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.renderer.seqfeatures.FeatureColourFinder;
  50 import jalview.schemes.JalviewColourScheme;
  51 import jalview.schemes.ResidueColourScheme;
  52 import jalview.util.ColorUtils;
  53 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
  54
  55 import java.awt.Color;
  56 import java.io.IOException;
  57 import java.io.Reader;
  58 import java.util.ArrayList;
  59 import java.util.Hashtable;
  60 import java.util.Iterator;
  61 import java.util.List;
  62 import java.util.Vector;
  63
  64 import org.json.simple.JSONArray;
  65 import org.json.simple.JSONObject;
  66 import org.json.simple.parser.JSONParser;
  67
  68 public class JSONFile extends AlignFile implements ComplexAlignFile
  69 {
  70   private static String version = new BuildDetails().getVersion();
  71
  72   private String webstartUrl = "http://www.jalview.org/services/launchApp";
  73
  74   private String application = "Jalview";
  75
  76   private String globalColourScheme;
  77
  78   private boolean showSeqFeatures;
  79
  80   private Hashtable<String, Sequence> seqMap;
  81
  82   private FeaturesDisplayedI displayedFeatures;
  83
  84   private FeatureRenderer fr;
  85
  86   private List<int[]> hiddenColumns;
  87
  88   private ColumnSelection columnSelection;
  89
  90   private List<String> hiddenSeqRefs;
  91
  92   private ArrayList<SequenceI> hiddenSequences;
  93
  94   private final static String TCOFFEE_SCORE = "TCoffeeScore";
  95
  96   public JSONFile()
  97   {
  98     super();
  99   }
 100
 101   public JSONFile(FileParse source) throws IOException
 102   {
 103     super(source);
 104   }
 105
 106   public JSONFile(String inFile, DataSourceType sourceType)
 107           throws IOException
 108   {
 109     super(inFile, sourceType);
 110   }
 111
 112   @Override
 113   public void parse() throws IOException
 114   {
 115     parse(getReader());
 116
 117   }
 118
 119   @Override
 120   public String print(SequenceI[] sqs, boolean jvsuffix)
 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 : sqs)
 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
 221                 .equalsIgnoreCase(JalviewColourScheme.RNAHelices.toString())
 222                 || globalColourScheme
 223                         .equalsIgnoreCase(JalviewColourScheme.TCoffee
 224                                 .toString()))
 225         {
 226           jsonAlignmentPojo.setGlobalColorScheme(ResidueColourScheme.NONE);
 227         }
 228       }
 229
 230       if (exportSettings.isExportFeatures())
 231       {
 232         jsonAlignmentPojo
 233                 .setSeqFeatures(sequenceFeatureToJsonPojo(sqs, fr));
 234       }
 235
 236       if (exportSettings.isExportGroups() && seqGroups != null
 237               && seqGroups.size() > 0)
 238       {
 239         for (SequenceGroup seqGrp : seqGroups)
 240         {
 241           SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
 242           seqGrpPojo.setGroupName(seqGrp.getName());
 243           seqGrpPojo.setColourScheme(seqGrp.getColourScheme()
 244                   .getSchemeName());
 245           seqGrpPojo.setColourText(seqGrp.getColourText());
 246           seqGrpPojo.setDescription(seqGrp.getDescription());
 247           seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
 248           seqGrpPojo.setDisplayText(seqGrp.getDisplayText());
 249           seqGrpPojo.setEndRes(seqGrp.getEndRes());
 250           seqGrpPojo.setStartRes(seqGrp.getStartRes());
 251           seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
 252           for (SequenceI seq : seqGrp.getSequences())
 253           {
 254             seqGrpPojo.getSequenceRefs()
 255                     .add(String.valueOf(seq.hashCode()));
 256           }
 257           jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
 258         }
 259       }
 260       org.json.JSONObject generatedJSon = new org.json.JSONObject(
 261               jsonAlignmentPojo);
 262       jsonOutput = generatedJSon.toString();
 263       return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
 264               "xEnd");
 265     } catch (Exception e)
 266     {
 267       e.printStackTrace();
 268     }
 269     return jsonOutput;
 270   }
 271
 272   public String[] getHiddenSections()
 273   {
 274     String[] hiddenSections = new String[2];
 275     if (getViewport() == null)
 276     {
 277       return null;
 278     }
 279
 280     // hidden column business
 281     if (getViewport().hasHiddenColumns())
 282     {
 283       List<int[]> hiddenCols = getViewport().getColumnSelection()
 284               .getHiddenColumns();
