src/jalview/io/JSONFile.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21
  22 package jalview.io;
  23
  24 import jalview.api.AlignExportSettingI;
  25 import jalview.api.AlignViewportI;
  26 import jalview.api.AlignmentViewPanel;
  27 import jalview.api.ComplexAlignFile;
  28 import jalview.api.FeatureRenderer;
  29 import jalview.api.FeatureSettingsModelI;
  30 import jalview.api.FeaturesDisplayedI;
  31 import jalview.bin.BuildDetails;
  32 import jalview.datamodel.AlignmentAnnotation;
  33 import jalview.datamodel.AlignmentI;
  34 import jalview.datamodel.Annotation;
  35 import jalview.datamodel.HiddenColumns;
  36 import jalview.datamodel.HiddenSequences;
  37 import jalview.datamodel.Sequence;
  38 import jalview.datamodel.SequenceFeature;
  39 import jalview.datamodel.SequenceGroup;
  40 import jalview.datamodel.SequenceI;
  41 import jalview.json.binding.biojson.v1.AlignmentAnnotationPojo;
  42 import jalview.json.binding.biojson.v1.AlignmentPojo;
  43 import jalview.json.binding.biojson.v1.AnnotationDisplaySettingPojo;
  44 import jalview.json.binding.biojson.v1.AnnotationPojo;
  45 import jalview.json.binding.biojson.v1.ColourSchemeMapper;
  46 import jalview.json.binding.biojson.v1.SequenceFeaturesPojo;
  47 import jalview.json.binding.biojson.v1.SequenceGrpPojo;
  48 import jalview.json.binding.biojson.v1.SequencePojo;
  49 import jalview.renderer.seqfeatures.FeatureColourFinder;
  50 import jalview.schemes.ColourSchemeProperty;
  51 import jalview.schemes.JalviewColourScheme;
  52 import jalview.schemes.ResidueColourScheme;
  53 import jalview.util.ColorUtils;
  54 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
  55
  56 import java.awt.Color;
  57 import java.io.IOException;
  58 import java.io.Reader;
  59 import java.util.ArrayList;
  60 import java.util.Hashtable;
  61 import java.util.Iterator;
  62 import java.util.List;
  63 import java.util.Vector;
  64
  65 import org.json.simple.JSONArray;
  66 import org.json.simple.JSONObject;
  67 import org.json.simple.parser.JSONParser;
  68
  69 public class JSONFile extends AlignFile implements ComplexAlignFile
  70 {
  71   private static String version = new BuildDetails().getVersion();
  72
  73   private String webstartUrl = "http://www.jalview.org/services/launchApp";
  74
  75   private String application = "Jalview";
  76
  77   private String globalColourScheme;
  78
  79   private boolean showSeqFeatures;
  80
  81   private Hashtable<String, Sequence> seqMap;
  82
  83   private FeaturesDisplayedI displayedFeatures;
  84
  85   private FeatureRenderer fr;
  86
  87   private HiddenColumns hiddenColumns;
  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.equalsIgnoreCase(
 222                         JalviewColourScheme.TCoffee.toString()))
 223         {
 224           jsonAlignmentPojo.setGlobalColorScheme(ResidueColourScheme.NONE);
 225         }
 226       }
 227
 228       if (exportSettings.isExportFeatures())
 229       {
 230         jsonAlignmentPojo
 231                 .setSeqFeatures(sequenceFeatureToJsonPojo(sqs, fr));
 232       }
 233
 234       if (exportSettings.isExportGroups() && seqGroups != null
 235               && seqGroups.size() > 0)
 236       {
 237         for (SequenceGroup seqGrp : seqGroups)
 238         {
 239           SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
 240           seqGrpPojo.setGroupName(seqGrp.getName());
 241           seqGrpPojo.setColourScheme(ColourSchemeProperty
 242                   .getColourName(seqGrp.getColourScheme()));
 243           seqGrpPojo.setColourText(seqGrp.getColourText());
 244           seqGrpPojo.setDescription(seqGrp.getDescription());
 245           seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
 246           seqGrpPojo.setDisplayText(seqGrp.getDisplayText());
 247           seqGrpPojo.setEndRes(seqGrp.getEndRes());
 248           seqGrpPojo.setStartRes(seqGrp.getStartRes());
 249           seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
 250           for (SequenceI seq : seqGrp.getSequences())
 251           {
 252             seqGrpPojo.getSequenceRefs()
 253                     .add(String.valueOf(seq.hashCode()));
 254           }
 255           jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
 256         }
 257       }
 258       org.json.JSONObject generatedJSon = new org.json.JSONObject(
 259               jsonAlignmentPojo);
 260       jsonOutput = generatedJSon.toString();
 261       return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
 262               "xEnd");
 263     } catch (Exception e)
 264     {
 265       e.printStackTrace();
 266     }
 267     return jsonOutput;
 268   }
 269
 270   public String[] getHiddenSections()
 271   {
