Package org.sbml.jsbml.ext

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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    }
   
    // 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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    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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    //      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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    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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    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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    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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    }

    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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    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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