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(
 215                 annotations, seqs));
 216       }
 217       else
 218       {
 219         if (globalColourScheme.equalsIgnoreCase("RNA Helices"))
 220         {
 221           jsonAlignmentPojo.setGlobalColorScheme("None");
 222         }
 223       }
 224
 225       if (exportSettings.isExportFeatures())
 226       {
 227         jsonAlignmentPojo
 228                 .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
 229       }
 230
 231       if (exportSettings.isExportGroups() && seqGroups != null
 232               && seqGroups.size() > 0)
 233       {
 234         for (SequenceGroup seqGrp : seqGroups)
 235         {
 236           SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
 237           seqGrpPojo.setGroupName(seqGrp.getName());
 238           seqGrpPojo.setColourScheme(ColourSchemeProperty
 239                   .getColourName(seqGrp.cs));
 240           seqGrpPojo.setColourText(seqGrp.getColourText());
 241           seqGrpPojo.setDescription(seqGrp.getDescription());
 242           seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
 243           seqGrpPojo.setDisplayText(seqGrp.getDisplayText());
 244           seqGrpPojo.setEndRes(seqGrp.getEndRes());
 245           seqGrpPojo.setStartRes(seqGrp.getStartRes());
 246           seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
 247           for (SequenceI seq : seqGrp.getSequences())
 248           {
 249             seqGrpPojo.getSequenceRefs()
 250                     .add(String.valueOf(seq.hashCode()));
 251           }
 252           jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
 253         }
 254       }
 255       org.json.JSONObject generatedJSon = new org.json.JSONObject(
 256               jsonAlignmentPojo);
 257       jsonOutput = generatedJSon.toString();
 258       return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
 259               "xEnd");
 260     } catch (Exception e)
 261     {
 262       e.printStackTrace();
 263     }
 264     return jsonOutput;
 265   }
 266
 267   public String[] getHiddenSections()
 268   {
 269     String[] hiddenSections = new String[2];
 270     if (getViewport() == null)
 271     {
 272       return null;
 273     }
 274
 275     // hidden column business
 276     if (getViewport().hasHiddenColumns())
 277     {
 278       List<int[]> hiddenCols = getViewport().getColumnSelection()
 279               .getHiddenColumns();
 280       StringBuilder hiddenColsBuilder = new StringBuilder();
 281       for (int[] range : hiddenCols)
 282       {
 283         hiddenColsBuilder.append(";").append(range[0]).append("-")
 284                 .append(range[1]);
 285       }
 286
 287       hiddenColsBuilder.deleteCharAt(0);
 288       hiddenSections[0] = hiddenColsBuilder.toString();
 289     }
 290
 291     // hidden rows/seqs business
 292     HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
 293             .getHiddenSequences();
 294     if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
 295     {
 296       return hiddenSections;
 297     }
 298
 299     SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
 300     StringBuilder hiddenSeqsBuilder = new StringBuilder();
 301     for (SequenceI hiddenSeq : hiddenSeqs)
 302     {
 303       if (hiddenSeq != null)
 304       {
 305         hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
 306       }
 307     }
 308     if (hiddenSeqsBuilder.length() > 0)
 309     {
 310       hiddenSeqsBuilder.deleteCharAt(0);
 311     }
 312     hiddenSections[1] = hiddenSeqsBuilder.toString();
 313
 314     return hiddenSections;
 315   }
 316
 317   public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
 318           List<SequenceI> seqs, FeatureRenderer fr)
 319   {
 320     displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
 321     List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
 322     for (SequenceI seq : seqs)
 323     {
 324       SequenceI dataSetSequence = seq.getDatasetSequence();
 325       SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
 326               : seq.getDatasetSequence().getSequenceFeatures();
 327
 328       seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
 329               : seqFeatures;
 330       if (seqFeatures == null)
 331       {
 332         continue;
 333       }
 334
 335       for (SequenceFeature sf : seqFeatures)
 336       {
 337         if (displayedFeatures != null
 338                 && displayedFeatures.isVisible(sf.getType()))
 339         {
 340           SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
 341                   String.valueOf(seq.hashCode()));
 342
 343           String featureColour = (fr == null) ? null : jalview.util.Format
 344                   .getHexString(fr.findFeatureColour(Color.white, seq,
 345                           seq.findIndex(sf.getBegin())));
