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.centreColLabels);
 388       annotSetting.setShowAllColLabels(annot.showAllColLabels);
 389       annotSetting.setVisible(annot.visible);
 390       alignAnnotPojo.setAnnotationSettings(annotSetting);
 391       SequenceI refSeq = annot.sequenceRef;
 392       if (refSeq != null)
 393       {
 394         alignAnnotPojo.setSequenceRef(String.valueOf(refSeq.hashCode()));
 395       }
 396       for (Annotation annotation : annot.annotations)
 397       {
 398         AnnotationPojo annotationPojo = new AnnotationPojo();
 399         if (annotation != null)
 400         {
 401           annotationPojo.setDescription(annotation.description);
 402           annotationPojo.setValue(annotation.value);
 403           annotationPojo
 404                   .setSecondaryStructure(annotation.secondaryStructure);
 405           annotationPojo.setDisplayCharacter(annotation.displayCharacter);
 406           if (annotation.colour != null)
 407           {
 408             annotationPojo.setColour(jalview.util.Format
 409                     .getHexString(annotation.colour));
 410           }
 411           alignAnnotPojo.getAnnotations().add(annotationPojo);
 412         }
 413         else
 414         {
 415           if (annot.getCalcId() != null
 416                   && annot.getCalcId().equalsIgnoreCase(TCOFFEE_SCORE))
 417           {
 418             // do nothing
 419           }
 420           else
 421           {
 422             alignAnnotPojo.getAnnotations().add(annotationPojo);
 423           }
 424         }
 425       }
 426       jsonAnnotations.add(alignAnnotPojo);
 427     }
 428     return jsonAnnotations;
 429   }
 430
 431   @SuppressWarnings("unchecked")
 432   public JSONFile parse(Reader jsonAlignmentString)
 433   {
 434     try
 435     {
 436       JSONParser jsonParser = new JSONParser();
 437       JSONObject alignmentJsonObj = (JSONObject) jsonParser
 438               .parse(jsonAlignmentString);
 439       JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
 440       JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
 441               .get("alignAnnotation");
 442       JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
 443               .get("seqFeatures");
 444       JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
 445               .get("seqGroups");
 446       JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
 447               .get("appSettings");
 448
 449       if (jvSettingsJsonObj != null)
 450       {
 451         globalColourScheme = (String) jvSettingsJsonObj
 452                 .get("globalColorScheme");
 453         Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
 454                 "showSeqFeatures").toString());
 455         setShowSeqFeatures(showFeatures);
 456         parseHiddenSeqRefsAsList(jvSettingsJsonObj);
 457         parseHiddenCols(jvSettingsJsonObj);
 458       }
 459
 460       hiddenSequences = new ArrayList<SequenceI>();
 461       seqMap = new Hashtable<String, Sequence>();
 462       for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
 463               .hasNext();)
 464       {
 465         JSONObject sequence = sequenceIter.next();
 466         String sequcenceString = sequence.get("seq").toString();
 467         String sequenceName = sequence.get("name").toString();
 468         String seqUniqueId = sequence.get("id").toString();
 469         int start = Integer.valueOf(sequence.get("start").toString());
 470         int end = Integer.valueOf(sequence.get("end").toString());
 471         Sequence seq = new Sequence(sequenceName, sequcenceString, start,
 472                 end);
 473         if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
 474         {
 475           hiddenSequences.add(seq);
 476         }
 477         seqs.add(seq);
 478         seqMap.put(seqUniqueId, seq);
 479       }
 480
 481
 482       parseFeatures(jsonSeqArray);
 483
 484       for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
 485               .hasNext();)
 486       {
 487         JSONObject seqGrpObj = seqGrpIter.next();
 488         String grpName = seqGrpObj.get("groupName").toString();
 489         String colourScheme = seqGrpObj.get("colourScheme").toString();
 490         String description = (seqGrpObj.get("description") == null) ? null
 491                 : seqGrpObj.get("description").toString();
 492         boolean displayBoxes = Boolean.valueOf(seqGrpObj
