Examples of IdentifiedAnnotation

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

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  public String calcAlias () {
    try{
    if (m1.getContent() instanceof IdentifiedAnnotation &&
      m2.getContent() instanceof IdentifiedAnnotation) {
      IdentifiedAnnotation ne1 = (IdentifiedAnnotation) m1.getContent();
      IdentifiedAnnotation ne2 = (IdentifiedAnnotation) m2.getContent();

      ArrayList<String> l = new ArrayList<String>();
      FSArray fsa = ne1.getOntologyConceptArr();
      for (int i = 0; i < fsa.size(); ++i)
        if (fsa.get(i) instanceof UmlsConcept)
          l.add(((UmlsConcept)fsa.get(i)).getCui());

      fsa = ne2.getOntologyConceptArr();
      for (int i = 0; i < fsa.size(); ++i)
        if (fsa.get(i) instanceof UmlsConcept &&
          l.contains(((UmlsConcept)fsa.get(i)).getCui()))
          return "C";
    }
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Examples of org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation

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    EventMention event = null;
    TimeMention time = null;
   
    // swap the order if necessary:
    if(arg2.getBegin() <= arg1.getBegin() && arg2.getEnd() <= arg1.getEnd()){
      IdentifiedAnnotation temp = arg1;
      arg1 = arg2;
      arg2 = temp;
    }

    if(arg1 instanceof EventMention){
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Examples of org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation

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            fileName, category, arg1Type, arg1Begin, arg1End, arg2Type, arg2Begin, arg2End);
      }
    }
   
    protected static String formatRelation(BinaryTextRelation relation) {
      IdentifiedAnnotation arg1 = (IdentifiedAnnotation)relation.getArg1().getArgument();
      IdentifiedAnnotation arg2 = (IdentifiedAnnotation)relation.getArg2().getArgument();
      String arg1Type ="E";
      String arg2Type ="T";
      if(arg1 instanceof TimeMention) arg1Type = "T";
      if(arg2 instanceof EventMention) arg2Type = "E";
      String text = arg1.getCAS().getDocumentText();
      int begin = Math.min(arg1.getBegin(), arg2.getBegin());
      int end = Math.max(arg1.getBegin(), arg2.getBegin());
      begin = Math.max(0, begin - 50);
      end = Math.min(text.length(), end + 50);
      return String.format(
          "%s(%s(type=%d!%d-%d!%s), %s(type=%d!%d-%d!%s)) in ...%s...",
          relation.getCategory(),
          arg1.getCoveredText(),
          arg1.getTypeID(),
          //add extra
          arg1.getBegin(),
          arg1.getEnd(),
          arg1Type,
         
          arg2.getCoveredText(),
          arg2.getTypeID(),
          //add extra
          arg2.getBegin(),
          arg2.getEnd(),
          arg2Type,
          text.substring(begin, end).replaceAll("[\r\n]", " "));
    }
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Examples of org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation

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      features.add(new TreeFeature("TK_PATH", fakeTree.toString()));
      return features;
    }
    // swap the order if necessary:
    if(arg2.getBegin() <= arg1.getBegin() && arg2.getEnd() <= arg1.getEnd()){
      IdentifiedAnnotation temp = arg1;
      arg1 = arg2;
      arg2 = temp;
    }
   
    String a1type="", a2type="";
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Examples of org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation

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      return features;
    }
   
    // swap the order if necessary:
    if(arg2.getBegin() <= arg1.getBegin() && arg2.getEnd() <= arg1.getEnd()){
      IdentifiedAnnotation temp = arg1;
      arg1 = arg2;
      arg2 = temp;
    }
   
    String a1type="", a2type="";
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Examples of org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation

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      return features;
    }
   
    // swap the order if necessary:
    if(arg2.getBegin() <= arg1.getBegin() && arg2.getEnd() <= arg1.getEnd()){
      IdentifiedAnnotation temp = arg1;
      arg1 = arg2;
      arg2 = temp;
    }
   
    String a1type="", a2type="";
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Examples of org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation

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      IdentifiedAnnotation arg2) throws AnalysisEngineProcessException {
    List<Feature> feats = new ArrayList<Feature>();
   
    // make sure they're in the correct order
    if(arg1.getBegin() > arg2.getBegin()){
      IdentifiedAnnotation temp = arg1;
      arg1 = arg2;
      arg2 = temp;
    }
   
    SimpleTree bopTree = getTree(jcas, arg1, arg2, "BOP", new Function<BaseToken,String>(){public String apply(BaseToken t){ return t.getPartOfSpeech();}});
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Examples of org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation

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  @Override
  public List<Feature> extract(JCas view, Annotation focusAnnotation)
      throws CleartkExtractorException {
    List<Feature> featList = new ArrayList<Feature>();
   
    IdentifiedAnnotation mention = (IdentifiedAnnotation) focusAnnotation;
    featList.add(new Feature("IsNegated", mention.getPolarity() == CONST.NE_POLARITY_NEGATION_PRESENT));
    return featList;
  }
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Examples of org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation

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    // allowable arg2 types for location_of
  // Per CTAKES-190, only link anatomical sites in LocationOf to EventMentions, but these three are EventMentions now,
  // so this check of type ID now already handles if it is an EventMention.
    HashSet<Integer> okArg2Types = new HashSet<Integer>(Arrays.asList(CONST.NE_TYPE_ID_DISORDER, CONST.NE_TYPE_ID_FINDING, CONST.NE_TYPE_ID_PROCEDURE));
   
    IdentifiedAnnotation arg1 = pair.getArg1(); // Argument (should be anatomical site)
    IdentifiedAnnotation arg2 = pair.getArg2(); // Related_to (should be either disorder, sign/symptom, or procedure)
    int type1 = arg1.getTypeID();
    int type2 = arg2.getTypeID();
   
    if(type1 == CONST.NE_TYPE_ID_ANATOMICAL_SITE && okArg2Types.contains(type2)) {
      return true;
    }
   
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Examples of org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation

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    // allowable arg1 types
  // Per CTAKES-190, only link SeverityModifiers to EventMention, but the 2 type IDs below are EventMentions now,
    // so this check of type ID now already handles if it is an EventMention.
    HashSet<Integer> okArg1Types = new HashSet<Integer>(Arrays.asList(CONST.NE_TYPE_ID_DISORDER, CONST.NE_TYPE_ID_FINDING));

    IdentifiedAnnotation arg1 = pair.getArg1(); // Argument (should be either disease/disorder or sign/symptom
    int type1 = arg1.getTypeID();

    if(okArg1Types.contains(type1)) {
      return true; // assume arg2 is a modifier
    }
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