Examples of org.apache.uima.jcas.tcas.Annotation

org.apache.uima.jcas.tcas.Annotation
the JCas class model for the CAS type uima.cas.Annotation. It defines two integer valued features indicating the begin and end of the span being annotated. There is also a method to retrieve the spanned text as a string.

      Map<List<Annotation>, TemporalTextRelation> dischargeTimeRelationLookup;
        dischargeTimeRelationLookup = new HashMap<>();
        if (this.isTraining()) {
          dischargeTimeRelationLookup = new HashMap<>();
          for (TemporalTextRelation relation : JCasUtil.select(jCas, TemporalTextRelation.class)) {
            Annotation arg1 = relation.getArg1().getArgument();
            Annotation arg2 = relation.getArg2().getArgument();
            // The key is a list of args so we can do bi-directional lookup
            if(arg1 instanceof TimeMention && arg2 instanceof EventMention ){
              if( arg1==admissionTime){
                dischargeTimeRelationLookup.put(Arrays.asList(arg1, arg2), relation);
                continue;

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  public void process(JCas jCas) throws AnalysisEngineProcessException {
    for(TemporalLink link : JCasUtil.select(jCas, TemporalLink.class)){
      BinaryTextRelation rel = new BinaryTextRelation(jCas);
      RelationArgument arg1 = new RelationArgument(jCas);
      Anchor source = link.getSource();
      arg1.setArgument(new Annotation(jCas, source.getBegin(), source.getEnd()));
      arg1.addToIndexes();
      
      RelationArgument arg2 = new RelationArgument(jCas);
      Anchor target = link.getTarget();
      arg2.setArgument(new Annotation(jCas, target.getBegin(), target.getEnd()));
      arg2.addToIndexes();
      
      String cat = getMappedCategory(link.getRelationType());
      if(cat.endsWith("-1")){
        rel.setArg1(arg2);

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      // /
      if (!filteredIterator.hasNext()) {
              throw new RuntimeException(
                              "Surrounding sentence annotation not found!!");
      }
      Annotation sentenceAnnotation = filteredIterator.next();
      Sentence sentence = (Sentence) sentenceAnnotation;
      int lineNumber = sentence.getSentenceNumber() + 1;


      // FSIterator<Annotation> tokensInSentenceIterator = jcas
      // .getAnnotationIndex(baseTokenTypeId).subiterator(sentence);
      //
      // if (!tokensInSentenceIterator.hasNext()) {
      // throw new RuntimeException("First token in sentence not found!!");
      // }
      // Annotation firstTokenAnnotation = tokensInSentenceIterator.next();
      // BaseToken firstToken = (BaseToken) firstTokenAnnotation;
      // int firstTokenInSentenceNumber = firstToken.getTokenNumber();


      FSIterator<Annotation> beginTokenInSentenceIterator = constraintConstructorFindContainedWithin
                      .createFilteredIterator(problemBegin, problemEnd, baseTokenType);


      // if (!beginTokenInSentenceIterator.hasNext()) {
      // throw new RuntimeException("First token in sentence not found!!");
      // }
      // Annotation beginTokenAnnotation =
      // beginTokenInSentenceIterator.next();
      // BaseToken beginToken = (BaseToken) beginTokenAnnotation;
      // int beginTokenNumber = beginToken.getTokenNumber();
      // int beginTokenWordNumber = beginTokenNumber
      // - firstTokenInSentenceNumber;
      BaseToken beginToken = this
                      .getNextNonEOLToken(beginTokenInSentenceIterator);
      int beginTokenWordNumber = this.sentenceToTokenNumberMap.get(sentence)
                      .indexOf(beginToken);


      beginTokenInSentenceIterator.moveToLast();
      if (!beginTokenInSentenceIterator.hasNext()) {
              throw new RuntimeException("First token in sentence not found!!");
      }
      Annotation endTokenAnnotation = beginTokenInSentenceIterator.next();
      BaseToken endToken = (BaseToken) endTokenAnnotation;
      // int endTokenNumber = endToken.getTokenNumber();
      // int endTokenWordNumber = endTokenNumber - firstTokenInSentenceNumber;
      int endTokenWordNumber = this.sentenceToTokenNumberMap.get(sentence)
                      .indexOf(endToken);

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  private int printAnnos(JCas jCas, int type) {
    AnnotationIndex<Annotation> sentences = jCas.getAnnotationIndex(type);
    Iterator<Annotation> iter = sentences.iterator();
    int sentCount = 0;
    while (iter.hasNext()) {
      Annotation sent = (Annotation) iter.next();
      System.out.println(sent.getClass().getSimpleName() + " ["
          + sent.getCoveredText() + "]");
      sentCount++;
    }
    return sentCount;
  }

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          if (spanEnd > end) {
            end = spanEnd;
          }
        }


        Annotation annotation;
        if (type.equals("EVENT")) {
          String docTimeRel = removeSingleChildText(propertiesElem, "DocTimeRel", id);
          if (docTimeRel == null) {
            error("no docTimeRel, assuming OVERLAP", id);
            docTimeRel = "OVERLAP";

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      String targetID,
      String category,
      Map<String, Annotation> idToAnnotation,
      String causeID) {
    if (sourceID != null && targetID != null) {
      Annotation source = getArgument(sourceID, idToAnnotation, causeID);
      Annotation target = getArgument(targetID, idToAnnotation, causeID);
      if (source != null && target != null) {
        RelationArgument sourceArg = new RelationArgument(jCas);
        sourceArg.setArgument(source);
        sourceArg.addToIndexes();
        RelationArgument targetArg = new RelationArgument(jCas);

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  private static Annotation getArgument(
      String id,
      Map<String, Annotation> idToAnnotation,
      String causeID) {
    Annotation annotation = idToAnnotation.get(id);
    if (annotation == null) {
      error("no annotation with id " + id, causeID);
    }
    return annotation;
  }

View Full Code Here

      _entityIdCollection = entityIdCollection;
      populateTlinkTypesArray( tlinkList );
   }


   public TlinkTypeSet getTlinkTypes( final BinaryTextRelation tlink ) {
      final Annotation entityA = tlink.getArg1().getArgument();
      final Annotation entityB = tlink.getArg2().getArgument();
      final int entityIdA = _entityIdCollection.getAnnotationId( entityA );
      final int entityIdB = _entityIdCollection.getAnnotationId( entityB );
      final int indexA = _entityIdList.indexOf( entityIdA );
      final int indexB = _entityIdList.indexOf( entityIdB );
      return getTlinkTypes( indexA, indexB );

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      return closedTlinks;
   }


   private BinaryTextRelation createTlink( final JCas jCas, int row, final int column, final TlinkType tlinkType ) {
     //      final ClassType tlinkClass = new CustomClassType( "TLINK" );
     final Annotation entityA = getAnnotation( row );
     final Annotation entityB = getAnnotation( column );
     if ( entityA == null || entityB == null ) {
       return null;
     }
     //      final Attribute tlinkAttribute = tlinkType.getAsAttribute();
     ////      if ( entityB instanceof Timex ) {

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      goldMentions.addAll(JCasUtil.select(goldView, EntityMention.class));
      goldMentions.addAll(JCasUtil.select(goldView, Modifier.class));
      CasCopier copier = new CasCopier(goldView.getCas(), systemView.getCas());
      for (IdentifiedAnnotation goldMention : goldMentions)
      {
        Annotation copy = (Annotation) copier.copyFs(goldMention);
        Feature sofaFeature = copy.getType().getFeatureByBaseName("sofa");
        copy.setFeatureValue(sofaFeature, systemView.getSofa());
        copy.addToIndexes();
      }
    }

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