src/jalview/io/JSONFile.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21
  22 package jalview.io;
  23
  24 import jalview.api.AlignExportSettingI;
  25 import jalview.api.AlignViewportI;
  26 import jalview.api.AlignmentViewPanel;
  27 import jalview.api.ComplexAlignFile;
  28 import jalview.api.FeatureRenderer;
  29 import jalview.api.FeatureSettingsModelI;
  30 import jalview.api.FeaturesDisplayedI;
  31 import jalview.bin.BuildDetails;
  32 import jalview.datamodel.AlignmentAnnotation;
  33 import jalview.datamodel.AlignmentI;
  34 import jalview.datamodel.Annotation;
  35 import jalview.datamodel.ColumnSelection;
  36 import jalview.datamodel.HiddenSequences;
  37 import jalview.datamodel.Sequence;
  38 import jalview.datamodel.SequenceFeature;
  39 import jalview.datamodel.SequenceGroup;
  40 import jalview.datamodel.SequenceI;
  41 import jalview.json.binding.biojson.v1.AlignmentAnnotationPojo;
  42 import jalview.json.binding.biojson.v1.AlignmentPojo;
  43 import jalview.json.binding.biojson.v1.AnnotationDisplaySettingPojo;
  44 import jalview.json.binding.biojson.v1.AnnotationPojo;
  45 import jalview.json.binding.biojson.v1.ColourSchemeMapper;
  46 import jalview.json.binding.biojson.v1.SequenceFeaturesPojo;
  47 import jalview.json.binding.biojson.v1.SequenceGrpPojo;
  48 import jalview.json.binding.biojson.v1.SequencePojo;
  49 import jalview.schemes.ColourSchemeProperty;
  50 import jalview.schemes.UserColourScheme;
  51 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
  52
  53 import java.awt.Color;
  54 import java.io.IOException;
  55 import java.io.Reader;
  56 import java.util.ArrayList;
  57 import java.util.Hashtable;
  58 import java.util.Iterator;
  59 import java.util.List;
  60 import java.util.Vector;
  61
  62 import org.json.simple.JSONArray;
  63 import org.json.simple.JSONObject;
  64 import org.json.simple.parser.JSONParser;
  65
  66 public class JSONFile extends AlignFile implements ComplexAlignFile
  67 {
  68   private static String version = new BuildDetails().getVersion();
  69
  70   private String webstartUrl = "http://www.jalview.org/services/launchApp";
  71
  72   private String application = "Jalview";
  73
  74   public static final String FILE_EXT = "json";
  75
  76   public static final String FILE_DESC = "JSON";
  77
  78   private String globalColourScheme;
  79
  80   private boolean showSeqFeatures;
  81
  82   private Hashtable<String, Sequence> seqMap;
  83
  84   private FeaturesDisplayedI displayedFeatures;
  85
  86   private FeatureRenderer fr;
  87
  88   private List<int[]> hiddenColumns;
  89
  90   private ColumnSelection columnSelection;
  91
  92   private List<String> hiddenSeqRefs;
  93
  94   private ArrayList<SequenceI> hiddenSequences;
  95
  96   private final static String TCOFFEE_SCORE = "TCoffeeScore";
  97
  98   public JSONFile()
  99   {
 100     super();
 101   }
 102
 103   public JSONFile(FileParse source) throws IOException
 104   {
 105     super(source);
 106   }
 107
 108   public JSONFile(String inFile, String type) throws IOException
 109   {
 110     super(inFile, type);
 111   }
 112
 113   @Override
 114   public void parse() throws IOException
 115   {
 116     parse(getReader());
 117
 118   }
 119
 120   @Override
 121   public String print()
 122   {
 123     String jsonOutput = null;
 124     try
 125     {
 126       AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
 127       AlignExportSettingI exportSettings = getExportSettings();
 128
 129       // if no export settings were supplied use the following with all values
 130       // defaulting to true
 131       if (exportSettings == null)
 132       {
 133         exportSettings = new AlignExportSettingI()
 134         {
 135           @Override
 136           public boolean isExportHiddenSequences()
 137           {
 138             return true;
 139           }
 140
 141           @Override
 142           public boolean isExportHiddenColumns()
 143           {
 144             return true;
 145           }
 146
 147           @Override
 148           public boolean isExportGroups()
 149           {
 150             return true;
 151           }
 152
 153           @Override
 154           public boolean isExportFeatures()
 155           {
 156             return true;
 157           }
 158
 159           @Override
 160           public boolean isExportAnnotations()
 161           {
 162             return true;