 493                 .get("displayBoxes").toString());
 494         boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
 495                 .toString());
 496         boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
 497                 .toString());
 498         boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
 499                 "showNonconserved").toString());
 500         int startRes = Integer
 501                 .valueOf(seqGrpObj.get("startRes").toString());
 502         int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
 503         JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
 504
 505         ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
 506         if (sequenceRefs.size() > 0)
 507         {
 508           Iterator<String> seqHashIter = sequenceRefs.iterator();
 509           while (seqHashIter.hasNext())
 510           {
 511             String seqHash = seqHashIter.next();
 512             Sequence sequence = seqMap.get(seqHash);
 513             if (sequence != null)
 514             {
 515               grpSeqs.add(sequence);
 516             }
 517           }
 518         }
 519         SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
 520                 displayBoxes, displayText, colourText,
 521                 startRes, endRes);
 522         seqGrp.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme,
 523                 seqGrp);
 524         seqGrp.setShowNonconserved(showNonconserved);
 525         seqGrp.setDescription(description);
 526         this.seqGroups.add(seqGrp);
 527
 528       }
 529
 530       for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
 531               .hasNext();)
 532       {
 533         JSONObject alAnnot = alAnnotIter.next();
 534         JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
 535         Annotation[] annotations = new Annotation[annotJsonArray.size()];
 536         int count = 0;
 537         for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
 538                 .hasNext();)
 539         {
 540           JSONObject annot = annotIter.next();
 541           if (annot == null)
 542           {
 543             annotations[count] = null;
 544           }
 545           else
 546           {
 547             float val = annot.get("value") == null ? null : Float
 548                     .valueOf(annot.get("value").toString());
 549             String desc = annot.get("description") == null ? null : annot
 550                     .get("description").toString();
 551             char ss = annot.get("secondaryStructure") == null
 552                     || annot.get("secondaryStructure").toString()
 553                             .equalsIgnoreCase("u0000") ? ' ' : annot
 554                     .get("secondaryStructure").toString().charAt(0);
 555             String displayChar = annot.get("displayCharacter") == null ? ""
 556                     : annot.get("displayCharacter").toString();
 557             Color color = annot.get("colour") == null ? Color.white
 558                     : UserColourScheme.getColourFromString(annot.get(
 559                     "colour").toString());
 560             annotations[count] = new Annotation(displayChar, desc, ss, val,
 561                     color);
 562           }
 563           ++count;
 564         }
 565
 566         AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
 567                 .get("label").toString(), alAnnot.get("description")
 568                 .toString(), annotations);
 569         alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0 : Integer
 570                 .valueOf(alAnnot.get("graphType")
 571                         .toString());
 572
 573         JSONObject diplaySettings = (JSONObject) alAnnot
 574                 .get("annotationSettings");
 575         if (diplaySettings != null)
 576         {
 577
 578           alignAnnot.scaleColLabel = (diplaySettings.get("scaleColLabel") == null) ? false
 579                   : Boolean.valueOf(diplaySettings.get("scaleColLabel")
 580                           .toString());
 581           alignAnnot.showAllColLabels = (diplaySettings
 582                   .get("showAllColLabels") == null) ? true : Boolean
 583                   .valueOf(diplaySettings.get("showAllColLabels")
 584                           .toString());
 585           alignAnnot.centreColLabels = (diplaySettings
 586                   .get("centreColLabels") == null) ? true
