net.maizegenetics.analysis.data

Class ExportPlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.analysis.data.ExportPlugin

All Implemented Interfaces:

Runnable, Plugin, PluginListener, ProgressListener

public class ExportPlugin
extends AbstractPlugin

Author:

Terry Casstevens

Field Summary

Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin

DEFAULT_CITATION, POSITION_LIST_NONE, TAXA_LIST_NONE

Constructor Summary

Constructors

Constructor and Description
ExportPlugin(Frame parentFrame, boolean isInteractive) Creates a new instance of ExportPlugin

Method Summary

Modifier and Type	Method and Description
FileLoadPlugin.TasselFileType	fileType() Export file format
ExportPlugin	fileType(FileLoadPlugin.TasselFileType value) Set Format.
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	includeTaxaAnnotations() Whether to include taxa annotations if format supports taxa annotations.
ExportPlugin	includeTaxaAnnotations(Boolean value) Set Include Taxa Annotations.
Boolean	keepDepth() Whether to keep depth if format supports depth.
ExportPlugin	keepDepth(Boolean value) Set Keep Depth.
String	performFunctionForAlignment(GenotypeTable inputAlignment)
String	performFunctionForDistanceMatrix(DistanceMatrix input)
String	performFunctionForFilter(FilterList filter)
String	performFunctionForPhenotype(Phenotype input)
String	performFunctionForPositionList(PositionList input)
String	performFunctionForSimpleTree(SimpleTree input)
String	performFunctionForTableReport(TableReport input)
String	performFunctionForTaxaList(TaxaList input)
String	pluginUserManualURL() Returns URL to User Manual.
DataSet	processData(DataSet input) For the new Generic Plugin Parameter design, performFunction() will automatically call this.
String	saveFile() Save file as...
ExportPlugin	saveFile(String value) Save file as...
ExportPlugin	setAlignmentFileType(FileLoadPlugin.TasselFileType type) Deprecated.
ExportPlugin	setSaveFile(String saveFile) Deprecated.

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

ExportPlugin

public ExportPlugin(Frame parentFrame,
                    boolean isInteractive)

Creates a new instance of ExportPlugin

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.

performFunctionForDistanceMatrix

public String performFunctionForDistanceMatrix(DistanceMatrix input)

performFunctionForTableReport

public String performFunctionForTableReport(TableReport input)

performFunctionForFilter

public String performFunctionForFilter(FilterList filter)

performFunctionForPhenotype

public String performFunctionForPhenotype(Phenotype input)

performFunctionForAlignment

public String performFunctionForAlignment(GenotypeTable inputAlignment)

performFunctionForSimpleTree

public String performFunctionForSimpleTree(SimpleTree input)

performFunctionForTaxaList

public String performFunctionForTaxaList(TaxaList input)

performFunctionForPositionList

public String performFunctionForPositionList(PositionList input)

getIcon

public ImageIcon getIcon()

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

Returns:

ImageIcon

getButtonName

public String getButtonName()

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

Returns:

String

getToolTipText

public String getToolTipText()

Tool Tip Text for this plugin

Returns:

String

pluginUserManualURL

public String pluginUserManualURL()

Description copied from interface: Plugin

Returns URL to User Manual.

Specified by:

pluginUserManualURL in interface Plugin

Overrides:

pluginUserManualURL in class AbstractPlugin

Returns:

URL

saveFile

public String saveFile()

Save file as...

Returns:

Save As

saveFile

public ExportPlugin saveFile(String value)

Save file as...

Parameters:

value - filename

Returns:

this plugin

setSaveFile

@Deprecated
public ExportPlugin setSaveFile(String saveFile)

Deprecated.

fileType

public FileLoadPlugin.TasselFileType fileType()

Export file format

Returns:

Format

fileType

public ExportPlugin fileType(FileLoadPlugin.TasselFileType value)

Set Format. Export file format

Parameters:

value - Format

Returns:

this plugin

setAlignmentFileType

@Deprecated
public ExportPlugin setAlignmentFileType(FileLoadPlugin.TasselFileType type)

Deprecated.

keepDepth

public Boolean keepDepth()

Whether to keep depth if format supports depth.

Returns:

Keep Depth

keepDepth

public ExportPlugin keepDepth(Boolean value)

Set Keep Depth. Whether to keep depth if format supports depth.

Parameters:

value - Keep Depth

Returns:

this plugin

includeTaxaAnnotations

public Boolean includeTaxaAnnotations()

Whether to include taxa annotations if format supports taxa annotations.

Returns:

Include Taxa Annotations

includeTaxaAnnotations

public ExportPlugin includeTaxaAnnotations(Boolean value)

Set Include Taxa Annotations. Whether to include taxa annotations if format supports taxa annotations.

Parameters:

value - Include Taxa Annotations

Returns:

this plugin