 163           }
 164
 165           @Override
 166           public boolean isCancelled()
 167           {
 168             return false;
 169           }
 170         };
 171       }
 172
 173       int count = 0;
 174       for (SequenceI seq : seqs)
 175       {
 176         StringBuilder name = new StringBuilder();
 177         name.append(seq.getName()).append("/").append(seq.getStart())
 178                 .append("-").append(seq.getEnd());
 179         SequencePojo jsonSeqPojo = new SequencePojo();
 180         jsonSeqPojo.setId(String.valueOf(seq.hashCode()));
 181         jsonSeqPojo.setOrder(++count);
 182         jsonSeqPojo.setEnd(seq.getEnd());
 183         jsonSeqPojo.setStart(seq.getStart());
 184         jsonSeqPojo.setName(name.toString());
 185         jsonSeqPojo.setSeq(seq.getSequenceAsString());
 186         jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
 187       }
 188       jsonAlignmentPojo.setGlobalColorScheme(globalColourScheme);
 189       jsonAlignmentPojo.getAppSettings().put("application", application);
 190       jsonAlignmentPojo.getAppSettings().put("version", version);
 191       jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
 192       jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
 193               String.valueOf(showSeqFeatures));
 194
 195       String[] hiddenSections = getHiddenSections();
 196       if (hiddenSections != null)
 197       {
 198         if (hiddenSections[0] != null
 199                 && exportSettings.isExportHiddenColumns())
 200         {
 201           jsonAlignmentPojo.getAppSettings().put("hiddenCols",
 202                   String.valueOf(hiddenSections[0]));
 203         }
 204         if (hiddenSections[1] != null
 205                 && exportSettings.isExportHiddenSequences())
 206         {
 207           jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
 208                   String.valueOf(hiddenSections[1]));
 209         }
 210       }
 211
 212       if (exportSettings.isExportAnnotations())
 213       {
 214         jsonAlignmentPojo
 215                 .setAlignAnnotation(annotationToJsonPojo(annotations));
 216       }
 217       else
 218       {
 219         // These color schemes require annotation, disable them if annotations
 220         // are not exported
 221         if (globalColourScheme.equalsIgnoreCase("RNA Helices")
 222                 || globalColourScheme.equalsIgnoreCase("T-COFFEE SCORES"))
 223         {
 224           jsonAlignmentPojo.setGlobalColorScheme("None");
 225         }
 226       }
 227
 228       if (exportSettings.isExportFeatures())
 229       {
 230         jsonAlignmentPojo
 231                 .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
 232       }
 233
 234       if (exportSettings.isExportGroups() && seqGroups != null
 235               && seqGroups.size() > 0)
 236       {
 237         for (SequenceGroup seqGrp : seqGroups)
 238         {
 239           SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
 240           seqGrpPojo.setGroupName(seqGrp.getName());
 241           seqGrpPojo.setColourScheme(ColourSchemeProperty
 242                   .getColourName(seqGrp.cs));
 243           seqGrpPojo.setColourText(seqGrp.getColourText());
 244           seqGrpPojo.setDescription(seqGrp.getDescription());
 245           seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
 246           seqGrpPojo.setDisplayText(seqGrp.getDisplayText());
 247           seqGrpPojo.setEndRes(seqGrp.getEndRes());
 248           seqGrpPojo.setStartRes(seqGrp.getStartRes());
 249           seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
 250           for (SequenceI seq : seqGrp.getSequences())
 251           {
 252             seqGrpPojo.getSequenceRefs()
 253                     .add(String.valueOf(seq.hashCode()));
 254           }
 255           jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
 256         }
 257       }
 258       org.json.JSONObject generatedJSon = new org.json.JSONObject(
 259               jsonAlignmentPojo);
 260       jsonOutput = generatedJSon.toString();
 261       return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
 262               "xEnd");
 263     } catch (Exception e)
 264     {
 265       e.printStackTrace();
 266     }
 267     return jsonOutput;
 268   }
 269
 270   public String[] getHiddenSections()
 271   {
 272     String[] hiddenSections = new String[2];
