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.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[]> hiddenColumnsList;
  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
 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().getAlignment()
 284               .getHiddenColumns()
 285               .getListOfCols();
 286       StringBuilder hiddenColsBuilder = new StringBuilder();
 287       for (int[] range : hiddenCols)
 288       {
 289         hiddenColsBuilder.append(";").append(range[0]).append("-")
 290                 .append(range[1]);
 291       }
 292
 293       hiddenColsBuilder.deleteCharAt(0);
 294       hiddenSections[0] = hiddenColsBuilder.toString();
 295     }
 296
 297     // hidden rows/seqs business
 298     HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
 299             .getHiddenSequences();
 300     if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
 301     {
 302       return hiddenSections;
 303     }
 304
 305     SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
 306     StringBuilder hiddenSeqsBuilder = new StringBuilder();
 307     for (SequenceI hiddenSeq : hiddenSeqs)
 308     {
 309       if (hiddenSeq != null)
 310       {
 311         hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
 312       }
 313     }
 314     if (hiddenSeqsBuilder.length() > 0)
 315     {
 316       hiddenSeqsBuilder.deleteCharAt(0);
 317     }
 318     hiddenSections[1] = hiddenSeqsBuilder.toString();
 319
 320     return hiddenSections;
 321   }
 322
 323   public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
 324           SequenceI[] sqs, FeatureRenderer fr)
 325   {
 326     displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
 327     List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
 328     if (sqs == null)
 329     {
 330       return sequenceFeaturesPojo;
 331     }
 332
 333     FeatureColourFinder finder = new FeatureColourFinder(fr);
 334
 335     for (SequenceI seq : sqs)
 336     {
 337       SequenceI dataSetSequence = seq.getDatasetSequence();
 338       SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
 339               : seq.getDatasetSequence().getSequenceFeatures();
 340
 341       seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
 342               : seqFeatures;
 343       if (seqFeatures == null)
 344       {
 345         continue;
 346       }
 347
 348       for (SequenceFeature sf : seqFeatures)
 349       {
 350         if (displayedFeatures != null
 351                 && displayedFeatures.isVisible(sf.getType()))
 352         {
 353           SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
 354                   String.valueOf(seq.hashCode()));
 355
 356           String featureColour = (fr == null) ? null : jalview.util.Format
 357                   .getHexString(finder.findFeatureColour(Color.white, seq,
 358                           seq.findIndex(sf.getBegin())));
 359           jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
 360           jsonFeature.setXend(seq.findIndex(sf.getEnd()));
 361           jsonFeature.setType(sf.getType());
 362           jsonFeature.setDescription(sf.getDescription());
 363           jsonFeature.setLinks(sf.links);
 364           jsonFeature.setOtherDetails(sf.otherDetails);
 365           jsonFeature.setScore(sf.getScore());
 366           jsonFeature.setFillColor(featureColour);
 367           jsonFeature.setFeatureGroup(sf.getFeatureGroup());
 368           sequenceFeaturesPojo.add(jsonFeature);
 369         }
 370       }
 371     }
 372     return sequenceFeaturesPojo;
 373   }
 374
 375   public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
 376           Vector<AlignmentAnnotation> annotations)
 377   {
 378     List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
 379     if (annotations == null)
 380     {
 381       return jsonAnnotations;
 382     }
 383     for (AlignmentAnnotation annot : annotations)
 384     {
 385       AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
 386       alignAnnotPojo.setDescription(annot.description);
 387       alignAnnotPojo.setLabel(annot.label);
 388       if (!Double.isNaN(annot.score))
 389       {
 390         alignAnnotPojo.setScore(annot.score);
 391       }
 392       alignAnnotPojo.setCalcId(annot.getCalcId());
 393       alignAnnotPojo.setGraphType(annot.graph);
 394
 395       AnnotationDisplaySettingPojo annotSetting = new AnnotationDisplaySettingPojo();
 396       annotSetting.setBelowAlignment(annot.belowAlignment);
 397       annotSetting.setCentreColLabels(annot.centreColLabels);