 587                   : Boolean.valueOf(diplaySettings.get("centreColLabels")
 588                           .toString());
 589           alignAnnot.belowAlignment = (diplaySettings.get("belowAlignment") == null) ? false
 590                   : Boolean.valueOf(diplaySettings.get("belowAlignment")
 591                           .toString());
 592           alignAnnot.visible = (diplaySettings.get("visible") == null) ? true
 593                   : Boolean.valueOf(diplaySettings.get("visible")
 594                           .toString());
 595
 596         }
 597         if (alAnnot.get("score") != null)
 598         {
 599           alignAnnot.score = Double
 600                   .valueOf(alAnnot.get("score").toString());
 601         }
 602
 603         String calcId = (alAnnot.get("calcId") == null) ? "" : alAnnot.get(
 604                 "calcId").toString();
 605         alignAnnot.setCalcId(calcId);
 606         String seqHash = (alAnnot.get("sequenceRef") != null) ? alAnnot
 607                 .get("sequenceRef").toString() : null;
 608
 609         Sequence sequence = (seqHash != null) ? seqMap.get(seqHash) : null;
 610         if (sequence != null)
 611         {
 612           alignAnnot.sequenceRef = sequence;
 613           sequence.addAlignmentAnnotation(alignAnnot);
 614           if (alignAnnot.label.equalsIgnoreCase("T-COFFEE"))
 615           {
 616             alignAnnot.createSequenceMapping(sequence, sequence.getStart(),
 617                     false);
 618             sequence.addAlignmentAnnotation(alignAnnot);
 619             alignAnnot.adjustForAlignment();
 620           }
 621         }
 622         this.annotations.add(alignAnnot);
 623       }
 624     } catch (Exception e)
 625     {
 626       e.printStackTrace();
 627     }
 628     return this;
 629   }
 630
 631   public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
 632   {
 633     hiddenSeqRefs = new ArrayList<String>();
 634     String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
 635     if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
 636     {
 637       String[] seqRefs = hiddenSeqs.split(";");
 638       for (String seqRef : seqRefs)
 639       {
 640         hiddenSeqRefs.add(seqRef);
 641       }
 642     }
 643   }
 644
 645   public void parseHiddenCols(JSONObject jvSettingsJson)
 646   {
 647     String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
 648     if (hiddenCols != null && !hiddenCols.isEmpty())
 649     {
 650       columnSelection = new ColumnSelection();
 651       String[] rangeStrings = hiddenCols.split(";");
 652       for (String rangeString : rangeStrings)
 653       {
 654         String[] range = rangeString.split("-");
 655         columnSelection.hideColumns(Integer.valueOf(range[0]),
 656                 Integer.valueOf(range[1]));
 657       }
 658     }
 659   }
 660
 661   @SuppressWarnings("unchecked")
 662   private void parseFeatures(JSONArray jsonSeqFeatures)
 663   {
 664     if (jsonSeqFeatures != null)
 665     {
 666       displayedFeatures = new FeaturesDisplayed();
 667       for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
 668               .hasNext();)
 669       {
 670         JSONObject jsonFeature = seqFeatureItr.next();
 671         Long begin = (Long) jsonFeature.get("xStart");
 672         Long end = (Long) jsonFeature.get("xEnd");
 673         String type = (String) jsonFeature.get("type");
 674         String featureGrp = (String) jsonFeature.get("featureGroup");
 675         String descripiton = (String) jsonFeature.get("description");
 676         String seqRef = (String) jsonFeature.get("sequenceRef");
 677         Float score = Float.valueOf(jsonFeature.get("score").toString());
 678
 679         Sequence seq = seqMap.get(seqRef);
 680         SequenceFeature sequenceFeature = new SequenceFeature();
 681         JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
 682         if (linksJsonArray != null && linksJsonArray.size() > 0)
 683         {
 684           Iterator<String> linkList = linksJsonArray.iterator();
 685           while (linkList.hasNext())
 686           {
 687             String link = linkList.next();
 688             sequenceFeature.addLink(link);
 689           }
 690         }
 691         sequenceFeature.setFeatureGroup(featureGrp);
 692         sequenceFeature.setScore(score);
 693         sequenceFeature.setDescription(descripiton);
 694         sequenceFeature.setType(type);
