src/jalview/io/JSONFile.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21
  22 package jalview.io;
  23
  24 import jalview.api.AlignExportSettingI;
  25 import jalview.api.AlignViewportI;
  26 import jalview.api.AlignmentViewPanel;
  27 import jalview.api.ComplexAlignFile;
  28 import jalview.api.FeatureRenderer;
  29 import jalview.api.FeatureSettingsModelI;
  30 import jalview.api.FeaturesDisplayedI;
  31 import jalview.bin.BuildDetails;
  32 import jalview.datamodel.AlignmentAnnotation;
  33 import jalview.datamodel.AlignmentI;
  34 import jalview.datamodel.Annotation;
  35 import jalview.datamodel.ColumnSelection;
  36 import jalview.datamodel.HiddenSequences;
  37 import jalview.datamodel.Sequence;
  38 import jalview.datamodel.SequenceFeature;
  39 import jalview.datamodel.SequenceGroup;
  40 import jalview.datamodel.SequenceI;
  41 import jalview.json.binding.biojson.v1.AlignmentAnnotationPojo;
  42 import jalview.json.binding.biojson.v1.AlignmentPojo;
  43 import jalview.json.binding.biojson.v1.AnnotationDisplaySettingPojo;
  44 import jalview.json.binding.biojson.v1.AnnotationPojo;
  45 import jalview.json.binding.biojson.v1.ColourSchemeMapper;
  46 import jalview.json.binding.biojson.v1.SequenceFeaturesPojo;
  47 import jalview.json.binding.biojson.v1.SequenceGrpPojo;
  48 import jalview.json.binding.biojson.v1.SequencePojo;
  49 import jalview.schemes.JalviewColourScheme;
  50 import jalview.schemes.ResidueColourScheme;
  51 import jalview.util.ColorUtils;
  52 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
  53
  54 import java.awt.Color;
  55 import java.io.IOException;
  56 import java.io.Reader;
  57 import java.util.ArrayList;
  58 import java.util.Hashtable;
  59 import java.util.Iterator;
  60 import java.util.List;
  61 import java.util.Vector;
  62
  63 import org.json.simple.JSONArray;
  64 import org.json.simple.JSONObject;
  65 import org.json.simple.parser.JSONParser;
  66
  67 public class JSONFile extends AlignFile implements ComplexAlignFile
  68 {
  69   private static String version = new BuildDetails().getVersion();
  70
  71   private String webstartUrl = "http://www.jalview.org/services/launchApp";
  72
  73   private String application = "Jalview";
  74
  75   private String globalColourScheme;
  76
  77   private boolean showSeqFeatures;
  78
  79   private Hashtable<String, Sequence> seqMap;
  80
  81   private FeaturesDisplayedI displayedFeatures;
  82
  83   private FeatureRenderer fr;
  84
  85   private List<int[]> hiddenColumns;
  86
  87   private ColumnSelection columnSelection;
  88
  89   private List<String> hiddenSeqRefs;
  90
  91   private ArrayList<SequenceI> hiddenSequences;
  92
  93   private final static String TCOFFEE_SCORE = "TCoffeeScore";
  94
  95   public JSONFile()
  96   {
  97     super();
  98   }
  99
 100   public JSONFile(FileParse source) throws IOException
 101   {
 102     super(source);
 103   }
 104
 105   public JSONFile(String inFile, DataSourceType sourceType)
 106           throws IOException
 107   {
 108     super(inFile, sourceType);
 109   }
 110
 111   @Override
 112   public void parse() throws IOException
 113   {
 114     parse(getReader());
 115
 116   }
 117
 118   @Override
 119   public String print(SequenceI[] sqs, boolean jvsuffix)
 120   {
 121     String jsonOutput = null;
 122     try
 123     {
 124       AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
 125       AlignExportSettingI exportSettings = getExportSettings();
 126
 127       // if no export settings were supplied use the following with all values
 128       // defaulting to true
 129       if (exportSettings == null)
 130       {
 131         exportSettings = new AlignExportSettingI()
 132         {
 133           @Override
 134           public boolean isExportHiddenSequences()
 135           {
 136             return true;
 137           }
 138
 139           @Override
 140           public boolean isExportHiddenColumns()
 141           {
 142             return true;
 143           }
 144
 145           @Override
 146           public boolean isExportGroups()
 147           {
 148             return true;
 149           }
 150
 151           @Override
 152           public boolean isExportFeatures()
