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