 273     if (getViewport() == null)
 274     {
 275       return null;
 276     }
 277
 278     // hidden column business
 279     if (getViewport().hasHiddenColumns())
 280     {
 281       List<int[]> hiddenCols = getViewport().getColumnSelection()
 282               .getHiddenColumns();
 283       StringBuilder hiddenColsBuilder = new StringBuilder();
 284       for (int[] range : hiddenCols)
 285       {
 286         hiddenColsBuilder.append(";").append(range[0]).append("-")
 287                 .append(range[1]);
 288       }
 289
 290       hiddenColsBuilder.deleteCharAt(0);
 291       hiddenSections[0] = hiddenColsBuilder.toString();
 292     }
 293
 294     // hidden rows/seqs business
 295     HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
 296             .getHiddenSequences();
 297     if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
 298     {
 299       return hiddenSections;
 300     }
 301
 302     SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
 303     StringBuilder hiddenSeqsBuilder = new StringBuilder();
 304     for (SequenceI hiddenSeq : hiddenSeqs)
 305     {
 306       if (hiddenSeq != null)
 307       {
 308         hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
 309       }
 310     }
 311     if (hiddenSeqsBuilder.length() > 0)
 312     {
 313       hiddenSeqsBuilder.deleteCharAt(0);
 314     }
 315     hiddenSections[1] = hiddenSeqsBuilder.toString();
 316
 317     return hiddenSections;
 318   }
 319
 320   public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
 321           List<SequenceI> seqs, FeatureRenderer fr)
 322   {
 323     displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
 324     List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
 325     for (SequenceI seq : seqs)
 326     {
 327       SequenceI dataSetSequence = seq.getDatasetSequence();
 328       SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
 329               : seq.getDatasetSequence().getSequenceFeatures();
 330
 331       seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
 332               : seqFeatures;
 333       if (seqFeatures == null)
 334       {
 335         continue;
 336       }
 337
 338       for (SequenceFeature sf : seqFeatures)
 339       {
 340         if (displayedFeatures != null
 341                 && displayedFeatures.isVisible(sf.getType()))
 342         {
 343           SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
 344                   String.valueOf(seq.hashCode()));
 345
 346           String featureColour = (fr == null) ? null : jalview.util.Format
 347                   .getHexString(fr.findFeatureColour(Color.white, seq,
 348                           seq.findIndex(sf.getBegin())));
 349           jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
 350           jsonFeature.setXend(seq.findIndex(sf.getEnd()));
 351           jsonFeature.setType(sf.getType());
 352           jsonFeature.setDescription(sf.getDescription());
 353           jsonFeature.setLinks(sf.links);
 354           jsonFeature.setOtherDetails(sf.otherDetails);
 355           jsonFeature.setScore(sf.getScore());
 356           jsonFeature.setFillColor(featureColour);
 357           jsonFeature.setFeatureGroup(sf.getFeatureGroup());
 358           sequenceFeaturesPojo.add(jsonFeature);
 359         }
 360       }
 361     }
 362     return sequenceFeaturesPojo;
 363   }
 364
 365   public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
 366           Vector<AlignmentAnnotation> annotations)
 367   {
 368     List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
 369     if (annotations == null)
 370     {
 371       return jsonAnnotations;
 372     }
 373     for (AlignmentAnnotation annot : annotations)
 374     {
 375       AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
 376       alignAnnotPojo.setDescription(annot.description);
 377       alignAnnotPojo.setLabel(annot.label);
 378       if (!Double.isNaN(annot.score))
 379       {
 380         alignAnnotPojo.setScore(annot.score);
 381       }
 382       alignAnnotPojo.setCalcId(annot.getCalcId());
 383       alignAnnotPojo.setGraphType(annot.graph);
 384
 385       AnnotationDisplaySettingPojo annotSetting = new AnnotationDisplaySettingPojo();
 386       annotSetting.setBelowAlignment(annot.belowAlignment);
 387       annotSetting.setCentreColLabels(annot.centreColLabels);
 388       annotSetting.setScaleColLabel(annot.scaleColLabel);
