net.maizegenetics.analysis.numericaltransform

Class TransformDataPlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.analysis.numericaltransform.TransformDataPlugin

All Implemented Interfaces:

Runnable, Plugin, PluginListener, ProgressListener

public class TransformDataPlugin
extends AbstractPlugin

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	TransformDataPlugin.BASE

Field Summary

Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin

DEFAULT_CITATION, POSITION_LIST_NONE, TAXA_LIST_NONE

Constructor Summary

Constructors

Constructor and Description
TransformDataPlugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
String	getButtonName() Button name for this plugin to be used in buttons, etc.
ImageIcon	getIcon() Icon for this plugin to be used in buttons, etc.
String	getToolTipText() Tool Tip Text for this plugin
String	getUsage() Gets the Usage Statement for this Plugin.
NumericAttribute	logTransform(NumericAttribute original)
float[]	meanStdDev(float[] data)
NumericAttribute	powerTransform(NumericAttribute original)
DataSet	processData(DataSet input) For the new Generic Plugin Parameter design, performFunction() will automatically call this.
void	setByFactor(List<CategoricalAttribute> byFactor)
void	setFactors(String namelist)
void	setLogTransform(boolean logTransform)
void	setMyBase(TransformDataPlugin.BASE myBase)
void	setParameters(String[] args) Allows self-describing Plugins to use args to set parameters specific to itself.
void	setPower(double power)
void	setPowerTransform(boolean powerTransform)
void	setStandardize(boolean standardize)
void	setTraits(String namelist)
void	setTraitsToTransform(List<NumericAttribute> traitsToTransform)
NumericAttribute	standardize(NumericAttribute original)
NumericAttribute	standardize(NumericAttribute original, List<CategoricalAttribute> byFactors)
List<int[]>	subsets(List<CategoricalAttribute> byFactors)
PhenotypeAttribute	transformAttribute(PhenotypeAttribute myAttribute)
DataSet	transformTraits(Phenotype myPhenotype, Datum myData)

Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin

addListener, cancel, convert, dataSetReturned, getCitation, getInputs, getMenu, getPanel, getParameter, getParameter, getParentFrame, getUsageHTML, isInteractive, performFunction, pluginDescription, pluginUserManualURL, progress, progress, receiveInput, reverseTrace, run, setConfigParameters, setParameter, setParameter, setParameter, setParametersToDefault, setThreaded, trace, wasCancelled

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface net.maizegenetics.plugindef.Plugin

getPluginInstance, getPluginInstance, isPlugin

Constructor Detail

TransformDataPlugin

public TransformDataPlugin(Frame parentFrame,
                           boolean isInteractive)

Method Detail

processData

public DataSet processData(DataSet input)

Description copied from interface: Plugin

For the new Generic Plugin Parameter design, performFunction() will automatically call this. Therefore, coders of Plugins should override this instead of performFunction().

Specified by:

processData in interface Plugin

Overrides:

processData in class AbstractPlugin

Parameters:

input - input

Returns:

resulting data set or null.

transformTraits

public DataSet transformTraits(Phenotype myPhenotype,
                               Datum myData)

transformAttribute

public PhenotypeAttribute transformAttribute(PhenotypeAttribute myAttribute)

getIcon

public ImageIcon getIcon()

Description copied from interface: Plugin

Icon for this plugin to be used in buttons, etc.

Returns:

ImageIcon

getButtonName

public String getButtonName()

Description copied from interface: Plugin

Button name for this plugin to be used in buttons, etc.

Returns:

String

getToolTipText

public String getToolTipText()

Description copied from interface: Plugin

Tool Tip Text for this plugin

Returns:

String

powerTransform

public NumericAttribute powerTransform(NumericAttribute original)

logTransform

public NumericAttribute logTransform(NumericAttribute original)

standardize

public NumericAttribute standardize(NumericAttribute original)

meanStdDev

public float[] meanStdDev(float[] data)

standardize

public NumericAttribute standardize(NumericAttribute original,
                                    List<CategoricalAttribute> byFactors)

subsets

public List<int[]> subsets(List<CategoricalAttribute> byFactors)

setParameters

public void setParameters(String[] args)

Description copied from interface: Plugin

Allows self-describing Plugins to use args to set parameters specific to itself.

Specified by:

setParameters in interface Plugin

Overrides:

setParameters in class AbstractPlugin

Parameters:

args - arguments

getUsage

public String getUsage()

Description copied from interface: Plugin

Gets the Usage Statement for this Plugin.

Specified by:

getUsage in interface Plugin

Overrides:

getUsage in class AbstractPlugin

Returns:

Usage Statement

setTraits

public void setTraits(String namelist)

setFactors

public void setFactors(String namelist)

setTraitsToTransform

public void setTraitsToTransform(List<NumericAttribute> traitsToTransform)

setByFactor

public void setByFactor(List<CategoricalAttribute> byFactor)

setLogTransform

public void setLogTransform(boolean logTransform)

setPowerTransform

public void setPowerTransform(boolean powerTransform)

setStandardize

public void setStandardize(boolean standardize)

setMyBase

public void setMyBase(TransformDataPlugin.BASE myBase)

setPower

public void setPower(double power)