AbstractPlugin (net.maizegenetics:tassel 5.2.46 API)

java.lang.Object
- net.maizegenetics.plugindef.AbstractPlugin

All Implemented Interfaces:

Runnable, Plugin, PluginListener, ProgressListener

Direct Known Subclasses:

AbstractDisplayPlugin, AddDistanceMatrixPlugin, AdditiveSiteStorePlugin, AddReferenceAlleleToHDF5Plugin, AdjustPhasingPlugin, AMatrixPlugin, AnnotateTOPMwSAMPlugin, ArchaeopteryxPlugin, AvgPhenotypeByTaxaPlugin, BinaryToTextPlugin, BoxCoxTransformationPlugin, BuildUnfinishedHDF5GenotypesPlugin, CallParentAllelesPlugin, 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, KeepSpecifiedReadsinFastqPlugin, KeepSpecifiedSitesInTOPMPlugin, KinshipPlugin, KmerToTagCountPlugin, KmerToTBTPlugin, LDKNNiImputationHetV2Plugin, LDKNNiImputationHetV3Plugin, LDKNNiImputationPlugin, LinkageDisequilibriumPlugin, ListPlugins, LIXPlugin, LoadRNAContigsToGBSDBPlugin, 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, 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, TagAgainstAnchorPlugin, TagCountToFastqPlugin, TagExportToFastqPlugin, TasselLogging, TextToBinaryPlugin, ThinSitesByPositionPlugin, TOPMSummaryPlugin, TransformDataPlugin, UnionAlignmentPlugin, UpdateSNPPositionQualityPlugin, UTagCountToTagPairPlugin, UTagPairToTOPMPlugin, VCAPScanPlugin, ViterbiAlgorithmPlugin, WorkflowPlugin, WritePopulationAlignmentPlugin
```
public abstract class AbstractPlugin
extends Object
implements Plugin
```
Author:

Terry Casstevens

Field Summary

Fields
Modifier and Type Field and Description

static String DEFAULT_CITATION

static String POSITION_LIST_NONE

static String TAXA_LIST_NONE

Fields
Modifier and Type	Field and Description
`static String`	`DEFAULT_CITATION`
`static String`	`POSITION_LIST_NONE`
`static String`	`TAXA_LIST_NONE`

Constructor Summary

Constructors
Constructor and Description
`AbstractPlugin()` Creates a new instance of AbstractPlugin
`AbstractPlugin(Frame parentFrame, boolean isInteractive)` Creates a new instance of AbstractPlugin

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addListener(PluginListener listener)` Adds listener to this plugin.
`boolean`	`cancel()` Attempt to cancel processing.
`static <T> T`	`convert(String input, Class<T> outputClass)`
`void`	`dataSetReturned(PluginEvent event)` Returns data set after complete.
`String`	`getCitation()` Returns Citation for this plugin.
`List<Plugin>`	`getInputs()`
`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.
`String`	`getUsage()` Gets the Usage Statement for this Plugin.
`String`	`getUsageHTML()`
`boolean`	`isInteractive()` If interactive = true, the plugin will create dialogs and panels to interacts with the user
`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`	`progress(int percent, Object meta)` Returns progress of execution.
`void`	`progress(PluginEvent event)` No operation for this abstract class.
`void`	`receiveInput(Plugin input)` Sets up this plugin to receive input from another plugin.
`void`	`reverseTrace(int indent)`
`void`	`run()`
`void`	`setConfigParameters()`
`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.
`void`	`trace(int indent)`
`boolean`	`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
getButtonName, getIcon, getPluginInstance, getPluginInstance, getToolTipText, isPlugin

- Field Detail
  - DEFAULT_CITATION
```
public static final String DEFAULT_CITATION
```
    See Also:
    
    Constant Field Values
  - POSITION_LIST_NONE
```
public static final String POSITION_LIST_NONE
```
    See Also:
    
