net.maizegenetics.plugindef

Interface Plugin

All Superinterfaces:

PluginListener, ProgressListener, Runnable

All Known Implementing Classes:

AbstractDisplayPlugin, AbstractPlugin, AddDistanceMatrixPlugin, AdditiveSiteStorePlugin, AddReferenceAlleleToHDF5Plugin, AdjustPhasingPlugin, AMatrixPlugin, AnnotateTOPMwSAMPlugin, ArchaeopteryxPlugin, AvgPhenotypeByTaxaPlugin, BinaryToTextPlugin, BoxCoxTransformationPlugin, BuildUnfinishedHDF5GenotypesPlugin, CallParentAllelesPlugin, ChartDisplayPlugin, ClusterGenotypesPlugin, ColumnsToBinaryFullGenomeTablePlugin, ColumnsToBinarySNPOnlyTablePlugin, CombineDataSetsPlugin, CompareGenosBetweenHapMapFilesPlugin, ContigPETagCountPlugin, ConvertAlignmentCoordinatesPlugin, CreateHybridGenotypesPlugin, CreateTreePlugin, DiscoverySNPCallerPlugin, DiscoverySNPCallerPluginV2, DistanceMatrixPlugin, DistanceMatrixRangesPlugin, EqtlAssociationPlugin, ExportMultiplePlugin, ExportPlugin, ExtractHapmapSubsetPlugin, FastMultithreadedAssociationPlugin, FastqToPETagCountPlugin, FastqToTagCountPlugin, FastqToTBTPlugin, FeatureListToPositionsPlugin, FileLoadPlugin, FILLINFindHaplotypesPlugin, FILLINImputationPlugin, FilterAlignmentPlugin, FilterDataSetPlugin, FilterSiteBuilderPlugin, FilterSiteNamePlugin, FilterSubsetPlugin, FilterTaxaBuilderPlugin, FilterTaxaPropertiesPlugin, FilterTraitsPlugin, FindInversionsPlugin, FindMergeHaplotypesPlugin, FixedEffectLMPlugin, FSFHapImputationPlugin, GBSSeqToTagDBPlugin, GenomeAnnosDBQueryToPositionListPlugin, GenomicSelectionPlugin, GenosToABHPlugin, GenotypeSummaryPlugin, GetPhenotypeFromB4RPlugin, GetPositionListPlugin, GetTagSequenceFromDBPlugin, GetTagTaxaDistFromDBPlugin, GetTaxaListPlugin, GOBIIPlugin, GWAS_IFLPlugin, HapBreakpoints_IFLFilePlugin, HDF5SummaryPlugin, HetsToUnknownPlugin, HMatrixPlugin, IdentityRecognitionPlugin, ImputationAccuracyPlugin, ImputationPlugin, ImputeProgenyStatesPlugin, IndelsToUnknownPlugin, IntersectionAlignmentPlugin, KeepSpecifiedReadsinFastqPlugin, KeepSpecifiedSitesInTOPMPlugin, KinshipPlugin, KmerToTagCountPlugin, KmerToTBTPlugin, LDKNNiImputationHetV2Plugin, LDKNNiImputationHetV3Plugin, LDKNNiImputationPlugin, LinkageDiseqDisplayPlugin, LinkageDisequilibriumPlugin, ListPlugins, LIXPlugin, LoadRNAContigsToGBSDBPlugin, ManhattanDisplayPlugin, MarkerDNARun_IFLFilePlugin, MaskGenotypePlugin, MemoryUsagePlugin, MergeAlignmentsSameSitesPlugin, MergeBreakpointFilesPlugin, MergeDuplicateSNPsPlugin, MergeGenotypeTablesPlugin, MergeGenotypeTablesPluginV2, MergeHDF5GenotypesSameSitesPlugin, MergeMultipleTagCountPlugin, MergeMultipleTOPMPlugin, MergePETagCountPlugin, MergeRenameDeleteTaxaPlugin, MergeTagsByTaxaFilesByRowPlugin, MergeTagsByTaxaFilesPlugin, MLMPlugin, ModifyTBTHDF5Plugin, MonetDB_IFLFilePlugin, MultiDimensionalScalingPlugin, NumericalGenotypePlugin, PanAAddPosToTagMapPlugin, PanABuildPivotTBTPlugin, PanABuildTagBlockPosPlugin, PanABuildTagGWASMapPlugin, PanABuildTrainingSetPlugin, PanAFilteringTagMapPlugin, PanAH5ToAnchorPlugin, PanAMergeMappingResultPlugin, PanAModelTrainingPlugin, PanAPredictionPlugin, PanAReadDigestPlugin, PanAReadToKmerPlugin, PanASamToMultiPositionTOPMPlugin, PanASplitTagBlockPosPlugin, PanASplitTBTPlugin, PanATagGWASMappingPlugin, PanATagMapToFastaPlugin, ParentPhasingPlugin, PassThroughPlugin, PlinkLoadPlugin, PreferencesDialog, PreProcessGOBIIMappingFilePlugin, PrincipalComponentsPlugin, ProductionPipeline, ProductionSNPCallerPlugin, ProductionSNPCallerPluginV2, ProjectionLoadPlugin, ProjectPcsAndRunModelSelectionPlugin, QQDisplayPlugin, QseqToPETagCountPlugin, QseqToTagCountPlugin, QseqToTBTPlugin, RampSeqAlignFromBlastTags, RandomGenotypeImputationPlugin, ReImputeUpdatedTaxaByFILLINPlugin, RemoveIndelsForBeaglePlugin, RemoveNaNFromDistanceMatrixPlugin, RepGenAlignerPlugin, RepGenLDAnalysisPlugin, RepGenLoadSeqToDBPlugin, RepGenPhase2AlignerPlugin, ResamplingGWASPlugin, RGBSProductionSNPCallerPlugin, RidgeRegressionEmmaPlugin, RNADeMultiplexProductionPlugin, RNADeMultiPlexSeqToDBPlugin, SAMConverterPlugin, SAMToGBSdbPlugin, SAMWGMapConverterPlugin, SeparatePlugin, SeqToTBTHDF5Plugin, SequenceDiversityPlugin, SetLowDepthGenosToMissingPlugin, SNPCutPosTagVerificationPlugin, SNPQualityProfilerPlugin, SortGenotypeFilePlugin, SortTaxaAlphabeticallyPlugin, SplitFile_IFLFilePlugin, SplitHDF5ByChromosomePlugin, StepwiseAdditiveModelFitterPlugin, StepwiseOLSModelFitterPlugin, SubtractDistanceMatrixPlugin, SubtractGenotypesPlugin, SubtractPhenotypeByTaxaPlugin, SynonymizerPlugin, TableDisplayPlugin, TagAgainstAnchorPlugin, TagCountToFastqPlugin, TagExportToFastqPlugin, TasselLogging, TextToBinaryPlugin, ThinSitesByPositionPlugin, TOPMSummaryPlugin, TransformDataPlugin, UnionAlignmentPlugin, UpdateSNPPositionQualityPlugin, UTagCountToTagPairPlugin, UTagPairToTOPMPlugin, VCAPScanPlugin, ViterbiAlgorithmPlugin, WeightedMLMPlugin, WorkflowPlugin, WritePopulationAlignmentPlugin

