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.ColourSchemeProperty;
  50 import jalview.schemes.UserColourScheme;
  51 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
  52
  53 import java.awt.Color;
  54 import java.io.IOException;
  55 import java.io.Reader;
  56 import java.util.ArrayList;
  57 import java.util.Hashtable;
  58 import java.util.Iterator;
  59 import java.util.List;
  60 import java.util.Vector;
  61
  62 import org.json.simple.JSONArray;
  63 import org.json.simple.JSONObject;
  64 import org.json.simple.parser.JSONParser;
  65
  66 public class JSONFile extends AlignFile implements ComplexAlignFile
  67 {
  68   private static String version = new BuildDetails().getVersion();
  69
  70   private String webstartUrl = "http://www.jalview.org/services/launchApp";
  71
  72   private String application = "Jalview";
  73
  74   private String globalColourScheme;
  75
  76   private boolean showSeqFeatures;
  77
  78   private Hashtable<String, Sequence> seqMap;
  79
  80   private FeaturesDisplayedI displayedFeatures;
  81
  82   private FeatureRenderer fr;
  83
  84   private List<int[]> hiddenColumns;
  85
  86   private ColumnSelection columnSelection;
  87
  88   private List<String> hiddenSeqRefs;
  89
  90   private ArrayList<SequenceI> hiddenSequences;
  91
  92   private final static String TCOFFEE_SCORE = "TCoffeeScore";
  93
  94   public JSONFile()
  95   {
  96     super();
  97   }
  98
  99   public JSONFile(FileParse source) throws IOException
 100   {
 101     super(source);
 102   }
 103
 104   public JSONFile(String inFile, DataSourceType sourceType)
 105           throws IOException
 106   {
 107     super(inFile, sourceType);
 108   }
 109
 110   @Override
 111   public void parse() throws IOException
 112   {
 113     parse(getReader());
 114
 115   }
 116
 117   @Override
 118   public String print(SequenceI[] sqs, boolean jvsuffix)
 119   {
 120     String jsonOutput = null;
 121     try
 122     {
 123       AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
 124       AlignExportSettingI exportSettings = getExportSettings();
 125
 126       // if no export settings were supplied use the following with all values
 127       // defaulting to true
 128       if (exportSettings == null)
 129       {
 130         exportSettings = new AlignExportSettingI()
 131         {
 132           @Override
 133           public boolean isExportHiddenSequences()
 134           {
 135             return true;
 136           }
 137
 138           @Override
 139           public boolean isExportHiddenColumns()
 140           {
 141             return true;
 142           }
 143
 144           @Override
 145           public boolean isExportGroups()
 146           {
 147             return true;
 148           }
 149
 150           @Override
 151           public boolean isExportFeatures()
 152           {
 153             return true;
 154           }
 155
 156           @Override
 157           public boolean isExportAnnotations()
 158           {
 159             return true;
 160           }
 161
 162           @Override
 163           public boolean isCancelled()
 164           {
 165             return false;
 166           }
 167         };
 168       }
 169
 170       int count = 0;
 171       for (SequenceI seq : sqs)
 172       {
 173         StringBuilder name = new StringBuilder();
 174         name.append(seq.getName()).append("/").append(seq.getStart())
 175                 .append("-").append(seq.getEnd());
 176         SequencePojo jsonSeqPojo = new SequencePojo();
 177         jsonSeqPojo.setId(String.valueOf(seq.hashCode()));
 178         jsonSeqPojo.setOrder(++count);
 179         jsonSeqPojo.setEnd(seq.getEnd());
 180         jsonSeqPojo.setStart(seq.getStart());
 181         jsonSeqPojo.setName(name.toString());
 182         jsonSeqPojo.setSeq(seq.getSequenceAsString());
 183         jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
 184       }
 185       jsonAlignmentPojo.setGlobalColorScheme(globalColourScheme);
 186       jsonAlignmentPojo.getAppSettings().put("application", application);
 187       jsonAlignmentPojo.getAppSettings().put("version", version);
 188       jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
 189       jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
 190               String.valueOf(showSeqFeatures));
 191
 192       String[] hiddenSections = getHiddenSections();
 193       if (hiddenSections != null)
 194       {
 195         if (hiddenSections[0] != null
 196                 && exportSettings.isExportHiddenColumns())
 197         {
 198           jsonAlignmentPojo.getAppSettings().put("hiddenCols",
 199                   String.valueOf(hiddenSections[0]));
 200         }