 346           jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
 347           jsonFeature.setXend(seq.findIndex(sf.getEnd()));
 348           jsonFeature.setType(sf.getType());
 349           jsonFeature.setDescription(sf.getDescription());
 350           jsonFeature.setLinks(sf.links);
 351           jsonFeature.setOtherDetails(sf.otherDetails);
 352           jsonFeature.setScore(sf.getScore());
 353           jsonFeature.setFillColor(featureColour);
 354           jsonFeature.setFeatureGroup(sf.getFeatureGroup());
 355           sequenceFeaturesPojo.add(jsonFeature);
 356         }
 357       }
 358     }
 359     return sequenceFeaturesPojo;
 360   }
 361
 362   public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
 363           Vector<AlignmentAnnotation> annotations, Vector<SequenceI> seqs)
 364   {
 365     List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
 366     if (annotations == null)
 367     {
 368       return jsonAnnotations;
 369     }
 370     for (AlignmentAnnotation annot : annotations)
 371     {
 372       AnnotationDisplaySettingPojo annotSetting = new AnnotationDisplaySettingPojo();
 373       annotSetting.setBelowAlignment(annot.belowAlignment);
 374       annotSetting.setCentreColLabels(annot.centreColLabels);
 375       annotSetting.setScaleColLabel(annot.centreColLabels);
 376       annotSetting.setShowAllColLabels(annot.showAllColLabels);
 377       annotSetting.setVisible(annot.visible);
 378
 379
 380       AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
 381       alignAnnotPojo.setScore(annot.score);
 382       alignAnnotPojo.setCalcId(annot.getCalcId());
 383       alignAnnotPojo.setDescription(annot.description);
 384       alignAnnotPojo.setLabel(annot.label);
 385       alignAnnotPojo.setGraphType(annot.graph);
 386       alignAnnotPojo.setAnnotationSettings(annotSetting);
 387       int seqHash = setAnnotationRefSeq(annot, seqs);
 388       alignAnnotPojo.setSequenceRef(seqHash == 0 ? null : String
 389               .valueOf(seqHash));
 390       for (Annotation annotation : annot.annotations)
 391       {
 392         AnnotationPojo annotationPojo = new AnnotationPojo();
 393         if (annotation != null)
 394         {
 395           annotationPojo.setDescription(annotation.description);
 396           annotationPojo.setValue(annotation.value);
 397           annotationPojo
 398                   .setSecondaryStructure(annotation.secondaryStructure);
 399           annotationPojo.setDisplayCharacter(annotation.displayCharacter);
 400           if (annotation.colour != null)
 401           {
 402             annotationPojo.setColour(jalview.util.Format
 403                     .getHexString(annotation.colour));
 404           }
 405           alignAnnotPojo.getAnnotations().add(annotationPojo);
 406         }
 407         else
 408         {
 409           if (annot.getCalcId() != null
 410                   && annot.getCalcId().equalsIgnoreCase(TCOFFEE_SCORE))
 411           {
 412             // do nothing
 413           }
 414           else
 415           {
 416             alignAnnotPojo.getAnnotations().add(null);
 417           }
 418         }
 419       }
 420       jsonAnnotations.add(alignAnnotPojo);
 421     }
 422     return jsonAnnotations;
 423   }
 424
 425   private static int setAnnotationRefSeq(AlignmentAnnotation annot,
 426           Vector<SequenceI> seqs)
 427   {
 428     if (annot == null || seqs == null || seqs.size() == 0)
 429     {
 430       return 0;
 431     }
 432     for (SequenceI seq : seqs)
 433     {
 434       if (seq == null || seq.getAnnotation() == null)
 435       {
 436         continue;
 437       }
 438       for (AlignmentAnnotation seqAnnot : seq.getAnnotation())
 439       {
 440         if (seqAnnot == annot)
 441         {
 442           return seq.hashCode();
 443         }
 444       }
 445     }
 446     return 0;
 447   }
 448   @SuppressWarnings("unchecked")
 449   public JSONFile parse(Reader jsonAlignmentString)
 450   {
 451     try
 452     {
 453       JSONParser jsonParser = new JSONParser();
 454       JSONObject alignmentJsonObj = (JSONObject) jsonParser
 455               .parse(jsonAlignmentString);
 456       JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
 457       JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
 458               .get("alignAnnotation");
 459       JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
 460               .get("seqFeatures");
 461       JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
 462               .get("seqGroups");
 463       JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
 464               .get("appSettings");
 465
 466       if (jvSettingsJsonObj != null)
 467       {
 468         globalColourScheme = (String) jvSettingsJsonObj
 469                 .get("globalColorScheme");