 285       StringBuilder hiddenColsBuilder = new StringBuilder();
 286       for (int[] range : hiddenCols)
 287       {
 288         hiddenColsBuilder.append(";").append(range[0]).append("-")
 289                 .append(range[1]);
 290       }
 291
 292       hiddenColsBuilder.deleteCharAt(0);
 293       hiddenSections[0] = hiddenColsBuilder.toString();
 294     }
 295
 296     // hidden rows/seqs business
 297     HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
 298             .getHiddenSequences();
 299     if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
 300     {
 301       return hiddenSections;
 302     }
 303
 304     SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
 305     StringBuilder hiddenSeqsBuilder = new StringBuilder();
 306     for (SequenceI hiddenSeq : hiddenSeqs)
 307     {
 308       if (hiddenSeq != null)
 309       {
 310         hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
 311       }
 312     }
 313     if (hiddenSeqsBuilder.length() > 0)
 314     {
 315       hiddenSeqsBuilder.deleteCharAt(0);
 316     }
 317     hiddenSections[1] = hiddenSeqsBuilder.toString();
 318
 319     return hiddenSections;
 320   }
 321
 322   public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
 323           SequenceI[] sqs, FeatureRenderer fr)
 324   {
 325     displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
 326     List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
 327     if (sqs == null)
 328     {
 329       return sequenceFeaturesPojo;
 330     }
 331
 332     FeatureColourFinder finder = new FeatureColourFinder(fr);
 333
 334     for (SequenceI seq : sqs)
 335     {
 336       SequenceI dataSetSequence = seq.getDatasetSequence();
 337       SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
 338               : seq.getDatasetSequence().getSequenceFeatures();
 339
 340       seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
 341               : seqFeatures;
 342       if (seqFeatures == null)
 343       {
 344         continue;
 345       }
 346
 347       for (SequenceFeature sf : seqFeatures)
 348       {
 349         if (displayedFeatures != null
 350                 && displayedFeatures.isVisible(sf.getType()))
 351         {
 352           SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
 353                   String.valueOf(seq.hashCode()));
 354
 355           String featureColour = (fr == null) ? null : jalview.util.Format
 356                   .getHexString(finder.findFeatureColour(Color.white, seq,
 357                           seq.findIndex(sf.getBegin())));
 358           jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
 359           jsonFeature.setXend(seq.findIndex(sf.getEnd()));
 360           jsonFeature.setType(sf.getType());
 361           jsonFeature.setDescription(sf.getDescription());
 362           jsonFeature.setLinks(sf.links);
 363           jsonFeature.setOtherDetails(sf.otherDetails);
 364           jsonFeature.setScore(sf.getScore());
 365           jsonFeature.setFillColor(featureColour);
 366           jsonFeature.setFeatureGroup(sf.getFeatureGroup());
 367           sequenceFeaturesPojo.add(jsonFeature);
 368         }
 369       }
 370     }
 371     return sequenceFeaturesPojo;
 372   }
 373
 374   public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
 375           Vector<AlignmentAnnotation> annotations)
 376   {
 377     List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
 378     if (annotations == null)
 379     {
 380       return jsonAnnotations;
 381     }
 382     for (AlignmentAnnotation annot : annotations)
 383     {
 384       AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
 385       alignAnnotPojo.setDescription(annot.description);
 386       alignAnnotPojo.setLabel(annot.label);
 387       if (!Double.isNaN(annot.score))
 388       {
 389         alignAnnotPojo.setScore(annot.score);
 390       }
 391       alignAnnotPojo.setCalcId(annot.getCalcId());
 392       alignAnnotPojo.setGraphType(annot.graph);
 393
 394       AnnotationDisplaySettingPojo annotSetting = new AnnotationDisplaySettingPojo();
 395       annotSetting.setBelowAlignment(annot.belowAlignment);
 396       annotSetting.setCentreColLabels(annot.centreColLabels);
 397       annotSetting.setScaleColLabel(annot.scaleColLabel);
 398       annotSetting.setShowAllColLabels(annot.showAllColLabels);
 399       annotSetting.setVisible(annot.visible);
 400       annotSetting.setHasIcon(annot.hasIcons);
 401       alignAnnotPojo.setAnnotationSettings(annotSetting);
 402       SequenceI refSeq = annot.sequenceRef;
 403       if (refSeq != null)
 404       {
 405         alignAnnotPojo.setSequenceRef(String.valueOf(refSeq.hashCode()));
