Package adams.gui.visualization.sequence.metadatacolor

Class Density

java.lang.Object

adams.core.logging.LoggingObject

adams.core.logging.CustomLoggingLevelObject

adams.core.option.AbstractOptionHandler

adams.gui.visualization.sequence.metadatacolor.AbstractMetaDataColor<XYSequencePoint>

adams.gui.visualization.sequence.metadatacolor.Density

All Implemented Interfaces:

Destroyable, GlobalInfoSupporter, LoggingLevelHandler, LoggingSupporter, OptionHandler, SizeOfHandler, Serializable

public class Density
extends AbstractMetaDataColor<XYSequencePoint>

Generates colors based on the point density in the grid of numBins x numBins bins.

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	Density.Mode	The mode for calculating the density.
static class	Density.RenderState	The rendering state.

Field Summary

Fields

Modifier and Type	Field	Description
protected double	m_Bandwidth	the bandwidth.
protected Map<DataContainer,Density.RenderState>	m_Cache	the cached states.
protected ColorGradientGenerator	m_Generator	the generator to use.
protected Density.Mode	m_Mode	the mode to use.
protected int	m_NumBins	the number of bins to generate on X and Y.

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
Density()

Method Summary

Modifier and Type	Method	Description
String	bandwidthTipText()	Returns the tip text for this property.
void	defineOptions()	Adds options to the internal list of options.
String	generatorTipText()	Returns the tip text for this property.
double	getBandwidth()	Returns the bandwidth for kernel density estimates.
Color	getColor(XYSequencePoint point, Color defColor)	Extracts the color from the meta-data.
ColorGradientGenerator	getGenerator()	Returns the color generator.
Density.Mode	getMode()	Returns the mode to use.
int	getNumBins()	Returns the number of bins to generate on X and Y axis.
String	globalInfo()	Returns a string describing the object.
void	initialize(List<XYSequencePoint> points)	Initializes the meta-data color scheme.
String	modeTipText()	Returns the tip text for this property.
String	numBinsTipText()	Returns the tip text for this property.
protected void	reset()	Resets the scheme.
void	setBandwidth(double value)	Sets the bandwidth for kernel density estimates.
void	setGenerator(ColorGradientGenerator value)	Sets the color generator.
void	setMode(Density.Mode value)	Sets the mode to use.
void	setNumBins(int value)	Sets the number of bins to generate on X and Y axis.

Methods inherited from class adams.core.option.AbstractOptionHandler

cleanUpOptions, destroy, finishInit, getDefaultLoggingLevel, getOptionManager, 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, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface adams.core.logging.LoggingLevelHandler

getLoggingLevel

Field Detail

m_Mode

protected Density.Mode m_Mode

the mode to use.

m_NumBins

protected int m_NumBins

the number of bins to generate on X and Y.

m_Bandwidth

protected double m_Bandwidth

the bandwidth.

m_Generator

protected ColorGradientGenerator m_Generator

the generator to use.

m_Cache

protected transient Map<DataContainer,Density.RenderState> m_Cache

the cached states.

Constructor Detail

Density

public Density()

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 AbstractOptionHandler

reset

protected void reset()

Resets the scheme.

Overrides:

reset in class AbstractOptionHandler

setMode

public void setMode(Density.Mode value)

Sets the mode to use.

Parameters:

value - the mode

getMode

public Density.Mode getMode()

Returns the mode to use.

Returns:

the mode

modeTipText

public String modeTipText()

Returns the tip text for this property.

Returns:

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

setNumBins

public void setNumBins(int value)

Sets the number of bins to generate on X and Y axis.

Parameters:

value - the number of bins

getNumBins

public int getNumBins()

Returns the number of bins to generate on X and Y axis.

Returns:

the number of bins

numBinsTipText

public String numBinsTipText()

Returns the tip text for this property.

Returns:

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

setBandwidth

public void setBandwidth(double value)

Sets the bandwidth for kernel density estimates.

Parameters:

value - the bandwidth

getBandwidth

public double getBandwidth()

Returns the bandwidth for kernel density estimates.

Returns:

the bandwidth

bandwidthTipText

public String bandwidthTipText()

Returns the tip text for this property.

Returns:

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

setGenerator

public void setGenerator(ColorGradientGenerator value)

Sets the color generator.

Parameters:

value - the generator

getGenerator

public ColorGradientGenerator getGenerator()

Returns the color generator.

Returns:

the generator

generatorTipText

public String generatorTipText()

Returns the tip text for this property.

Returns:

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

initialize

public void initialize(List<XYSequencePoint> points)

Initializes the meta-data color scheme.

Specified by:

initialize in class AbstractMetaDataColor<XYSequencePoint>

Parameters:

points - the points to initialize with

getColor

public Color getColor(XYSequencePoint point,
                      Color defColor)

Extracts the color from the meta-data.

Specified by:

getColor in class AbstractMetaDataColor<XYSequencePoint>

Parameters:

point - the point to get the color from

defColor - the default color to use

Returns:

the color