Examples of MedicationMention

Examples of org.apache.ctakes.typesystem.type.textsem.MedicationMention

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      {
    boolean noPriorMention = false;
    boolean noPostMention = false;
    int originalEndSpan = endSpan;
    int originalBeginSpan = beginSpan;
    MedicationMention neAnnot = new MedicationMention(jcas, tokenDrugNER.getBegin(),
        tokenDrugNER.getEnd());
    int beginChunk = drugChangeStatus.getEnd();
    DrugMention compareDM = new DrugMention(jcas, beginChunk, endSpan);
    DrugMention priorDM = new DrugMention(jcas, beginSpan, drugChangeStatus.getBegin());
    if ((priorDM.dosage == null) && (priorDM.strength == null) && (priorDM.frequency == null ) )
      noPriorMention = true;
    if ((compareDM.dosage == null) && (compareDM.strength == null) && (compareDM.frequency == null ) )
      noPostMention = true;
    count++;
    if ( !noPriorMention)  {
      if (priorDM.dosage != null) {
        tokenDrugNER.setDosage(priorDM.getDosageElement());
        tokenDrugNER.setDosageBegin(priorDM.getDosageBegin());
        tokenDrugNER.setDosageEnd(priorDM.getDosageEnd());
      }
      if (priorDM.strength != null) {
        tokenDrugNER.setStrength(priorDM.getStrengthElement());
        tokenDrugNER.setStrengthBegin(priorDM.getStrengthBegin());
        tokenDrugNER.setStrengthEnd(priorDM.getStrengthEnd());
        tokenDrugNER.setStrengthUnit(priorDM.getStrengthUnitElement());
        tokenDrugNER.setSuBegin(priorDM.getStrengthUnitBegin());
        tokenDrugNER.setSuEnd(priorDM.getStrengthUnitEnd());
      }
      if (priorDM.frequency != null) {
        tokenDrugNER.setFrequency(priorDM.getFrequencyElement());
        tokenDrugNER.setFrequencyBegin(priorDM.getFrequencyBegin());
        tokenDrugNER.setFrequencyEnd(priorDM.getFrequencyEnd());
      }
    }
    neAnnot.setTypeID(NERTypeIdentifier);
    int [] updatedSpan = {beginSpan, endSpan};

    List<MedicationMention> buildNewNER = new ArrayList<MedicationMention>();

    buildNewNER.add(neAnnot);

