Package de.jstacs.parameters

This package provides classes for parameters that establish a general convention for the description of parameters as defined in the Parameter-interface.

See: Description

Interface Summary

Interface	Description
GalaxyConvertible	Interface for Parameters that can be converted to and extracted from Galaxy representations.
Rangeable	Interface for Parameters that potentially can be varied over a certain interval or a list of values.
RangeIterator	Interface for a Parameter or ParameterSet that can have multiple values at the same time.

Class Summary

Class	Description
AbstractSelectionParameter	Class for a collection parameter, i.e.
ArrayParameterSet	Class for a ParameterSet that consists of a length-Parameter that defines the length of the array and an array of ParameterSetContainers of this length.
EnumParameter	This class implements a SelectionParameter based on an Enum.
ExpandableParameterSet	A class for a ParameterSet that can be expanded by additional Parameters at runtime.
FileParameter	Class for a Parameter that represents a local file.
FileParameter.FileRepresentation	Class that represents a file.
InstanceParameterSet<T extends InstantiableFromParameterSet>	Container class for a set of Parameters that can be used to instantiate another class.
MultiSelectionParameter	Class for a Parameter that provides a collection of possible values.
Parameter	Abstract class for a parameter that shall be used as the parameter of some method, constructor, etc.
ParameterSet	(Container) class for a set of Parameters.
ParameterSetContainer	Class for a ParameterSetContainer that contains a ParameterSet as value.
ParameterSetTagger	This class implements a tagger for Parameter of ParameterSet.
ParameterSetTagger.KeyEntryComparator<K extends Comparable<K>,V>	This class implements a comparator on Map.Entry that sorts by the key of the Map.Entry.
RangeParameter	Class for a parameter wrapper that allows SimpleParameters to be set to a set of values. These values may be given either as a list of values separated by spaces, as a range between a first and a last value with a given number of steps between these values, or a single value.
SelectionParameter	Class for a collection parameter, i.e.
SequenceScoringParameterSet<T extends InstantiableFromParameterSet>	Abstract class for a ParameterSet containing all parameters necessary to construct an Object that implements InstantiableFromParameterSet.
SimpleParameter	Class for a "simple" parameter.
SimpleParameterSet	Class for a ParameterSet that is constructed from an array of Parameters.

Enum Summary

Enum	Description
RangeParameter.RangeType	The possible types of defining ranges for a RangeParameter.
RangeParameter.Scale	This enum defines possible scales, if RangeParameter.RangeType is RangeParameter.RangeType.RANGE.

Exception Summary

Exception	Description
ParameterException	Class for an exception that is thrown if some error occurs while setting a parameter's value or constructing a parameter.
SimpleParameter.DatatypeNotValidException	Class for an Exception that can be thrown if the provided int-value that represents a data type is not one of the values defined in DataType.
SimpleParameter.IllegalValueException	This exception is thrown if a parameter is not valid.

Package de.jstacs.parameters Description

This package provides classes for parameters that establish a general convention for the description of parameters as defined in the Parameter-interface. This convention includes that each parameter has

• a name that should be meaningful for a potential user,
• a comment that adds supplementary information additional to the name
• a data type that can be used to render the parameter in some interface and to validate possible inputs
• optionally a ParameterValidator that allows for a stricter validation, e.g. a specified range of allowed parameter values

The package also provides some predefined parameter types for primitive data types and Strings in SimpleParameter, collections of possible parameter values in CollectionParameter, input files in FileParameter, and for parameters that can have a number of different parameter values in RangeParameter.

All of these Parameter-types can be combined to ParameterSets that contain a set of Parameters. As SimpleParameters can also have ParameterSets as values (the corresponding data type is DataType.PARAMETERSET) and these can also be used inside CollectionParameters, a tree of parameters can be built that allows to select between different options in a collection and set the parameters that belong to the selected option, or to bundle sets of parameters into subsets to allow for a clearer organization of parameters.