Class SDParameters

  • Direct Known Subclasses:
    HBParameters, LDParameters

    @PublicAPI
    public class SDParameters
    extends MDParameters
    Manages ScalarDescriptor parameters. This class reads, stores and provides parameters for the ScalarDescriptor class. The native format of the parameter configuraton is XML.
    Since:
    JChem 2.2
    • Constructor Detail

      • SDParameters

        public SDParameters()
        Creates an empty object.
      • SDParameters

        public SDParameters​(File configFile)
                     throws MDParametersException
        Creates a new object from the given configuration file.
        Parameters:
        configFile - XML configuration file
        Throws:
        MDParametersException - missing or bad XML configuration
      • SDParameters

        public SDParameters​(String XMLconfig)
                     throws MDParametersException
        Creates a new object from the given configuration string.
        Parameters:
        XMLconfig - XML configuration string
        Throws:
        MDParametersException - missing or bad XML configuration
    • Method Detail

      • fromString

        public void fromString​(String parameterString)
                        throws MDParametersException
        Sets parameters from a string representation. This method processes an XML format, but derived classes may overload this and define their own formats.
        Overrides:
        fromString in class MDParameters
        Parameters:
        parameterString - parameters in string
        Throws:
        MDParametersException - when the parameter string is not well-formed
      • fromFile

        public void fromFile​(File parameterFile)
                      throws MDParametersException
        Sets parameters from an XML file. Derived classes may overload this and define their own format (other than XML).
        Overrides:
        fromFile in class MDParameters
        Parameters:
        parameterFile - initialized parameter file
        Throws:
        MDParametersException - failed to process parameter file
      • getNumberOfMetrics

        public int getNumberOfMetrics()
        Gets the total number of parametrized metrics available in the present configuration.
        Overrides:
        getNumberOfMetrics in class MDParameters
        Returns:
        number of metrics
      • init

        protected void init()
        This method is called by the constructors before processing the XML configuration. It creates a ScalarDescriptor object stored in MDParameters.md.
      • initParameters

        protected void initParameters()
        Initializes those data members that depend on the XML configuration but are not directly taken from it.
        Overrides:
        initParameters in class MDParameters
      • processDocument

        protected void processDocument​(boolean all)
                                throws MDParametersException
        Processes parts of the XML configuration specific to ScalarDescriptor. Find the node in the DOM tree and leaves the rest of the work to the parent class.
        Overrides:
        processDocument in class MDParameters
        Parameters:
        all - indicates if the entire document has to be processed in which case the existing configuration is overwritten
        Throws:
        MDParametersException
      • getType

        public String getType()