net.maizegenetics.pangenome.hapCalling

Class HapCountBestPathPlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin

All Implemented Interfaces:

Runnable, net.maizegenetics.plugindef.Plugin, net.maizegenetics.plugindef.PluginListener, net.maizegenetics.util.ProgressListener

public class HapCountBestPathPlugin
extends net.maizegenetics.plugindef.AbstractPlugin

Field Summary

Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin

DEFAULT_CITATION, POSITION_LIST_NONE, TAXA_LIST_NONE

Constructor Summary

Constructors

Constructor and Description
HapCountBestPathPlugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
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.
ReferenceRangeEmissionProbability.METHOD	emissionMethod() Emission Method
HapCountBestPathPlugin	emissionMethod(ReferenceRangeEmissionProbability.METHOD value) Set Emission Method.
String	getButtonName()
ImageIcon	getIcon()
String	getToolTipText()
String	graphExportBasename() The base name for R-igraph export files.
HapCountBestPathPlugin	graphExportBasename(String value) Set Graph Export.
Integer	haplotypeCountsId() DB assigned haplotype_counts_id from the haplotype_counts table.
HapCountBestPathPlugin	haplotypeCountsId(Integer value) Set Hap Counts Id.
String	inclusionFilename() The name of the file containing read inclusion and exclusion counts for hapids.
HapCountBestPathPlugin	inclusionFilename(String value) Set Inclusion File.
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.
Double	minProbBF() Only nodes with minP or greater probability will be kept in the path when using the Backward-Forward algorithm,
Integer	minReads() minimum number of reads per anchor reference range.
HapCountBestPathPlugin	minReads(Integer value) Set Min Reads.
Integer	minTaxaPerRange() minimum number of taxa per anchor reference range.
HapCountBestPathPlugin	minTaxaPerRange(Integer value) Set Min Taxa.
Double	minTransitionProb() minimum probability of a transition between nodes at adjacent reference ranges.
HapCountBestPathPlugin	minTransitionProb(Double value) Set Min Transition Prob.
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	pluginDescription()
Double	probReadMappedCorrectly() minimum number of reads per anchor reference range.
HapCountBestPathPlugin	probReadMappedCorrectly(Double value) Set Prob Correct.
net.maizegenetics.plugindef.DataSet	processData(net.maizegenetics.plugindef.DataSet input)
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.
String	targetTaxon() The taxon that will be used to evaluate the node list returned.
HapCountBestPathPlugin	targetTaxon(String value) Set Target.
String	taxaFilterString() A comma delimited list of taxa (no spaces allowed) to include in graph.
HapCountBestPathPlugin	taxaFilterString(String value) Set Taxa.
Boolean	useBackwardForward() Use the Backward-Forward algorithm instead of the Viterbi algorithm for the HMM.
HapCountBestPathPlugin	useBackwardForward(Boolean value) Set Usebf.
void	writeGraphInfoFilesForChr(String outbase, List<HaplotypeNode> path, HaplotypeGraph graph, Map<Integer,Integer> inclusionMap, Map<Integer,Integer> exclusionMap, net.maizegenetics.dna.map.Chromosome chr, String target)
void	writePathInformation(String outFilename, List<HaplotypeNode> nodeList, HaplotypeGraph filteredGraph, Map<Integer,Integer> inclusionMap, Map<Integer,Integer> exclusionMap) Method is used to write diagnostic information about a path to a file.

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

HapCountBestPathPlugin

public HapCountBestPathPlugin(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

writePathInformation

public void writePathInformation(String outFilename,
                                 List<HaplotypeNode> nodeList,
                                 HaplotypeGraph filteredGraph,
                                 Map<Integer,Integer> inclusionMap,
                                 Map<Integer,Integer> exclusionMap)

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.

Parameters:

outFilename -

nodeList -

filteredGraph -

writeGraphInfoFilesForChr

public void writeGraphInfoFilesForChr(String outbase,
                                      List<HaplotypeNode> path,
                                      HaplotypeGraph graph,
                                      Map<Integer,Integer> inclusionMap,
                                      Map<Integer,Integer> exclusionMap,
                                      net.maizegenetics.dna.map.Chromosome chr,
                                      String target)

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

minTaxaPerRange

public Integer minTaxaPerRange()

minimum number of taxa per anchor reference range. Ranges with fewer taxa will not be included in the output node list.