 201         if (hiddenSections[1] != null
 202                 && exportSettings.isExportHiddenSequences())
 203         {
 204           jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
 205                   String.valueOf(hiddenSections[1]));
 206         }
 207       }
 208
 209       if (exportSettings.isExportAnnotations())
 210       {
 211         jsonAlignmentPojo
 212                 .setAlignAnnotation(annotationToJsonPojo(annotations));
 213       }
 214       else
 215       {
 216         // These color schemes require annotation, disable them if annotations
 217         // are not exported
 218         if (globalColourScheme.equalsIgnoreCase("RNA Helices")
 219                 || globalColourScheme.equalsIgnoreCase("T-COFFEE SCORES"))
 220         {
 221           jsonAlignmentPojo.setGlobalColorScheme("None");
 222         }
 223       }
 224
 225       if (exportSettings.isExportFeatures())
 226       {
 227         jsonAlignmentPojo
 228                 .setSeqFeatures(sequenceFeatureToJsonPojo(sqs, fr));
 229       }
 230
 231       if (exportSettings.isExportGroups() && seqGroups != null
 232               && seqGroups.size() > 0)
 233       {
 234         for (SequenceGroup seqGrp : seqGroups)
 235         {
 236           SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
 237           seqGrpPojo.setGroupName(seqGrp.getName());
 238           seqGrpPojo.setColourScheme(ColourSchemeProperty
 239                   .getColourName(seqGrp.cs));
 240           seqGrpPojo.setColourText(seqGrp.getColourText());
 241           seqGrpPojo.setDescription(seqGrp.getDescription());
 242           seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
 243           seqGrpPojo.setDisplayText(seqGrp.getDisplayText());
 244           seqGrpPojo.setEndRes(seqGrp.getEndRes());
 245           seqGrpPojo.setStartRes(seqGrp.getStartRes());
 246           seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
 247           for (SequenceI seq : seqGrp.getSequences())
 248           {
 249             seqGrpPojo.getSequenceRefs()
 250                     .add(String.valueOf(seq.hashCode()));
 251           }
 252           jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
 253         }
 254       }
 255       org.json.JSONObject generatedJSon = new org.json.JSONObject(
 256               jsonAlignmentPojo);
 257       jsonOutput = generatedJSon.toString();
 258       return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
 259               "xEnd");
 260     } catch (Exception e)
 261     {
 262       e.printStackTrace();
 263     }
 264     return jsonOutput;
 265   }
 266
 267   public String[] getHiddenSections()
 268   {
 269     String[] hiddenSections = new String[2];
 270     if (getViewport() == null)
 271     {
 272       return null;
 273     }
 274
 275     // hidden column business
 276     if (getViewport().hasHiddenColumns())
 277     {
 278       List<int[]> hiddenCols = getViewport().getColumnSelection()
 279               .getHiddenColumns();
 280       StringBuilder hiddenColsBuilder = new StringBuilder();
 281       for (int[] range : hiddenCols)
 282       {
 283         hiddenColsBuilder.append(";").append(range[0]).append("-")
 284                 .append(range[1]);
 285       }
 286
 287       hiddenColsBuilder.deleteCharAt(0);
 288       hiddenSections[0] = hiddenColsBuilder.toString();
 289     }
 290
 291     // hidden rows/seqs business
 292     HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
 293             .getHiddenSequences();
 294     if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
 295     {
 296       return hiddenSections;
 297     }
 298
 299     SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
 300     StringBuilder hiddenSeqsBuilder = new StringBuilder();
 301     for (SequenceI hiddenSeq : hiddenSeqs)
 302     {
 303       if (hiddenSeq != null)
 304       {
 305         hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
 306       }
 307     }
 308     if (hiddenSeqsBuilder.length() > 0)
 309     {
 310       hiddenSeqsBuilder.deleteCharAt(0);
 311     }
 312     hiddenSections[1] = hiddenSeqsBuilder.toString();
 313
 314     return hiddenSections;
 315   }
 316
 317   public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
 318           SequenceI[] sqs, FeatureRenderer fr)
 319   {
 320     displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
 321     List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
 322     if (sqs == null)
 323     {
 324       return sequenceFeaturesPojo;
 325     }
 326
 327     for (SequenceI seq : sqs)
 328     {
 329       SequenceI dataSetSequence = seq.getDatasetSequence();
 330       SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
