de.jstacs.utils.galaxy
Class GalaxyAdaptor.FileResult

java.lang.Object
  de.jstacs.AnnotatedEntity
      de.jstacs.results.Result
          de.jstacs.utils.galaxy.GalaxyAdaptor.FileResult

All Implemented Interfaces:

Storable

Enclosing class:

GalaxyAdaptor

public static class GalaxyAdaptor.FileResult
extends Result

Result for files that are results of some computation. Also used to link e.g. PDFs of images to GalaxyAdaptor.LinkedImageResults.

Author:

Jan Grau

Field Summary

Fields inherited from class de.jstacs.AnnotatedEntity

comment, datatype, name

Constructor Summary

GalaxyAdaptor.FileResult(StringBuffer rep)
Creates a new GalaxyAdaptor.FileResult from its XML-representation

GalaxyAdaptor.FileResult(String name, String comment, String fullPath)
Creates a new GalaxyAdaptor.FileResult with name, comment, and path to the file.

GalaxyAdaptor.FileResult(String name, String comment, String path, String filename, String extension)
Creates a new GalaxyAdaptor.FileResult with name, comment, path to the file, filename and extension.

Method Summary

protected void	appendFurtherInfos(StringBuffer sb) This method can be used in the method Storable.toXML() to extract further information (name, comment, datatype).
protected void	extractFurtherInfos(StringBuffer rep) This method can be used in the constructor with parameter StringBuffer to extract the further information.
String	getExtension() Returns the filename extension
String	getFilename() Returns the filename.
String	getPath() Returns the path of the directory containing the file
File	getValue() Returns the value of the AnnotatedEntity.
String	getXMLTag() This method returns a tag used as outer tag of the XML description.
void	setExtension(String extension) Sets the filename extension
void	setFilename(String filename) Sets the file
void	setPath(String path) Sets the path of the directory containing the file to path

Methods inherited from class de.jstacs.results.Result

checkDatatype, createResult, isCastableResult, isComparableResult

Methods inherited from class de.jstacs.AnnotatedEntity

getComment, getDatatype, getName, toXML

Methods inherited from class java.lang.Object

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

Constructor Detail

GalaxyAdaptor.FileResult

public GalaxyAdaptor.FileResult(String name,
                                String comment,
                                String fullPath)

Creates a new GalaxyAdaptor.FileResult with name, comment, and path to the file.

Parameters:

name - the name of the result

comment - the comment for the result

fullPath - the path to the file

GalaxyAdaptor.FileResult

public GalaxyAdaptor.FileResult(String name,
                                String comment,
                                String path,
                                String filename,
                                String extension)

Creates a new GalaxyAdaptor.FileResult with name, comment, path to the file, filename and extension.

Parameters:

name - the name of the result

comment - the comment for the result

path - the path to the directory containing the file

filename - the filename without extension

extension - the filename extension

GalaxyAdaptor.FileResult

public GalaxyAdaptor.FileResult(StringBuffer rep)
                         throws NonParsableException

Creates a new GalaxyAdaptor.FileResult from its XML-representation

Parameters:

rep - the representation

Throws:

NonParsableException - if pre could not be parsed

Method Detail

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 sb)

Description copied from class: AnnotatedEntity

This method can be used in the method Storable.toXML() to extract further information (name, comment, datatype).

Specified by:

appendFurtherInfos in class AnnotatedEntity

Parameters:

sb - a XML representation of the main information as StringBuffer

See Also:

Storable.toXML()

extractFurtherInfos

protected void extractFurtherInfos(StringBuffer rep)
                            throws NonParsableException

Description copied from class: AnnotatedEntity

This method can be used in the constructor with parameter StringBuffer to extract the further information.

Specified by:

extractFurtherInfos in class AnnotatedEntity

Parameters:

rep - a XML represenation of the main information as StringBuffer

Throws:

NonParsableException - if the XML representation is not parsable

See Also:

AnnotatedEntity.AnnotatedEntity(StringBuffer)

getValue

public File getValue()

Description copied from class: AnnotatedEntity

Returns the value of the AnnotatedEntity.

Specified by:

getValue in class AnnotatedEntity

Returns:

the value of the AnnotatedEntity

getPath

public String getPath()

Returns the path of the directory containing the file

Returns:

the path

setPath

public void setPath(String path)

Sets the path of the directory containing the file to path

Parameters:

path - the new path

getFilename

public String getFilename()

Returns the filename.

Returns:

the filename

setFilename

public void setFilename(String filename)

Sets the file

Parameters:

filename - the new filename

getExtension

public String getExtension()

Returns the filename extension

Returns:

the extension

setExtension

public void setExtension(String extension)

Sets the filename extension

Parameters:

extension - the new extension