de.jstacs.parameters

Class ExpandableParameterSet

java.lang.Object

de.jstacs.parameters.ParameterSet

de.jstacs.parameters.ExpandableParameterSet

All Implemented Interfaces:

GalaxyConvertible, Storable, Cloneable

Direct Known Subclasses:

AbstractPerformanceMeasureParameterSet, AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet, ArrayParameterSet

public class ExpandableParameterSet
extends ParameterSet

A class for a ParameterSet that can be expanded by additional Parameters at runtime. The Parameters are all of type ParameterSetContainer. The contents of these Parameters are provided by a ParameterSet-template, which is cloned each time addParameterToSet() is called and set as value of a ParameterSetContainer that is added to the Parameters of the ExpandableParameterSet. Already added Parameters can also be removed from the set using removeParameterFromSet().

Author:

Jan Grau

Nested Class Summary

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

ParameterSet.ParameterList

Field Summary

Fields

Modifier and Type	Field and Description
protected String	commentTemplate A template for the comment of the enclosing ParameterSetContainer
protected String	nameTemplate A template for the name of the enclosing ParameterSetContainer
protected ParameterSet	template The template for each ParameterSet

Fields inherited from class de.jstacs.parameters.ParameterSet

errorMessage, parameters, parent

Constructor Summary

Constructors

Constructor and Description
ExpandableParameterSet(ParameterSet[] templateAndContent, String nameTemplate, String commentTemplate) Creates a new ExpandableParameterSet from a ParameterSet -array.
ExpandableParameterSet(ParameterSet template, String nameTemplate, String commentTemplate) Creates a new ExpandableParameterSet from a Class that can be instantiated using this ExpandableParameterSet and templates for the ParameterSet in each element of the array, the name and the comment that are displayed for the ParameterSetContainers enclosing the ParameterSets.
ExpandableParameterSet(ParameterSet template, String nameTemplate, String commentTemplate, int initCount) Creates a new ExpandableParameterSet from a Class that can be instantiated using this ExpandableParameterSet and templates for the ParameterSet in each element of the array, the name and the comment that are displayed for the ParameterSetContainers enclosing the ParameterSets.
ExpandableParameterSet(StringBuffer representation) The standard constructor for the interface Storable.

Method Summary

Modifier and Type	Method and Description
void	addParameterToSet() Adds a new ParameterSetContainer containing a clone of the ParameterSet-template to the set of Parameters.
ExpandableParameterSet	clone() Creates a full clone (deep copy) of this ParameterSet.
void	fromGalaxy(String namePrefix, StringBuffer command) Parses the contents of command in the format defined by configBuffer of GalaxyConvertible.toGalaxy(String, String, int, StringBuffer, StringBuffer, boolean) and sets the values of the Parameter or ParameterSet accordingly.
protected void	fromXML(StringBuffer representation) Parses the instance fields of a ParameterSet from the XML representation as returned by ParameterSet.toXML().
boolean	parameterRemovable() Returns true if there is still a Parameter that can be removed from the set.
void	removeParameterFromSet() Removes the last Parameter from set.
boolean	replaceContentWith(ParameterSet[] paramSetArray) First removes all previous added ParameterSetContainers and afterwards adds all given ParameterSets (in the given order) enclosed in new ParameterSetContainers.
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.
StringBuffer	toXML() This method returns an XML representation as StringBuffer of an instance of the implementing class.

Methods inherited from class de.jstacs.parameters.ParameterSet

getAllParameterNames, getComment, getComment, getErrorMessage, getIndex, getName, getName, getNumberOfParameters, getParameterAt, getParameterForName, getParent, hasDefaultOrIsSet, initParameterList, initParameterList, isAtomic, isComparable, parametersLoaded, reset, setParent

Methods inherited from class java.lang.Object

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

Field Detail

template

protected ParameterSet template

The template for each ParameterSet

nameTemplate

protected String nameTemplate

A template for the name of the enclosing ParameterSetContainer

commentTemplate

protected String commentTemplate

A template for the comment of the enclosing ParameterSetContainer

Constructor Detail

ExpandableParameterSet

public ExpandableParameterSet(ParameterSet template,
                              String nameTemplate,
                              String commentTemplate)
                       throws CloneNotSupportedException

Creates a new ExpandableParameterSet from a Class that can be instantiated using this ExpandableParameterSet and templates for the ParameterSet in each element of the array, the name and the comment that are displayed for the ParameterSetContainers enclosing the ParameterSets.

