Package adams.flow.sink

Class PlotContainerSink

java.lang.Object

adams.core.logging.LoggingObject

adams.core.logging.CustomLoggingLevelObject

adams.core.option.AbstractOptionHandler

adams.flow.core.AbstractActor

adams.flow.sink.AbstractSink

adams.flow.sink.AbstractFileWriter

adams.flow.sink.PlotContainerSink

All Implemented Interfaces:

AdditionalInformationHandler, CleanUpHandler, Destroyable, GlobalInfoSupporter, FileWriter, LoggingLevelHandler, LoggingSupporter, OptionHandler, QuickInfoSupporter, ShallowCopySupporter<Actor>, SizeOfHandler, Stoppable, StoppableWithFeedback, VariablesInspectionHandler, VariableChangeListener, Actor, ErrorHandler, InputConsumer, Serializable, Comparable

public class PlotContainerSink
extends AbstractFileWriter

Actor that outputs the plot containers in various formats.

Input/output:
- accepts:
adams.flow.container.SequencePlotterContainer


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: PlotContainerSink
 

-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.
 

-output <adams.core.io.PlaceholderFile> (property: outputFile)
    The file to save the generated output to.
    default: .
 

-writer <adams.core.io.AbstractSpreadSheetWriter> (property: writer)
    The writer to use for outputting the plot containers.
    default: adams.core.io.CsvSpreadSheetWriter
 

Version:

$Revision$

Author:

fracpete (fracpete at waikato dot ac dot nz)

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	PlotContainerSink.DoubleComparator	Comparator for doubles that are stored as string.

Field Summary

Fields

Modifier and Type	Field	Description
static String	BACKUP_SPREADSHEET	the key for storing the spreadsheet generated so far in the backup.
static String	BACKUP_TOKENCOUNTS	the key for storing the token counts in the backup.
static String	COLUMN_X	the key for storing the X value in the spreadsheet.
protected PlotContainerSink.DoubleComparator	m_Comparator	the comparator to use.
protected SpreadSheet	m_SpreadSheet	stores the content of the plot containers.
protected NamedCounter	m_TokenCounts	for keeping track of the number of tokens being added for a specific sequence, in case the X value is undefined (seqname - count relation).
protected SpreadSheetWriter	m_Writer	the writer to use.

Fields inherited from class adams.flow.sink.AbstractFileWriter

m_OutputFile

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_LoggingPrefix, m_Name, m_Parent, m_ScopeHandler, m_Self, m_Silent, m_Skip, m_StopFlowOnError, m_StopMessage, m_Stopped, m_StorageHandler, m_VariablesUpdated

Fields inherited from class adams.core.option.AbstractOptionHandler

m_OptionManager

Fields inherited from class adams.core.logging.LoggingObject

m_Logger, m_LoggingIsEnabled, m_LoggingLevel

Fields inherited from interface adams.flow.core.Actor

FILE_EXTENSION, FILE_EXTENSION_GZ

Constructor Summary

Constructors

Constructor	Description
PlotContainerSink()

Method Summary

Modifier and Type	Method	Description
Class[]	accepts()	Returns the class that the consumer accepts.
protected Hashtable<String,Object>	backupState()	Backs up the current state of the actor before update the variables.
void	defineOptions()	Adds options to the internal list of options.
protected String	doExecute()	Executes the flow item.
String	getQuickInfo()	Returns a quick info about the actor, which will be displayed in the GUI.
SpreadSheetWriter	getWriter()	Returns the writer to use for outputting the plot containers.
String	globalInfo()	Returns a string describing the object.
protected void	initialize()	Initializes the members.
String	outputFileTipText()	Returns the tip text for this property.
protected void	pruneBackup()	Removes entries from the backup.
protected void	reset()	Initializes the members.
protected void	restoreState(Hashtable<String,Object> state)	Restores the state of the actor before the variables got updated.
void	setWriter(SpreadSheetWriter value)	Sets the writer to use for outputting the plot containers.
void	wrapUp()	Cleans up after the execution has finished.
String	writerTipText()	Returns the tip text for this property.

