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()
 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 : seqs)
 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(seqs, 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           List<SequenceI> seqs, FeatureRenderer fr)
 319   {
 320     displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
 321     List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
 322     for (SequenceI seq : seqs)
 323     {
 324       SequenceI dataSetSequence = seq.getDatasetSequence();
 325       SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
 326               : seq.getDatasetSequence().getSequenceFeatures();
 327
 328       seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
 329               : seqFeatures;
 330       if (seqFeatures == null)
 331       {
 332         continue;
 333       }
 334
 335       for (SequenceFeature sf : seqFeatures)
 336       {
 337         if (displayedFeatures != null
 338                 && displayedFeatures.isVisible(sf.getType()))
 339         {
 340           SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
 341                   String.valueOf(seq.hashCode()));
 342
 343           String featureColour = (fr == null) ? null : jalview.util.Format
 344                   .getHexString(fr.findFeatureColour(Color.white, seq,
 345                           seq.findIndex(sf.getBegin())));
 346           jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
 347           jsonFeature.setXend(seq.findIndex(sf.getEnd()));
 348           jsonFeature.setType(sf.getType());
 349           jsonFeature.setDescription(sf.getDescription());
 350           jsonFeature.setLinks(sf.links);
 351           jsonFeature.setOtherDetails(sf.otherDetails);
 352           jsonFeature.setScore(sf.getScore());
 353           jsonFeature.setFillColor(featureColour);
 354           jsonFeature.setFeatureGroup(sf.getFeatureGroup());
 355           sequenceFeaturesPojo.add(jsonFeature);
 356         }
 357       }
 358     }
 359     return sequenceFeaturesPojo;
 360   }
 361
 362   public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
 363           Vector<AlignmentAnnotation> annotations)
 364   {
 365     List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
 366     if (annotations == null)
 367     {
 368       return jsonAnnotations;
 369     }
 370     for (AlignmentAnnotation annot : annotations)
 371     {
 372       AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
 373       alignAnnotPojo.setDescription(annot.description);
 374       alignAnnotPojo.setLabel(annot.label);
 375       if (!Double.isNaN(annot.score))
 376       {
 377         alignAnnotPojo.setScore(annot.score);
 378       }
 379       alignAnnotPojo.setCalcId(annot.getCalcId());
 380       alignAnnotPojo.setGraphType(annot.graph);
 381
 382       AnnotationDisplaySettingPojo annotSetting = new AnnotationDisplaySettingPojo();
 383       annotSetting.setBelowAlignment(annot.belowAlignment);
 384       annotSetting.setCentreColLabels(annot.centreColLabels);
 385       annotSetting.setScaleColLabel(annot.scaleColLabel);
 386       annotSetting.setShowAllColLabels(annot.showAllColLabels);
 387       annotSetting.setVisible(annot.visible);
 388       annotSetting.setHasIcon(annot.hasIcons);
 389       alignAnnotPojo.setAnnotationSettings(annotSetting);
 390       SequenceI refSeq = annot.sequenceRef;
 391       if (refSeq != null)
 392       {
 393         alignAnnotPojo.setSequenceRef(String.valueOf(refSeq.hashCode()));
 394       }
 395       for (Annotation annotation : annot.annotations)
 396       {
 397         AnnotationPojo annotationPojo = new AnnotationPojo();
 398         if (annotation != null)
 399         {
 400           annotationPojo.setDescription(annotation.description);
 401           annotationPojo.setValue(annotation.value);
 402           annotationPojo
 403                   .setSecondaryStructure(annotation.secondaryStructure);
 404           String displayChar = annotation.displayCharacter == null ? null
 405                   : annotation.displayCharacter;
 406           // System.out.println("--------------------->[" + displayChar + "]");
 407           annotationPojo.setDisplayCharacter(displayChar);
 408           if (annotation.colour != null)
 409           {
 410             annotationPojo.setColour(jalview.util.Format
 411                     .getHexString(annotation.colour));
