Package fr.ens.biologie.genomique.eoulsan.util.r

Class RserveRExecutor

java.lang.Object

fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor

fr.ens.biologie.genomique.eoulsan.util.r.RserveRExecutor

All Implemented Interfaces:

RExecutor

public class RserveRExecutor
extends AbstractRExecutor

This class define a RServe RExecutor.

Since:

2.0

Author:

Laurent Jourdren

Field Summary

Fields

Modifier and Type	Field	Description
static final String	REXECUTOR_NAME

Constructor Summary

Constructors

Constructor	Description
RserveRExecutor(File outputDirectory, File temporaryDirectory, String serverName)	Public constructor.

Method Summary

Modifier and Type	Method	Description
void	closeConnection()	Close the connection.
void	executeR(String code, File workflowOutputDir)
String	getName()	Get the name of the RExecutor.
void	getOutputFiles()	Get the output files of the analysis
void	openConnection()	Open the connection.
void	writeFile(String content, String outputFilename)	Write a file.

Methods inherited from class fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor

executeRScript, executeRScript, putInputFile, putInputFile, removeInputFiles

Methods inherited from class java.lang.Object

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

Field Details

REXECUTOR_NAME

public static final String REXECUTOR_NAME

See Also:

• Constant Field Values

Constructor Details

RserveRExecutor

public RserveRExecutor(File outputDirectory,
 File temporaryDirectory,
 String serverName)
                throws IOException

Public constructor.

Parameters:

outputDirectory - the output directory

temporaryDirectory - the temporary directory

serverName - Rserve server name

Throws:

IOException - if an error occurs

Method Details

getName

public String getName()

Description copied from interface: RExecutor

Get the name of the RExecutor.

Returns:

the name of the RExecutor

getOutputFiles

public void getOutputFiles()
                    throws IOException

Description copied from interface: RExecutor

Get the output files of the analysis

Specified by:

getOutputFiles in interface RExecutor

Overrides:

getOutputFiles in class AbstractRExecutor

Throws:

IOException - if an error occurs while getting the output files

openConnection

public void openConnection()
                    throws IOException

Description copied from interface: RExecutor

Open the connection.

Specified by:

openConnection in interface RExecutor

Overrides:

openConnection in class AbstractRExecutor

Throws:

IOException - if an error occurs while opening the connection

closeConnection

public void closeConnection()
                     throws IOException

Description copied from interface: RExecutor

Close the connection.

Specified by:

closeConnection in interface RExecutor

Overrides:

closeConnection in class AbstractRExecutor

Throws:

IOException - if an error occurs while closing the connection

writeFile

public void writeFile(String content,
 String outputFilename)
               throws IOException

Description copied from interface: RExecutor

Write a file.

Parameters:

content - the content of the file

outputFilename - the output filename

Throws:

IOException - if an exception occurs while writing a file

executeR

public void executeR(String code,
 File workflowOutputDir)
              throws IOException

Throws:

IOException