net.maizegenetics.pangenome.processAssemblyGenomes

Class ResizeRefBlockPlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.pangenome.processAssemblyGenomes.ResizeRefBlockPlugin

All Implemented Interfaces:

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

public class ResizeRefBlockPlugin
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
ResizeRefBlockPlugin(Frame parentFrame)
ResizeRefBlockPlugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
String	getButtonName()
ImageIcon	getIcon()
String	getToolTipText()
net.maizegenetics.plugindef.DataSet	processData(net.maizegenetics.plugindef.DataSet input)
String	ref() Reference fasta File
ResizeRefBlockPlugin	ref(String value) Set Reference.
String	taxon() Name to be assigned for the taxon
ResizeRefBlockPlugin	taxon(String value) Set Taxon Name.
String	vCFFile() Normalized VCF file which needs to be corrected
ResizeRefBlockPlugin	vCFFile(String value) Set Normalized VCF File.
String	vCFFileCorrected() Corrected RefBlock VCF file
ResizeRefBlockPlugin	vCFFileCorrected(String value) Set Output VCF File.

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

ResizeRefBlockPlugin

public ResizeRefBlockPlugin(Frame parentFrame)

ResizeRefBlockPlugin

public ResizeRefBlockPlugin(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()

vCFFile

public String vCFFile()

Normalized VCF file which needs to be corrected

Returns:

Normalized VCF File

vCFFile

public ResizeRefBlockPlugin vCFFile(String value)

Set Normalized VCF File. Normalized VCF file which needs to be corrected

Parameters:

value - Normalized VCF File

Returns:

this plugin

vCFFileCorrected

public String vCFFileCorrected()

Corrected RefBlock VCF file

Returns:

Output VCF File

vCFFileCorrected

public ResizeRefBlockPlugin vCFFileCorrected(String value)

Set Output VCF File. Corrected RefBlock VCF file

Parameters:

value - Output VCF File

Returns:

this plugin

ref

public String ref()

Reference fasta File

Returns:

Reference

ref

public ResizeRefBlockPlugin ref(String value)

Set Reference. Reference fasta File

Parameters:

value - Reference

Returns:

this plugin

taxon

public String taxon()

Name to be assigned for the taxon

Returns:

Taxon Name

taxon

public ResizeRefBlockPlugin taxon(String value)

Set Taxon Name. Name to be assigned for the taxon

Parameters:

value - Taxon Name

Returns:

this plugin