HapCountBestPathToTextPlugin (net.maizegenetics:phg 0.0.1 API)

java.lang.Object
- net.maizegenetics.plugindef.AbstractPlugin
- - net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin

All Implemented Interfaces:

Runnable, net.maizegenetics.plugindef.Plugin, net.maizegenetics.plugindef.PluginListener, net.maizegenetics.util.ProgressListener
```
public class HapCountBestPathToTextPlugin
extends net.maizegenetics.plugindef.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.

Author:

Terry Casstevens, Zack Miller, Lynn Johnson

Field Summary
- Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin
  DEFAULT_CITATION, POSITION_LIST_NONE, TAXA_LIST_NONE

Constructor Summary

Constructors
Constructor and Description

HapCountBestPathToTextPlugin(Frame parentFrame, boolean isInteractive)

Constructors
Constructor and Description
`HapCountBestPathToTextPlugin(Frame parentFrame, boolean isInteractive)`

Method Summary

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

Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin
addListener, cancel, convert, dataSetReturned, getCitation, getInputs, getMenu, getPanel, getParameter, getParameter, getParentFrame, getUsage, getUsageHTML, isInteractive, performFunction, pluginUserManualURL, progress, progress, receiveInput, reverseTrace, run, setConfigParameters, setParameter, setParameter, setParameter, setParameters, setParametersToDefault, setThreaded, trace, wasCancelled

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface net.maizegenetics.plugindef.Plugin
getPluginInstance, getPluginInstance, isPlugin

- Constructor Detail
  - HapCountBestPathToTextPlugin
```
public HapCountBestPathToTextPlugin(Frame parentFrame,
                                    boolean isInteractive)
```
- Method Detail
  - processData
```
public net.maizegenetics.plugindef.DataSet processData(net.maizegenetics.plugindef.DataSet input)
```
    Specified by:
    
    processData in interface net.maizegenetics.plugindef.Plugin
    
    Overrides:
    
    processData in class net.maizegenetics.plugindef.AbstractPlugin
  - getIcon
```
public ImageIcon getIcon()
```
  - getButtonName
```
public String getButtonName()
```
  - getToolTipText
```
public String getToolTipText()
```
  - pluginDescription
```
public String pluginDescription()
```
    Specified by:
    
    pluginDescription in interface net.maizegenetics.plugindef.Plugin
    
    Overrides:
    
    pluginDescription in class net.maizegenetics.plugindef.AbstractPlugin
  - configFile
```
public String configFile()
```
    Database configuration file
    
    Returns:
    
    Database Config File
  - configFile
```
public HapCountBestPathToTextPlugin configFile(String value)
```
    Set Database Config File. Database configuration file
    
    Parameters:
    
    value - Database Config File
    
    Returns:
    
    this plugin
  - taxaFilterString
```
public 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.
    
    Returns:
    
    Taxa
  - taxaFilterString
```
public 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
    
    Returns:
    
    this plugin
  - inclusionFilenameDir
```
public String inclusionFilenameDir()
```
    The name of the file containing read inclusion and exclusion counts for hapids.
    
    Returns:
    
    Inclusion File Dir
  - inclusionFilenameDir
```
public 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
    
    Returns:
    
    this plugin
  - targetTaxon
```
public String targetTaxon()
```
    The taxon that will be used to evaluate the node list returned.
    
    Returns:
    
    Target
  - targetTaxon
```
public HapCountBestPathToTextPlugin targetTaxon(String value)
```
    Set Target. The taxon that will be used to evaluate the node list returned.
    
    Parameters:
    
    value - Target
    
    Returns:
    
    this plugin
  - refRangeFile
```
public String refRangeFile()
```
    The name of the file containing the reference ranges to keep.
    
    Returns:
    
    Ref Range File
  - refRangeFile
```
public HapCountBestPathToTextPlugin refRangeFile(String value)
```
    Set Ref Range File. The name of the file containing the reference ranges to keep.
    
    Parameters:
    
    value - Ref Range File
    
    Returns:
    
    this plugin
  - referenceFileName
```
public String referenceFileName()
```
    Reference file name in case you want to index on the fly
    
    Returns:
    
    Ref File Name
  - referenceFileName
```
public 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
    
    Returns:
    
    this plugin
  - outputDir
```
public String outputDir()
```
    Output Directory
    
    Returns:
    
    Output Dir
  - outputDir
```
public HapCountBestPathToTextPlugin outputDir(String value)
```
    Set Output Dir. Output Directory
    
    Parameters:
    
    value - Output Dir
    
    Returns:
    
    this plugin
  - hapCountMethod
```
public String hapCountMethod()
```
    Name of method used to creates inclusion/exclusion counts in FastqToHapCountPLugin
    
    Returns:
    
    Hc Method
  - hapCountMethod
```
public HapCountBestPathToTextPlugin hapCountMethod(String value)
```
    Set Hap Count Method. Name of method used to creates inclusion/exclusion counts in FastqToHapCountPLugin
    
    Parameters:
    
    value - Hap Count Method
    
    Returns:
    
    this plugin
  - pathMethod
```
public String pathMethod()
```
    Name of method to be used to create paths through the graph.
    
    Returns:
    
    Path Method
  - pathMethod
```
public HapCountBestPathToTextPlugin pathMethod(String value)
```
    Set P Method. Name of method to be used to create paths through the graph.
    
    Parameters:
    
    value - P Method
    
    Returns:
    
    this plugin

Class HapCountBestPathToTextPlugin

Field Summary

Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin

Constructor Summary

Method Summary

Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin

Methods inherited from class java.lang.Object

Methods inherited from interface net.maizegenetics.plugindef.Plugin

Constructor Detail

HapCountBestPathToTextPlugin

Method Detail

processData

getIcon

getButtonName

getToolTipText

pluginDescription

configFile

configFile

taxaFilterString

taxaFilterString

inclusionFilenameDir

inclusionFilenameDir

targetTaxon

targetTaxon

refRangeFile

refRangeFile

referenceFileName

referenceFileName

outputDir

outputDir

hapCountMethod

hapCountMethod

pathMethod

pathMethod