Parameters:

template - the template of the ParameterSet

nameTemplate - the name-template

commentTemplate - the comment-template

Throws:

CloneNotSupportedException - if the template could not be cloned

ExpandableParameterSet

public ExpandableParameterSet(ParameterSet template,
                              String nameTemplate,
                              String commentTemplate,
                              int initCount)
                       throws CloneNotSupportedException

Creates a new ExpandableParameterSet from a Class that can be instantiated using this ExpandableParameterSet and templates for the ParameterSet in each element of the array, the name and the comment that are displayed for the ParameterSetContainers enclosing the ParameterSets.

Parameters:

template - the template of the ParameterSet

nameTemplate - the name-template

commentTemplate - the comment-template

initCount - the number of initial copies of the template

Throws:

CloneNotSupportedException - if the template could not be cloned

ExpandableParameterSet

public ExpandableParameterSet(StringBuffer representation)
                       throws NonParsableException

The standard constructor for the interface Storable. Creates a new ExpandableParameterSet from its XML representation.

Parameters:

representation - the XML represenation as StringBuffer

Throws:

NonParsableException - if the StringBuffer representation could not be parsed

ExpandableParameterSet

public ExpandableParameterSet(ParameterSet[] templateAndContent,
                              String nameTemplate,
                              String commentTemplate)

Creates a new ExpandableParameterSet from a ParameterSet -array. The first element of this array is taken as a template for further calls of addParameterToSet().

Parameters:

templateAndContent - the content (and template)

nameTemplate - the name-template

commentTemplate - the comment-template

Method Detail

clone

public ExpandableParameterSet 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

addParameterToSet

public void addParameterToSet()
                       throws CloneNotSupportedException

Adds a new ParameterSetContainer containing a clone of the ParameterSet-template to the set of Parameters.

Throws:

CloneNotSupportedException - if the template could not be cloned

replaceContentWith

public boolean replaceContentWith(ParameterSet[] paramSetArray)

First removes all previous added ParameterSetContainers and afterwards adds all given ParameterSets (in the given order) enclosed in new ParameterSetContainers.

Parameters:

paramSetArray - the ParameterSets to be set

Returns:

true, if all given ParameterSets are of the same class as the defined template-ParameterSet of this ExpandableParameterSet, false otherwise (In this case, neither the previous added ParameterSetContainers are removed nor is any given ParameterSet added. Hence the ExpandableParameterSet stays unchanged.)

parameterRemovable

public boolean parameterRemovable()

Returns true if there is still a Parameter that can be removed from the set.

Returns:

true if a Parameter can be removed from the set

removeParameterFromSet

public void removeParameterFromSet()

Removes the last Parameter from set.

toXML

public StringBuffer toXML()

Description copied from interface: Storable

This method returns an XML representation as StringBuffer of an instance of the implementing class.

Specified by:

toXML in interface Storable

Overrides:

toXML in class ParameterSet

Returns:

the XML representation

fromXML

protected void fromXML(StringBuffer representation)
                throws NonParsableException

Description copied from class: ParameterSet

Parses the instance fields of a ParameterSet from the XML representation as returned by ParameterSet.toXML().

Overrides:

fromXML in class ParameterSet

Parameters:

representation - the XML representation as StringBuffer

Throws:

NonParsableException - if the XML code could not be parsed

See Also:

ParameterSet.toXML()

toGalaxy

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

Description copied from interface: GalaxyConvertible

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.

Specified by:

toGalaxy in interface GalaxyConvertible

Overrides:

toGalaxy in class ParameterSet

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

Throws:

Exception - if the conversion fails

fromGalaxy

public void fromGalaxy(String namePrefix,
                       StringBuffer command)
                throws Exception

Description copied from interface: GalaxyConvertible

Parses the contents of command in the format defined by configBuffer of GalaxyConvertible.toGalaxy(String, String, int, StringBuffer, StringBuffer, boolean) and sets the values of the Parameter or ParameterSet accordingly.

Specified by:

fromGalaxy in interface GalaxyConvertible

Overrides:

fromGalaxy in class ParameterSet

Parameters:

namePrefix - the prefix of the variable name

command - the command string

Throws:

Exception - if the command string could not be parsed