 406       }
 407       for (Annotation annotation : annot.annotations)
 408       {
 409         AnnotationPojo annotationPojo = new AnnotationPojo();
 410         if (annotation != null)
 411         {
 412           annotationPojo.setDescription(annotation.description);
 413           annotationPojo.setValue(annotation.value);
 414           annotationPojo
 415                   .setSecondaryStructure(annotation.secondaryStructure);
 416           String displayChar = annotation.displayCharacter == null ? null
 417                   : annotation.displayCharacter;
 418           // System.out.println("--------------------->[" + displayChar + "]");
 419           annotationPojo.setDisplayCharacter(displayChar);
 420           if (annotation.colour != null)
 421           {
 422             annotationPojo.setColour(jalview.util.Format
 423                     .getHexString(annotation.colour));
 424           }
 425           alignAnnotPojo.getAnnotations().add(annotationPojo);
 426         }
 427         else
 428         {
 429           if (annot.getCalcId() != null
 430                   && annot.getCalcId().equalsIgnoreCase(TCOFFEE_SCORE))
 431           {
 432             // do nothing
 433           }
 434           else
 435           {
 436             alignAnnotPojo.getAnnotations().add(annotationPojo);
 437           }
 438         }
 439       }
 440       jsonAnnotations.add(alignAnnotPojo);
 441     }
 442     return jsonAnnotations;
 443   }
 444
 445   @SuppressWarnings("unchecked")
 446   public JSONFile parse(Reader jsonAlignmentString)
 447   {
 448     try
 449     {
 450       JSONParser jsonParser = new JSONParser();
 451       JSONObject alignmentJsonObj = (JSONObject) jsonParser
 452               .parse(jsonAlignmentString);
 453       JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
 454       JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
 455               .get("alignAnnotation");
 456       JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
 457               .get("seqFeatures");
 458       JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
 459               .get("seqGroups");
 460       JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
 461               .get("appSettings");
 462
 463       if (jvSettingsJsonObj != null)
 464       {
 465         globalColourScheme = (String) jvSettingsJsonObj
 466                 .get("globalColorScheme");
 467         Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
 468                 "showSeqFeatures").toString());
 469         setShowSeqFeatures(showFeatures);
 470         parseHiddenSeqRefsAsList(jvSettingsJsonObj);
 471         parseHiddenCols(jvSettingsJsonObj);
 472       }
 473
 474       hiddenSequences = new ArrayList<SequenceI>();
 475       seqMap = new Hashtable<String, Sequence>();
 476       for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
 477               .hasNext();)
 478       {
 479         JSONObject sequence = sequenceIter.next();
 480         String sequcenceString = sequence.get("seq").toString();
 481         String sequenceName = sequence.get("name").toString();
 482         String seqUniqueId = sequence.get("id").toString();
 483         int start = Integer.valueOf(sequence.get("start").toString());
 484         int end = Integer.valueOf(sequence.get("end").toString());
 485         Sequence seq = new Sequence(sequenceName, sequcenceString, start,
 486                 end);
 487         if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
 488         {
 489           hiddenSequences.add(seq);
 490         }
 491         seqs.add(seq);
 492         seqMap.put(seqUniqueId, seq);
 493       }
 494
 495       parseFeatures(jsonSeqArray);
 496
 497       for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
 498               .hasNext();)
 499       {
 500         JSONObject seqGrpObj = seqGrpIter.next();
 501         String grpName = seqGrpObj.get("groupName").toString();
 502         String colourScheme = seqGrpObj.get("colourScheme").toString();
 503         String description = (seqGrpObj.get("description") == null) ? null
 504                 : seqGrpObj.get("description").toString();
 505         boolean displayBoxes = Boolean.valueOf(seqGrpObj
 506                 .get("displayBoxes").toString());
 507         boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
 508                 .toString());
 509         boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
 510                 .toString());
 511         boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
 512                 "showNonconserved").toString());