 153           {
 154             return true;
 155           }
 156
 157           @Override
 158           public boolean isExportAnnotations()
 159           {
 160             return true;
 161           }
 162
 163           @Override
 164           public boolean isCancelled()
 165           {
 166             return false;
 167           }
 168         };
 169       }
 170
 171       int count = 0;
 172       for (SequenceI seq : sqs)
 173       {
 174         StringBuilder name = new StringBuilder();
 175         name.append(seq.getName()).append("/").append(seq.getStart())
 176                 .append("-").append(seq.getEnd());
 177         SequencePojo jsonSeqPojo = new SequencePojo();
 178         jsonSeqPojo.setId(String.valueOf(seq.hashCode()));
 179         jsonSeqPojo.setOrder(++count);
 180         jsonSeqPojo.setEnd(seq.getEnd());
 181         jsonSeqPojo.setStart(seq.getStart());
 182         jsonSeqPojo.setName(name.toString());
 183         jsonSeqPojo.setSeq(seq.getSequenceAsString());
 184         jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
 185       }
 186       jsonAlignmentPojo.setGlobalColorScheme(globalColourScheme);
 187       jsonAlignmentPojo.getAppSettings().put("application", application);
 188       jsonAlignmentPojo.getAppSettings().put("version", version);
 189       jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
 190       jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
 191               String.valueOf(showSeqFeatures));
 192
 193       String[] hiddenSections = getHiddenSections();
 194       if (hiddenSections != null)
 195       {
 196         if (hiddenSections[0] != null
 197                 && exportSettings.isExportHiddenColumns())
 198         {
 199           jsonAlignmentPojo.getAppSettings().put("hiddenCols",
 200                   String.valueOf(hiddenSections[0]));
 201         }
 202         if (hiddenSections[1] != null
 203                 && exportSettings.isExportHiddenSequences())
 204         {
 205           jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
 206                   String.valueOf(hiddenSections[1]));
 207         }
 208       }
 209
 210       if (exportSettings.isExportAnnotations())
 211       {
 212         jsonAlignmentPojo
 213                 .setAlignAnnotation(annotationToJsonPojo(annotations));
 214       }
 215       else
 216       {
 217         // These color schemes require annotation, disable them if annotations
 218         // are not exported
 219         if (globalColourScheme
 220                 .equalsIgnoreCase(JalviewColourScheme.RNAHelices.toString())
 221                 || globalColourScheme
 222                         .equalsIgnoreCase(JalviewColourScheme.TCoffee
 223                                 .toString()))
 224         {
 225           jsonAlignmentPojo.setGlobalColorScheme(ResidueColourScheme.NONE);
 226         }
 227       }
 228
 229       if (exportSettings.isExportFeatures())
 230       {
 231         jsonAlignmentPojo
 232                 .setSeqFeatures(sequenceFeatureToJsonPojo(sqs, fr));
 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(seqGrp.cs.getSchemeName());
 243           seqGrpPojo.setColourText(seqGrp.getColourText());
 244           seqGrpPojo.setDescription(seqGrp.getDescription());
 245           seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
 246           seqGrpPojo.setDisplayText(seqGrp.getDisplayText());
 247           seqGrpPojo.setEndRes(seqGrp.getEndRes());
 248           seqGrpPojo.setStartRes(seqGrp.getStartRes());
 249           seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
 250           for (SequenceI seq : seqGrp.getSequences())
 251           {
 252             seqGrpPojo.getSequenceRefs()
 253                     .add(String.valueOf(seq.hashCode()));
 254           }
 255           jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
 256         }
 257       }
 258       org.json.JSONObject generatedJSon = new org.json.JSONObject(
 259               jsonAlignmentPojo);
 260       jsonOutput = generatedJSon.toString();
 261       return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
 262               "xEnd");
 263     } catch (Exception e)
 264     {
