All Implemented Interfaces:

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

Enum Constant Summary

Enum Constants
Enum Constant	Description

Method Summary

Modifier and Type	Method	Description
`DataSet`	`processData(DataSet input)`
`void`	`writePathInformation(String outFilename, List<HaplotypeNode> nodeList, HaplotypeGraph filteredGraph, Multimap<ReferenceRange, SingleHapMapping> readMap)`	Method is used to write diagnostic information about a path to a file.
`void`	`writeGraphInfoFilesForChr(String outbase, List<HaplotypeNode> path, HaplotypeGraph graph, Multimap<ReferenceRange, SingleHapMapping> readMap, Chromosome chr, String target)`
`ImageIcon`	`getIcon()`
`String`	`getButtonName()`
`String`	`getToolTipText()`
`String`	`pluginDescription()`
`Integer`	`minTaxaPerRange()`	minimum number of taxa per anchor reference range.
`HapCountBestPathPlugin`	`minTaxaPerRange(Integer value)`	Set Min Taxa.
`Integer`	`minReads()`	minimum number of reads per anchor reference range.
`HapCountBestPathPlugin`	`minReads(Integer value)`	Set Min Reads.
`Integer`	`maxNodesPerRange()`	maximum number of nodes per reference range.
`HapCountBestPathPlugin`	`maxNodesPerRange(Integer value)`	Set Max Nodes.
`Integer`	`maxReadsPerKB()`	maximum number of include counts per anchor reference range.
`HapCountBestPathPlugin`	`maxReadsPerKB(Integer value)`	Set Max Reads.
`String`	`taxaFilterString()`	A comma delimited list of taxa (no spaces allowed) to include in graph.
`HapCountBestPathPlugin`	`taxaFilterString(String value)`	Set Taxa.
`Double`	`minTransitionProb()`	minimum probability of a transition between nodes at adjacent reference ranges.
`HapCountBestPathPlugin`	`minTransitionProb(Double value)`	Set Min Transition Prob.
`Double`	`probReadMappedCorrectly()`	minimum number of reads per anchor reference range.
`HapCountBestPathPlugin`	`probReadMappedCorrectly(Double value)`	Set Prob Correct.
`String`	`inclusionFilename()`	The name of the file containing read inclusion and exclusion counts for hapids.
`HapCountBestPathPlugin`	`inclusionFilename(String value)`	Set Inclusion File.
`String`	`targetTaxon()`	The taxon that will be used to evaluate the node list returned.
`HapCountBestPathPlugin`	`targetTaxon(String value)`	Set Target.
`ReferenceRangeEmissionProbability.METHOD`	`emissionMethod()`	Emission Method
`HapCountBestPathPlugin`	`emissionMethod(ReferenceRangeEmissionProbability.METHOD value)`	Set Emission Method.
`String`	`refRangeFile()`	The name of the file containing the reference ranges to keep.
`HapCountBestPathPlugin`	`refRangeFile(String value)`	Set Ref Range File.
`Boolean`	`splitTaxa()`	split consensus nodes into one node per taxon.
`HapCountBestPathPlugin`	`splitTaxa(Boolean value)`	Set Split Taxa.
`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.
`HapCountBestPathPlugin`	`splitTransitionProb(Double value)`	Set Split Prob.
`Boolean`	`useBackwardForward()`	Use the Backward-Forward algorithm instead of the Viterbi algorithm for the HMM.
`HapCountBestPathPlugin`	`useBackwardForward(Boolean value)`	Set Usebf.
`Double`	`minProbBF()`	Only nodes with minP or greater probability will be kept in the path when using the Backward-Forward algorithm,
`HapCountBestPathPlugin`	`minProbBF(Double value)`	Set Min P.
`String`	`bfInfoFilename()`	The name of the file to node probabilities from the backward-forward algorithm will be written.
`HapCountBestPathPlugin`	`bfInfoFilename(String value)`	Set Bf Info File.
`Integer`	`haplotypeCountsId()`	DB assigned haplotype_counts_id from the haplotype_counts table.
`HapCountBestPathPlugin`	`haplotypeCountsId(Integer value)`	Set Hap Counts Id.
`String`	`pathInfoFilename()`	The name of the file to which detailed path diagnostic information will be written.
`HapCountBestPathPlugin`	`pathInfoFilename(String value)`	Set Path Info File.
`String`	`graphExportBasename()`	The base name for R-igraph export files.
`HapCountBestPathPlugin`	`graphExportBasename(String value)`	Set Graph Export.
`Boolean`	`removeRangesWithEqualCounts()`	Ranges with equal read counts for all haplotypes should be removed from the graph.
`HapCountBestPathPlugin`	`removeRangesWithEqualCounts(Boolean value)`	Set Remove Equal.

