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 = "https://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.equalsIgnoreCase(
 223                         JalviewColourScheme.TCoffee.toString()))
 224         {
 225           jsonAlignmentPojo.setGlobalColorScheme(ResidueColourScheme.NONE);
 226         }
 227       }
 228
 229       if (exportSettings.isExportFeatures())
 230       {
 231         jsonAlignmentPojo.setSeqFeatures(sequenceFeatureToJsonPojo(sqs));
 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.getColourScheme()));
 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       hiddenSections[0] = getViewport().getAlignment().getHiddenColumns()
 282               .regionsToString(";", "-");
 283     }
 284
 285     // hidden rows/seqs business
 286     HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
 287             .getHiddenSequences();
 288     if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
 289     {
 290       return hiddenSections;
 291     }
 292
 293     SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
 294     StringBuilder hiddenSeqsBuilder = new StringBuilder();
 295     for (SequenceI hiddenSeq : hiddenSeqs)
 296     {
 297       if (hiddenSeq != null)
 298       {
 299         hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
 300       }
 301     }
 302     if (hiddenSeqsBuilder.length() > 0)
 303     {
 304       hiddenSeqsBuilder.deleteCharAt(0);
 305     }
 306     hiddenSections[1] = hiddenSeqsBuilder.toString();
 307
 308     return hiddenSections;
 309   }
 310
 311   protected List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
 312           SequenceI[] sqs)
 313   {
 314     displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
 315     List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<>();
 316     if (sqs == null)
 317     {
 318       return sequenceFeaturesPojo;
 319     }
 320
 321     FeatureColourFinder finder = new FeatureColourFinder(fr);
 322
 323     String[] visibleFeatureTypes = displayedFeatures == null ? null
 324             : displayedFeatures.getVisibleFeatures().toArray(
 325                     new String[displayedFeatures.getVisibleFeatureCount()]);
 326
 327     for (SequenceI seq : sqs)
 328     {
 329       /*
 330        * get all features currently visible (and any non-positional features)
 331        */
 332       List<SequenceFeature> seqFeatures = seq.getFeatures().getAllFeatures(
 333               visibleFeatureTypes);
 334       for (SequenceFeature sf : seqFeatures)
 335       {
 336         SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
 337                 String.valueOf(seq.hashCode()));
 338
 339         String featureColour = (fr == null) ? null : Format
 340                 .getHexString(finder.findFeatureColour(Color.white, seq,
 341                         seq.findIndex(sf.getBegin())));
 342         int xStart = sf.getBegin() == 0 ? 0
 343                 : seq.findIndex(sf.getBegin()) - 1;
 344         int xEnd = sf.getEnd() == 0 ? 0 : seq.findIndex(sf.getEnd());
 345         jsonFeature.setXstart(xStart);
 346         jsonFeature.setXend(xEnd);
 347         jsonFeature.setType(sf.getType());
 348         jsonFeature.setDescription(sf.getDescription());
 349         jsonFeature.setLinks(sf.links);
 350         jsonFeature.setOtherDetails(sf.otherDetails);
 351         jsonFeature.setScore(sf.getScore());
 352         jsonFeature.setFillColor(featureColour);
 353         jsonFeature.setFeatureGroup(sf.getFeatureGroup());
 354         sequenceFeaturesPojo.add(jsonFeature);
 355       }
 356     }
 357     return sequenceFeaturesPojo;
 358   }
 359
 360   public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
 361           Vector<AlignmentAnnotation> annotations)
 362   {
 363     List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<>();
 364     if (annotations == null)
 365     {
 366       return jsonAnnotations;
 367     }
 368     for (AlignmentAnnotation annot : annotations)
 369     {
 370       AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
 371       alignAnnotPojo.setDescription(annot.description);
 372       alignAnnotPojo.setLabel(annot.label);
 373       if (!Double.isNaN(annot.score))
 374       {
 375         alignAnnotPojo.setScore(annot.score);
 376       }
 377       alignAnnotPojo.setCalcId(annot.getCalcId());
 378       alignAnnotPojo.setGraphType(annot.graph);
 379
 380       AnnotationDisplaySettingPojo annotSetting = new AnnotationDisplaySettingPojo();
 381       annotSetting.setBelowAlignment(annot.belowAlignment);
 382       annotSetting.setCentreColLabels(annot.centreColLabels);
 383       annotSetting.setScaleColLabel(annot.scaleColLabel);
