Examples of processLite()

Examples of uk.ac.cam.ch.wwmm.oscar3.flow.OscarFlow.processLite()

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  }
 
  public void autoAnnotate() throws Exception {
    clearAnnotations();
    OscarFlow oscarFlow = new OscarFlow(doc);
    oscarFlow.processLite();
    doc = SciXMLDocument.makeFromDoc(oscarFlow.getInlineXML());
    writeScrapBook();
  }

  public void autoAnnotateReactions() throws Exception {
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Examples of uk.ac.cam.ch.wwmm.oscar3.flow.OscarFlow.processLite()

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    nodes = parseDoc.query("//cmlPile");
    for(int i=0;i<nodes.size();i++) {
      nodes.get(i).detach();
    }   
    OscarFlow oscarFlow = new OscarFlow(parseDoc);
    oscarFlow.processLite();
    parseDoc = oscarFlow.getInlineXML();
   
    Nodes parsedIds = parseDoc.query("//snippet/@id");
    Nodes goodIds = doc.query("//snippet/@id");
    Set<String> parsedIdStrs = new LinkedHashSet<String>();
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Examples of uk.ac.cam.ch.wwmm.oscar3.flow.OscarFlow.processLite()

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   * @throws Exception
   */
  public static String stringToString(String input) throws Exception {
    Document doc = TextToSciXML.textToSciXML(input);
    OscarFlow flow = new OscarFlow(doc);
    flow.processLite();
    return flow.getInlineXML().toXML();
  }

 
  /** Prints out a useful help message.
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Examples of uk.ac.cam.ch.wwmm.oscar3.flow.OscarFlow.processLite()

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    }
   
    OscarFlow oscarFlow = new OscarFlow(doc);

    if(mode.equals("Process")) {
      oscarFlow.processLite();
      return oscarFlow.getInlineXML();
    } else if(mode.equals("SAF")) {
      oscarFlow.processToSAF();
      return oscarFlow.getSafXML();
    } else if(mode.equals("Data")) {
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Examples of uk.ac.cam.ch.wwmm.oscar3.flow.OscarFlow.processLite()

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      return oscarFlow.getSafXML();
    } else if(mode.equals("Data")) {
      oscarFlow.parseData();
      return oscarFlow.getDataXML();
    } else if(mode.equals("RoundTrip")) {
      oscarFlow.processLite();
      ptsx.setSciXMLDoc(oscarFlow.getInlineXML());
      return ptsx.getAnnotatedPubXML();
    }
    return null;
  }
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Examples of uk.ac.cam.ch.wwmm.oscar3.flow.OscarFlow.processLite()

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          request.getParameter("flowcommand").trim().length() > 0) {
        oscarFlow.runFlow(request.getParameter("flowcommand"));
      } else if(outputMode.equals("data")) {
        oscarFlow.parseData();
      } else {
        oscarFlow.processLite();
      }
      if(outputMode.equals("default") && request.getParameter("flowcommand") != null &&
          !request.getParameter("flowcommand").toLowerCase().contains("inline")) {
        outputMode = "saf";
      }
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