net.maizegenetics.pangenome.pipelineTests

Class CompareToKnownSNPPlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.pangenome.pipelineTests.CompareToKnownSNPPlugin

All Implemented Interfaces:

Runnable, net.maizegenetics.plugindef.Plugin, net.maizegenetics.plugindef.PluginListener, net.maizegenetics.util.ProgressListener

public class CompareToKnownSNPPlugin
extends net.maizegenetics.plugindef.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.

Field Summary

Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin

DEFAULT_CITATION, POSITION_LIST_NONE, TAXA_LIST_NONE

Constructor Summary

Constructors

Constructor and Description
CompareToKnownSNPPlugin(Frame parentFrame, boolean isInteractive)

Method Summary

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

Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin

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

Methods inherited from class java.lang.Object

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

Methods inherited from interface net.maizegenetics.plugindef.Plugin

getPluginInstance, getPluginInstance, isPlugin

Constructor Detail

CompareToKnownSNPPlugin

public CompareToKnownSNPPlugin(Frame parentFrame,
                               boolean isInteractive)

Method Detail

processData

public net.maizegenetics.plugindef.DataSet processData(net.maizegenetics.plugindef.DataSet input)

Specified by:

processData in interface net.maizegenetics.plugindef.Plugin

Overrides:

processData in class net.maizegenetics.plugindef.AbstractPlugin

getIcon

public ImageIcon getIcon()

getButtonName

public String getButtonName()

getToolTipText

public String getToolTipText()

anchorRegionBed

public String anchorRegionBed()

Bed File

Returns:

Bed File

anchorRegionBed

public CompareToKnownSNPPlugin anchorRegionBed(String value)

Set Bed File. Bed File

Parameters:

value - Bed File

Returns:

this plugin