    if (drugChangeStatus.getChangeStatus().compareTo(
        DrugChangeStatusToken.DECREASE) == 0)
    {
      int endChunk = 0;
      int startChunk = 0;
      int midChunk = 0;
      if (noPriorMention) {//Look for highest value on right side
        startChunk =  getAdjustedWindowSpan(jcas,  beginChunk, endSpan, false)[0];
        midChunk =  getAdjustedWindowSpan(jcas,  beginChunk, endSpan, true)[0];
        endChunk = getAdjustedWindowSpan(jcas,  beginChunk, endSpan, true)[1];
      }
      updatedSpan[0] = beginChunk;
      String [] changeStatusArray = new String [] {DrugChangeStatusToken.DECREASE, new Integer (drugChangeStatus.getBegin()).toString(), new Integer(drugChangeStatus.getEnd()).toString()};
      generateDrugMentionsAndAnnotations(jcas, buildNewNER, beginChunk,
          midChunk, tokenDrugNER, changeStatusArray, count,
          globalNER);
      if (noPriorMention) {
        compareDM = new DrugMention(jcas, startChunk, endChunk);
        if (compareDM.dosage != null) {
          tokenDrugNER.setDosage(compareDM.getDosageElement());
          tokenDrugNER.setDosageBegin(compareDM.getDosageBegin());
          tokenDrugNER.setDosageEnd(compareDM.getDosageEnd());
        }
        if (compareDM.strength != null) {
          tokenDrugNER.setStrength(compareDM.getStrengthElement());
          tokenDrugNER.setStrengthBegin(compareDM.getStrengthBegin());
          tokenDrugNER.setStrengthEnd(compareDM.getStrengthEnd());
          tokenDrugNER.setStrengthUnit(compareDM.getStrengthUnitElement());
          tokenDrugNER.setSuBegin(compareDM.getStrengthUnitBegin());
          tokenDrugNER.setSuEnd(compareDM.getStrengthUnitEnd());
        }
        if (compareDM.frequency != null) {
          tokenDrugNER.setFrequency(compareDM.getFrequencyElement());
          tokenDrugNER.setFrequencyBegin(compareDM.getFrequencyBegin());
          tokenDrugNER.setFrequencyEnd(compareDM.getFrequencyEnd());
        }
      }
      tokenDrugNER.setDrugChangeStatus(DrugChangeStatusToken.NOCHANGE);
    } else if (drugChangeStatus.getChangeStatus().compareTo(
        DrugChangeStatusToken.DECREASEFROM) == 0)
    {
      if (noPriorMention) {//Look for lowest value on right side
        beginChunk = getAdjustedWindowSpan(jcas,  beginChunk, endSpan, true)[0];
        if (beginChunk == -1) {
          beginChunk = drugChangeStatus.getEnd();
        }
      }
      String [] changeStatusArray = new String [] {DrugChangeStatusToken.DECREASE, new Integer (drugChangeStatus.getBegin()).toString(), new Integer(drugChangeStatus.getEnd()).toString()};
      generateDrugMentionsAndAnnotations(jcas,
          buildNewNER, beginChunk, endSpan,
          tokenDrugNER, changeStatusArray, count, globalNER);
      if (noPriorMention) {
        priorDM = new DrugMention(jcas, originalBeginSpan, beginChunk);
        if (priorDM.dosage != null) {
          tokenDrugNER.setDosage(priorDM.getDosageElement());
          tokenDrugNER.setDosageBegin(priorDM.getDosageBegin());
          tokenDrugNER.setDosageEnd(priorDM.getDosageEnd());
        }
        if (priorDM.strength != null) {
          tokenDrugNER.setStrength(priorDM.getStrengthElement());
          tokenDrugNER.setStrengthBegin(priorDM.getStrengthBegin());
          tokenDrugNER.setStrengthEnd(priorDM.getStrengthEnd());
          tokenDrugNER.setStrengthUnit(compareDM.getStrengthUnitElement());
          tokenDrugNER.setSuBegin(compareDM.getStrengthUnitBegin());
          tokenDrugNER.setSuEnd(compareDM.getStrengthUnitEnd());
        }
        if (priorDM.frequency != null) {
          tokenDrugNER.setFrequency(priorDM.getFrequencyElement());
          tokenDrugNER.setFrequencyBegin(priorDM.getFrequencyBegin());
          tokenDrugNER.setFrequencyEnd(priorDM.getFrequencyEnd());
        }
      }
      tokenDrugNER.setDrugChangeStatus(DrugChangeStatusToken.NOCHANGE);

