Examples of org.apache.ctakes.padtermspotter.type.PADLocation

Package org.apache.ctakes.padtermspotter.type

Examples of org.apache.ctakes.padtermspotter.type.PADLocation

org.apache.ctakes.padtermspotter.type.PADLocation

      iv_logger.debug("Processing term and loc["+prevAnn.getCoveredText()+"] currAnn["+currAnn.getCoveredText()+"]");
    
    if(isAdjacentWithWindowSize(jcas, prevAnn, currAnn, iAnnotationType, iWindowSize))
    {
      boolean isHit = false;
      PADLocation ual = null;
      PADTerm uat = null;
      
      if((prevAnn != null && prevAnn instanceof PADLocation) && 
          (currAnn != null && currAnn instanceof PADTerm))
      {

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    Iterator<?> annotItr = indexes.getAnnotationIndex(iAnnTypePartTwoOfPair).iterator();


    //if terms present store them
    while(annotItr.hasNext())
    {
      PADLocation uaLoc = (PADLocation)annotItr.next();


      if((uaLoc.getPolarity()<0 && filterOutNegated) || isInIgnoreTypesPartTwo(uaLoc))//negated, so get next
      {
        iv_logger.info(uaLoc.getHitDictionaryValue() + " ignoring because negated");
        continue;
      }
      storePartTwoHit(uaLoc);
    }    
  }

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        else if (uaHit.getUaLocation() != null)
          casConsumerOutData.append(((PADLocation) uaHit
              .getUaLocation()).getSegmentID());


        // add location and term data
        PADLocation ual = uaHit.getUaLocation();
        PADTerm uat = uaHit.getUaTerm();


        if (ual != null) {
          casConsumerOutData.append(COLLECTION_SEPARATOR
              + ual.getCoveredText());
          casConsumerOffSetData.append(ual.getBegin() + "-"
              + ual.getEnd() + ":");
          if (ual.getPolarity() == -1
              && uat == null
              || (ual.getPolarity() == -1 && uat != null
                  && uat.getTypeID() != disorderStenosis && ual
                  .getPolarity() == -1)) {
            negatedCase = true;
          } else if (ual.getIsStandAlone() != 1
              && ual.getPolarity() != -1
              && ual.getUncertainty() == disorderPatent) {
            probableCase = true;
            probableCount++;
          } else
            probableCase = false;
        } else {
          casConsumerOutData.append(COLLECTION_SEPARATOR + " ");
          casConsumerOffSetData.append("-1:");
          if (uat.getTypeID() == disorderStenosis
              && uat.getPolarity() != -1)
            noStenosis = false;
          if (uat != null && uat.getPolarity() == -1
              && uat.getTypeID() != disorderStenosis
              && uat.getTypeID() != anatomicalSiteExclusion)
            negatedCase = true;
          else if (uat != null
              && ((uat.getIsStandAlone() != 1 || uat.getTypeID() == disorderPatent) && uat
                  .getPolarity() != -1)) {
            probableCase = true;
            probableCount++;
          } else
            probableCase = false;
        }


        if (uat != null) {
          casConsumerOutData.append(COLLECTION_SEPARATOR
              + uat.getCoveredText());
          casConsumerOffSetData.append(uat.getBegin() + "-"
              + uat.getEnd() + ")");
          if (uat.getTypeID() == disorderStenosis
              && uat.getPolarity() != -1)
            noStenosis = false;
          if (uat.getPolarity() == -1
              && uat.getTypeID() != disorderStenosis
              && uat.getUncertainty() != disorderPatent
              && uat.getTypeID() != anatomicalSiteExclusion
              && uat.getIsStandAlone() != 1)


            negatedCase = true;
          else if (uat.getUncertainty() == disorderPatent
              && uat.getIsStandAlone() != 1) {
            probableCase = true;
            probableCount++;
          } else if (!negatedCase)
            probableCase = false;
        } else {
          casConsumerOutData.append(COLLECTION_SEPARATOR + " ");
          casConsumerOffSetData.append("-1)");
          if (ual != null && ual.getPolarity() == -1
              && ual.getUncertainty() != disorderPatent)
            negatedCase = true;
          else if (ual.getIsStandAlone() != 1
              && ual.getPolarity() != -1
              && ual.getUncertainty() == disorderPatent) {
            probableCase = true;
            probableCount++;
          }


          else
            probableCase = false;
        }


        if (probableCase)
          globalProbable = true;
        if ((negatedCase || probableCase)) {
          count--;
          negCount = true;
          if (uat != null && !probableCase
              && uat.getTypeID() != disorderStenosis
              && uat.getTypeID() != disorderPatent) {
            if (ual == null || (ual != null)
                && ual.getTypeID() != disorderPatent
                && ual.getPolarity() == -1)
              balanceCount--;


