Interface StandardizerConfigurationReader

All Known Implementing Classes:
StandardizerActionStringReader, StandardizerXMLReader

@PublicAPI public interface StandardizerConfigurationReader
This interface is provided for classes which can read the configuration of StandardizerActionRunner
Configuration error
There are 2 kinds of configuration errors for execution configuration.
  • the configuration contain unrecognized standardizer actions
  • the recognized standardizer action has unrecognized, or invalid parameters
In the first case in the place of the unrecognized action the configuration should contain an instance of InvalidStandardizerAction containing the text representation of the error. Exceptions should not be thrown, so all errors can be found in the configuration. This way, partially correct configurations can be executed on the target molecules.
In the second case the particular standardizer action contains information on the error. If an error like this occurred, the StandardizerAction.isValid() function should return false.
  • Field Details


      static final String USER_STANDARDIZERS_CONFIG_PATH
      path to user-defined standardizer action configuration list

      path to default standardizer action configuration list
      See Also:
  • Method Details

    • getConfiguration

      StandardizerConfiguration getConfiguration()
      Gets the configuration defined by the pre-set configuration file.
      the StandardizerConfiguration instance which can be run by a StandardizerActionRunner instance
    • setPath

      void setPath(String path)
      Sets the base path of the configuration. External references within the configuration file mist be based on the path set with this method.
      path - the base path of the configuration