    } else if (drugChangeStatus.getChangeStatus().compareTo(
        DrugChangeStatusToken.INCREASE) == 0)
    {
      if (noPriorMention) {//Look for highest value on right side
        endSpan =  getAdjustedWindowSpan(jcas,  beginChunk, endSpan, true)[0];
      }
      updatedSpan[0] = beginChunk;
      String [] changeStatusArray = new String [] {DrugChangeStatusToken.INCREASE, new Integer (drugChangeStatus.getBegin()).toString(), new Integer(drugChangeStatus.getEnd()).toString()};
      generateDrugMentionsAndAnnotations(jcas, buildNewNER, beginChunk,
          endSpan, tokenDrugNER, changeStatusArray, count,
          globalNER);
      if (noPriorMention) {
        compareDM = new DrugMention(jcas, endSpan, originalEndSpan);
        if (compareDM.dosage != null) {
          tokenDrugNER.setDosage(compareDM.getDosageElement());
          tokenDrugNER.setDosageBegin(compareDM.getDosageBegin());
          tokenDrugNER.setDosageEnd(compareDM.getDosageEnd());
        }
        if (compareDM.strength != null) {
          tokenDrugNER.setStrength(compareDM.getStrengthElement());
          tokenDrugNER.setStrengthBegin(compareDM.getStrengthBegin());
          tokenDrugNER.setStrengthEnd(compareDM.getStrengthEnd());
          tokenDrugNER.setStrengthUnit(compareDM.getStrengthUnitElement());
          tokenDrugNER.setSuBegin(compareDM.getStrengthUnitBegin());
          tokenDrugNER.setSuEnd(compareDM.getStrengthUnitEnd());
        }
        if (compareDM.frequency != null) {
          tokenDrugNER.setFrequency(compareDM.getFrequencyElement());
          tokenDrugNER.setFrequencyBegin(compareDM.getFrequencyBegin());
          tokenDrugNER.setFrequencyEnd(compareDM.getFrequencyEnd());
        }
      }
      tokenDrugNER.setDrugChangeStatus(DrugChangeStatusToken.OTHER);
    } else if (drugChangeStatus.getChangeStatus().compareTo(
        DrugChangeStatusToken.INCREASEFROM) == 0)
    {
      int startChunk = 0;
      int endChunk = 0;
      int midChunk = 0;
      if (noPriorMention) {//Look for lowest value on right side
        startChunk = getAdjustedWindowSpan(jcas,  beginChunk, endSpan, false)[0];
        midChunk =  getAdjustedWindowSpan(jcas,  beginChunk, endSpan, false)[1];
        endChunk = getAdjustedWindowSpan(jcas,  beginChunk, endSpan, true)[1];
      }
      String [] changeStatusArray = new String [] {DrugChangeStatusToken.INCREASE, new Integer (drugChangeStatus.getBegin()).toString(), new Integer(drugChangeStatus.getEnd()).toString()};
      generateDrugMentionsAndAnnotations(jcas, buildNewNER, startChunk,
          endChunk, tokenDrugNER,
          changeStatusArray, count, globalNER);
      if (noPriorMention) {
        priorDM = new DrugMention(jcas, originalBeginSpan, midChunk);
        if (priorDM.dosage != null) {
          tokenDrugNER.setDosage(priorDM.getDosageElement());
          tokenDrugNER.setDosageBegin(priorDM.getDosageBegin());
          tokenDrugNER.setDosageEnd(priorDM.getDosageEnd());
        }
        if (priorDM.strength != null) {
          tokenDrugNER.setStrength(priorDM.getStrengthElement());
          tokenDrugNER.setStrengthBegin(priorDM.getStrengthBegin());
          tokenDrugNER.setStrengthEnd(priorDM.getStrengthEnd());
          tokenDrugNER.setStrengthUnit(priorDM.getStrengthUnitElement());
          tokenDrugNER.setSuBegin(priorDM.getStrengthUnitBegin());
          tokenDrugNER.setSuEnd(priorDM.getStrengthUnitEnd());
        }
        if (priorDM.frequency != null) {
          tokenDrugNER.setFrequency(priorDM.getFrequencyElement());
          tokenDrugNER.setFrequencyBegin(priorDM.getFrequencyBegin());
          tokenDrugNER.setFrequencyEnd(priorDM.getFrequencyEnd());
        }
      }
      tokenDrugNER.setDrugChangeStatus(DrugChangeStatusToken.NOCHANGE);
    } else if (drugChangeStatus.getChangeStatus().compareTo(
        DrugChangeStatusToken.STOP) == 0)
    {
      tokenDrugNER.setDrugChangeStatus(tokenDrugNER.getDrugChangeStatus());
    } else if ((drugChangeStatus.getChangeStatus().compareTo(
        DrugChangeStatusToken.OTHER) == 0)
        || drugChangeStatus.getChangeStatus().compareTo(
            DrugChangeStatusToken.SUM) == 0)
    {


