net.maizegenetics.pangenome.hapCalling

Class ExportVCForTaxonMethodPlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin

All Implemented Interfaces:

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

public class ExportVCForTaxonMethodPlugin
extends net.maizegenetics.plugindef.AbstractPlugin

Exports variant context lists to vcf file. NOTE: PathsToVCF is not used as that method only exports SNPs. Input: taxon and method to identify haplotypes table entries A single chromosome may also be supplied. If no chromoseom is given, data for all chromosomes will be pulled. Output: vcf file TODO: create hmp or vcf based on file extension.

Author:

lcj34

Field Summary

Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin

DEFAULT_CITATION, POSITION_LIST_NONE, TAXA_LIST_NONE

Constructor Summary

Constructors

Constructor and Description
ExportVCForTaxonMethodPlugin()
ExportVCForTaxonMethodPlugin(Frame parentFrame)
ExportVCForTaxonMethodPlugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
String	chrom() If a chrom is specified, pull only data for that chromosome.
ExportVCForTaxonMethodPlugin	chrom(String value) Set Chrom.
String	configFile() Config file that specifies database connection parameters
ExportVCForTaxonMethodPlugin	configFile(String value) Set Config File.
String	getButtonName()
ImageIcon	getIcon()
String	getToolTipText()
String	method() Name of method used when creating the haplotypes to be pulled
ExportVCForTaxonMethodPlugin	method(String value) Set Method.
Boolean	onlyGenic() True means create vcf only for hte genic intervals.
ExportVCForTaxonMethodPlugin	onlyGenic(Boolean value) Set Only Genic.
String	outputFile() FUll path to output file created by this plugin .
ExportVCForTaxonMethodPlugin	outputFile(String value) Set Output File.
net.maizegenetics.plugindef.DataSet	processData(net.maizegenetics.plugindef.DataSet input)
String	taxon() Name of taxon whose variant contexts should be pulled.
ExportVCForTaxonMethodPlugin	taxon(String value) Set Taxon.

Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin

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

ExportVCForTaxonMethodPlugin

public ExportVCForTaxonMethodPlugin()

ExportVCForTaxonMethodPlugin

public ExportVCForTaxonMethodPlugin(Frame parentFrame)

ExportVCForTaxonMethodPlugin

public ExportVCForTaxonMethodPlugin(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

getIcon

public ImageIcon getIcon()

getButtonName

public String getButtonName()

getToolTipText

public String getToolTipText()

configFile

public String configFile()

Config file that specifies database connection parameters

Returns:

Config File

configFile

public ExportVCForTaxonMethodPlugin configFile(String value)

Set Config File. Config file that specifies database connection parameters

Parameters:

value - Config File

Returns:

this plugin

taxon

public String taxon()

Name of taxon whose variant contexts should be pulled.

Returns:

Taxon

taxon

public ExportVCForTaxonMethodPlugin taxon(String value)

Set Taxon. Name of taxon whose variant contexts should be pulled.

Parameters:

value - Taxon

Returns:

this plugin

method

public String method()

Name of method used when creating the haplotypes to be pulled

Returns:

Method

method

public ExportVCForTaxonMethodPlugin method(String value)

Set Method. Name of method used when creating the haplotypes to be pulled

Parameters:

value - Method

Returns:

this plugin

outputFile

public String outputFile()

FUll path to output file created by this plugin .

Returns:

Output File

outputFile

public ExportVCForTaxonMethodPlugin outputFile(String value)

Set Output File. FUll path to output file created by this plugin .

Parameters:

value - Output File

Returns:

this plugin

onlyGenic

public Boolean onlyGenic()

True means create vcf only for hte genic intervals. False means include both genic and inter-genic intervals

Returns:

Only Genic

onlyGenic

public ExportVCForTaxonMethodPlugin onlyGenic(Boolean value)

Set Only Genic. True means create vcf only for hte genic intervals. False means include both genic and inter-genic intervals

Parameters:

value - Only Genic

Returns:

this plugin

chrom

public String chrom()

If a chrom is specified, pull only data for that chromosome. If no chromosome is specified, data for all chromsomes will be pulled.

Returns:

Chrom

chrom

public ExportVCForTaxonMethodPlugin chrom(String value)

Set Chrom. If a chrom is specified, pull only data for that chromosome. If no chromosome is specified, data for all chromsomes will be pulled.

Parameters:

value - Chrom

Returns:

this plugin