Class ParameterDefinition


  • public class ParameterDefinition
    extends Object
    Represents a parameter definition for the external program. A name and type is required. All other settings are optional. Supported values for type is:
    • string: The parameter is a free-text string parameter with a maximum length of 255 characters.
    • text: The parameter is a free-text string parameter with a maximum length of 64K characters.
    • integer, float: The parameter is a numeric parameter. Options 'min' and 'max' can be set to restrict the range of valid values.
    • boolean: The parameter is a true/false parameter.
    • enumeration: The parameter is an enumeration that must take it's value from a predefined list of values. The predefined list should be set in the 'enum' option with a line break as a delimiter between values.
    • factor: The parameter is an enumeration among the experimental factors that has been defined for the experiment. The default value is matched against the name/external id of the annotation types.
    • spotformula: The parameter is an enumeration among the formulas that can be used with the current source bioassay set. The default value is matched against the name of the formulas.
    • assays: The parameter is an enumeration among the bioassays in the current source bioassay set. The default value is matched against the name of the bioassays.
    Since:
    2.15
    Author:
    Nicklas
    • Field Detail

      • dtdFile

        private static final URL dtdFile
      • required

        private boolean required
      • multiple

        private boolean multiple
      • defaultValue

        private String defaultValue
      • description

        private String description
    • Constructor Detail

      • ParameterDefinition

        public ParameterDefinition()
        Create a new empty parameter definition. Before it can be used a name and type must be specified.
    • Method Detail

      • parseXml

        public static List<ParameterDefinition> parseXml​(String xml,
                                                         boolean validate)
        Parse an XML document containing parameter definitions.
        Parameters:
        xml - The xml as a string (with or without a DOCTYPE declaration)
        validate - TRUE to validate the XML against the dtd (external-plugin-parameters.dtd)
        Returns:
        A list with parameter definition
      • getType

        public String getType()
        Get the type of the parameter.
      • setType

        public void setType​(String type)
        Set the type of the parameter. For supported values see the class documentation.
      • getName

        public String getName()
        Get the name of the parameter. This value is required.
      • setName

        public void setName​(String name)
        Set the name of the parameter.
      • isRequired

        public boolean isRequired()
        Is this parameter a required parameter or not?
      • setRequired

        public void setRequired​(boolean required)
        Set if this parameter should be a required or optional parameter.
      • isMultiple

        public boolean isMultiple()
        Can this parameter have multiple values or only one?
      • setMultiple

        public void setMultiple​(boolean multiple)
        Set if this parameter can have multiple values or only one.
      • getDefaultValue

        public String getDefaultValue()
        Get the default value for this parameter.
      • setDefaultValue

        public void setDefaultValue​(String defaultValue)
        Set the default value for this parameter.
      • getDescription

        public String getDescription()
        Get a description/help text about this parameter.
      • setDescription

        public void setDescription​(String description)
        Set a description/help text for this parmeter.
      • getOptions

        public Set<String> getOptions()
        Get the names of other options that are defined for this parmeter. Useful options depend on the parameter type and are described in the class documentation.
      • getOption

        public String getOption​(String key)
        Get the value for an option.
      • setOption

        public void setOption​(String key,
                              String value)
        Set the value for an option.
      • toXmlFragment

        public String toXmlFragment​(boolean compact)
        Render this parameter definition as an XML fragment. Multiple fragments can be concatenated and then wrapped with:
        <!DOCTYPE parameter-definition SYSTEM "external-plugin-parameters.dtd">
        <parameter-definition>
        ...
        </parameter-definition>
        
        Parameters:
        compact - If TRUE, the generated XML is compacted and without line breaks.
        Returns:
        An XML representation of this parameter definition
      • toPluginParameter

        public PluginParameter<?> toPluginParameter​(DbControl dc,
                                                    BioAssaySet source)
        Convert this parameter definition to a PluginParameter object.
        Parameters:
        dc - A DbControl to use for database access
        source - The source bioassay set