net.maizegenetics.analysis.imputation

Class CallParentAllelesPlugin

AbstractPlugin

net.maizegenetics.analysis.imputation.CallParentAllelesPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class CallParentAllelesPlugin
extends AbstractPlugin

Constructor Detail

CallParentAllelesPlugin

public CallParentAllelesPlugin(java.awt.Frame parentFrame)

Method Detail

performFunction

public DataSet performFunction(DataSet input)

setParameters

public void setParameters(java.lang.String[] args)

setPedfileName

public void setPedfileName(java.lang.String pedfileName)

setWindowSize

public void setWindowSize(int windowSize)

setMinRforSnps

public void setMinRforSnps(double minRforSnps)

setMaxDifference

public void setMaxDifference(int maxDifference)

setMinUsedClusterSize

public void setMinUsedClusterSize(int minUsedClusterSize)

setCheckSubPops

public void setCheckSubPops(boolean checkSubPops)

setMaxMissing

public void setMaxMissing(double maxMissing)

setMinMinorAlleleFrequency

public void setMinMinorAlleleFrequency(double minMinorAlleleFrequency)

setUseBCFilter

public void setUseBCFilter(boolean useBCFilter)

setUseMultipleBCFilter

public void setUseMultipleBCFilter(boolean useMultipleBCFilter)

setUseClusterAlgorithm

public void setUseClusterAlgorithm(boolean useClusterAlgorithm)

setUseHets

public void setUseHets(boolean useHets)

setUseWindowLD

public void setUseWindowLD(boolean useWindowLD)

setMaxHetDev

public void setMaxHetDev(double maxHetDev)

setOverlap

public void setOverlap(int overlap)

setLogFile

public void setLogFile(java.lang.String logname)

includeParents

public void includeParents(boolean include)

haplotypesFromParents

public void haplotypesFromParents(boolean useparents)

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

getToolTipText

public java.lang.String getToolTipText()

getUsage

public java.lang.String getUsage()

setFamilyList

public void setFamilyList(java.util.ArrayList<net.maizegenetics.analysis.imputation.PopulationData> familyList)