Examples of uk.ac.cam.ch.wwmm.oscar3.flow.OscarFlow

uk.ac.cam.ch.wwmm.oscar3.recogniser.document.TokenSequence
This runs Oscar modules on SciXML Documents. You put the SciXML in with the constructor, call methods to run the modules, and then use getter methods to get various Documents back. @author ptc24

    String tag = bestLast;
    for(int i=t.size()-1;i>=0;i--) {
      tags.set(i, tag);
      tag = prevsByLabel.get(i).get(tag);
    }
    Token startToken = null;
    for(int i=0;i<t.size();i++) {
      //System.out.println(t.getToken(i).getValue() + "\t" + tags.get(i));
      if(startToken != null && !tags.get(i).matches("[IE]-ONT.*")) {
        //System.out.println(t.getSubstring(startToken.getId(), t.getToken(i-1).getId()));
        results.add("[" + startToken.getStart() + ":" + t.getToken(i-1).getEnd() + "]");
        startToken = null;
      }
      if(tags.get(i).equals("B-ONT")) startToken = t.getToken(i);
    }
    if(startToken != null) {
      results.add("[" + startToken.getStart() + ":" + t.getToken(t.size()-1).getEnd() + "]");
      //System.out.println(t.getSubstring(startToken.getId(), t.size()-1));
    }
    return results;
  }

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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"));
        if(tokSeqs.containsKey(tokSeq)) {
          if(isReact) tokSeqs.put(tokSeq, true);
        } else {
          tokSeqs.put(tokSeq, isReact);

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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) {
        for(int i=1;i<=1;i++) {
          if(TokenTypes.isRef(tt) && tt.getNAfter(-1) != null) {
            //  features.add(prefix + "skiprefprev");
            tt = tt.getNAfter(-1);
          }
          String ttv = tt.getValue();
          ttv = ttv.replaceAll("\\s+", "_");
          //if(i == 1) features.add("prev" + 1 + "=" + ttv);
          features.add("pbg" + i + "=" + ttv + "_" + surface.replaceAll("\\s+", "_"));
          //features.add("pbg" + (i+1) + "=" + ttv + "_" + surface.replaceAll("\\s+", "_"));
          //features.add("pbg" + 0 + "=" + ttv + "_" + surface.replaceAll("\\s+", "_"));
          //features.add("uibg" + 0 + "=" + ttv + "_" + surface.replaceAll("\\s+", "_"));
          
          tt = tt.getNAfter(-1);
          if(tt == null) break;
        }        


        
        //if(ttv.length() > 4) features.add("prevs=" + ttv.substring(ttv.length()-4) + "_" + surface.replaceAll("\\s+", "_"));
        //features.add("psbg=" + ttv + "_" + suffix.replaceAll("\\s+", "_"));
        //features.add("pstbg=" + ttv + "_" + stem);
        
      }
    }
    
    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) {
        for(int i=1;i<=1;i++) {
          if(TokenTypes.isRef(tt) && tt.getNAfter(1) != null) {
            tt = tt.getNAfter(1);
          }
          
          String ttv = tt.getValue();
          ttv = ttv.replaceAll("\\s+", "_");
          //if(i == 1) features.add("next=" + ttv);
          features.add("nbg" + i + "=" + surface.replaceAll("\\s+", "_")  + "_" + ttv);
          
          //features.add("uibg" + 0 + "=" + ttv + "_" + surface.replaceAll("\\s+", "_"));


          
          tt = tt.getNAfter(1);
          if(tt == null) break;
        }
        //if(ttv.length() > 4) features.add("nexts=" + surface.replaceAll("\\s+", "_")  + "_" + ttv.substring(ttv.length()-4));
        //features.add("nsbg=" + suffix.replaceAll("\\s+", "_")  + "_" + ttv);
        //features.add("nstbg=" + stem  + "_" + ttv);

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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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   * 
   * @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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