 265       e.printStackTrace();
 266     }
 267     return jsonOutput;
 268   }
 269
 270   public String[] getHiddenSections()
 271   {
 272     String[] hiddenSections = new String[2];
 273     if (getViewport() == null)
 274     {
 275       return null;
 276     }
 277
 278     // hidden column business
 279     if (getViewport().hasHiddenColumns())
 280     {
 281       List<int[]> hiddenCols = getViewport().getColumnSelection()
 282               .getHiddenColumns();
 283       StringBuilder hiddenColsBuilder = new StringBuilder();
 284       for (int[] range : hiddenCols)
 285       {
 286         hiddenColsBuilder.append(";").append(range[0]).append("-")
 287                 .append(range[1]);
 288       }
 289
 290       hiddenColsBuilder.deleteCharAt(0);
 291       hiddenSections[0] = hiddenColsBuilder.toString();
 292     }
 293
 294     // hidden rows/seqs business
 295     HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
 296             .getHiddenSequences();
 297     if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
 298     {
 299       return hiddenSections;
 300     }
 301
 302     SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
 303     StringBuilder hiddenSeqsBuilder = new StringBuilder();
 304     for (SequenceI hiddenSeq : hiddenSeqs)
 305     {
 306       if (hiddenSeq != null)
 307       {
 308         hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
 309       }
 310     }
 311     if (hiddenSeqsBuilder.length() > 0)
 312     {
 313       hiddenSeqsBuilder.deleteCharAt(0);
 314     }
 315     hiddenSections[1] = hiddenSeqsBuilder.toString();
 316
 317     return hiddenSections;
 318   }
 319
 320   public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
 321           SequenceI[] sqs, FeatureRenderer fr)
 322   {
 323     displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
 324     List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
 325     if (sqs == null)
 326     {
 327       return sequenceFeaturesPojo;
 328     }
 329
 330     for (SequenceI seq : sqs)
 331     {
 332       SequenceI dataSetSequence = seq.getDatasetSequence();
 333       SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
 334               : seq.getDatasetSequence().getSequenceFeatures();
 335
 336       seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
 337               : seqFeatures;
 338       if (seqFeatures == null)
 339       {
 340         continue;
 341       }
 342
 343       for (SequenceFeature sf : seqFeatures)
 344       {
 345         if (displayedFeatures != null
 346                 && displayedFeatures.isVisible(sf.getType()))
 347         {
 348           SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
 349                   String.valueOf(seq.hashCode()));
 350
 351           String featureColour = (fr == null) ? null : jalview.util.Format
 352                   .getHexString(fr.findFeatureColour(Color.white, seq,
 353                           seq.findIndex(sf.getBegin())));
 354           jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
 355           jsonFeature.setXend(seq.findIndex(sf.getEnd()));
 356           jsonFeature.setType(sf.getType());
 357           jsonFeature.setDescription(sf.getDescription());
 358           jsonFeature.setLinks(sf.links);
 359           jsonFeature.setOtherDetails(sf.otherDetails);
 360           jsonFeature.setScore(sf.getScore());
 361           jsonFeature.setFillColor(featureColour);
 362           jsonFeature.setFeatureGroup(sf.getFeatureGroup());
 363           sequenceFeaturesPojo.add(jsonFeature);
 364         }
 365       }
 366     }
 367     return sequenceFeaturesPojo;
 368   }
 369
 370   public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
 371           Vector<AlignmentAnnotation> annotations)
 372   {
 373     List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
 374     if (annotations == null)
 375     {
 376       return jsonAnnotations;
 377     }
 378     for (AlignmentAnnotation annot : annotations)
 379     {
 380       AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
 381       alignAnnotPojo.setDescription(annot.description);
 382       alignAnnotPojo.setLabel(annot.label);
 383       if (!Double.isNaN(annot.score))
