Examples of org.apache.uima.jcas.cas.TOP

org.apache.uima.jcas.cas.TOP
The Java Class model corresponding to the Cas TOP type. This type is the super type of all feature structures. This type implements FeatureStructure since subclasses of it are the FSs generated by this system.

      } catch (CASException e1) {
       logAndThrow(e1, jcasView);
      }
     
     // Return eq fs instance if already created
      TOP fs = jcasView.getJfsFromCaddr(addr);
      if (null != fs) {
        fs.jcasType = jcasView.getType(type);
      } else {
        initargs[0] = Integer.valueOf(addr);
        initargs[1] = jcasView.getType(type);

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    // covert to array for spring batch update
    // final Integer[] annoIdArray = annoIds.toArray(new Integer[] {});
    final List<Integer> annoIdList = new ArrayList<Integer>(annoIds);
    // get mappinginfo
    // final TOP t = mapIdToAnno.get(annoIdArray[0]);
    final TOP t = mapIdToAnno.get(annoIdList.get(0));
    final Type type = t.getType();
    final AnnoMappingInfo mapInfo = this.getMapInfo(t);
    // get non primitive fields, insert them after inserting the annotation
    final Set<String> fsNames = this.tl_mapFieldInfo.get().get(
        type.getName());
    final ListMultimap<String, AnnoFSAttribute> mapAnnoToFS = ArrayListMultimap

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    Collection<? extends TOP> srcObjs = JCasUtil.select(jcas, srcClass);
    for(TOP srcObj : srcObjs){
      Object[] constrArgVals = { jcas };
      try {
        // create new destination object
        TOP destObj = (TOP) iv_destContr.newInstance(constrArgVals);


        // copy data from source to destination
        Iterator<Method> getterItr = iv_getSetMap.keySet().iterator();
        while (getterItr.hasNext()) {
          Method getterMeth = getterItr.next();
          Method setterMeth = iv_getSetMap.get(getterMeth);


          Object val = getterMeth.invoke(srcObj, (Object[]) null);
          Object[] setterArgs = { val };
          setterMeth.invoke(destObj, setterArgs);
        }
        // add new destination object to JCas
        destObj.addToIndexes();
      } catch (Exception e) {
        throw new AnalysisEngineProcessException(e);
      }
    }
  }

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      this.featureValue = featureValue;
    }


    public void setValueFrom(Map<String, ? extends TOP> idAnnotationMap) {
      if (this.featureValue != null) {
        TOP valueAnnotation = idAnnotationMap.get(this.featureValue.id);
        if (valueAnnotation == null) {
          LOGGER.warn(String.format(
              "unable to set feature; found no annotation for %s",
              this.featureValue.id));
        } else {

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      this.featureValue = featureValue;
    }


    public void setValueFrom(Map<String, ? extends TOP> idAnnotationMap) {
      if (this.featureValue != null) {
        TOP valueAnnotation = idAnnotationMap.get(this.featureValue.id);
        if (valueAnnotation == null) {
          LOGGER.warn(String.format(
              "unable to set feature; found no annotation for %s",
              this.featureValue.id));
        } else {

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        // remove old NominalAttributeValue objects from CAS
        Iterator<NominalAttributeValue> removalItr = removalList.iterator();
        while (removalItr.hasNext())
        {
            TOP top = (TOP) removalItr.next();
            top.removeFromIndexes();
        }
      
        /**
         * 
         * This is to deal with cases like "nonsmoker" and "non-smoker"

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    Iterator srcObjItr = indexes.getAnnotationIndex(org.apache.ctakes.typesystem.type.textspan.Segment.type).iterator();
    org.apache.ctakes.typesystem.type.textspan.Segment segment = null;
    
    while (srcObjItr.hasNext())
    {
      TOP srcObj = (TOP) srcObjItr.next();


      Object[] constrArgVals = { jcas };
      try
      {
        // create new destination object
        TOP destObj = (TOP) iv_destContr.newInstance(constrArgVals);
        
        // Find the segments that are to be handled as complete sections
                boolean okayToSkip = false;
                boolean segmentMissing = iv_skipSegmentsSet.isEmpty();
        if (!segmentMissing){
          Iterator getSkipSegs = iv_skipSegmentsSet.iterator();
          segment = (org.apache.ctakes.typesystem.type.textspan.Segment) srcObj;
          while (getSkipSegs.hasNext()  && !okayToSkip){
            if (getSkipSegs.next().equals(segment.getId())){


              okayToSkip = true;
            }
          }
          
        }
        // copy data from source to destination
        Iterator getterItr = iv_getSetMap.keySet().iterator();
        


        while (getterItr.hasNext() && (okayToSkip || segmentMissing))
        {
          Method getterMeth = (Method) getterItr.next();
          Method setterMeth = (Method) iv_getSetMap.get(getterMeth);


          Object val = getterMeth.invoke(srcObj, (Object []) null);
          Object[] setterArgs = { val };
          setterMeth.invoke(destObj, setterArgs);
          
        }
        // add new destination object to JCas
        if (okayToSkip) {
          destObj.addToIndexes();
        } else {
          Iterator lookupWindows = FSUtil.getAnnotationsInSpanIterator(jcas, org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation.type, segment.getBegin(), segment.getEnd());
          while (lookupWindows.hasNext()){
            org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation lookup = (org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation) lookupWindows.next();
            org.apache.ctakes.typesystem.type.textspan.DrugLookupWindowAnnotation drugLookup = new org.apache.ctakes.typesystem.type.textspan.DrugLookupWindowAnnotation(jcas, lookup.getBegin(), lookup.getEnd()); //Reorganized paths in 3.0 SPM

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    // iterate over source objects in JCas
    JFSIndexRepository indexes = jcas.getJFSIndexRepository();
    FSIterator<Annotation> srcObjItr = indexes.getAnnotationIndex(
        iv_srcType).iterator();
    while (srcObjItr.hasNext()) {
      TOP srcObj = (TOP) srcObjItr.next();


      Object[] constrArgVals = { jcas };
      try {
        // create new destination object
        TOP destObj = (TOP) iv_destContr.newInstance(constrArgVals);


        // copy data from source to destination
        Iterator<Method> getterItr = iv_getSetMap.keySet().iterator();
        while (getterItr.hasNext()) {
          Method getterMeth = (Method) getterItr.next();
          Method setterMeth = (Method) iv_getSetMap.get(getterMeth);


          Object val = getterMeth.invoke(srcObj, (Object[]) null);
          Object[] setterArgs = { val };
          setterMeth.invoke(destObj, setterArgs);
        }
        // add new destination object to JCas
        destObj.addToIndexes();
      } catch (Exception e) {
        throw new AnalysisEngineProcessException(e);
      }
    }
  }

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      this.featureValue = featureValue;
    }


    public void setValueFrom(Map<String, ? extends TOP> idAnnotationMap) {
      if (this.featureValue != null) {
        TOP valueAnnotation = idAnnotationMap.get(this.featureValue.id);
        if (valueAnnotation == null) {
          LOGGER.warn(String.format(
              "unable to set feature; found no annotation for %s",
              this.featureValue.id));
        } else {

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        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;
        gatherFeatures(newStructure, features, matchedAnnotation, element, match, stream);
        newStructure.addToIndexes();
      }
    }


  }

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TOP

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