Examples of SBasePlugin

org.sbml.jsbml.ext.SBasePlugin
Defines the methods necessary for an SBase Plugin. When a SBML level 3 is extending one of the core SBML elements with additional attributes or child elements, a {@link SBasePlugin}is created to serve as a place holder for there new attributes or elements. @author Nicolas Rodriguez @version $Rev: 1533 $ @since 1.0

Examples of org.sbml.jsbml.ext.SBasePlugin

      // we will have to change that !!!
      return null;
    } 
    else if (sbase instanceof SBasePlugin) 
    {
      SBasePlugin elementPlugin = (SBasePlugin) sbase;
      
      children = elementPlugin.children();
    }
    else if (sbase instanceof TreeNode) 
    {
      children = ((TreeNode) sbase).children();

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Examples of org.sbml.jsbml.ext.SBasePlugin

    }
    
    // Add all additional attributes from extension packages if there are any:
    if ((extensions != null) && (extensions.size() > 0)) {
      for (String key : extensions.keySet()) {
        SBasePlugin plugin = extensions.get(key);
        if (plugin != null) {
          Map<String, String> pluginAttributes = plugin.writeXMLAttributes();
          if (pluginAttributes != null) {
            attributes.putAll(pluginAttributes);
          }
        } else {
          logger.warn(MessageFormat.format(

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Examples of org.sbml.jsbml.ext.SBasePlugin


    List<Object> listOfElementsToWrite = new ArrayList<Object>();


    // test if this treeNode is an extended SBase.
    if (treeNode instanceof SBase && (! (treeNode instanceof Model)) && ((SBase) treeNode).getExtension(getNamespaceURI()) != null) {
      SBasePlugin sbasePlugin = ((SBase) treeNode).getExtension(getNamespaceURI());


      if (sbasePlugin != null) {
        listOfElementsToWrite = super.getListOfSBMLElementsToWrite(sbasePlugin);
        logger.debug("getListOfSBMLElementsToWrite: nb children = " + sbasePlugin.getChildCount());
      }
    } else {
      listOfElementsToWrite = super.getListOfSBMLElementsToWrite(treeNode);
    }

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Examples of org.sbml.jsbml.ext.SBasePlugin

    //      while (children.hasMoreElements()) {
    //        listOfElementsToWrite.add(children.nextElement());
    //      }
    //    }
    if (treeNode instanceof SBase && (! (treeNode instanceof Model)) && ((SBase) treeNode).getExtension(getNamespaceURI()) != null) {
      SBasePlugin sbasePlugin = ((SBase) treeNode).getExtension(getNamespaceURI());


      if (sbasePlugin != null) {
        listOfElementsToWrite = super.getListOfSBMLElementsToWrite(sbasePlugin);
        logger.debug("getListOfSBMLElementsToWrite: nb children = " + sbasePlugin.getChildCount());
      }
    } else {
      listOfElementsToWrite = super.getListOfSBMLElementsToWrite(treeNode);
    }

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Examples of org.sbml.jsbml.ext.SBasePlugin


    List<Object> listOfElementsToWrite = new ArrayList<Object>();


    // test if this treeNode is an extended SBase.
    if (treeNode instanceof SBase && ((SBase) treeNode).getExtension(getNamespaceURI()) != null) {
      SBasePlugin sbasePlugin = ((SBase) treeNode).getExtension(getNamespaceURI());


      if (sbasePlugin != null) {
        listOfElementsToWrite = super.getListOfSBMLElementsToWrite(sbasePlugin);
        logger.debug("getListOfSBMLElementsToWrite: nb children = " + sbasePlugin.getChildCount());
      }
    } else {
      listOfElementsToWrite = super.getListOfSBMLElementsToWrite(treeNode);
    }

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Examples of org.sbml.jsbml.ext.SBasePlugin

    logger.debug("getListOfSBMLElementsToWrite: " + sbase.getClass().getCanonicalName());


    List<Object> listOfElementsToWrite = new ArrayList<Object>();


    if (sbase instanceof Model) {
      SBasePlugin modelPlugin = ((Model) sbase).getExtension(getNamespaceURI());


      if (modelPlugin != null) {
        listOfElementsToWrite = super.getListOfSBMLElementsToWrite(modelPlugin);
      }
    } else {

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Examples of org.sbml.jsbml.ext.SBasePlugin


    List<Object> listOfElementsToWrite = new ArrayList<Object>();


    // test if this sbase is an extended SBase.
    if (sbase instanceof SBase && ((SBase) sbase).getExtension(getNamespaceURI()) != null) {
      SBasePlugin sbasePlugin = ((SBase) sbase).getExtension(getNamespaceURI());


      listOfElementsToWrite = super.getListOfSBMLElementsToWrite(sbasePlugin);
      logger.debug("getListOfSBMLElementsToWrite: nb children = " + sbasePlugin.getChildCount());
    } else {
      listOfElementsToWrite = super.getListOfSBMLElementsToWrite(sbase);
    }


    return listOfElementsToWrite;

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Examples of org.sbml.jsbml.ext.SBasePlugin

    }


    List<Object> listOfElementsToWrite = new ArrayList<Object>();


    if (sbase instanceof Model) {
      SBasePlugin modelPlugin = ((Model) sbase).getExtension(getNamespaceURI());


      if (modelPlugin != null) {
        listOfElementsToWrite = super.getListOfSBMLElementsToWrite(modelPlugin);
      }
    } else {

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Examples of org.sbml.jsbml.ext.SBasePlugin


    List<Object> listOfElementsToWrite = new ArrayList<Object>();


    // test if this treeNode is an extended SBase.
    if (treeNode instanceof SBase && ((SBase) treeNode).getExtension(getNamespaceURI()) != null) {
      SBasePlugin sbasePlugin = ((Model) treeNode).getExtension(getNamespaceURI());


      if (sbasePlugin != null) {
        listOfElementsToWrite = super.getListOfSBMLElementsToWrite(sbasePlugin);
        logger.debug("getListOfSBMLElementsToWrite: nb children = " + sbasePlugin.getChildCount());
      }
    } else {
      listOfElementsToWrite = super.getListOfSBMLElementsToWrite(treeNode);
    }

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