 398       annotSetting.setScaleColLabel(annot.scaleColLabel);
 399       annotSetting.setShowAllColLabels(annot.showAllColLabels);
 400       annotSetting.setVisible(annot.visible);
 401       annotSetting.setHasIcon(annot.hasIcons);
 402       alignAnnotPojo.setAnnotationSettings(annotSetting);
 403       SequenceI refSeq = annot.sequenceRef;
 404       if (refSeq != null)
 405       {
 406         alignAnnotPojo.setSequenceRef(String.valueOf(refSeq.hashCode()));
 407       }
 408       for (Annotation annotation : annot.annotations)
 409       {
 410         AnnotationPojo annotationPojo = new AnnotationPojo();
 411         if (annotation != null)
 412         {
 413           annotationPojo.setDescription(annotation.description);
 414           annotationPojo.setValue(annotation.value);
 415           annotationPojo
 416                   .setSecondaryStructure(annotation.secondaryStructure);
 417           String displayChar = annotation.displayCharacter == null ? null
 418                   : annotation.displayCharacter;
 419           // System.out.println("--------------------->[" + displayChar + "]");
 420           annotationPojo.setDisplayCharacter(displayChar);
 421           if (annotation.colour != null)
 422           {
 423             annotationPojo.setColour(jalview.util.Format
 424                     .getHexString(annotation.colour));
 425           }
 426           alignAnnotPojo.getAnnotations().add(annotationPojo);
 427         }
 428         else
 429         {
 430           if (annot.getCalcId() != null
 431                   && annot.getCalcId().equalsIgnoreCase(TCOFFEE_SCORE))
 432           {
 433             // do nothing
 434           }
 435           else
 436           {
 437             alignAnnotPojo.getAnnotations().add(annotationPojo);
 438           }
 439         }
 440       }
 441       jsonAnnotations.add(alignAnnotPojo);
 442     }
 443     return jsonAnnotations;
 444   }
 445
 446   @SuppressWarnings("unchecked")
 447   public JSONFile parse(Reader jsonAlignmentString)
 448   {
 449     try
 450     {
 451       JSONParser jsonParser = new JSONParser();
 452       JSONObject alignmentJsonObj = (JSONObject) jsonParser
 453               .parse(jsonAlignmentString);
 454       JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
 455       JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
 456               .get("alignAnnotation");
 457       JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
 458               .get("seqFeatures");
 459       JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
 460               .get("seqGroups");
 461       JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
 462               .get("appSettings");
 463
 464       if (jvSettingsJsonObj != null)
 465       {
 466         globalColourScheme = (String) jvSettingsJsonObj
 467                 .get("globalColorScheme");
 468         Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
 469                 "showSeqFeatures").toString());
 470         setShowSeqFeatures(showFeatures);
 471         parseHiddenSeqRefsAsList(jvSettingsJsonObj);
 472         parseHiddenCols(jvSettingsJsonObj);
 473       }
 474
 475       hiddenSequences = new ArrayList<SequenceI>();
 476       seqMap = new Hashtable<String, Sequence>();
 477       for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
 478               .hasNext();)
 479       {
 480         JSONObject sequence = sequenceIter.next();
 481         String sequcenceString = sequence.get("seq").toString();
 482         String sequenceName = sequence.get("name").toString();
 483         String seqUniqueId = sequence.get("id").toString();
 484         int start = Integer.valueOf(sequence.get("start").toString());
 485         int end = Integer.valueOf(sequence.get("end").toString());
 486         Sequence seq = new Sequence(sequenceName, sequcenceString, start,
 487                 end);
 488         if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
 489         {
 490           hiddenSequences.add(seq);
 491         }
 492         seqs.add(seq);
 493         seqMap.put(seqUniqueId, seq);
 494       }
 495
 496       parseFeatures(jsonSeqArray);
 497
 498       for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
 499               .hasNext();)
 500       {
 501         JSONObject seqGrpObj = seqGrpIter.next();
 502         String grpName = seqGrpObj.get("groupName").toString();
 503         String colourScheme = seqGrpObj.get("colourScheme").toString();
 504         String description = (seqGrpObj.get("description") == null) ? null
