Examples of org.sbml.jsbml.ext.fbc.FBCModelPlugin

org.sbml.jsbml.ext.fbc.FBCModelPlugin
@author Nicolas Rodriguez @version $Rev: 1639 $ @since 1.0 @date 27.10.2011

  public Object processStartElement(String elementName, String uri, String prefix,
    boolean hasAttributes, boolean hasNamespaces, Object contextObject)
  {
    if (contextObject instanceof Model) {
      Model model = (Model) contextObject;
      FBCModelPlugin fbcModel = null;


      if (model.getExtension(FBCConstants.namespaceURI) != null) {
        fbcModel = (FBCModelPlugin) model.getExtension(FBCConstants.namespaceURI);
      } else {
        fbcModel = new FBCModelPlugin(model);
        model.addExtension(FBCConstants.namespaceURI, fbcModel);
      }


      if (elementName.equals(FBCList.listOfFluxBounds.name())) {


        ListOf<FluxBound> listOfFluxBounds = fbcModel.getListOfFluxBounds();
        groupList = FBCList.listOfFluxBounds;
        return listOfFluxBounds;
      }
      else if (elementName.equals(FBCList.listOfObjectives.name())) {


        ListOf<Objective> listOfObjectives = fbcModel.getListOfObjectives();
        groupList = FBCList.listOfObjectives;
        return listOfObjectives;
      }
    } else if (contextObject instanceof Objective) {
      Objective objective = (Objective) contextObject;


      if (elementName.equals("listOfFluxObjectives") || elementName.equals("listOfFluxes")) {
        // listOfFluxes was the first name of listOfFluxObjectives in the preliminary specifications
        ListOf<FluxObjective> listOfFluxObjectives = objective.getListOfFluxObjectives();
        groupList = FBCList.listOfFluxObjectives;
        return listOfFluxObjectives;
      }
    }


    else if (contextObject instanceof ListOf<?>) {
      ListOf<SBase> listOf = (ListOf<SBase>) contextObject;


      if (elementName.equals("fluxBound")
          && groupList.equals(FBCList.listOfFluxBounds)) {
        Model model = (Model) listOf.getParentSBMLObject();
        FBCModelPlugin extendeModel = (FBCModelPlugin) model.getExtension(FBCConstants.namespaceURI);


        FluxBound fluxBound = new FluxBound();
        extendeModel.addFluxBound(fluxBound);
        return fluxBound;


      } else if (elementName.equals("objective")
          && groupList.equals(FBCList.listOfObjectives)) {
        Model model = (Model) listOf.getParentSBMLObject();
        FBCModelPlugin extendeModel = (FBCModelPlugin) model.getExtension(FBCConstants.namespaceURI);


        Objective objective = new Objective();
        extendeModel.addObjective(objective);


        return objective;
      } else if (elementName.equals("fluxObjective")
          && groupList.equals(FBCList.listOfFluxObjectives)) {
        Objective objective = (Objective) listOf.getParentSBMLObject();

View Full Code Here

        testDocument = new SBMLReader().readSBMLFromFile(fileName);
        System.out.printf("Reading done\n");
        System.out.println(Calendar.getInstance().getTime());
        afterRead = Calendar.getInstance().getTimeInMillis();


        FBCModelPlugin fbcModel = (FBCModelPlugin) testDocument.getModel().getExtension(FBCConstants.namespaceURI);


        if (fbcModel != null)
        {
          System.out.println("nb fluxBounds found: " + fbcModel.getListOfFluxBounds().size());
          System.out.println("nb objectives found: " + fbcModel.getListOfObjectives().size());
          System.out.println("nb fluxObjectives found: " + fbcModel.getObjective(0).getListOfFluxObjectives().size());
          System.out.println("Active objective: " + fbcModel.getActiveObjective());
          System.out.println("Active objective: " + fbcModel.getListOfObjectives().getActiveObjective());
        }
        else
        {
          System.out.println("!!!!!!!!!! not FBC model plugin defined !!!!!!!!!!!!");
        }

View Full Code Here

  @Override
  public SBasePlugin createPluginFor(SBase sbase) {


    if (sbase != null) {
      if (sbase instanceof Model) {
        return new FBCModelPlugin((Model) sbase);
      } else if (sbase instanceof Species) {
        return new FBCSpeciesPlugin((Species) sbase);
      }
    }
    return null;

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Related Classes of org.sbml.jsbml.ext.fbc.FBCModelPlugin

org.sbml.jsbml.xml.parsers.FBCParser

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