All Implemented Interfaces:

java.lang.Runnable , net.maizegenetics.plugindef.Plugin , net.maizegenetics.plugindef.PluginListener , net.maizegenetics.util.ProgressListener
```
public class AddRefRangeAsAssemblyPlugin
extends AbstractPlugin
                    
```
This function is fairly obsolete. IT was used before the graph was able to take multiple methods as parameters. This class created to load a reference genome as an assembly. The method is hard-coded to "mummer4", which is the assembly method name at the time of this writing. All the variants are reference records. The addition of these haplotypes allows for pulling TODO: IT it is deemd this class is still useful, it should be updated to create a gvcf file as is done in LoadAllIntervalsToPHGdbPlugin, store the gvcf file data to the genomeFileData table, and save the gvcfFileId to the anchorDataPHG object.

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

Enum Constant Summary

Enum Constants
Enum Constant	Description

Method Summary

Modifier and Type	Method	Description
`DataSet`	`processData(DataSet input)`
`static void`	`main(Array<String> args)`
`ImageIcon`	`getIcon()`
`String`	`getButtonName()`
`String`	`getToolTipText()`
`String`	`refGenome()`	Referemce Genome File for aligning against
`AddRefRangeAsAssemblyPlugin`	`refGenome(String value)`	Set Reference Genome File.
`String`	`configFile()`	Path to config file for db loading
`AddRefRangeAsAssemblyPlugin`	`configFile(String value)`	Set config file for db access
`String`	`haplotypeMethod()`	Name of method to be stored in db
`AddRefRangeAsAssemblyPlugin`	`haplotypeMethod(String value)`	Set methodName
`String`	`pathName()`	Name of method used for create PHG Path.
`AddRefRangeAsAssemblyPlugin`	`pathName(String value)`	Set Path Method Name.
`String`	`lineName()`	Name name to be stored in the genotypes table, e.g.
`AddRefRangeAsAssemblyPlugin`	`lineName(String value)`	Set Line Name.

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
  - AddRefRangeAsAssemblyPlugin
```
AddRefRangeAsAssemblyPlugin()
```
  - AddRefRangeAsAssemblyPlugin
```
AddRefRangeAsAssemblyPlugin(Frame parentFrame)
```
  - AddRefRangeAsAssemblyPlugin
```
AddRefRangeAsAssemblyPlugin(Frame parentFrame, boolean isInteractive)
```
- Method Detail
  - processData
```
 DataSet processData(DataSet input)
```
  - main
```
 static void main(Array<String> args)
```
  - getIcon
```
 ImageIcon getIcon()
```
  - getButtonName
```
 String getButtonName()
```
  - getToolTipText
```
 String getToolTipText()
```
  - refGenome
```
 String refGenome()
```
    Referemce Genome File for aligning against
  - refGenome
```
 AddRefRangeAsAssemblyPlugin refGenome(String value)
```
    Set Reference Genome File. Referemce Genome File for aligning against
    
    Parameters:
    
    value - Reference Genome File
  - configFile
```
 String configFile()
```
    Path to config file for db loading
  - configFile
```
 AddRefRangeAsAssemblyPlugin configFile(String value)
```
    Set config file for db access
    
    Parameters:
    
    value - config file
  - haplotypeMethod
```
 String haplotypeMethod()
```
    Name of method to be stored in db
  - haplotypeMethod
```
 AddRefRangeAsAssemblyPlugin haplotypeMethod(String value)
```
    Set methodName
    
    Parameters:
    
    value - methodName
  - pathName
```
 String pathName()
```
    Name of method used for create PHG Path. Should match the assembly path method - that default is mummer4_PATH
  - pathName
```
 AddRefRangeAsAssemblyPlugin pathName(String value)
```
    Set Path Method Name. Name of method used for create PHG Path. Should match the assembly path method - that default is mummer4_PATH
    
    Parameters:
    
    value - Path Method Name
  - lineName
```
 String lineName()
```
    Name name to be stored in the genotypes table, e.g. B73_Assembly
  - lineName
```
 AddRefRangeAsAssemblyPlugin lineName(String value)
```
    Set Line Name. Name name to be stored in the genotypes table, e.g. B73_Assembly
    
    Parameters:
    
    value - Line Name

Class AddRefRangeAsAssemblyPlugin

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

AddRefRangeAsAssemblyPlugin

AddRefRangeAsAssemblyPlugin

AddRefRangeAsAssemblyPlugin

Method Detail

processData

main

getIcon

getButtonName

getToolTipText

refGenome

refGenome

configFile

configFile

haplotypeMethod

haplotypeMethod

pathName

pathName

lineName

lineName