Package 

Class CompareToKnownSNPPlugin

  • All Implemented Interfaces:
    java.lang.Runnable , net.maizegenetics.plugindef.Plugin , net.maizegenetics.plugindef.PluginListener , net.maizegenetics.util.ProgressListener 
    
public class CompareToKnownSNPPlugin
extends AbstractPlugin

    Plugin to compare A GenotypeTable to a known trusted GenotypeTable Inputs: -DataSet of at least 2 GenotypeTables, First one is the known SNP set you wish to compare to, the rest are compared in order. -bedFile, bed file of regions you want to compare. If not specified will compare all base pairs in the known SNP set Outputs: - Will print out the Number of HetIndelMissing base pairs, the number of missing base pairs, the number of base pairs compared and the error rate to the console. Created by zrm22 on 12/18/17.

    • Nested Class Summary

      Nested Classes 
      Modifier and Type Class Description

    • Enum Constant Summary

      Enum Constants 
      Enum Constant Description

    • Method Summary

      Modifier and Type Method Description
      DataSet processData(DataSet input)
      ImageIcon getIcon()
      String getButtonName()
      String getToolTipText()
      String anchorRegionBed() Bed File
      CompareToKnownSNPPlugin anchorRegionBed(String value) Set Bed File.

      • Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin

        addListener, cancel, convert, dataSetReturned, getCitation, getInputs, getListeners, getMenu, getPanel, getParameter, getParentFrame, getUsage, getUsageHTML, hasListeners, isInteractive, isPluginParameter, performFunction, pluginDescription, pluginParameters, pluginUserManualURL, progress, receiveInput, reverseTrace, run, setConfigParameters, setParameter, setParameters, setParametersToDefault, setThreaded, trace, usageParameters, wasCancelled

      • Methods inherited from class net.maizegenetics.plugindef.Plugin

        getPluginInstance, isPlugin

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait