       jsonAnnotations.add(alignAnnotPojo);
 431     }
 432     return jsonAnnotations;
 433   }
 434
 435   @SuppressWarnings("unchecked")
 436   public JSONFile parse(Reader jsonAlignmentString)
 437   {
 438     try
 439     {
 440       JSONParser jsonParser = new JSONParser();
 441       JSONObject alignmentJsonObj = (JSONObject) jsonParser
 442               .parse(jsonAlignmentString);
 443       JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
 444       JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
 445               .get("alignAnnotation");
 446       JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
 447               .get("seqFeatures");
 448       JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
 449               .get("seqGroups");
 450       JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
 451               .get("appSettings");
 452
 453       if (jvSettingsJsonObj != null)
 454       {
 455         globalColourScheme = (String) jvSettingsJsonObj
 456                 .get("globalColorScheme");
 457         Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
 458                 "showSeqFeatures").toString());
 459         setShowSeqFeatures(showFeatures);
 460         parseHiddenSeqRefsAsList(jvSettingsJsonObj);
 461         parseHiddenCols(jvSettingsJsonObj);
 462       }
 463
 464       hiddenSequences = new ArrayList<SequenceI>();
 465       seqMap = new Hashtable<String, Sequence>();
 466       for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
 467               .hasNext();)
 468       {
 469         JSONObject sequence = sequenceIter.next();
 470         String sequcenceString = sequence.get("seq").toString();
 471         String sequenceName = sequence.get("name").toString();
 472         String seqUniqueId = sequence.get("id").toString();
 473         int start = Integer.valueOf(sequence.get("start").toString());
 474         int end = Integer.valueOf(sequence.get("end").toString());
 475         Sequence seq = new Sequence(sequenceName, sequcenceString, start,
 476                 end);
 477         if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
 478         {
 479           hiddenSequences.add(seq);
 480         }
 481         seqs.add(seq);
 482         seqMap.put(seqUniqueId, seq);
 483       }
 484
 485       parseFeatures(jsonSeqArray);
 486
 487       for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
 488               .hasNext();)
 489       {
 490         JSONObject seqGrpObj = seqGrpIter.next();
 491         String grpName = seqGrpObj.get("groupName").toString();
 492         String colourScheme = seqGrpObj.get("colourScheme").toString();
 493         String description = (seqGrpObj.get("description") == null) ? null
 494                 : seqGrpObj.get("description").toString();
 495         boolean displayBoxes = Boolean.valueOf(seqGrpObj
 496                 .get("displayBoxes").toString());
 497         boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
 498                 .toString());
 499         boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
 500                 .toString());
 501         boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
 502                 "showNonconserved").toString());
 503         int startRes = Integer
 504                 .valueOf(seqGrpObj.get("startRes").toString());
 505         int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
 506         JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
 507
 508         ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
 509         if (sequenceRefs.size() > 0)
 510         {
 511           Iterator<String> seqHashIter = sequenceRefs.iterator();
 512           while (seqHashIter.hasNext())
 513           {
 514             String seqHash = seqHashIter.next();
 515             Sequence sequence = seqMap.get(seqHash);
 516             if (sequence != null)
 517             {
 518               grpSeqs.add(sequence);
 519             }
 520           }
 521         }
 522         SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
 523                 displayBoxes, displayText, colourText, startRes, endRes);
 524         seqGrp.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme,
 525                 seqGrp);
 526         seqGrp.setShowNonconserved(showNonconserved);
 527         seqGrp.setDescription(description);
 528         this.seqGroups.add(seqGrp);
 529
 530       }
 531
 532       for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
 533               .hasNext();)
 534       {
 535         JSONObject alAnnot = alAnnotIter.next();
 536         JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
 537         Annotation[] annotations = new Annotation[annotJsonArray.size()];
 538         int count = 0;
 539         for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
 540                 .hasNext();)
 541         {
 542           JSONObject annot = annotIter.next();
 543           if (annot == null)
 544           {
 545             annotations[count] = null;
 546           }
 547           else
 548           {
 549             float val = annot.get("value") == null ? null : Float
 550                     .valueOf(annot.get("value").toString());
 551             String desc = annot.get("description") == null ? null : annot
 552                     .get("description").toString();
 553             char ss = annot.get("secondaryStructure") == null
 554                     || annot.get("secondaryStructure").toString()