 505                 : seqGrpObj.get("description").toString();
 506         boolean displayBoxes = Boolean.valueOf(seqGrpObj
 507                 .get("displayBoxes").toString());
 508         boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
 509                 .toString());
 510         boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
 511                 .toString());
 512         boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
 513                 "showNonconserved").toString());
 514         int startRes = Integer
 515                 .valueOf(seqGrpObj.get("startRes").toString());
 516         int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
 517         JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
 518
 519         ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
 520         if (sequenceRefs.size() > 0)
 521         {
 522           Iterator<String> seqHashIter = sequenceRefs.iterator();
 523           while (seqHashIter.hasNext())
 524           {
 525             String seqHash = seqHashIter.next();
 526             Sequence sequence = seqMap.get(seqHash);
 527             if (sequence != null)
 528             {
 529               grpSeqs.add(sequence);
 530             }
 531           }
 532         }
 533         SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
 534                 displayBoxes, displayText, colourText, startRes, endRes);
 535         seqGrp.setColourScheme(ColourSchemeMapper.getJalviewColourScheme(
 536                 colourScheme, seqGrp));
 537         seqGrp.setShowNonconserved(showNonconserved);
 538         seqGrp.setDescription(description);
 539         this.seqGroups.add(seqGrp);
 540
 541       }
 542
 543       for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
 544               .hasNext();)
 545       {
 546         JSONObject alAnnot = alAnnotIter.next();
 547         JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
 548         Annotation[] annotations = new Annotation[annotJsonArray.size()];
 549         int count = 0;
 550         for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
 551                 .hasNext();)
 552         {
 553           JSONObject annot = annotIter.next();
 554           if (annot == null)
 555           {
 556             annotations[count] = null;
 557           }
 558           else
 559           {
 560             float val = annot.get("value") == null ? null : Float
 561                     .valueOf(annot.get("value").toString());
 562             String desc = annot.get("description") == null ? null : annot
 563                     .get("description").toString();
 564             char ss = annot.get("secondaryStructure") == null
 565                     || annot.get("secondaryStructure").toString()
 566                             .equalsIgnoreCase("u0000") ? ' ' : annot
 567                     .get("secondaryStructure").toString().charAt(0);
 568             String displayChar = annot.get("displayCharacter") == null ? ""
 569                     : annot.get("displayCharacter").toString();
 570
 571             annotations[count] = new Annotation(displayChar, desc, ss, val);
 572             if (annot.get("colour") != null)
 573             {
 574               Color color = ColorUtils.parseColourString(annot.get(
 575                       "colour").toString());
 576               annotations[count].colour = color;
 577             }
 578           }
 579           ++count;
 580         }
 581
 582         AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
 583                 .get("label").toString(), alAnnot.get("description")
 584                 .toString(), annotations);
 585         alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0 : Integer
 586                 .valueOf(alAnnot.get("graphType").toString());
 587
 588         JSONObject diplaySettings = (JSONObject) alAnnot
 589                 .get("annotationSettings");
 590         if (diplaySettings != null)
 591         {
 592
 593           alignAnnot.scaleColLabel = (diplaySettings.get("scaleColLabel") == null) ? false
 594                   : Boolean.valueOf(diplaySettings.get("scaleColLabel")
 595                           .toString());
 596           alignAnnot.showAllColLabels = (diplaySettings
 597                   .get("showAllColLabels") == null) ? true : Boolean
 598                   .valueOf(diplaySettings.get("showAllColLabels")
 599                           .toString());
 600           alignAnnot.centreColLabels = (diplaySettings
 601                   .get("centreColLabels") == null) ? true
