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

Class DataFile

java.lang.Object

fr.ens.biologie.genomique.eoulsan.data.DataFile

All Implemented Interfaces:

Serializable, Comparable<DataFile>

public class DataFile
extends Object
implements Comparable<DataFile>, Serializable

This class define a DataFile.

Since:

1.0

Author:

Laurent Jourdren

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
static String	separator	The separator char ('/') as a String.
static char	separatorChar	The separator char ('/').

Constructor Summary

Constructors

Constructor	Description
DataFile(DataFile parentFile, String filename)	Public constructor.
DataFile(File file)	Public constructor.
DataFile(File parentFile, String filename)	Public constructor.
DataFile(String source)	Public constructor.
DataFile(URI uri)	Public constructor.
DataFile(Path path)	Public constructor.
DataFile(Path parentPath, String filename)	Public constructor.

Method Summary

Modifier and Type	Method	Description
int	compareTo(DataFile o)
void	copyTo(DataFile dest)	Copy this DataFile in a other DataFile.
OutputStream	create()	Create an OutputStream for the DataFile.
void	delete()	Delete the DataFile.
void	delete(boolean recursive)	Delete the DataFile.
boolean	equals(Object o)
boolean	exists()	Check if this DataFile exists.
boolean	exists(boolean followLink)	Check if this DataFile exists.
String	getBasename()	Get the base name of this DataFile without all its extensions.
String	getCompressionExtension()	Get the compression extension of this DataFile.
fr.ens.biologie.genomique.kenetre.io.CompressionType	getCompressionType()	Get the compression Type of this DataFile.
DataFormat	getDataFormat()	Get the DataFormat of the DataFile.
String	getExtension()	Get the extension of this DataFile without compression extension.
String	getFullExtension()	Get the base name of this DataFile with all its extensions (include compression extension).
DataFileMetadata	getMetaData()	Get the metadata for this DataFile.
String	getName()	Get the name of this DataFile.
DataFile	getParent()	Get the parent of this DataFile.
DataProtocol	getProtocol()	Get the protocol of this DataFile.
String	getProtocolPrefixInSource()	Get the prefix of the protocol in the source name of the DataFile.
String	getSource()	Get the source of this DataFile.
int	hashCode()
boolean	isLocalFile()	Test if the DataFile use the defaultProtocol.
List<DataFile>	list()	List the content of a directory.
void	mkdir()	Create a directory with the path of the DataFile.
void	mkdirs()	Create a directory and its parents if not exists with the path of the DataFile.
InputStream	open()	Create an InputStream for the DataFile.
OutputStream	rawCreate()	Create an OutputStream for the DataFile.
InputStream	rawOpen()	Create an InputStream for the DataFile.
void	renameTo(DataFile dest)	Rename the DataFile.
void	symlink(DataFile link)	Create a symbolic link that target is the current file.
void	symlink(DataFile link, boolean relativize)	Create a symbolic link that target is the current file.
DataFile	toAbsoluteDataFile()	Convert the the DataFile to a absolute DataFile.
File	toFile()	Convert the DataFile object to File object if the underlying protocol allow it.
Path	toPath()	Convert the DataFile object to Path object if the underlying protocol allow it.
DataFile	toRealDataFile()	Convert the the DataFile to a DataFile where all the indirection has been solved.
String	toString()
URI	toUri()	Convert the DataFile object to an URI.

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

separatorChar

public static final char separatorChar

The separator char ('/').

See Also:

Constant Field Values

separator

public static final String separator

The separator char ('/') as a String.

See Also:

Constant Field Values

Constructor Detail

DataFile

public DataFile(String source)

Public constructor.

Parameters:

source - the source of the DataFile

DataFile

public DataFile(DataFile parentFile,
                String filename)

Public constructor.

Parameters:

parentFile - the parent file of the DataFile

filename - the filename of the DataFile

DataFile

public DataFile(File parentFile,
                String filename)

Public constructor.

Parameters:

parentFile - the parent file of the DataFile

filename - the filename of the DataFile

DataFile

public DataFile(Path parentPath,
                String filename)

Public constructor.

Parameters:

parentPath - the parent file of the DataFile

filename - the filename of the DataFile

DataFile

public DataFile(File file)

Public constructor.

Parameters:

file - the source file of the DataFile

DataFile

public DataFile(Path path)

Public constructor.

Parameters:

path - the source path of the DataFile

DataFile

public DataFile(URI uri)

Public constructor.

Parameters:

uri - the URI of the DataFile

Method Detail

getSource

public String getSource()

Get the source of this DataFile.

Returns:

a String with the source of this DataFile

getName

public String getName()

Get the name of this DataFile.

Returns:

a String with the name of this DataFile

getBasename

public String getBasename()

Get the base name of this DataFile without all its extensions. The result is computed with the output of the getName() method.

Returns:

a String with the base name of this DataFile

getExtension

public String getExtension()

Get the extension of this DataFile without compression extension. The result is computed with the output of the getName() method.

Returns:

a String with the extension of this DataFile. The result String is empty if there is no extension

getFullExtension

public String getFullExtension()

Get the base name of this DataFile with all its extensions (include compression extension). The result is computed with the output of the getName() method.

Returns:

a String with the base name of this DataFile. The result String is empty if there is no extension

getCompressionExtension

public String getCompressionExtension()

Get the compression extension of this DataFile. The result is computed with the output of the getName() method.

