Package edu.pitt.dbmi.nlp.noble.terminology

Examples of edu.pitt.dbmi.nlp.noble.terminology.Concept.addMatchedTerm()

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            acr.add(c);
        }
        // if expanded form was matched as a single concept
        if(exp != null){
          // fix annotations
          exp.addMatchedTerm(acronym);
          exp.setAnnotations(null);
          exp.setText(null);
          // save acronym with expanded form code
          getAcronyms().put(acronym,exp.getCode());
          // if there was a different acronym selected, then remove them
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      if(!isFilteredOut(c)){
        c.setScore(1.0);
        if(result.containsKey(c)){
          Concept oc = result.get(c);
          for(String ot: c.getMatchedTerms())
            oc.addMatchedTerm(ot);
          for(Annotation a: c.getAnnotations())
            oc.addAnnotation(a);
        }else
          result.put(c,c);
      }
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          c = new Concept(code,term);
        }
        // clone
        c = c.clone();
        c.setTerminology(this);
        c.addMatchedTerm(oterm);
        c.setSearchString(text);
       
        if(ignoreAcronyms && isAcronym(c))
          continue;
     
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        if(!isFilteredOut(c)){
          // if we have multipe annotations, deal with it better
          if(result.containsKey(c)){
            Concept oc = result.get(c);
            for(String ot: c.getMatchedTerms())
              oc.addMatchedTerm(ot);
            // this actually fails to identify multiple mentions
            //for(Annotation a: c.getAnnotations())
            //  oc.addAnnotation(a);
          }else
            result.put(c,c);
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          c = new Concept(code,term);
        }
        // clone
        c = c.clone();
        c.setTerminology(this);
        c.addMatchedTerm(oterm);
        c.setSearchString(text);
       
        if(ignoreAcronyms && isAcronym(c))
          continue;
     
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