 272     String[] hiddenSections = new String[2];
 273     if (getViewport() == null)
 274     {
 275       return null;
 276     }
 277
 278     // hidden column business
 279     if (getViewport().hasHiddenColumns())
 280     {
 281       hiddenSections[0] = getViewport().getAlignment().getHiddenColumns()
 282               .regionsToString(";", "-");
 283     }
 284
 285     // hidden rows/seqs business
 286     HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
 287             .getHiddenSequences();
 288     if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
 289     {
 290       return hiddenSections;
 291     }
 292
 293     SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
 294     StringBuilder hiddenSeqsBuilder = new StringBuilder();
 295     for (SequenceI hiddenSeq : hiddenSeqs)
 296     {
 297       if (hiddenSeq != null)
 298       {
 299         hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
 300       }
 301     }
 302     if (hiddenSeqsBuilder.length() > 0)
 303     {
 304       hiddenSeqsBuilder.deleteCharAt(0);
 305     }
 306     hiddenSections[1] = hiddenSeqsBuilder.toString();
 307
 308     return hiddenSections;
 309   }
 310
 311   public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
 312           SequenceI[] sqs, FeatureRenderer fr)
 313   {
 314     displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
 315     List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<>();
 316     if (sqs == null)
 317     {
 318       return sequenceFeaturesPojo;
 319     }
 320
 321     FeatureColourFinder finder = new FeatureColourFinder(fr);
 322
 323     for (SequenceI seq : sqs)
 324     {
 325       SequenceI dataSetSequence = seq.getDatasetSequence();
 326       SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
 327               : seq.getDatasetSequence().getSequenceFeatures();
 328
 329       seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
 330               : seqFeatures;
 331       if (seqFeatures == null)
 332       {
 333         continue;
 334       }
 335
 336       for (SequenceFeature sf : seqFeatures)
 337       {
 338         if (displayedFeatures != null
 339                 && displayedFeatures.isVisible(sf.getType()))
 340         {
 341           SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
 342                   String.valueOf(seq.hashCode()));
 343
 344           String featureColour = (fr == null) ? null
 345                   : jalview.util.Format.getHexString(
 346                           finder.findFeatureColour(Color.white, seq,
 347                                   seq.findIndex(sf.getBegin())));
 348           jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
 349           jsonFeature.setXend(seq.findIndex(sf.getEnd()));
 350           jsonFeature.setType(sf.getType());
 351           jsonFeature.setDescription(sf.getDescription());
 352           jsonFeature.setLinks(sf.links);
 353           jsonFeature.setOtherDetails(sf.otherDetails);
 354           jsonFeature.setScore(sf.getScore());
 355           jsonFeature.setFillColor(featureColour);
 356           jsonFeature.setFeatureGroup(sf.getFeatureGroup());
 357           sequenceFeaturesPojo.add(jsonFeature);
 358         }
 359       }
 360     }
 361     return sequenceFeaturesPojo;
 362   }
 363
 364   public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
 365           Vector<AlignmentAnnotation> annotations)
 366   {
 367     List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<>();
 368     if (annotations == null)
 369     {
 370       return jsonAnnotations;
 371     }
 372     for (AlignmentAnnotation annot : annotations)
 373     {
 374       AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
 375       alignAnnotPojo.setDescription(annot.description);
 376       alignAnnotPojo.setLabel(annot.label);
 377       if (!Double.isNaN(annot.score))
 378       {
 379         alignAnnotPojo.setScore(annot.score);
 380       }
 381       alignAnnotPojo.setCalcId(annot.getCalcId());
 382       alignAnnotPojo.setGraphType(annot.graph);
 383
 384       AnnotationDisplaySettingPojo annotSetting = new AnnotationDisplaySettingPojo();
 385       annotSetting.setBelowAlignment(annot.belowAlignment);
 386       annotSetting.setCentreColLabels(annot.centreColLabels);
 387       annotSetting.setScaleColLabel(annot.scaleColLabel);
 388       annotSetting.setShowAllColLabels(annot.showAllColLabels);
 389       annotSetting.setVisible(annot.visible);
 390       annotSetting.setHasIcon(annot.hasIcons);
 391       alignAnnotPojo.setAnnotationSettings(annotSetting);
 392       SequenceI refSeq = annot.sequenceRef;
 393       if (refSeq != null)
 394       {
 395         alignAnnotPojo.setSequenceRef(String.valueOf(refSeq.hashCode()));
