Package org.apache.ctakes.drugner.type

Examples of org.apache.ctakes.drugner.type.StrengthUnitAnnotation.addToIndexes()

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        Object mt = (Object)  measurementTokenItr.next();
        if (mt instanceof  StrengthUnitToken) {
          // StrengthUnitToken mt = (StrengthUnitToken) measurementTokenItr.next();
          int begSeg = ((StrengthUnitToken) mt).getStartOffset(), endSeg = ((StrengthUnitToken) mt).getEndOffset();
          StrengthUnitAnnotation ma = new StrengthUnitAnnotation(jcas, begSeg, endSeg);
          ma.addToIndexes();
        } else {
          int begSeg = ((StrengthUnitCombinedToken) mt).getStartOffset(), endSeg = ((StrengthUnitCombinedToken) mt).getEndOffset();
          StrengthUnitAnnotation ma = new StrengthUnitAnnotation(jcas, begSeg, endSeg);
          ma.setBegin(findTextualStringOffset(ma.getCoveredText()) + begSeg);
          ma.addToIndexes();
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          ma.addToIndexes();
        } else {
          int begSeg = ((StrengthUnitCombinedToken) mt).getStartOffset(), endSeg = ((StrengthUnitCombinedToken) mt).getEndOffset();
          StrengthUnitAnnotation ma = new StrengthUnitAnnotation(jcas, begSeg, endSeg);
          ma.setBegin(findTextualStringOffset(ma.getCoveredText()) + begSeg);
          ma.addToIndexes();
        }
        //TODO: Does this need to be commented out? Created Strength       
      }
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      while (formTokenItr.hasNext())
      {
        FormToken mt = (FormToken) formTokenItr.next();
        FormAnnotation ma = new FormAnnotation(jcas, mt.getStartOffset(), mt.getEndOffset());

        ma.addToIndexes();
        // if (defaultNE != null && defaultNE.getCoveredText() != null)
        // defaultNE.setForm(ma.getCoveredText());

      }
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          int endOff = mt.getEndOffset();
          StrengthAnnotation ma = new StrengthAnnotation(jcas, begOff, endOff);
          Iterator subStrengthItr = FSUtil.getAnnotationsIteratorInSpan(jcas, StrengthUnitAnnotation.type, begOff, endOff);
          if (subStrengthItr.hasNext() )
                ma.setEnd(((StrengthUnitAnnotation)subStrengthItr.next()).getBegin());
          ma.addToIndexes();
          // loadandAppend("./strengthTable.csv", ma.getCoveredText(),
          // true);

        }
//      }
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        begSegDose = mt.getStartOffset();
        endSegDose = mt.getEndOffset();
        DosagesAnnotation ma = new DosagesAnnotation(jcas, begSegDose,
            endSegDose);

        ma.addToIndexes();

      }
      Set suffixTokenSet = iv_suffixFSM.execute(baseTokenList, strengthTokenSet);

      Iterator suffixTokenItr = suffixTokenSet.iterator();
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      Iterator suffixTokenItr = suffixTokenSet.iterator();
      while (suffixTokenItr.hasNext())
      {
        SuffixStrengthToken mt = (SuffixStrengthToken) suffixTokenItr.next();
        SuffixStrengthAnnotation ma = new SuffixStrengthAnnotation(jcas, mt.getStartOffset(), mt.getEndOffset());
        ma.addToIndexes();
      }
      // This needs to be handled differently. But since I'm not sure if this feature will be utilized
      // I am going to leave 'as is' for now.

      Set routeTokenSet = iv_routeFSM.execute(baseTokenList);
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        RouteToken mt = (RouteToken) routeTokenItr.next();
        begSegRT = mt.getStartOffset();
        endSegRT = mt.getEndOffset();
        RouteAnnotation ma = new RouteAnnotation(jcas, begSegRT, endSegRT);
        ma.setIntakeMethod(new Integer(mt.getFormMethod()).toString());
        ma.addToIndexes();

      }

      Set frequencyUnitTokenSet = iv_frequencyUnitFSM.execute(baseTokenList);
      boolean foundFrequencyUnit = false;
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        begSegFUT = fut.getStartOffset();
        endSegFUT = fut.getEndOffset();
        FrequencyUnitAnnotation ma = new FrequencyUnitAnnotation(jcas,
            begSegFUT, endSegFUT);
        ma.setPeriod(new Float(fut.getFrequencyUnitQuantity()).floatValue());
        ma.addToIndexes();

      }
      // The frequencyFSM can take advantage of the frequencyUnit to
      // establish conditions via the override
      Set frequencyTokenSet = iv_frequencyFSM.execute(baseTokenList,
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        FrequencyToken ft = (FrequencyToken) frequencyTokenItr.next();
        begSegFT = ft.getStartOffset();
        endSegFT = ft.getEndOffset();
        FrequencyAnnotation ma = new FrequencyAnnotation(jcas, begSegFT,
            endSegFT);
        ma.addToIndexes();

      }

      /* Check again if confidence was found during frequency check */

 
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        DurationToken du = (DurationToken) durationTokenItr.next();
        begSegDU = du.getStartOffset();
        endSegDU = du.getEndOffset();
        DurationAnnotation ma = new DurationAnnotation(jcas, begSegDU, endSegDU);
        // dm.setDurationElement(jcas, begSegDU, endSegDU);
        ma.addToIndexes();
        // loadandAppend("./frequencyTable.csv", ma.getCoveredText(),
        // true);
      }

    } catch (Exception e)
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