adams.flow.sink
Class RSink

java.lang.Object
  adams.core.ConsoleObject
      adams.core.option.AbstractOptionHandler
          adams.flow.core.AbstractActor
              adams.flow.sink.AbstractSink
                  adams.flow.sink.RSink

All Implemented Interfaces:

AdditionalInformationHandler, CleanUpHandler, Debuggable, DebugOutputHandler, Destroyable, OptionHandler, QuickInfoSupporter, ShallowCopySupporter<AbstractActor>, SizeOfHandler, Stoppable, VariableChangeListener, Actor, ErrorHandler, InputConsumer, Serializable, Comparable

public class RSink
extends AbstractSink

Carries out an r command on the token passed in. The input can be accessed via 'X'.
Variables are supported as well, e.g.: pow(X,@{exp}) with '@{exp}' being a variable available at execution time.

Input/output:
- accepts:
java.lang.Integer
java.lang.String
java.lang.Double
java.lang.Double[]
java.lang.Double[][]
adams.data.spreadsheet.SpreadSheet

Valid options are:

-D <int> (property: debugLevel)
    The greater the number the more additional info the scheme may output to 
    the console (0 = off).
    default: 0
    minimum: 0
 

-name <java.lang.String> (property: name)
    The name of the actor.
    default: RSink
 

-annotation <adams.core.base.BaseText> (property: annotations)
    The annotations to attach to this actor.
    default: 
 

-skip (property: skip)
    If set to true, transformation is skipped and the input token is just forwarded 
    as it is.
 

-stop-flow-on-error (property: stopFlowOnError)
    If set to true, the flow gets stopped in case this actor encounters an error;
     useful for critical actors.
 

-script <adams.core.scripting.RScript> (property: script)
    Script to pass into r. The input value can be accessed via 'X'.
    default: 
 

Version:

$Revision: 6830 $

Author:

rsmith

See Also:

Serialized Form

Field Summary

static String	INPUT the placeholder for the input value.
protected org.rosuda.REngine.Rserve.RConnection	m_RConn Connection to Rserve
protected Rserve	m_Rserve the Rserve actor.
protected RScript	m_Script Script to pass to r

Fields inherited from class adams.flow.sink.AbstractSink

BACKUP_INPUT, m_InputToken

Fields inherited from class adams.flow.core.AbstractActor

m_Annotations, m_BackupState, m_DetectedObjectVariables, m_DetectedVariables, m_ErrorHandler, m_Executed, m_Executing, m_ExecutionListeningSupporter, m_FullName, m_Headless, m_Name, m_Parent, m_Root, m_ScopeHandler, m_Self, m_Skip, m_StopFlowOnError, m_StopMessage, m_Stopped, m_StorageHandler, m_VariablesUpdated

Fields inherited from class adams.core.option.AbstractOptionHandler

m_DebugLevel, m_OptionManager

Fields inherited from interface adams.flow.core.Actor

FILE_EXTENSION, FILE_EXTENSION_GZ

Constructor Summary

RSink()

Method Summary

Class[]	accepts() List of classes that can be used as input.
void	defineOptions() Adds to the internal list of options.
protected String	doExecute() Executes the flow, including reading the input and returning R's output.
String	getQuickInfo() Returns a quick info about the actor, which will be displayed in the GUI.
RScript	getScript() Gets the script.
String	globalInfo() Info about this flow.
protected void	reset() Ressets the members.
String	scriptTipText() Tool tip about the script.
void	setScript(RScript val) Sets the script.
String	setUp() Sets up the connection to Rserve.
void	wrapUp() Closes the Rserve connection as the flow finishes.

