-
- 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.
-
-
Field Summary
Fields Modifier and Type Field Description public final static String
DEFAULT_CITATION
public final static String
POSITION_LIST_NONE
public final static String
TAXA_LIST_NONE
-
Constructor Summary
Constructors Constructor Description CompareToKnownSNPPlugin(Frame parentFrame, boolean isInteractive)
-
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
-
-
Constructor Detail
-
CompareToKnownSNPPlugin
CompareToKnownSNPPlugin(Frame parentFrame, boolean isInteractive)
-
-
Method Detail
-
processData
DataSet processData(DataSet input)
-
getButtonName
String getButtonName()
-
getToolTipText
String getToolTipText()
-
anchorRegionBed
String anchorRegionBed()
Bed File
-
anchorRegionBed
CompareToKnownSNPPlugin anchorRegionBed(String value)
Set Bed File. Bed File
- Parameters:
value
- Bed File
-
-
-
-