de.jstacs.parameters

Class SimpleParameter

java.lang.Object

de.jstacs.AnnotatedEntity

de.jstacs.parameters.Parameter

de.jstacs.parameters.SimpleParameter

All Implemented Interfaces:

GalaxyConvertible, Rangeable, Storable, Cloneable

Direct Known Subclasses:

DataColumnParameter, MultilineSimpleParameter

public class SimpleParameter
extends Parameter
implements Rangeable, GalaxyConvertible

Class for a "simple" parameter. Simple parameters are those of the primitive types and single Strings.

Author:

Jan Grau

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	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.
static class	SimpleParameter.IllegalValueException This exception is thrown if a parameter is not valid.

Field Summary

Fields

Modifier and Type	Field and Description
protected Object	defaultValue The default value of the parameter
protected boolean	required Determines if the parameter is required
protected ParameterValidator	validator The validator for the parameter values
protected Object	value The current value of the parameter

Fields inherited from class de.jstacs.parameters.Parameter

parent

Fields inherited from class de.jstacs.AnnotatedEntity

comment, datatype, name

Constructor Summary

Constructors

Constructor and Description
SimpleParameter(DataType datatype, String name, String comment, boolean required) Constructor for a SimpleParameter without ParameterValidator.
SimpleParameter(DataType datatype, String name, String comment, boolean required, Object defaultVal) Constructor for a SimpleParameter without ParameterValidator but with a default value.
SimpleParameter(DataType datatype, String name, String comment, boolean required, ParameterValidator validator) Constructor for a SimpleParameter with a ParameterValidator.
SimpleParameter(DataType datatype, String name, String comment, boolean required, ParameterValidator validator, Object defaultVal) Constructor for a SimpleParameter with validator and default value.
SimpleParameter(StringBuffer representation) The standard constructor for the interface Storable.

Method Summary

Modifier and Type	Method and Description
protected void	appendFurtherInfos(StringBuffer buf) This method can be used in the method Storable.toXML() to extract further information (name, comment, datatype).
boolean	checkValue(Object value) Checks the value for correctness, e.g.
SimpleParameter	clone()
protected String	dataTypeToGalaxy() Returns the Galaxy identifier for the DataType of this parameter
boolean	equals(Object o2)
protected void	extractFurtherInfos(StringBuffer representation) This method can be used in the constructor with parameter StringBuffer to extract the further information.
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.
String	getErrorMessage() If a value could not be set successfully this method returns the corresponding error message.
Parameter	getRangedInstance() Returns an instance of RangeIterator that has the same properties as the current instance, but accepts a range or list of values.
ParameterValidator	getValidator() Returns the ParameterValidator used in this SimpleParameter.
Object	getValue() Returns the value of the AnnotatedEntity.
String	getXMLTag() This method returns a tag used as outer tag of the XML description.
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	isRequired() Returns true if the Parameter is required, false otherwise.
boolean	isSet() Returns true if the parameter was set by the user, false otherwise.
void	reset() Resets the parameter and its contents to the default values or null if no defaults are given.
void	setDefault(Object defaultValue) Sets the default value of the Parameter to defaultValue.
void	setRangeable(boolean rangeable) Sets the value returned by isRangeable() to rangeable.
void	setValidator(ParameterValidator validator) Sets a new ParameterValidator for this SimpleParameter.
void	setValue(Object value2) Sets the value of this Parameter to value.
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.
String	toString()

Methods inherited from class de.jstacs.parameters.Parameter

getParent, isComparable, setParent

Methods inherited from class de.jstacs.AnnotatedEntity

getComment, getDatatype, getName, toXML

Methods inherited from class java.lang.Object

finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

required

protected boolean required

Determines if the parameter is required

value

protected Object value

The current value of the parameter

defaultValue

protected Object defaultValue

The default value of the parameter

validator

protected ParameterValidator validator

The validator for the parameter values

Constructor Detail

SimpleParameter

public SimpleParameter(StringBuffer representation)
                throws NonParsableException

The standard constructor for the interface Storable. Constructs a SimpleParameter out of an XML representation.

Parameters:

representation - the XML representation as StringBuffer

Throws:

NonParsableException - if the SimpleParameter could not be restored from the StringBuffer representation

SimpleParameter

public SimpleParameter(DataType datatype,
                       String name,
                       String comment,
                       boolean required)
                throws SimpleParameter.DatatypeNotValidException

Constructor for a SimpleParameter without ParameterValidator.

Parameters:

datatype - the data type of the parameter value

name - the name of the parameter

comment - a comment on the parameter that tells the user some details about it

required - determines if the parameter is required

Throws:

SimpleParameter.DatatypeNotValidException - if datatype is not one of the allowed DataTypes

SimpleParameter

public SimpleParameter(DataType datatype,
                       String name,
                       String comment,
                       boolean required,
                       Object defaultVal)
                throws SimpleParameter.DatatypeNotValidException,
                       SimpleParameter.IllegalValueException

Constructor for a SimpleParameter without ParameterValidator but with a default value.