Methods inherited from class adams.flow.sink.AbstractFileWriter

getDefaultOutputFile, getOutputFile, setOutputFile, setUp

Methods inherited from class adams.flow.sink.AbstractSink

currentInput, hasInput, input, postExecute

Methods inherited from class adams.flow.core.AbstractActor

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

Methods inherited from class adams.core.option.AbstractOptionHandler

cleanUpOptions, finishInit, getDefaultLoggingLevel, getOptionManager, loggingLevelTipText, newOptionManager, setLoggingLevel, toCommandLine, toString

Methods inherited from class adams.core.logging.LoggingObject

getLogger, getLoggingLevel, initializeLogging, isLoggingEnabled

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

Methods inherited from interface adams.core.AdditionalInformationHandler

getAdditionalInformation

Methods inherited from interface adams.core.logging.LoggingLevelHandler

getLoggingLevel, setLoggingLevel

Methods inherited from interface adams.core.logging.LoggingSupporter

getLogger, isLoggingEnabled

Methods inherited from interface adams.core.option.OptionHandler

cleanUpOptions, getOptionManager

Methods inherited from interface adams.core.VariablesInspectionHandler

canInspectOptions

Field Detail

BACKUP_SPREADSHEET

public static final String BACKUP_SPREADSHEET

the key for storing the spreadsheet generated so far in the backup.

See Also:

Constant Field Values

BACKUP_TOKENCOUNTS

public static final String BACKUP_TOKENCOUNTS

the key for storing the token counts in the backup.

See Also:

Constant Field Values

COLUMN_X

public static final String COLUMN_X

the key for storing the X value in the spreadsheet.

See Also:

Constant Field Values

m_Writer

protected SpreadSheetWriter m_Writer

the writer to use.

m_SpreadSheet

protected SpreadSheet m_SpreadSheet

stores the content of the plot containers.

m_TokenCounts

protected NamedCounter m_TokenCounts

for keeping track of the number of tokens being added for a specific sequence, in case the X value is undefined (seqname - count relation).

m_Comparator

protected PlotContainerSink.DoubleComparator m_Comparator

the comparator to use.

Constructor Detail

PlotContainerSink

public PlotContainerSink()

Method Detail

globalInfo

public String globalInfo()

Returns a string describing the object.

Specified by:

globalInfo in interface GlobalInfoSupporter

Specified by:

globalInfo in class AbstractOptionHandler

Returns:

a description suitable for displaying in the gui

defineOptions

public void defineOptions()

Adds options to the internal list of options.

Specified by:

defineOptions in interface OptionHandler

Overrides:

defineOptions in class AbstractFileWriter

getQuickInfo

public String getQuickInfo()

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

Specified by:

getQuickInfo in interface Actor

Specified by:

getQuickInfo in interface QuickInfoSupporter

Overrides:

getQuickInfo in class AbstractFileWriter

Returns:

null if no info available, otherwise short string

initialize

protected void initialize()

Initializes the members.

Overrides:

initialize in class AbstractActor

reset

protected void reset()

Initializes the members.

Overrides:

reset in class AbstractActor

outputFileTipText

public String outputFileTipText()

Returns the tip text for this property.

Specified by:

outputFileTipText in interface FileWriter

Specified by:

outputFileTipText in class AbstractFileWriter

Returns:

tip text for this property suitable for displaying in the GUI or for listing the options.

setWriter

public void setWriter(SpreadSheetWriter value)

Sets the writer to use for outputting the plot containers.

Parameters:

value - the writer

getWriter

public SpreadSheetWriter getWriter()

Returns the writer to use for outputting the plot containers.

Returns:

the writer

writerTipText

public String writerTipText()

Returns the tip text for this property.

Returns:

tip text for this property suitable for displaying in the GUI or for listing the options.

pruneBackup

protected void pruneBackup()

Removes entries from the backup.

Overrides:

pruneBackup in class AbstractActor

See Also:

AbstractActor.reset()

backupState

protected Hashtable<String,Object> backupState()

Backs up the current state of the actor before update the variables.

Overrides:

backupState in class AbstractSink

Returns:

the backup

See Also:

AbstractActor.updateVariables(), AbstractActor.restoreState(Hashtable)

restoreState

protected void restoreState(Hashtable<String,Object> state)

Restores the state of the actor before the variables got updated.

Overrides:

restoreState in class AbstractSink

Parameters:

state - the backup of the state to restore from

See Also:

AbstractActor.updateVariables(), AbstractActor.backupState()

accepts

public Class[] accepts()

Returns the class that the consumer accepts.

Returns:

adams.flow.container.SequencePlotterContainer.class

doExecute

protected String doExecute()

Executes the flow item.

Specified by:

doExecute in class AbstractActor

Returns:

null if everything is fine, otherwise error message

wrapUp

public void wrapUp()

Cleans up after the execution has finished. Graphical output is left untouched.

Specified by:

wrapUp in interface Actor

Overrides:

wrapUp in class AbstractSink