Package adams.data.filter

Class BaselineCorrection<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.BaselineCorrection<T>

Type Parameters:

T - the type of data to process

All Implemented Interfaces:

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

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

A filter that runs a baseline correction scheme over the data.

Valid options are:

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

-baseline <adams.data.baseline.AbstractBaselineCorrection [options]> (property: baselineCorrection)
    The baseline correction algorithm to use for correcting the baseline of
    the data.
    default: adams.data.baseline.PassThrough
 

Default options for adams.data.baseline.PassThrough (-baseline/baselineCorrection):

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

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 AbstractBaselineCorrection	m_BaselineCorrection	the baseline correction 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
BaselineCorrection()

Method Summary

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

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_BaselineCorrection

protected AbstractBaselineCorrection m_BaselineCorrection

the baseline correction algorithm.

Constructor Detail

BaselineCorrection

public BaselineCorrection()

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

setBaselineCorrection

public void setBaselineCorrection(AbstractBaselineCorrection value)

Sets the baseline correction algorithm.

Parameters:

value - the algorithm

getBaselineCorrection

public AbstractBaselineCorrection getBaselineCorrection()

Returns the current baseline correction algorithm.

Returns:

the algorithm

baselineCorrectionTipText

public String baselineCorrectionTipText()

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 baseline correction.

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