src/jalview/io/JSONFile.java

   1 package jalview.io;
   2
   3 import jalview.api.FeaturesDisplayedI;
   4 import jalview.datamodel.AlignmentAnnotation;
   5 import jalview.datamodel.Annotation;
   6 import jalview.datamodel.Sequence;
   7 import jalview.datamodel.SequenceFeature;
   8 import jalview.datamodel.SequenceGroup;
   9 import jalview.datamodel.SequenceI;
  10 import jalview.gui.AlignFrame;
  11 import jalview.gui.Desktop;
  12 import jalview.json.binding.v1.AlignmentAnnotationPojo;
  13 import jalview.json.binding.v1.AlignmentPojo;
  14 import jalview.json.binding.v1.AlignmentPojo.JalviewBioJsColorSchemeMapper;
  15 import jalview.json.binding.v1.AnnotationPojo;
  16 import jalview.json.binding.v1.FeaturePojo;
  17 import jalview.json.binding.v1.SequenceGrpPojo;
  18 import jalview.json.binding.v1.SequencePojo;
  19 import jalview.schemes.ColourSchemeI;
  20 import jalview.schemes.ColourSchemeProperty;
  21 import jalview.viewmodel.AlignmentViewport;
  22
  23 import java.awt.Color;
  24 import java.io.IOException;
  25 import java.util.ArrayList;
  26 import java.util.Hashtable;
  27 import java.util.Iterator;
  28
  29 import org.json.simple.JSONArray;
  30 import org.json.simple.JSONObject;
  31 import org.json.simple.parser.JSONParser;
  32
  33 public class JSONFile extends AlignFile
  34 {
  35   private ColourSchemeI cs;
  36
  37   private String jalviewVersion;
  38
  39   private String webStartLaunchServletUrl = "http://www.jalview.org/services/launchApp";
  40
  41   public static final String FILE_EXT = "json";
  42
  43   public static final String FILE_DESC = "JSON";
  44
  45   private String globalColorScheme;
  46
  47   private Hashtable<String, Sequence> seqMap;
  48
  49   private FeaturesDisplayedI displayedFeatures;
  50
  51   // private AlignmentI al;
  52
  53   private AlignmentViewport av;
  54
  55   private jalview.api.FeatureRenderer fr;
  56
  57   public JSONFile()
  58   {
  59     super();
  60   }
  61
  62   public JSONFile(FileParse source) throws IOException
  63   {
  64     super(source);
  65   }
  66
  67   public JSONFile(String inFile, String type) throws IOException
  68   {
  69     super(inFile, type);
  70   }
  71
  72
  73   @Override
  74   public void parse() throws IOException
  75   {
  76     StringBuilder jsonStringBuilder = new StringBuilder();
  77     String currentLine;
  78     while ((currentLine = nextLine()) != null)
  79     {
  80       jsonStringBuilder.append(currentLine);
  81     }
  82     parse(jsonStringBuilder.toString());
  83
  84   }
  85
  86   @Override
  87   public String print()
  88   {
  89     AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
  90     if (Desktop.getCurrentAlignFrame() != null)
  91     {
  92       jsonAlignmentPojo.setGlobalColorScheme(ColourSchemeProperty
  93               .getColourName(Desktop.getCurrentAlignFrame().getViewport()
  94                       .getGlobalColourScheme()));
  95       this.av = Desktop.getCurrentAlignFrame().getCurrentView();
  96       this.fr = Desktop.getCurrentAlignFrame().alignPanel
  97               .cloneFeatureRenderer();
  98       displayedFeatures = av.getFeaturesDisplayed();
  99     }
 100     jsonAlignmentPojo.setJalviewVersion(jalviewVersion);
 101     jsonAlignmentPojo.setWebStartUrl(webStartLaunchServletUrl);
 102
 103     System.out.println(">>>>>>>>>>>>>> found grps : " + seqGroups.size());
 104     if (seqGroups.size() > 0)
 105     {
 106       ArrayList<SequenceGrpPojo> sequenceGroupsPojo = new ArrayList<SequenceGrpPojo>();
 107       for (SequenceGroup seqGrp : seqGroups)
 108       {
 109         System.out.println(">>>>>>>>>>>> grp : " + seqGrp.getName());
 110         SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
 111         seqGrpPojo.setGroupName(seqGrp.getName());
 112         seqGrpPojo.setColourScheme(ColourSchemeProperty
 113                 .getColourName(seqGrp.cs));
 114         seqGrpPojo.setColourText(seqGrp.getColourText());
 115         seqGrpPojo.setDescription(seqGrp.getDescription());
 116         seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
 117         seqGrpPojo.setDisplayText(seqGrp.getDisplayText());
