Package fr.ens.biologie.genomique.eoulsan

Class LocalEoulsanRuntime

java.lang.Object

fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime

fr.ens.biologie.genomique.eoulsan.LocalEoulsanRuntime

public final class LocalEoulsanRuntime
extends AbstractEoulsanRuntime

This class define the Runtime to execute low level IO operation for Eoulsan in local mode.

Since:

1.0

Author:

Laurent Jourdren

Nested Class Summary

Nested classes/interfaces inherited from class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime

AbstractEoulsanRuntime.EoulsanExecMode

Method Summary

Modifier and Type	Method	Description
InputStream	getInputStream(String dataSource)	Create an InputStream to load data.
AbstractEoulsanRuntime.EoulsanExecMode	getMode()	Get Eoulsan mode.
OutputStream	getOutputStream(String dataSource)	Create an OutputStream to load data.
InputStream	getRawInputStream(String dataSource)	Create a raw InputStream (without decompression of input data) to load data.
File	getTempDirectory()	Get the temporary directory.
static void	initEoulsanRuntimeForExternalApp()	Initialization Eoulsan runtime for external application who needed Eoulsan
static LocalEoulsanRuntime	newEoulsanRuntime(Settings settings)	Public constructor, initialize the runtime.
void	setMode(AbstractEoulsanRuntime.EoulsanExecMode mode)	Set the cluster mode.

Methods inherited from class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime

createFileInTempDir, createTempDir, createTempDir, createTempFile, decompressInputStreamIsNeeded, getSettings

Methods inherited from class java.lang.Object

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

Method Detail

getMode

public AbstractEoulsanRuntime.EoulsanExecMode getMode()

Description copied from class: AbstractEoulsanRuntime

Get Eoulsan mode.

Specified by:

getMode in class AbstractEoulsanRuntime

Returns:

the Eoulsan mode

getTempDirectory

public File getTempDirectory()

Description copied from class: AbstractEoulsanRuntime

Get the temporary directory.

Specified by:

getTempDirectory in class AbstractEoulsanRuntime

Returns:

the temporary directory as a File object

getInputStream

public InputStream getInputStream(String dataSource)
                           throws IOException

Description copied from class: AbstractEoulsanRuntime

Create an InputStream to load data.

Specified by:

getInputStream in class AbstractEoulsanRuntime

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 InputStream getRawInputStream(String dataSource)
                              throws IOException

Description copied from class: AbstractEoulsanRuntime

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

Specified by:

getRawInputStream in class AbstractEoulsanRuntime

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 OutputStream getOutputStream(String dataSource)
                             throws IOException

Description copied from class: AbstractEoulsanRuntime

Create an OutputStream to load data.

Specified by:

getOutputStream in class AbstractEoulsanRuntime

Parameters:

dataSource - the source of the data to load

Returns:

an OutputStream corresponding to the source

Throws:

IOException - if an error occurs the OutputStream

setMode

public void setMode(AbstractEoulsanRuntime.EoulsanExecMode mode)

Set the cluster mode.

Parameters:

mode - Eoulsan execution mode

newEoulsanRuntime

public static LocalEoulsanRuntime newEoulsanRuntime(Settings settings)

Public constructor, initialize the runtime.

Parameters:

settings - Settings of the application

initEoulsanRuntimeForExternalApp

public static void initEoulsanRuntimeForExternalApp()
                                             throws IOException,
                                                    EoulsanException

Initialization Eoulsan runtime for external application who needed Eoulsan

Throws:

IOException - if an error occurs while initializing the runtime

EoulsanException - if an error occurs while initializing the runtime