net.maizegenetics.analysis.distance

Class HMatrixPlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.analysis.distance.HMatrixPlugin

All Implemented Interfaces:

Runnable, Plugin, PluginListener, ProgressListener

public class HMatrixPlugin
extends AbstractPlugin

Author:

Josh Lamos-Sweeney, Yaw Nti-Addae, Kelly Robbins, Terry Casstevens

Field Summary

Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin

DEFAULT_CITATION, POSITION_LIST_NONE, TAXA_LIST_NONE

Constructor Summary

Constructors

Constructor and Description
HMatrixPlugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
DistanceMatrix	aMatrix() Pedigree Matrix
HMatrixPlugin	aMatrix(DistanceMatrix value) Set Pedigree Matrix.
static DistanceMatrix	generateCombinedMatrix(DistanceMatrix aInverse, DistanceMatrix gStarInverse) Given the inverse of an A matrix (Pedigree Kinship matrix) and a G Matrix (Genetic Kinship Matrix) which contains mostly entries in the A Matrix creates a combined (H) matrix.
String	getButtonName() Button name for this plugin to be used in buttons, etc.
String	getCitation() Returns Citation for this plugin.
ImageIcon	getIcon() Icon for this plugin to be used in buttons, etc.
String	getToolTipText() Tool Tip Text for this plugin
DistanceMatrix	gMatrix() Kinship Matrix
HMatrixPlugin	gMatrix(DistanceMatrix value) Set Kinship Matrix.
DataSet	processData(DataSet input) For the new Generic Plugin Parameter design, performFunction() will automatically call this.
Double	weight() Weight
HMatrixPlugin	weight(Double value) Set Weight.

Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin

addListener, cancel, convert, dataSetReturned, getInputs, getMenu, getPanel, getParameter, getParameter, getParentFrame, getUsage, getUsageHTML, isInteractive, performFunction, pluginDescription, pluginUserManualURL, progress, progress, receiveInput, reverseTrace, run, setConfigParameters, setParameter, setParameter, setParameter, setParameters, 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

HMatrixPlugin

public HMatrixPlugin(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.

aMatrix

public DistanceMatrix aMatrix()

Pedigree Matrix

Returns:

Pedigree Matrix

aMatrix

public HMatrixPlugin aMatrix(DistanceMatrix value)

Set Pedigree Matrix. Pedigree Matrix

Parameters:

value - Pedigree Matrix

Returns:

this plugin

gMatrix

public DistanceMatrix gMatrix()

Kinship Matrix

Returns:

Kinship Matrix

gMatrix

public HMatrixPlugin gMatrix(DistanceMatrix value)

Set Kinship Matrix. Kinship Matrix

Parameters:

value - Kinship Matrix

Returns:

this plugin

weight

public Double weight()

Weight

Returns:

Weight

weight

public HMatrixPlugin weight(Double value)

Set Weight. Weight

Parameters:

value - Weight

Returns:

this plugin

generateCombinedMatrix

public static DistanceMatrix generateCombinedMatrix(DistanceMatrix aInverse,
                                                    DistanceMatrix gStarInverse)

Given the inverse of an A matrix (Pedigree Kinship matrix) and a G Matrix (Genetic Kinship Matrix) which contains mostly entries in the A Matrix creates a combined (H) matrix.

Parameters:

aInverse - Inverted Pedigree kinship(A) matrix

gStarInverse - Inverted and weighted kinship(G*) matrix. Should contain mostly Taxa in common with A matrix for best results

Returns:

Combined matrix based on aInverse and gInverse

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

getCitation

public String getCitation()

Description copied from interface: Plugin

Returns Citation for this plugin.

Specified by:

getCitation in interface Plugin

Overrides:

getCitation in class AbstractPlugin

Returns:

Citation