 470         Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
 471                 "showSeqFeatures").toString());
 472         setShowSeqFeatures(showFeatures);
 473         parseHiddenSeqRefsAsList(jvSettingsJsonObj);
 474         parseHiddenCols(jvSettingsJsonObj);
 475       }
 476
 477       hiddenSequences = new ArrayList<SequenceI>();
 478       seqMap = new Hashtable<String, Sequence>();
 479       for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
 480               .hasNext();)
 481       {
 482         JSONObject sequence = sequenceIter.next();
 483         String sequcenceString = sequence.get("seq").toString();
 484         String sequenceName = sequence.get("name").toString();
 485         String seqUniqueId = sequence.get("id").toString();
 486         int start = Integer.valueOf(sequence.get("start").toString());
 487         int end = Integer.valueOf(sequence.get("end").toString());
 488         Sequence seq = new Sequence(sequenceName, sequcenceString, start,
 489                 end);
 490         if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
 491         {
 492           hiddenSequences.add(seq);
 493         }
 494         seqs.add(seq);
 495         seqMap.put(seqUniqueId, seq);
 496       }
 497
 498
 499       parseFeatures(jsonSeqArray);
 500
 501       for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
 502               .hasNext();)
 503       {
 504         JSONObject seqGrpObj = seqGrpIter.next();
 505         String grpName = seqGrpObj.get("groupName").toString();
 506         String colourScheme = seqGrpObj.get("colourScheme").toString();
 507         String description = (seqGrpObj.get("description") == null) ? null
 508                 : seqGrpObj.get("description").toString();
 509         boolean displayBoxes = Boolean.valueOf(seqGrpObj
 510                 .get("displayBoxes").toString());
 511         boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
 512                 .toString());
 513         boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
 514                 .toString());
 515         boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
 516                 "showNonconserved").toString());
 517         int startRes = Integer
 518                 .valueOf(seqGrpObj.get("startRes").toString());
 519         int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
 520         JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
 521
 522         ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
 523         if (sequenceRefs.size() > 0)
 524         {
 525           Iterator<String> seqHashIter = sequenceRefs.iterator();
 526           while (seqHashIter.hasNext())
 527           {
 528             String seqHash = seqHashIter.next();
 529             Sequence sequence = seqMap.get(seqHash);
 530             if (sequence != null)
 531             {
 532               grpSeqs.add(sequence);
 533             }
 534           }
 535         }
 536         SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
 537                 displayBoxes, displayText, colourText,
 538                 startRes, endRes);
 539         seqGrp.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme,
 540                 seqGrp);
 541         seqGrp.setShowNonconserved(showNonconserved);
 542         seqGrp.setDescription(description);
 543         this.seqGroups.add(seqGrp);
 544
 545       }
 546
 547       for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
 548               .hasNext();)
 549       {
 550         JSONObject alAnnot = alAnnotIter.next();
 551         if (alAnnot == null)
 552         {
 553           continue;
 554         }
 555         JSONObject diplaySettings = (JSONObject) alAnnot
 556                 .get("annotationSettings");
 557
 558         JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
 559         Annotation[] annotations = new Annotation[annotJsonArray.size()];
 560         int count = 0;
 561         String calcId = alAnnot.get("calcId") == null ? "" : alAnnot.get(
 562                 "calcId").toString();
 563         for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
 564                 .hasNext();)
 565         {
 566           JSONObject annot = annotIter.next();
 567           if (annot == null)
 568           {
 569             annotations[count] = null;
 570           }
 571           else
 572           {
 573             float val = annot.get("value") == null ? null : Float
 574                     .valueOf(annot.get("value").toString());
 575             String desc = annot.get("description") == null ? null : annot
 576                     .get("description").toString();
 577             char ss = annot.get("secondaryStructure") == null
 578                     || annot.get("secondaryStructure").toString()
 579                             .equalsIgnoreCase("u0000") ? ' ' : annot
