de.jstacs.utils
Class REnvironment

java.lang.Object
  de.jstacs.utils.REnvironment

public class REnvironment
extends Object

This is an environment class for R and Rserve that helps you to handle all things in a more gentle way.

Author:

Jens Keilwagen

See Also:

RUtils

Constructor Summary

REnvironment()
This constructor creates a connection to an R instance on the "localhost" with empty login and password.

REnvironment(String server, int port, String user, String passwd)
Creates a new REnvironment with initial size 10 using the given port.

REnvironment(String server, int port, String user, String passwd, int initSize)
Creates a new REnvironment using the given port.

REnvironment(String server, String user, String passwd)
Creates a new REnvironment with initial size 10 using the default port.

REnvironment(String server, String user, String passwd, int initSize)
Creates a new REnvironment using the default port.

Method Summary

void	close() Closes the REnvironment and removes all files from the server.
boolean	copyFileFromServer(String serverFileName, String clientFileName, boolean overwriteExistingFile) Copies a file from the server to the local machine.
boolean	copyFileToServer(String clientFileName, String serverFileName, boolean overwriteExistingFile) Copies a file from the local machine to the server.
REXP	createMatrix(String matrixName, double[][] matrix) Creates a matrix of doubles.
REXP	createMatrix(String matrixName, int[][] matrix) Creates a matrix of ints.
REXP	createVector(String vectorName, double[] vector) Creates a vector of doubles.
REXP	createVector(String vectorName, int[] vector) Creates a vector of ints.
REXP	createVector(String vectorName, long[] vector) Creates a vector of longs.
REXP	createVector(String vectorName, String[] vector) Creates a vector of Strings.
void	deleteAllFilesAtTheServer() Deletes all files that have been copied to the server or created on the server.
REXP	eval(CharSequence cmd) Evaluates the String as R commands.
protected void	finalize()
String	getVersionInformation() Returns information about the version of R that is used.
void	installScript(String clientFileName, String serverFileName, boolean overwriteExistingFile) Installs a script on the server.
BufferedImage	plot(CharSequence pltcmd) Creates a buffered image from a given plot command.
BufferedImage	plot(CharSequence pltcmd, double width, double height) Creates a buffered image with given dimension from a given plot command.
void	plot(CharSequence pltcmd, double width, double height, String formatName, OutputStream out) This method creates an image with given dimension from a given plot command and pipes it to the output stream.
boolean	plotToPDF(CharSequence pltcmd, double width, double height, String fileName, boolean overwriteExistingFile) Creates a pdf file with given dimension from a given plot command.
boolean	plotToPDF(CharSequence pltcmd, String fileName, boolean overwriteExistingFile) Creates a pdf file from a given plot command.
boolean	plotToTexFile(CharSequence pltcmd, double width, double height, String fileName, boolean overwriteExistingFile) Creates a tex file with given dimension from a given plot command.
boolean	plotToTexFile(CharSequence pltcmd, String fileName, boolean overwriteExistingFile) Creates a tex file from a given plot command.
static JFrame	showImage(String title, BufferedImage img) Enables you to show an image.
static JFrame	showImage(String title, BufferedImage img, int defaultCloseOperation) Enables you to show an image.
void	voidEval(CharSequence cmd) Evaluates the String as R commands.

Methods inherited from class java.lang.Object

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

Constructor Detail

REnvironment

public REnvironment()
             throws Exception

This constructor creates a connection to an R instance on the "localhost" with empty login and password.

Throws:

Exception - if something went wrong

See Also:

REnvironment(String, String, String)

REnvironment

public REnvironment(String server,
                    String user,
                    String passwd,
                    int initSize)
             throws Exception

Creates a new REnvironment using the default port.

Parameters:

server - the name of the server

user - the login

passwd - the password for the login

initSize - the initial number of slots for files on the server (has to be at least 1)

Throws:

Exception - if something went wrong

REnvironment

public REnvironment(String server,
                    String user,
                    String passwd)
             throws Exception

Creates a new REnvironment with initial size 10 using the default port.

Parameters:

server - the name of the server

user - the login

passwd - the password for the login

Throws:

Exception - if something went wrong

See Also:

REnvironment(String, String, String, int)

REnvironment

public REnvironment(String server,
                    int port,
                    String user,
                    String passwd,
                    int initSize)
             throws Exception

Creates a new REnvironment using the given port.

