org.nuiton.j2r

Class REngineAbstract

java.lang.Object

org.nuiton.j2r.REngineAbstract

All Implemented Interfaces:

REngine

Direct Known Subclasses:

RJniEngine, RNetEngine

public abstract class REngineAbstract
extends Object
implements REngine

Abstract REngine that provides utility R methods (such as clear session, set working directory, import data, ...) for all R engines.

Author:

couteau

Field Summary

Fields

Modifier and Type	Field and Description
protected Boolean	autocommit If true, commit each R instruction on the fly, if false, commit only when the commit() method is called.

Constructor Summary

Constructors

Constructor and Description
REngineAbstract()

Method Summary

Modifier and Type	Method and Description
void	clearSession() Method to clear the R session.
void	cp(String source, String destination) Copy a R Object into another one (similar to the linux cp instruction).
void	dget(String rObject, File inputFile) Use the dget rInstruction to store the content of a file (created with the dput instruction) into a R object.
void	dget(String rObject, String inputFileName) Use the dget rInstruction to store the content of a file (created with the dput instruction) into a R object.
void	dput(String rObject, File outputFile) Use the dput R instruction to store the content of a R object to a file.
void	dput(String rObject, String outputFileName) Use the dput R instruction to store the content of a R object to a file.
File	getwd() Get the actual R session working directory
Boolean	isAutoCommit() Method to know if engine is in autocommit mode.
void	loadRData(File directory) Load a specific R session : Load .RData file located in directory
void	loadRData(File directory, String fileName) Load a specific R session : Load the "fileName.RData" file located in directory.
void	loadRData(String fileName) Load the "fileName.RData" file located in current working directory.
String[]	ls() Method to get all the R object in session.
void	mv(String source, String destination) Method similar to the linux mv instruction : move an object to a destination, or in this case, rename a R object.
void	plot(String filename, String x, String y, String type, String main, String sub, String xlab, String ylab, String asp)
void	remove(String rObject) Remove a R object from the R session using the R method : remove(rObject).
void	saveRData(File directory) Save the session in a .RData file in directory
void	saveRData(File directory, String fileName) Save a R session in a fileName.RData file located in directory.
void	saveRData(String filename) Save the session in a .RData file in current working directory
void	setAutoCommit(Boolean autocommit) Change the autocommit mode of the engine.
void	setwd(File directory) Set the R working directory

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.nuiton.j2r.REngine

commit, eval, evalScript, init, terminate, voidEval

Field Detail

autocommit

protected Boolean autocommit

If true, commit each R instruction on the fly, if false, commit only when the commit() method is called.

Constructor Detail

REngineAbstract

public REngineAbstract()

Method Detail

loadRData

public void loadRData(File directory)
               throws RException

Load a specific R session : Load .RData file located in directory

Specified by:

loadRData in interface REngine

Parameters:

directory - directory where the .RData file is located

Throws:

RException - if an error occur while loading the R session file

loadRData

public void loadRData(File directory,
                      String fileName)
               throws RException

Load a specific R session : Load the "fileName.RData" file located in directory.

Specified by:

loadRData in interface REngine

Parameters:

directory - directory where the ".RData" file is located

fileName - name of the file to load (will load the fileName.RData file)

Throws:

RException - if an error occur while loading the R session file.

loadRData

public void loadRData(String fileName)
               throws RException

Load the "fileName.RData" file located in current working directory.

Specified by:

loadRData in interface REngine

Parameters:

fileName - name of the file to load (will load the fileName.RData file)

Throws:

RException - if an error occur while loading the R session file.

saveRData

public void saveRData(File directory)
               throws RException

Save the session in a .RData file in directory

Specified by:

saveRData in interface REngine

Parameters:

directory - where the .RData file will be saved

Throws:

RException - if an error occur while saving the R session.

saveRData

public void saveRData(String filename)
               throws RException

Save the session in a .RData file in current working directory

Specified by:

saveRData in interface REngine

Parameters:

filename - the .RData filename (will be followed by .RData)

Throws:

RException - if an error occur while saving the R session.

saveRData

public void saveRData(File directory,
                      String fileName)
               throws RException

Save a R session in a fileName.RData file located in directory.