 396       }
 397       for (Annotation annotation : annot.annotations)
 398       {
 399         AnnotationPojo annotationPojo = new AnnotationPojo();
 400         if (annotation != null)
 401         {
 402           annotationPojo.setDescription(annotation.description);
 403           annotationPojo.setValue(annotation.value);
 404           annotationPojo
 405                   .setSecondaryStructure(annotation.secondaryStructure);
 406           String displayChar = annotation.displayCharacter == null ? null
 407                   : annotation.displayCharacter;
 408           // System.out.println("--------------------->[" + displayChar + "]");
 409           annotationPojo.setDisplayCharacter(displayChar);
 410           if (annotation.colour != null)
 411           {
 412             annotationPojo.setColour(
 413                     jalview.util.Format.getHexString(annotation.colour));
 414           }
 415           alignAnnotPojo.getAnnotations().add(annotationPojo);
 416         }
 417         else
 418         {
 419           if (annot.getCalcId() != null
 420                   && annot.getCalcId().equalsIgnoreCase(TCOFFEE_SCORE))
 421           {
 422             // do nothing
 423           }
 424           else
 425           {
 426             alignAnnotPojo.getAnnotations().add(annotationPojo);
 427           }
 428         }
 429       }
 430       jsonAnnotations.add(alignAnnotPojo);
 431     }
 432     return jsonAnnotations;
 433   }
 434
 435   @SuppressWarnings("unchecked")
 436   public JSONFile parse(Reader jsonAlignmentString)
 437   {
 438     try
 439     {
 440       JSONParser jsonParser = new JSONParser();
 441       JSONObject alignmentJsonObj = (JSONObject) jsonParser
 442               .parse(jsonAlignmentString);
 443       JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
 444       JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
 445               .get("alignAnnotation");
 446       JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
 447               .get("seqFeatures");
 448       JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
 449               .get("seqGroups");
 450       JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
 451               .get("appSettings");
 452
 453       if (jvSettingsJsonObj != null)
 454       {
 455         globalColourScheme = (String) jvSettingsJsonObj
 456                 .get("globalColorScheme");
 457         Boolean showFeatures = Boolean.valueOf(
 458                 jvSettingsJsonObj.get("showSeqFeatures").toString());
 459         setShowSeqFeatures(showFeatures);
 460         parseHiddenSeqRefsAsList(jvSettingsJsonObj);
 461         parseHiddenCols(jvSettingsJsonObj);
 462       }
 463
 464       hiddenSequences = new ArrayList<>();
 465       seqMap = new Hashtable<>();
 466       for (Iterator<JSONObject> sequenceIter = seqJsonArray
 467               .iterator(); sequenceIter.hasNext();)
 468       {
 469         JSONObject sequence = sequenceIter.next();
 470         String sequcenceString = sequence.get("seq").toString();
 471         String sequenceName = sequence.get("name").toString();
 472         String seqUniqueId = sequence.get("id").toString();
 473         int start = Integer.valueOf(sequence.get("start").toString());
 474         int end = Integer.valueOf(sequence.get("end").toString());
 475         Sequence seq = new Sequence(sequenceName, sequcenceString, start,
 476                 end);
 477         if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
 478         {
 479           hiddenSequences.add(seq);
 480         }
 481         seqs.add(seq);
 482         seqMap.put(seqUniqueId, seq);
 483       }
 484
 485       parseFeatures(jsonSeqArray);
 486
 487       for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray
 488               .iterator(); seqGrpIter.hasNext();)
 489       {
 490         JSONObject seqGrpObj = seqGrpIter.next();
 491         String grpName = seqGrpObj.get("groupName").toString();
 492         String colourScheme = seqGrpObj.get("colourScheme").toString();
 493         String description = (seqGrpObj.get("description") == null) ? null
 494                 : seqGrpObj.get("description").toString();
 495         boolean displayBoxes = Boolean
 496                 .valueOf(seqGrpObj.get("displayBoxes").toString());
 497         boolean displayText = Boolean
 498                 .valueOf(seqGrpObj.get("displayText").toString());
 499         boolean colourText = Boolean
 500                 .valueOf(seqGrpObj.get("colourText").toString());
 501         boolean showNonconserved = Boolean
 502                 .valueOf(seqGrpObj.get("showNonconserved").toString());
 503         int startRes = Integer
