picard.util

Class RExecutor

java.lang.Object

picard.util.RExecutor

public class RExecutor
extends java.lang.Object

Util class for executing R scripts.

Author:

Doug Voet (dvoet at broadinstitute dot org)

Constructor Summary

Constructors

Constructor and Description
RExecutor()

Method Summary

Modifier and Type	Method and Description
static int	executeFromClasspath(java.lang.String rScriptName, java.lang.String... arguments) Executes the given R script that is stored in a file on the classpath.
static int	executeFromFile(java.io.File scriptFile, java.lang.String... arguments) Executes the given R script that is stored in a file by a call to Rscript.

Methods inherited from class java.lang.Object

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

Constructor Detail

RExecutor

public RExecutor()

Method Detail

executeFromClasspath

public static int executeFromClasspath(java.lang.String rScriptName,
                                       java.lang.String... arguments)

Executes the given R script that is stored in a file on the classpath. The script file is read from the classpath and written to a temp file then executed by a call to Rscript. Blocks until the R script is complete.

Parameters:

rScriptName - the fully qualified name of the classpath resource of the script

arguments - any arguments required by the script

Returns:

the return code of the R process

executeFromFile

public static int executeFromFile(java.io.File scriptFile,
                                  java.lang.String... arguments)

Executes the given R script that is stored in a file by a call to Rscript. Blocks until the R script is complete.

Parameters:

scriptFile - the file object for the script

arguments - any arguments required by the script

Returns:

the return code of the R process