All Implemented Interfaces:

java.lang.Runnable , net.maizegenetics.plugindef.Plugin , net.maizegenetics.plugindef.PluginListener , net.maizegenetics.util.ProgressListener
```
public class HaplotypeGraphBuilderPlugin
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
`HaplotypeGraphBuilderPlugin(Frame parentFrame, boolean isInteractive)`

Enum Constant Summary

Enum Constants
Enum Constant	Description

Method Summary

Modifier and Type	Method	Description
`DataSet`	`processData(DataSet input)`
`HaplotypeGraph`	`build()`
`static List<Tuple<String, String>>`	`convertMethods(String methodPairs)`
`String`	`configFile()`	Database configuration file
`HaplotypeGraphBuilderPlugin`	`configFile(String value)`	Set Database Config File.
`String`	`methods()`	Pairs of methods (haplotype method name and range group method name).
`HaplotypeGraphBuilderPlugin`	`methods(String value)`	Set Methods.
`Boolean`	`includeSequences()`	Whether to include sequences in haplotype nodes.
`HaplotypeGraphBuilderPlugin`	`includeSequences(Boolean value)`	Set Include Sequences.
`Boolean`	`includeVariantContexts()`	Whether to include variant contexts in haplotype nodes.
`HaplotypeGraphBuilderPlugin`	`includeVariantContexts(Boolean value)`	Set Include Variant Contexts.
`SortedSet<Integer>`	`hapids()`	List of haplotype ids to include in the graph.
`HaplotypeGraphBuilderPlugin`	`hapids(SortedSet<Integer> value)`	Set Haplotype Ids.
`List<String>`	`chromosomes()`	Chromosomes
`HaplotypeGraphBuilderPlugin`	`chromosomes(List<String> value)`	Set Chromosomes.
`TaxaList`	`taxaList()`	Optional list of taxa to include.
`HaplotypeGraphBuilderPlugin`	`taxaList(TaxaList value)`	Set Taxa.
`HaplotypeGraphBuilderPlugin`	`taxaList(String value)`
`String`	`localGVCFFolder()`	Local folder to which gvcf file will be downloaded.
`HaplotypeGraphBuilderPlugin`	`localGVCFFolder(String value)`	Set local gvcf folder path
`ImageIcon`	`getIcon()`
`String`	`getButtonName()`
`String`	`getToolTipText()`
`static void`	`main(Array<String> args)`

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
  - HaplotypeGraphBuilderPlugin
```
HaplotypeGraphBuilderPlugin(Frame parentFrame, boolean isInteractive)
```
- Method Detail
  - processData
```
 DataSet processData(DataSet input)
```
  - build
```
 HaplotypeGraph build()
```
  - convertMethods
```
 static List<Tuple<String, String>> convertMethods(String methodPairs)
```
  - configFile
```
 String configFile()
```
    Database configuration file
  - configFile
```
 HaplotypeGraphBuilderPlugin configFile(String value)
```
    Set Database Config File. Database configuration file
    
    Parameters:
    
    value - Database Config File
  - methods
```
 String methods()
```
    Pairs of methods (haplotype method name and range group method name). Method pair separated by a comma, and pairs separated by semicolon. The range group is optional Usage: ,
  - methods
```
 HaplotypeGraphBuilderPlugin methods(String value)
```
    Set Methods. Pairs of methods (haplotype method name and range group method name). Method pair separated by a comma, and pairs separated by semicolon. The range group is optional Usage: ,
    
    Parameters:
    
    value - Methods
  - includeSequences
```
 Boolean includeSequences()
```
    Whether to include sequences in haplotype nodes.
  - includeSequences
```
 HaplotypeGraphBuilderPlugin includeSequences(Boolean value)
```
    Set Include Sequences. Whether to include sequences in haplotype nodes.
    
    Parameters:
    
    value - Include Sequences
  - includeVariantContexts
```
 Boolean includeVariantContexts()
```
    Whether to include variant contexts in haplotype nodes.
  - includeVariantContexts
```
 HaplotypeGraphBuilderPlugin includeVariantContexts(Boolean value)
```
    Set Include Variant Contexts. Whether to include variant contexts in haplotype nodes.
    
    Parameters:
    
    value - Include Variant Contexts
  - hapids
```
 SortedSet<Integer> hapids()
```
    List of haplotype ids to include in the graph. If not specified, all ids are included.
  - hapids
```
 HaplotypeGraphBuilderPlugin hapids(SortedSet<Integer> value)
```
    Set Haplotype Ids. List of haplotype ids to include in the graph. If not specified, all ids are included.
    
    Parameters:
    
    value - Haplotype Ids
  - chromosomes
```
 List<String> chromosomes()
```
    Chromosomes
  - chromosomes
```
 HaplotypeGraphBuilderPlugin chromosomes(List<String> value)
```
    Set Chromosomes. Chromosomes
    
    Parameters:
    
    value - Chromosomes
  - taxaList
```
 TaxaList taxaList()
```
    Optional list of taxa to include. This can be a comma separated list of taxa (no spaces unless surrounded by quotes), file (.txt) with list of taxa names to include, or a taxa list file (.json or .json.gz). By default, all taxa will be included.
  - taxaList
```
 HaplotypeGraphBuilderPlugin taxaList(TaxaList value)
```
    Set Taxa. Optional list of taxa to include. This can be a comma separated list of taxa (no spaces unless surrounded by quotes), file (.txt) with list of taxa names to include, or a taxa list file (.json or .json.gz). By default, all taxa will be included.
    
    Parameters:
    
    value - Taxa
  - taxaList
```
 HaplotypeGraphBuilderPlugin taxaList(String value)
```
  - localGVCFFolder
```
 String localGVCFFolder()
```
    Local folder to which gvcf file will be downloaded.
  - localGVCFFolder
```
 HaplotypeGraphBuilderPlugin localGVCFFolder(String value)
```
    Set local gvcf folder path
    
    Parameters:
    
    value - Local GVCF Folder path
  - getIcon
```
 ImageIcon getIcon()
```
  - getButtonName
```
 String getButtonName()
```
  - getToolTipText
```
 String getToolTipText()
```
  - main
```
 static void main(Array<String> args)
```

Class HaplotypeGraphBuilderPlugin

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

HaplotypeGraphBuilderPlugin

Method Detail

processData

build

convertMethods

configFile

configFile

methods

methods

includeSequences

includeSequences

includeVariantContexts

includeVariantContexts

hapids

hapids

chromosomes

chromosomes

taxaList

taxaList

taxaList

localGVCFFolder

localGVCFFolder

getIcon

getButtonName

getToolTipText

main