Returns:

a String with the compression extension of this DataFile. The result String is empty if there is no compression extension

getCompressionType

public fr.ens.biologie.genomique.kenetre.io.CompressionType getCompressionType()

Get the compression Type of this DataFile. The result is computed with the output of the getName() method.

Returns:

a CompressionType object

getDataFormat

public DataFormat getDataFormat()

Get the DataFormat of the DataFile. The result is computed with the output of the getName() method. This is an alias for getDataFormatFromFilename() of the DataFormatRegistry.

Returns:

the DataFormat of the DataFile

getParent

public DataFile getParent()
                   throws IOException

Get the parent of this DataFile.

Returns:

the parent DataFile

Throws:

IOException - if an error occurs while the parent

getProtocol

public DataProtocol getProtocol()
                         throws IOException

Get the protocol of this DataFile.

Returns:

a DataProtocol

Throws:

IOException

getMetaData

public DataFileMetadata getMetaData()
                             throws IOException

Get the metadata for this DataFile.

Returns:

a DataFileMetadata with all metadata information about this DataFile

Throws:

IOException - if the protocol is unknown or if the DataFile does not exists

getProtocolPrefixInSource

public String getProtocolPrefixInSource()

Get the prefix of the protocol in the source name of the DataFile.

Returns:

the prefix of the protocol

isLocalFile

public boolean isLocalFile()

Test if the DataFile use the defaultProtocol.

Returns:

true if the DataFile use the default protocol

toFile

public File toFile()

Convert the DataFile object to File object if the underlying protocol allow it. Only local protocol can return a value.

Returns:

a File object or null if the underlying protocol does not allow it

toPath

public Path toPath()

Convert the DataFile object to Path object if the underlying protocol allow it.

Returns:

a Path object or null if the underlying protocol does not allow it

toUri

public URI toUri()

Convert the DataFile object to an URI.

Returns:

an URI object or null if the DataFile cannot be converted into URI

toRealDataFile

public DataFile toRealDataFile()

Convert the the DataFile to a DataFile where all the indirection has been solved. This method use the JDK Path.toRealPath() method. This method has only an effect for local DataFiles.

Returns:

a DataFile

toAbsoluteDataFile

public DataFile toAbsoluteDataFile()

Convert the the DataFile to a absolute DataFile. This method use the JDK File.getAbsoluteFile() method. This method has only an effect for local DataFiles.

Returns:

a DataFile

create

public OutputStream create()
                    throws IOException

Create an OutputStream for the DataFile. If the DataFile is declared as compressed by its content type or its extension, the output stream will be automatically compress data.

Returns:

an OutputStream object

Throws:

IOException - if an error occurs while creating the DataFile

rawCreate

public OutputStream rawCreate()
                       throws IOException

Create an OutputStream for the DataFile. The output stream will not automatically compress data.

Returns:

an OutputStream object

Throws:

IOException - if an error occurs while creating the DataFile

open

public InputStream open()
                 throws IOException

Create an InputStream for the DataFile. If the DataFile is compressed, the input stream will be automatically uncompress.

Returns:

an InputStream object

Throws:

IOException - if an error occurs while opening the DataFile

rawOpen

public InputStream rawOpen()
                    throws IOException

Create an InputStream for the DataFile. The input stream will not automatically uncompress data.

Returns:

an InputStream object

Throws:

IOException - if an error occurs while opening the DataFile

copyTo

public void copyTo(DataFile dest)
            throws IOException

Copy this DataFile in a other DataFile.

Parameters:

dest - destination DataFile

Throws:

IOException - if an error occurs while copying the DataFile

exists

public boolean exists()

Check if this DataFile exists.

Returns:

true if this DataFile exists

exists

public boolean exists(boolean followLink)

Check if this DataFile exists.

Parameters:

followLink - follow the link target if the file is a symbolic link

Returns:

true if this DataFile exists

mkdir

public void mkdir()
           throws IOException

Create a directory with the path of the DataFile.

Throws:

IOException - if an error occurs while creating the directory

mkdirs

public void mkdirs()
            throws IOException

Create a directory and its parents if not exists with the path of the DataFile.

Throws:

IOException - if an error occurs while creating the directory

symlink

public void symlink(DataFile link)
             throws IOException

Create a symbolic link that target is the current file.

Parameters:

link - symbolic file

Throws:

IOException - if an error occurs while creating the symbolic link

symlink

public void symlink(DataFile link,
                    boolean relativize)
             throws IOException

Create a symbolic link that target is the current file.

Parameters:

link - symbolic file

relativize - relativize the link target path

Throws:

IOException - if an error occurs while creating the symbolic link

delete

public void delete()
            throws IOException

Delete the DataFile.

Throws:

IOException - if an error occurs while deleting the DataFile

delete

public void delete(boolean recursive)
            throws IOException

Delete the DataFile.

Parameters:

recursive - recursive deletion

Throws:

IOException - if an error occurs while deleting the DataFile

list

public List<DataFile> list()
                    throws IOException

List the content of a directory.

Returns:

a List with the content of the directory

Throws:

IOException - if an error occurs while listing the directory

renameTo

public void renameTo(DataFile dest)
              throws IOException

Rename the DataFile.

Parameters:

dest - destination DataFile

Throws:

IOException - if an error occurs while renaming the DataFile

compareTo

public int compareTo(DataFile o)

Specified by:

compareTo in interface Comparable<DataFile>

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Overrides:

toString in class Object