Examples of SBMLGraphReader

cysbml.SBMLGraphReader
Modified: 2013-11-05 @author Matthias KoenigInstances of the CySBMLGraphReader class should normally only be generated from within the Cytoscape.createNetwork(new GraphReader, ...), to be sure all the necessary Cytoscape processing is performed when the SBML is loaded. The work is based upon the original SBML2 Reader for Cytoscape. Created on September 27, 2005, 9:23 AM and reuses the way the filter for SBML files is generated and how the GraphReader is hooked into Cytoscape. @author W.P.A. Ligtenberg, Eindhoven University of Technology @author Mike Smoot

Examples of cysbml.SBMLGraphReader

    return pass;
  }


  /** Gets the SBML Graph Reader. */
  public GraphReader getReader(String fileName) {
      return new SBMLGraphReader(fileName);
  }

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Examples of cysbml.SBMLGraphReader

      }
      else{
        InputStream instream = new ByteArrayInputStream(sbml.getBytes("UTF-8"));
        taskMonitor.setPercentCompleted(40);
        taskMonitor.setStatus("Creating Cytoscape network from SBML ...");
        Cytoscape.createNetwork(new SBMLGraphReader(instream),true, null);
      }
    } catch (Exception e) {
      e.printStackTrace();
    }  
    taskMonitor.setPercentCompleted(100);

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Examples of cysbml.SBMLGraphReader

   * Uses the CySBMLGraphReader with the given SBML file. 
   */
  public boolean performTest(){
    boolean success = false;
    try {
      SBMLGraphReader reader = new SBMLGraphReader(filename);
      reader.read();
      Cytoscape.getCurrentNetwork().getIdentifier();
      //reader.doPostProcessing(Cytoscape.getCurrentNetwork());
      
      // Destroy the network nodes
      for (Object node : Cytoscape.getCyNodesList()) {

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