 331               : seq.getDatasetSequence().getSequenceFeatures();
 332
 333       seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
 334               : seqFeatures;
 335       if (seqFeatures == null)
 336       {
 337         continue;
 338       }
 339
 340       for (SequenceFeature sf : seqFeatures)
 341       {
 342         if (displayedFeatures != null
 343                 && displayedFeatures.isVisible(sf.getType()))
 344         {
 345           SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
 346                   String.valueOf(seq.hashCode()));
 347
 348           String featureColour = (fr == null) ? null : jalview.util.Format
 349                   .getHexString(fr.findFeatureColour(Color.white, seq,
 350                           seq.findIndex(sf.getBegin())));
 351           jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
 352           jsonFeature.setXend(seq.findIndex(sf.getEnd()));
 353           jsonFeature.setType(sf.getType());
 354           jsonFeature.setDescription(sf.getDescription());
 355           jsonFeature.setLinks(sf.links);
 356           jsonFeature.setOtherDetails(sf.otherDetails);
 357           jsonFeature.setScore(sf.getScore());
 358           jsonFeature.setFillColor(featureColour);
 359           jsonFeature.setFeatureGroup(sf.getFeatureGroup());
 360           sequenceFeaturesPojo.add(jsonFeature);
 361         }
 362       }
 363     }
 364     return sequenceFeaturesPojo;
 365   }
 366
 367   public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
 368           Vector<AlignmentAnnotation> annotations)
 369   {
 370     List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
 371     if (annotations == null)
 372     {
 373       return jsonAnnotations;
 374     }
 375     for (AlignmentAnnotation annot : annotations)
 376     {
 377       AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
 378       alignAnnotPojo.setDescription(annot.description);
 379       alignAnnotPojo.setLabel(annot.label);
 380       if (!Double.isNaN(annot.score))
 381       {
 382         alignAnnotPojo.setScore(annot.score);
 383       }
 384       alignAnnotPojo.setCalcId(annot.getCalcId());
 385       alignAnnotPojo.setGraphType(annot.graph);
 386
 387       AnnotationDisplaySettingPojo annotSetting = new AnnotationDisplaySettingPojo();
 388       annotSetting.setBelowAlignment(annot.belowAlignment);
 389       annotSetting.setCentreColLabels(annot.centreColLabels);
 390       annotSetting.setScaleColLabel(annot.scaleColLabel);
 391       annotSetting.setShowAllColLabels(annot.showAllColLabels);
 392       annotSetting.setVisible(annot.visible);
 393       annotSetting.setHasIcon(annot.hasIcons);
 394       alignAnnotPojo.setAnnotationSettings(annotSetting);
 395       SequenceI refSeq = annot.sequenceRef;
 396       if (refSeq != null)
 397       {
 398         alignAnnotPojo.setSequenceRef(String.valueOf(refSeq.hashCode()));
 399       }
 400       for (Annotation annotation : annot.annotations)
 401       {
 402         AnnotationPojo annotationPojo = new AnnotationPojo();
 403         if (annotation != null)
 404         {
 405           annotationPojo.setDescription(annotation.description);
 406           annotationPojo.setValue(annotation.value);
 407           annotationPojo
 408                   .setSecondaryStructure(annotation.secondaryStructure);
 409           String displayChar = annotation.displayCharacter == null ? null
 410                   : annotation.displayCharacter;
 411           // System.out.println("--------------------->[" + displayChar + "]");
 412           annotationPojo.setDisplayCharacter(displayChar);
 413           if (annotation.colour != null)
 414           {
 415             annotationPojo.setColour(jalview.util.Format
 416                     .getHexString(annotation.colour));
 417           }
 418           alignAnnotPojo.getAnnotations().add(annotationPojo);
 419         }
 420         else
 421         {
 422           if (annot.getCalcId() != null
 423                   && annot.getCalcId().equalsIgnoreCase(TCOFFEE_SCORE))
 424           {
 425             // do nothing
 426           }
 427           else
 428           {
 429             alignAnnotPojo.getAnnotations().add(annotationPojo);
 430           }
 431         }
 432       }
 433       jsonAnnotations.add(alignAnnotPojo);
 434     }
 435     return jsonAnnotations;
 436   }
 437
 438   @SuppressWarnings("unchecked")
 439   public JSONFile parse(Reader jsonAlignmentString)
 440   {
 441     try
 442     {
 443       JSONParser jsonParser = new JSONParser();
 444       JSONObject alignmentJsonObj = (JSONObject) jsonParser
 445               .parse(jsonAlignmentString);
 446       JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
