com.eco.bio7.rbridge

Class RServe

java.lang.Object

com.eco.bio7.rbridge.RServe

public class RServe
extends java.lang.Object

This class provides methods for the communication with the Rserve application.

Author:

Bio7

Constructor Summary

Constructors

Constructor and Description
RServe()

Method Summary

Modifier and Type	Method and Description
static void	callRScript(java.lang.String path) A method to call a RScript.
static void	callRScriptSilent(java.lang.String path) A method to call a RScript without to capture (print) the output.
static void	closeAndDisplay()
static void	evaluateExt(java.lang.String expression) Evaluates an R expression without running in a job.
static org.rosuda.REngine.Rserve.RConnection	getConnection() Returns a Rserve connection.
static int	getDisplayNumber()
static java.lang.String	getRout() Internal method of Bio7.
static org.rosuda.REngine.Rserve.RSession	getRsession() A method to get the current stored RSession.
static java.lang.String[]	getShellSelections() A method to get the selected variable names in the left Objects tab in the R-Shell view (variables in the R workspace!).
static boolean	isAlive() Returns if the connection to Rserve is alive.
static boolean	isAliveDialog() Returns if the connection to Rserve is alive visible by means of a dialog.
static boolean	isConnected() Returns if the Bio7 application is connected to the Rserve application.
static boolean	isIsconnecting() Internal method of Bio7.
static boolean	isPdf() Returns if the plotting device is the pdf device.
static boolean	isRrunning() Returns if the Rserve application is running.
static java.io.File[]	ListFilesDirectory(java.io.File filedirectory, java.lang.String[] extensions)
static void	openPDF(java.lang.String plotPathR, java.lang.String fileName, boolean useBrowser, java.lang.String openInJavaFXBrowser)
static void	plotLinux(java.lang.String finalpath)
static void	print(java.lang.String expression) Evaluates and prints an expression to the Bio7 console.
static void	printJob(java.lang.String expression) Evaluates and prints an expression to the Bio7 console executed in a job.
static void	printJobs(java.lang.String[] expressions) Evaluates and prints an array of expressions to the Bio7 console executed in a job.
static void	setConnection(org.rosuda.REngine.Rserve.RConnection connection) Sets a Rserve connection.
static void	setPdf(boolean pdf) Set the plotting device to pdf.
static void	setPlotInch(double inchx, double inchy) Set the plot size in inch for a pdf plot.
static void	setPlotPixel(int imageWidth, int imageHeight) Set the plot size in pixel for a png plot.
static void	setRout(java.lang.String rout) Internal method of Bio7.
static void	setRrunning(boolean running) Set the Rserve running value.
static void	setRsession(org.rosuda.REngine.Rserve.RSession rSess) A method to store the current RSession.

Methods inherited from class java.lang.Object

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

Constructor Detail

RServe

public RServe()

Method Detail

evaluateExt

public static void evaluateExt(java.lang.String expression)

Evaluates an R expression without running in a job. This method can be used to evaluate R scripts from e.g. Groovy (running already in a job). R plots a possible, too.

Parameters:

expression - a R expression.

printJob

public static void printJob(java.lang.String expression)

Evaluates and prints an expression to the Bio7 console executed in a job.

Parameters:

expression - a R expression as a string.

printJobs

public static void printJobs(java.lang.String[] expressions)

Evaluates and prints an array of expressions to the Bio7 console executed in a job.

Parameters:

expressions - a R expression as a string.

print

public static void print(java.lang.String expression)

Evaluates and prints an expression to the Bio7 console.

Parameters:

expression - a R expression as a string.

getConnection

public static org.rosuda.REngine.Rserve.RConnection getConnection()

Returns a Rserve connection.

Returns:

a R connection.

isAliveDialog

public static boolean isAliveDialog()

Returns if the connection to Rserve is alive visible by means of a dialog.

Returns:

a boolean value.

isAlive

public static boolean isAlive()

Returns if the connection to Rserve is alive.

Returns:

a boolean value.

setConnection

public static void setConnection(org.rosuda.REngine.Rserve.RConnection connection)

Sets a Rserve connection.

Parameters:

connection - a R connection.

isPdf

public static boolean isPdf()

Returns if the plotting device is the pdf device.

Returns:

a boolean value.

setPdf

public static void setPdf(boolean pdf)

Set the plotting device to pdf.

Parameters:

pdf - a boolean value.

isIsconnecting

public static boolean isIsconnecting()

Internal method of Bio7.

Returns:

a boolean value.

isRrunning

public static boolean isRrunning()

Returns if the Rserve application is running.

Returns:

a boolean value.

setRrunning

public static void setRrunning(boolean running)

Set the Rserve running value.

Parameters:

running - a boolean value.

setRout

public static void setRout(java.lang.String rout)

Internal method of Bio7.

Parameters:

rout - a string value.

getRout

public static java.lang.String getRout()

Internal method of Bio7.

Returns:

a string value.

isConnected

public static boolean isConnected()

Returns if the Bio7 application is connected to the Rserve application.

Returns:

a boolean value.

setPlotInch

public static void setPlotInch(double inchx,
                               double inchy)

Set the plot size in inch for a pdf plot.

Parameters:

inchx - the width of the plot in inch units.

inchy - the height of the plot in inch units.

setPlotPixel

public static void setPlotPixel(int imageWidth,
                                int imageHeight)

Set the plot size in pixel for a png plot.

Parameters:

imageWidth - the width of the plot in pixel units.

imageHeight - the height of the plot in pixel units.

callRScript

public static void callRScript(java.lang.String path)

A method to call a RScript.

Parameters:

path - the relative path from the Bio7 Workspace to the script.

callRScriptSilent

public static void callRScriptSilent(java.lang.String path)

A method to call a RScript without to capture (print) the output.

Parameters:

path - the relative path from the Bio7 Workspace to the script.

getShellSelections

public static java.lang.String[] getShellSelections()

A method to get the selected variable names in the left Objects tab in the R-Shell view (variables in the R workspace!).

Returns:

the selected workspace variables.

closeAndDisplay

public static void closeAndDisplay()

openPDF

public static void openPDF(java.lang.String plotPathR,
                           java.lang.String fileName,
                           boolean useBrowser,
                           java.lang.String openInJavaFXBrowser)

getDisplayNumber

public static int getDisplayNumber()

ListFilesDirectory

public static java.io.File[] ListFilesDirectory(java.io.File filedirectory,
                                                java.lang.String[] extensions)

plotLinux

public static void plotLinux(java.lang.String finalpath)

setRsession

public static void setRsession(org.rosuda.REngine.Rserve.RSession rSess)

A method to store the current RSession.

Parameters:

rSess - the RSession

getRsession

public static org.rosuda.REngine.Rserve.RSession getRsession()

A method to get the current stored RSession.

Returns:

the RSession