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

Examples of uk.ac.cam.ch.wwmm.oscar3.terms.OBOOntology

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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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   *
   * @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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    int nb = 0;
    int b = 0;
   
    for(int i=0;i<n.size();i++) {
      TokenSequence t = Tokeniser.getInstance().tokenise(n.get(i).getValue());
      boolean isBoring = true;
      for(String s : t.getTokenStringList()) {
        s = StringTools.normaliseName(s);
        if(!s.matches(".*[A-Za-z].*")) continue;
        if(boring.contains(s)) continue;
        boring.add(s);
        isBoring = false;
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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);
        wordCounts.add(word);
      }
    } 
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