Package org.mitre.medfacts.zoner

Examples of org.mitre.medfacts.zoner.CharacterOffsetToLineTokenConverterDefaultImpl

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          PrintWriter writer = new PrintWriter(new java.io.File(odir + "/" + file.getName()));
            XmiCasDeserializer.deserialize(inputStream, cas);
            JCas jcas = cas.getJCas();
            String sofaString = jcas.getDocumentText();
            System.err.println("Converting text string: " + sofaString);
            CharacterOffsetToLineTokenConverterDefaultImpl converter = new CharacterOffsetToLineTokenConverterDefaultImpl(sofaString);
          AnnotationIndex<Annotation> aIndex = jcas.getAnnotationIndex(assertionType);
          for (Annotation a : aIndex) {
            Assertion ai = (Assertion) a;
            int begin = ai.getBegin();
            int end = ai.getEnd();
            LineAndTokenPosition begPos = converter.convert(begin);
            LineAndTokenPosition endPos = converter.convert(end);
            writer.println("c=\"" + sofaString.substring(begin,end) + "\" " + begPos.getLine() + ":" + begPos.getTokenOffset() +
                " " + endPos.getLine() + ":" + endPos.getTokenOffset() + "||t=\"problem\"||a=\"" + ai.getAssertionType() + "\"");
          }
          writer.close();
        } catch (Exception e) {
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//          new LineTokenToCharacterOffsetConverter(contents);
//    }
    if (converter2 == null)
    {
      converter2 =
          new CharacterOffsetToLineTokenConverterDefaultImpl(contents);
    }
  }
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        textLookup = textLookupTemp.toArray(twoDimensionalStringArray);
        wholeText = builder.toString();
    }

    public void addConceptAnnotation(int startCharOffset, int endCharOffset, String typ, ConceptTypeParam conceptType) {
      CharacterOffsetToLineTokenConverter converter = new CharacterOffsetToLineTokenConverterDefaultImpl(wholeText);

      LineAndTokenPosition startLineAndTokenPosition = converter.convert(startCharOffset);
      LineAndTokenPosition endLineAndTokenPosition = converter.convert(endCharOffset);

      ConceptAnnotation conceptAnnotation = new ConceptAnnotation();

      Location beginLocation = new Location();
      beginLocation.setLine(startLineAndTokenPosition.getLine());
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  {
    try
      {
        processTextFile();
       
        this.converter = new CharacterOffsetToLineTokenConverterDefaultImpl(entireContents);
       
        processAnnotationFiles();
        MedFactsRunner.postProcessForCueWords(textLookup, allAnnotationList, annotationsByType);
        processZones();
        //validateAnnotations();
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          PrintWriter writer = new PrintWriter(new java.io.File(odir + "/" + file.getName()));
            XmiCasDeserializer.deserialize(inputStream, cas);
            JCas jcas = cas.getJCas();
            String sofaString = jcas.getDocumentText();
            System.err.println("Converting text string: " + sofaString);
            CharacterOffsetToLineTokenConverterDefaultImpl converter = new CharacterOffsetToLineTokenConverterDefaultImpl(sofaString);
          AnnotationIndex<Annotation> aIndex = jcas.getAnnotationIndex(assertionType);
          for (Annotation a : aIndex) {
            Assertion ai = (Assertion) a;
            int begin = ai.getBegin();
            int end = ai.getEnd();
            LineAndTokenPosition begPos = converter.convert(begin);
            LineAndTokenPosition endPos = converter.convert(end);
            writer.println("c=\"" + sofaString.substring(begin,end) + "\" " + begPos.getLine() + ":" + begPos.getTokenOffset() +
                " " + endPos.getLine() + ":" + endPos.getTokenOffset() + "||t=\"problem\"||a=\"" + ai.getAssertionType() + "\"");
          }
          writer.close();
        } catch (Exception e) {
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Related Classes of org.mitre.medfacts.zoner.CharacterOffsetToLineTokenConverterDefaultImpl

  • org.apache.ctakes.assertion.medfacts.ConvertXMIAssertionsToi2b2Format
  • org.mitre.medfacts.i2b2.api.SingleDocumentProcessor
  • org.mitre.medfacts.i2b2.cli.AssertionDocumentObject
  • org.mitre.medfacts.i2b2.cli.MedFactsRunner
  • org.mitre.medfacts.uima.assertion.ConvertXMIAssertionsToi2b2Format
  • java.util.regex.Matcher
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