net.maizegenetics.analysis.association

Class MLMPlugin

AbstractPlugin

net.maizegenetics.analysis.association.MLMPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

Direct Known Subclasses:

WeightedMLMPlugin

public class MLMPlugin
extends AbstractPlugin

Field Detail

kinshipMatrix

protected DistanceMatrix kinshipMatrix

analyzeByColumn

protected boolean analyzeByColumn

useP3D

protected boolean useP3D

compressionType

protected net.maizegenetics.analysis.association.MLMPlugin.CompressionType compressionType

compression

protected double compression

Constructor Detail

MLMPlugin

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

Method Detail

isUseP3D

public boolean isUseP3D()

setUseP3D

public void setUseP3D(boolean useP3D)

isUseGenotype

public boolean isUseGenotype()

setUseGenotype

public void setUseGenotype(boolean useGenotype)

isUseRefProb

public boolean isUseRefProb()

setUseRefProb

public void setUseRefProb(boolean useRefProb)

processData

public DataSet processData(DataSet input)

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

getToolTipText

public java.lang.String getToolTipText()

setAnalyzeByColumn

public void setAnalyzeByColumn(boolean analyzeByColumn)

setMaximumNumOfIteration

public void setMaximumNumOfIteration(int max)

setFinalIterMarker

public void setFinalIterMarker(boolean myFinalIterMarker)

addFactors

public void addFactors(kotlin.Array[] factors)

setColumnTypes

public void setColumnTypes(java.lang.String[] types)

addFactors

public void addFactors(java.lang.String[] names)

updateProgress

public void updateProgress(int progress)

setVarCompEst

public void setVarCompEst(java.lang.String value)

setCompressionType

public void setCompressionType(net.maizegenetics.analysis.association.MLMPlugin.CompressionType type)

isWriteOutputToFile

public boolean isWriteOutputToFile()

setWriteOutputToFile

public void setWriteOutputToFile(boolean writeOutputToFile)

getOutputName

public java.lang.String getOutputName()

setOutputName

public void setOutputName(java.lang.String outputName)

isFilterOutput

public boolean isFilterOutput()

setFilterOutput

public void setFilterOutput(boolean filterOutput)

getMaxp

public double getMaxp()

setMaxp

public void setMaxp(double maxp)

getCustomCompression

public double getCustomCompression()

setCustomCompression

public void setCustomCompression(double value)

useGenotypeCalls

public void useGenotypeCalls()

useReferenceProbability

public void useReferenceProbability()

useAlleleProbabilities

public void useAlleleProbabilities()