org.broadinstitute.hellbender.utils.R

Class RScriptExecutor

java.lang.Object

org.broadinstitute.hellbender.utils.runtime.ScriptExecutor

org.broadinstitute.hellbender.utils.R.RScriptExecutor

public final class RScriptExecutor
extends ScriptExecutor

Generic service for executing RScripts

Field Summary

Fields inherited from class org.broadinstitute.hellbender.utils.runtime.ScriptExecutor

externalScriptExecutableName, ignoreExceptions

Constructor Summary

Constructors

Constructor and Description
RScriptExecutor()
RScriptExecutor(boolean ensureExecutableExists)

Method Summary

Modifier and Type	Method and Description
void	addArgs(java.lang.Object... args) Adds args to the end of the Rscript command line.
void	addLibrary(RScriptLibrary library)
void	addScript(java.io.File script)
void	addScript(Resource script)
boolean	exec()
java.lang.String	getApproximateCommandLine() Return a (not necessarily executable) string representing the command line for this executor for error reporting purposes.
RScriptExecutorException	getScriptException(java.lang.String message) Return an exception specific to this executor type, to be thrown on error conditions.

Methods inherited from class org.broadinstitute.hellbender.utils.runtime.ScriptExecutor

executableMissing, executeCuratedArgs, externalExecutableExists, setIgnoreExceptions

Methods inherited from class java.lang.Object

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

Constructor Detail

RScriptExecutor

public RScriptExecutor()

RScriptExecutor

public RScriptExecutor(boolean ensureExecutableExists)

Parameters:

ensureExecutableExists - throw if the RScript executable cannot be located

Method Detail

addLibrary

public void addLibrary(RScriptLibrary library)

addScript

public void addScript(Resource script)

addScript

public void addScript(java.io.File script)

addArgs

public void addArgs(java.lang.Object... args)

Adds args to the end of the Rscript command line.

Parameters:

args - the args.

Throws:

java.lang.NullPointerException - if any of the args are null.

getApproximateCommandLine

public java.lang.String getApproximateCommandLine()

Description copied from class: ScriptExecutor

Return a (not necessarily executable) string representing the command line for this executor for error reporting purposes.

Specified by:

getApproximateCommandLine in class ScriptExecutor

Returns:

Command line string.

getScriptException

public RScriptExecutorException getScriptException(java.lang.String message)

Return an exception specific to this executor type, to be thrown on error conditions.

Specified by:

getScriptException in class ScriptExecutor

Parameters:

message -

Returns:

a {#ScriptExecutorException}-derived exception object

exec

public boolean exec()