Package uk.ac.cam.ch.wwmm.oscar3.dataparse

Examples of uk.ac.cam.ch.wwmm.oscar3.dataparse.RPNode

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    }
   
    //if(surface.matches("([Pp]oly).+")) features.add("polymer");
    //if(surface.matches(".+\\(\\d\\d\\d+\\)")) features.add("surfacenotation");
   
    Token t = state.procDoc.getTokenByStart(annot.getAttributeValue("from"));
    if(fPrevious && t != null) {
      Token tt = t.getNAfter(-1);
      if(tt != null) {
        if(TokenTypes.isRef(tt) && tt.getNAfter(-1) != null) {
          //  features.add(prefix + "skiprefprev");
          tt = tt.getNAfter(-1);
        }
        String ttv = tt.getValue();
        ttv = ttv.replaceAll("\\s+", "_");
        features.add("prev=" + ttv);
      }
    }
   
    t = state.procDoc.getTokenByEnd(annot.getAttributeValue("to"));
    if(fNext && t != null) {
      Token tt = t.getNAfter(1);
      if(tt != null && tt.getValue().equals("-")) {
        tt = t.getNAfter(2);
      }
      if(tt != null) {
        if(TokenTypes.isRef(tt) && tt.getNAfter(1) != null) {
          tt = tt.getNAfter(1);
        }
       
        String ttv = tt.getValue();
        ttv = ttv.replaceAll("\\s+", "_");
        features.add("next=" + ttv);
      }
    }
   
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    Map<TokenSequence,Boolean> tokSeqs = new HashMap<TokenSequence,Boolean>();
    Map<TokenSequence,Bag<String>> tokSeqPRWs = new HashMap<TokenSequence,Bag<String>>();
   
    for(int i=0;i<n.size();i++) {
      Element e = (Element)n.get(i);
      Token token = procDoc.getTokenByStart(e.getAttributeValue("from"));
      if(token == null) token = procDoc.getTokenByEnd(e.getAttributeValue("to"));
      if(token == null) {
        System.out.println("Eeep!");
      } else {
        TokenSequence tokSeq = token.getTokenSequence();
        //boolean isReact = "REACT".equals(SafTools.getSlotValue(e, "subtype"));
        boolean isPubmed = f.toString().contains("pubmed");
        if(tokSeqs.containsKey(tokSeq)) {
          if(isPubmed) tokSeqs.put(tokSeq, true);
        } else {
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      }
      prevCell = cell;
    }
    //System.out.println("**************************");
    // Parenthetical phrases
    Token beforeBracket = null;
    Token prevToken = null;
    for(Token token : tokSeq.getTokens()) {
      if(prevToken == null) {
        prevToken = token;
        continue;
      }
      if(beforeBracket == null) {
        if(token.getValue().equals("(")) beforeBracket = prevToken;
      } else if(token.getValue().equals(")")) {
        LatticeCell beforeBracketCell = tokensToTokenCells.get(beforeBracket);
        LatticeCell bracketCell = tokensToTokenCells.get(token);
        if(beforeBracketCell != null || bracketCell != null) {
          beforeBracketCell.addInheritance(bracketCell);
          //System.out.println("Parenthetical: " + tokSeq.getSubstring(beforeBracket.getId(), token.getId()));
        }
        beforeBracket = null;
      }
      prevToken = token;
    }
   
    // Build in named entities
    for(Token token : tokSeq.getTokens()) {
      if(startsToNEs.containsKey(token.getStart())) {
        for(Element neElem : startsToNEs.get(token.getStart())) {
          Token endToken = procDoc.getTokenByEnd(neElem.getAttributeValue("to"));
          if(endToken == null) continue;
          prevCell = tokenToPrev.get(token);
          LatticeCell endTokenCell = tokensToTokenCells.get(endToken);
          if(endTokenCell == null) continue;
          LatticeCell neCell = new LatticeCell(neElem, endTokenCell);
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   *
   * @param word The string to test.
   */
  public static void destroyInstanceIfWordTokenises(String word) {
    if(myInstance == null) return;
    TokenSequence ts = Tokeniser.getInstance().tokenise(word);
    if(ts.getTokens().size() > 1) myInstance = null;
  }
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   *
   * @param word The string to test.
   */
  public static void destroyInstanceIfWordTokenises(String word) {
    if(myInstance == null) return;
    TokenSequence ts = Tokeniser.getInstance().tokenise(word);
    if(ts.getTokens().size() > 1) myInstance = null;
  }
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        ontDFANumber++;
      }
      type = type + "_" + ontDFANumber;*/
    }

    TokenSequence ts = Tokeniser.getInstance().tokenise(ne);
    List<String> tokens = ts.getTokenStringList();

    if(!alwaysAdd && tokens.size() == 1 && !ne.contains("$")) return;
    StringBuffer sb = new StringBuffer();
    for(String token : tokens) {
      sb.append(getRepForToken(token));
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                featuresForAbbrev.add(abbrMode + "abbr<" + thresh);
              }             
            }
          } else {
            int tokID = ne.getFirstToken().getId();
            TokenSequence tokSeq = ne.getFirstToken().getTokenSequence();
            int length = surf.length();
            boolean isAcro = false;
            if(allCaps.matcher(surf).matches()) {
              if(length <= (tokID - 1)) {
                isAcro = true;
                for(int i=0;i<length;i++) {
                  if(!tokSeq.getToken(tokID - length - 1 + i).getValue().toUpperCase().startsWith(surf.substring(i,i+1))) isAcro = false;
                }
                if(isAcro) {
                  featuresForAbbrev.add("allUpperAbbrev");
                }
              }
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    double conf = ne.getConfidence();
    double confLog = Math.log(conf) - Math.log(1 - conf);

    List<String> features = new ArrayList<String>();
   
    TokenSequence t = ne.getTokens().get(0).getTokenSequence();
    int entityLength = ne.getTokens().size();
    int startID = ne.getTokens().get(0).getId();
    int endID = startID + entityLength - 1;
    String surf = ne.getSurface();
   
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      Bag<String> wordCounts = new Bag<String>();
     
      ss.reset();
      for(String s : ss) {
        TokenSequence t = Tokeniser.getInstance().tokenise(s);
        for(String word : t.getTokenStringList()) {
          if(!word.matches(".*[a-z][a-z].*")) continue;
          word = StringTools.normaliseName(word);
          if(!knownWords.contains(NGram.parseWord(word))) wordCounts.add(word);
        }
      } 
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      Elements lineElems = elems.get(i).getChildElements();
      //List<String> wordsForWord = new ArrayList<String>();
      Set<String> wordsForWord = new HashSet<String>();
      for(int j=0;j<lineElems.size();j++) {
        String lineVal = lineElems.get(j).getValue();
        TokenSequence t = Tokeniser.getInstance().tokenise(lineVal);
        boolean found = false;
        List<String> tl = new ArrayList<String>();
        for(String s : t.getTokenStringList()) {
          if(s.compareToIgnoreCase(name) == 0) {
            tl.add("*WORD*");
            found = true;
          } else {
            //tl.add(StringTools.normaliseName2(s));
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Related Classes of uk.ac.cam.ch.wwmm.oscar3.dataparse.RPNode

  • dk.brics.automaton.Automaton
  • jregex.Pattern
  • nu.xom.Attribute
  • nu.xom.Builder
  • nu.xom.Document
  • nu.xom.Element
  • nu.xom.Elements
  • nu.xom.Node
  • nu.xom.Nodes
  • nu.xom.Serializer
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