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