 555                             .equalsIgnoreCase("u0000") ? ' ' : annot
 556                     .get("secondaryStructure").toString().charAt(0);
 557             String displayChar = annot.get("displayCharacter") == null ? ""
 558                     : annot.get("displayCharacter").toString();
 559
 560             annotations[count] = new Annotation(displayChar, desc, ss, val);
 561             if (annot.get("colour") != null)
 562             {
 563               Color color = UserColourScheme.getColourFromString(annot.get(
 564                       "colour").toString());
 565               annotations[count].colour = color;
 566             }
 567           }
 568           ++count;
 569         }
 570
 571         AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
 572                 .get("label").toString(), alAnnot.get("description")
 573                 .toString(), annotations);
 574         alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0 : Integer
 575                 .valueOf(alAnnot.get("graphType")
 576                         .toString());
 577
 578         JSONObject diplaySettings = (JSONObject) alAnnot
 579                 .get("annotationSettings");
 580         if (diplaySettings != null)
 581         {
 582
 583           alignAnnot.scaleColLabel = (diplaySettings.get("scaleColLabel") == null) ? false
 584                   : Boolean.valueOf(diplaySettings.get("scaleColLabel")
 585                           .toString());
 586           alignAnnot.showAllColLabels = (diplaySettings
 587                   .get("showAllColLabels") == null) ? true : Boolean
 588                   .valueOf(diplaySettings.get("showAllColLabels")
 589                           .toString());
 590           alignAnnot.centreColLabels = (diplaySettings
 591                   .get("centreColLabels") == null) ? true
 592                   : Boolean.valueOf(diplaySettings.get("centreColLabels")
 593                           .toString());
 594           alignAnnot.belowAlignment = (diplaySettings.get("belowAlignment") == null) ? false
 595                   : Boolean.valueOf(diplaySettings.get("belowAlignment")
 596                           .toString());
 597           alignAnnot.visible = (diplaySettings.get("visible") == null) ? true
 598                   : Boolean.valueOf(diplaySettings.get("visible")
 599                           .toString());
 600           alignAnnot.hasIcons = (diplaySettings.get("hasIcon") == null) ? true
 601                   : Boolean.valueOf(diplaySettings.get("hasIcon")
 602                           .toString());
 603
 604         }
 605         if (alAnnot.get("score") != null)
 606         {
 607           alignAnnot.score = Double
 608                   .valueOf(alAnnot.get("score").toString());
 609         }
 610
 611         String calcId = (alAnnot.get("calcId") == null) ? "" : alAnnot.get(
 612                 "calcId").toString();
 613         alignAnnot.setCalcId(calcId);
 614         String seqHash = (alAnnot.get("sequenceRef") != null) ? alAnnot
 615                 .get("sequenceRef").toString() : null;
 616
 617         Sequence sequence = (seqHash != null) ? seqMap.get(seqHash) : null;
 618         if (sequence != null)
 619         {
 620           alignAnnot.sequenceRef = sequence;
 621           sequence.addAlignmentAnnotation(alignAnnot);
 622           if (alignAnnot.label.equalsIgnoreCase("T-COFFEE"))
 623           {
 624             alignAnnot.createSequenceMapping(sequence, sequence.getStart(),
 625                     false);
 626             sequence.addAlignmentAnnotation(alignAnnot);
 627             alignAnnot.adjustForAlignment();
 628           }
 629         }
 630         alignAnnot.validateRangeAndDisplay();
 631         this.annotations.add(alignAnnot);
 632
 633       }
 634     } catch (Exception e)
 635     {
 636       e.printStackTrace();
 637     }
 638     return this;
 639   }
 640
 641   public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
 642   {
 643     hiddenSeqRefs = new ArrayList<String>();
 644     String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
 645     if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
 646     {
 647       String[] seqRefs = hiddenSeqs.split(";");
 648       for (String seqRef : seqRefs)
 649       {
 650         hiddenSeqRefs.add(seqRef);
 651       }
 652     }
 653   }
 654
 655   public void parseHiddenCols(JSONObject jvSettingsJson)
 656   {
 657     String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
 658     if (hiddenCols != null && !hiddenCols.isEmpty())
 659     {
 660       columnSelection = new ColumnSelection();
 661       String[] rangeStrings = hiddenCols.split(";");
 662       for (String rangeString : rangeStrings)
 663       {
 664         String[] range = rangeString.split("-");
 665         columnSelection.hideColumns(Integer.valueOf(range[0]),
 666                 Integer.valueOf(range[1]));
 667       }
 668     }
 669   }
 670
 671   @SuppressWarnings("unchecked")
 672   private void parseFeatures(JSONArray jsonSeqFeatures)
 673   {
 674     if (jsonSeqFeatures != null)
 675     {
 676       displayedFeatures = new FeaturesDisplayed();
 677       for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
 678               .hasNext();)
 679       {
 680         JSONObject jsonFeature = seqFeatureItr.next();
 681         Long begin = (Long) jsonFeature.get("xStart");
 682         Long end = (Long) jsonFeature.get("xEnd");
 683         String type = (String) jsonFeature.get("type");