public interface Plugin
extends PluginListener, ProgressListener, Runnable

Author:

Terry Casstevens

Field Summary

Fields

Modifier and Type	Field and Description
static org.apache.log4j.Logger	myLogger

Method Summary

Modifier and Type	Method and Description
void	addListener(PluginListener listener) Adds listener to this plugin.
boolean	cancel() Attempt to cancel processing.
String	getButtonName() Button name for this plugin to be used in buttons, etc.
String	getCitation() Returns Citation for this plugin.
ImageIcon	getIcon() Icon for this plugin to be used in buttons, etc.
JMenu	getMenu() Returns menu that can be added to main menu bar.
JPanel	getPanel() GUI Panel for this plugin.
Object	getParameter(Enum key) Returns parameter value for given parameter key.
Object	getParameter(String key) Returns parameter value for given parameter key.
Frame	getParentFrame() Parent Frame for this plugin.
static Plugin	getPluginInstance(String className, Frame frame)
static Plugin	getPluginInstance(String className, Frame frame, boolean isInteractive) Gets instance of Plugin
String	getToolTipText() Tool Tip Text for this plugin
String	getUsage() Gets the Usage Statement for this Plugin.
boolean	isInteractive() If interactive = true, the plugin will create dialogs and panels to interacts with the user
static boolean	isPlugin(String className) Returns whether given class name is Plugin.
DataSet	performFunction(DataSet input) Performs function of this plugin.
String	pluginDescription() Returns description of the plugin.
String	pluginUserManualURL() Returns URL to User Manual.
DataSet	processData(DataSet input) For the new Generic Plugin Parameter design, performFunction() will automatically call this.
void	receiveInput(Plugin input) Sets up this plugin to receive input from another plugin.
Plugin	setParameter(PluginParameter<?> param, Object value) Sets parameter value for a given plugin
Plugin	setParameter(String key, Object value) Sets parameter value for given parameter key.
Plugin	setParameter(String key, String value) Sets parameter value for given parameter key.
void	setParameters(String[] args) Allows self-describing Plugins to use args to set parameters specific to itself.
void	setParametersToDefault() Sets all parameter values to default.
void	setThreaded(boolean threaded) Set whether this plugin is threaded.
boolean	wasCancelled()