      double strengthChange = 1;
      double dosageChange = 1;
      double frequencyChange = 1;
      if (noPriorMention) {
        int [] updateSpan =   getAdjustedWindowSpan(jcas,  beginChunk, endSpan, false);
        compareDM = new DrugMention(jcas, endSpan, originalEndSpan);
        if (compareDM.dosage != null) {
          tokenDrugNER.setDosage(compareDM.getDosageElement());
          tokenDrugNER.setDosageBegin(compareDM.getDosageBegin());
          tokenDrugNER.setDosageEnd(compareDM.getDosageEnd());
        }
        if (compareDM.strength != null) {
          tokenDrugNER.setStrength(compareDM.getStrengthElement());
          tokenDrugNER.setStrengthBegin(compareDM.getStrengthBegin());
          tokenDrugNER.setStrengthEnd(compareDM.getStrengthEnd());
          tokenDrugNER.setStrengthUnit(compareDM.getStrengthUnitElement());
          tokenDrugNER.setSuBegin(compareDM.getStrengthUnitBegin());
          tokenDrugNER.setSuEnd(compareDM.getStrengthUnitEnd());
        }
        if (compareDM.frequency != null) {
          tokenDrugNER.setFrequency(compareDM.getFrequencyElement());
          tokenDrugNER.setFrequencyBegin(compareDM.getFrequencyBegin());
          tokenDrugNER.setFrequencyEnd(compareDM.getFrequencyEnd());
        }
      }
      tokenDrugNER.setDrugChangeStatus(DrugChangeStatusToken.OTHER);
      if (compareDM.getStrengthElement() != null
          && compareDM.getStrengthElement().compareTo("") != 0
          && compareDM != null)
      {
        strengthChange = new Double(compareDM.parseDoubleValue(compareDM.getStrengthElement())).doubleValue();

      } else if (priorDM.getStrengthElement() != null
          && priorDM.getStrengthElement().compareTo("") != 0
          && priorDM.getStrengthElement().length() > 0)
      {
        int spacePosition = priorDM.getStrengthElement().indexOf(" ");
        if (spacePosition > 0)
        {
          strengthChange = new Double(priorDM.parseDoubleValue(priorDM.getStrengthElement().substring(0, spacePosition))).doubleValue();

        } else
        {
          strengthChange = new Double(priorDM.parseDoubleValue(priorDM.getStrengthElement())).doubleValue();

        }
      }
      if (compareDM.getDosageElement() != null
          && compareDM.getDosageElement().compareTo("") != 0)
      {
        dosageChange = new Double(compareDM.parseDoubleValue(compareDM.getDosageElement())).doubleValue();
      } else if (priorDM.getDosageElement() != null
          && priorDM.getDosageElement().compareTo("") != 0)
      {
        dosageChange = new Double(priorDM.parseDoubleValue(priorDM.getDosageElement())).doubleValue();
      }
      if (compareDM.getFrequencyElement() != null
          && compareDM.getFrequencyElement().compareTo("") != 0)
      {
        frequencyChange = new Double(compareDM.parseDoubleValue(compareDM.getFrequencyElement())).doubleValue();
      } else if (priorDM.getFrequencyElement() != null
          && priorDM.getFrequencyElement().compareTo("") != 0)
      {
        frequencyChange = new Double(priorDM.parseDoubleValue(priorDM.getFrequencyElement())).doubleValue();
      }

      double strengthBefore = 1;
      double dosageBefore = 1;
      double frequencyBefore = 1;

      if (priorDM.getStrengthElement() != null
          && priorDM.getStrengthElement().compareTo("") != 0
          && priorDM.getStrengthElement().length() > 0)
      {
        strengthBefore = new Double(priorDM.parseDoubleValue(priorDM.getStrengthElement())).doubleValue();
        tokenDrugNER.setStrength(priorDM.getStrengthElement());
        tokenDrugNER.setStrengthBegin(priorDM.getStrengthBegin());
        tokenDrugNER.setStrengthEnd(priorDM.getStrengthEnd());
        tokenDrugNER.setStrengthUnit(priorDM.getStrengthUnitElement());
        tokenDrugNER.setSuBegin(priorDM.getStrengthUnitBegin());
        tokenDrugNER.setSuEnd(priorDM.getStrengthUnitEnd());
      } else if (tokenDrugNER.getStrength() != null
          && tokenDrugNER.getStrength().compareTo("") != 0
          && tokenDrugNER.getStrength().length() > 0)
      {
        boolean handledSeparator = false;
        int hyphPosition = tokenDrugNER.getStrength().indexOf('-');
        String hyphString = tokenDrugNER.getStrength();
        if (hyphPosition > 0)
        {
          hyphString = tokenDrugNER.getStrength().substring(0, hyphPosition);

