Package org.mitre.medfacts.zoner

Examples of org.mitre.medfacts.zoner.LineTokenToCharacterOffsetConverter.convert()

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        sentStart.setLine(i+1);
        sentStart.setTokenOffset(0);
        LineAndTokenPosition sentEnd = new LineAndTokenPosition();
        sentEnd.setLine(i+1);
        sentEnd.setTokenOffset(tokenArrays[i].length-1);
        LineTokenToCharacterOffsetConverter.BeginAndEndCharacterOffsetPair sStart = converter.convert(sentStart);
        LineTokenToCharacterOffsetConverter.BeginAndEndCharacterOffsetPair sEnd = converter.convert(sentEnd);
        if ((sStart == null) || (sEnd == null)) {
          sent.setBegin(0);
          sent.setEnd(0);
          sent.setSentenceNumber(sentNum);
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        sentStart.setTokenOffset(0);
        LineAndTokenPosition sentEnd = new LineAndTokenPosition();
        sentEnd.setLine(i+1);
        sentEnd.setTokenOffset(tokenArrays[i].length-1);
        LineTokenToCharacterOffsetConverter.BeginAndEndCharacterOffsetPair sStart = converter.convert(sentStart);
        LineTokenToCharacterOffsetConverter.BeginAndEndCharacterOffsetPair sEnd = converter.convert(sentEnd);
        if ((sStart == null) || (sEnd == null)) {
          sent.setBegin(0);
          sent.setEnd(0);
          sent.setSentenceNumber(sentNum);
        } else {
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        for (int j=0; j < tokenArrays[i].length; j++) {
          WordToken tok = new WordToken(jcas);
          LineAndTokenPosition word = new LineAndTokenPosition();
          word.setLine(i+1);
          word.setTokenOffset(j);
          LineTokenToCharacterOffsetConverter.BeginAndEndCharacterOffsetPair tPos = converter.convert(word);
          if (tPos == null) {
            tok.setBegin(0);
            tok.setEnd(1);
          } else {
            tok.setBegin(tPos.getBegin());
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//        assertion.setBegin(converter.convert(assertionStart).getBegin());
//        assertion.setEnd(converter.convert(assertionEnd).getEnd() + 1);
//        assertion.setConceptType("PROBLEM");
//        assertion.addToIndexes();
       
        entityOrEventMention.setBegin(converter.convert(assertionStart).getBegin());
        entityOrEventMention.setEnd(converter.convert(assertionEnd).getEnd());
        entityOrEventMention.setConfidence(1.0f);
       
        FSArray ontologyConceptArray = ConceptLookup.reverseLookup(conceptType, jcas);
        entityOrEventMention.setOntologyConceptArr(ontologyConceptArray);
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//        assertion.setEnd(converter.convert(assertionEnd).getEnd() + 1);
//        assertion.setConceptType("PROBLEM");
//        assertion.addToIndexes();
       
        entityOrEventMention.setBegin(converter.convert(assertionStart).getBegin());
        entityOrEventMention.setEnd(converter.convert(assertionEnd).getEnd());
        entityOrEventMention.setConfidence(1.0f);
       
        FSArray ontologyConceptArray = ConceptLookup.reverseLookup(conceptType, jcas);
        entityOrEventMention.setOntologyConceptArr(ontologyConceptArray);
       
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        sentStart.setLine(i+1);
        sentStart.setTokenOffset(0);
        LineAndTokenPosition sentEnd = new LineAndTokenPosition();
        sentEnd.setLine(i+1);
        sentEnd.setTokenOffset(tokenArrays[i].length-1);
        LineTokenToCharacterOffsetConverter.BeginAndEndCharacterOffsetPair sStart = converter.convert(sentStart);
        LineTokenToCharacterOffsetConverter.BeginAndEndCharacterOffsetPair sEnd = converter.convert(sentEnd);
        if ((sStart == null) || (sEnd == null)) {
          sent.setBegin(0);
          sent.setEnd(0);
          sent.setSentenceNumber(sentNum);
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        sentStart.setTokenOffset(0);
        LineAndTokenPosition sentEnd = new LineAndTokenPosition();
        sentEnd.setLine(i+1);
        sentEnd.setTokenOffset(tokenArrays[i].length-1);
        LineTokenToCharacterOffsetConverter.BeginAndEndCharacterOffsetPair sStart = converter.convert(sentStart);
        LineTokenToCharacterOffsetConverter.BeginAndEndCharacterOffsetPair sEnd = converter.convert(sentEnd);
        if ((sStart == null) || (sEnd == null)) {
          sent.setBegin(0);
          sent.setEnd(0);
          sent.setSentenceNumber(sentNum);
        } else {
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        for (int j=0; j < tokenArrays[i].length; j++) {
          WordToken tok = new WordToken(jcas);
          LineAndTokenPosition word = new LineAndTokenPosition();
          word.setLine(i+1);
          word.setTokenOffset(j);
          LineTokenToCharacterOffsetConverter.BeginAndEndCharacterOffsetPair tPos = converter.convert(word);
          if (tPos == null) {
            tok.setBegin(0);
            tok.setEnd(1);
          } else {
            tok.setBegin(tPos.getBegin());
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        LineAndTokenPosition assertionEnd = new LineAndTokenPosition();
        assertionStart.setLine(a.getBegin().getLine());
        assertionStart.setTokenOffset(a.getBegin().getTokenOffset());
        assertionEnd.setLine(a.getEnd().getLine());
        assertionEnd.setTokenOffset(a.getEnd().getTokenOffset());
        assertion.setBegin(converter.convert(assertionStart).getBegin());
        assertion.setEnd(converter.convert(assertionEnd).getEnd() + 1);
        assertion.setConceptType("PROBLEM");
        assertion.addToIndexes();
      }
      writeXmi(cas,outFile);
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        assertionStart.setLine(a.getBegin().getLine());
        assertionStart.setTokenOffset(a.getBegin().getTokenOffset());
        assertionEnd.setLine(a.getEnd().getLine());
        assertionEnd.setTokenOffset(a.getEnd().getTokenOffset());
        assertion.setBegin(converter.convert(assertionStart).getBegin());
        assertion.setEnd(converter.convert(assertionEnd).getEnd() + 1);
        assertion.setConceptType("PROBLEM");
        assertion.addToIndexes();
      }
      writeXmi(cas,outFile);
    }
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