net.maizegenetics.pangenome.hapCalling

Class PathsToVCFPlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin

All Implemented Interfaces:

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

public class PathsToVCFPlugin
extends net.maizegenetics.plugindef.AbstractPlugin

Author:

Terry Casstevens Created October 04, 2017

Field Summary

Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin

DEFAULT_CITATION, POSITION_LIST_NONE, TAXA_LIST_NONE

Constructor Summary

Constructors

Constructor and Description
PathsToVCFPlugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
String	getButtonName()
ImageIcon	getIcon()
String	getToolTipText()
Boolean	outputAllSNPs() Whether to output all SNPs known by haplotype graph.
PathsToVCFPlugin	outputAllSNPs(Boolean value) Set Output All SNPs.
String	outputFile() Output file name
PathsToVCFPlugin	outputFile(String value) Set Output File.
net.maizegenetics.plugindef.DataSet	processData(net.maizegenetics.plugindef.DataSet input)
String	refRangeForSNPFile() Reference Range file used to further subset the paths for only specified regions of the genome.
PathsToVCFPlugin	refRangeForSNPFile(String value) Set Ref Range File V C F.

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

PathsToVCFPlugin

public PathsToVCFPlugin(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

outputFile

public String outputFile()

Output file name

Returns:

Output File

outputFile

public PathsToVCFPlugin outputFile(String value)

Set Output File. Output file name

Parameters:

value - Output File

Returns:

this plugin

refRangeForSNPFile

public String refRangeForSNPFile()

Reference Range file used to further subset the paths for only specified regions of the genome.

Returns:

Ref Range File VCF

refRangeForSNPFile

public PathsToVCFPlugin refRangeForSNPFile(String value)

Set Ref Range File V C F. Reference Range file used to further subset the paths for only specified regions of the genome.

Parameters:

value - Ref Range File VCF

Returns:

this plugin

outputAllSNPs

public Boolean outputAllSNPs()

Whether to output all SNPs known by haplotype graph.

Returns:

Output All SNPs

outputAllSNPs

public PathsToVCFPlugin outputAllSNPs(Boolean value)

Set Output All SNPs. Whether to output all SNPs known by haplotype graph.

Parameters:

value - Output All SNPs

Returns:

this plugin

getIcon

public ImageIcon getIcon()

getButtonName

public String getButtonName()

getToolTipText

public String getToolTipText()