net.maizegenetics.analysis.gbs

Class ModifyTBTHDF5Plugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.analysis.gbs.ModifyTBTHDF5Plugin

All Implemented Interfaces:

Runnable, Plugin, PluginListener, ProgressListener

public class ModifyTBTHDF5Plugin
extends AbstractPlugin

This pipeline modifies TagsByTaxa HDF5 file with data organized by taxa. It can: 1. Create an empty TBT. 2. Merge two TBT 3. Combined similarly named taxa 4. Pivot a taxa TBT to a tag TBT

Author:

ed

Field Summary

Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin

DEFAULT_CITATION, POSITION_LIST_NONE, TAXA_LIST_NONE

Constructor Summary

Constructors

Constructor and Description
ModifyTBTHDF5Plugin()
ModifyTBTHDF5Plugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
String	additionTaxaFile()
ModifyTBTHDF5Plugin	additionTaxaFile(String value)
String	getButtonName() Button name for this plugin to be used in buttons, etc.
ImageIcon	getIcon() Icon for this plugin to be used in buttons, etc.
String	getToolTipText() Tool Tip Text for this plugin
Boolean	mergeTaxa()
ModifyTBTHDF5Plugin	mergeTaxa(Boolean value)
String	pivotTBTHDF5File()
ModifyTBTHDF5Plugin	pivotTBTHDF5File(String value)
DataSet	processData(DataSet input) For the new Generic Plugin Parameter design, performFunction() will automatically call this.
String	targetTBTHDF5File()
ModifyTBTHDF5Plugin	targetTBTHDF5File(String value)

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

ModifyTBTHDF5Plugin

public ModifyTBTHDF5Plugin()

ModifyTBTHDF5Plugin

public ModifyTBTHDF5Plugin(Frame parentFrame,
                           boolean isInteractive)

Method Detail

processData

public DataSet processData(DataSet input)

Description copied from interface: Plugin

For the new Generic Plugin Parameter design, performFunction() will automatically call this. Therefore, coders of Plugins should override this instead of performFunction().

Specified by:

processData in interface Plugin

Overrides:

processData in class AbstractPlugin

Parameters:

input - input

Returns:

resulting data set or null.

targetTBTHDF5File

public String targetTBTHDF5File()

targetTBTHDF5File

public ModifyTBTHDF5Plugin targetTBTHDF5File(String value)

additionTaxaFile

public String additionTaxaFile()

additionTaxaFile

public ModifyTBTHDF5Plugin additionTaxaFile(String value)

mergeTaxa

public Boolean mergeTaxa()

mergeTaxa

public ModifyTBTHDF5Plugin mergeTaxa(Boolean value)

pivotTBTHDF5File

public String pivotTBTHDF5File()

pivotTBTHDF5File

public ModifyTBTHDF5Plugin pivotTBTHDF5File(String value)

getIcon

public ImageIcon getIcon()

Description copied from interface: Plugin

Icon for this plugin to be used in buttons, etc.

Returns:

ImageIcon

getButtonName

public String getButtonName()

Description copied from interface: Plugin

Button name for this plugin to be used in buttons, etc.

Returns:

String

getToolTipText

public String getToolTipText()

Description copied from interface: Plugin

Tool Tip Text for this plugin

Returns:

String