 513         int startRes = Integer
 514                 .valueOf(seqGrpObj.get("startRes").toString());
 515         int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
 516         JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
 517
 518         ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
 519         if (sequenceRefs.size() > 0)
 520         {
 521           Iterator<String> seqHashIter = sequenceRefs.iterator();
 522           while (seqHashIter.hasNext())
 523           {
 524             String seqHash = seqHashIter.next();
 525             Sequence sequence = seqMap.get(seqHash);
 526             if (sequence != null)
 527             {
 528               grpSeqs.add(sequence);
 529             }
 530           }
 531         }
 532         SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
 533                 displayBoxes, displayText, colourText, startRes, endRes);
 534         seqGrp.setColourScheme(ColourSchemeMapper.getJalviewColourScheme(
 535                 colourScheme, seqGrp));
 536         seqGrp.setShowNonconserved(showNonconserved);
 537         seqGrp.setDescription(description);
 538         this.seqGroups.add(seqGrp);
 539
 540       }
 541
 542       for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
 543               .hasNext();)
 544       {
 545         JSONObject alAnnot = alAnnotIter.next();
 546         JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
 547         Annotation[] annotations = new Annotation[annotJsonArray.size()];
 548         int count = 0;
 549         for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
 550                 .hasNext();)
 551         {
 552           JSONObject annot = annotIter.next();
 553           if (annot == null)
 554           {
 555             annotations[count] = null;
 556           }
 557           else
 558           {
 559             float val = annot.get("value") == null ? null : Float
 560                     .valueOf(annot.get("value").toString());
 561             String desc = annot.get("description") == null ? null : annot
 562                     .get("description").toString();
 563             char ss = annot.get("secondaryStructure") == null
 564                     || annot.get("secondaryStructure").toString()
 565                             .equalsIgnoreCase("u0000") ? ' ' : annot
 566                     .get("secondaryStructure").toString().charAt(0);
 567             String displayChar = annot.get("displayCharacter") == null ? ""
 568                     : annot.get("displayCharacter").toString();
 569
 570             annotations[count] = new Annotation(displayChar, desc, ss, val);
 571             if (annot.get("colour") != null)
 572             {
 573               Color color = ColorUtils.parseColourString(annot.get(
 574                       "colour").toString());
 575               annotations[count].colour = color;
 576             }
 577           }
 578           ++count;
 579         }
 580
 581         AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
 582                 .get("label").toString(), alAnnot.get("description")
 583                 .toString(), annotations);
 584         alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0 : Integer
 585                 .valueOf(alAnnot.get("graphType").toString());
 586
 587         JSONObject diplaySettings = (JSONObject) alAnnot
 588                 .get("annotationSettings");
 589         if (diplaySettings != null)
 590         {
 591
 592           alignAnnot.scaleColLabel = (diplaySettings.get("scaleColLabel") == null) ? false
 593                   : Boolean.valueOf(diplaySettings.get("scaleColLabel")
 594                           .toString());
 595           alignAnnot.showAllColLabels = (diplaySettings
 596                   .get("showAllColLabels") == null) ? true : Boolean
 597                   .valueOf(diplaySettings.get("showAllColLabels")
 598                           .toString());
 599           alignAnnot.centreColLabels = (diplaySettings
 600                   .get("centreColLabels") == null) ? true
 601                   : Boolean.valueOf(diplaySettings.get("centreColLabels")
 602                           .toString());
 603           alignAnnot.belowAlignment = (diplaySettings.get("belowAlignment") == null) ? false
 604                   : Boolean.valueOf(diplaySettings.get("belowAlignment")
 605                           .toString());
 606           alignAnnot.visible = (diplaySettings.get("visible") == null) ? true
 607                   : Boolean.valueOf(diplaySettings.get("visible")
 608                           .toString());
 609           alignAnnot.hasIcons = (diplaySettings.get("hasIcon") == null) ? true
