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.

      Collection<AnnotationFS> endAnchors = stream.getEndAnchor(eachMatched.getEnd()).getEndAnchors(
              targetType);
      allAnchoredAnnotations.addAll(beginAnchors);
      allAnchoredAnnotations.addAll(endAnchors);
      for (AnnotationFS eachAnchored : allAnchoredAnnotations) {
        Annotation a = (Annotation) eachAnchored;
        stream.removeAnnotation(a);
        a.setBegin(eachDestination.getBegin());
        a.setEnd(eachDestination.getEnd());
        stream.addAnnotation(a, true, match);
      }
    }
  }

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    List<Annotation> result = new ArrayList<Annotation>();
    moveTo(annotation);
    while (currentIt.isValid()) {
      currentIt.moveToNext();
      if (currentIt.isValid()) {
        Annotation nextAnnotation = (Annotation) currentIt.get();
        if (nextAnnotation.getBegin() == annotation.getEnd()) {
          result.add(nextAnnotation);
        } else if (nextAnnotation.getBegin() >= annotation.getEnd()) {
          break;
        }
      }
    }
    return result;

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      completeIt.moveToNext();
    }


    while (completeIt.isValid()
            && ((Annotation) completeIt.get()).getBegin() >= windowAnnotation.getBegin()) {
      Annotation annotation = (Annotation) completeIt.get();
      if (getCas().getTypeSystem().subsumes(type, annotation.getType())
              && annotation.getEnd() <= windowAnnotation.getEnd()) {
        result.add(annotation);
      }
      completeIt.moveToNext();
    }
    return result;

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        return;
      }
      Type type = structureType.getType(element.getParent());
      FeatureStructure newFS = stream.getCas().createFS(type);
      if (newFS instanceof Annotation) {
        Annotation a = (Annotation) newFS;
        a.setBegin(matchedAnnotation.getBegin());
        a.setEnd(matchedAnnotation.getEnd());
        stream.addAnnotation(a, match);
      }
      TOP newStructure = null;
      if (newFS instanceof TOP) {
        newStructure = (TOP) newFS;

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            int end = textsMatched.get(textsMatched.size() - 1).getEnd();
            RutaFrame frame = new RutaFrame(jcas, begin, end);
            FSIterator<Annotation> iterator = jcas.getAnnotationIndex(range).iterator(frame);
            AnnotationFS newA = null;
            while (iterator.isValid()) {
              Annotation a = iterator.get();
              if (a.getBegin() == begin && a.getEnd() == end
                      && jcas.getTypeSystem().subsumes(range, a.getType())) {
                newA = a;
              } else if (a.getBegin() > begin || a.getEnd() < end) {
                break;
              }
              iterator.moveToNext();
            }
            if (newA == null) {

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      List<RutaBasic> basicsToAdd = new ArrayList<RutaBasic>();
      basicsToAdd.add(anchorBasic);
      String text = anchorBasic.getCoveredText();
      StringBuilder candidate = new StringBuilder(text);
      // String lastCandidate = candidate.toString();
      Annotation interResult = null;
      while (streamPointer.isValid()) {
        if (containsFragment(candidate.toString(), ignoreCase, size, ignoreChars, maxIgnoredChars,
                ignoreWS)) {
          streamPointer.moveToNext();
          if (streamPointer.isValid()) {
            RutaBasic next = (RutaBasic) streamPointer.get();
            if (contains(candidate.toString(), ignoreCase, size, ignoreChars, maxIgnoredChars,
                    ignoreWS)) {
              interResult = new Annotation(stream.getJCas(), basicsToAdd.get(0).getBegin(),
                      basicsToAdd.get(basicsToAdd.size() - 1).getEnd());
            }
            // lastCandidate = candidate.toString();
            candidate.append(next.getCoveredText());
            basicsToAdd.add(next);

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          ArrayList<AnnotationFS> results, List<RutaBasic> basicsToAdd, String lastCandidate,
          Annotation interResult, char[] ignoreChars, int maxIgnoredChars, boolean ignoreWS) {
    if (basicsToAdd.size() >= 1
            && contains(lastCandidate, ignoreCase, size, ignoreChars, maxIgnoredChars, ignoreWS)) {


      results.add(new Annotation(stream.getJCas(), basicsToAdd.get(0).getBegin(), basicsToAdd.get(
              basicsToAdd.size() - 1).getEnd()));
    } else if (interResult != null) {
      results.add(interResult);
    }
  }

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    for (Annotation annotation : annotationIndex) {
      // TODO be careful here, because some people inherit from DocumentAnnotation
      if (typeSystem.subsumes(docType, annotation.getType())) {
        continue;
      }
      Annotation clone = (Annotation) casCopier.copyFs(annotation);
      // change the view/sofa of the new annotation...
      // see: http://osdir.com/ml/apache.uima.general/2007-09/msg00107.html
      clone.setFeatureValue(modview.getTypeSystem()
              .getFeatureByFullName(CAS.FEATURE_FULL_NAME_SOFA), modview.getSofa());
      final int mappedBegin = map[clone.getBegin()];
      final int mappedEnd = map[clone.getEnd()];
      if (mappedBegin < mappedEnd) {
        if (mappedEnd > fromJcas.getCas().getDocumentAnnotation().getEnd()) {
          getContext().getLogger().log(Level.WARNING, "illegal annotation offset mapping");
        } else {
          int max = modview.getCas().getDocumentAnnotation().getEnd();
          if (mappedBegin < max && mappedEnd <= max && mappedBegin >= 0 && mappedEnd > 0) {
            clone.setBegin(mappedBegin);
            clone.setEnd(mappedEnd);
            // TODO handle nested annotation features
            modview.addFsToIndexes(clone);
            indexedFs.add(clone);
          } else {
            getContext().getLogger().log(Level.WARNING, "illegal annotation offset mapping");

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    CasCopier casCopier = new CasCopier(fromJcas.getCas(), modview.getCas());
    for (Annotation annotation : annotationIndex) {
      if (typeSystem.subsumes(docType, annotation.getType())) {
        continue;
      }
      Annotation clone = (Annotation) casCopier.copyFs(annotation);
      // change the view/sofa of the new annotation...
      // see: http://osdir.com/ml/apache.uima.general/2007-09/msg00107.html
      clone.setFeatureValue(modview.getTypeSystem()
              .getFeatureByFullName(CAS.FEATURE_FULL_NAME_SOFA), modview.getSofa());
      final int mappedBegin = map[clone.getBegin()];
      final int mappedEnd = map[clone.getEnd()];
      if (mappedBegin < mappedEnd) {
        if (mappedEnd > fromJcas.getCas().getDocumentAnnotation().getEnd()) {
          getContext().getLogger().log(Level.WARNING, "illegal annotation offset mapping");
        } else {
          int max = modview.getCas().getDocumentAnnotation().getEnd();
          if (mappedBegin < max && mappedEnd <= max && mappedBegin >= 0 && mappedEnd > 0) {
            clone.setBegin(mappedBegin);
            clone.setEnd(mappedEnd);
            // TODO handle nested annotation features
            modview.addFsToIndexes(clone);
            indexedFs.add(clone);
          } else {
            getContext().getLogger().log(Level.WARNING, "illegal annotation offset mapping");

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      beginNew = valueBegin - deltaBefore;
      endNew = valueEnd + deltaAfter;
    }


    if (newFS instanceof Annotation) {
      Annotation newA = (Annotation) newFS;
      newA.setBegin(beginNew);
      newA.setEnd(endNew);
      stream.addAnnotation(newA, match);
    }
    return newFS;
  }

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