net.maizegenetics.pangenome.hapCalling

Class ExportHaplotypePathToFilePlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin

All Implemented Interfaces:

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

public class ExportHaplotypePathToFilePlugin
extends net.maizegenetics.plugindef.AbstractPlugin

Plugin to export the Multimap exported by a Path finding algorithm to a directory of text files Created by zrm22 on 10/13/17.

Field Summary

Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin

DEFAULT_CITATION, POSITION_LIST_NONE, TAXA_LIST_NONE

Constructor Summary

Constructors

Constructor and Description
ExportHaplotypePathToFilePlugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
String	getButtonName()
ImageIcon	getIcon()
String	getToolTipText()
String	hapCountMethod() Method name used to create haplotype counts, as stored in db table methods
ExportHaplotypePathToFilePlugin	hapCountMethod(String value) Set Hap Count Method.
String	outputFileDirectory() Output file directory
ExportHaplotypePathToFilePlugin	outputFileDirectory(String value) Set Output File Directory.
String	pathMethod() Name of method used to create paths, as it should appear in the paths table
ExportHaplotypePathToFilePlugin	pathMethod(String value) Set Path Method.
String	pathMethodDetails() Description of method used to create paths - optional
ExportHaplotypePathToFilePlugin	pathMethodDetails(String value) Set Path Method Details.
net.maizegenetics.plugindef.DataSet	processData(net.maizegenetics.plugindef.DataSet input)
String	refVersion() Name of reference version as stored in the DB table genome_inteval_versions
ExportHaplotypePathToFilePlugin	refVersion(String value) Set Ref Version.

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

ExportHaplotypePathToFilePlugin

public ExportHaplotypePathToFilePlugin(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()

outputFileDirectory

public String outputFileDirectory()

Output file directory

Returns:

Output File Directory

outputFileDirectory

public ExportHaplotypePathToFilePlugin outputFileDirectory(String value)

Set Output File Directory. Output file directory

Parameters:

value - Output File Directory

Returns:

this plugin

refVersion

public String refVersion()

Name of reference version as stored in the DB table genome_inteval_versions

Returns:

Ref Version

refVersion

public ExportHaplotypePathToFilePlugin refVersion(String value)

Set Ref Version. Name of reference version as stored in the DB table genome_inteval_versions

Parameters:

value - Ref Version

Returns:

this plugin

hapCountMethod

public String hapCountMethod()

Method name used to create haplotype counts, as stored in db table methods

Returns:

Hap Counts Method

hapCountMethod

public ExportHaplotypePathToFilePlugin hapCountMethod(String value)

Set Hap Count Method. Method name used to create haplotype counts, as stored in db table methods

Parameters:

value - Hap Counts Method

Returns:

this plugin

pathMethod

public String pathMethod()

Name of method used to create paths, as it should appear in the paths table

Returns:

Path Method

pathMethod

public ExportHaplotypePathToFilePlugin pathMethod(String value)

Set Path Method. Name of method used to create paths, as it should appear in the paths table

Parameters:

value - Path Method

Returns:

this plugin

pathMethodDetails

public String pathMethodDetails()

Description of method used to create paths - optional

Returns:

Path Method Details

pathMethodDetails

public ExportHaplotypePathToFilePlugin pathMethodDetails(String value)

Set Path Method Details. Description of method used to create paths - optional

Parameters:

value - Path Method Details

Returns:

this plugin