de.jstacs.parameters
Class ParameterSetContainer

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

All Implemented Interfaces:

GalaxyConvertible, Storable, Cloneable

public class ParameterSetContainer
extends Parameter
implements 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

parent

Fields inherited from class de.jstacs.AnnotatedEntity

comment, datatype, name

Constructor Summary

ParameterSetContainer(Class<? extends ParameterSet> contentClazz)
Creates an new ParameterSetContainer out of the class of a ParameterSet.

ParameterSetContainer(ParameterSet p)
Creates an new ParameterSetContainer out of a ParameterSet.

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

ParameterSetContainer(String name, String comment, Class<? extends ParameterSet> contentClazz)
Creates an new ParameterSetContainer out of the class of a ParameterSet.

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

Method Summary

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. for numerical parameters this might be checking if the value is within specified bounds.
ParameterSetContainer	clone()
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) 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.
ParameterSet	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	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	setValue(Object value) Sets the value of this Parameter to value.
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.

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

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(ParameterSet p)

Creates an new ParameterSetContainer out of a ParameterSet.

Parameters:

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

See Also:

ParameterSet.getName(ParameterSet), ParameterSet.getComment(ParameterSet)

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(Class<? extends ParameterSet> contentClazz)

Creates an new ParameterSetContainer out of the class of a ParameterSet.

Parameters:

contentClazz - the class of the contained ParameterSet

See Also:

ParameterSet.getName(Class), ParameterSet.getComment(Class)

ParameterSetContainer

public ParameterSetContainer(String name,
                             String comment,
                             Class<? extends ParameterSet> contentClazz)

Creates an new ParameterSetContainer out of the class of a ParameterSet.

Parameters:

name - the name of the ParameterSetContainer

comment - a comment on the ParameterSetContainer

contentClazz - the class of 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

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: AnnotatedEntity

Returns the value of the AnnotatedEntity.

Specified by:

getValue in class AnnotatedEntity

Returns:

the value of the AnnotatedEntity

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

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. 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:

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

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)

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