ScoreRangesByInclusionCountsPlugin

All Implemented Interfaces:

java.lang.Runnable , net.maizegenetics.plugindef.Plugin , net.maizegenetics.plugindef.PluginListener , net.maizegenetics.util.ProgressListener
```
@Deprecated() 
public class ScoreRangesByInclusionCountsPlugin
extends AbstractPlugin
                    
```
Created by zrm22 on 10/11/17. This plugin will take in any number of inclusion file and will score each reference range by counting how many taxa hit this ref range at least once

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
`ScoreRangesByInclusionCountsPlugin(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`	`pluginDescription()`
`String`	`pluginUserManualURL()`
`String`	`inclusionFilenameDir()`	The name of the file containing read inclusion and exclusion counts for hapids.
`ScoreRangesByInclusionCountsPlugin`	`inclusionFilenameDir(String value)`	Set Inclusion File Dir.
`String`	`outputFileName()`	Name of output file
`ScoreRangesByInclusionCountsPlugin`	`outputFileName(String value)`	Set Output File.
`String`	`filterRefRanges()`	Name of ref range filter file
`ScoreRangesByInclusionCountsPlugin`	`filterRefRanges(String value)`	Set Filter Ref Range 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, pluginParameters, 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
  - ScoreRangesByInclusionCountsPlugin
```
ScoreRangesByInclusionCountsPlugin(Frame parentFrame, boolean isInteractive)
```
- Method Detail
  - processData
```
 DataSet processData(DataSet input)
```
  - getIcon
```
 ImageIcon getIcon()
```
  - getButtonName
```
 String getButtonName()
```
  - getToolTipText
```
 String getToolTipText()
```
  - pluginDescription
```
 String pluginDescription()
```
  - pluginUserManualURL
```
 String pluginUserManualURL()
```
  - inclusionFilenameDir
```
 String inclusionFilenameDir()
```
    The name of the file containing read inclusion and exclusion counts for hapids.
  - inclusionFilenameDir
```
 ScoreRangesByInclusionCountsPlugin inclusionFilenameDir(String value)
```
    Set Inclusion File Dir. The name of the file containing read inclusion and exclusion counts for hapids.
    
    Parameters:
    
    value - Inclusion File Dir
  - outputFileName
```
 String outputFileName()
```
    Name of output file
  - outputFileName
```
 ScoreRangesByInclusionCountsPlugin outputFileName(String value)
```
    Set Output File. Name of output file
    
    Parameters:
    
    value - Output File
  - filterRefRanges
```
 String filterRefRanges()
```
    Name of ref range filter file
  - filterRefRanges
```
 ScoreRangesByInclusionCountsPlugin filterRefRanges(String value)
```
    Set Filter Ref Range File. Name of ref range filter file
    
    Parameters:
    
    value - Filter Ref Range File