de.jstacs.utils.galaxy
Class MultilineSimpleParameter

java.lang.Object
  de.jstacs.AnnotatedEntity
      de.jstacs.parameters.Parameter
          de.jstacs.parameters.SimpleParameter
              de.jstacs.utils.galaxy.MultilineSimpleParameter

All Implemented Interfaces:

GalaxyConvertible, Rangeable, Storable, Cloneable

public class MultilineSimpleParameter
extends SimpleParameter

An extension of SimpleParameter that renders as a textarea in Galaxy, which is only suitable for DataType.STRINGs. Besides the toGalaxy(String, String, int, StringBuffer, StringBuffer, boolean) and fromGalaxy(String, StringBuffer), all functionality is inherited from SimpleParameter.

Author:

Jan Grau

Nested Class Summary

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

SimpleParameter.DatatypeNotValidException, SimpleParameter.IllegalValueException

Field Summary

Fields inherited from class de.jstacs.parameters.SimpleParameter

defaultValue, required, validator, value

Fields inherited from class de.jstacs.parameters.Parameter

parent

Fields inherited from class de.jstacs.AnnotatedEntity

comment, datatype, name

Constructor Summary

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

MultilineSimpleParameter(String name, String comment, boolean required)
Creates a new MultilineSimpleParameter with no default value.

MultilineSimpleParameter(String name, String comment, boolean required, Object defaultVal)
Creates a new MultilineSimpleParameter with given default value.

MultilineSimpleParameter(String name, String comment, boolean required, ParameterValidator validator)
Creates a new MultilineSimpleParameter with no default value and a ParameterValidator.

MultilineSimpleParameter(String name, String comment, boolean required, ParameterValidator validator, Object defaultVal)
Creates a new MultilineSimpleParameter with given default value and a ParameterValidator.

Method Summary

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.
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.SimpleParameter

appendFurtherInfos, checkValue, clone, equals, extractFurtherInfos, getErrorMessage, getRangedInstance, getValidator, getValue, getXMLTag, hasDefaultOrIsSet, isAtomic, isRangeable, isRequired, isSet, reset, setDefault, setRangeable, setValidator, setValue, 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

Constructor Detail

MultilineSimpleParameter

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

Creates a new MultilineSimpleParameter with given default value.

Parameters:

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:

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

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

SimpleParameter.DatatypeNotValidException

SimpleParameter.IllegalValueException

MultilineSimpleParameter

public MultilineSimpleParameter(String name,
                                String comment,
                                boolean required,
                                ParameterValidator validator,
                                Object defaultVal)
                         throws ParameterException

Creates a new MultilineSimpleParameter with given default value and a ParameterValidator.

Parameters:

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

MultilineSimpleParameter

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

Creates a new MultilineSimpleParameter with no default value and a ParameterValidator.

Parameters:

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:

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

SimpleParameter.DatatypeNotValidException

MultilineSimpleParameter

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

Creates a new MultilineSimpleParameter with no default value.

Parameters:

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:

DatatypeNotValidException - if datatype is not one of the allowed DataTypes

SimpleParameter.DatatypeNotValidException

MultilineSimpleParameter

public MultilineSimpleParameter(StringBuffer representation)
                         throws NonParsableException

The standard constructor for the interface Storable. Constructs a MultilineSimpleParameter 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

Method Detail

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 SimpleParameter

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 SimpleParameter

Parameters:

namePrefix - the prefix of the variable name

command - the command string

Throws:

Exception - if the command string could not be parsed