 610                   : Boolean.valueOf(diplaySettings.get("hasIcon")
 611                           .toString());
 612
 613         }
 614         if (alAnnot.get("score") != null)
 615         {
 616           alignAnnot.score = Double
 617                   .valueOf(alAnnot.get("score").toString());
 618         }
 619
 620         String calcId = (alAnnot.get("calcId") == null) ? "" : alAnnot.get(
 621                 "calcId").toString();
 622         alignAnnot.setCalcId(calcId);
 623         String seqHash = (alAnnot.get("sequenceRef") != null) ? alAnnot
 624                 .get("sequenceRef").toString() : null;
 625
 626         Sequence sequence = (seqHash != null) ? seqMap.get(seqHash) : null;
 627         if (sequence != null)
 628         {
 629           alignAnnot.sequenceRef = sequence;
 630           sequence.addAlignmentAnnotation(alignAnnot);
 631           if (alignAnnot.label.equalsIgnoreCase("T-COFFEE"))
 632           {
 633             alignAnnot.createSequenceMapping(sequence, sequence.getStart(),
 634                     false);
 635             sequence.addAlignmentAnnotation(alignAnnot);
 636             alignAnnot.adjustForAlignment();
 637           }
 638         }
 639         alignAnnot.validateRangeAndDisplay();
 640         this.annotations.add(alignAnnot);
 641
 642       }
 643     } catch (Exception e)
 644     {
 645       e.printStackTrace();
 646     }
 647     return this;
 648   }
 649
 650   public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
 651   {
 652     hiddenSeqRefs = new ArrayList<String>();
 653     String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
 654     if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
 655     {
 656       String[] seqRefs = hiddenSeqs.split(";");
 657       for (String seqRef : seqRefs)
 658       {
 659         hiddenSeqRefs.add(seqRef);
 660       }
 661     }
 662   }
 663
 664   public void parseHiddenCols(JSONObject jvSettingsJson)
 665   {
 666     String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
 667     if (hiddenCols != null && !hiddenCols.isEmpty())
 668     {
 669       columnSelection = new ColumnSelection();
 670       String[] rangeStrings = hiddenCols.split(";");
 671       for (String rangeString : rangeStrings)
 672       {
 673         String[] range = rangeString.split("-");
 674         columnSelection.hideColumns(Integer.valueOf(range[0]),
 675                 Integer.valueOf(range[1]));
 676       }
 677     }
 678   }
 679
 680   @SuppressWarnings("unchecked")
 681   private void parseFeatures(JSONArray jsonSeqFeatures)
 682   {
 683     if (jsonSeqFeatures != null)
 684     {
 685       displayedFeatures = new FeaturesDisplayed();
 686       for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
 687               .hasNext();)
 688       {
 689         JSONObject jsonFeature = seqFeatureItr.next();
 690         Long begin = (Long) jsonFeature.get("xStart");
 691         Long end = (Long) jsonFeature.get("xEnd");
 692         String type = (String) jsonFeature.get("type");
 693         String featureGrp = (String) jsonFeature.get("featureGroup");
 694         String descripiton = (String) jsonFeature.get("description");
 695         String seqRef = (String) jsonFeature.get("sequenceRef");
 696         Float score = Float.valueOf(jsonFeature.get("score").toString());
 697
 698         Sequence seq = seqMap.get(seqRef);
 699         SequenceFeature sequenceFeature = new SequenceFeature();
 700         JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
 701         if (linksJsonArray != null && linksJsonArray.size() > 0)
 702         {
 703           Iterator<String> linkList = linksJsonArray.iterator();
 704           while (linkList.hasNext())
 705           {
 706             String link = linkList.next();
 707             sequenceFeature.addLink(link);
 708           }
 709         }
 710         sequenceFeature.setFeatureGroup(featureGrp);
 711         sequenceFeature.setScore(score);
 712         sequenceFeature.setDescription(descripiton);
 713         sequenceFeature.setType(type);
 714         sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
 715         sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
 716         seq.addSequenceFeature(sequenceFeature);
 717         displayedFeatures.setVisible(type);
 718       }
 719     }
 720   }
 721
 722   @Override
 723   public String getGlobalColourScheme()
 724   {
 725     return globalColourScheme;
 726   }
 727
 728   public void setGlobalColorScheme(String globalColourScheme)
 729   {
 730     this.globalColourScheme = globalColourScheme;
 731   }
 732
 733   @Override
