Package adams.data.filter

Class Smoothing<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.Smoothing<T>

Type Parameters:

T - the type of data to smooth

All Implemented Interfaces:

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

public class Smoothing<T extends DataContainer>
extends AbstractDatabaseConnectionFilter<T>

A filter that runs a smoothing scheme over the data.

Valid options are:

-D (property: debug)
         If set to true, scheme may output additional info to the console.
 

-smoother <gcms.data.smoothing.AbstractSmoother [options]> (property: smoother)
         The smoothing algorithm to use for smoothing the GC points (abundances)
         of the chromatogram.
         default: gcms.data.smoothing.SlidingWindow -window 20 -measure MEDIAN
 

Default options for gcms.data.smoothing.SlidingWindow (-smoother/smoother):

-D (property: debug)
         If set to true, scheme may output additional info to the console.
 

-window <int> (property: windowSize)
         The window size for determining the 'smoothed' abundances.
         default: 20
 

-measure <MEDIAN|MEAN> (property: measure)
         The measure to use for calculating the 'smoothed' abundances.
         default: MEDIAN
 

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 AbstractSmoother	m_Smoother	the smoothing scheme.

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
Smoothing()

Method Summary

Modifier and Type	Method	Description
void	defineOptions()	Adds options to the internal list of options.
protected AbstractDatabaseConnection	getDefaultDatabaseConnection()	Returns the default database connection.
AbstractSmoother	getSmoother()	Returns the current smoothing algorithm.
String	globalInfo()	Returns a string describing the object.
protected T	processData(T data)	Performs the actual filtering.
void	setSmoother(AbstractSmoother value)	Sets the smoothing algorithm.
String	smootherTipText()	Returns the tip text for this property.
protected void	updateDatabaseConnection()	Updates the database connection in the smoother.

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.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_Smoother

protected AbstractSmoother m_Smoother

the smoothing scheme.

Constructor Detail

Smoothing

public Smoothing()

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

setSmoother

public void setSmoother(AbstractSmoother value)

Sets the smoothing algorithm.

Parameters:

value - the algorithm

getSmoother

public AbstractSmoother getSmoother()

Returns the current smoothing algorithm.

Returns:

the algorithm

smootherTipText

public String smootherTipText()

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 smoother.

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