de.jstacs.parameters

Class FileParameter

java.lang.Object

de.jstacs.AnnotatedEntity

de.jstacs.parameters.Parameter

de.jstacs.parameters.FileParameter

All Implemented Interfaces:

GalaxyConvertible, Storable, Cloneable

public class FileParameter
extends Parameter
implements GalaxyConvertible

Class for a Parameter that represents a local file.

Author:

Jan Grau

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	FileParameter.FileRepresentation Class that represents a file.

Field Summary

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
FileParameter(StringBuffer buf) The standard constructor for the interface Storable.
FileParameter(String name, String comment, String filetype, boolean required) Creates a FileParameter.
FileParameter(String name, String comment, String filetype, boolean required, ParameterValidator validator) Constructs a FileParameter.

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.
FileParameter	clone()
protected void	extractFurtherInfos(StringBuffer buf) 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	getAcceptedMimeType() Returns the type(s) of the allowed files as list of file extensions, separated by commas
String	getErrorMessage() If a value could not be set successfully this method returns the corresponding error message.
String	getExtendedType() Returns the extended type (or null if not set) of this FileParameter.
FileParameter.FileRepresentation	getFileContents() Returns the content of the file.
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	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 FileParameter to its original state.
void	setDefault(Object defaultValue) Sets the default value of the Parameter to defaultValue.
void	setExtendedType(String extendedType) Sets the extended type of this FileParameter.
void	setValue(Object value) 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

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

Constructor Detail

FileParameter

public FileParameter(StringBuffer buf)
              throws NonParsableException

The standard constructor for the interface Storable. Restores a FileParameter from an XML representation.

Parameters:

buf - the XML representation as StringBuffer

Throws:

NonParsableException - if the XML code could not be parsed

FileParameter

public FileParameter(String name,
                     String comment,
                     String filetype,
                     boolean required)

Creates a FileParameter.

Parameters:

name - the name of the parameter

comment - a comment on the parameter

filetype - the type of allowed files, may be allowed file extensions, separated by commas

required - true if this FileParameter is required to continue, false otherwise

FileParameter

public FileParameter(String name,
                     String comment,
                     String filetype,
                     boolean required,
                     ParameterValidator validator)

Constructs a FileParameter.

Parameters:

name - the name of the parameter

comment - a comment on the parameter

filetype - the type of allowed files, may be allowed file extensions, separated by commas

required - true if this FileParameter is required

validator - a validator that validates e.g. the contents of the file

Method Detail

clone

public FileParameter clone()
                    throws CloneNotSupportedException

Overrides:

clone in class Parameter

Throws:

CloneNotSupportedException

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

reset

public void reset()

Resets the FileParameter to its original state.

Specified by:

reset in class Parameter

getFileContents

public FileParameter.FileRepresentation getFileContents()

Returns the content of the file.

Returns:

the content of the file

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

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

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

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 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

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

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 buf)
                            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:

buf - a XML represenation of the main information as StringBuffer

Throws:

NonParsableException - if the XML representation is not parsable

See Also:

AnnotatedEntity.AnnotatedEntity(StringBuffer)

getAcceptedMimeType

public String getAcceptedMimeType()

Returns the type(s) of the allowed files as list of file extensions, separated by commas

Returns:

the type(s) of the allowed files

getExtendedType

public String getExtendedType()

Returns the extended type (or null if not set) of this FileParameter.

Returns:

the extended type

setExtendedType

public void setExtendedType(String extendedType)

Sets the extended type of this FileParameter.

Parameters:

extendedType - the extended type

toGalaxy

public void toGalaxy(String namePrefix,
                     String configPrefix,
                     int depth,
                     StringBuffer descBuffer,
                     StringBuffer configBuffer,
                     boolean addLine)

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

toString

public String toString()

Overrides:

toString in class Object

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