 447       JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
 448               .get("alignAnnotation");
 449       JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
 450               .get("seqFeatures");
 451       JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
 452               .get("seqGroups");
 453       JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
 454               .get("appSettings");
 455
 456       if (jvSettingsJsonObj != null)
 457       {
 458         globalColourScheme = (String) jvSettingsJsonObj
 459                 .get("globalColorScheme");
 460         Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
 461                 "showSeqFeatures").toString());
 462         setShowSeqFeatures(showFeatures);
 463         parseHiddenSeqRefsAsList(jvSettingsJsonObj);
 464         parseHiddenCols(jvSettingsJsonObj);
 465       }
 466
 467       hiddenSequences = new ArrayList<SequenceI>();
 468       seqMap = new Hashtable<String, Sequence>();
 469       for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
 470               .hasNext();)
 471       {
 472         JSONObject sequence = sequenceIter.next();
 473         String sequcenceString = sequence.get("seq").toString();
 474         String sequenceName = sequence.get("name").toString();
 475         String seqUniqueId = sequence.get("id").toString();
 476         int start = Integer.valueOf(sequence.get("start").toString());
 477         int end = Integer.valueOf(sequence.get("end").toString());
 478         Sequence seq = new Sequence(sequenceName, sequcenceString, start,
 479                 end);
 480         if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
 481         {
 482           hiddenSequences.add(seq);
 483         }
 484         seqs.add(seq);
 485         seqMap.put(seqUniqueId, seq);
 486       }
 487
 488       parseFeatures(jsonSeqArray);
 489
 490       for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
 491               .hasNext();)
 492       {
 493         JSONObject seqGrpObj = seqGrpIter.next();
 494         String grpName = seqGrpObj.get("groupName").toString();
 495         String colourScheme = seqGrpObj.get("colourScheme").toString();
 496         String description = (seqGrpObj.get("description") == null) ? null
 497                 : seqGrpObj.get("description").toString();
 498         boolean displayBoxes = Boolean.valueOf(seqGrpObj
 499                 .get("displayBoxes").toString());
 500         boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
 501                 .toString());
 502         boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
 503                 .toString());
 504         boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
 505                 "showNonconserved").toString());
 506         int startRes = Integer
 507                 .valueOf(seqGrpObj.get("startRes").toString());
 508         int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
 509         JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
 510
 511         ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
 512         if (sequenceRefs.size() > 0)
 513         {
 514           Iterator<String> seqHashIter = sequenceRefs.iterator();
 515           while (seqHashIter.hasNext())
 516           {
 517             String seqHash = seqHashIter.next();
 518             Sequence sequence = seqMap.get(seqHash);
 519             if (sequence != null)
 520             {
 521               grpSeqs.add(sequence);
 522             }
 523           }
 524         }
 525         SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
 526                 displayBoxes, displayText, colourText, startRes, endRes);
 527         seqGrp.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme,
 528                 seqGrp);
 529         seqGrp.setShowNonconserved(showNonconserved);
 530         seqGrp.setDescription(description);
 531         this.seqGroups.add(seqGrp);
 532
 533       }
 534
 535       for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
 536               .hasNext();)
 537       {
 538         JSONObject alAnnot = alAnnotIter.next();
 539         JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
 540         Annotation[] annotations = new Annotation[annotJsonArray.size()];
 541         int count = 0;
 542         for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
 543                 .hasNext();)
 544         {
 545           JSONObject annot = annotIter.next();
 546           if (annot == null)
 547           {
 548             annotations[count] = null;
 549           }
 550           else
 551           {
 552             float val = annot.get("value") == null ? null : Float
