All Implemented Interfaces:

java.lang.Runnable , net.maizegenetics.plugindef.Plugin , net.maizegenetics.plugindef.PluginListener , net.maizegenetics.util.ProgressListener
```
@Deprecated() 
public class RunHapCollapsePipelinePlugin
extends AbstractPlugin
                    
```
Simple plugin to run the full Haplotype Collapse plugin. Will do the following steps: Steps: 1. Loop through each reference range in the graph: 1.a Extract the HaplotypeNodes with the VariantContexts(We assume that the user has not pulled these yet for memory reasons) 1.b Merge all the VariantContext records for each BP of the reference range 1.c Export a GenotypeTable containing each bp 1.d Run HapCollapse Finding algorithm on this genotype table 2. For each VCF file exported, upload them to the DB as a consensus Created by zrm22 on 11/8/17.

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
`RunHapCollapsePipelinePlugin(Frame parentFrame, boolean isInteractive)`

Enum Constant Summary

Enum Constants
Enum Constant	Description

Method Summary

Modifier and Type	Method	Description
`DataSet`	`processData(DataSet input)`
`void`	`runCollapsePipeline(HaplotypeGraph graph, String referenceFasta)`	This method will loop through each reference range in the graph and will: 1.
`String`	`getButtonName()`
`String`	`getToolTipText()`
`String`	`pluginDescription()`
`ImageIcon`	`getIcon()`
`String`	`reference()`	Input Reference Fasta
`RunHapCollapsePipelinePlugin`	`reference(String value)`	Set Ref.
`String`	`dbConfigFile()`	File holding the DB config information
`RunHapCollapsePipelinePlugin`	`dbConfigFile(String value)`	Set Db Config File.
`String`	`consensusVCFOutputDir()`	Directory where you want to store the output VCFs from the consensus process
`RunHapCollapsePipelinePlugin`	`consensusVCFOutputDir(String value)`	Set Consensus VCF Output Dir.
`String`	`consensusFastaOutputDir()`	Directory where you want to store the output fastas from the consensus process
`RunHapCollapsePipelinePlugin`	`consensusFastaOutputDir(String value)`	Set Consensus Fasta Output Dir.
`String`	`collapseMethod()`	Name of the collapse method to be stored in the database
`RunHapCollapsePipelinePlugin`	`collapseMethod(String value)`	Set Collapse Method.
`String`	`collapseMethodDetails()`	Details for the collapse method to be stored in the database
`RunHapCollapsePipelinePlugin`	`collapseMethodDetails(String value)`	Set Collapse Method Details.
`FindHaplotypeClustersPlugin.CLUSTER_METHOD`	`clusterMethod()`	The method used to cluster taxa.
`RunHapCollapsePipelinePlugin`	`clusterMethod(FindHaplotypeClustersPlugin.CLUSTER_METHOD value)`	Set Cluster Method.
`FillIndelsIntoConsensus.INDEL_MERGE_RULE`	`mergeRule()`	The rule in which to resolve the conflicting Indels after consensus has been found.
`RunHapCollapsePipelinePlugin`	`mergeRule(FillIndelsIntoConsensus.INDEL_MERGE_RULE value)`	Set Indel Merge Rule.

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, 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
  - RunHapCollapsePipelinePlugin
```
RunHapCollapsePipelinePlugin(Frame parentFrame, boolean isInteractive)
```
- Method Detail
  - processData
```
 DataSet processData(DataSet input)
```
  - runCollapsePipeline
```
 void runCollapsePipeline(HaplotypeGraph graph, String referenceFasta)
```
    This method will loop through each reference range in the graph and will: 1. Merge all the gvcf records for a given haplotype method: 2. Cluster the haplotypes together into groups Then when done with all reference ranges, load the exported gvcfs and fastas to the db. This is the main function that processes each reference range in the graph
    