          }
        } else
          balanceCount++;


      }
      annotItr = indexes.getAnnotationIndex(PADLocation.type).iterator();
      while (annotItr.hasNext()) {
        PADLocation location = (PADLocation) annotItr.next();
        Iterator<?> annotHitItr = indexes.getAnnotationIndex(
            PADHit.type).iterator();
        boolean skip = false;
        if (location.getCoveredText().indexOf("vein") != -1) {
          noVein = false;
          veinCount++;
        }
        while (annotHitItr.hasNext() && !skip) {
          PADHit uaHit = ((PADHit) annotHitItr.next());
          if (uaHit.getUaLocation() != null
              && location.getBegin() == uaHit.getUaLocation()
                  .getBegin())
            skip = true;


        }
        if (!skip) {
          if (location.getPolarity() == -1) {
            locTermsOnly = true;
          }


          if (location.getPolarity() != -1) {


            locOnlyCount++;
            casConsumerOffSetData.append("(");


            casConsumerOffSetData.append("-1:");
            casConsumerOffSetData.append(location.getBegin() + "-"
                + location.getEnd() + ")");
            casConsumerOutData.append(COLLECTION_SEPARATOR);
            casConsumerOutData.append(location.getSegmentID());
            casConsumerOutData.append(COLLECTION_SEPARATOR
                + "**NO TERM**");
            casConsumerOutData.append(COLLECTION_SEPARATOR
                + location.getCoveredText());


          } else if (location.getPolarity() != -1
              && location.getTypeID() != disorderStenosis
              && location.getTypeID() != anatomicalSiteExclusion
              && location.getUncertainty() == disorderPatent)
            locOnlyCount--;
        }
      }
      annotItr = indexes.getAnnotationIndex(PADTerm.type).iterator();
      while (annotItr.hasNext()) {

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    //check if the location is standalone...
    String standAlone = metaData.getMetaFieldValue("2");
    
    iv_logger.log(Level.INFO, "Meta field 1 ["+mfValue+"] col2["+standAlone+"]");
    int cutOffForRevision = findOriginalReportSubSection(jcas);
    PADLocation locationTerm = new PADLocation(jcas);
    locationTerm.setHitDictionaryValue(mfValue);


    if(standAlone != null && standAlone.equalsIgnoreCase(STAND_ALONE))
      locationTerm.setIsStandAlone(TRUE);
    else {
      locationTerm.setIsStandAlone(FALSE);
      locationTerm.setTypeID(new Integer(standAlone).intValue());
    }
    locationTerm.setBegin(neBegin);
    locationTerm.setEnd(neEnd);
    
    List list = getTokenData(jcas, locationTerm);
    FSArray fsArr = new FSArray(jcas, list.size());


    for(int i=0; i<list.size(); i++) {
      BaseToken wta = (BaseToken)list.get(i);
      if (wta.getCoveredText().compareToIgnoreCase("at")!=0 || 
          (wta.getCoveredText().compareTo("AT")==0 && wta.getPartOfSpeech().compareTo("IN")!= 0))
        fsArr.set(i, wta);
      else if (i ==0)
        skipTerm = true;
    }
    String segStatus = getSubSectionStatus(locationTerm, jcas, cutOffForRevision);
    
    if (!skipTerm && (segStatus.compareTo("-1")==0 || segStatus.compareTo("1")!=0)) {
      locationTerm.setRelatedTokens(fsArr);
      String segId = getSegmentIdContaining(locationTerm, jcas);
      locationTerm.setSegmentID(segId);
    
    //fsArr.addToIndexes();
      locationTerm.addToIndexes();
    }
  }

View Full Code Here

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Related Classes of org.apache.ctakes.padtermspotter.type.PADLocation

org.apache.ctakes.padtermspotter.ae.PADHitAnnotator

org.apache.ctakes.padtermspotter.cc.PADOffSetsRecord

org.apache.ctakes.padtermspotter.impl.PADLocationConsumerImpl

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