de.jstacs.parameters
Class SimpleParameterSet

java.lang.Object
  de.jstacs.parameters.ParameterSet
      de.jstacs.parameters.SimpleParameterSet

All Implemented Interfaces:

GalaxyConvertible, Storable, Cloneable

public class SimpleParameterSet
extends ParameterSet

Class for a ParameterSet that is constructed from an array of Parameters.

Author:

Jan Grau

Nested Class Summary

Nested classes/interfaces inherited from class de.jstacs.parameters.ParameterSet

ParameterSet.ParameterList

Field Summary

Fields inherited from class de.jstacs.parameters.ParameterSet

errorMessage, parameters, parent

Constructor Summary

SimpleParameterSet(Parameter... parameters)
Creates a new SimpleParameterSet from an array of Parameters.

SimpleParameterSet(StringBuffer representation)
The standard constructor for the interface Storable.

Method Summary

SimpleParameterSet	clone() Creates a full clone (deep copy) of this ParameterSet.
void	reset() Resets all Parameters in this ParameterSet to their default values or null if not default value was provided.
void	toGalaxy(String namePrefix, String configPrefix, int depth, StringBuffer descBuffer, StringBuffer configBuffer, boolean[] addLine) Creates an Galaxy XML-representation of the parameters and appends it to descBuffer and variable configuration and appends it to configBuffer.

Methods inherited from class de.jstacs.parameters.ParameterSet

fromGalaxy, fromXML, getAllParameterNames, getComment, getComment, getErrorMessage, getIndex, getName, getName, getNumberOfParameters, getParameterAt, getParameterForName, getParent, hasDefaultOrIsSet, initParameterList, initParameterList, isAtomic, isComparable, parametersLoaded, setParent, toGalaxy, toXML

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SimpleParameterSet

public SimpleParameterSet(Parameter... parameters)

Creates a new SimpleParameterSet from an array of Parameters.

Parameters:

parameters - the parameters

SimpleParameterSet

public SimpleParameterSet(StringBuffer representation)
                   throws NonParsableException

The standard constructor for the interface Storable. Constructs a SimpleParameterSet from its XML representation.

Parameters:

representation - the XML representation as StringBuffer

Throws:

NonParsableException - if the StringBuffer representation could not be parsed

Method Detail

clone

public SimpleParameterSet clone()
                         throws CloneNotSupportedException

Description copied from class: ParameterSet

Creates a full clone (deep copy) of this ParameterSet. As a convenience-method the user can use fillWithStandardFieldsForClone(ParameterSet) on a newly created instance of a subclass of ParameterSet to obtain a clone/copy of all standard member variables (those already defined in ParameterSet) in the passed ParameterSet. Using this method, the cloning process becomes merely three-step:

• Create a new instance of your subclass of ParameterSet, most likely with an empty constructor or the one taking just the instance class.
• Call this.fillWithStandardFieldsForClone on this instance.
• Return the instance.

This method fulfills the conventions of Object's method Object.clone().

Overrides:

clone in class ParameterSet

Returns:

a deep clone/copy of this ParameterSet

Throws:

CloneNotSupportedException

reset

public void reset()

Description copied from class: ParameterSet

Resets all Parameters in this ParameterSet to their default values or null if not default value was provided.

Overrides:

reset in class ParameterSet

See Also:

Parameter.reset()

toGalaxy

public void toGalaxy(String namePrefix,
                     String configPrefix,
                     int depth,
                     StringBuffer descBuffer,
                     StringBuffer configBuffer,
                     boolean[] addLine)
              throws Exception

Creates an Galaxy XML-representation of the parameters and appends it to descBuffer and variable configuration and appends it to configBuffer. The variable configuration is also used to parse user-supplied values returned by Galaxy.

Parameters:

namePrefix - the prefix of the variable name used in Galaxy

configPrefix - the prefix for conditionals

depth - the depth in the parameter hierarchy, used for graphical representation of nesting

descBuffer - the buffer for the parameter description

configBuffer - the buffer for the configuration line

addLine - if true, a line is added before the title of a parameter with the corresponding index

Throws:

Exception - if the conversion fails