    Parameters:
    
    graph - haplotype graph
    
    referenceFasta - reference fasta
  - getButtonName
```
 String getButtonName()
```
  - getToolTipText
```
 String getToolTipText()
```
  - pluginDescription
```
 String pluginDescription()
```
  - getIcon
```
 ImageIcon getIcon()
```
  - reference
```
 String reference()
```
    Input Reference Fasta
  - reference
```
 RunHapCollapsePipelinePlugin reference(String value)
```
    Set Ref. Input Reference Fasta
    
    Parameters:
    
    value - Ref
  - dbConfigFile
```
 String dbConfigFile()
```
    File holding the DB config information
  - dbConfigFile
```
 RunHapCollapsePipelinePlugin dbConfigFile(String value)
```
    Set Db Config File. File holding the DB config information
    
    Parameters:
    
    value - Db Config File
  - consensusVCFOutputDir
```
 String consensusVCFOutputDir()
```
    Directory where you want to store the output VCFs from the consensus process
  - consensusVCFOutputDir
```
 RunHapCollapsePipelinePlugin consensusVCFOutputDir(String value)
```
    Set Consensus VCF Output Dir. Directory where you want to store the output VCFs from the consensus process
    
    Parameters:
    
    value - Consensus VCF Output Dir
  - consensusFastaOutputDir
```
 String consensusFastaOutputDir()
```
    Directory where you want to store the output fastas from the consensus process
  - consensusFastaOutputDir
```
 RunHapCollapsePipelinePlugin consensusFastaOutputDir(String value)
```
    Set Consensus Fasta Output Dir. Directory where you want to store the output fastas from the consensus process
    
    Parameters:
    
    value - Consensus Fasta Output Dir
  - collapseMethod
```
 String collapseMethod()
```
    Name of the collapse method to be stored in the database
  - collapseMethod
```
 RunHapCollapsePipelinePlugin collapseMethod(String value)
```
    Set Collapse Method. Name of the collapse method to be stored in the database
    
    Parameters:
    
    value - Collapse Method
  - collapseMethodDetails
```
 String collapseMethodDetails()
```
    Details for the collapse method to be stored in the database
  - collapseMethodDetails
```
 RunHapCollapsePipelinePlugin collapseMethodDetails(String value)
```
    Set Collapse Method Details. Details for the collapse method to be stored in the database
    
    Parameters:
    
    value - Collapse Method Details
  - clusterMethod
```
 FindHaplotypeClustersPlugin.CLUSTER_METHOD clusterMethod()
```
    The method used to cluster taxa. Coverage seeds the first cluster with the highest coverage taxon. UPGMA builds a UPGMA tree then cuts it at maxDistance.
  - clusterMethod
```
 RunHapCollapsePipelinePlugin clusterMethod(FindHaplotypeClustersPlugin.CLUSTER_METHOD value)
```
    Set Cluster Method. The method used to cluster taxa. Coverage seeds the first cluster with the highest coverage taxon. UPGMA builds a UPGMA tree then cuts it at maxDistance.
    
    Parameters:
    
    value - Cluster Method
  - mergeRule
```
 FillIndelsIntoConsensus.INDEL_MERGE_RULE mergeRule()
```
    The rule in which to resolve the conflicting Indels after consensus has been found.
  - mergeRule
```
 RunHapCollapsePipelinePlugin mergeRule(FillIndelsIntoConsensus.INDEL_MERGE_RULE value)
```
    Set Indel Merge Rule. The rule in which to resolve the conflicting Indels after consensus has been found.
    
    Parameters:
    
    value - Indel Merge Rule

Class RunHapCollapsePipelinePlugin

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

RunHapCollapsePipelinePlugin

Method Detail

processData

runCollapsePipeline

getButtonName

getToolTipText

pluginDescription

getIcon

reference

reference

dbConfigFile

dbConfigFile

consensusVCFOutputDir

consensusVCFOutputDir

consensusFastaOutputDir

consensusFastaOutputDir

collapseMethod

collapseMethod

collapseMethodDetails

collapseMethodDetails

clusterMethod

clusterMethod

mergeRule

mergeRule