 553                     .valueOf(annot.get("value").toString());
 554             String desc = annot.get("description") == null ? null : annot
 555                     .get("description").toString();
 556             char ss = annot.get("secondaryStructure") == null
 557                     || annot.get("secondaryStructure").toString()
 558                             .equalsIgnoreCase("u0000") ? ' ' : annot
 559                     .get("secondaryStructure").toString().charAt(0);
 560             String displayChar = annot.get("displayCharacter") == null ? ""
 561                     : annot.get("displayCharacter").toString();
 562
 563             annotations[count] = new Annotation(displayChar, desc, ss, val);
 564             if (annot.get("colour") != null)
 565             {
 566               Color color = UserColourScheme.getColourFromString(annot.get(
 567                       "colour").toString());
 568               annotations[count].colour = color;
 569             }
 570           }
 571           ++count;
 572         }
 573
 574         AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
 575                 .get("label").toString(), alAnnot.get("description")
 576                 .toString(), annotations);
 577         alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0 : Integer
 578                 .valueOf(alAnnot.get("graphType").toString());
 579
 580         JSONObject diplaySettings = (JSONObject) alAnnot
 581                 .get("annotationSettings");
 582         if (diplaySettings != null)
 583         {
 584
 585           alignAnnot.scaleColLabel = (diplaySettings.get("scaleColLabel") == null) ? false
 586                   : Boolean.valueOf(diplaySettings.get("scaleColLabel")
 587                           .toString());
 588           alignAnnot.showAllColLabels = (diplaySettings
 589                   .get("showAllColLabels") == null) ? true : Boolean
 590                   .valueOf(diplaySettings.get("showAllColLabels")
 591                           .toString());
 592           alignAnnot.centreColLabels = (diplaySettings
 593                   .get("centreColLabels") == null) ? true
 594                   : Boolean.valueOf(diplaySettings.get("centreColLabels")
 595                           .toString());
 596           alignAnnot.belowAlignment = (diplaySettings.get("belowAlignment") == null) ? false
 597                   : Boolean.valueOf(diplaySettings.get("belowAlignment")
 598                           .toString());
 599           alignAnnot.visible = (diplaySettings.get("visible") == null) ? true
 600                   : Boolean.valueOf(diplaySettings.get("visible")
 601                           .toString());
 602           alignAnnot.hasIcons = (diplaySettings.get("hasIcon") == null) ? true
 603                   : Boolean.valueOf(diplaySettings.get("hasIcon")
 604                           .toString());
 605
 606         }
 607         if (alAnnot.get("score") != null)
 608         {
 609           alignAnnot.score = Double
 610                   .valueOf(alAnnot.get("score").toString());
 611         }
 612
 613         String calcId = (alAnnot.get("calcId") == null) ? "" : alAnnot.get(
 614                 "calcId").toString();
 615         alignAnnot.setCalcId(calcId);
 616         String seqHash = (alAnnot.get("sequenceRef") != null) ? alAnnot
 617                 .get("sequenceRef").toString() : null;
 618
 619         Sequence sequence = (seqHash != null) ? seqMap.get(seqHash) : null;
 620         if (sequence != null)
 621         {
 622           alignAnnot.sequenceRef = sequence;
 623           sequence.addAlignmentAnnotation(alignAnnot);
 624           if (alignAnnot.label.equalsIgnoreCase("T-COFFEE"))
 625           {
 626             alignAnnot.createSequenceMapping(sequence, sequence.getStart(),
 627                     false);
 628             sequence.addAlignmentAnnotation(alignAnnot);
 629             alignAnnot.adjustForAlignment();
 630           }
 631         }
 632         alignAnnot.validateRangeAndDisplay();
 633         this.annotations.add(alignAnnot);
 634
 635       }
 636     } catch (Exception e)
 637     {
 638       e.printStackTrace();
 639     }
 640     return this;
 641   }
 642
 643   public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
 644   {
 645     hiddenSeqRefs = new ArrayList<String>();
 646     String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
 647     if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
 648     {
 649       String[] seqRefs = hiddenSeqs.split(";");
 650       for (String seqRef : seqRefs)
 651       {
 652         hiddenSeqRefs.add(seqRef);
 653       }
 654     }
 655   }
 656
 657   public void parseHiddenCols(JSONObject jvSettingsJson)
 658   {