 384       {
 385         alignAnnotPojo.setScore(annot.score);
 386       }
 387       alignAnnotPojo.setCalcId(annot.getCalcId());
 388       alignAnnotPojo.setGraphType(annot.graph);
 389
 390       AnnotationDisplaySettingPojo annotSetting = new AnnotationDisplaySettingPojo();
 391       annotSetting.setBelowAlignment(annot.belowAlignment);
 392       annotSetting.setCentreColLabels(annot.centreColLabels);
 393       annotSetting.setScaleColLabel(annot.scaleColLabel);
 394       annotSetting.setShowAllColLabels(annot.showAllColLabels);
 395       annotSetting.setVisible(annot.visible);
 396       annotSetting.setHasIcon(annot.hasIcons);
 397       alignAnnotPojo.setAnnotationSettings(annotSetting);
 398       SequenceI refSeq = annot.sequenceRef;
 399       if (refSeq != null)
 400       {
 401         alignAnnotPojo.setSequenceRef(String.valueOf(refSeq.hashCode()));
 402       }
 403       for (Annotation annotation : annot.annotations)
 404       {
 405         AnnotationPojo annotationPojo = new AnnotationPojo();
 406         if (annotation != null)
 407         {
 408           annotationPojo.setDescription(annotation.description);
 409           annotationPojo.setValue(annotation.value);
 410           annotationPojo
 411                   .setSecondaryStructure(annotation.secondaryStructure);
 412           String displayChar = annotation.displayCharacter == null ? null
 413                   : annotation.displayCharacter;
 414           // System.out.println("--------------------->[" + displayChar + "]");
 415           annotationPojo.setDisplayCharacter(displayChar);
 416           if (annotation.colour != null)
 417           {
 418             annotationPojo.setColour(jalview.util.Format
 419                     .getHexString(annotation.colour));
 420           }
 421           alignAnnotPojo.getAnnotations().add(annotationPojo);
 422         }
 423         else
 424         {
 425           if (annot.getCalcId() != null
 426                   && annot.getCalcId().equalsIgnoreCase(TCOFFEE_SCORE))
 427           {
 428             // do nothing
 429           }
 430           else
 431           {
 432             alignAnnotPojo.getAnnotations().add(annotationPojo);
 433           }
 434         }
 435       }
 436       jsonAnnotations.add(alignAnnotPojo);
 437     }
 438     return jsonAnnotations;
 439   }
 440
 441   @SuppressWarnings("unchecked")
 442   public JSONFile parse(Reader jsonAlignmentString)
 443   {
 444     try
 445     {
 446       JSONParser jsonParser = new JSONParser();
 447       JSONObject alignmentJsonObj = (JSONObject) jsonParser
 448               .parse(jsonAlignmentString);
 449       JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
 450       JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
 451               .get("alignAnnotation");
 452       JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
 453               .get("seqFeatures");
 454       JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
 455               .get("seqGroups");
 456       JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
 457               .get("appSettings");
 458
 459       if (jvSettingsJsonObj != null)
 460       {
 461         globalColourScheme = (String) jvSettingsJsonObj
 462                 .get("globalColorScheme");
 463         Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
 464                 "showSeqFeatures").toString());
 465         setShowSeqFeatures(showFeatures);
 466         parseHiddenSeqRefsAsList(jvSettingsJsonObj);
 467         parseHiddenCols(jvSettingsJsonObj);
 468       }
 469
 470       hiddenSequences = new ArrayList<SequenceI>();
 471       seqMap = new Hashtable<String, Sequence>();
 472       for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
 473               .hasNext();)
 474       {
 475         JSONObject sequence = sequenceIter.next();
 476         String sequcenceString = sequence.get("seq").toString();
 477         String sequenceName = sequence.get("name").toString();
 478         String seqUniqueId = sequence.get("id").toString();
 479         int start = Integer.valueOf(sequence.get("start").toString());
 480         int end = Integer.valueOf(sequence.get("end").toString());