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
  - HapCountBestPathPlugin
```
HapCountBestPathPlugin(Frame parentFrame, boolean isInteractive)
```
- Method Detail
  - processData
```
 DataSet processData(DataSet input)
```
  - writePathInformation
```
 void writePathInformation(String outFilename, List<HaplotypeNode> nodeList, HaplotypeGraph filteredGraph, Multimap<ReferenceRange, SingleHapMapping> readMap)
```
    Method is used to write diagnostic information about a path to a file. Information about each node on the path is written to a text file. Where a node in the path does not contain the target taxon, information is written for both that node and the node containing the target taxon from the same range.
  - writeGraphInfoFilesForChr
```
 void writeGraphInfoFilesForChr(String outbase, List<HaplotypeNode> path, HaplotypeGraph graph, Multimap<ReferenceRange, SingleHapMapping> readMap, Chromosome chr, String target)
```
  - getIcon
```
 ImageIcon getIcon()
```
  - getButtonName
```
 String getButtonName()
```
  - getToolTipText
```
 String getToolTipText()
```
  - pluginDescription
```
 String pluginDescription()
```
  - minTaxaPerRange
```
 Integer minTaxaPerRange()
```
    minimum number of taxa per anchor reference range. Ranges with fewer taxa will not be included in the output node list.
  - minTaxaPerRange
```
 HapCountBestPathPlugin minTaxaPerRange(Integer value)
```
    Set Min Taxa. minimum number of taxa per anchor reference range. Ranges with fewer taxa will not be included in the output node list.
    
    Parameters:
    
    value - Min Taxa
  - minReads
```
 Integer minReads()
```
    minimum number of reads per anchor reference range. Ranges with fewer reads will not be included in the output node list.
  - minReads
```
 HapCountBestPathPlugin minReads(Integer value)
```
    Set Min Reads. minimum number of reads per anchor reference range. Ranges with fewer reads will not be included in the output node list.
    
    Parameters:
    
    value - Min Reads
  - maxNodesPerRange
```
 Integer maxNodesPerRange()
```
    maximum number of nodes per reference range. Ranges with more nodes will not be included in the output node list.
  - maxNodesPerRange
```
 HapCountBestPathPlugin maxNodesPerRange(Integer value)
```
    Set Max Nodes. maximum number of nodes per reference range. Ranges with more nodes will not be included in the output node list.
    
    Parameters:
    
    value - Max Nodes
  - maxReadsPerKB
```
 Integer maxReadsPerKB()
```
    maximum number of include counts per anchor reference range. Ranges with more reads will not be included in the output node list.
  - maxReadsPerKB
```
 HapCountBestPathPlugin maxReadsPerKB(Integer value)
```
    Set Max Reads. maximum number of include counts per anchor reference range. Ranges with more reads will not be included in the output node list.
    
    Parameters:
    
    value - Max Reads
  - 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
```
 HapCountBestPathPlugin 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
  - minTransitionProb
```
 Double minTransitionProb()
```
    minimum probability of a transition between nodes at adjacent reference ranges.
  - minTransitionProb
```
 HapCountBestPathPlugin minTransitionProb(Double value)
```
    Set Min Transition Prob. minimum probability of a transition between nodes at adjacent reference ranges.
    
    Parameters:
    
    value - Min Transition Prob
  - probReadMappedCorrectly
```
 Double probReadMappedCorrectly()
```
    minimum number of reads per anchor reference range. Ranges with fewer reads will not be included in the output node list.
  - probReadMappedCorrectly
```
 HapCountBestPathPlugin probReadMappedCorrectly(Double value)
```
    Set Prob Correct. minimum number of reads per anchor reference range. Ranges with fewer reads will not be included in the output node list.
    
    Parameters:
    
    value - Prob Correct
  - inclusionFilename
```
 String inclusionFilename()
```
    The name of the file containing read inclusion and exclusion counts for hapids.
  - inclusionFilename
```
 HapCountBestPathPlugin inclusionFilename(String value)
```
    Set Inclusion File. The name of the file containing read inclusion and exclusion counts for hapids.
    
    Parameters:
    
    value - Inclusion File
  - targetTaxon
```
 String targetTaxon()
```
    The taxon that will be used to evaluate the node list returned.
  - targetTaxon
```
 HapCountBestPathPlugin targetTaxon(String value)
```
    Set Target. The taxon that will be used to evaluate the node list returned.
    
    Parameters:
    
    value - Target
  - emissionMethod
```
 ReferenceRangeEmissionProbability.METHOD emissionMethod()
```
    Emission Method
  - emissionMethod
```
 HapCountBestPathPlugin emissionMethod(ReferenceRangeEmissionProbability.METHOD value)
```
    Set Emission Method. Emission Method
    
    Parameters:
    
    value - Emission Method
  - refRangeFile
```
 String refRangeFile()
```
    The name of the file containing the reference ranges to keep.
  - refRangeFile
```
 HapCountBestPathPlugin refRangeFile(String value)
```
    Set Ref Range File. The name of the file containing the reference ranges to keep.
    
    Parameters:
    
    value - Ref Range File
  - splitTaxa
```
 Boolean splitTaxa()
```
    split consensus nodes into one node per taxon.
  - splitTaxa
```
 HapCountBestPathPlugin splitTaxa(Boolean value)
```
    Set Split Taxa. split consensus nodes into one node per taxon.
    
    Parameters:
    
    value - Split Taxa
  - 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
```
 HapCountBestPathPlugin 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
  - useBackwardForward
```
 Boolean useBackwardForward()
```
    Use the Backward-Forward algorithm instead of the Viterbi algorithm for the HMM.
  - useBackwardForward
```
 HapCountBestPathPlugin useBackwardForward(Boolean value)
```
    Set Usebf. Use the Backward-Forward algorithm instead of the Viterbi algorithm for the HMM.
    
