de.jstacs.parameters
Class ParameterSetContainer

java.lang.Object
  de.jstacs.parameters.Parameter
      de.jstacs.parameters.ParameterSetContainer

All Implemented Interfaces:

GalaxyConvertible, Rangeable, RangeIterator, Storable, Cloneable

public class ParameterSetContainer
extends Parameter
implements Rangeable, RangeIterator, GalaxyConvertible

Class for a ParameterSetContainer that contains a ParameterSet as value. This ParameterSet can be set either using the constructor or using the method setValue(Object) and can be obtained by the method getValue(). ParameterSetContainers can be used to build tree-structures of Parameters.

Author:

Jan Grau, Jens Keilwagen

Field Summary

protected String

errorMessage The message of the last error or null if no error occurred.

Fields inherited from class de.jstacs.parameters.Parameter

neededReference, neededReferenceId, parent

Constructor Summary

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

ParameterSetContainer(String name, String comment, ParameterSet content)
Creates an new ParameterSetContainer out of a ParameterSet.

Method Summary

boolean	checkValue(Object value) Checks the value for correctness, e.g. for numerical parameters this might be checking if the value is within specified bounds.
ParameterSetContainer	clone()
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) and sets the values of the Parameter or ParameterSet accordingly.
protected void	fromXML(StringBuffer representation) Parses a Parameter from a XML representation as returned by Parameter.toXML().
String	getComment() Returns a comment on this Parameter that tells something about useful values, domains, usage of this parameter, etc.
DataType	getDatatype() Returns the data type of the Parameter.
String	getErrorMessage() If a value could not be set successfully this method returns the corresponding error message.
String	getName() Returns the name of the Parameter.
int	getNumberOfValues() Returns the number of values in the collection.
Parameter	getRangedInstance() Returns an instance of RangeIterator that has the same properties as the current instance, but accepts a range or list of values.
ParameterSet	getValue() Returns the current value of this Parameter.
boolean	hasDefaultOrIsSet() Returns true if the parameter either has a default value or the value was set by the user, false otherwise.
boolean	isAtomic() Returns true if the parameter is of an atomic data type, false otherwise.
boolean	isRangeable() Returns true if the parameters can be varied over a range of values.
boolean	isRanged() Returns true if this RangeIterator is ranging over a set of values.
boolean	isRequired() Returns true if the Parameter is required, false otherwise.
boolean	isSet() Returns true if the parameter was set by the user, false otherwise.
boolean	next() Switches to the next value in the collection of values in the specified range.
void	reset() Resets the parameter and its contents to the default values or null if no defaults are given.
void	resetToFirst() Resets the current value in the collection to the first value.
void	setDefault(Object defaultValue) Sets the default value of the Parameter to defaultValue.
void	setValue(Object value) Sets the value of this Parameter to value.
void	simplify() Simplifies the Parameter and its contents to the relevant information.
void	toGalaxy(String namePrefix, String configPrefix, int depth, StringBuffer descBuffer, StringBuffer configBuffer) 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.
String	valuesToString() Returns a String representation of the set of values.

Methods inherited from class de.jstacs.parameters.Parameter

getId, getNeededReference, getNeededReferenceId, getParent, setNeededReference, setParent

Methods inherited from class java.lang.Object

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

Field Detail

errorMessage

protected String errorMessage

The message of the last error or null if no error occurred.

Constructor Detail

ParameterSetContainer

public ParameterSetContainer(String name,
                             String comment,
                             ParameterSet content)

Creates an new ParameterSetContainer out of a ParameterSet.

Parameters:

name - the name of the ParameterSetContainer

comment - a comment on the ParameterSetContainer

content - the content of the ParameterSetContainer (the contained ParameterSet)

ParameterSetContainer

public ParameterSetContainer(StringBuffer representation)
                      throws NonParsableException

The standard constructor for the interface Storable. Creates a new ParameterSetContainer 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 ParameterSetContainer clone()
                            throws CloneNotSupportedException

Overrides:

clone in class Parameter

Throws:

CloneNotSupportedException

getName

public String getName()

Description copied from class: Parameter

Returns the name of the Parameter.

Specified by:

getName in class Parameter

Returns:

the name of the Parameter

getDatatype

public DataType getDatatype()

Description copied from class: Parameter

Returns the data type of the Parameter.

Specified by:

getDatatype in class Parameter

Returns:

the data type of the Parameter

getComment

public String getComment()

Description copied from class: Parameter

Returns a comment on this Parameter that tells something about useful values, domains, usage of this parameter, etc.

Specified by:

getComment in class Parameter

Returns:

the comment

isRequired

public boolean isRequired()

Description copied from class: Parameter

Returns true if the Parameter is required, false otherwise.

Specified by:

isRequired in class Parameter

Returns:

true if the Parameter is required, false otherwise

checkValue

public boolean checkValue(Object value)

Description copied from class: Parameter

Checks the value for correctness, e.g. for numerical parameters this might be checking if the value is within specified bounds.