Returns:

Min Taxa

minTaxaPerRange

public 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

Returns:

this plugin

minReads

public Integer minReads()

minimum number of reads per anchor reference range. Ranges with fewer reads will not be included in the output node list.

Returns:

Min Reads

minReads

public 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

Returns:

this plugin

maxNodesPerRange

public Integer maxNodesPerRange()

maximum number of nodes per reference range. Ranges with more nodes will not be included in the output node list.

Returns:

Max Nodes

maxNodesPerRange

public 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

Returns:

this plugin

maxReadsPerKB

public Integer maxReadsPerKB()

maximum number of include counts per anchor reference range. Ranges with more reads will not be included in the output node list.

Returns:

Max Reads

maxReadsPerKB

public 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

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 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

Returns:

this plugin

minTransitionProb

public Double minTransitionProb()

minimum probability of a transition between nodes at adjacent reference ranges.

Returns:

Min Transition Prob

minTransitionProb

public HapCountBestPathPlugin minTransitionProb(Double value)

Set Min Transition Prob. minimum probability of a transition between nodes at adjacent reference ranges.

Parameters:

value - Min Transition Prob

Returns:

this plugin

probReadMappedCorrectly

public Double probReadMappedCorrectly()

minimum number of reads per anchor reference range. Ranges with fewer reads will not be included in the output node list.

Returns:

Prob Correct

probReadMappedCorrectly

public 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

Returns:

this plugin

inclusionFilename

public String inclusionFilename()

The name of the file containing read inclusion and exclusion counts for hapids.

Returns:

Inclusion File

inclusionFilename

public HapCountBestPathPlugin inclusionFilename(String value)

Set Inclusion File. The name of the file containing read inclusion and exclusion counts for hapids.

Parameters:

value - Inclusion File

Returns:

this plugin

targetTaxon

public String targetTaxon()

The taxon that will be used to evaluate the node list returned.

Returns:

Target

targetTaxon

public HapCountBestPathPlugin targetTaxon(String value)

Set Target. The taxon that will be used to evaluate the node list returned.

Parameters:

value - Target

Returns:

this plugin

emissionMethod

public ReferenceRangeEmissionProbability.METHOD emissionMethod()

Emission Method

Returns:

Emission Method

emissionMethod

public HapCountBestPathPlugin emissionMethod(ReferenceRangeEmissionProbability.METHOD value)

Set Emission Method. Emission Method

Parameters:

value - Emission Method

Returns:

this plugin

refRangeFile

public String refRangeFile()

The name of the file containing the reference ranges to keep.

Returns:

Ref Range File

refRangeFile

public HapCountBestPathPlugin 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

splitTaxa

public Boolean splitTaxa()

split consensus nodes into one node per taxon.

Returns:

Split Taxa

splitTaxa

public HapCountBestPathPlugin splitTaxa(Boolean value)

Set Split Taxa. split consensus nodes into one node per taxon.

Parameters:

value - Split Taxa

Returns:

this plugin

splitTransitionProb

public 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.

Returns:

Split Prob

splitTransitionProb

public 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

Returns:

this plugin

useBackwardForward

public Boolean useBackwardForward()

Use the Backward-Forward algorithm instead of the Viterbi algorithm for the HMM.

Returns:

Usebf

useBackwardForward

public HapCountBestPathPlugin useBackwardForward(Boolean value)

Set Usebf. Use the Backward-Forward algorithm instead of the Viterbi algorithm for the HMM.

Parameters:

value - Usebf

Returns:

this plugin

minProbBF

public Double minProbBF()

Only nodes with minP or greater probability will be kept in the path when using the Backward-Forward algorithm,

Returns:

Min P

bfInfoFilename

public 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.

Returns:

Bf Info File

bfInfoFilename

public 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

Returns:

this plugin

haplotypeCountsId

public 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.

Returns:

Hap Counts Id

haplotypeCountsId

public 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

Returns:

this plugin

pathInfoFilename

public 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.

Returns:

Path Info File

pathInfoFilename

public 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

Returns:

this plugin

graphExportBasename

public String graphExportBasename()

The base name for R-igraph export files. If a value is supplied, vertices, edges, and a layout will be exported.

Returns:

Graph Export

graphExportBasename

public 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

Returns:

this plugin