 602                   : Boolean.valueOf(diplaySettings.get("centreColLabels")
 603                           .toString());
 604           alignAnnot.belowAlignment = (diplaySettings.get("belowAlignment") == null) ? false
 605                   : Boolean.valueOf(diplaySettings.get("belowAlignment")
 606                           .toString());
 607           alignAnnot.visible = (diplaySettings.get("visible") == null) ? true
 608                   : Boolean.valueOf(diplaySettings.get("visible")
 609                           .toString());
 610           alignAnnot.hasIcons = (diplaySettings.get("hasIcon") == null) ? true
 611                   : Boolean.valueOf(diplaySettings.get("hasIcon")
 612                           .toString());
 613
 614         }
 615         if (alAnnot.get("score") != null)
 616         {
 617           alignAnnot.score = Double
 618                   .valueOf(alAnnot.get("score").toString());
 619         }
 620
 621         String calcId = (alAnnot.get("calcId") == null) ? "" : alAnnot.get(
 622                 "calcId").toString();
 623         alignAnnot.setCalcId(calcId);
 624         String seqHash = (alAnnot.get("sequenceRef") != null) ? alAnnot
 625                 .get("sequenceRef").toString() : null;
 626
 627         Sequence sequence = (seqHash != null) ? seqMap.get(seqHash) : null;
 628         if (sequence != null)
 629         {
 630           alignAnnot.sequenceRef = sequence;
 631           sequence.addAlignmentAnnotation(alignAnnot);
 632           if (alignAnnot.label.equalsIgnoreCase("T-COFFEE"))
 633           {
 634             alignAnnot.createSequenceMapping(sequence, sequence.getStart(),
 635                     false);
 636             sequence.addAlignmentAnnotation(alignAnnot);
 637             alignAnnot.adjustForAlignment();
 638           }
 639         }
 640         alignAnnot.validateRangeAndDisplay();
 641         this.annotations.add(alignAnnot);
 642
 643       }
 644     } catch (Exception e)
 645     {
 646       e.printStackTrace();
 647     }
 648     return this;
 649   }
 650
 651   public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
 652   {
 653     hiddenSeqRefs = new ArrayList<String>();
 654     String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
 655     if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
 656     {
 657       String[] seqRefs = hiddenSeqs.split(";");
 658       for (String seqRef : seqRefs)
 659       {
 660         hiddenSeqRefs.add(seqRef);
 661       }
 662     }
 663   }
 664
 665   public void parseHiddenCols(JSONObject jvSettingsJson)
 666   {
 667     String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
 668     if (hiddenCols != null && !hiddenCols.isEmpty())
 669     {
 670       HiddenColumns hidden = new HiddenColumns();
 671       String[] rangeStrings = hiddenCols.split(";");
 672       for (String rangeString : rangeStrings)
 673       {
 674         String[] range = rangeString.split("-");
 675         hidden.hideColumns(Integer.valueOf(range[0]),
 676                 Integer.valueOf(range[1]));
 677       }
 678     }
 679   }
 680
 681   @SuppressWarnings("unchecked")
 682   private void parseFeatures(JSONArray jsonSeqFeatures)
 683   {
 684     if (jsonSeqFeatures != null)
 685     {
 686       displayedFeatures = new FeaturesDisplayed();
 687       for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
 688               .hasNext();)
 689       {
 690         JSONObject jsonFeature = seqFeatureItr.next();
 691         Long begin = (Long) jsonFeature.get("xStart");
 692         Long end = (Long) jsonFeature.get("xEnd");
 693         String type = (String) jsonFeature.get("type");
 694         String featureGrp = (String) jsonFeature.get("featureGroup");
 695         String descripiton = (String) jsonFeature.get("description");
 696         String seqRef = (String) jsonFeature.get("sequenceRef");
 697         Float score = Float.valueOf(jsonFeature.get("score").toString());
 698
 699         Sequence seq = seqMap.get(seqRef);
 700         SequenceFeature sequenceFeature = new SequenceFeature();
 701         JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
 702         if (linksJsonArray != null && linksJsonArray.size() > 0)
 703         {
 704           Iterator<String> linkList = linksJsonArray.iterator();
 705           while (linkList.hasNext())
 706           {
 707             String link = linkList.next();
 708             sequenceFeature.addLink(link);
 709           }
 710         }
 711         sequenceFeature.setFeatureGroup(featureGrp);
 712         sequenceFeature.setScore(score);