 389       annotSetting.setShowAllColLabels(annot.showAllColLabels);
 390       annotSetting.setVisible(annot.visible);
 391       annotSetting.setHasIcon(annot.hasIcons);
 392       alignAnnotPojo.setAnnotationSettings(annotSetting);
 393       SequenceI refSeq = annot.sequenceRef;
 394       if (refSeq != null)
 395       {
 396         alignAnnotPojo.setSequenceRef(String.valueOf(refSeq.hashCode()));
 397       }
 398       for (Annotation annotation : annot.annotations)
 399       {
 400         AnnotationPojo annotationPojo = new AnnotationPojo();
 401         if (annotation != null)
 402         {
 403           annotationPojo.setDescription(annotation.description);
 404           annotationPojo.setValue(annotation.value);
 405           annotationPojo
 406                   .setSecondaryStructure(annotation.secondaryStructure);
 407           String displayChar = annotation.displayCharacter == null ? null
 408                   : annotation.displayCharacter;
 409           // System.out.println("--------------------->[" + displayChar + "]");
 410           annotationPojo.setDisplayCharacter(displayChar);
 411           if (annotation.colour != null)
 412           {
 413             annotationPojo.setColour(jalview.util.Format
 414                     .getHexString(annotation.colour));
 415           }
 416           alignAnnotPojo.getAnnotations().add(annotationPojo);
 417         }
 418         else
 419         {
 420           if (annot.getCalcId() != null
 421                   && annot.getCalcId().equalsIgnoreCase(TCOFFEE_SCORE))
 422           {
 423             // do nothing
 424           }
 425           else
 426           {
 427             alignAnnotPojo.getAnnotations().add(annotationPojo);
 428           }
 429         }
 430       }
 431       jsonAnnotations.add(alignAnnotPojo);
 432     }
 433     return jsonAnnotations;
 434   }
 435
 436   @SuppressWarnings("unchecked")
 437   public JSONFile parse(Reader jsonAlignmentString)
 438   {
 439     try
 440     {
 441       JSONParser jsonParser = new JSONParser();
 442       JSONObject alignmentJsonObj = (JSONObject) jsonParser
 443               .parse(jsonAlignmentString);
 444       JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
 445       JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
 446               .get("alignAnnotation");
 447       JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
 448               .get("seqFeatures");
 449       JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
 450               .get("seqGroups");
 451       JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
 452               .get("appSettings");
 453
 454       if (jvSettingsJsonObj != null)
 455       {
 456         globalColourScheme = (String) jvSettingsJsonObj
 457                 .get("globalColorScheme");
 458         Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
 459                 "showSeqFeatures").toString());
 460         setShowSeqFeatures(showFeatures);
 461         parseHiddenSeqRefsAsList(jvSettingsJsonObj);
 462         parseHiddenCols(jvSettingsJsonObj);
 463       }
 464
 465       hiddenSequences = new ArrayList<SequenceI>();
 466       seqMap = new Hashtable<String, Sequence>();
 467       for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
 468               .hasNext();)
 469       {
 470         JSONObject sequence = sequenceIter.next();
 471         String sequcenceString = sequence.get("seq").toString();
 472         String sequenceName = sequence.get("name").toString();
 473         String seqUniqueId = sequence.get("id").toString();
 474         int start = Integer.valueOf(sequence.get("start").toString());
 475         int end = Integer.valueOf(sequence.get("end").toString());
 476         Sequence seq = new Sequence(sequenceName, sequcenceString, start,
 477                 end);
 478         if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
 479         {
 480           hiddenSequences.add(seq);
 481         }
 482         seqs.add(seq);
 483         seqMap.put(seqUniqueId, seq);
 484       }
 485
 486       parseFeatures(jsonSeqArray);
 487
 488       for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
 489               .hasNext();)
 490       {
 491         JSONObject seqGrpObj = seqGrpIter.next();
 492         String grpName = seqGrpObj.get("groupName").toString();
 493         String colourScheme = seqGrpObj.get("colourScheme").toString();
