net.maizegenetics.pangenome.db_loading

Class CreateIntervalBedFilesPlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin

All Implemented Interfaces:

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

public class CreateIntervalBedFilesPlugin
extends net.maizegenetics.plugindef.AbstractPlugin

Created by zrm22 on 1/16/18. Simple Plugin to Create The interval BED files from the database. If the user provides a extendedBedFile name, it will add the windowSize to both ends of the genome interval.

Field Summary

Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin

DEFAULT_CITATION, POSITION_LIST_NONE, TAXA_LIST_NONE

Constructor Summary

Constructors

Constructor and Description
CreateIntervalBedFilesPlugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
String	bedFile() Name for the bed file
CreateIntervalBedFilesPlugin	bedFile(String value) Set Bed File.
String	dbConfigFile() File holding the DB config information
CreateIntervalBedFilesPlugin	dbConfigFile(String value) Set Db Config File.
String	extendedBedFile() Name for the extended bed file
CreateIntervalBedFilesPlugin	extendedBedFile(String value) Set Extended Bed File.
String	getButtonName()
ImageIcon	getIcon()
String	getToolTipText()
String	pluginDescription()
net.maizegenetics.plugindef.DataSet	processData(net.maizegenetics.plugindef.DataSet input)
Integer	windowSize() Window size to add to the extendedBedFile
CreateIntervalBedFilesPlugin	windowSize(Integer value) Set Window Size.

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

CreateIntervalBedFilesPlugin

public CreateIntervalBedFilesPlugin(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

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

getIcon

public ImageIcon getIcon()

dbConfigFile

public String dbConfigFile()

File holding the DB config information

Returns:

Db Config File

dbConfigFile

public CreateIntervalBedFilesPlugin dbConfigFile(String value)

Set Db Config File. File holding the DB config information

Parameters:

value - Db Config File

Returns:

this plugin

bedFile

public String bedFile()

Name for the bed file

Returns:

Bed File

bedFile

public CreateIntervalBedFilesPlugin bedFile(String value)

Set Bed File. Name for the bed file

Parameters:

value - Bed File

Returns:

this plugin

extendedBedFile

public String extendedBedFile()

Name for the extended bed file

Returns:

Extended Bed File

extendedBedFile

public CreateIntervalBedFilesPlugin extendedBedFile(String value)

Set Extended Bed File. Name for the extended bed file

Parameters:

value - Extended Bed File

Returns:

this plugin

windowSize

public Integer windowSize()

Window size to add to the extendedBedFile

Returns:

Window Size

windowSize

public CreateIntervalBedFilesPlugin windowSize(Integer value)

Set Window Size. Window size to add to the extendedBedFile

Parameters:

value - Window Size

Returns:

this plugin