 481         Sequence seq = new Sequence(sequenceName, sequcenceString, start,
 482                 end);
 483         if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
 484         {
 485           hiddenSequences.add(seq);
 486         }
 487         seqs.add(seq);
 488         seqMap.put(seqUniqueId, seq);
 489       }
 490
 491       parseFeatures(jsonSeqArray);
 492
 493       for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
 494               .hasNext();)
 495       {
 496         JSONObject seqGrpObj = seqGrpIter.next();
 497         String grpName = seqGrpObj.get("groupName").toString();
 498         String colourScheme = seqGrpObj.get("colourScheme").toString();
 499         String description = (seqGrpObj.get("description") == null) ? null
 500                 : seqGrpObj.get("description").toString();
 501         boolean displayBoxes = Boolean.valueOf(seqGrpObj
 502                 .get("displayBoxes").toString());
 503         boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
 504                 .toString());
 505         boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
 506                 .toString());
 507         boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
 508                 "showNonconserved").toString());
 509         int startRes = Integer
 510                 .valueOf(seqGrpObj.get("startRes").toString());
 511         int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
 512         JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
 513
 514         ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
 515         if (sequenceRefs.size() > 0)
 516         {
 517           Iterator<String> seqHashIter = sequenceRefs.iterator();
 518           while (seqHashIter.hasNext())
 519           {
 520             String seqHash = seqHashIter.next();
 521             Sequence sequence = seqMap.get(seqHash);
 522             if (sequence != null)
 523             {
 524               grpSeqs.add(sequence);
 525             }
 526           }
 527         }
 528         SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
 529                 displayBoxes, displayText, colourText, startRes, endRes);
 530         seqGrp.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme,
 531                 seqGrp);
 532         seqGrp.setShowNonconserved(showNonconserved);
 533         seqGrp.setDescription(description);
 534         this.seqGroups.add(seqGrp);
 535
 536       }
 537
 538       for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
 539               .hasNext();)
 540       {
 541         JSONObject alAnnot = alAnnotIter.next();
 542         JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
 543         Annotation[] annotations = new Annotation[annotJsonArray.size()];
 544         int count = 0;
 545         for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
 546                 .hasNext();)
 547         {
 548           JSONObject annot = annotIter.next();
 549           if (annot == null)
 550           {
 551             annotations[count] = null;
 552           }
 553           else
 554           {
 555             float val = annot.get("value") == null ? null : Float
 556                     .valueOf(annot.get("value").toString());
 557             String desc = annot.get("description") == null ? null : annot
 558                     .get("description").toString();
 559             char ss = annot.get("secondaryStructure") == null
 560                     || annot.get("secondaryStructure").toString()
 561                             .equalsIgnoreCase("u0000") ? ' ' : annot
 562                     .get("secondaryStructure").toString().charAt(0);
 563             String displayChar = annot.get("displayCharacter") == null ? ""
 564                     : annot.get("displayCharacter").toString();
 565
 566             annotations[count] = new Annotation(displayChar, desc, ss, val);
 567             if (annot.get("colour") != null)
 568             {
 569               Color color = ColorUtils.parseColourString(annot.get(
 570                       "colour").toString());
 571               annotations[count].colour = color;
 572             }
 573           }