 494         String description = (seqGrpObj.get("description") == null) ? null
 495                 : seqGrpObj.get("description").toString();
 496         boolean displayBoxes = Boolean.valueOf(seqGrpObj
 497                 .get("displayBoxes").toString());
 498         boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
 499                 .toString());
 500         boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
 501                 .toString());
 502         boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
 503                 "showNonconserved").toString());
 504         int startRes = Integer
 505                 .valueOf(seqGrpObj.get("startRes").toString());
 506         int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
 507         JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
 508
 509         ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
 510         if (sequenceRefs.size() > 0)
 511         {
 512           Iterator<String> seqHashIter = sequenceRefs.iterator();
 513           while (seqHashIter.hasNext())
 514           {
 515             String seqHash = seqHashIter.next();
 516             Sequence sequence = seqMap.get(seqHash);
 517             if (sequence != null)
 518             {
 519               grpSeqs.add(sequence);
 520             }
 521           }
 522         }
 523         SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
 524                 displayBoxes, displayText, colourText, startRes, endRes);
 525         seqGrp.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme,
 526                 seqGrp);
 527         seqGrp.setShowNonconserved(showNonconserved);
 528         seqGrp.setDescription(description);
 529         this.seqGroups.add(seqGrp);
 530
 531       }
 532
 533       for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
 534               .hasNext();)
 535       {
 536         JSONObject alAnnot = alAnnotIter.next();
 537         JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
 538         Annotation[] annotations = new Annotation[annotJsonArray.size()];
 539         int count = 0;
 540         for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
 541                 .hasNext();)
 542         {
 543           JSONObject annot = annotIter.next();
 544           if (annot == null)
 545           {
 546             annotations[count] = null;
 547           }
 548           else
 549           {
 550             float val = annot.get("value") == null ? null : Float
 551                     .valueOf(annot.get("value").toString());
 552             String desc = annot.get("description") == null ? null : annot
 553                     .get("description").toString();
 554             char ss = annot.get("secondaryStructure") == null
 555                     || annot.get("secondaryStructure").toString()
 556                             .equalsIgnoreCase("u0000") ? ' ' : annot
 557                     .get("secondaryStructure").toString().charAt(0);
 558             String displayChar = annot.get("displayCharacter") == null ? ""
 559                     : annot.get("displayCharacter").toString();
 560
 561             annotations[count] = new Annotation(displayChar, desc, ss, val);
 562             if (annot.get("colour") != null)
 563             {
 564               Color color = UserColourScheme.getColourFromString(annot.get(
 565                       "colour").toString());
 566               annotations[count].colour = color;
 567             }
 568           }
 569           ++count;
 570         }
 571
 572         AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
 573                 .get("label").toString(), alAnnot.get("description")
 574                 .toString(), annotations);
 575         alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0 : Integer
 576                 .valueOf(alAnnot.get("graphType").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   @Override
 714   public String getGlobalColourScheme()
 715   {
 716     return globalColourScheme;
 717   }
 718
 719   public void setGlobalColorScheme(String globalColourScheme)
 720   {
 721     this.globalColourScheme = globalColourScheme;
 722   }
 723
 724   @Override
 725   public FeaturesDisplayedI getDisplayedFeatures()
 726   {
 727     return displayedFeatures;
 728   }
 729
 730   public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
 731   {