 384       annotSetting.setShowAllColLabels(annot.showAllColLabels);
 385       annotSetting.setVisible(annot.visible);
 386       annotSetting.setHasIcon(annot.hasIcons);
 387       alignAnnotPojo.setAnnotationSettings(annotSetting);
 388       SequenceI refSeq = annot.sequenceRef;
 389       if (refSeq != null)
 390       {
 391         alignAnnotPojo.setSequenceRef(String.valueOf(refSeq.hashCode()));
 392       }
 393       for (Annotation annotation : annot.annotations)
 394       {
 395         AnnotationPojo annotationPojo = new AnnotationPojo();
 396         if (annotation != null)
 397         {
 398           annotationPojo.setDescription(annotation.description);
 399           annotationPojo.setValue(annotation.value);
 400           annotationPojo
 401                   .setSecondaryStructure(annotation.secondaryStructure);
 402           String displayChar = annotation.displayCharacter == null ? null
 403                   : annotation.displayCharacter;
 404           // System.out.println("--------------------->[" + displayChar + "]");
 405           annotationPojo.setDisplayCharacter(displayChar);
 406           if (annotation.colour != null)
 407           {
 408             annotationPojo.setColour(
 409                     jalview.util.Format.getHexString(annotation.colour));
 410           }
 411           alignAnnotPojo.getAnnotations().add(annotationPojo);
 412         }
 413         else
 414         {
 415           if (annot.getCalcId() != null
 416                   && annot.getCalcId().equalsIgnoreCase(TCOFFEE_SCORE))
 417           {
 418             // do nothing
 419           }
 420           else
 421           {
 422             alignAnnotPojo.getAnnotations().add(annotationPojo);
 423           }
 424         }
 425       }
 426       jsonAnnotations.add(alignAnnotPojo);
 427     }
 428     return jsonAnnotations;
 429   }
 430
 431   @SuppressWarnings("unchecked")
 432   public JSONFile parse(Reader jsonAlignmentString)
 433   {
 434     try
 435     {
 436       JSONParser jsonParser = new JSONParser();
 437       JSONObject alignmentJsonObj = (JSONObject) jsonParser
 438               .parse(jsonAlignmentString);
 439       JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
 440       JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
 441               .get("alignAnnotation");
 442       JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
 443               .get("seqFeatures");
 444       JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
 445               .get("seqGroups");
 446       JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
 447               .get("appSettings");
 448
 449       if (jvSettingsJsonObj != null)
 450       {
 451         globalColourScheme = (String) jvSettingsJsonObj
 452                 .get("globalColorScheme");
 453         Boolean showFeatures = Boolean.valueOf(
 454                 jvSettingsJsonObj.get("showSeqFeatures").toString());
 455         setShowSeqFeatures(showFeatures);
 456         parseHiddenSeqRefsAsList(jvSettingsJsonObj);
 457         parseHiddenCols(jvSettingsJsonObj);
 458       }
 459
 460       hiddenSequences = new ArrayList<>();
 461       seqMap = new Hashtable<>();
 462       for (Iterator<JSONObject> sequenceIter = seqJsonArray
 463               .iterator(); sequenceIter.hasNext();)
 464       {
 465         JSONObject sequence = sequenceIter.next();
 466         String sequcenceString = sequence.get("seq").toString();
 467         String sequenceName = sequence.get("name").toString();
 468         String seqUniqueId = sequence.get("id").toString();
 469         int start = Integer.valueOf(sequence.get("start").toString());
 470         int end = Integer.valueOf(sequence.get("end").toString());
 471         Sequence seq = new Sequence(sequenceName, sequcenceString, start,
 472                 end);
 473         if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
 474         {
 475           hiddenSequences.add(seq);
 476         }
 477         seqs.add(seq);
 478         seqMap.put(seqUniqueId, seq);
 479       }
 480
 481       parseFeatures(jsonSeqArray);
 482
 483       for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray
 484               .iterator(); seqGrpIter.hasNext();)
 485       {
 486         JSONObject seqGrpObj = seqGrpIter.next();
 487         String grpName = seqGrpObj.get("groupName").toString();
 488         String colourScheme = seqGrpObj.get("colourScheme").toString();
 489         String description = (seqGrpObj.get("description") == null) ? null
 490                 : seqGrpObj.get("description").toString();
 491         boolean displayBoxes = Boolean
