Package adams.data.noise

Class AbstractDenoiser<T extends DataContainer>

java.lang.Object

adams.core.logging.LoggingObject

adams.core.logging.CustomLoggingLevelObject

adams.core.option.AbstractOptionHandler

adams.data.noise.AbstractDenoiser<T>

Type Parameters:

T - the type of data the denoiser is handling

All Implemented Interfaces:

CleanUpHandler, Destroyable, GlobalInfoSupporter, LoggingLevelHandler, LoggingSupporter, OptionHandler, ShallowCopySupporter<AbstractDenoiser>, SizeOfHandler, RegionRecorder<T>, Serializable, Comparable

Direct Known Subclasses:

AbstractDatabaseConnectionDenoiser, PassThrough

public abstract class AbstractDenoiser<T extends DataContainer>
extends AbstractOptionHandler
implements RegionRecorder<T>, Comparable, CleanUpHandler, ShallowCopySupporter<AbstractDenoiser>

An abstract super class for algorithms that remove noise from data.

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	AbstractDenoiser.DenoiserJob<T extends DataContainer>	A job class specific to denoisers.

Field Summary

Fields

Modifier and Type	Field	Description
protected boolean	m_RecordRegions	whether to record elution regions as well.
protected List<T>	m_Regions	the collected elution regions.

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
AbstractDenoiser()

Method Summary

Modifier and Type	Method	Description
protected void	checkData(T data)	The default implementation only checks whether there is any data set.
void	cleanUp()	Cleans up data structures, frees up memory.
int	compareTo(Object o)	Compares this object with the specified object for order.
void	defineOptions()	Adds options to the internal list of options.
T	denoise(T data)	Returns the denoised data.
void	destroy()	Frees up memory in a "destructive" non-reversible way.
boolean	equals(Object o)	Returns whether the two objects are the same.
static AbstractDenoiser	forCommandLine(String cmdline)	Instantiates the denoiser algorithm from the given commandline (i.e., classname and optional options).
static AbstractDenoiser	forName(String classname, String[] options)	Instantiates the denoiser algorithm with the given options.
static String[]	getDenoisers()	Returns a list with classnames of denoiser algorithms.
boolean	getRecordRegions()	Returns whether noisy regions are recorded.
List<T>	getRegions()	Returns the noisy regions that were recorded.
protected T	postprocessData(T original, T denoised)	Post-processes the data.
protected abstract T	processData(T data)	Performs the actual denoising.
String	recordRegionsTipText()	Returns the tip text for this property.
protected void	reset()	Resets the noise algorithm.
void	setRecordRegions(boolean value)	Sets whether the noisy regions are recorded as well.
AbstractDenoiser	shallowCopy()	Returns a shallow copy of itself, i.e., based on the commandline options.
AbstractDenoiser	shallowCopy(boolean expand)	Returns a shallow copy of itself, i.e., based on the commandline options.
String	toStringRegions()	Turns the recorded regions as a string.

Methods inherited from class adams.core.option.AbstractOptionHandler

cleanUpOptions, finishInit, getDefaultLoggingLevel, getOptionManager, globalInfo, initialize, 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

Field Detail

m_RecordRegions

protected boolean m_RecordRegions

whether to record elution regions as well.

m_Regions

protected List<T extends DataContainer> m_Regions

the collected elution regions.

Constructor Detail

AbstractDenoiser

public AbstractDenoiser()

Method Detail

reset

protected void reset()

Resets the noise algorithm. Derived classes must call this method in set-methods of parameters to assure the invalidation of previously generated data.

Overrides:

reset in class AbstractOptionHandler

cleanUp

public void cleanUp()

Cleans up data structures, frees up memory. Sets the input data to null.

Specified by:

cleanUp in interface CleanUpHandler

destroy

public void destroy()

Frees up memory in a "destructive" non-reversible way.

Calls cleanUp() and cleans up the options.