 732     this.displayedFeatures = displayedFeatures;
 733   }
 734
 735   @Override
 736   public void configureForView(AlignmentViewPanel avpanel)
 737   {
 738     if (avpanel == null)
 739     {
 740       return;
 741     }
 742     super.configureForView(avpanel);
 743     AlignViewportI viewport = avpanel.getAlignViewport();
 744     AlignmentI alignment = viewport.getAlignment();
 745     AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
 746
 747     seqGroups = alignment.getGroups();
 748     fr = avpanel.cloneFeatureRenderer();
 749
 750     // Add non auto calculated annotation to AlignFile
 751     if (annots != null)
 752     {
 753       for (AlignmentAnnotation annot : annots)
 754       {
 755         if (annot != null && !annot.autoCalculated)
 756         {
 757           annotations.add(annot);
 758         }
 759       }
 760     }
 761     globalColourScheme = ColourSchemeProperty.getColourName(viewport
 762             .getGlobalColourScheme());
 763     setDisplayedFeatures(viewport.getFeaturesDisplayed());
 764     showSeqFeatures = viewport.isShowSequenceFeatures();
 765
 766   }
 767
 768   @Override
 769   public boolean isShowSeqFeatures()
 770   {
 771     return showSeqFeatures;
 772   }
 773
 774   public void setShowSeqFeatures(boolean showSeqFeatures)
 775   {
 776     this.showSeqFeatures = showSeqFeatures;
 777   }
 778
 779   public Vector<AlignmentAnnotation> getAnnotations()
 780   {
 781     return annotations;
 782   }
 783
 784   public List<int[]> getHiddenColumns()
 785   {
 786     return hiddenColumns;
 787   }
 788
 789   @Override
 790   public ColumnSelection getColumnSelection()
 791   {
 792     return columnSelection;
 793   }
 794
 795   public void setColumnSelection(ColumnSelection columnSelection)
 796   {
 797     this.columnSelection = columnSelection;
 798   }
 799
 800   @Override
 801   public SequenceI[] getHiddenSequences()
 802   {
 803     if (hiddenSequences == null || hiddenSequences.isEmpty())
 804     {
 805       return new SequenceI[] {};
 806     }
 807     synchronized (hiddenSequences)
 808     {
 809       return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
 810     }
 811   }
 812
 813   public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
 814   {
 815     this.hiddenSequences = hiddenSequences;
 816   }
 817
 818   public class JSONExportSettings
 819   {
 820     private boolean exportSequence;
 821
 822     private boolean exportSequenceFeatures;
 823
 824     private boolean exportAnnotations;
 825
 826     private boolean exportGroups;
 827
 828     private boolean exportJalviewSettings;
 829
 830     public boolean isExportSequence()
 831     {
 832       return exportSequence;
 833     }
 834
 835     public void setExportSequence(boolean exportSequence)
 836     {
 837       this.exportSequence = exportSequence;
 838     }
 839
 840     public boolean isExportSequenceFeatures()
 841     {
 842       return exportSequenceFeatures;
 843     }
 844
 845     public void setExportSequenceFeatures(boolean exportSequenceFeatures)
 846     {
 847       this.exportSequenceFeatures = exportSequenceFeatures;
 848     }
 849
 850     public boolean isExportAnnotations()
 851     {
 852       return exportAnnotations;
 853     }
 854
 855     public void setExportAnnotations(boolean exportAnnotations)
 856     {
 857       this.exportAnnotations = exportAnnotations;
 858     }
 859
 860     public boolean isExportGroups()
 861     {
 862       return exportGroups;
 863     }
 864
 865     public void setExportGroups(boolean exportGroups)
 866     {
 867       this.exportGroups = exportGroups;
 868     }
 869
 870     public boolean isExportJalviewSettings()
 871     {
 872       return exportJalviewSettings;
 873     }
 874
 875     public void setExportJalviewSettings(boolean exportJalviewSettings)
 876     {
 877       this.exportJalviewSettings = exportJalviewSettings;
 878     }
 879   }
 880
 881   /**
 882    * Returns a descriptor for suitable feature display settings with
 883    * <ul>
 884    * <li>ResNums or insertions features visible</li>
 885    * <li>insertions features coloured red</li>
 886    * <li>ResNum features coloured by label</li>
 887    * <li>Insertions displayed above (on top of) ResNums</li>
 888    * </ul>
 889    */
 890   @Override
 891   public FeatureSettingsModelI getFeatureColourScheme()
 892   {
 893     return new PDBFeatureSettings();
 894   }
 895 }