All Implemented Interfaces:

java.lang.Runnable , net.maizegenetics.plugindef.Plugin , net.maizegenetics.plugindef.PluginListener , net.maizegenetics.util.ProgressListener
```
public class CreateGeneIntervalsFromConservedGFFPlugin
extends AbstractPlugin
                    
```
Creates bed file with chromosome and coordinates to be used to create PHG reference ranges. Gene names are included with each reference range. The gene name column is ignored when loading the bed file - it is there for when we want to associate reference ranges with the genes on which they were based.

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

Enum Constant Summary

Enum Constants
Enum Constant	Description

Method Summary

Modifier and Type	Method	Description
`static void`	`main(Array<String> args)`
`DataSet`	`processData(DataSet input)`
`ImageIcon`	`getIcon()`
`String`	`getButtonName()`
`String`	`getToolTipText()`
`String`	`gffFile()`	Tab delimited .
`CreateGeneIntervalsFromConservedGFFPlugin`	`gffFile(String value)`	Set Gene File.
`String`	`outputFile()`	Name of output file to be written
`CreateGeneIntervalsFromConservedGFFPlugin`	`outputFile(String value)`	Set Output File.
`String`	`conservedGeneFile()`	File containing list of conserved genes to include as anchor regions
`CreateGeneIntervalsFromConservedGFFPlugin`	`conservedGeneFile(String value)`	Set Conserved Gene File.

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
  - CreateGeneIntervalsFromConservedGFFPlugin
```
CreateGeneIntervalsFromConservedGFFPlugin()
```
  - CreateGeneIntervalsFromConservedGFFPlugin
```
CreateGeneIntervalsFromConservedGFFPlugin(Frame parentFrame)
```
  - CreateGeneIntervalsFromConservedGFFPlugin
```
CreateGeneIntervalsFromConservedGFFPlugin(Frame parentFrame, boolean isInteractive)
```
- Method Detail
  - main
```
 static void main(Array<String> args)
```
  - processData
```
 DataSet processData(DataSet input)
```
  - getIcon
```
 ImageIcon getIcon()
```
  - getButtonName
```
 String getButtonName()
```
  - getToolTipText
```
 String getToolTipText()
```
  - gffFile
```
 String gffFile()
```
    Tab delimited .txt file containing gene-only GFF data from reference GFF file for all desired chromosomes,
  - gffFile
```
 CreateGeneIntervalsFromConservedGFFPlugin gffFile(String value)
```
    Set Gene File. Tab delimited .txt file containing gene-only GFF data from reference GFF file for all desired chromosomes,
    
    Parameters:
    
    value - Gene File
  - outputFile
```
 String outputFile()
```
    Name of output file to be written
  - outputFile
```
 CreateGeneIntervalsFromConservedGFFPlugin outputFile(String value)
```
    Set Output File. Name of file to be written
    
    Parameters:
    
    value - Output Directory
  - conservedGeneFile
```
 String conservedGeneFile()
```
    File containing list of conserved genes to include as anchor regions
  - conservedGeneFile
```
 CreateGeneIntervalsFromConservedGFFPlugin conservedGeneFile(String value)
```
    Set Conserved Gene File. File containing list of conserved genes to include as anchor regions
    
    Parameters:
    
    value - Conserved Gene File

Class CreateGeneIntervalsFromConservedGFFPlugin

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

CreateGeneIntervalsFromConservedGFFPlugin

CreateGeneIntervalsFromConservedGFFPlugin

CreateGeneIntervalsFromConservedGFFPlugin

Method Detail

main

processData

getIcon

getButtonName

getToolTipText

gffFile

gffFile

outputFile

outputFile

conservedGeneFile

conservedGeneFile