 574           ++count;
 575         }
 576
 577         AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
 578                 .get("label").toString(), alAnnot.get("description")
 579                 .toString(), annotations);
 580         alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0 : Integer
 581                 .valueOf(alAnnot.get("graphType").toString());
 582
 583         JSONObject diplaySettings = (JSONObject) alAnnot
 584                 .get("annotationSettings");
 585         if (diplaySettings != null)
 586         {
 587
 588           alignAnnot.scaleColLabel = (diplaySettings.get("scaleColLabel") == null) ? false
 589                   : Boolean.valueOf(diplaySettings.get("scaleColLabel")
 590                           .toString());
 591           alignAnnot.showAllColLabels = (diplaySettings
 592                   .get("showAllColLabels") == null) ? true : Boolean
 593                   .valueOf(diplaySettings.get("showAllColLabels")
 594                           .toString());
 595           alignAnnot.centreColLabels = (diplaySettings
 596                   .get("centreColLabels") == null) ? true
 597                   : Boolean.valueOf(diplaySettings.get("centreColLabels")
 598                           .toString());
 599           alignAnnot.belowAlignment = (diplaySettings.get("belowAlignment") == null) ? false
 600                   : Boolean.valueOf(diplaySettings.get("belowAlignment")
 601                           .toString());
 602           alignAnnot.visible = (diplaySettings.get("visible") == null) ? true
 603                   : Boolean.valueOf(diplaySettings.get("visible")
 604                           .toString());
 605           alignAnnot.hasIcons = (diplaySettings.get("hasIcon") == null) ? true
 606                   : Boolean.valueOf(diplaySettings.get("hasIcon")
 607                           .toString());
 608
 609         }
 610         if (alAnnot.get("score") != null)
 611         {
 612           alignAnnot.score = Double
 613                   .valueOf(alAnnot.get("score").toString());
 614         }
 615
 616         String calcId = (alAnnot.get("calcId") == null) ? "" : alAnnot.get(
 617                 "calcId").toString();
 618         alignAnnot.setCalcId(calcId);
 619         String seqHash = (alAnnot.get("sequenceRef") != null) ? alAnnot
 620                 .get("sequenceRef").toString() : null;
 621
 622         Sequence sequence = (seqHash != null) ? seqMap.get(seqHash) : null;
 623         if (sequence != null)
 624         {
 625           alignAnnot.sequenceRef = sequence;
 626           sequence.addAlignmentAnnotation(alignAnnot);
 627           if (alignAnnot.label.equalsIgnoreCase("T-COFFEE"))
 628           {
 629             alignAnnot.createSequenceMapping(sequence, sequence.getStart(),
 630                     false);
 631             sequence.addAlignmentAnnotation(alignAnnot);
 632             alignAnnot.adjustForAlignment();
 633           }
 634         }
 635         alignAnnot.validateRangeAndDisplay();
 636         this.annotations.add(alignAnnot);
 637
 638       }
 639     } catch (Exception e)
 640     {
 641       e.printStackTrace();
 642     }
 643     return this;
 644   }
 645
 646   public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
 647   {
 648     hiddenSeqRefs = new ArrayList<String>();
 649     String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
 650     if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
 651     {
 652       String[] seqRefs = hiddenSeqs.split(";");
 653       for (String seqRef : seqRefs)
 654       {
 655         hiddenSeqRefs.add(seqRef);
 656       }
 657     }
 658   }
 659
 660   public void parseHiddenCols(JSONObject jvSettingsJson)
 661   {
 662     String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
 663     if (hiddenCols != null && !hiddenCols.isEmpty())
 664     {
 665       columnSelection = new ColumnSelection();
 666       String[] rangeStrings = hiddenCols.split(";");
 667       for (String rangeString : rangeStrings)
 668       {
 669         String[] range = rangeString.split("-");
 670         columnSelection.hideColumns(Integer.valueOf(range[0]),
 671                 Integer.valueOf(range[1]));
 672       }