 118         seqGrpPojo.setEndRes(seqGrp.getEndRes());
 119         seqGrpPojo.setStartRes(seqGrp.getStartRes());
 120         seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
 121         jsonAlignmentPojo.getSequenceGroups().add(seqGrpPojo);
 122         for(SequenceI seq : seqGrp.getSequences()){
 123           seqGrpPojo.getSeqsHash().add(seq.getName() + "_" + seq.hashCode());
 124         }
 125         // sequenceGroupsPojo.add(seqGrpPojo);
 126       }
 127     }
 128     for (AlignmentAnnotation annot : annotations)
 129     {
 130       AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
 131       alignAnnotPojo.setDescription(annot.description);
 132       alignAnnotPojo.setLabel(annot.label);
 133       for (Annotation annotation : annot.annotations)
 134       {
 135         AnnotationPojo annotationPojo = new AnnotationPojo();
 136         if (annotation != null)
 137         {
 138           annotationPojo.setDescription(annotation.description);
 139           annotationPojo.setValue(annotation.value);
 140           annotationPojo
 141                   .setSecondaryStructure(annotation.secondaryStructure);
 142           annotationPojo.setDisplayCharacter(annotation.displayCharacter);
 143           alignAnnotPojo.getAnnotations().add(annotationPojo);
 144         }
 145         else
 146         {
 147           alignAnnotPojo.getAnnotations().add(annotationPojo);
 148         }
 149       }
 150       jsonAlignmentPojo.getAlignmentAnnotation().add(alignAnnotPojo);
 151     }
 152
 153     int count = 0;
 154     for (SequenceI seq : seqs)
 155     {
 156       StringBuilder name = new StringBuilder();
 157       name.append(seq.getName()).append("/").append(seq.getStart())
 158               .append("-").append(seq.getEnd());
 159
 160       SequencePojo jsonSeqPojo = new SequencePojo();
 161
 162       jsonSeqPojo.setId(seq.getName() + "_" + seq.hashCode());
 163       jsonSeqPojo.setOrder(++count);
 164       jsonSeqPojo.setEnd(seq.getEnd());
 165       jsonSeqPojo.setStart(seq.getStart());
 166       jsonSeqPojo.setName(name.toString());
 167       jsonSeqPojo.setSeq(seq.getSequenceAsString());
 168       jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
 169
 170       if (seq.getDatasetSequence() != null
 171               && seq.getDatasetSequence().getSequenceFeatures() != null)
 172       {
 173         ArrayList<FeaturePojo> seqFeaturesPojo = new ArrayList<FeaturePojo>();
 174         for (SequenceFeature sf : seq.getDatasetSequence()
 175                 .getSequenceFeatures())
 176         {
 177
 178           if (displayedFeatures != null
 179                   && displayedFeatures.isVisible(sf.getType()))
 180           {
 181
 182             String fillColor = ((fr != null) ? jalview.util.Format
 183                     .getHexString(fr.findFeatureColour(Color.white, seq,
 184                             seq.findIndex(sf.getBegin()))) : null);
 185             FeaturePojo jsonFeature = new FeaturePojo();
 186             jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
 187             jsonFeature.setXend(seq.findIndex(sf.getEnd()));
 188             jsonFeature.setType(sf.getType());
 189             jsonFeature.setDescription(sf.getDescription());
 190             jsonFeature.setLinks(sf.links);
 191             jsonFeature.setOtherDetails(sf.otherDetails);
 192             jsonFeature.setScore(sf.getScore());
 193             jsonFeature.setFillColor(fillColor);
 194             jsonFeature.setFeatureGroup(sf.getFeatureGroup());
 195             seqFeaturesPojo.add(jsonFeature);
 196           }
 197         }
 198         jsonSeqPojo.setFeatures(seqFeaturesPojo);
 199       }
 200     }
 201     return new com.json.JSONObject(jsonAlignmentPojo).toString()
 202             .replaceAll("xstart", "xStart").replaceAll("xend", "xEnd");
 203   }
 204
 205   public void parse(String jsonAlignmentString)
 206   {
 207     try
 208     {
 209       JSONParser jsonParser = new JSONParser();
 210       JSONObject alignmentJsonObj = (JSONObject) jsonParser
 211               .parse(jsonAlignmentString);
 212       JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