 492                 .valueOf(seqGrpObj.get("displayBoxes").toString());
 493         boolean displayText = Boolean
 494                 .valueOf(seqGrpObj.get("displayText").toString());
 495         boolean colourText = Boolean
 496                 .valueOf(seqGrpObj.get("colourText").toString());
 497         boolean showNonconserved = Boolean
 498                 .valueOf(seqGrpObj.get("showNonconserved").toString());
 499         int startRes = Integer
 500                 .valueOf(seqGrpObj.get("startRes").toString());
 501         int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
 502         JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
 503
 504         ArrayList<SequenceI> grpSeqs = new ArrayList<>();
 505         if (sequenceRefs.size() > 0)
 506         {
 507           Iterator<String> seqHashIter = sequenceRefs.iterator();
 508           while (seqHashIter.hasNext())
 509           {
 510             String seqHash = seqHashIter.next();
 511             Sequence sequence = seqMap.get(seqHash);
 512             if (sequence != null)
 513             {
 514               grpSeqs.add(sequence);
 515             }
 516           }
 517         }
 518         SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
 519                 displayBoxes, displayText, colourText, startRes, endRes);
 520         seqGrp.setColourScheme(ColourSchemeMapper
 521                 .getJalviewColourScheme(colourScheme, seqGrp));
 522         seqGrp.setShowNonconserved(showNonconserved);
 523         seqGrp.setDescription(description);
 524         this.seqGroups.add(seqGrp);
 525
 526       }
 527
 528       for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray
 529               .iterator(); alAnnotIter.hasNext();)
 530       {
 531         JSONObject alAnnot = alAnnotIter.next();
 532         JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
 533         Annotation[] annotations = new Annotation[annotJsonArray.size()];
 534         int count = 0;
 535         for (Iterator<JSONObject> annotIter = annotJsonArray
 536                 .iterator(); annotIter.hasNext();)
 537         {
 538           JSONObject annot = annotIter.next();
 539           if (annot == null)
 540           {
 541             annotations[count] = null;
 542           }
 543           else
 544           {
 545             float val = annot.get("value") == null ? null
 546                     : Float.valueOf(annot.get("value").toString());
 547             String desc = annot.get("description") == null ? null
 548                     : annot.get("description").toString();
 549             char ss = annot.get("secondaryStructure") == null
 550                     || annot.get("secondaryStructure").toString()
 551                             .equalsIgnoreCase("u0000") ? ' '
 552                                     : annot.get("secondaryStructure")
 553                                             .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
 561                       .parseColourString(annot.get("colour").toString());
 562               annotations[count].colour = color;
 563             }
 564           }
 565           ++count;
 566         }
 567
 568         AlignmentAnnotation alignAnnot = new AlignmentAnnotation(
 569                 alAnnot.get("label").toString(),
 570                 alAnnot.get("description").toString(), annotations);
 571         alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0
 572                 : Integer.valueOf(alAnnot.get("graphType").toString());
 573
 574         JSONObject diplaySettings = (JSONObject) alAnnot
 575                 .get("annotationSettings");
 576         if (diplaySettings != null)
 577         {
 578
 579           alignAnnot.scaleColLabel = (diplaySettings
 580                   .get("scaleColLabel") == null) ? false
 581                           : Boolean.valueOf(diplaySettings
 582                                   .get("scaleColLabel").toString());
 583           alignAnnot.showAllColLabels = (diplaySettings
 584                   .get("showAllColLabels") == null) ? true
 585                           : Boolean.valueOf(diplaySettings
 586                                   .get("showAllColLabels").toString());
 587           alignAnnot.centreColLabels = (diplaySettings
 588                   .get("centreColLabels") == null) ? true
 589                           : Boolean.valueOf(diplaySettings
 590                                   .get("centreColLabels").toString());
 591           alignAnnot.belowAlignment = (diplaySettings
 592                   .get("belowAlignment") == null) ? false
 593                           : Boolean.valueOf(diplaySettings
 594                                   .get("belowAlignment").toString());
