All Implemented Interfaces:

java.lang.Runnable , net.maizegenetics.plugindef.Plugin , net.maizegenetics.plugindef.PluginListener , net.maizegenetics.util.ProgressListener
```
@Deprecated() 
public class HapCountBestPathToTextPlugin
extends AbstractPlugin
                    
```
This plugin processes haplotype node data either from of an inclusion file, or from PHG database tables. The HapCountBestPathPlugin is called to find the best path through the provided haplotype graph. The output will be either stored to the PHG db, printed to text files or both depending on the input type. Assumptions made by this software: 1. This method can determine paths from haplotype counts (perfect hits/exclusion) that are stored in the db's haplotype_counts table, or from haplotype counts (perfect hits/exclusion) pulled from an inclusion file If an inclusion file is present, its data is used. Otherwise the DB table is used. 2. When the DB is used to pull haplotype_counts data, any paths created will be stored in the DB. If an inclusion file is used, paths are NOT stored to the DB. This is because the paths table needs the haplotype_counts_id. When an inclusion file is used, the assumption is that these hapltoype counts are NOT stored in the DB. 3. The exported inclusion files (that are input to this Plugin) and the exported path files (created by this plugin) each contain "header" data needed to load their contents into the DB. These are the first lines in the file, and each begin with #. A separate plugin should be written to load these files to db if desired.

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
`HapCountBestPathToTextPlugin(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()`	Database configuration file
`HapCountBestPathToTextPlugin`	`configFile(String value)`	Set Database Config File.
`String`	`taxaFilterString()`	A comma delimited list of taxa (no spaces allowed) to include in graph.
`HapCountBestPathToTextPlugin`	`taxaFilterString(String value)`	Set Taxa.
`String`	`inclusionFilenameDir()`	The name of the file containing read inclusion and exclusion counts for hapids.
`HapCountBestPathToTextPlugin`	`inclusionFilenameDir(String value)`	Set Inclusion File Dir.
`String`	`targetTaxon()`	The taxon that will be used to evaluate the node list returned.
`HapCountBestPathToTextPlugin`	`targetTaxon(String value)`	Set Target.
`String`	`refRangeFile()`	The name of the file containing the reference ranges to keep.
`HapCountBestPathToTextPlugin`	`refRangeFile(String value)`	Set Ref Range File.
`String`	`referenceFileName()`	Reference file name in case you want to index on the fly
`HapCountBestPathToTextPlugin`	`referenceFileName(String value)`	Set Ref File Name.
`String`	`outputDir()`	Output Directory
`HapCountBestPathToTextPlugin`	`outputDir(String value)`	Set Output Dir.
`String`	`hapCountMethod()`	Name of method used to creates inclusion/exclusion counts in FastqToHapCountPLugin
`HapCountBestPathToTextPlugin`	`hapCountMethod(String value)`	Set Hap Count Method.
`String`	`pathMethod()`	Name of method to be used to create paths through the graph.
`HapCountBestPathToTextPlugin`	`pathMethod(String value)`	Set P Method.

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
  - HapCountBestPathToTextPlugin
```
HapCountBestPathToTextPlugin(Frame parentFrame, boolean isInteractive)
```
- Method Detail
  - processData
```
 DataSet processData(DataSet input)
```
  - getIcon
```
 ImageIcon getIcon()
```
  - getButtonName
```
 String getButtonName()
```
  - getToolTipText
```
 String getToolTipText()
```
  - configFile
```
 String configFile()
```
    Database configuration file
  - configFile
```
 HapCountBestPathToTextPlugin configFile(String value)
```
    Set Database Config File. Database configuration file
    
    Parameters:
    
    value - Database Config File
  - taxaFilterString
```
 String taxaFilterString()
```
    A comma delimited list of taxa (no spaces allowed) to include in graph. Only nodes containing these taxa will be included in the graph. If no taxa list is supplied, then all taxa in the full graph will be used.
  - taxaFilterString
```
 HapCountBestPathToTextPlugin taxaFilterString(String value)
```
    Set Taxa. A comma delimited list of taxa (no spaces allowed) to include in graph. Only nodes containing these taxa will be included in the graph. If no taxa list is supplied, then all taxa in the full graph will be used.
    
    Parameters:
    
    value - Taxa
  - inclusionFilenameDir
```
 String inclusionFilenameDir()
```
    The name of the file containing read inclusion and exclusion counts for hapids.
  - inclusionFilenameDir
```
 HapCountBestPathToTextPlugin 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
  - targetTaxon
```
 String targetTaxon()
```
    The taxon that will be used to evaluate the node list returned.
  - targetTaxon
```
 HapCountBestPathToTextPlugin targetTaxon(String value)
```
    Set Target. The taxon that will be used to evaluate the node list returned.
    
    Parameters:
    
    value - Target
  - refRangeFile
```
 String refRangeFile()
```
    The name of the file containing the reference ranges to keep.
  - refRangeFile
```
 HapCountBestPathToTextPlugin refRangeFile(String value)
```
    Set Ref Range File. The name of the file containing the reference ranges to keep.
    
    Parameters:
    
    value - Ref Range File
  - referenceFileName
```
 String referenceFileName()
```
    Reference file name in case you want to index on the fly
  - referenceFileName
```
 HapCountBestPathToTextPlugin referenceFileName(String value)
```
    Set Ref File Name. Reference file name in case you want to index on the fly
    
    Parameters:
    
    value - Ref File Name
  - outputDir
```
 String outputDir()
```
    Output Directory
  - outputDir
```
 HapCountBestPathToTextPlugin outputDir(String value)
```
    Set Output Dir. Output Directory
    
    Parameters:
    
    value - Output Dir
  - hapCountMethod
```
 String hapCountMethod()
```
    Name of method used to creates inclusion/exclusion counts in FastqToHapCountPLugin
  - hapCountMethod
```
 HapCountBestPathToTextPlugin hapCountMethod(String value)
```
    Set Hap Count Method. Name of method used to creates inclusion/exclusion counts in FastqToHapCountPLugin
    
    Parameters:
    
    value - Hap Count Method
  - pathMethod
```
 String pathMethod()
```
    Name of method to be used to create paths through the graph.
  - pathMethod
```
 HapCountBestPathToTextPlugin pathMethod(String value)
```
    Set P Method. Name of method to be used to create paths through the graph.
    
    Parameters:
    
    value - P Method

Class HapCountBestPathToTextPlugin

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

HapCountBestPathToTextPlugin

Method Detail

processData

getIcon

getButtonName

getToolTipText

configFile

configFile

taxaFilterString

taxaFilterString

inclusionFilenameDir

inclusionFilenameDir

targetTaxon

targetTaxon

refRangeFile

refRangeFile

referenceFileName

referenceFileName

outputDir

outputDir

hapCountMethod

hapCountMethod

pathMethod

pathMethod