Methods inherited from interface net.maizegenetics.plugindef.PluginListener

dataSetReturned, progress

Methods inherited from interface net.maizegenetics.util.ProgressListener

progress

Methods inherited from interface java.lang.Runnable

run

Field Detail

myLogger

static final org.apache.log4j.Logger myLogger

Method Detail

getMenu

JMenu getMenu()

Returns menu that can be added to main menu bar.

Returns:

menu

performFunction

DataSet performFunction(DataSet input)

Performs function of this plugin.

Parameters:

input - input

Returns:

resulting data set or null.

processData

DataSet processData(DataSet input)

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

Parameters:

input - input

Returns:

resulting data set or null.

getParameter

Object getParameter(Enum key)

Returns parameter value for given parameter key.

Parameters:

key - key

Returns:

value

getParameter

Object getParameter(String key)

Returns parameter value for given parameter key.

Parameters:

key - key

Returns:

value

setParameter

Plugin setParameter(PluginParameter<?> param,
                    Object value)

Sets parameter value for a given plugin

Parameters:

param - parameter

value - value

Returns:

this plugin

setParameter

Plugin setParameter(String key,
                    Object value)

Sets parameter value for given parameter key.

Parameters:

key - key

value - value

Returns:

this plugin

setParameter

Plugin setParameter(String key,
                    String value)

Sets parameter value for given parameter key.

Parameters:

key - key

value - value

Returns:

this plugin

setParametersToDefault

void setParametersToDefault()

Sets all parameter values to default.

receiveInput

void receiveInput(Plugin input)

Sets up this plugin to receive input from another plugin.

Parameters:

input - input

getPanel

JPanel getPanel()

GUI Panel for this plugin.

Returns:

panel

isInteractive

boolean isInteractive()

If interactive = true, the plugin will create dialogs and panels to interacts with the user

Returns:

boolean

getParentFrame

Frame getParentFrame()

Parent Frame for this plugin. Can be null.

Returns:

frame

getIcon

ImageIcon getIcon()

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

Returns:

ImageIcon

getButtonName

String getButtonName()

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

Returns:

String

getToolTipText

String getToolTipText()

Tool Tip Text for this plugin

Returns:

String

addListener

void addListener(PluginListener listener)

Adds listener to this plugin.

Parameters:

listener - listener to add

setThreaded

void setThreaded(boolean threaded)

Set whether this plugin is threaded.

Parameters:

threaded - whether to be threaded.

cancel

boolean cancel()

Attempt to cancel processing.

Returns:

true if plugin will cancel itself.

setParameters

void setParameters(String[] args)

Allows self-describing Plugins to use args to set parameters specific to itself.

Parameters:

args - arguments

getCitation

String getCitation()

Returns Citation for this plugin.

Returns:

Citation

pluginDescription

String pluginDescription()

Returns description of the plugin.

Returns:

description

pluginUserManualURL

String pluginUserManualURL()

Returns URL to User Manual.

Returns:

URL

getUsage

String getUsage()

Gets the Usage Statement for this Plugin.

Returns:

Usage Statement

wasCancelled

boolean wasCancelled()

getPluginInstance

static Plugin getPluginInstance(String className,
                                Frame frame)

getPluginInstance

static Plugin getPluginInstance(String className,
                                Frame frame,
                                boolean isInteractive)

Gets instance of Plugin

Parameters:

className - class name

frame - frame (can be null)

isInteractive - is interactive

Returns:

Plugin

isPlugin

static boolean isPlugin(String className)

Returns whether given class name is Plugin.

Parameters:

className - class name

Returns:

true if class is Plugin