Methods inherited from class adams.flow.sink.AbstractSink

backupState, input, restoreState

Methods inherited from class adams.flow.core.AbstractActor

annotationsTipText, canInspectOptions, canPerformSetUpCheck, cleanUp, compareTo, debug, destroy, equals, execute, findVariables, findVariables, findVariables, forceVariables, forCommandLine, forName, getAdditionalInformation, getAnnotations, getDefaultName, getDetectedVariables, getErrorHandler, getFlowActors, getFlowExecutionListeningSupporter, getFullName, getName, getNextSibling, getParent, getParentComponent, getPreviousSibling, getRoot, getScopeHandler, getSkip, getStopFlowOnError, getStopMessage, getStorageHandler, getVariables, handleError, handleException, hasErrorHandler, hasStopMessage, index, initialize, isBackedUp, isExecuted, isExecuting, isFinished, isHeadless, isStopped, nameTipText, performSetUpChecks, postExecute, preExecute, pruneBackup, pruneBackup, setAnnotations, setErrorHandler, setHeadless, setName, setParent, setSkip, setStopFlowOnError, setVariables, shallowCopy, shallowCopy, sizeOf, skipTipText, stopExecution, stopExecution, stopFlowOnErrorTipText, updateDetectedVariables, updatePrefix, updateVariables, variableChanged

Methods inherited from class adams.core.option.AbstractOptionHandler

cleanUpOptions, debug, debugLevelTipText, finishInit, getDebugLevel, getOptionManager, isDebugOn, newOptionManager, setDebugLevel, toCommandLine, toString

Methods inherited from class adams.core.ConsoleObject

getDebugging, getSystemErr, getSystemOut

Methods inherited from class java.lang.Object

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

Methods inherited from interface adams.flow.core.Actor

cleanUp, compareTo, debug, destroy, equals, execute, findVariables, getAnnotations, getDefaultName, getDetectedVariables, getErrorHandler, getFlowExecutionListeningSupporter, getFullName, getName, getNextSibling, getParent, getParentComponent, getPreviousSibling, getRoot, getScopeHandler, getSkip, getStopFlowOnError, getStopMessage, getStorageHandler, getVariables, handleError, hasErrorHandler, hasStopMessage, index, isExecuted, isFinished, isHeadless, isStopped, setAnnotations, setErrorHandler, setHeadless, setName, setParent, setSkip, setStopFlowOnError, setVariables, sizeOf, stopExecution, stopExecution, variableChanged

Methods inherited from interface adams.core.AdditionalInformationHandler

getAdditionalInformation

Methods inherited from interface adams.core.option.OptionHandler

cleanUpOptions, getOptionManager

Field Detail

INPUT

public static final String INPUT

the placeholder for the input value.

See Also:

Constant Field Values

m_Script

protected RScript m_Script

Script to pass to r

m_RConn

protected org.rosuda.REngine.Rserve.RConnection m_RConn

Connection to Rserve

m_Rserve

protected Rserve m_Rserve

the Rserve actor.

Constructor Detail

RSink

public RSink()

Method Detail

defineOptions

public void defineOptions()

Adds to the internal list of options.

Specified by:

defineOptions in interface OptionHandler

Overrides:

defineOptions in class AbstractActor

reset

protected void reset()

Ressets the members.

Overrides:

reset in class AbstractActor

setScript

public void setScript(RScript val)

Sets the script.

Parameters:

val - the script

getScript

public RScript getScript()

Gets the script.

Returns:

the script

scriptTipText

public String scriptTipText()

Tool tip about the script.

Returns:

tool tip message

getQuickInfo

public String getQuickInfo()

Returns a quick info about the actor, which will be displayed in the GUI.

Specified by:

getQuickInfo in interface QuickInfoSupporter

Specified by:

getQuickInfo in interface Actor

Overrides:

getQuickInfo in class AbstractActor

Returns:

null if no info available, otherwise short string

accepts

public Class[] accepts()

List of classes that can be used as input.

setUp

public String setUp()

Sets up the connection to Rserve.

Specified by:

setUp in interface Actor

Overrides:

setUp in class AbstractActor

doExecute

protected String doExecute()

Executes the flow, including reading the input and returning R's output.

Specified by:

doExecute in class AbstractActor

globalInfo

public String globalInfo()

Info about this flow.

Specified by:

globalInfo in class AbstractOptionHandler

wrapUp

public void wrapUp()

Closes the Rserve connection as the flow finishes.

Specified by:

wrapUp in interface Actor

Overrides:

wrapUp in class AbstractSink