Examples of addToIndexes()

Examples of org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation.addToIndexes()

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            neAnnot.setTypeID(neType.intValue());
            neAnnot.setBegin(neBegin);
            neAnnot.setEnd(neEnd);
            neAnnot.setDiscoveryTechnique(CONST.NE_DISCOVERY_TECH_DICT_LOOKUP);
            neAnnot.setOntologyConceptArr(conceptArr);
            neAnnot.addToIndexes();
          }
         
        }
      }
    }
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Examples of org.apache.ctakes.typesystem.type.textsem.LabEstimatedModifier.addToIndexes()

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      } else if ("estimated_flag_indicator".equals(annotation.type)) {
        boolean value = booleanSlots.remove("estimated_normalization");
        LabEstimatedModifier modifier = new LabEstimatedModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setIndicated(value);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("lab_interpretation_indicator".equals(annotation.type)) {
        String value = stringSlots.remove("lab_interpretation_normalization");
        LabInterpretationModifier modifier = new LabInterpretationModifier(jCas, coveringSpan.begin, coveringSpan.end);
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Examples of org.apache.ctakes.typesystem.type.textsem.LabInterpretationModifier.addToIndexes()

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      } else if ("lab_interpretation_indicator".equals(annotation.type)) {
        String value = stringSlots.remove("lab_interpretation_normalization");
        LabInterpretationModifier modifier = new LabInterpretationModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setTypeID(CONST.MODIFIER_TYPE_ID_LAB_INTERPRETATION_INDICATOR);
        modifier.setValue(value);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("reference_range".equals(annotation.type)) {
        LabReferenceRangeModifier modifier = new LabReferenceRangeModifier(jCas, coveringSpan.begin, coveringSpan.end);
        LabReferenceRange attribute = new LabReferenceRange(jCas);
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Examples of org.apache.ctakes.typesystem.type.textsem.LabMention.addToIndexes()

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        date.setMonth(month);
        date.setDay(day);
        date.addToIndexes();
        TimeMention mention = new TimeMention(jCas, coveringSpan.begin, coveringSpan.end);
        mention.setDate(date);
        mention.addToIndexes();
        idAnnotationMap.put(annotation.id, mention);

      } else if (eventRelationTypes.contains(annotation.type)) {
        // store the ALINK information for later, once all annotations are in the CAS
        DelayedRelation relation = new DelayedRelation();
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Examples of org.apache.ctakes.typesystem.type.textsem.LabReferenceRangeModifier.addToIndexes()

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        LabReferenceRangeModifier modifier = new LabReferenceRangeModifier(jCas, coveringSpan.begin, coveringSpan.end);
        LabReferenceRange attribute = new LabReferenceRange(jCas);
        attribute.setValue(modifier.getCoveredText());
        attribute.addToIndexes();
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("Value".equals(annotation.type)) {
        KnowtatorAnnotation unit = annotationSlots.remove("value_unit");
        KnowtatorAnnotation number = annotationSlots.remove("value_number");
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Examples of org.apache.ctakes.typesystem.type.textsem.LabValueModifier.addToIndexes()

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          attribute.setNumber(numberString);
        }
        attribute.addToIndexes();
        LabValueModifier modifier = new LabValueModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("Value number".equals(annotation.type)) {
        // already handled in "Value" above
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Examples of org.apache.ctakes.typesystem.type.textsem.MeasurementAnnotation.addToIndexes()

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      Set<MeasurementToken> measurementTokenSet = iv_measurementFSM.execute(baseTokenList, rangeTokenSet);
      Iterator<MeasurementToken> measurementTokenItr = measurementTokenSet.iterator();
      while (measurementTokenItr.hasNext()) {
        MeasurementToken mt = measurementTokenItr.next();
        MeasurementAnnotation ma = new MeasurementAnnotation(jcas, mt.getStartOffset(), mt.getEndOffset());
        ma.addToIndexes();
      }

      Set<PersonTitleToken> personTitleTokenSet = iv_personTitleFSM.execute(baseTokenList);
      Iterator<PersonTitleToken> personTitleTokenItr = personTitleTokenSet.iterator();
      while (personTitleTokenItr.hasNext()) {
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Examples of org.apache.ctakes.typesystem.type.textsem.MedicationAllergyModifier.addToIndexes()

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          LOGGER.error(String.format(
              "unrecognized allergy-indicator value \"%s\" on annotation with id \"%s\"",
              value,
              annotation.id));
        }
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("Dosage".equals(annotation.type)) {
        String value = stringSlots.remove("dosage_values");
        MedicationDosage attribute = new MedicationDosage(jCas);
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Examples of org.apache.ctakes.typesystem.type.textsem.MedicationDosageModifier.addToIndexes()

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        MedicationDosage attribute = new MedicationDosage(jCas);
        attribute.setValue(value);
        attribute.addToIndexes();
        MedicationDosageModifier modifier = new MedicationDosageModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("Duration".equals(annotation.type)) {
        String value = stringSlots.remove("duration_values");
        MedicationDuration attribute = new MedicationDuration(jCas);
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Examples of org.apache.ctakes.typesystem.type.textsem.MedicationDurationModifier.addToIndexes()

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        MedicationDuration attribute = new MedicationDuration(jCas);
        attribute.setValue(value);
        attribute.addToIndexes();
        MedicationDurationModifier modifier = new MedicationDurationModifier(jCas, coveringSpan.begin, coveringSpan.end);
        modifier.setNormalizedForm(attribute);
        modifier.addToIndexes();
        idAnnotationMap.put(annotation.id, modifier);

      } else if ("Form".equals(annotation.type)) {
        String value = stringSlots.remove("form_values");
        MedicationForm attribute = new MedicationForm(jCas);
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