Parameters:

server - the name of the server

port - the port

user - the login

passwd - the password for the login

initSize - the initial number of slots for files on the server (has to be at least 1)

Throws:

Exception - if something went wrong

REnvironment

public REnvironment(String server,
                    int port,
                    String user,
                    String passwd)
             throws Exception

Creates a new REnvironment with initial size 10 using the given port.

Parameters:

server - the name of the server

port - the port

user - the login

passwd - the password for the login

Throws:

Exception - if something went wrong

See Also:

REnvironment(String, String, String, int)

Method Detail

copyFileFromServer

public boolean copyFileFromServer(String serverFileName,
                                  String clientFileName,
                                  boolean overwriteExistingFile)
                           throws Exception

Copies a file from the server to the local machine.

Parameters:

serverFileName - name of the file on the server

clientFileName - name of the file on the client (local machine)

overwriteExistingFile - whether to overwrite the file, if already existing on the client

Returns:

true if the file is copied successfully

Throws:

Exception - if something went wrong

copyFileToServer

public boolean copyFileToServer(String clientFileName,
                                String serverFileName,
                                boolean overwriteExistingFile)
                         throws Exception

Copies a file from the local machine to the server.

Parameters:

serverFileName - name of the file on the server

clientFileName - name of the file on the client (local machine)

overwriteExistingFile - whether to overwrite the file, if already existing on the server

Returns:

true if the file is copied successfully

Throws:

Exception - if something went wrong

close

public void close()
           throws Exception

Closes the REnvironment and removes all files from the server.

Throws:

Exception - if something went wrong

createMatrix

public REXP createMatrix(String matrixName,
                         int[][] matrix)
                  throws RserveException,
                         IllegalArgumentException

Creates a matrix of ints.

Parameters:

matrixName - the name of the matrix

matrix - the matrix of ints

Returns:

an R expression

Throws:

RserveException - if something with Rserve went wrong

IllegalArgumentException - if matrix[i].length != matrix[j].length

createMatrix

public REXP createMatrix(String matrixName,
                         double[][] matrix)
                  throws RserveException,
                         IllegalArgumentException

Creates a matrix of doubles.

Parameters:

matrixName - the name of the matrix

matrix - the matrix of doubles

Returns:

an R expression

Throws:

RserveException - if something with Rserve went wrong

IllegalArgumentException - if matrix[i].length != matrix[j].length

createVector

public REXP createVector(String vectorName,
                         String[] vector)
                  throws RserveException

Creates a vector of Strings.

Parameters:

vectorName - the name of the vector

vector - the vector of Strings

Returns:

an R expression

Throws:

RserveException - if something with Rserve went wrong

createVector

public REXP createVector(String vectorName,
                         int[] vector)
                  throws RserveException

Creates a vector of ints.

Parameters:

vectorName - the name of the vector

vector - the vector of ints

Returns:

an R expression

Throws:

RserveException - if something with Rserve went wrong

createVector

public REXP createVector(String vectorName,
                         long[] vector)
                  throws RserveException

Creates a vector of longs.

Parameters:

vectorName - the name of the vector

vector - the vector of longs

Returns:

an R expression

Throws:

RserveException - if something with Rserve went wrong

createVector

public REXP createVector(String vectorName,
                         double[] vector)
                  throws RserveException

Creates a vector of doubles.

Parameters:

vectorName - the name of the vector

vector - the vector of doubles

Returns:

an R expression

Throws:

RserveException - if something with Rserve went wrong

deleteAllFilesAtTheServer

public void deleteAllFilesAtTheServer()
                               throws Exception

Deletes all files that have been copied to the server or created on the server.

Throws:

Exception - if something went wrong

eval

public REXP eval(CharSequence cmd)
          throws Exception

Evaluates the String as R commands.

Parameters:

cmd - the String to be evaluated

Returns:

the result from R

Throws:

Exception - if something went wrong

getVersionInformation

public String getVersionInformation()
                             throws Exception

Returns information about the version of R that is used.

Returns:

information about the version of R that is used

Throws:

Exception - if something went wrong

installScript

public void installScript(String clientFileName,
                          String serverFileName,
                          boolean overwriteExistingFile)
                   throws Exception

Installs a script on the server.

Parameters:

clientFileName - the name of the scriptfile on the client

serverFileName - the name of the scriptfile on the server

overwriteExistingFile - if true the method is enabled to overwrite an existing file

Throws:

Exception - if something went wrong

plot

public BufferedImage plot(CharSequence pltcmd)
                   throws Exception

Creates a buffered image from a given plot command.