 504                 .valueOf(seqGrpObj.get("startRes").toString());
 505         int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
 506         JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
 507
 508         ArrayList<SequenceI> grpSeqs = new ArrayList<>();
 509         if (sequenceRefs.size() > 0)
 510         {
 511           Iterator<String> seqHashIter = sequenceRefs.iterator();
 512           while (seqHashIter.hasNext())
 513           {
 514             String seqHash = seqHashIter.next();
 515             Sequence sequence = seqMap.get(seqHash);
 516             if (sequence != null)
 517             {
 518               grpSeqs.add(sequence);
 519             }
 520           }
 521         }
 522         SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
 523                 displayBoxes, displayText, colourText, startRes, endRes);
 524         seqGrp.setColourScheme(ColourSchemeMapper
 525                 .getJalviewColourScheme(colourScheme, seqGrp));
 526         seqGrp.setShowNonconserved(showNonconserved);
 527         seqGrp.setDescription(description);
 528         this.seqGroups.add(seqGrp);
 529
 530       }
 531
 532       for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray
 533               .iterator(); alAnnotIter.hasNext();)
 534       {
 535         JSONObject alAnnot = alAnnotIter.next();
 536         JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
 537         Annotation[] annotations = new Annotation[annotJsonArray.size()];
 538         int count = 0;
 539         for (Iterator<JSONObject> annotIter = annotJsonArray
 540                 .iterator(); annotIter.hasNext();)
 541         {
 542           JSONObject annot = annotIter.next();
 543           if (annot == null)
 544           {
 545             annotations[count] = null;
 546           }
 547           else
 548           {
 549             float val = annot.get("value") == null ? null
 550                     : Float.valueOf(annot.get("value").toString());
 551             String desc = annot.get("description") == null ? null
 552                     : annot.get("description").toString();
 553             char ss = annot.get("secondaryStructure") == null
 554                     || annot.get("secondaryStructure").toString()
 555                             .equalsIgnoreCase("u0000") ? ' '
 556                                     : annot.get("secondaryStructure")
 557                                             .toString().charAt(0);
 558             String displayChar = annot.get("displayCharacter") == null ? ""
 559                     : annot.get("displayCharacter").toString();
 560
 561             annotations[count] = new Annotation(displayChar, desc, ss, val);
 562             if (annot.get("colour") != null)
 563             {
 564               Color color = ColorUtils
 565                       .parseColourString(annot.get("colour").toString());
 566               annotations[count].colour = color;
 567             }
 568           }
 569           ++count;
 570         }
 571
 572         AlignmentAnnotation alignAnnot = new AlignmentAnnotation(
 573                 alAnnot.get("label").toString(),
 574                 alAnnot.get("description").toString(), annotations);
 575         alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0
 576                 : Integer.valueOf(alAnnot.get("graphType").toString());
 577
 578         JSONObject diplaySettings = (JSONObject) alAnnot
 579                 .get("annotationSettings");
 580         if (diplaySettings != null)
 581         {
 582
 583           alignAnnot.scaleColLabel = (diplaySettings
 584                   .get("scaleColLabel") == null) ? false
 585                           : Boolean.valueOf(diplaySettings
 586                                   .get("scaleColLabel").toString());
 587           alignAnnot.showAllColLabels = (diplaySettings
 588                   .get("showAllColLabels") == null) ? true
 589                           : Boolean.valueOf(diplaySettings
 590                                   .get("showAllColLabels").toString());
 591           alignAnnot.centreColLabels = (diplaySettings
 592                   .get("centreColLabels") == null) ? true
 593                           : Boolean.valueOf(diplaySettings
 594                                   .get("centreColLabels").toString());
 595           alignAnnot.belowAlignment = (diplaySettings
 596                   .get("belowAlignment") == null) ? false
 597                           : Boolean.valueOf(diplaySettings
 598                                   .get("belowAlignment").toString());
 599           alignAnnot.visible = (diplaySettings.get("visible") == null)
 600                   ? true
 601                   : Boolean.valueOf(
