All Implemented Interfaces:

java.lang.Runnable , net.maizegenetics.plugindef.Plugin , net.maizegenetics.plugindef.PluginListener , net.maizegenetics.util.ProgressListener
```
@Deprecated() 
public class PathToIgraphPlugin
extends AbstractPlugin
                    
```

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
`PathToIgraphPlugin(Frame parentFrame, boolean isInteractive)`

Enum Constant Summary

Enum Constants
Enum Constant	Description

Method Summary

Modifier and Type	Method	Description
`DataSet`	`processData(DataSet input)`
`void`	`writeGraphInfoAllChr(String outbase, Array<int> pathids, HaplotypeGraph graph, Array<Array<int>> inclusionExclusionCounts, String target)`
`void`	`writeGraphInfoFilesForChr(String outbase, Array<int> pathids, HaplotypeGraph graph, Map<Integer, Integer> inclusionMap, Map<Integer, Integer> exclusionMap, Chromosome chr, String target)`
`ImageIcon`	`getIcon()`
`String`	`getButtonName()`
`String`	`getToolTipText()`
`void`	`runPlugin(DataSet input)`	Convenience method to run plugin that returns nothing.
`String`	`taxonName()`	The name of the taxon for which the path is requested.
`PathToIgraphPlugin`	`taxonName(String value)`	Set Taxon name.
`String`	`targetName()`	The name of the taxon to which the path will be compared.
`PathToIgraphPlugin`	`targetName(String value)`	Set Taxon name.
`String`	`pathName()`	The path method name assigned when the path was created and stored in the DB.
`PathToIgraphPlugin`	`pathName(String value)`	Set Path method name.
`String`	`countMethod()`	The haplotype count method name assigned when the counts were created and stored in the DB.
`PathToIgraphPlugin`	`countMethod(String value)`	Set Haplotype count method name.
`String`	`fastqName()`	The name of the fastq file used to create the path.
`PathToIgraphPlugin`	`fastqName(String value)`	Set Fastq name.
`String`	`configFile()`	Database configuration file
`PathToIgraphPlugin`	`configFile(String value)`	Set Database Config File.
`Double`	`splitTransitionProb()`	When the consensus nodes are split by taxa, this is the transition probability for moving from a node to the next node of the same taxon.
`PathToIgraphPlugin`	`splitTransitionProb(Double value)`	Set Split Prob.
`TaxaList`	`taxaFilterString()`	A list of taxa to include in graph.
`PathToIgraphPlugin`	`taxaFilter(TaxaList value)`	Set Taxa.
`String`	`refRangeFile()`	The name of the file containing the reference ranges to keep.
`PathToIgraphPlugin`	`refRangeFile(String value)`	Set Ref Range File.
`String`	`outputBase()`	base name for output files from this Plugin.
`PathToIgraphPlugin`	`outputBase(String value)`	Set Output file base.

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
  - PathToIgraphPlugin
```
PathToIgraphPlugin(Frame parentFrame, boolean isInteractive)
```
- Method Detail
  - processData
```
 DataSet processData(DataSet input)
```
  - writeGraphInfoAllChr
```
 void writeGraphInfoAllChr(String outbase, Array<int> pathids, HaplotypeGraph graph, Array<Array<int>> inclusionExclusionCounts, String target)
```
  - writeGraphInfoFilesForChr
```
 void writeGraphInfoFilesForChr(String outbase, Array<int> pathids, HaplotypeGraph graph, Map<Integer, Integer> inclusionMap, Map<Integer, Integer> exclusionMap, Chromosome chr, String target)
```
  - getIcon
```
 ImageIcon getIcon()
```
  - getButtonName
```
 String getButtonName()
```
  - getToolTipText
```
 String getToolTipText()
```
  - runPlugin
```
 void runPlugin(DataSet input)
```
    Convenience method to run plugin that returns nothing.
  - taxonName
```
 String taxonName()
```
    The name of the taxon for which the path is requested.
  - taxonName
```
 PathToIgraphPlugin taxonName(String value)
```
    Set Taxon name. The name of the taxon for which the path is requested.
    
