net.maizegenetics.pangenome.gvcfFiltering

Class FilterGVCFSingleFilePlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFSingleFilePlugin

All Implemented Interfaces:

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

public class FilterGVCFSingleFilePlugin
extends net.maizegenetics.plugindef.AbstractPlugin

Field Summary

Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin

DEFAULT_CITATION, POSITION_LIST_NONE, TAXA_LIST_NONE

Constructor Summary

Constructors

Constructor and Description
FilterGVCFSingleFilePlugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
String	configFile() Config folder containing the filtering parameters.
FilterGVCFSingleFilePlugin	configFile(String value) Set Config File.
String	getButtonName()
ImageIcon	getIcon()
String	getToolTipText()
String	inputFile() GVCF File to be filtered.
FilterGVCFSingleFilePlugin	inputFile(String value) Set Input G V C F File.
String	outputFile() Output GVCF File Path and Name.
FilterGVCFSingleFilePlugin	outputFile(String value) Set Output G V C F File.
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

FilterGVCFSingleFilePlugin

public FilterGVCFSingleFilePlugin(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()

inputFile

public String inputFile()

GVCF File to be filtered.

Returns:

Input G V C F File

inputFile

public FilterGVCFSingleFilePlugin inputFile(String value)

Set Input G V C F File. GVCF File to be filtered.

Parameters:

value - Input G V C F File

Returns:

this plugin

outputFile

public String outputFile()

Output GVCF File Path and Name.

Returns:

Output G V C F File

outputFile

public FilterGVCFSingleFilePlugin outputFile(String value)

Set Output G V C F File. Output GVCF File Path and Name.

Parameters:

value - Output G V C F File

Returns:

this plugin

configFile

public String configFile()

Config folder containing the filtering parameters.

Returns:

Config File

configFile

public FilterGVCFSingleFilePlugin configFile(String value)

Set Config File. Config folder containing the filtering parameters.

Parameters:

value - Config File

Returns:

this plugin