net.maizegenetics.analysis.distance

Class HMatrixPlugin

AbstractPlugin

net.maizegenetics.analysis.distance.HMatrixPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class HMatrixPlugin
extends AbstractPlugin

Constructor Detail

HMatrixPlugin

public HMatrixPlugin(java.awt.Frame parentFrame,
                     boolean isInteractive)

Method Detail

processData

public DataSet processData(DataSet input)

aMatrix

public DistanceMatrix aMatrix()

Pedigree Matrix

Returns:

org.jetbrains.dokka.NodeRenderContent@44c21e2d: Pedigree Matrix

aMatrix

public HMatrixPlugin aMatrix(DistanceMatrix value)

Set Pedigree Matrix. Pedigree Matrix

Parameters:

value - Pedigree Matrix

Returns:

org.jetbrains.dokka.NodeRenderContent@6ecd5619: this plugin

gMatrix

public DistanceMatrix gMatrix()

Kinship Matrix

Returns:

org.jetbrains.dokka.NodeRenderContent@18bb0f55: Kinship Matrix

gMatrix

public HMatrixPlugin gMatrix(DistanceMatrix value)

Set Kinship Matrix. Kinship Matrix

Parameters:

value - Kinship Matrix

Returns:

org.jetbrains.dokka.NodeRenderContent@1d10c0c3: this plugin

weight

public java.lang.Double weight()

Weight

Returns:

org.jetbrains.dokka.NodeRenderContent@49f7863a: Weight

weight

public HMatrixPlugin weight(java.lang.Double value)

Set Weight. Weight

Parameters:

value - Weight

Returns:

org.jetbrains.dokka.NodeRenderContent@4d0e7c83: 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:

org.jetbrains.dokka.NodeRenderContent@d8f13d0: Combined matrix based on aInverse and gInverse

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

getToolTipText

public java.lang.String getToolTipText()

getCitation

public java.lang.String getCitation()