 213       JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj.get("alignmentAnnotation");
 214       JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj.get("sequenceGroups");
 215       String jsColourScheme = (String) alignmentJsonObj
 216               .get("globalColorScheme");
 217       System.out.println(">>>>>>>>>>>>>>>> global cs : " + jsColourScheme);
 218       cs = getJalviewColorScheme(jsColourScheme);
 219       seqMap = new Hashtable<String, Sequence>();
 220       Desktop.setCurrentGlobalColourScheme(cs);
 221       for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
 222               .hasNext();)
 223       {
 224         JSONObject sequence = sequenceIter.next();
 225         String sequcenceString = sequence.get("seq").toString();
 226         String sequenceName = sequence.get("name").toString();
 227         String seqUniqueId = sequence.get("id").toString();
 228         int start = Integer.valueOf(sequence.get("start").toString());
 229         int end = Integer.valueOf(sequence.get("end").toString());
 230         Sequence seq = new Sequence(sequenceName, sequcenceString, start,
 231                 end);
 232         JSONArray jsonSeqArray = (JSONArray) sequence.get("features");
 233         SequenceFeature[] retrievedSeqFeatures = getJalviewSequenceFeatures(
 234                 jsonSeqArray, seq);
 235         if (retrievedSeqFeatures != null)
 236         {
 237           seq.setSequenceFeatures(retrievedSeqFeatures);
 238         }
 239         seqs.add(seq);
 240         seqMap.put(seqUniqueId, seq);
 241       }
 242
 243       // for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator();
 244       // seqGrpIter
 245       // .hasNext();)
 246       // {
 247       // JSONObject seqGrpObj = seqGrpIter.next();
 248       // String grpName = seqGrpObj.get("groupName").toString();
 249       // String colourScheme = seqGrpObj.get("colourScheme").toString();
 250       // String description = (seqGrpObj.get("description") == null) ? null
 251       // : seqGrpObj.get("description").toString();
 252       // boolean displayBoxes = Boolean.valueOf(seqGrpObj
 253       // .get("displayBoxes").toString());
 254       // boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
 255       // .toString());
 256       // boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
 257       // .toString());
 258       // boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
 259       // "showNonconserved").toString());
 260       // int startRes = Integer
 261       // .valueOf(seqGrpObj.get("startRes").toString());
 262       // int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
 263       // JSONArray seqsHashArray = (JSONArray) seqGrpObj.get("seqsHash");
 264       //
 265       // ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
 266       // if (seqsHashArray.size() > 0)
 267       // {
 268       // Iterator<String> seqHashIter = seqsHashArray.iterator();
 269       //
 270       // while (seqHashIter.hasNext())
 271       // {
 272       // String seqHash = seqHashIter.next();
 273       // Sequence sequence = seqMap.get(seqHash);
 274       // if (sequence != null)
 275       // {
 276       // grpSeqs.add(sequence);
 277       // }
 278       // // System.out.println(">>>>>>>>>>>>>>>>>>>>>>> seqHash : "
 279       // // + seqHash);
 280       // }
 281       // }
 282       // System.out.println(">>>>>>>>>>>>>>>>>> scheme string : "
 283       // + colourScheme);
 284       // ColourSchemeI scheme = getJalviewColorScheme(colourScheme);
 285       // System.out.println(">>>>>>>>>>>>>>>>>> scheme: " + scheme);
 286       // SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, scheme,
 287       // displayBoxes, displayText, colourText, startRes, endRes);
 288       // this.seqGroups.add(seqGrp);
 289       //
 290       // }
 291
 292
 293       for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
 294               .hasNext();)
 295       {
 296         JSONObject alAnnot = alAnnotIter.next();
 297         JSONArray annotJsonArray = (JSONArray) alAnnot
 298                 .get("annotations");