 412           }
 413           alignAnnotPojo.getAnnotations().add(annotationPojo);
 414         }
 415         else
 416         {
 417           if (annot.getCalcId() != null
 418                   && annot.getCalcId().equalsIgnoreCase(TCOFFEE_SCORE))
 419           {
 420             // do nothing
 421           }
 422           else
 423           {
 424             alignAnnotPojo.getAnnotations().add(annotationPojo);
 425           }
 426         }
 427       }
 428       jsonAnnotations.add(alignAnnotPojo);
 429     }
 430     return jsonAnnotations;
 431   }
 432
 433   @SuppressWarnings("unchecked")
 434   public JSONFile parse(Reader jsonAlignmentString)
 435   {
 436     try
 437     {
 438       JSONParser jsonParser = new JSONParser();
 439       JSONObject alignmentJsonObj = (JSONObject) jsonParser
 440               .parse(jsonAlignmentString);
 441       JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
 442       JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
 443               .get("alignAnnotation");
 444       JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
 445               .get("seqFeatures");
 446       JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
 447               .get("seqGroups");
 448       JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
 449               .get("appSettings");
 450
 451       if (jvSettingsJsonObj != null)
 452       {
 453         globalColourScheme = (String) jvSettingsJsonObj
 454                 .get("globalColorScheme");
 455         Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
 456                 "showSeqFeatures").toString());
 457         setShowSeqFeatures(showFeatures);
 458         parseHiddenSeqRefsAsList(jvSettingsJsonObj);
 459         parseHiddenCols(jvSettingsJsonObj);
 460       }
 461
 462       hiddenSequences = new ArrayList<SequenceI>();
 463       seqMap = new Hashtable<String, Sequence>();
 464       for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
 465               .hasNext();)
 466       {
 467         JSONObject sequence = sequenceIter.next();
 468         String sequcenceString = sequence.get("seq").toString();
 469         String sequenceName = sequence.get("name").toString();
 470         String seqUniqueId = sequence.get("id").toString();
 471         int start = Integer.valueOf(sequence.get("start").toString());
 472         int end = Integer.valueOf(sequence.get("end").toString());
 473         Sequence seq = new Sequence(sequenceName, sequcenceString, start,
 474                 end);
 475         if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
 476         {
 477           hiddenSequences.add(seq);
 478         }
 479         seqs.add(seq);
 480         seqMap.put(seqUniqueId, seq);
 481       }
 482
 483       parseFeatures(jsonSeqArray);
 484
 485       for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
 486               .hasNext();)
 487       {
 488         JSONObject seqGrpObj = seqGrpIter.next();
 489         String grpName = seqGrpObj.get("groupName").toString();
 490         String colourScheme = seqGrpObj.get("colourScheme").toString();
 491         String description = (seqGrpObj.get("description") == null) ? null
 492                 : seqGrpObj.get("description").toString();
 493         boolean displayBoxes = Boolean.valueOf(seqGrpObj
 494                 .get("displayBoxes").toString());
 495         boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
 496                 .toString());
 497         boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
 498                 .toString());
 499         boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
 500                 "showNonconserved").toString());
 501         int startRes = Integer
 502                 .valueOf(seqGrpObj.get("startRes").toString());
 503         int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
 504         JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
 505
 506         ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
 507         if (sequenceRefs.size() > 0)
 508         {
 509           Iterator<String> seqHashIter = sequenceRefs.iterator();
 510           while (seqHashIter.hasNext())
 511           {
 512             String seqHash = seqHashIter.next();
 513             Sequence sequence = seqMap.get(seqHash);
 514             if (sequence != null)
 515             {
