Package fr.ens.biologie.genomique.eoulsan

Class AbstractEoulsanRuntime

java.lang.Object

fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime

Direct Known Subclasses:

HadoopEoulsanRuntime, LocalEoulsanRuntime

public abstract class AbstractEoulsanRuntime
extends Object

This class define an abstract EoulsanRuntime.

Since:

1.0

Author:

Laurent Jourdren

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	AbstractEoulsanRuntime.EoulsanExecMode	This Enum define the Eoulsan execution mode.

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	AbstractEoulsanRuntime(Settings settings)

Method Summary

Modifier and Type	Method	Description
File	createFileInTempDir(String filename)	Create a file in the temporary directory.
File	createTempDir()	Create a new temporary directory.
File	createTempDir(String prefix)	Create a new temporary directory.
File	createTempFile(String prefix, String suffix)	Create a new temporary file.
protected InputStream	decompressInputStreamIsNeeded(InputStream is, String source)	Decompress an inputStream if needed.
abstract InputStream	getInputStream(String dataSource)	Create an InputStream to load data.
abstract AbstractEoulsanRuntime.EoulsanExecMode	getMode()	Get Eoulsan mode.
abstract OutputStream	getOutputStream(String dataSource)	Create an OutputStream to load data.
abstract InputStream	getRawInputStream(String dataSource)	Create a raw InputStream (without decompression of input data) to load data.
Settings	getSettings()	Get Settings.
abstract File	getTempDirectory()	Get the temporary directory.

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractEoulsanRuntime

protected AbstractEoulsanRuntime(Settings settings)

Method Detail

getSettings

public Settings getSettings()

Get Settings.

Returns:

a Settings object

getTempDirectory

public abstract File getTempDirectory()

Get the temporary directory.

Returns:

the temporary directory as a File object

getMode

public abstract AbstractEoulsanRuntime.EoulsanExecMode getMode()

Get Eoulsan mode.

Returns:

the Eoulsan mode

getInputStream

public abstract InputStream getInputStream(String dataSource)
                                    throws IOException

Create an InputStream to load data.

Parameters:

dataSource - the source of the data to load

Returns:

an InputStream corresponding to the source

Throws:

IOException - if an error occurs the InputStream

getRawInputStream

public abstract InputStream getRawInputStream(String dataSource)
                                       throws IOException

Create a raw InputStream (without decompression of input data) to load data.

Parameters:

dataSource - the source of the data to load

Returns:

an InputStream corresponding to the source

Throws:

IOException - if an error occurs the InputStream

getOutputStream

public abstract OutputStream getOutputStream(String dataSource)
                                      throws IOException

Create an OutputStream to load data.

Parameters:

dataSource - the source of the data to load

Returns:

an OutputStream corresponding to the source

Throws:

IOException - if an error occurs the OutputStream

decompressInputStreamIsNeeded

protected InputStream decompressInputStreamIsNeeded(InputStream is,
                                                    String source)
                                             throws IOException

Decompress an inputStream if needed.

Parameters:

is - the InputStream

source - source of the inputStream

Returns:

a InputStream with decompression integrated or not

Throws:

IOException - if an error occurs while creating decompressor InputStream

createTempDir

public File createTempDir()
                   throws IOException

Create a new temporary directory.

Returns:

the new directory

Throws:

IOException - if there is an error creating the temporary directory

createTempDir

public File createTempDir(String prefix)
                   throws IOException

Create a new temporary directory.

Parameters:

prefix - prefix of the temporary directory

Returns:

the new directory

Throws:

IOException - if there is an error creating the temporary directory

createTempFile

public File createTempFile(String prefix,
                           String suffix)
                    throws IOException

Create a new temporary file.

Parameters:

prefix - Prefix of the temporary file

suffix - suffix of the temporary file

Returns:

the new temporary file

Throws:

IOException - if there is an error creating the temporary directory

createFileInTempDir

public File createFileInTempDir(String filename)

Create a file in the temporary directory.

Parameters:

filename - The filename to create

Returns:

The new File