net.maizegenetics.pangenome.hapCalling

Class FastqToKmerCountPlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin

All Implemented Interfaces:

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

public class FastqToKmerCountPlugin
extends net.maizegenetics.plugindef.AbstractPlugin

Created by zrm22 on 10/23/17.

Field Summary

Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin

DEFAULT_CITATION, POSITION_LIST_NONE, TAXA_LIST_NONE

Constructor Summary

Constructors

Constructor and Description
FastqToKmerCountPlugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
String	debugTaxon() Debug taxon
FastqToKmerCountPlugin	debugTaxon(String value) Set Debug Taxon.
String	exportHaplotypeFile() Text file to store haplotype scoring
FastqToKmerCountPlugin	exportHaplotypeFile(String value) Set Export Haplo File.
String	getButtonName()
ImageIcon	getIcon()
String	getToolTipText()
String	haplotypesGenomeFile() Fasta file and associated BWA indices for haplotypes
FastqToKmerCountPlugin	haplotypesGenomeFile(String value) Set Haplotype File.
Integer	numErrorAllowed() Maximum allowable error in order to count the read mapping
FastqToKmerCountPlugin	numErrorAllowed(Integer value) Set Allowed Error.
String	pluginUserManualURL()
net.maizegenetics.plugindef.DataSet	processData(net.maizegenetics.plugindef.DataSet input)
String	readFile() Raw Read file aligned to the reference
FastqToKmerCountPlugin	readFile(String value) Set Raw Read File.
String	refGenomeFile() Reference genome file - temporary need until we can back convert coordinates
FastqToKmerCountPlugin	refGenomeFile(String value) Set Ref File.

Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin

addListener, cancel, convert, dataSetReturned, getCitation, getInputs, getMenu, getPanel, getParameter, getParameter, getParentFrame, getUsage, getUsageHTML, isInteractive, performFunction, pluginDescription, 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

FastqToKmerCountPlugin

public FastqToKmerCountPlugin(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

pluginUserManualURL

public String pluginUserManualURL()

Specified by:

pluginUserManualURL in interface net.maizegenetics.plugindef.Plugin

Overrides:

pluginUserManualURL in class net.maizegenetics.plugindef.AbstractPlugin

getIcon

public ImageIcon getIcon()

getButtonName

public String getButtonName()

getToolTipText

public String getToolTipText()

haplotypesGenomeFile

public String haplotypesGenomeFile()

Fasta file and associated BWA indices for haplotypes

Returns:

Haplotype File

haplotypesGenomeFile

public FastqToKmerCountPlugin haplotypesGenomeFile(String value)

Set Haplotype File. Fasta file and associated BWA indices for haplotypes

Parameters:

value - Haplotype File

Returns:

this plugin

refGenomeFile

public String refGenomeFile()

Reference genome file - temporary need until we can back convert coordinates

Returns:

Ref File

refGenomeFile

public FastqToKmerCountPlugin refGenomeFile(String value)

Set Ref File. Reference genome file - temporary need until we can back convert coordinates

Parameters:

value - Ref File

Returns:

this plugin

readFile

public String readFile()

Raw Read file aligned to the reference

Returns:

Raw Read File

readFile

public FastqToKmerCountPlugin readFile(String value)

Set Raw Read File. Raw Read file aligned to the reference

Parameters:

value - Raw Read File

Returns:

this plugin

numErrorAllowed

public Integer numErrorAllowed()

Maximum allowable error in order to count the read mapping

Returns:

Allowed Error

numErrorAllowed

public FastqToKmerCountPlugin numErrorAllowed(Integer value)

Set Allowed Error. Maximum allowable error in order to count the read mapping

Parameters:

value - Allowed Error

Returns:

this plugin

exportHaplotypeFile

public String exportHaplotypeFile()

Text file to store haplotype scoring

Returns:

Export Haplo File

exportHaplotypeFile

public FastqToKmerCountPlugin exportHaplotypeFile(String value)

Set Export Haplo File. Text file to store haplotype scoring

Parameters:

value - Export Haplo File

Returns:

this plugin

debugTaxon

public String debugTaxon()

Debug taxon

Returns:

Debug Taxon

debugTaxon

public FastqToKmerCountPlugin debugTaxon(String value)

Set Debug Taxon. Debug taxon

Parameters:

value - Debug Taxon

Returns:

this plugin