 516               grpSeqs.add(sequence);
 517             }
 518           }
 519         }
 520         SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
 521                 displayBoxes, displayText, colourText, startRes, endRes);
 522         seqGrp.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme,
 523                 seqGrp);
 524         seqGrp.setShowNonconserved(showNonconserved);
 525         seqGrp.setDescription(description);
 526         this.seqGroups.add(seqGrp);
 527
 528       }
 529
 530       for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
 531               .hasNext();)
 532       {
 533         JSONObject alAnnot = alAnnotIter.next();
 534         JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
 535         Annotation[] annotations = new Annotation[annotJsonArray.size()];
 536         int count = 0;
 537         for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
 538                 .hasNext();)
 539         {
 540           JSONObject annot = annotIter.next();
 541           if (annot == null)
 542           {
 543             annotations[count] = null;
 544           }
 545           else
 546           {
 547             float val = annot.get("value") == null ? null : Float
 548                     .valueOf(annot.get("value").toString());
 549             String desc = annot.get("description") == null ? null : annot
 550                     .get("description").toString();
 551             char ss = annot.get("secondaryStructure") == null
 552                     || annot.get("secondaryStructure").toString()
 553                             .equalsIgnoreCase("u0000") ? ' ' : annot
 554                     .get("secondaryStructure").toString().charAt(0);
 555             String displayChar = annot.get("displayCharacter") == null ? ""
 556                     : annot.get("displayCharacter").toString();
 557
 558             annotations[count] = new Annotation(displayChar, desc, ss, val);
 559             if (annot.get("colour") != null)
 560             {
 561               Color color = UserColourScheme.getColourFromString(annot.get(
 562                       "colour").toString());
 563               annotations[count].colour = color;
 564             }
 565           }
 566           ++count;
 567         }
 568
 569         AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
 570                 .get("label").toString(), alAnnot.get("description")
 571                 .toString(), annotations);
 572         alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0 : Integer
 573                 .valueOf(alAnnot.get("graphType").toString());
 574
 575         JSONObject diplaySettings = (JSONObject) alAnnot
 576                 .get("annotationSettings");
 577         if (diplaySettings != null)
 578         {
 579
 580           alignAnnot.scaleColLabel = (diplaySettings.get("scaleColLabel") == null) ? false
 581                   : Boolean.valueOf(diplaySettings.get("scaleColLabel")
 582                           .toString());
 583           alignAnnot.showAllColLabels = (diplaySettings
 584                   .get("showAllColLabels") == null) ? true : Boolean
 585                   .valueOf(diplaySettings.get("showAllColLabels")
 586                           .toString());
 587           alignAnnot.centreColLabels = (diplaySettings
 588                   .get("centreColLabels") == null) ? true
 589                   : Boolean.valueOf(diplaySettings.get("centreColLabels")
 590                           .toString());
 591           alignAnnot.belowAlignment = (diplaySettings.get("belowAlignment") == null) ? false
 592                   : Boolean.valueOf(diplaySettings.get("belowAlignment")
 593                           .toString());
 594           alignAnnot.visible = (diplaySettings.get("visible") == null) ? true
 595                   : Boolean.valueOf(diplaySettings.get("visible")
 596                           .toString());
 597           alignAnnot.hasIcons = (diplaySettings.get("hasIcon") == null) ? true
 598                   : Boolean.valueOf(diplaySettings.get("hasIcon")
 599                           .toString());
 600
 601         }
 602         if (alAnnot.get("score") != null)
 603         {
 604           alignAnnot.score = Double
 605                   .valueOf(alAnnot.get("score").toString());
 606         }
 607
 608         String calcId = (alAnnot.get("calcId") == null) ? "" : alAnnot.get(