 713         sequenceFeature.setDescription(descripiton);
 714         sequenceFeature.setType(type);
 715         sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
 716         sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
 717         seq.addSequenceFeature(sequenceFeature);
 718         displayedFeatures.setVisible(type);
 719       }
 720     }
 721   }
 722
 723   @Override
 724   public String getGlobalColourScheme()
 725   {
 726     return globalColourScheme;
 727   }
 728
 729   public void setGlobalColorScheme(String globalColourScheme)
 730   {
 731     this.globalColourScheme = globalColourScheme;
 732   }
 733
 734   @Override
 735   public FeaturesDisplayedI getDisplayedFeatures()
 736   {
 737     return displayedFeatures;
 738   }
 739
 740   public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
 741   {
 742     this.displayedFeatures = displayedFeatures;
 743   }
 744
 745   @Override
 746   public void configureForView(AlignmentViewPanel avpanel)
 747   {
 748     if (avpanel == null)
 749     {
 750       return;
 751     }
 752     super.configureForView(avpanel);
 753     AlignViewportI viewport = avpanel.getAlignViewport();
 754     AlignmentI alignment = viewport.getAlignment();
 755     AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
 756
 757     seqGroups = alignment.getGroups();
 758     fr = avpanel.cloneFeatureRenderer();
 759
 760     // Add non auto calculated annotation to AlignFile
 761     if (annots != null)
 762     {
 763       for (AlignmentAnnotation annot : annots)
 764       {
 765         if (annot != null && !annot.autoCalculated)
 766         {
 767           annotations.add(annot);
 768         }
 769       }
 770     }
 771     globalColourScheme = 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   @Override
 794   public HiddenColumns getHiddenColumns()
 795   {
 796     return hiddenColumns;
 797   }
 798
 799   public void setHiddenColumns(HiddenColumns hidden)
 800   {
 801     this.hiddenColumns = hidden;
 802   }
 803
 804   @Override
 805   public SequenceI[] getHiddenSequences()
 806   {
 807     if (hiddenSequences == null || hiddenSequences.isEmpty())
 808     {
 809       return new SequenceI[] {};
 810     }
 811     synchronized (hiddenSequences)
 812     {
 813       return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
 814     }
 815   }
 816
 817   public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
 818   {
 819     this.hiddenSequences = hiddenSequences;
 820   }
 821
 822   public class JSONExportSettings
 823   {
 824     private boolean exportSequence;
 825
 826     private boolean exportSequenceFeatures;
 827
 828     private boolean exportAnnotations;
 829
 830     private boolean exportGroups;
 831
 832     private boolean exportJalviewSettings;
 833
 834     public boolean isExportSequence()
 835     {
 836       return exportSequence;
 837     }
 838
 839     public void setExportSequence(boolean exportSequence)
 840     {
 841       this.exportSequence = exportSequence;
 842     }
 843
 844     public boolean isExportSequenceFeatures()
 845     {
 846       return exportSequenceFeatures;
 847     }
 848
 849     public void setExportSequenceFeatures(boolean exportSequenceFeatures)
 850     {
 851       this.exportSequenceFeatures = exportSequenceFeatures;
 852     }
 853
 854     public boolean isExportAnnotations()
 855     {
 856       return exportAnnotations;
 857     }
 858
 859     public void setExportAnnotations(boolean exportAnnotations)
 860     {
 861       this.exportAnnotations = exportAnnotations;
 862     }
 863
 864     public boolean isExportGroups()
 865     {
 866       return exportGroups;
 867     }
 868
 869     public void setExportGroups(boolean exportGroups)
 870     {
 871       this.exportGroups = exportGroups;
 872     }
 873
 874     public boolean isExportJalviewSettings()
 875     {
 876       return exportJalviewSettings;
 877     }
 878
 879     public void setExportJalviewSettings(boolean exportJalviewSettings)
 880     {
 881       this.exportJalviewSettings = exportJalviewSettings;
 882     }
 883   }
 884
 885   /**
 886    * Returns a descriptor for suitable feature display settings with
 887    * <ul>
 888    * <li>ResNums or insertions features visible</li>
 889    * <li>insertions features coloured red</li>
 890    * <li>ResNum features coloured by label</li>
 891    * <li>Insertions displayed above (on top of) ResNums</li>
 892    * </ul>
 893    */
 894   @Override
 895   public FeatureSettingsModelI getFeatureColourScheme()
 896   {
 897     return new PDBFeatureSettings();
 898   }
 899 }