 595           alignAnnot.visible = (diplaySettings.get("visible") == null)
 596                   ? true
 597                   : Boolean.valueOf(
 598                           diplaySettings.get("visible").toString());
 599           alignAnnot.hasIcons = (diplaySettings.get("hasIcon") == null)
 600                   ? true
 601                   : Boolean.valueOf(
 602                           diplaySettings.get("hasIcon").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) ? ""
 612                 : alAnnot.get("calcId").toString();
 613         alignAnnot.setCalcId(calcId);
 614         String seqHash = (alAnnot.get("sequenceRef") != null)
 615                 ? alAnnot.get("sequenceRef").toString()
 616                 : null;
 617
 618         Sequence sequence = (seqHash != null) ? seqMap.get(seqHash) : null;
 619         if (sequence != null)
 620         {
 621           alignAnnot.sequenceRef = sequence;
 622           sequence.addAlignmentAnnotation(alignAnnot);
 623           if (alignAnnot.label.equalsIgnoreCase("T-COFFEE"))
 624           {
 625             alignAnnot.createSequenceMapping(sequence, sequence.getStart(),
 626                     false);
 627             sequence.addAlignmentAnnotation(alignAnnot);
 628             alignAnnot.adjustForAlignment();
 629           }
 630         }
 631         alignAnnot.validateRangeAndDisplay();
 632         this.annotations.add(alignAnnot);
 633
 634       }
 635     } catch (Exception e)
 636     {
 637       e.printStackTrace();
 638     }
 639     return this;
 640   }
 641
 642   public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
 643   {
 644     hiddenSeqRefs = new ArrayList<>();
 645     String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
 646     if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
 647     {
 648       String[] seqRefs = hiddenSeqs.split(";");
 649       for (String seqRef : seqRefs)
 650       {
 651         hiddenSeqRefs.add(seqRef);
 652       }
 653     }
 654   }
 655
 656   public void parseHiddenCols(JSONObject jvSettingsJson)
 657   {
 658     String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
 659     if (hiddenCols != null && !hiddenCols.isEmpty())
 660     {
 661       hiddenColumns = new HiddenColumns();
 662       String[] rangeStrings = hiddenCols.split(";");
 663       for (String rangeString : rangeStrings)
 664       {
 665         String[] range = rangeString.split("-");
 666         hiddenColumns.hideColumns(Integer.valueOf(range[0]),
 667                 Integer.valueOf(range[1]));
 668       }
 669     }
 670   }
 671
 672   @SuppressWarnings("unchecked")
 673   private void parseFeatures(JSONArray jsonSeqFeatures)
 674   {
 675     if (jsonSeqFeatures != null)
 676     {
 677       displayedFeatures = new FeaturesDisplayed();
 678       for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures
 679               .iterator(); seqFeatureItr.hasNext();)
 680       {
 681         JSONObject jsonFeature = seqFeatureItr.next();
 682         Long begin = (Long) jsonFeature.get("xStart");
 683         Long end = (Long) jsonFeature.get("xEnd");
 684         String type = (String) jsonFeature.get("type");
 685         String featureGrp = (String) jsonFeature.get("featureGroup");
 686         String description = (String) jsonFeature.get("description");
 687         String seqRef = (String) jsonFeature.get("sequenceRef");
 688         Float score = Float.valueOf(jsonFeature.get("score").toString());
 689
 690         Sequence seq = seqMap.get(seqRef);
 691
 692         /*
 693          * begin/end of 0 is for a non-positional feature
 694          */
 695         int featureBegin = begin.intValue() == 0 ? 0 : seq
 696                 .findPosition(begin.intValue());
 697         int featureEnd = end.intValue() == 0 ? 0 : seq.findPosition(end
 698                 .intValue()) - 1;
 699
 700         SequenceFeature sequenceFeature = new SequenceFeature(type,
 701                 description, featureBegin, featureEnd, score, featureGrp);
 702
 703         JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
 704         if (linksJsonArray != null && linksJsonArray.size() > 0)
 705         {
 706           Iterator<String> linkList = linksJsonArray.iterator();
 707           while (linkList.hasNext())
 708           {
 709             String link = linkList.next();
 710             sequenceFeature.addLink(link);
 711           }
 712         }
 713
 714         seq.addSequenceFeature(sequenceFeature);
 715         displayedFeatures.setVisible(type);
 716       }
 717     }
 718   }
 719
 720   @Override
 721   public String getGlobalColourScheme()
 722   {