 299         Annotation[] annotations = new Annotation[annotJsonArray.size()];
 300         int count = 0;
 301         for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
 302                 .hasNext();)
 303         {
 304           JSONObject annot = annotIter.next();
 305           if (annot == null)
 306           {
 307             annotations[count] = null;
 308           }
 309           else
 310           {
 311             float val = annot.get("value") == null ? null
 312                     : Float.valueOf(annot.get("value")
 313                     .toString());
 314             String desc = annot.get("description") == null ? null : annot
 315                     .get("description").toString();
 316
 317             char ss = annot.get("secondaryStructure") == null ? null
 318                     : annot
 319                     .get("secondaryStructure").toString().charAt(0);
 320             String displayChar = annot.get(
 321                     "displayCharacter").toString();
 322
 323             annotations[count] = new Annotation(displayChar, desc, ss, val);
 324           }
 325           ++count;
 326         }
 327
 328         AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
 329                 .get("label").toString(), alAnnot.get("description")
 330                 .toString(), annotations);
 331         this.annotations.add(alignAnnot);
 332       }
 333
 334     } catch (Exception e)
 335     {
 336       e.printStackTrace();
 337     }
 338   }
 339
 340   public SequenceFeature[] getJalviewSequenceFeatures(
 341           JSONArray jsonSeqFeatures, Sequence seq)
 342   {
 343     SequenceFeature[] seqFeatures = null;
 344     int count = 0;
 345     if (jsonSeqFeatures != null)
 346     {
 347       seqFeatures = new SequenceFeature[jsonSeqFeatures.size()];
 348       for (@SuppressWarnings("unchecked")
 349       Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
 350               .hasNext();)
 351       {
 352
 353         SequenceFeature sequenceFeature = new SequenceFeature();
 354         JSONObject jsonFeature = seqFeatureItr.next();
 355         Long begin = (Long) jsonFeature.get("xStart");
 356         Long end = (Long) jsonFeature.get("xEnd");
 357         String type = (String) jsonFeature.get("type");
 358         // String color = (String) jsonFeature.get("fillColor");
 359         String featureGrp = (String) jsonFeature.get("featureGroup");
 360         String descripiton = (String) jsonFeature.get("description");
 361         Float score = Float.valueOf(jsonFeature.get("score").toString());
 362         // Hashtable otherDetails = (Hashtable) jsonFeature
 363         // .get("otherDetails");
 364         // Vector<String> links = (Vector<String>) jsonFeature.get("links");
 365
 366         // sequenceFeature.links = links;
 367         // sequenceFeature.otherDetails = otherDetails;
 368         sequenceFeature.setScore(score);
 369         sequenceFeature.setDescription(descripiton);
 370
 371         sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
 372         sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
 373         sequenceFeature.setType(type);
 374         seqFeatures[count++] = sequenceFeature;
 375       }
 376     }
 377     return seqFeatures;
 378   }
 379
 380   private ColourSchemeI getJalviewColorScheme(String bioJsColourSchemeName)
 381   {
 382     ColourSchemeI jalviewColor = null;
 383     for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
 384             .values())
 385     {
 386       if (cs.getBioJsName().equalsIgnoreCase(bioJsColourSchemeName))
 387       {
 388         jalviewColor = cs.getJvColourScheme();
 389         break;
 390       }
 391     }
 392     return jalviewColor;
 393   }
 394
 395   public void LoadAlignmentFeatures(AlignFrame af)
 396   {
 397     af.setShowSeqFeatures(true);
 398     af.changeColour(cs);
 399     af.setMenusForViewport();
 400   }
 401
 402   public String getGlobalColorScheme()
 403   {
 404     return globalColorScheme;
 405   }
 406
 407   public void setGlobalColorScheme(String globalColorScheme)
 408   {
 409     this.globalColorScheme = globalColorScheme;
 410   }
 411 }