Interface StandardizerConfigurationReader

  • All Known Implementing Classes:
    StandardizerActionStringReader, StandardizerXMLReader

    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 Detail


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

        path to default standardizer action configuration list
        See Also:
        Constant Field Values
    • Method Detail

      • 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