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.

    JFSIndexRepository indexes = jcas.getJFSIndexRepository();
    FSIterator<Annotation> srcObjItr = indexes.getAnnotationIndex(
        retainAnnType).iterator();


    while (srcObjItr.hasNext()) {
      Annotation ann = (Annotation) srcObjItr.next();
      if (!isValid(ann))
        removeList.add(ann);
    }


    for (int i = 0; i < removeList.size(); i++)

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  {
    List list = new ArrayList();


    while (annotItr.hasNext())
    {
      Annotation annot = (Annotation) annotItr.next();


      // only consider if it's within the window
      if ((annot.getBegin() >= begin) && (annot.getEnd() <= end))
      {
        list.add(new LookupAnnotationToJCasAdapter(annot));
      }
    }
    return list;

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        LookupInitializer lInit = ls.getLookupInitializer();


        Iterator windowItr = lInit.getLookupWindowIterator(jcas);
        while (windowItr.hasNext()) {


          Annotation window = (Annotation) windowItr.next();
          List lookupTokensInWindow = constrainToWindow(
              window,
              lInit.getLookupTokenIterator(jcas));


          Map ctxMap = lInit.getContextMap(
              jcas,
              window.getBegin(),
              window.getEnd());
          performLookup(jcas, ls, lookupTokensInWindow, ctxMap);
        }
      }


    }

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      return "N";
  }


  // FIXME use parser output instead of LWA
  public String calcmNPHead () {
    Annotation a = m.getContent();
    FSIterator iter = jcas.getJFSIndexRepository().getAnnotationIndex(LookupWindowAnnotation.type).iterator();
    while (iter.hasNext()) {
      LookupWindowAnnotation lwa = (LookupWindowAnnotation) iter.next();
      if (lwa.getBegin()<=a.getBegin() && lwa.getEnd()==a.getEnd())
        return "yes";
    }
    return "no";
  }

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    }
    return "I";
  }


  public String calcNPHead () {
    Annotation a = m1.getContent();
//    return (a.getEnd()==m1.getEnd() && a.getBegin()>m1.getBegin()) ? "yes" : "no";
    FSIterator iter = jcas.getJFSIndexRepository().getAnnotationIndex(LookupWindowAnnotation.type).iterator();
    while (iter.hasNext()) {
      LookupWindowAnnotation lwa = (LookupWindowAnnotation) iter.next();
      if (lwa.getBegin()<=a.getBegin() && lwa.getEnd()==a.getEnd())
        return "yes";
    }
    return "no";
  }

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                append(uimaObject.hashCode()).toString()), existingNode.getGraph());
        log.info(new StringBuilder("Node created for Type ").append(uimaObject.getType().toString()).toString());


        // set Annotation specific properties for the node
        if (uimaObject instanceof Annotation) {
          Annotation annotation = (Annotation) uimaObject;
          String coveredText = annotation.getCoveredText();
          annotationNode.addPropertyValue(ENTITY.coveredText, coveredText);
          log.info(new StringBuilder("Node wraps Annotation with coveredText:").append(coveredText).toString());
        }


        //XXX : in OpenCalais the type is an URI so it maybe reasonable to put another node here

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  @Test
  public void testFailingGetSingletonFS() {
    try {
      JCas cas = getCAS().getJCas();
      cas.setDocumentText(DOCUMENT_TEXT);
      Annotation simpleAnnotation = new Annotation(cas);
      simpleAnnotation.setBegin(10);
      simpleAnnotation.setEnd(24);
      simpleAnnotation.addToIndexes();


      Annotation secondSimpleAnnotation = new Annotation(cas);
      secondSimpleAnnotation.setBegin(32);
      secondSimpleAnnotation.setEnd(44);
      secondSimpleAnnotation.addToIndexes();


      UIMAUtils.getSingletonFeatureStructure(Annotation.type, cas);
      fail("should raise exception since there are 3 annotations of type Annotation");
    } catch (Exception e) {
      // if here, test passed

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    try {
      JCas cas = getCAS().getJCas();
      cas.setDocumentText(DOCUMENT_TEXT);


      Annotation simpleAnnotation = new Annotation(cas);
      simpleAnnotation.setBegin(10);
      simpleAnnotation.setEnd(24);
      simpleAnnotation.addToIndexes();


      Annotation secondSimpleAnnotation = new Annotation(cas);
      secondSimpleAnnotation.setBegin(32);
      secondSimpleAnnotation.setEnd(44);
      secondSimpleAnnotation.addToIndexes();


      MGraph mGraph = new SimpleMGraph();
      GraphNode node = new GraphNode(new UriRef(cas.toString()), mGraph);


      UIMAUtils.enhanceNode(node, UIMAUtils.getAllAnnotationsOfType(Annotation.type, cas));

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              if (uimaObject.getType().toString().equals("uima.tcas.DocumentAnnotation")) {
                continue;
              }


              // Get persistent URI for region in document
              Annotation annot = (Annotation) uimaObject;
              log.info("annotation index " + annotCnt);
              annotIndex.put(annot, annotCnt);
              annotCnt++;
          }
      }


      UriRef annotationSetUri = new UriRef(
              new StringBuilder(AO.AnnotationSet.getUnicodeString()).toString());
      log.info("AO: Annotation set uri " + annotationSetUri);


      GraphNode annotationSet = new GraphNode(annotationSetUri, node.getGraph());
      log.info(new StringBuilder("AO: Set created ").toString());
      annotationSet.addProperty(new UriRef("http://www.w3.org/1999/02/22-rdf-syntax-ns#type"),
              AO.AnnotationSet);


      for (FeatureStructure uimaObject : UIMAUtils.getAllFSofType(TOP.type, cas.getJCas())) {


        // set Annotation specific properties for the node
        if (uimaObject instanceof Annotation) {


          // If type is DocumentAnnotation I skip it
          if (uimaObject.getType().toString().equals("uima.tcas.DocumentAnnotation")) {
            continue;
          }


          // Get persistent URI for region in document
          Annotation annot = (Annotation) uimaObject;
          UriRef selectorUri = selectorRegistry.get(annot.getBegin(), annot.getEnd());


          // Annotation URI
          int annotId = annotIndex.get((Annotation) uimaObject);
          UriRef annotationUri = new UriRef(new StringBuilder(AO.Annotation.getUnicodeString())
                  .append("/").append(annotId).toString());

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            externalServicesFacade.setParameterSetting(parameterSettings);
            List<FeatureStructure> entities = externalServicesFacade.getNamedEntities(ANOTHER_ENGLISH_TEXT);
            assertTrue(entities != null);
            assertTrue(!entities.isEmpty());
            for (FeatureStructure fs : entities) {
              Annotation annotation = (Annotation) fs;
              assertTrue(annotation.getType()!=null && annotation.getType().getName()!=null);
              assertTrue(annotation.getBegin()>0);
              assertTrue(annotation.getEnd()>0);
              assertTrue(annotation.getCoveredText()!=null);
            }
        }
        catch (Exception e) {
            e.printStackTrace();
            fail(e.getLocalizedMessage());

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