 659     String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
 660     if (hiddenCols != null && !hiddenCols.isEmpty())
 661     {
 662       columnSelection = new ColumnSelection();
 663       String[] rangeStrings = hiddenCols.split(";");
 664       for (String rangeString : rangeStrings)
 665       {
 666         String[] range = rangeString.split("-");
 667         columnSelection.hideColumns(Integer.valueOf(range[0]),
 668                 Integer.valueOf(range[1]));
 669       }
 670     }
 671   }
 672
 673   @SuppressWarnings("unchecked")
 674   private void parseFeatures(JSONArray jsonSeqFeatures)
 675   {
 676     if (jsonSeqFeatures != null)
 677     {
 678       displayedFeatures = new FeaturesDisplayed();
 679       for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
 680               .hasNext();)
 681       {
 682         JSONObject jsonFeature = seqFeatureItr.next();
 683         Long begin = (Long) jsonFeature.get("xStart");
 684         Long end = (Long) jsonFeature.get("xEnd");
 685         String type = (String) jsonFeature.get("type");
 686         String featureGrp = (String) jsonFeature.get("featureGroup");
 687         String descripiton = (String) jsonFeature.get("description");
 688         String seqRef = (String) jsonFeature.get("sequenceRef");
 689         Float score = Float.valueOf(jsonFeature.get("score").toString());
 690
 691         Sequence seq = seqMap.get(seqRef);
 692         SequenceFeature sequenceFeature = new SequenceFeature();
 693         JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
 694         if (linksJsonArray != null && linksJsonArray.size() > 0)
 695         {
 696           Iterator<String> linkList = linksJsonArray.iterator();
 697           while (linkList.hasNext())
 698           {
 699             String link = linkList.next();
 700             sequenceFeature.addLink(link);
 701           }
 702         }
 703         sequenceFeature.setFeatureGroup(featureGrp);
 704         sequenceFeature.setScore(score);
 705         sequenceFeature.setDescription(descripiton);
 706         sequenceFeature.setType(type);
 707         sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
 708         sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
 709         seq.addSequenceFeature(sequenceFeature);
 710         displayedFeatures.setVisible(type);
 711       }
 712     }
 713   }
 714
 715   @Override
 716   public String getGlobalColourScheme()
 717   {
 718     return globalColourScheme;
 719   }
 720
 721   public void setGlobalColorScheme(String globalColourScheme)
 722   {
 723     this.globalColourScheme = globalColourScheme;
 724   }
 725
 726   @Override
 727   public FeaturesDisplayedI getDisplayedFeatures()
 728   {
 729     return displayedFeatures;
 730   }
 731
 732   public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
 733   {
 734     this.displayedFeatures = displayedFeatures;
 735   }
 736
 737   @Override
 738   public void configureForView(AlignmentViewPanel avpanel)
 739   {
 740     if (avpanel == null)
 741     {
 742       return;
 743     }
 744     super.configureForView(avpanel);
 745     AlignViewportI viewport = avpanel.getAlignViewport();
 746     AlignmentI alignment = viewport.getAlignment();
 747     AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
 748
 749     seqGroups = alignment.getGroups();
 750     fr = avpanel.cloneFeatureRenderer();
 751
 752     // Add non auto calculated annotation to AlignFile
 753     if (annots != null)
 754     {
 755       for (AlignmentAnnotation annot : annots)
 756       {
 757         if (annot != null && !annot.autoCalculated)
 758         {
 759           annotations.add(annot);
 760         }
 761       }
 762     }
 763     globalColourScheme = ColourSchemeProperty.getColourName(viewport
 764             .getGlobalColourScheme());
 765     setDisplayedFeatures(viewport.getFeaturesDisplayed());
 766     showSeqFeatures = viewport.isShowSequenceFeatures();
 767
 768   }
 769
 770   @Override
 771   public boolean isShowSeqFeatures()
 772   {
 773     return showSeqFeatures;
 774   }
 775
 776   public void setShowSeqFeatures(boolean showSeqFeatures)
 777   {
 778     this.showSeqFeatures = showSeqFeatures;
 779   }
 780
 781   public Vector<AlignmentAnnotation> getAnnotations()
 782   {
 783     return annotations;
 784   }
 785
 786   public List<int[]> getHiddenColumns()
 787   {
 788     return hiddenColumns;
 789   }
 790
 791   @Override
 792   public ColumnSelection getColumnSelection()
 793   {
 794     return columnSelection;
 795   }
 796
 797   public void setColumnSelection(ColumnSelection columnSelection)
 798   {
 799     this.columnSelection = columnSelection;
 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 }