de.jstacs.tools

Class DataColumnParameter

java.lang.Object

de.jstacs.AnnotatedEntity

de.jstacs.parameters.Parameter

de.jstacs.parameters.SimpleParameter

de.jstacs.tools.DataColumnParameter

All Implemented Interfaces:

GalaxyConvertible, Rangeable, Storable, Cloneable

public class DataColumnParameter
extends SimpleParameter

SimpleParameter that represents a data column parameter in Galaxy and JstacsFX.

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

Constructors

Constructor and Description
DataColumnParameter(StringBuffer representation) The standard constructor for the interface Storable.
DataColumnParameter(String dataRef, String name, String comment, boolean required) Creates a new DataColumnParameter with given name, comment, and reference.
DataColumnParameter(String dataRef, String name, String comment, boolean required, Integer defaultVal) Creates a new DataColumnParameter with given name, comment, and reference.
DataColumnParameter(String dataRef, String name, String comment, boolean required, ParameterValidator validator) Creates a new DataColumnParameter with given name, comment, and reference.
DataColumnParameter(String dataRef, String name, String comment, boolean required, ParameterValidator validator, Integer defaultVal) Creates a new DataColumnParameter with given name, comment, and reference.

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).
protected String	dataTypeToGalaxy() Returns the Galaxy identifier for the DataType of this parameter
protected void	extractFurtherInfos(StringBuffer representation) This method can be used in the constructor with parameter StringBuffer to extract the further information.
static FileParameter	find(ParameterSet top, String dataRef) Finds the parameter for the given ID in a 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.
String	getDataRef() Returns the ID of the referenced parameter (tabular) in Galaxy.
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

checkValue, clone, equals, 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

DataColumnParameter

public DataColumnParameter(String dataRef,
                           String name,
                           String comment,
                           boolean required,
                           Integer defaultVal)
                    throws SimpleParameter.DatatypeNotValidException,
                           SimpleParameter.IllegalValueException

Creates a new DataColumnParameter with given name, comment, and reference.

Parameters:

dataRef - the ID of the referenced parameter (tabular) in Galaxy.

name - the name of the parameter

comment - a comment on the parameter

required - if this parameter is required

defaultVal - the default value

Throws:

DatatypeNotValidException - should not happen

IllegalValueException - should not happen

SimpleParameter.DatatypeNotValidException

SimpleParameter.IllegalValueException

DataColumnParameter

public DataColumnParameter(String dataRef,
                           String name,
                           String comment,
                           boolean required,
                           ParameterValidator validator,
                           Integer defaultVal)
                    throws ParameterException

Creates a new DataColumnParameter with given name, comment, and reference.

Parameters:

dataRef - the ID of the referenced parameter (tabular) in Galaxy.

name - the name of the parameter

comment - a comment on the parameter

required - if this parameter is required

validator - a validator of admissible values

defaultVal - the default value

Throws:

ParameterException - if the default value is not admissible

DataColumnParameter

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

Creates a new DataColumnParameter with given name, comment, and reference.

Parameters:

dataRef - the ID of the referenced parameter (tabular) in Galaxy.

name - the name of the parameter

comment - a comment on the parameter

required - if this parameter is required

validator - a validator of admissible values

Throws:

DatatypeNotValidException - should not happen

SimpleParameter.DatatypeNotValidException

DataColumnParameter

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

Creates a new DataColumnParameter with given name, comment, and reference.

Parameters:

dataRef - the ID of the referenced parameter (tabular) in Galaxy.

name - the name of the parameter

comment - a comment on the parameter

required - if this parameter is required

Throws:

DatatypeNotValidException - should not happen

SimpleParameter.DatatypeNotValidException

DataColumnParameter

public DataColumnParameter(StringBuffer representation)
                    throws NonParsableException

The standard constructor for the interface Storable. Creates a new DataColumnParameter out of its XML representation.

Parameters:

representation - the XML representation as StringBuffer

Throws:

NonParsableException - if the DataColumnParameter could not be reconstructed out of the XML representation (the StringBuffer could not be parsed)

See Also:

Storable

Method Detail

dataTypeToGalaxy

protected String dataTypeToGalaxy()

Description copied from class: SimpleParameter

Returns the Galaxy identifier for the DataType of this parameter

Overrides:

dataTypeToGalaxy in class SimpleParameter

Returns:

the Galaxy identifier of the data type

getDataRef

public String getDataRef()

Returns the ID of the referenced parameter (tabular) in Galaxy.

Returns:

the ID

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

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 SimpleParameter

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 SimpleParameter

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)

find

public static FileParameter find(ParameterSet top,
                                 String dataRef)

Finds the parameter for the given ID in a ParameterSet.

Parameters:

top - the ParameterSet

dataRef - the ID

Returns:

the parameter