 684         String featureGrp = (String) jsonFeature.get("featureGroup");
 685         String descripiton = (String) jsonFeature.get("description");
 686         String seqRef = (String) jsonFeature.get("sequenceRef");
 687         Float score = Float.valueOf(jsonFeature.get("score").toString());
 688
 689         Sequence seq = seqMap.get(seqRef);
 690         SequenceFeature sequenceFeature = new SequenceFeature();
 691         JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
 692         if (linksJsonArray != null && linksJsonArray.size() > 0)
 693         {
 694           Iterator<String> linkList = linksJsonArray.iterator();
 695           while (linkList.hasNext())
 696           {
 697             String link = linkList.next();
 698             sequenceFeature.addLink(link);
 699           }
 700         }
 701         sequenceFeature.setFeatureGroup(featureGrp);
 702         sequenceFeature.setScore(score);
 703         sequenceFeature.setDescription(descripiton);
 704         sequenceFeature.setType(type);
 705         sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
 706         sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
 707         seq.addSequenceFeature(sequenceFeature);
 708         displayedFeatures.setVisible(type);
 709       }
 710     }
 711   }
 712
 713   public String getGlobalColourScheme()
 714   {
 715     return globalColourScheme;
 716   }
 717
 718   public void setGlobalColorScheme(String globalColourScheme)
 719   {
 720     this.globalColourScheme = globalColourScheme;
 721   }
 722
 723   @Override
 724   public FeaturesDisplayedI getDisplayedFeatures()
 725   {
 726     return displayedFeatures;
 727   }
 728
 729   public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
 730   {
 731     this.displayedFeatures = displayedFeatures;
 732   }
 733
 734   public void configureForView(AlignmentViewPanel avpanel)
 735   {
 736     super.configureForView(avpanel);
 737     AlignViewportI viewport = avpanel.getAlignViewport();
 738     AlignmentI alignment = viewport.getAlignment();
 739     AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
 740
 741     seqGroups = alignment.getGroups();
 742     fr = avpanel.cloneFeatureRenderer();
 743
 744     // Add non auto calculated annotation to AlignFile
 745     for (AlignmentAnnotation annot : annots)
 746     {
 747       if (annot != null && !annot.autoCalculated)
 748       {
 749         annotations.add(annot);
 750       }
 751     }
 752     globalColourScheme = ColourSchemeProperty.getColourName(viewport
 753             .getGlobalColourScheme());
 754     setDisplayedFeatures(viewport.getFeaturesDisplayed());
 755     showSeqFeatures = viewport.isShowSequenceFeatures();
 756
 757   }
 758
 759   public boolean isShowSeqFeatures()
 760   {
 761     return showSeqFeatures;
 762   }
 763
 764   public void setShowSeqFeatures(boolean showSeqFeatures)
 765   {
 766     this.showSeqFeatures = showSeqFeatures;
 767   }
 768
 769   public Vector<AlignmentAnnotation> getAnnotations()
 770   {
 771     return annotations;
 772   }
 773
 774   public List<int[]> getHiddenColumns()
 775   {
 776     return hiddenColumns;
 777   }
 778
 779   public ColumnSelection getColumnSelection()
 780   {
 781     return columnSelection;
 782   }
 783
 784   public void setColumnSelection(ColumnSelection columnSelection)
 785   {
 786     this.columnSelection = columnSelection;
 787   }
 788
 789   public SequenceI[] getHiddenSequences()
 790   {
 791     if (hiddenSequences == null || hiddenSequences.isEmpty())
 792     {
 793       return new SequenceI[] {};
 794     }
 795     synchronized (hiddenSequences)
 796     {
 797       return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
 798     }
 799   }
 800
 801   public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
 802   {
 803     this.hiddenSequences = hiddenSequences;
 804   }
 805
 806   public class JSONExportSettings
 807   {
 808     private boolean exportSequence;
 809
 810     private boolean exportSequenceFeatures;
 811
 812     private boolean exportAnnotations;
 813
 814     private boolean exportGroups;
 815
 816     private boolean exportJalviewSettings;
 817
 818     public boolean isExportSequence()
 819     {
 820       return exportSequence;
 821     }
 822
 823     public void setExportSequence(boolean exportSequence)
 824     {
 825       this.exportSequence = exportSequence;
 826     }
 827
 828     public boolean isExportSequenceFeatures()
 829     {
 830       return exportSequenceFeatures;
 831     }
 832
 833     public void setExportSequenceFeatures(boolean exportSequenceFeatures)
 834     {
 835       this.exportSequenceFeatures = exportSequenceFeatures;
 836     }
 837
 838     public boolean isExportAnnotations()
 839     {
 840       return exportAnnotations;
 841     }
 842
 843     public void setExportAnnotations(boolean exportAnnotations)
 844     {
 845       this.exportAnnotations = exportAnnotations;
 846     }
 847
 848     public boolean isExportGroups()
 849     {
 850       return exportGroups;
 851     }
 852
 853     public void setExportGroups(boolean exportGroups)
 854     {
 855       this.exportGroups = exportGroups;
 856     }
 857
 858     public boolean isExportJalviewSettings()
 859     {
 860       return exportJalviewSettings;
 861     }
 862
 863     public void setExportJalviewSettings(boolean exportJalviewSettings)
 864     {
 865       this.exportJalviewSettings = exportJalviewSettings;
 866     }
 867   }
 868 }