Parameters:

datatype - the data type of the parameter value

name - the name of the parameter

comment - a comment on the parameter that tells the user some details about it

required - determines if the parameter is required

defaultVal - the default value

Throws:

SimpleParameter.DatatypeNotValidException - if datatype is not in the values allowed for a SimpleParameter

SimpleParameter.IllegalValueException - if the default value is not a valid value with respect to datatype

SimpleParameter

public SimpleParameter(DataType datatype,
                       String name,
                       String comment,
                       boolean required,
                       ParameterValidator validator)
                throws SimpleParameter.DatatypeNotValidException

Constructor for a SimpleParameter with a ParameterValidator.

Parameters:

datatype - the data type of the parameter value

name - the name of the parameter

comment - a comment on the parameter that tells the user some details about it

required - determines if the parameter is required

validator - the validator for the parameter values

Throws:

SimpleParameter.DatatypeNotValidException - if datatype is not in the values allowed for a SimpleParameter

SimpleParameter

public SimpleParameter(DataType datatype,
                       String name,
                       String comment,
                       boolean required,
                       ParameterValidator validator,
                       Object defaultVal)
                throws ParameterException

Constructor for a SimpleParameter with validator and default value.

Parameters:

datatype - the data type of the parameter value

name - the name of the parameter

comment - a comment on the parameter that tells the user some details about it

required - determines if the parameter is required

validator - the validator for the parameter values

defaultVal - the default value

Throws:

ParameterException - if either the default value is not a valid value with respect to datatype or datatype is not in the values allowed for a SimpleParameter

Method Detail

clone

public SimpleParameter clone()
                      throws CloneNotSupportedException

Overrides:

clone in class Parameter

Throws:

CloneNotSupportedException

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

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

setRangeable

public void setRangeable(boolean rangeable)

Sets the value returned by isRangeable() to rangeable.

Parameters:

rangeable - the new value that determines if this SimpleParameter is rangeable

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

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

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

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

setDefault

public void setDefault(Object defaultValue)
                throws SimpleParameter.IllegalValueException

Description copied from class: Parameter

Sets the default value of the Parameter to defaultValue. This method also sets the current value of this Parameter to the default.

Specified by:

setDefault in class Parameter

Parameters:

defaultValue - the default value

Throws:

SimpleParameter.IllegalValueException

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

setValue

public void setValue(Object value2)
              throws SimpleParameter.IllegalValueException

Description copied from class: Parameter

Sets the value of this Parameter to value.

Specified by:

setValue in class Parameter

Parameters:

value2 - the new value of the Parameter

Throws:

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

getValue

public Object getValue()

Description copied from class: AnnotatedEntity

Returns the value of the AnnotatedEntity.

Specified by:

getValue in class AnnotatedEntity

Returns:

the value of the AnnotatedEntity

getXMLTag

public String getXMLTag()

Description copied from class: AnnotatedEntity

This method returns a tag used as outer tag of the XML description.

Specified by:

getXMLTag in class AnnotatedEntity

Returns:

a tag used as outer tag of the XML description

appendFurtherInfos

protected void appendFurtherInfos(StringBuffer buf)

Description copied from class: AnnotatedEntity

This method can be used in the method Storable.toXML() to extract further information (name, comment, datatype).

Overrides:

appendFurtherInfos in class Parameter

Parameters:

buf - a XML representation of the main information as StringBuffer

See Also:

Storable.toXML()

extractFurtherInfos

protected void extractFurtherInfos(StringBuffer representation)
                            throws NonParsableException

Description copied from class: AnnotatedEntity

This method can be used in the constructor with parameter StringBuffer to extract the further information.

Overrides:

extractFurtherInfos in class Parameter

Parameters:

representation - a XML represenation of the main information as StringBuffer

Throws:

NonParsableException - if the XML representation is not parsable

See Also:

AnnotatedEntity.AnnotatedEntity(StringBuffer)

equals

public boolean equals(Object o2)

Overrides:

equals in class Object

getValidator

public ParameterValidator getValidator()

Returns the ParameterValidator used in this SimpleParameter. This may be null.

Returns:

the validator used in this SimpleParameter

setValidator

public void setValidator(ParameterValidator validator)

Sets a new ParameterValidator for this SimpleParameter.

Parameters:

validator - the new parameter validator

toString

public String toString()

Overrides:

toString in class Object

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

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

dataTypeToGalaxy

protected String dataTypeToGalaxy()

Returns the Galaxy identifier for the DataType of this parameter

Returns:

the Galaxy identifier of the data type

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

Parameters:

namePrefix - the prefix of the variable name

command - the command string

Throws:

Exception - if the command string could not be parsed