Specified by:

destroy in interface Destroyable

Overrides:

destroy in class AbstractOptionHandler

See Also:

AbstractOptionHandler.cleanUpOptions()

defineOptions

public void defineOptions()

Adds options to the internal list of options.

Specified by:

defineOptions in interface OptionHandler

Overrides:

defineOptions in class AbstractOptionHandler

setRecordRegions

public void setRecordRegions(boolean value)

Sets whether the noisy regions are recorded as well.

Specified by:

setRecordRegions in interface RegionRecorder<T extends DataContainer>

Parameters:

value - if true the regions will be recorded

See Also:

getRegions()

getRecordRegions

public boolean getRecordRegions()

Returns whether noisy regions are recorded.

Specified by:

getRecordRegions in interface RegionRecorder<T extends DataContainer>

Returns:

true if the regions are recorded

See Also:

getRegions()

recordRegionsTipText

public String recordRegionsTipText()

Returns the tip text for this property.

Specified by:

recordRegionsTipText in interface RegionRecorder<T extends DataContainer>

Returns:

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

getRegions

public List<T> getRegions()

Returns the noisy regions that were recorded.

Specified by:

getRegions in interface RegionRecorder<T extends DataContainer>

Returns:

the regions

See Also:

m_RecordRegions

checkData

protected void checkData(T data)

The default implementation only checks whether there is any data set.

Parameters:

data - the data to process

processData

protected abstract T processData(T data)

Performs the actual denoising.

Parameters:

data - the data to process

Returns:

the denoised data

postprocessData

protected T postprocessData(T original,
                            T denoised)

Post-processes the data.

Default implementation only returns the denoised data as it is.

Parameters:

original - the original input data

denoised - the denoised data

Returns:

the postprocessed data

denoise

public T denoise(T data)

Returns the denoised data.

Parameters:

data - the data to denoise

Returns:

the denoised data

toStringRegions

public String toStringRegions()

Turns the recorded regions as a string.

Returns:

the regions

compareTo

public int compareTo(Object o)

Compares this object with the specified object for order. Returns a negative integer, zero, or a positive integer as this object is less than, equal to, or greater than the specified object.

Only compares the commandlines of the two objects.

Specified by:

compareTo in interface Comparable<T extends DataContainer>

Parameters:

o - the object to be compared.

Returns:

a negative integer, zero, or a positive integer as this object is less than, equal to, or greater than the specified object.

Throws:

ClassCastException - if the specified object's type prevents it from being compared to this object.

equals

public boolean equals(Object o)

Returns whether the two objects are the same.

Only compares the commandlines of the two objects.

Overrides:

equals in class Object

Parameters:

o - the object to be compared

Returns:

true if the object is the same as this one

shallowCopy

public AbstractDenoiser shallowCopy()

Returns a shallow copy of itself, i.e., based on the commandline options.

Specified by:

shallowCopy in interface ShallowCopySupporter<T extends DataContainer>

Returns:

the shallow copy

shallowCopy

public AbstractDenoiser shallowCopy(boolean expand)

Returns a shallow copy of itself, i.e., based on the commandline options.

Specified by:

shallowCopy in interface ShallowCopySupporter<T extends DataContainer>

Parameters:

expand - whether to expand variables to their current values

Returns:

the shallow copy

getDenoisers

public static String[] getDenoisers()

Returns a list with classnames of denoiser algorithms.

Returns:

the denoiser algorithm classnames

forName

public static AbstractDenoiser forName(String classname,
                                       String[] options)

Instantiates the denoiser algorithm with the given options.

Parameters:

classname - the classname of the denoiser algorithm to instantiate

options - the options for the denoiser algorithm

Returns:

the instantiated denoiser algorithm or null if an error occurred

forCommandLine

public static AbstractDenoiser forCommandLine(String cmdline)

Instantiates the denoiser algorithm from the given commandline (i.e., classname and optional options).

Parameters:

cmdline - the classname (and optional options) of the denoiser algorithm to instantiate

Returns:

the instantiated denoiser algorithm or null if an error occurred