If you use a java version below 1.6 your image is internally encoded as jpeg.
If you use a java version at least 1.6 your image is internally encoded as png.

Parameters:

pltcmd - the plot command

Returns:

the buffered image

Throws:

Exception - if something went wrong

See Also:

plot(CharSequence, double, double), showImage(String, BufferedImage), ImageIO.write(java.awt.image.RenderedImage, String, File)

plot

public BufferedImage plot(CharSequence pltcmd,
                          double width,
                          double height)
                   throws Exception

Creates a buffered image with given dimension from a given plot command.

If you use a java version below 1.6 your image is internally encoded as jpeg.
If you use a java version at least 1.6 your image is internally encoded as png.

Parameters:

pltcmd - the plot command

width - the width of the image (in pixel)

height - the height of the image (in pixel)

Returns:

the buffered image

Throws:

Exception - if something went wrong

See Also:

showImage(String, BufferedImage), ImageIO.write(java.awt.image.RenderedImage, java.lang.String, java.io.File)

plot

public void plot(CharSequence pltcmd,
                 double width,
                 double height,
                 String formatName,
                 OutputStream out)
          throws IOException,
                 Exception

This method creates an image with given dimension from a given plot command and pipes it to the output stream.

Parameters:

pltcmd - the plotting command

width - the width of the image

height - the height of the image

formatName - the name of the image format used for writing the image (see ImageIO)

out - the OutputStream used for writing the image

Throws:

IOException - see ImageIO.write(java.awt.image.RenderedImage, String, OutputStream)

Exception - see plot(CharSequence, double, double)

See Also:

ImageIO.write(java.awt.image.RenderedImage, String, OutputStream)

plotToPDF

public boolean plotToPDF(CharSequence pltcmd,
                         String fileName,
                         boolean overwriteExistingFile)
                  throws Exception

Creates a pdf file from a given plot command.

Parameters:

pltcmd - the plot command

fileName - the name of the pdf file

overwriteExistingFile - if true the method is enabled to overwrite an existing file

Returns:

true if the plot is done

Throws:

Exception - if something went wrong

plotToPDF

public boolean plotToPDF(CharSequence pltcmd,
                         double width,
                         double height,
                         String fileName,
                         boolean overwriteExistingFile)
                  throws Exception

Creates a pdf file with given dimension from a given plot command.

Parameters:

pltcmd - the plot command

width - the width of the image

height - the height of the image

fileName - the name of the pdf file

overwriteExistingFile - if true the method is enabled to overwrite an existing file

Returns:

true if the plot is done

Throws:

Exception - if something went wrong

plotToTexFile

public boolean plotToTexFile(CharSequence pltcmd,
                             String fileName,
                             boolean overwriteExistingFile)
                      throws Exception

Creates a tex file from a given plot command.

Parameters:

pltcmd - the plot command

fileName - the name of the tex file

overwriteExistingFile - if true the method is enabled to overwrite an existing file

Returns:

true if the plot is done

Throws:

Exception - if something went wrong

plotToTexFile

public boolean plotToTexFile(CharSequence pltcmd,
                             double width,
                             double height,
                             String fileName,
                             boolean overwriteExistingFile)
                      throws Exception

Creates a tex file with given dimension from a given plot command.

Parameters:

pltcmd - the plot command

width - the width of the image

height - the height of the image

fileName - the name of the tex file

overwriteExistingFile - if true the method is enabled to overwrite an existing file

Returns:

true if the plot is done

Throws:

Exception - if something went wrong

voidEval

public void voidEval(CharSequence cmd)
              throws Exception

Evaluates the String as R commands.

Parameters:

cmd - the String to be evaluated

Throws:

Exception - if something went wrong

finalize

protected void finalize()
                 throws Throwable

Overrides:

finalize in class Object

Throws:

Throwable

showImage

public static JFrame showImage(String title,
                               BufferedImage img)
                        throws InterruptedException

Enables you to show an image.

Parameters:

title - the title of the frame

img - the image

Returns:

a frame showing the image

Throws:

InterruptedException - if the process is interrupted

See Also:

showImage(String, BufferedImage, int)

showImage

public static JFrame showImage(String title,
                               BufferedImage img,
                               int defaultCloseOperation)
                        throws InterruptedException

Enables you to show an image.

Parameters:

title - the title of the frame

img - the image

defaultCloseOperation - the variable used to control the window-closing operation

Returns:

a frame showing the image

Throws:

InterruptedException - if the process is interrupted

See Also:

WindowConstants