 673     }
 674   }
 675
 676   @SuppressWarnings("unchecked")
 677   private void parseFeatures(JSONArray jsonSeqFeatures)
 678   {
 679     if (jsonSeqFeatures != null)
 680     {
 681       displayedFeatures = new FeaturesDisplayed();
 682       for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
 683               .hasNext();)
 684       {
 685         JSONObject jsonFeature = seqFeatureItr.next();
 686         Long begin = (Long) jsonFeature.get("xStart");
 687         Long end = (Long) jsonFeature.get("xEnd");
 688         String type = (String) jsonFeature.get("type");
 689         String featureGrp = (String) jsonFeature.get("featureGroup");
 690         String descripiton = (String) jsonFeature.get("description");
 691         String seqRef = (String) jsonFeature.get("sequenceRef");
 692         Float score = Float.valueOf(jsonFeature.get("score").toString());
 693
 694         Sequence seq = seqMap.get(seqRef);
 695         SequenceFeature sequenceFeature = new SequenceFeature();
 696         JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
 697         if (linksJsonArray != null && linksJsonArray.size() > 0)
 698         {
 699           Iterator<String> linkList = linksJsonArray.iterator();
 700           while (linkList.hasNext())
 701           {
 702             String link = linkList.next();
 703             sequenceFeature.addLink(link);
 704           }
 705         }
 706         sequenceFeature.setFeatureGroup(featureGrp);
 707         sequenceFeature.setScore(score);
 708         sequenceFeature.setDescription(descripiton);
 709         sequenceFeature.setType(type);
 710         sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
 711         sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
 712         seq.addSequenceFeature(sequenceFeature);
 713         displayedFeatures.setVisible(type);
 714       }
 715     }
 716   }
 717
 718   @Override
 719   public String getGlobalColourScheme()
 720   {
 721     return globalColourScheme;
 722   }
 723
 724   public void setGlobalColorScheme(String globalColourScheme)
 725   {
 726     this.globalColourScheme = globalColourScheme;
 727   }
 728
 729   @Override
 730   public FeaturesDisplayedI getDisplayedFeatures()
 731   {
 732     return displayedFeatures;
 733   }
 734
 735   public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
 736   {
 737     this.displayedFeatures = displayedFeatures;
 738   }
 739
 740   @Override
 741   public void configureForView(AlignmentViewPanel avpanel)
 742   {
 743     if (avpanel == null)
 744     {
 745       return;
 746     }
 747     super.configureForView(avpanel);
 748     AlignViewportI viewport = avpanel.getAlignViewport();
 749     AlignmentI alignment = viewport.getAlignment();
 750     AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
 751
 752     seqGroups = alignment.getGroups();
 753     fr = avpanel.cloneFeatureRenderer();
 754
 755     // Add non auto calculated annotation to AlignFile
 756     if (annots != null)
 757     {
 758       for (AlignmentAnnotation annot : annots)
 759       {
 760         if (annot != null && !annot.autoCalculated)
 761         {
 762           annotations.add(annot);
 763         }
 764       }
 765     }
 766     globalColourScheme = viewport.getGlobalColourScheme().getSchemeName();
 767     setDisplayedFeatures(viewport.getFeaturesDisplayed());
 768     showSeqFeatures = viewport.isShowSequenceFeatures();
 769
 770   }
 771
 772   @Override
 773   public boolean isShowSeqFeatures()
 774   {
 775     return showSeqFeatures;
 776   }
 777
 778   public void setShowSeqFeatures(boolean showSeqFeatures)
 779   {
 780     this.showSeqFeatures = showSeqFeatures;
 781   }
 782
 783   public Vector<AlignmentAnnotation> getAnnotations()
 784   {
 785     return annotations;
 786   }
 787
 788   public List<int[]> getHiddenColumns()
 789   {
 790     return hiddenColumns;
 791   }
 792
 793   @Override
 794   public ColumnSelection getColumnSelection()
 795   {
 796     return columnSelection;
 797   }
 798
 799   public void setColumnSelection(ColumnSelection columnSelection)
 800   {
 801     this.columnSelection = columnSelection;
 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 }