Specified by:

checkValue in class Parameter

Parameters:

value - the value to be checked

Returns:

true if the value is valid, false otherwise

setValue

public void setValue(Object value)
              throws SimpleParameter.IllegalValueException

Description copied from class: Parameter

Sets the value of this Parameter to value.

Specified by:

setValue in class Parameter

Parameters:

value - the new value of the Parameter

Throws:

SimpleParameter.IllegalValueException - if the specified value is not valid for this Parameter

getValue

public ParameterSet getValue()

Description copied from class: Parameter

Returns the current value of this Parameter.

Specified by:

getValue in class Parameter

Returns:

the current value of the Parameter

hasDefaultOrIsSet

public boolean hasDefaultOrIsSet()

Description copied from class: Parameter

Returns true if the parameter either has a default value or the value was set by the user, false otherwise.

Specified by:

hasDefaultOrIsSet in class Parameter

Returns:

true if value has a default value or was set, false otherwise

isSet

public boolean isSet()

Description copied from class: Parameter

Returns true if the parameter was set by the user, false otherwise.

Specified by:

isSet in class Parameter

Returns:

true if the parameter was set, false otherwise

isAtomic

public boolean isAtomic()

Description copied from class: Parameter

Returns true if the parameter is of an atomic data type, false otherwise.

Specified by:

isAtomic in class Parameter

Returns:

true if the parameter is atomic, false otherwise

getErrorMessage

public String getErrorMessage()

Description copied from class: Parameter

If a value could not be set successfully this method returns the corresponding error message.

Specified by:

getErrorMessage in class Parameter

Returns:

an error message if a value could not be set successfully

simplify

public void simplify()

Description copied from class: Parameter

Simplifies the Parameter and its contents to the relevant information. This could be e.g. to reset the contents of those values of a CollectionParameter that are not selected.

Specified by:

simplify in class Parameter

reset

public void reset()

Description copied from class: Parameter

Resets the parameter and its contents to the default values or null if no defaults are given.

Specified by:

reset in class Parameter

setDefault

public void setDefault(Object defaultValue)
                throws Exception

Description copied from class: Parameter

Sets the default value of the Parameter to defaultValue.

Specified by:

setDefault in class Parameter

Parameters:

defaultValue - the default value

Throws:

Exception - if the default value is not an appropriate value for this Parameter

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 Parameter

Returns:

the XML representation

fromXML

protected void fromXML(StringBuffer representation)
                throws NonParsableException

Description copied from class: Parameter

Parses a Parameter from a XML representation as returned by Parameter.toXML().

Overrides:

fromXML in class Parameter

Parameters:

representation - the XML representation as StringBuffer

Throws:

NonParsableException - if the XML code could not be parsed

See Also:

Parameter.toXML()

isRangeable

public boolean isRangeable()

Description copied from interface: Rangeable

Returns true if the parameters can be varied over a range of values.

Specified by:

isRangeable in interface Rangeable

Returns:

true if the parameter can be varied, false otherwise

getRangedInstance

public Parameter getRangedInstance()
                            throws Exception

Description copied from interface: Rangeable

Returns an instance of RangeIterator that has the same properties as the current instance, but accepts a range or list of values. These values can be obtained by the methods of RangeIterator.

Specified by:

getRangedInstance in interface Rangeable

Returns:

an instance with the same properties as the current instance

Throws:

Exception - is thrown if Rangeable.isRangeable() returns false or the ranged instance could not be created for some other reason

next

public boolean next()
             throws ParameterException

Description copied from interface: RangeIterator

Switches to the next value in the collection of values in the specified range.

Specified by:

next in interface RangeIterator

Returns:

true if the next element exists, false otherwise

Throws:

ParameterException - if the next value could not be fetched

resetToFirst

public void resetToFirst()

Description copied from interface: RangeIterator

Resets the current value in the collection to the first value.

Specified by:

resetToFirst in interface RangeIterator

isRanged

public boolean isRanged()

Description copied from interface: RangeIterator

Returns true if this RangeIterator is ranging over a set of values.

Specified by:

isRanged in interface RangeIterator

Returns:

true if this RangeIterator is ranging over a set of values, false otherwise

getNumberOfValues

public int getNumberOfValues()

Description copied from interface: RangeIterator

Returns the number of values in the collection.

Specified by:

getNumberOfValues in interface RangeIterator

Returns:

the number of values

valuesToString

public String valuesToString()

Description copied from interface: RangeIterator

Returns a String representation of the set of values.

Specified by:

valuesToString in interface RangeIterator

Returns:

the String representation

toGalaxy

public void toGalaxy(String namePrefix,
                     String configPrefix,
                     int depth,
                     StringBuffer descBuffer,
                     StringBuffer configBuffer)
              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 configuation is also used to parse user-supplied values returned by Galaxy.

Specified by:

toGalaxy in interface GalaxyConvertible

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

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) and sets the values of the Parameter or ParameterSet accordingly.

Specified by:

fromGalaxy in interface GalaxyConvertible

Parameters:

namePrefix - the prefix of the variable name

command - the command string

Throws:

Exception - if the command string could not be parsed