 602                           diplaySettings.get("visible").toString());
 603           alignAnnot.hasIcons = (diplaySettings.get("hasIcon") == null)
 604                   ? true
 605                   : Boolean.valueOf(
 606                           diplaySettings.get("hasIcon").toString());
 607
 608         }
 609         if (alAnnot.get("score") != null)
 610         {
 611           alignAnnot.score = Double
 612                   .valueOf(alAnnot.get("score").toString());
 613         }
 614
 615         String calcId = (alAnnot.get("calcId") == null) ? ""
 616                 : alAnnot.get("calcId").toString();
 617         alignAnnot.setCalcId(calcId);
 618         String seqHash = (alAnnot.get("sequenceRef") != null)
 619                 ? alAnnot.get("sequenceRef").toString()
 620                 : 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<>();
 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       hiddenColumns = new HiddenColumns();
 666       String[] rangeStrings = hiddenCols.split(";");
 667       for (String rangeString : rangeStrings)
 668       {
 669         String[] range = rangeString.split("-");
 670         hiddenColumns.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
 683               .iterator(); seqFeatureItr.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 = ColourSchemeProperty
 767             .getColourName(viewport.getGlobalColourScheme());
 768     setDisplayedFeatures(viewport.getFeaturesDisplayed());
 769     showSeqFeatures = viewport.isShowSequenceFeatures();
 770
 771   }
 772
 773   @Override
 774   public boolean isShowSeqFeatures()
 775   {
 776     return showSeqFeatures;
 777   }
 778
 779   public void setShowSeqFeatures(boolean showSeqFeatures)
 780   {
 781     this.showSeqFeatures = showSeqFeatures;
 782   }
 783
 784   public Vector<AlignmentAnnotation> getAnnotations()
 785   {
 786     return annotations;
 787   }
 788
 789   @Override
 790   public HiddenColumns getHiddenColumns()
 791   {
 792     return hiddenColumns;
 793   }
 794
 795   public void setHiddenColumns(HiddenColumns hidden)
 796   {
 797     this.hiddenColumns = hidden;
 798   }
 799
 800   @Override
 801   public SequenceI[] getHiddenSequences()
 802   {
 803     if (hiddenSequences == null || hiddenSequences.isEmpty())
 804     {
 805       return new SequenceI[] {};
 806     }
 807     synchronized (hiddenSequences)
 808     {
 809       return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
 810     }
 811   }
 812
 813   public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
 814   {
 815     this.hiddenSequences = hiddenSequences;
 816   }
 817
 818   public class JSONExportSettings
 819   {
 820     private boolean exportSequence;
 821
 822     private boolean exportSequenceFeatures;
 823
 824     private boolean exportAnnotations;
 825
 826     private boolean exportGroups;
 827
 828     private boolean exportJalviewSettings;
 829
 830     public boolean isExportSequence()
 831     {
 832       return exportSequence;
 833     }
 834
 835     public void setExportSequence(boolean exportSequence)
 836     {
 837       this.exportSequence = exportSequence;
 838     }
 839
 840     public boolean isExportSequenceFeatures()
 841     {
 842       return exportSequenceFeatures;
 843     }
 844
 845     public void setExportSequenceFeatures(boolean exportSequenceFeatures)
 846     {
 847       this.exportSequenceFeatures = exportSequenceFeatures;
 848     }
 849
 850     public boolean isExportAnnotations()
 851     {
 852       return exportAnnotations;
 853     }
 854
 855     public void setExportAnnotations(boolean exportAnnotations)
 856     {
 857       this.exportAnnotations = exportAnnotations;
 858     }
 859
 860     public boolean isExportGroups()
 861     {
 862       return exportGroups;
 863     }
 864
 865     public void setExportGroups(boolean exportGroups)
 866     {
 867       this.exportGroups = exportGroups;
 868     }
 869
 870     public boolean isExportJalviewSettings()
 871     {
 872       return exportJalviewSettings;
 873     }
 874
 875     public void setExportJalviewSettings(boolean exportJalviewSettings)
 876     {
 877       this.exportJalviewSettings = exportJalviewSettings;
 878     }
 879   }
 880
 881   /**
 882    * Returns a descriptor for suitable feature display settings with
 883    * <ul>
 884    * <li>ResNums or insertions features visible</li>
 885    * <li>insertions features coloured red</li>
 886    * <li>ResNum features coloured by label</li>
 887    * <li>Insertions displayed above (on top of) ResNums</li>
 888    * </ul>
 889    */
 890   @Override
 891   public FeatureSettingsModelI getFeatureColourScheme()
 892   {
 893     return new PDBFeatureSettings();
 894   }
 895 }