net.maizegenetics.analysis.popgen

Class LinkageDisequilibriumPlugin

AbstractPlugin

net.maizegenetics.analysis.popgen.LinkageDisequilibriumPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class LinkageDisequilibriumPlugin
extends AbstractPlugin

Constructor Detail

LinkageDisequilibriumPlugin

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

Creates a new instance of LinkageDisequilibriumPlugin

Method Detail

performFunction

public DataSet performFunction(DataSet input)

Workhorse function to actually run LD on a dataset

Parameters:

input - A DataSet containing one or more GenotypeTable objects

Returns:

org.jetbrains.dokka.NodeRenderContent@43b1f237: The input DataSet with the LinkageDisequilibrium object(s) added

isRapidAnalysis

public boolean isRapidAnalysis()

setRapidAnalysis

public void setRapidAnalysis(boolean rapidAnalysis)

isPermutationNumber

public int isPermutationNumber()

setPermutationNumber

public void setPermutationNumber(int permutationNumber)

setLDType

public void setLDType(net.maizegenetics.analysis.popgen.LinkageDisequilibrium.testDesign type)

getLDType

public net.maizegenetics.analysis.popgen.LinkageDisequilibrium.testDesign getLDType()

setWinSize

public void setWinSize(int winSize)

getWinSize

public int getWinSize()

setNumAccumulateIntervals

public void setNumAccumulateIntervals(int numIntervals)

getNumAccumulateIntervals

public int getNumAccumulateIntervals()

setIsAccumulateResults

public void setIsAccumulateResults(boolean accumulate)

getIsAccumulateResults

public boolean getIsAccumulateResults()

setTestSite

public void setTestSite(int site)

getTestSite

public int getTestSite()

setTestSiteName

public void setTestSiteName(java.lang.String siteName)

getTestSiteName

public java.lang.String getTestSiteName()

setHetTreatment

public void setHetTreatment(net.maizegenetics.analysis.popgen.LinkageDisequilibrium.HetTreatment treatment)

getHetTreatment

public net.maizegenetics.analysis.popgen.LinkageDisequilibrium.HetTreatment getHetTreatment()

getIcon

public javax.swing.ImageIcon getIcon()

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

Returns:

org.jetbrains.dokka.NodeRenderContent@69be952e: ImageIcon

getButtonName

public java.lang.String getButtonName()

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

Returns:

org.jetbrains.dokka.NodeRenderContent@46e279f5: String

getToolTipText

public java.lang.String getToolTipText()

Tool Tip Text for this plugin

Returns:

org.jetbrains.dokka.NodeRenderContent@7e136af6: String