 734   public FeaturesDisplayedI getDisplayedFeatures()
 735   {
 736     return displayedFeatures;
 737   }
 738
 739   public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
 740   {
 741     this.displayedFeatures = displayedFeatures;
 742   }
 743
 744   @Override
 745   public void configureForView(AlignmentViewPanel avpanel)
 746   {
 747     if (avpanel == null)
 748     {
 749       return;
 750     }
 751     super.configureForView(avpanel);
 752     AlignViewportI viewport = avpanel.getAlignViewport();
 753     AlignmentI alignment = viewport.getAlignment();
 754     AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
 755
 756     seqGroups = alignment.getGroups();
 757     fr = avpanel.cloneFeatureRenderer();
 758
 759     // Add non auto calculated annotation to AlignFile
 760     if (annots != null)
 761     {
 762       for (AlignmentAnnotation annot : annots)
 763       {
 764         if (annot != null && !annot.autoCalculated)
 765         {
 766           annotations.add(annot);
 767         }
 768       }
 769     }
 770     globalColourScheme = (viewport.getGlobalColourScheme() == null) ? ResidueColourScheme.NONE
 771             : viewport.getGlobalColourScheme().getSchemeName();
 772     setDisplayedFeatures(viewport.getFeaturesDisplayed());
 773     showSeqFeatures = viewport.isShowSequenceFeatures();
 774
 775   }
 776
 777   @Override
 778   public boolean isShowSeqFeatures()
 779   {
 780     return showSeqFeatures;
 781   }
 782
 783   public void setShowSeqFeatures(boolean showSeqFeatures)
 784   {
 785     this.showSeqFeatures = showSeqFeatures;
 786   }
 787
 788   public Vector<AlignmentAnnotation> getAnnotations()
 789   {
 790     return annotations;
 791   }
 792
 793   public List<int[]> getHiddenColumns()
 794   {
 795     return hiddenColumns;
 796   }
 797
 798   @Override
 799   public ColumnSelection getColumnSelection()
 800   {
 801     return columnSelection;
 802   }
 803
 804   public void setColumnSelection(ColumnSelection columnSelection)
 805   {
 806     this.columnSelection = columnSelection;
 807   }
 808
 809   @Override
 810   public SequenceI[] getHiddenSequences()
 811   {
 812     if (hiddenSequences == null || hiddenSequences.isEmpty())
 813     {
 814       return new SequenceI[] {};
 815     }
 816     synchronized (hiddenSequences)
 817     {
 818       return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
 819     }
 820   }
 821
 822   public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
 823   {
 824     this.hiddenSequences = hiddenSequences;
 825   }
 826
 827   public class JSONExportSettings
 828   {
 829     private boolean exportSequence;
 830
 831     private boolean exportSequenceFeatures;
 832
 833     private boolean exportAnnotations;
 834
 835     private boolean exportGroups;
 836
 837     private boolean exportJalviewSettings;
 838
 839     public boolean isExportSequence()
 840     {
 841       return exportSequence;
 842     }
 843
 844     public void setExportSequence(boolean exportSequence)
 845     {
 846       this.exportSequence = exportSequence;
 847     }
 848
 849     public boolean isExportSequenceFeatures()
 850     {
 851       return exportSequenceFeatures;
 852     }
 853
 854     public void setExportSequenceFeatures(boolean exportSequenceFeatures)
 855     {
 856       this.exportSequenceFeatures = exportSequenceFeatures;
 857     }
 858
 859     public boolean isExportAnnotations()
 860     {
 861       return exportAnnotations;
 862     }
 863
 864     public void setExportAnnotations(boolean exportAnnotations)
 865     {
 866       this.exportAnnotations = exportAnnotations;
 867     }
 868
 869     public boolean isExportGroups()
 870     {
 871       return exportGroups;
 872     }
 873
 874     public void setExportGroups(boolean exportGroups)
 875     {
 876       this.exportGroups = exportGroups;
 877     }
 878
 879     public boolean isExportJalviewSettings()
 880     {
 881       return exportJalviewSettings;
 882     }
 883
 884     public void setExportJalviewSettings(boolean exportJalviewSettings)
 885     {
 886       this.exportJalviewSettings = exportJalviewSettings;
 887     }
 888   }
 889
 890   /**
 891    * Returns a descriptor for suitable feature display settings with
 892    * <ul>
 893    * <li>ResNums or insertions features visible</li>
 894    * <li>insertions features coloured red</li>
 895    * <li>ResNum features coloured by label</li>
 896    * <li>Insertions displayed above (on top of) ResNums</li>
 897    * </ul>
 898    */
 899   @Override
 900   public FeatureSettingsModelI getFeatureColourScheme()
 901   {
 902     return new PDBFeatureSettings();
 903   }
 904 }