 609                 "calcId").toString();
 610         alignAnnot.setCalcId(calcId);
 611         String seqHash = (alAnnot.get("sequenceRef") != null) ? alAnnot
 612                 .get("sequenceRef").toString() : null;
 613
 614         Sequence sequence = (seqHash != null) ? seqMap.get(seqHash) : null;
 615         if (sequence != null)
 616         {
 617           alignAnnot.sequenceRef = sequence;
 618           sequence.addAlignmentAnnotation(alignAnnot);
 619           if (alignAnnot.label.equalsIgnoreCase("T-COFFEE"))
 620           {
 621             alignAnnot.createSequenceMapping(sequence, sequence.getStart(),
 622                     false);
 623             sequence.addAlignmentAnnotation(alignAnnot);
 624             alignAnnot.adjustForAlignment();
 625           }
 626         }
 627         alignAnnot.validateRangeAndDisplay();
 628         this.annotations.add(alignAnnot);
 629
 630       }
 631     } catch (Exception e)
 632     {
 633       e.printStackTrace();
 634     }
 635     return this;
 636   }
 637
 638   public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
 639   {
 640     hiddenSeqRefs = new ArrayList<String>();
 641     String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
 642     if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
 643     {
 644       String[] seqRefs = hiddenSeqs.split(";");
 645       for (String seqRef : seqRefs)
 646       {
 647         hiddenSeqRefs.add(seqRef);
 648       }
 649     }
 650   }
 651
 652   public void parseHiddenCols(JSONObject jvSettingsJson)
 653   {
 654     String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
 655     if (hiddenCols != null && !hiddenCols.isEmpty())
 656     {
 657       columnSelection = new ColumnSelection();
 658       String[] rangeStrings = hiddenCols.split(";");
 659       for (String rangeString : rangeStrings)
 660       {
 661         String[] range = rangeString.split("-");
 662         columnSelection.hideColumns(Integer.valueOf(range[0]),
 663                 Integer.valueOf(range[1]));
 664       }
 665     }
 666   }
 667
 668   @SuppressWarnings("unchecked")
 669   private void parseFeatures(JSONArray jsonSeqFeatures)
 670   {
 671     if (jsonSeqFeatures != null)
 672     {
 673       displayedFeatures = new FeaturesDisplayed();
 674       for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
 675               .hasNext();)
 676       {
 677         JSONObject jsonFeature = seqFeatureItr.next();
 678         Long begin = (Long) jsonFeature.get("xStart");
 679         Long end = (Long) jsonFeature.get("xEnd");
 680         String type = (String) jsonFeature.get("type");
 681         String featureGrp = (String) jsonFeature.get("featureGroup");
 682         String descripiton = (String) jsonFeature.get("description");
 683         String seqRef = (String) jsonFeature.get("sequenceRef");
 684         Float score = Float.valueOf(jsonFeature.get("score").toString());
 685
 686         Sequence seq = seqMap.get(seqRef);
 687         SequenceFeature sequenceFeature = new SequenceFeature();
 688         JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
 689         if (linksJsonArray != null && linksJsonArray.size() > 0)
 690         {
 691           Iterator<String> linkList = linksJsonArray.iterator();
 692           while (linkList.hasNext())
 693           {
 694             String link = linkList.next();
 695             sequenceFeature.addLink(link);
 696           }
 697         }
 698         sequenceFeature.setFeatureGroup(featureGrp);
 699         sequenceFeature.setScore(score);
 700         sequenceFeature.setDescription(descripiton);
 701         sequenceFeature.setType(type);
 702         sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
 703         sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
 704         seq.addSequenceFeature(sequenceFeature);
 705         displayedFeatures.setVisible(type);
 706       }
 707     }
 708   }
 709
 710   @Override
 711   public String getGlobalColourScheme()
 712   {
 713     return globalColourScheme;
 714   }
 715
 716   public void setGlobalColorScheme(String globalColourScheme)
 717   {
 718     this.globalColourScheme = globalColourScheme;
 719   }
 720
 721   @Override
 722   public FeaturesDisplayedI getDisplayedFeatures()
 723   {
 724     return displayedFeatures;
 725   }
 726