    Parameters:
    
    value - Usebf
  - minProbBF
```
 Double minProbBF()
```
    Only nodes with minP or greater probability will be kept in the path when using the Backward-Forward algorithm,
  - minProbBF
```
 HapCountBestPathPlugin minProbBF(Double value)
```
    Set Min P. Only nodes with minP or greater probability will be kept in the path when using the Backward-Forward algorithm,
    
    Parameters:
    
    value - Min P
  - bfInfoFilename
```
 String bfInfoFilename()
```
    The name of the file to node probabilities from the backward-forward algorithm will be written. If the name is not supplied the diagnostic information will not be reported. The target taxon name should be supplied as well.
  - bfInfoFilename
```
 HapCountBestPathPlugin bfInfoFilename(String value)
```
    Set Bf Info File. The name of the file to node probabilities from the backward-forward algorithm will be written. If the name is not supplied the diagnostic information will not be reported. The target taxon name should be supplied as well.
    
    Parameters:
    
    value - Bf Info File
  - haplotypeCountsId
```
 Integer haplotypeCountsId()
```
    DB assigned haplotype_counts_id from the haplotype_counts table. This is assigned programatically and only present when plugin is called from an internal method.
  - haplotypeCountsId
```
 HapCountBestPathPlugin haplotypeCountsId(Integer value)
```
    Set Hap Counts Id. DB assigned haplotype_counts_id from the haplotype_counts table. This is assigned programatically and only present when plugin is called from an internal method.
    
    Parameters:
    
    value - Hap Counts Id
  - pathInfoFilename
```
 String pathInfoFilename()
```
    The name of the file to which detailed path diagnostic information will be written. If the name is not supplied the diagnotic information will not be reported. The target taxon name must be supplied as well.
  - pathInfoFilename
```
 HapCountBestPathPlugin pathInfoFilename(String value)
```
    Set Path Info File. The name of the file to which detailed path diagnostic information will be written. If the name is not supplied the diagnotic information will not be reported. The target taxon name must be supplied as well.
    
    Parameters:
    
    value - Path Info File
  - graphExportBasename
```
 String graphExportBasename()
```
    The base name for R-igraph export files. If a value is supplied, vertices, edges, and a layout will be exported.
  - graphExportBasename
```
 HapCountBestPathPlugin graphExportBasename(String value)
```
    Set Graph Export. The base name for R-igraph export files. If a value is supplied, vertices, edges, and a layout will be exported.
    
    Parameters:
    
    value - Graph Export
  - removeRangesWithEqualCounts
```
 Boolean removeRangesWithEqualCounts()
```
    Ranges with equal read counts for all haplotypes should be removed from the graph. Defaults to true but will be always be false if minReads = 0.
  - removeRangesWithEqualCounts
```
 HapCountBestPathPlugin removeRangesWithEqualCounts(Boolean value)
```
    Set Remove Equal. Ranges with equal read counts for all haplotypes should be removed from the graph. Defaults to true but will be always be false if minReads = 0.
    
    Parameters:
    
    value - Remove Equal

Class HapCountBestPathPlugin

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

HapCountBestPathPlugin

Method Detail

processData

writePathInformation

writeGraphInfoFilesForChr

getIcon

getButtonName

getToolTipText

pluginDescription

minTaxaPerRange

minTaxaPerRange

minReads

minReads

maxNodesPerRange

maxNodesPerRange

maxReadsPerKB

maxReadsPerKB

taxaFilterString

taxaFilterString

minTransitionProb

minTransitionProb

probReadMappedCorrectly

probReadMappedCorrectly

inclusionFilename

inclusionFilename

targetTaxon

targetTaxon

emissionMethod

emissionMethod

refRangeFile

refRangeFile

splitTaxa

splitTaxa

splitTransitionProb

splitTransitionProb

useBackwardForward

useBackwardForward

minProbBF

minProbBF

bfInfoFilename

bfInfoFilename

haplotypeCountsId

haplotypeCountsId

pathInfoFilename

pathInfoFilename

graphExportBasename

graphExportBasename

removeRangesWithEqualCounts

removeRangesWithEqualCounts