 580                     .get("secondaryStructure").toString().charAt(0);
 581             String displayChar = annot.get("displayCharacter") == null ? ""
 582                     : annot.get("displayCharacter").toString();
 583             Color color = annot.get("colour") == null ? Color.white
 584                     : UserColourScheme.getColourFromString(annot.get(
 585                     "colour").toString());
 586             annotations[count] = new Annotation(displayChar, desc, ss, val,
 587                     color);
 588           }
 589           ++count;
 590         }
 591
 592         AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
 593                 .get("label").toString(), alAnnot.get("description")
 594                 .toString(), annotations);
 595         alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0 : Integer
 596                 .valueOf(alAnnot.get("graphType")
 597                         .toString());
 598         alignAnnot.scaleColLabel = (diplaySettings.get("scaleColLabel") == null) ? false
 599                 : Boolean.valueOf(diplaySettings.get("scaleColLabel")
 600                         .toString());
 601         alignAnnot.showAllColLabels = (diplaySettings
 602                 .get("showAllColLabels") == null) ? true : Boolean
 603                 .valueOf(diplaySettings.get("showAllColLabels").toString());
 604         alignAnnot.centreColLabels = (diplaySettings.get("centreColLabels") == null) ? true
 605                 : Boolean.valueOf(diplaySettings.get("centreColLabels")
 606                         .toString());
 607         alignAnnot.belowAlignment = (diplaySettings.get("belowAlignment") == null) ? false
 608                 : Boolean.valueOf(diplaySettings.get("belowAlignment")
 609                         .toString());
 610         alignAnnot.visible = (diplaySettings.get("visible") == null) ? true
 611                 : Boolean.valueOf(diplaySettings.get("visible").toString());
 612
 613
 614         alignAnnot.score = alAnnot.get("score") == null ? null : Double
 615                 .valueOf(alAnnot.get("score").toString());
 616         alignAnnot.setCalcId(calcId);
 617         String seqHash = (alAnnot.get("sequenceRef") != null) ? alAnnot
 618                 .get("sequenceRef").toString() : null;
 619
 620         Sequence sequence = (seqHash != null) ? seqMap.get(seqHash) : null;
 621         if (sequence != null)
 622         {
 623           alignAnnot.sequenceRef = sequence;
 624           sequence.addAlignmentAnnotation(alignAnnot);
 625           if (alignAnnot.label.equalsIgnoreCase("T-COFFEE"))
 626           {
 627             alignAnnot.createSequenceMapping(sequence, sequence.getStart(),
 628                     false);
 629             sequence.addAlignmentAnnotation(alignAnnot);
 630             alignAnnot.adjustForAlignment();
 631           }
 632         }
 633         this.annotations.add(alignAnnot);
 634         alignAnnot.validateRangeAndDisplay();
 635       }
 636     } catch (Exception e)
 637     {
 638       e.printStackTrace();
 639     }
 640     return this;
 641   }
 642
 643   public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
 644   {
 645     hiddenSeqRefs = new ArrayList<String>();
 646     String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
 647     if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
 648     {
 649       String[] seqRefs = hiddenSeqs.split(";");
 650       for (String seqRef : seqRefs)
 651       {
 652         hiddenSeqRefs.add(seqRef);
 653       }
 654     }
 655   }
 656
 657   public void parseHiddenCols(JSONObject jvSettingsJson)
 658   {
 659     String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
 660     if (hiddenCols != null && !hiddenCols.isEmpty())
 661     {
 662       columnSelection = new ColumnSelection();
 663       String[] rangeStrings = hiddenCols.split(";");
 664       for (String rangeString : rangeStrings)
 665       {
 666         String[] range = rangeString.split("-");
 667         columnSelection.hideColumns(Integer.valueOf(range[0]),
 668                 Integer.valueOf(range[1]));
 669       }
 670     }
 671   }
 672
 673   @SuppressWarnings("unchecked")
 674   private void parseFeatures(JSONArray jsonSeqFeatures)
 675   {
 676     if (jsonSeqFeatures != null)
 677     {
 678       displayedFeatures = new FeaturesDisplayed();
 679       for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
 680               .hasNext();)
 681       {
 682         JSONObject jsonFeature = seqFeatureItr.next();
 683         Long begin = (Long) jsonFeature.get("xStart");
 684         Long end = (Long) jsonFeature.get("xEnd");
 685         String type = (String) jsonFeature.get("type");
 686         String featureGrp = (String) jsonFeature.get("featureGroup");
 687         String descripiton = (String) jsonFeature.get("description");
