Package adams.data.filter

Class OutlierDetector<T extends DataContainer>

java.lang.Object

adams.core.logging.LoggingObject

adams.core.logging.CustomLoggingLevelObject

adams.core.option.AbstractOptionHandler

adams.data.filter.AbstractFilter<T>

adams.data.filter.AbstractDatabaseConnectionFilter<T>

adams.data.filter.OutlierDetector<T>

Type Parameters:

T - the type of data to pass through the filter

All Implemented Interfaces:

CleanUpHandler, Destroyable, GlobalInfoSupporter, LoggingLevelHandler, LoggingSupporter, OptionHandler, ShallowCopySupporter<Filter>, SizeOfHandler, BatchFilter<T>, Filter<T>, TrainableBatchFilter<T>, DatabaseConnectionHandler, DatabaseConnectionProvider, DatabaseConnectionUser, Serializable, Comparable

public class OutlierDetector<T extends DataContainer>
extends AbstractDatabaseConnectionFilter<T>
implements TrainableBatchFilter<T>

A filter that runs an outlier detector over the data and attaches the generated detections as notes to the chromatogram.

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
 

-detector <adams.data.outlier.AbstractOutlierDetector [options]> (property: detector)
    The outlier detector to use (the detections generated by the algorithm get
    attached to the chromatogram).
    default: adams.data.outlier.PassThrough
 

-only-warning (property: onlyWarning)
    If enabled, the detections get added merely as warnings instead of as errors.
 

Version:

$Revision$

Author:

fracpete (fracpete at waikato dot ac dot nz)

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class adams.data.filter.AbstractFilter

AbstractFilter.FilterJob<T extends DataContainer>

Field Summary

Fields

Modifier and Type	Field	Description
protected boolean	m_OnlyWarning	whether the detection is only added as warning instead of error.
protected AbstractOutlierDetector	m_OutlierDetector	the detector algorithm.

Fields inherited from class adams.data.filter.AbstractDatabaseConnectionFilter

m_DatabaseConnection

Fields inherited from class adams.data.filter.AbstractFilter

m_DontUpdateID

Fields inherited from class adams.core.option.AbstractOptionHandler

m_OptionManager

Fields inherited from class adams.core.logging.LoggingObject

m_Logger, m_LoggingIsEnabled, m_LoggingLevel

Constructor Summary

Constructors

Constructor	Description
OutlierDetector()

Method Summary

Modifier and Type	Method	Description
T[]	batchFilter(T[] data)	Batch filters the data.
void	defineOptions()	Adds options to the internal list of options.
String	detectorTipText()	Returns the tip text for this property.
protected AbstractDatabaseConnection	getDefaultDatabaseConnection()	Returns the default database connection.
AbstractOutlierDetector	getDetector()	Returns the current outlier detector.
boolean	getOnlyWarning()	Returns whether the detections are added as error or warning.
String	globalInfo()	Returns a string describing the object.
boolean	isTrained()	Returns whether the filter has been trained already and is ready to use.
String	onlyWarningTipText()	Returns the tip text for this property.
protected T	processData(T data)	Performs the actual filtering.
void	resetFilter()	Resets the filter, i.e., flags it as "not trained".
void	setDetector(AbstractOutlierDetector value)	Sets the outlier detector.
void	setOnlyWarning(boolean value)	Sets whether the detections are added as error or warning.
void	trainFilter(T[] data)	Trains the filter with the specified data.
protected void	updateDatabaseConnection()	Updates the database connection in the outlier detectors.

Methods inherited from class adams.data.filter.AbstractDatabaseConnectionFilter

getDatabaseConnection, initialize, setDatabaseConnection

Methods inherited from class adams.data.filter.AbstractFilter

checkData, cleanUp, compareTo, destroy, dontUpdateIDTipText, equals, filter, forCommandLine, getDontUpdateID, reset, setDontUpdateID, shallowCopy, shallowCopy

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

configureLogger, getLogger, getLoggingLevel, initializeLogging, isLoggingEnabled, sizeOf

Methods inherited from class java.lang.Object

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

Methods inherited from interface adams.data.filter.Filter

cleanUp, compareTo, destroy, dontUpdateIDTipText, equals, filter, getDontUpdateID, reset, setDontUpdateID, shallowCopy, shallowCopy

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, toCommandLine

Field Detail

m_OutlierDetector

protected AbstractOutlierDetector m_OutlierDetector

the detector algorithm.

m_OnlyWarning

protected boolean m_OnlyWarning

whether the detection is only added as warning instead of error.

Constructor Detail

OutlierDetector

public OutlierDetector()

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 AbstractFilter<T extends DataContainer>

getDefaultDatabaseConnection

protected AbstractDatabaseConnection getDefaultDatabaseConnection()

Returns the default database connection.

Specified by:

getDefaultDatabaseConnection in class AbstractDatabaseConnectionFilter<T extends DataContainer>

Returns:

the default database connection

setDetector

public void setDetector(AbstractOutlierDetector value)

Sets the outlier detector.

Parameters:

value - the algorithm

getDetector

public AbstractOutlierDetector getDetector()

Returns the current outlier detector.

Returns:

the algorithm

detectorTipText

public String detectorTipText()

Returns the tip text for this property.

Returns:

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

setOnlyWarning

public void setOnlyWarning(boolean value)

Sets whether the detections are added as error or warning.

Parameters:

value - if true then the detections are added as warning instead of as error

getOnlyWarning

public boolean getOnlyWarning()

Returns whether the detections are added as error or warning.

Returns:

true if the detections get added as warning instead of as error

onlyWarningTipText

public String onlyWarningTipText()

Returns the tip text for this property.

Returns:

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

updateDatabaseConnection

protected void updateDatabaseConnection()

Updates the database connection in the outlier detectors.

Overrides:

updateDatabaseConnection in class AbstractDatabaseConnectionFilter<T extends DataContainer>

processData

protected T processData(T data)

Performs the actual filtering.

Specified by:

processData in class AbstractFilter<T extends DataContainer>

Parameters:

data - the data to filter

Returns:

the filtered data

resetFilter

public void resetFilter()

Resets the filter, i.e., flags it as "not trained".

Specified by:

resetFilter in interface TrainableBatchFilter<T extends DataContainer>

See Also:

isTrained()

trainFilter

public void trainFilter(T[] data)

Trains the filter with the specified data.

Specified by:

trainFilter in interface TrainableBatchFilter<T extends DataContainer>

isTrained

public boolean isTrained()

Returns whether the filter has been trained already and is ready to use.

Specified by:

isTrained in interface TrainableBatchFilter<T extends DataContainer>

Returns:

true if already trained

batchFilter

public T[] batchFilter(T[] data)

Batch filters the data.

Specified by:

batchFilter in interface BatchFilter<T extends DataContainer>

Parameters:

data - the data to filter

Returns:

the filtered data