de.jstacs.parameters
Class FileParameter

java.lang.Object
  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

static class

FileParameter.FileRepresentation Class that represents a file.

Field Summary

Fields inherited from class de.jstacs.parameters.Parameter

neededReference, neededReferenceId, parent

Constructor Summary

FileParameter(StringBuffer buf)
The standard constructor for the interface Storable.

FileParameter(String name, String comment, String mime, boolean required)
Creates a FileParameter.

FileParameter(String name, String comment, String mime, boolean required, ParameterValidator validator)
Constructs a FileParameter.

Method Summary

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.
FileParameter	clone()
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.
protected void	fromXML(StringBuffer representation) Parses a Parameter from a XML representation as returned by Parameter.toXML().
String	getAcceptedMimeType() Returns the MIME-type of the allowed files.
String	getComment() Returns a comment on this Parameter that tells something about useful values, domains, usage of this parameter, etc.
DataType	getDatatype() Returns the data type of the Parameter.
String	getErrorMessage() If a value could not be set successfully this method returns the corresponding error message.
FileParameter.FileRepresentation	getFileContents() Returns the content of the file.
String	getName() Returns the name of the Parameter.
Object	getValue() Returns the current value of this Parameter.
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	setValue(Object value) Sets the value of this Parameter to value.
void	simplify() Simplifies the Parameter and its contents to the relevant information.
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.
StringBuffer	toXML() This method returns an XML representation as StringBuffer of an instance of the implementing class.

Methods inherited from class de.jstacs.parameters.Parameter

getId, getNeededReference, getNeededReferenceId, getParent, setNeededReference, setParent

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, toString, 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

See Also:

fromXML(StringBuffer)

FileParameter

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

Creates a FileParameter.

Parameters:

name - the name of the parameter

comment - a comment on the parameter

mime - the MIME-type of allowed files

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

FileParameter

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

Constructs a FileParameter.

Parameters:

name - the name of the parameter

comment - a comment on the parameter

mime - the MIME-type of allowed files

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

getName

public String getName()

Description copied from class: Parameter

Returns the name of the Parameter.

Specified by:

getName in class Parameter

Returns:

the name of the Parameter

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

getDatatype

public DataType getDatatype()

Description copied from class: Parameter

Returns the data type of the Parameter.

Specified by:

getDatatype in class Parameter

Returns:

the data type of the Parameter

getComment

public String getComment()

Description copied from class: Parameter

Returns a comment on this Parameter that tells something about useful values, domains, usage of this parameter, etc.

Specified by:

getComment in class Parameter

Returns:

the comment

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.

Specified by:

setDefault in class Parameter

Parameters:

defaultValue - the default value

Throws:

SimpleParameter.IllegalValueException

simplify

public void simplify()

Description copied from class: Parameter

Simplifies the Parameter and its contents to the relevant information. This could be e.g. to reset the contents of those values of a CollectionParameter that are not selected.

Specified by:

simplify in class Parameter

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: Parameter

Returns the current value of this Parameter.

Specified by:

getValue in class Parameter

Returns:

the current value of the Parameter

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

toXML

public StringBuffer toXML()

Description copied from interface: Storable

This method returns an XML representation as StringBuffer of an instance of the implementing class.

Specified by:

toXML in interface Storable

Overrides:

toXML in class Parameter

Returns:

the XML representation

fromXML

protected void fromXML(StringBuffer representation)
                throws NonParsableException

Description copied from class: Parameter

Parses a Parameter from a XML representation as returned by Parameter.toXML().

Overrides:

fromXML in class Parameter

Parameters:

representation - the XML representation as StringBuffer

Throws:

NonParsableException - if the XML code could not be parsed

See Also:

Parameter.toXML()

getAcceptedMimeType

public String getAcceptedMimeType()

Returns the MIME-type of the allowed files.

Returns:

the MIME-type of the allowed files

toGalaxy

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

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

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