Specified by:

saveRData in interface REngine

Parameters:

directory - where the ".RData" file will be located

fileName - name of the file to save (will save in the fileName.RData file)

Throws:

RException - if an error occur while saving the R session.

setwd

public void setwd(File directory)
           throws RException

Set the R working directory

Specified by:

setwd in interface REngine

Parameters:

directory - to set

Throws:

RException

getwd

public File getwd()
           throws RException

Get the actual R session working directory

Specified by:

getwd in interface REngine

Returns:

a File that is the actual R session working directory

Throws:

RException

dput

public void dput(String rObject,
                 String outputFileName)
          throws RException

Use the dput R instruction to store the content of a R object to a file. The file created will be in the working directory

Specified by:

dput in interface REngine

Parameters:

rObject - name of the R object to save

outputFileName - name of the file to save

Throws:

RException

dget

public void dget(String rObject,
                 String inputFileName)
          throws RException

Use the dget rInstruction to store the content of a file (created with the dput instruction) into a R object. The file used have to be in the working directory

Specified by:

dget in interface REngine

Parameters:

rObject - name of the R object created

inputFileName - name of the file to load

Throws:

RException

dput

public void dput(String rObject,
                 File outputFile)
          throws RException

Use the dput R instruction to store the content of a R object to a file.

Specified by:

dput in interface REngine

Parameters:

rObject - R object to save

outputFile - the file to save

Throws:

RException

dget

public void dget(String rObject,
                 File inputFile)
          throws RException

Use the dget rInstruction to store the content of a file (created with the dput instruction) into a R object.

Specified by:

dget in interface REngine

Parameters:

rObject - name of the R object created

inputFile - file to load

Throws:

RException

remove

public void remove(String rObject)
            throws RException

Remove a R object from the R session using the R method : remove(rObject).

Specified by:

remove in interface REngine

Parameters:

rObject - name of the R object to be removed.

Throws:

RException - if an error occur while trying to remove the R object.

mv

public void mv(String source,
               String destination)
        throws RException

Method similar to the linux mv instruction : move an object to a destination, or in this case, rename a R object. Does : destination<-source remove(source)

Specified by:

mv in interface REngine

Parameters:

source - source R object name

destination - destination R object name

Throws:

RException - if an error occur while trying to move the R object.

cp

public void cp(String source,
               String destination)
        throws RException

Copy a R Object into another one (similar to the linux cp instruction). Does : destination<-source

Specified by:

cp in interface REngine

Parameters:

source - source R object name

destination - destination R object name

Throws:

RException - if an error occur while trying to assign the source to the destination

ls

public String[] ls()
            throws RException

Method to get all the R object in session. Return the result of the R ls() function.

Specified by:

ls in interface REngine

Returns:

the names of the R objects present in session as a String[]. The order of the names is given by their order given by the R ls() method, e.g. alphabetic order.

Throws:

RException - if an error occur while trying to list the R objects in session.

clearSession

public void clearSession()
                  throws RException

Method to clear the R session. Does : rm(list=ls())

Specified by:

clearSession in interface REngine

Throws:

RException - if an error occur while trying to clear the session

setAutoCommit

public void setAutoCommit(Boolean autocommit)
                   throws RException

Change the autocommit mode of the engine. If switching from no-autocommit to autocommit mode, does a commit of all R instructions stored.

Specified by:

setAutoCommit in interface REngine

Parameters:

autocommit - true for autocommit mode, false for no-autocommit mode.

Throws:

RException - if an error occur while commiting all the R instructions stored.

isAutoCommit

public Boolean isAutoCommit()

Method to know if engine is in autocommit mode.

Specified by:

isAutoCommit in interface REngine

Returns:

true if in autocommit mode, false otherwise.

plot

public void plot(String filename,
                 String x,
                 String y,
                 String type,
                 String main,
                 String sub,
                 String xlab,
                 String ylab,
                 String asp)
          throws RException

Specified by:

plot in interface REngine

Parameters:

filename -

x -

y -

type -

main -

sub -

xlab -

ylab -

asp -

Throws:

RException