Package fr.ens.biologie.genomique.eoulsan.data.protocols

Class AdditionalAnnotationDataProtocol

java.lang.Object

fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol

fr.ens.biologie.genomique.eoulsan.data.protocols.AdditionalAnnotationDataProtocol

All Implemented Interfaces:

DataProtocol

public class AdditionalAnnotationDataProtocol
extends StorageDataProtocol

This class define a additional annotation protocol.

Since:

2.0

Author:

Laurent Jourdren

Constructor Summary

Constructors

Constructor	Description
AdditionalAnnotationDataProtocol()

Method Summary

Modifier and Type	Method	Description
boolean	canDelete()	Test if the delete() method is available with this protocol.
boolean	canList()	Test if the list() method is available with this protocol.
boolean	canMkdir()	Test if the mkdir() and mkdirs() methods are available with this protocol.
boolean	canRename()	Test if the renameTo() method is available with this protocol.
boolean	canSymlink()	Test if the symlink() method is available with this protocol.
void	delete(DataFile file, boolean recursive)	Delete a file.
protected String	getBasePath()	Get the path where searching the files.
DataFile	getDataFileParent(DataFile src)	Get the parent source of the source.
protected List<String>	getExtensions()	Get the list of the file extensions of the files to search.
String	getName()	Get Protocol name.
String	getSourceFilename(String source)	Get the name of the filename that correspond to the source.
List<DataFile>	list(DataFile file)	List a directory.
void	mkdir(DataFile dir)	Create a directory.
void	mkdirs(DataFile dir)	Create a directory and its parents if not exists.
void	putData(DataFile src, DataFile dest)	Copy data from a source to a destination source
OutputStream	putData(DataFile src, DataFileMetadata md)	Create an OutputStream from the source.
void	rename(DataFile oldName, DataFile newName)	Rename a file.
void	symlink(DataFile target, DataFile link)	Create a symbolic link.

Methods inherited from class fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol

canRead, canWrite, exists, getData, getExtension, getMetadata, getSourceAsFile, getUnderLyingData, putData

Methods inherited from class java.lang.Object

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

Constructor Detail

AdditionalAnnotationDataProtocol

public AdditionalAnnotationDataProtocol()

Method Detail

getName

public String getName()

Description copied from interface: DataProtocol

Get Protocol name.

Returns:

the name of the protocol

getExtensions

protected List<String> getExtensions()

Description copied from class: StorageDataProtocol

Get the list of the file extensions of the files to search.

Overrides:

getExtensions in class StorageDataProtocol

Returns:

a list with file extensions of the files to search

getBasePath

protected String getBasePath()

Description copied from class: StorageDataProtocol

Get the path where searching the files.

Specified by:

getBasePath in class StorageDataProtocol

Returns:

a string with the path where search the files

getSourceFilename

public String getSourceFilename(String source)

Description copied from interface: DataProtocol

Get the name of the filename that correspond to the source.

Specified by:

getSourceFilename in interface DataProtocol

Parameters:

source - the source

Returns:

a String with the filename

getDataFileParent

public DataFile getDataFileParent(DataFile src)

Description copied from interface: DataProtocol

Get the parent source of the source.

Specified by:

getDataFileParent in interface DataProtocol

Parameters:

src - source to use

Returns:

a String with the source of the parent or null if there is parent

putData

public OutputStream putData(DataFile src,
                            DataFileMetadata md)
                     throws IOException

Description copied from interface: DataProtocol

Create an OutputStream from the source.

Specified by:

putData in interface DataProtocol

Parameters:

src - source to use

md - metadata for the stream to write

Returns:

an OutputStream

Throws:

IOException - if an error occurs while creating the OutputStream

putData

public void putData(DataFile src,
                    DataFile dest)
             throws IOException

Description copied from interface: DataProtocol

Copy data from a source to a destination source

Specified by:

putData in interface DataProtocol

Parameters:

src - source source

dest - destination source

Throws:

IOException - if an error occurs while copying data

mkdir

public void mkdir(DataFile dir)
           throws IOException

Description copied from interface: DataProtocol

Create a directory.

Specified by:

mkdir in interface DataProtocol

Parameters:

dir - directory to create

Throws:

IOException - if an error occurs while creating the directory

mkdirs

public void mkdirs(DataFile dir)
            throws IOException

Description copied from interface: DataProtocol

Create a directory and its parents if not exists.

Specified by:

mkdirs in interface DataProtocol

Parameters:

dir - directory to create

Throws:

IOException - if an error occurs while creating the directory

canMkdir

public boolean canMkdir()

Description copied from interface: DataProtocol

Test if the mkdir() and mkdirs() methods are available with this protocol.

Specified by:

canMkdir in interface DataProtocol

Returns:

true if mkdir() and mkdirs() are available

symlink

public void symlink(DataFile target,
                    DataFile link)
             throws IOException

Description copied from interface: DataProtocol

Create a symbolic link.

Specified by:

symlink in interface DataProtocol

Parameters:

target - target file

link - symbolic link file

Throws:

IOException - if an error occurs while creating the symbolic link

canSymlink

public boolean canSymlink()

Description copied from interface: DataProtocol

Test if the symlink() method is available with this protocol.

Specified by:

canSymlink in interface DataProtocol

Returns:

true if symlink() is available

delete

public void delete(DataFile file,
                   boolean recursive)
            throws IOException

Description copied from interface: DataProtocol

Delete a file.

Specified by:

delete in interface DataProtocol

Parameters:

file - file to delete

recursive - recursive deletion

Throws:

IOException - if an error occurs while deleting the file

canDelete

public boolean canDelete()

Description copied from interface: DataProtocol

Test if the delete() method is available with this protocol.

Specified by:

canDelete in interface DataProtocol

Returns:

true if delete() is available

list

public List<DataFile> list(DataFile file)
                    throws IOException

Description copied from interface: DataProtocol

List a directory.

Specified by:

list in interface DataProtocol

Parameters:

file - directory to list

Returns:

a list of DataFile objects

Throws:

IOException - if an error occurs while listing the directory

canList

public boolean canList()

Description copied from interface: DataProtocol

Test if the list() method is available with this protocol.

Specified by:

canList in interface DataProtocol

Returns:

true if list() is available

canRename

public boolean canRename()

Description copied from interface: DataProtocol

Test if the renameTo() method is available with this protocol.

Specified by:

canRename in interface DataProtocol

Returns:

true if renameTo() is available

rename

public void rename(DataFile oldName,
                   DataFile newName)
            throws IOException

Description copied from interface: DataProtocol

Rename a file.

Specified by:

rename in interface DataProtocol

Parameters:

oldName - the file to rename

newName - the destination file

Throws:

IOException - if an error occurs while renaming the directory