 723     return globalColourScheme;
 724   }
 725
 726   public void setGlobalColorScheme(String globalColourScheme)
 727   {
 728     this.globalColourScheme = globalColourScheme;
 729   }
 730
 731   @Override
 732   public FeaturesDisplayedI getDisplayedFeatures()
 733   {
 734     return displayedFeatures;
 735   }
 736
 737   public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
 738   {
 739     this.displayedFeatures = displayedFeatures;
 740   }
 741
 742   @Override
 743   public void configureForView(AlignmentViewPanel avpanel)
 744   {
 745     if (avpanel == null)
 746     {
 747       return;
 748     }
 749     super.configureForView(avpanel);
 750     AlignViewportI viewport = avpanel.getAlignViewport();
 751     AlignmentI alignment = viewport.getAlignment();
 752     AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
 753
 754     seqGroups = alignment.getGroups();
 755     fr = avpanel.cloneFeatureRenderer();
 756
 757     // Add non auto calculated annotation to AlignFile
 758     if (annots != null)
 759     {
 760       for (AlignmentAnnotation annot : annots)
 761       {
 762         if (annot != null && !annot.autoCalculated)
 763         {
 764           annotations.add(annot);
 765         }
 766       }
 767     }
 768     globalColourScheme = ColourSchemeProperty
 769             .getColourName(viewport.getGlobalColourScheme());
 770     setDisplayedFeatures(viewport.getFeaturesDisplayed());
 771     showSeqFeatures = viewport.isShowSequenceFeatures();
 772
 773   }
 774
 775   @Override
 776   public boolean isShowSeqFeatures()
 777   {
 778     return showSeqFeatures;
 779   }
 780
 781   public void setShowSeqFeatures(boolean showSeqFeatures)
 782   {
 783     this.showSeqFeatures = showSeqFeatures;
 784   }
 785
 786   public Vector<AlignmentAnnotation> getAnnotations()
 787   {
 788     return annotations;
 789   }
 790
 791   @Override
 792   public HiddenColumns getHiddenColumns()
 793   {
 794     return hiddenColumns;
 795   }
 796
 797   public void setHiddenColumns(HiddenColumns hidden)
 798   {
 799     this.hiddenColumns = hidden;
 800   }
 801
 802   @Override
 803   public SequenceI[] getHiddenSequences()
 804   {
 805     if (hiddenSequences == null || hiddenSequences.isEmpty())
 806     {
 807       return new SequenceI[] {};
 808     }
 809     synchronized (hiddenSequences)
 810     {
 811       return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
 812     }
 813   }
 814
 815   public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
 816   {
 817     this.hiddenSequences = hiddenSequences;
 818   }
 819
 820   public class JSONExportSettings
 821   {
 822     private boolean exportSequence;
 823
 824     private boolean exportSequenceFeatures;
 825
 826     private boolean exportAnnotations;
 827
 828     private boolean exportGroups;
 829
 830     private boolean exportJalviewSettings;
 831
 832     public boolean isExportSequence()
 833     {
 834       return exportSequence;
 835     }
 836
 837     public void setExportSequence(boolean exportSequence)
 838     {
 839       this.exportSequence = exportSequence;
 840     }
 841
 842     public boolean isExportSequenceFeatures()
 843     {
 844       return exportSequenceFeatures;
 845     }
 846
 847     public void setExportSequenceFeatures(boolean exportSequenceFeatures)
 848     {
 849       this.exportSequenceFeatures = exportSequenceFeatures;
 850     }
 851
 852     public boolean isExportAnnotations()
 853     {
 854       return exportAnnotations;
 855     }
 856
 857     public void setExportAnnotations(boolean exportAnnotations)
 858     {
 859       this.exportAnnotations = exportAnnotations;
 860     }
 861
 862     public boolean isExportGroups()
 863     {
 864       return exportGroups;
 865     }
 866
 867     public void setExportGroups(boolean exportGroups)
 868     {
 869       this.exportGroups = exportGroups;
 870     }
 871
 872     public boolean isExportJalviewSettings()
 873     {
 874       return exportJalviewSettings;
 875     }
 876
 877     public void setExportJalviewSettings(boolean exportJalviewSettings)
 878     {
 879       this.exportJalviewSettings = exportJalviewSettings;
 880     }
 881   }
 882
 883   /**
 884    * Returns a descriptor for suitable feature display settings with
 885    * <ul>
 886    * <li>ResNums or insertions features visible</li>
 887    * <li>insertions features coloured red</li>
 888    * <li>ResNum features coloured by label</li>
 889    * <li>Insertions displayed above (on top of) ResNums</li>
 890    * </ul>
 891    */
 892   @Override
 893   public FeatureSettingsModelI getFeatureColourScheme()
 894   {
 895     return new PDBFeatureSettings();
 896   }
 897 }