    Parameters:
    
    value - Taxon name
  - targetName
```
 String targetName()
```
    The name of the taxon to which the path will be compared.
  - targetName
```
 PathToIgraphPlugin targetName(String value)
```
    Set Taxon name. The name of the taxon to which the path will be compared.
    
    Parameters:
    
    value - Taxon name
  - pathName
```
 String pathName()
```
    The path method name assigned when the path was created and stored in the DB. Not required if a path file name is supplied.
  - pathName
```
 PathToIgraphPlugin pathName(String value)
```
    Set Path method name. The path method name assigned when the path was created and stored in the DB. Not required if a path file name is supplied.
    
    Parameters:
    
    value - Path method name
  - countMethod
```
 String countMethod()
```
    The haplotype count method name assigned when the counts were created and stored in the DB. Not required if a path file name is supplied or if only one method was used to find a path for this taxon.
  - countMethod
```
 PathToIgraphPlugin countMethod(String value)
```
    Set Haplotype count method name. The haplotype count method name assigned when the counts were created and stored in the DB. Not required if a path file name is supplied or if only one method was used to find a path for this taxon.
    
    Parameters:
    
    value - Haplotype count method name
  - fastqName
```
 String fastqName()
```
    The name of the fastq file used to create the path. This must be the name only, not the full path. Not required if the path and count data can be retrieved using other parameters.
  - fastqName
```
 PathToIgraphPlugin fastqName(String value)
```
    Set Fastq name. The name of the fastq file used to create the path. This must be the name only, not the full path. Not required if the path and count data can be retrieved using other parameters.
    
    Parameters:
    
    value - Fastq name
  - configFile
```
 String configFile()
```
    Database configuration file
  - configFile
```
 PathToIgraphPlugin configFile(String value)
```
    Set Database Config File. Database configuration file
    
    Parameters:
    
    value - Database Config File
  - splitTransitionProb
```
 Double splitTransitionProb()
```
    When the consensus nodes are split by taxa, this is the transition probability for moving from a node to the next node of the same taxon. It equals 1 minus the probability of a recombination between adjacent nodes.
  - splitTransitionProb
```
 PathToIgraphPlugin splitTransitionProb(Double value)
```
    Set Split Prob. When the consensus nodes are split by taxa, this is the transition probability for moving from a node to the next node of the same taxon. It equals 1 minus the probability of a recombination between adjacent nodes.
    
    Parameters:
    
    value - Split Prob
  - taxaFilterString
```
 TaxaList taxaFilterString()
```
    A list of taxa 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.
  - taxaFilter
```
 PathToIgraphPlugin taxaFilter(TaxaList value)
```
    Set Taxa. A list of taxa 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
  - refRangeFile
```
 String refRangeFile()
```
    The name of the file containing the reference ranges to keep.
  - refRangeFile
```
 PathToIgraphPlugin refRangeFile(String value)
```
    Set Ref Range File. The name of the file containing the reference ranges to keep.
    
    Parameters:
    
    value - Ref Range File
  - outputBase
```
 String outputBase()
```
    base name for output files from this Plugin. Two files will be produced for each chromosome.
  - outputBase
```
 PathToIgraphPlugin outputBase(String value)
```
    Set Output file base. base name for output files from this Plugin. Two files will be produced for each chromosome.
    
    Parameters:
    
    value - Output file base

Class PathToIgraphPlugin

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

PathToIgraphPlugin

Method Detail

processData

writeGraphInfoAllChr

writeGraphInfoFilesForChr

getIcon

getButtonName

getToolTipText

runPlugin

taxonName

taxonName

targetName

targetName

pathName

pathName

countMethod

countMethod

fastqName

fastqName

configFile

configFile

splitTransitionProb

splitTransitionProb

taxaFilterString

taxaFilter

refRangeFile

refRangeFile

outputBase

outputBase