 727   public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
 728   {
 729     this.displayedFeatures = displayedFeatures;
 730   }
 731
 732   @Override
 733   public void configureForView(AlignmentViewPanel avpanel)
 734   {
 735     super.configureForView(avpanel);
 736     AlignViewportI viewport = avpanel.getAlignViewport();
 737     AlignmentI alignment = viewport.getAlignment();
 738     AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
 739
 740     seqGroups = alignment.getGroups();
 741     fr = avpanel.cloneFeatureRenderer();
 742
 743     // Add non auto calculated annotation to AlignFile
 744     if (annots != null)
 745     {
 746       for (AlignmentAnnotation annot : annots)
 747       {
 748         if (annot != null && !annot.autoCalculated)
 749         {
 750           annotations.add(annot);
 751         }
 752       }
 753     }
 754     globalColourScheme = ColourSchemeProperty.getColourName(viewport
 755             .getGlobalColourScheme());
 756     setDisplayedFeatures(viewport.getFeaturesDisplayed());
 757     showSeqFeatures = viewport.isShowSequenceFeatures();
 758
 759   }
 760
 761   @Override
 762   public boolean isShowSeqFeatures()
 763   {
 764     return showSeqFeatures;
 765   }
 766
 767   public void setShowSeqFeatures(boolean showSeqFeatures)
 768   {
 769     this.showSeqFeatures = showSeqFeatures;
 770   }
 771
 772   public Vector<AlignmentAnnotation> getAnnotations()
 773   {
 774     return annotations;
 775   }
 776
 777   public List<int[]> getHiddenColumns()
 778   {
 779     return hiddenColumns;
 780   }
 781
 782   @Override
 783   public ColumnSelection getColumnSelection()
 784   {
 785     return columnSelection;
 786   }
 787
 788   public void setColumnSelection(ColumnSelection columnSelection)
 789   {
 790     this.columnSelection = columnSelection;
 791   }
 792
 793   @Override
 794   public SequenceI[] getHiddenSequences()
 795   {
 796     if (hiddenSequences == null || hiddenSequences.isEmpty())
 797     {
 798       return new SequenceI[] {};
 799     }
 800     synchronized (hiddenSequences)
 801     {
 802       return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
 803     }
 804   }
 805
 806   public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
 807   {
 808     this.hiddenSequences = hiddenSequences;
 809   }
 810
 811   public class JSONExportSettings
 812   {
 813     private boolean exportSequence;
 814
 815     private boolean exportSequenceFeatures;
 816
 817     private boolean exportAnnotations;
 818
 819     private boolean exportGroups;
 820
 821     private boolean exportJalviewSettings;
 822
 823     public boolean isExportSequence()
 824     {
 825       return exportSequence;
 826     }
 827
 828     public void setExportSequence(boolean exportSequence)
 829     {
 830       this.exportSequence = exportSequence;
 831     }
 832
 833     public boolean isExportSequenceFeatures()
 834     {
 835       return exportSequenceFeatures;
 836     }
 837
 838     public void setExportSequenceFeatures(boolean exportSequenceFeatures)
 839     {
 840       this.exportSequenceFeatures = exportSequenceFeatures;
 841     }
 842
 843     public boolean isExportAnnotations()
 844     {
 845       return exportAnnotations;
 846     }
 847
 848     public void setExportAnnotations(boolean exportAnnotations)
 849     {
 850       this.exportAnnotations = exportAnnotations;
 851     }
 852
 853     public boolean isExportGroups()
 854     {
 855       return exportGroups;
 856     }
 857
 858     public void setExportGroups(boolean exportGroups)
 859     {
 860       this.exportGroups = exportGroups;
 861     }
 862
 863     public boolean isExportJalviewSettings()
 864     {
 865       return exportJalviewSettings;
 866     }
 867
 868     public void setExportJalviewSettings(boolean exportJalviewSettings)
 869     {
 870       this.exportJalviewSettings = exportJalviewSettings;
 871     }
 872   }
 873
 874   /**
 875    * Returns a descriptor for suitable feature display settings with
 876    * <ul>
 877    * <li>ResNums or insertions features visible</li>
 878    * <li>insertions features coloured red</li>
 879    * <li>ResNum features coloured by label</li>
 880    * <li>Insertions displayed above (on top of) ResNums</li>
 881    * </ul>
 882    */
 883   @Override
 884   public FeatureSettingsModelI getFeatureColourScheme()
 885   {
 886     return new PDBFeatureSettings();
 887   }
 888 }