 688         String seqRef = (String) jsonFeature.get("sequenceRef");
 689         Float score = Float.valueOf(jsonFeature.get("score").toString());
 690
 691         Sequence seq = seqMap.get(seqRef);
 692         SequenceFeature sequenceFeature = new SequenceFeature();
 693         JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
 694         if (linksJsonArray != null && linksJsonArray.size() > 0)
 695         {
 696           Iterator<String> linkList = linksJsonArray.iterator();
 697           while (linkList.hasNext())
 698           {
 699             String link = linkList.next();
 700             sequenceFeature.addLink(link);
 701           }
 702         }
 703         sequenceFeature.setFeatureGroup(featureGrp);
 704         sequenceFeature.setScore(score);
 705         sequenceFeature.setDescription(descripiton);
 706         sequenceFeature.setType(type);
 707         sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
 708         sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
 709         seq.addSequenceFeature(sequenceFeature);
 710         displayedFeatures.setVisible(type);
 711       }
 712     }
 713   }
 714
 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   public void configureForView(AlignmentViewPanel avpanel)
 737   {
 738     super.configureForView(avpanel);
 739     AlignViewportI viewport = avpanel.getAlignViewport();
 740     AlignmentI alignment = viewport.getAlignment();
 741     AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
 742
 743     seqGroups = alignment.getGroups();
 744     fr = avpanel.cloneFeatureRenderer();
 745
 746     // Add non auto calculated annotation to AlignFile
 747     for (AlignmentAnnotation annot : annots)
 748     {
 749       if (annot != null && !annot.autoCalculated)
 750       {
 751         annotations.add(annot);
 752       }
 753     }
 754     globalColourScheme = ColourSchemeProperty.getColourName(viewport
 755             .getGlobalColourScheme());
 756     setDisplayedFeatures(viewport.getFeaturesDisplayed());
 757     showSeqFeatures = viewport.isShowSequenceFeatures();
 758
 759   }
 760
 761   public boolean isShowSeqFeatures()
 762   {
 763     return showSeqFeatures;
 764   }
 765
 766   public void setShowSeqFeatures(boolean showSeqFeatures)
 767   {
 768     this.showSeqFeatures = showSeqFeatures;
 769   }
 770
 771   public Vector<AlignmentAnnotation> getAnnotations()
 772   {
 773     return annotations;
 774   }
 775
 776   public List<int[]> getHiddenColumns()
 777   {
 778     return hiddenColumns;
 779   }
 780
 781   public ColumnSelection getColumnSelection()
 782   {
 783     return columnSelection;
 784   }
 785
 786   public void setColumnSelection(ColumnSelection columnSelection)
 787   {
 788     this.columnSelection = columnSelection;
 789   }
 790
 791   public SequenceI[] getHiddenSequences()
 792   {
 793     if (hiddenSequences == null || hiddenSequences.isEmpty())
 794     {
 795       return new SequenceI[] {};
 796     }
 797     synchronized (hiddenSequences)
 798     {
 799       return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
 800     }
 801   }
 802
 803   public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
 804   {
 805     this.hiddenSequences = hiddenSequences;
 806   }
 807
 808   public class JSONExportSettings
 809   {
 810     private boolean exportSequence;
 811
 812     private boolean exportSequenceFeatures;
 813
 814     private boolean exportAnnotations;
 815
 816     private boolean exportGroups;
 817
 818     private boolean exportJalviewSettings;
 819
 820     public boolean isExportSequence()
 821     {
 822       return exportSequence;
 823     }
 824
 825     public void setExportSequence(boolean exportSequence)
 826     {
 827       this.exportSequence = exportSequence;
 828     }
 829
 830     public boolean isExportSequenceFeatures()
 831     {
 832       return exportSequenceFeatures;
 833     }
 834
 835     public void setExportSequenceFeatures(boolean exportSequenceFeatures)
 836     {
 837       this.exportSequenceFeatures = exportSequenceFeatures;
 838     }
 839
 840     public boolean isExportAnnotations()
 841     {
 842       return exportAnnotations;
 843     }
 844
 845     public void setExportAnnotations(boolean exportAnnotations)
 846     {
 847       this.exportAnnotations = exportAnnotations;
 848     }
 849
 850     public boolean isExportGroups()
 851     {
 852       return exportGroups;
 853     }
 854
 855     public void setExportGroups(boolean exportGroups)
 856     {
 857       this.exportGroups = exportGroups;
 858     }
 859
 860     public boolean isExportJalviewSettings()
 861     {
 862       return exportJalviewSettings;
 863     }
 864
 865     public void setExportJalviewSettings(boolean exportJalviewSettings)
 866     {
 867       this.exportJalviewSettings = exportJalviewSettings;
 868     }
 869   }
 870 }