Class CDParameters


  • @PublicAPI
    public class CDParameters
    extends MDParameters
    Manages parameters the CustomDescriptor class.
    Since:
    JChem 2.3
    • Field Detail

      • BINARY_DESCRIPTOR

        public static final int BINARY_DESCRIPTOR
        descriptor type constants
        See Also:
        Constant Field Values
      • descrType

        protected int descrType
        descriptor type
      • parameters

        protected org.dom4j.Element parameters
        node in the DOM tree built from the XML configuration
    • Constructor Detail

      • CDParameters

        public CDParameters()
        Creates an empty object. The type of the descriptor is not yet determined.
      • CDParameters

        public CDParameters​(int type)
        Creates an empty object of the given type. Initializes to default values.
      • CDParameters

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

        public CDParameters​(String XMLconfig)
                     throws MDParametersException
        Creates a new object based on a 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 format.
        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 (even other than XML).
        Overrides:
        fromFile in class MDParameters
        Parameters:
        parameterFile - initialized parameter file
        Throws:
        MDParametersException - failed to process parameter file
      • initGenerator

        protected void initGenerator()
                              throws MDParametersException
        This method is void in this class as custom descriptors are opaque, their internal structure is not known. Derived classes that implement user defined or 3rd party descriptors should overload this function and provide the procedure for descriptor generation.
        Throws:
        MDParametersException
      • init

        protected void init()
        This method is called by the constructors before processing the XML configuration. It creates a CustomDescriptor object defined in MDParameters.md. Metircs defined by the descirptor class are retrieved through this object.
      • initParameters

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

        public int getDescrType()
        Gets the type of the descriptor.
        Returns:
        type of the descriptor (BINARY_DESCRIPTOR, INTEGER_DESCRIPTOR or FLOAT_DESCRIPTOR)
      • getNumberOfWeights

        protected int getNumberOfWeights​(int parametrizedMetricIndex)
                                  throws IllegalArgumentException
        Gets the number of weight factors used by the specified metric. T
        Overrides:
        getNumberOfWeights in class MDParameters
        Parameters:
        parametrizedMetricIndex - parametrized metric index
        Returns:
        number of weights the metric uses
        Throws:
        IllegalArgumentException - if the given parameter is not a valid metric index
      • getDefaultDocumentFrame

        public String getDefaultDocumentFrame()
        Gets the XML configuration string. This is needed when the optional XML configuration is not specified.
        Overrides:
        getDefaultDocumentFrame in class MDParameters
        Returns:
        default XML configuration string of the CDParameters class
      • processDocument

        protected void processDocument​(boolean all)
                                throws MDParametersException
        Processes parts of the XML configuration that are specific to CustomDescriptor. 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
      • readValues

        protected void readValues​(boolean all)
                           throws MDParametersException
        Picks parameter values from the DOM tree.
        Overrides:
        readValues in class MDParameters
        Parameters:
        all - indicates if the entire document has to be processed in which case the existing configuration is overwritten
        Throws:
        MDParametersException