All Implemented Interfaces:

java.lang.Runnable , net.maizegenetics.plugindef.Plugin , net.maizegenetics.plugindef.PluginListener , net.maizegenetics.util.ProgressListener
```
public class AddRefRangeGroupPlugin
extends AbstractPlugin
                    
```
This class creates a user defined ref range group, adds it to the specified db, associates requested reference ranges with the new group. Input: 1. anchor bed file: Should be a subset of reference ranges currently existing in the DB. Format is tab-delimited file with columns: chr startpos endpos No header, positions are BED file formatted, ie 0-based, inclusive/exclusive 2. Name for the new method, which is the ref range group. 3. Method details: user description for method 4. Config file with db connection info Output: 1. Database tables "methods" and "ref_range_ref_range_method" are updated. Algorithm: 1. Read bed file into an object 2. Read all reference ranges from db 3. Verify all entries from the bed file exist in the reference_ranges table (throw exception if false) 4. Verify method name does not exist in methods table (throw exception if false) 5. Add method name to db. 6. Add specified reference ranges to the ref_range_ref_range_methods table with method_id = new method id.

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

Enum Constant Summary

Enum Constants
Enum Constant	Description

Method Summary

Modifier and Type	Method	Description
`DataSet`	`processData(DataSet input)`
`static List<Integer>`	`verifyRanges(String rangeFile, PHGDataWriter phg)`
`ImageIcon`	`getIcon()`
`String`	`getButtonName()`
`String`	`getToolTipText()`
`String`	`methodName()`	Method name for this reference range group.
`AddRefRangeGroupPlugin`	`methodName(String value)`	Set Method Name.
`String`	`methodDetails()`	Desscription for this group of reference ranges.
`AddRefRangeGroupPlugin`	`methodDetails(String value)`	Set Method Details.
`String`	`ranges()`	Tab-delimited, BED Formatted file containing chrom, ref range start position, ref range end position.
`AddRefRangeGroupPlugin`	`ranges(String value)`	Set Ranges File.
`String`	`configFile()`	Path to file containing database access information, separate lines for host=X, user=X, password=X, DB=X, DBtype=X where X is user defined, and DBtype is either sqlite or postgres.
`AddRefRangeGroupPlugin`	`configFile(String value)`	Set DataBase Configuration 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
  - AddRefRangeGroupPlugin
```
AddRefRangeGroupPlugin()
```
  - AddRefRangeGroupPlugin
```
AddRefRangeGroupPlugin(Frame parentFrame)
```
  - AddRefRangeGroupPlugin
```
AddRefRangeGroupPlugin(Frame parentFrame, boolean isInteractive)
```
- Method Detail
  - processData
```
 DataSet processData(DataSet input)
```
  - verifyRanges
```
 static List<Integer> verifyRanges(String rangeFile, PHGDataWriter phg)
```
  - getIcon
```
 ImageIcon getIcon()
```
  - getButtonName
```
 String getButtonName()
```
  - getToolTipText
```
 String getToolTipText()
```
  - methodName
```
 String methodName()
```
    Method name for this reference range group.
  - methodName
```
 AddRefRangeGroupPlugin methodName(String value)
```
    Set Method Name. Method name for this reference range group.
    
    Parameters:
    
    value - Method Name
  - methodDetails
```
 String methodDetails()
```
    Desscription for this group of reference ranges.
  - methodDetails
```
 AddRefRangeGroupPlugin methodDetails(String value)
```
    Set Method Details. Desscription for this group of reference ranges.
    
    Parameters:
    
    value - Method Details
  - ranges
```
 String ranges()
```
    Tab-delimited, BED Formatted file containing chrom, ref range start position, ref range end position. No header line.
  - ranges
```
 AddRefRangeGroupPlugin ranges(String value)
```
    Set Ranges File. Tab-delimited, BED Formatted file containing chrom, ref range start position, ref range end position. No header line.
    
    Parameters:
    
    value - Ranges File
  - configFile
```
 String configFile()
```
    Path to file containing database access information, separate lines for host=X, user=X, password=X, DB=X, DBtype=X where X is user defined, and DBtype is either sqlite or postgres.
  - configFile
```
 AddRefRangeGroupPlugin configFile(String value)
```
    Set DataBase Configuration File. Path to file containing database access information, separate lines for host=X, user=X, password=X, DB=X, DBtype=X where X is user defined, and DBtype is either sqlite or postgres.
    
    Parameters:
    
    value - DataBase Configuration File

Class AddRefRangeGroupPlugin

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

AddRefRangeGroupPlugin

AddRefRangeGroupPlugin

AddRefRangeGroupPlugin

Method Detail

processData

verifyRanges

getIcon

getButtonName

getToolTipText

methodName

methodName

methodDetails

methodDetails

ranges

ranges

configFile

configFile