All Implemented Interfaces:

java.lang.Runnable , net.maizegenetics.plugindef.Plugin , net.maizegenetics.plugindef.PluginListener , net.maizegenetics.util.ProgressListener
```
@Deprecated() 
public class ExportVCForTaxonMethodPlugin
extends AbstractPlugin
                    
```
Exports variant context lists to vcf file. NOTE: PathsToVCF is not used as that method only exports SNPs. Input: taxon and method to identify haplotypes table entries A single chromosome may also be supplied. If no chromoseom is given, data for all chromosomes will be pulled. Output: vcf file TODO: create hmp or vcf based on file extension.

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description

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
`ExportVCForTaxonMethodPlugin()`
`ExportVCForTaxonMethodPlugin(Frame parentFrame)`
`ExportVCForTaxonMethodPlugin(Frame parentFrame, boolean isInteractive)`

Enum Constant Summary

Enum Constants
Enum Constant	Description

Method Summary

Modifier and Type	Method	Description
`DataSet`	`processData(DataSet input)`
`ImageIcon`	`getIcon()`
`String`	`getButtonName()`
`String`	`getToolTipText()`
`String`	`configFile()`	Config file that specifies database connection parameters
`ExportVCForTaxonMethodPlugin`	`configFile(String value)`	Set Config File.
`String`	`taxon()`	Name of taxon whose variant contexts should be pulled.
`ExportVCForTaxonMethodPlugin`	`taxon(String value)`	Set Taxon.
`String`	`methods()`	Pairs of methods (haplotype method name and range group method name).
`ExportVCForTaxonMethodPlugin`	`methods(String value)`	Set Methods.
`String`	`outputFile()`	FUll path to output file created by this plugin .
`ExportVCForTaxonMethodPlugin`	`outputFile(String value)`	Set Output File.
`String`	`chrom()`	If a chrom is specified, pull only data for that chromosome.
`ExportVCForTaxonMethodPlugin`	`chrom(String value)`	Set Chrom.

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
  - ExportVCForTaxonMethodPlugin
```
ExportVCForTaxonMethodPlugin()
```
  - ExportVCForTaxonMethodPlugin
```
ExportVCForTaxonMethodPlugin(Frame parentFrame)
```
  - ExportVCForTaxonMethodPlugin
```
ExportVCForTaxonMethodPlugin(Frame parentFrame, boolean isInteractive)
```
- Method Detail
  - processData
```
 DataSet processData(DataSet input)
```
  - getIcon
```
 ImageIcon getIcon()
```
  - getButtonName
```
 String getButtonName()
```
  - getToolTipText
```
 String getToolTipText()
```
  - configFile
```
 String configFile()
```
    Config file that specifies database connection parameters
  - configFile
```
 ExportVCForTaxonMethodPlugin configFile(String value)
```
    Set Config File. Config file that specifies database connection parameters
    
    Parameters:
    
    value - Config File
  - taxon
```
 String taxon()
```
    Name of taxon whose variant contexts should be pulled.
  - taxon
```
 ExportVCForTaxonMethodPlugin taxon(String value)
```
    Set Taxon. Name of taxon whose variant contexts should be pulled.
    
    Parameters:
    
    value - Taxon
  - methods
```
 String methods()
```
    Pairs of methods (haplotype method name and range group method name). Method pair separated by a comma, and pairs separated by semicolon. The range group is optional Usage: ,
  - methods
```
 ExportVCForTaxonMethodPlugin methods(String value)
```
    Set Methods. Pairs of methods (haplotype method name and range group method name). Method pair separated by a comma, and pairs separated by semicolon. The range group is optional Usage: ,
    
    Parameters:
    
    value - Methods
  - outputFile
```
 String outputFile()
```
    FUll path to output file created by this plugin .
  - outputFile
```
 ExportVCForTaxonMethodPlugin outputFile(String value)
```
    Set Output File. FUll path to output file created by this plugin .
    
    Parameters:
    
    value - Output File
  - chrom
```
 String chrom()
```
    If a chrom is specified, pull only data for that chromosome. If no chromosome is specified, data for all chromsomes will be pulled.
  - chrom
```
 ExportVCForTaxonMethodPlugin chrom(String value)
```
    Set Chrom. If a chrom is specified, pull only data for that chromosome. If no chromosome is specified, data for all chromsomes will be pulled.
    
    Parameters:
    
    value - Chrom

Class ExportVCForTaxonMethodPlugin

Nested Class Summary

Field Summary

Constructor Summary

Enum Constant Summary

Method Summary

Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin

Methods inherited from class net.maizegenetics.plugindef.Plugin

Methods inherited from class java.lang.Object

Constructor Detail

ExportVCForTaxonMethodPlugin

ExportVCForTaxonMethodPlugin

ExportVCForTaxonMethodPlugin

Method Detail

processData

getIcon

getButtonName

getToolTipText

configFile

configFile

taxon

taxon

methods

methods

outputFile

outputFile

chrom

chrom