          strengthBefore = new Double(compareDM.parseDoubleValue(compareDM.convertFromTextToNum(hyphString))).doubleValue();
          handledSeparator = true;
        }
        int spacePosition = hyphString.indexOf(" ");
        if (spacePosition > 0)
        {
          hyphString = hyphString.substring(0, spacePosition);
          strengthBefore = new Double(priorDM.parseDoubleValue(priorDM.convertFromTextToNum(hyphString))).doubleValue();
          handledSeparator = true;
        }
        if (!handledSeparator)
          strengthBefore = new Double(compareDM.parseDoubleValue(tokenDrugNER.getStrength())).doubleValue();
      }
      if (priorDM.getDosageElement() != null
          && priorDM.getDosageElement().compareTo("") != 0
          && priorDM.dosage != null)
      {
        dosageBefore = new Double(priorDM.getDosageElement()).doubleValue();
        tokenDrugNER.setDosage(priorDM.getDosageElement());
        tokenDrugNER.setDosageBegin(priorDM.getDosageBegin());
        tokenDrugNER.setDosageEnd(priorDM.getDosageEnd());
      } else if (tokenDrugNER.getDosage() != null
          && tokenDrugNER.getDosage().compareTo("") != 0)
      {
        dosageBefore = new Double(compareDM.parseDoubleValue(tokenDrugNER.getDosage())).doubleValue();
      }
      if (priorDM.getFrequencyElement() != null
          && priorDM.getFrequencyElement().compareTo("") != 0)
      {
        frequencyBefore = new Double(priorDM.parseDoubleValue(priorDM.getFrequencyElement())).doubleValue();
        tokenDrugNER.setFrequency(priorDM.getFrequencyElement());

      } else if (tokenDrugNER.getFrequency() != null
          && tokenDrugNER.getFrequency().compareTo("") != 0)
      {
        frequencyBefore = new Double(compareDM.parseDoubleValue(tokenDrugNER.getFrequency())).doubleValue();
      }
      if ((drugChangeStatus.getChangeStatus().compareTo(
          DrugChangeStatusToken.SUM) == 0)
          && (strengthChange > 1 && strengthBefore > 1 || strengthChange == strengthBefore))
      {
        Iterator findLF = FSUtil.getAnnotationsIteratorInSpan(jcas,
            NewlineToken.type, neAnnot.getBegin(), beginChunk);
        if (!findLF.hasNext())
        {
          if (frequencyChange <= 1 && frequencyBefore > 1)
            tokenDrugNER.setFrequency("1.0");
          String [] changeStatusArray = new String [] {DrugChangeStatusToken.SUM, new Integer (0).toString(), new Integer(0).toString()};
View Full Code Here

Examples of org.apache.ctakes.typesystem.type.textsem.MedicationMention

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  }

  return span;
}
  private void findFSMInRange(JCas jcas, int begin, int end) throws Exception {
    MedicationMention ne = null;
    WordToken we = null;
    // grab iterator over tokens within this chunk
    Iterator btaItr = FSUtil.getAnnotationsInSpanIterator(jcas,
        BaseToken.type, begin,
        end+1);
View Full Code Here

Examples of org.apache.ctakes.typesystem.type.textsem.MedicationMention

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        }
      }

    } else if (elementType == MedicationMention.type) {
      while (neItr.hasNext()) {
        MedicationMention nea = (MedicationMention) neItr.next();
        if(nea.getTypeID()==1 || nea.getTypeID()==0) {
          lastLocation[0]= nea.getBegin();
          lastLocation[1] = nea.getEnd();
          if ((counter == 0 || lastLocation[0] != location[counter-1][0]) && (nea.getBegin()>=begin && nea.getEnd() <= end)) {
            location[counter][0]= lastLocation[0];
            location[counter][1]= lastLocation[1];
            counter++;
          }

        }
      }
    } else if (elementType == PunctuationToken.type) {
      while (neItr.hasNext()) {
        boolean foundPair = false;
        PunctuationToken nea = (PunctuationToken) neItr.next();
        if (nea.getCoveredText().compareTo("(")==0)
          lastLocation[0] = nea.getBegin();
        else if (nea.getCoveredText().compareTo(")")==0) {
          lastLocation[1] = nea.getEnd();
          foundPair = true;
        }
        if (nea.getBegin()>=begin && nea.getEnd() <= end && foundPair && (counter == 0  || (counter> 0 && lastLocation[0] !=  location[counter - 1][0]))) {
          location[counter][0]= lastLocation[0];
          location[counter][1]= lastLocation[1];
          counter++;
        }
      }
View Full Code Here