 695         sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
 696         sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
 697         seq.addSequenceFeature(sequenceFeature);
 698         displayedFeatures.setVisible(type);
 699       }
 700     }
 701   }
 702
 703   public String getGlobalColourScheme()
 704   {
 705     return globalColourScheme;
 706   }
 707
 708   public void setGlobalColorScheme(String globalColourScheme)
 709   {
 710     this.globalColourScheme = globalColourScheme;
 711   }
 712
 713   @Override
 714   public FeaturesDisplayedI getDisplayedFeatures()
 715   {
 716     return displayedFeatures;
 717   }
 718
 719   public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
 720   {
 721     this.displayedFeatures = displayedFeatures;
 722   }
 723
 724   public void configureForView(AlignmentViewPanel avpanel)
 725   {
 726     super.configureForView(avpanel);
 727     AlignViewportI viewport = avpanel.getAlignViewport();
 728     AlignmentI alignment = viewport.getAlignment();
 729     AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
 730
 731     seqGroups = alignment.getGroups();
 732     fr = avpanel.cloneFeatureRenderer();
 733
 734     // Add non auto calculated annotation to AlignFile
 735     for (AlignmentAnnotation annot : annots)
 736     {
 737       if (annot != null && !annot.autoCalculated)
 738       {
 739         annotations.add(annot);
 740       }
 741     }
 742     globalColourScheme = ColourSchemeProperty.getColourName(viewport
 743             .getGlobalColourScheme());
 744     setDisplayedFeatures(viewport.getFeaturesDisplayed());
 745     showSeqFeatures = viewport.isShowSequenceFeatures();
 746
 747   }
 748
 749   public boolean isShowSeqFeatures()
 750   {
 751     return showSeqFeatures;
 752   }
 753
 754   public void setShowSeqFeatures(boolean showSeqFeatures)
 755   {
 756     this.showSeqFeatures = showSeqFeatures;
 757   }
 758
 759   public Vector<AlignmentAnnotation> getAnnotations()
 760   {
 761     return annotations;
 762   }
 763
 764   public List<int[]> getHiddenColumns()
 765   {
 766     return hiddenColumns;
 767   }
 768
 769   public ColumnSelection getColumnSelection()
 770   {
 771     return columnSelection;
 772   }
 773
 774   public void setColumnSelection(ColumnSelection columnSelection)
 775   {
 776     this.columnSelection = columnSelection;
 777   }
 778
 779   public SequenceI[] getHiddenSequences()
 780   {
 781     if (hiddenSequences == null || hiddenSequences.isEmpty())
 782     {
 783       return new SequenceI[] {};
 784     }
 785     synchronized (hiddenSequences)
 786     {
 787       return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
 788     }
 789   }
 790
 791   public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
 792   {
 793     this.hiddenSequences = hiddenSequences;
 794   }
 795
 796   public class JSONExportSettings
 797   {
 798     private boolean exportSequence;
 799
 800     private boolean exportSequenceFeatures;
 801
 802     private boolean exportAnnotations;
 803
 804     private boolean exportGroups;
 805
 806     private boolean exportJalviewSettings;
 807
 808     public boolean isExportSequence()
 809     {
 810       return exportSequence;
 811     }
 812
 813     public void setExportSequence(boolean exportSequence)
 814     {
 815       this.exportSequence = exportSequence;
 816     }
 817
 818     public boolean isExportSequenceFeatures()
 819     {
 820       return exportSequenceFeatures;
 821     }
 822
 823     public void setExportSequenceFeatures(boolean exportSequenceFeatures)
 824     {
 825       this.exportSequenceFeatures = exportSequenceFeatures;
 826     }
 827
 828     public boolean isExportAnnotations()
 829     {
 830       return exportAnnotations;
 831     }
 832
 833     public void setExportAnnotations(boolean exportAnnotations)
 834     {
 835       this.exportAnnotations = exportAnnotations;
 836     }
 837
 838     public boolean isExportGroups()
 839     {
 840       return exportGroups;
 841     }
 842
 843     public void setExportGroups(boolean exportGroups)
 844     {
 845       this.exportGroups = exportGroups;
 846     }
 847
 848     public boolean isExportJalviewSettings()
 849     {
 850       return exportJalviewSettings;
 851     }
 852
 853     public void setExportJalviewSettings(boolean exportJalviewSettings)
 854     {
 855       this.exportJalviewSettings = exportJalviewSettings;
 856     }
 857   }
 858 }