Examples of org.apache.ctakes.typesystem.type.textsem.MedicationMention

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    Iterator neItr = FSUtil.getAnnotationsIteratorInSpan(jcas, MedicationMention.type, begin, end);

    int numDrugs=0;
    int beginOffset=0;
    while (neItr.hasNext()) {
      MedicationMention nea = (MedicationMention) neItr.next();
     
      if((nea.getTypeID()==1  || nea.getTypeID()==0) && beginOffset != nea.getBegin())    
        numDrugs++;
      beginOffset = nea.getBegin();
    }
    if(numDrugs>1) return true;
    else return false;        
  }
View Full Code Here

Examples of org.apache.ctakes.typesystem.type.textsem.MedicationMention

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    if (drugSpanLength > 1)
      for (int j = 0; j < drugSpanLength; j++) {
        Iterator drugListItr = FSUtil.getAnnotationsIteratorInSpan(jcas, MedicationMention.type, drugSpan[j][0], drugSpan[j][1]+1);
        Iterator drugListItrNext = FSUtil.getAnnotationsIteratorInSpan(jcas, MedicationMention.type, drugSpan[j+1][0], drugSpan[j+1][1]+1);
        if (drugListItr.hasNext()) {
          MedicationMention nea = (MedicationMention) drugListItr.next();
          drugSpanArray[j][0] = nea.getBegin();
          boolean patternFound = false;
          boolean hasNext = true;
          boolean isPairedDrug = false;
          boolean usingLeftParenthesisExclusive = false;
          boolean usingLeftParenthesisInclusive = false;
          boolean usingRightParenthesisInclusive = false;
          int endRange = 0;
          int countMultiplePre = 0;
          char highestInRange = ' ';
          char lowestPositiveInRange = ' ';
          char lowestInRange = ' ';
          int highestValueInRange = 0;
          int lowestValueInRange = 0;
          int lowestPositiveValueInRange = endPhrase;
          if (drugListItrNext.hasNext()) {
            MedicationMention neaNext = (MedicationMention) drugListItrNext.next();
            endPhrase = neaNext.getBegin();
          } else {
            hasNext = false;
            endPhrase = senSpan[1];
          }
          int [] testForMultipleElementsInRange = {0,0};
View Full Code Here

Examples of org.apache.ctakes.typesystem.type.textsem.MedicationMention

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      }

    } else if (elementType == MedicationMention.type) {
      int holdEndElement = 0;
      while (neItr.hasNext()) {
        MedicationMention nea = (MedicationMention) neItr.next();
        if(nea.getTypeID()==1 || nea.getTypeID()==0) {
          lastLocation[0]= nea.getBegin();
          lastLocation[1] = nea.getEnd();
          if ((counter == 0 || lastLocation[0] != location[counter-1][0]) && (nea.getBegin()>=begin && nea.getEnd() <= end)) {
            location[counter][0]= lastLocation[0];
            holdEndElement = location[counter][1] = lastLocation[1];
            counter++;
          } else if (counter > 0 && holdEndElement > lastLocation[1]) {
            holdEndElement = location[counter-1][1] = lastLocation[1];
          }

        }
      }
    } else if (elementType == PunctuationToken.type) {
      while (neItr.hasNext()) {
        int holdBeginElement = 0;
        boolean foundPair = false;
        PunctuationToken nea = (PunctuationToken) neItr.next();
        if (nea.getCoveredText().compareTo("(")==0 || nea.getCoveredText().compareTo("[")==0)
          lastLocation[0] = nea.getBegin();
        else if (nea.getCoveredText().compareTo(")")==0 || nea.getCoveredText().compareTo("]")==0) {
          lastLocation[1] = nea.getEnd();
          foundPair = true;
        }
        if (holdBeginElement < nea.getBegin() && nea.getBegin()>=begin && nea.getEnd() <= end && foundPair) {
          location[counter][0]= lastLocation[0];
          location[counter][1]= lastLocation[1];
          counter++;
        }
      }
View Full Code Here

Examples of org.apache.ctakes.typesystem.type.textsem.MedicationMention

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            }
         }
        
         IdentifiedAnnotation neAnnot = new IdentifiedAnnotation(jcas);
         if ( typeId == CONST.NE_TYPE_ID_DRUG ) {
            neAnnot = new MedicationMention( jcas );
         } else if ( typeId == CONST.NE_TYPE_ID_ANATOMICAL_SITE ) {
             neAnnot = new AnatomicalSiteMention( jcas );
         } else if ( typeId == CONST.NE_TYPE_ID_DISORDER ) {
             neAnnot = new DiseaseDisorderMention( jcas );
         } else if ( typeId == CONST.NE_TYPE_ID_FINDING ) {
View Full Code Here

Examples of org.apache.ctakes.typesystem.type.textsem.MedicationMention

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                  }

                  IdentifiedAnnotation neAnnot;
                  final int conceptKey = conceptEntry.getKey();
                  if ( conceptKey == CONST.NE_TYPE_ID_DRUG ) {
                     neAnnot = new MedicationMention( jcas );
                  } else if ( conceptKey == CONST.NE_TYPE_ID_ANATOMICAL_SITE ) {
                      neAnnot = new AnatomicalSiteMention( jcas );
                  } else if ( conceptKey == CONST.NE_TYPE_ID_DISORDER ) {
                      neAnnot = new DiseaseDisorderMention( jcas );
                  } else if ( conceptKey == CONST.NE_TYPE_ID_FINDING ) {
View Full Code Here

Examples of org.apache.ctakes.typesystem.type.textsem.MedicationMention

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               final MetaDataHit mdh = lookupHit.getDictMetaDataHit();
               final String code = mdh.getMetaFieldValue( CODE_MF );
               validCodes.add( code );
            }
            final FSArray ocArr = createOntologyConceptArr( jcas, validCodes );
            IdentifiedAnnotation neAnnot = new MedicationMention( jcas ); // medication NEs are EventMention
            neAnnot.setTypeID( CONST.NE_TYPE_ID_DRUG );
            neAnnot.setBegin( neBegin );
            neAnnot.setEnd( neEnd );
            neAnnot.setDiscoveryTechnique( CONST.NE_DISCOVERY_TECH_DICT_LOOKUP );
            neAnnot.setOntologyConceptArr( ocArr );
            neAnnot.addToIndexes();
         } else {
            iv_logger.warn( "Filtered out: " + text );
         }
      }
   }
View Full Code Here

Examples of org.apache.ctakes.typesystem.type.textsem.MedicationMention

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    if (drugSpanLength > 1)
      for (int j = 0; j < drugSpanLength; j++) {
        Iterator drugListItr = FSUtil.getAnnotationsIteratorInSpan(jcas, MedicationMention.type, drugSpan[j][0], drugSpan[j][1]+1);
        Iterator drugListItrNext = FSUtil.getAnnotationsIteratorInSpan(jcas, MedicationMention.type, drugSpan[j+1][0], drugSpan[j+1][1]+1);
        if (drugListItr.hasNext()) {
          MedicationMention nea = (MedicationMention) drugListItr.next();
          drugSpanArray[j][0] = nea.getBegin();
          boolean patternFound = false;
          boolean hasNext = true;
          boolean isPairedDrug = false;
          boolean usingLeftParenthesisExclusive = false;
          boolean usingLeftParenthesisInclusive = false;
          boolean usingRightParenthesisInclusive = false;
          int endRange = 0;
          int countMultiplePre = 0;
          char highestInRange = ' ';
          char lowestPositiveInRange = ' ';
          char lowestInRange = ' ';
          int highestValueInRange = 0;
          int lowestValueInRange = 0;
          int lowestPositiveValueInRange = endPhrase;
          if (drugListItrNext.hasNext()) {
            MedicationMention neaNext = (MedicationMention) drugListItrNext.next();
            endPhrase = neaNext.getBegin();
          } else {
            hasNext = false;
            endPhrase = senSpan[1];
          }
          int [] testForMultipleElementsInRange = {0,0};
View Full Code Here
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