    Constant Field Values
  - TAXA_LIST_NONE
```
public static final String TAXA_LIST_NONE
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - AbstractPlugin
```
public AbstractPlugin()
```
    Creates a new instance of AbstractPlugin
  - AbstractPlugin
```
public AbstractPlugin(Frame parentFrame,
                      boolean isInteractive)
```
    Creates a new instance of AbstractPlugin
- Method Detail
  - performFunction
```
public DataSet performFunction(DataSet input)
```
    Description copied from interface: Plugin
    
    Performs function of this plugin.
    
    Specified by:
    
    performFunction in interface Plugin
    
    Parameters:
    
    input - input
    
    Returns:
    
    resulting data set or null.
  - 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
    
    Parameters:
    
    input - input
    
    Returns:
    
    resulting data set or null.
  - convert
```
public static <T> T convert(String input,
                            Class<T> outputClass)
```
  - setParameters
```
public void setParameters(String[] args)
```
    Description copied from interface: Plugin
    
    Allows self-describing Plugins to use args to set parameters specific to itself.
    
    Specified by:
    
    setParameters in interface Plugin
    
    Parameters:
    
    args - arguments
  - setConfigParameters
```
public void setConfigParameters()
```
  - getUsage
```
public String getUsage()
```
    Description copied from interface: Plugin
    
    Gets the Usage Statement for this Plugin.
    
    Specified by:
    
    getUsage in interface Plugin
    
    Returns:
    
    Usage Statement
  - getParameter
```
public Object getParameter(Enum key)
```
    Description copied from interface: Plugin
    
    Returns parameter value for given parameter key.
    
    Specified by:
    
    getParameter in interface Plugin
    
    Parameters:
    
    key - key
    
    Returns:
    
    value
  - getParameter
```
public Object getParameter(String key)
```
    Description copied from interface: Plugin
    
    Returns parameter value for given parameter key.
    
    Specified by:
    
    getParameter in interface Plugin
    
    Parameters:
    
    key - key
    
    Returns:
    
    value
  - setParameter
```
public Plugin setParameter(PluginParameter<?> param,
                           Object value)
```
    Description copied from interface: Plugin
    
    Sets parameter value for a given plugin
    
    Specified by:
    
    setParameter in interface Plugin
    
    Parameters:
    
    param - parameter
    
    value - value
    
    Returns:
    
    this plugin
  - setParameter
```
public Plugin setParameter(String key,
                           Object value)
```
    Description copied from interface: Plugin
    
    Sets parameter value for given parameter key.
    
    Specified by:
    
    setParameter in interface Plugin
    
    Parameters:
    
    key - key
    
    value - value
    
    Returns:
    
    this plugin
  - setParameter
```
public Plugin setParameter(String key,
                           String value)
```
    Description copied from interface: Plugin
    
    Sets parameter value for given parameter key.
    
    Specified by:
    
    setParameter in interface Plugin
    
    Parameters:
    
    key - key
    
    value - value
    
    Returns:
    
    this plugin
  - setParametersToDefault
```
public void setParametersToDefault()
```
    Description copied from interface: Plugin
    
    Sets all parameter values to default.
    
    Specified by:
    
    setParametersToDefault in interface Plugin
  - getUsageHTML
```
public String getUsageHTML()
```
  - getMenu
```
public JMenu getMenu()
```
    Returns menu that can be added to main menu bar.
    
    Specified by:
    
    getMenu in interface Plugin
    
    Returns:
    
    menu
  - receiveInput
```
public void receiveInput(Plugin input)
```
    Sets up this plugin to receive input from another plugin.
    
    Specified by:
    
    receiveInput in interface Plugin
    
    Parameters:
    
    input - input
  - getPanel
```
public JPanel getPanel()
```
    GUI Panel for this plugin.
    
    Specified by:
    
    getPanel in interface Plugin
    
    Returns:
    
    panel
  - isInteractive
```
public boolean isInteractive()
```
    If interactive = true, the plugin will create dialogs and panels to interacts with the user
    
    Specified by:
    
    isInteractive in interface Plugin
    
    Returns:
    
    boolean
  - getParentFrame
```
public Frame getParentFrame()
```
    Parent Frame for this plugin. Can be null.
    
    Specified by:
    
    getParentFrame in interface Plugin
    
    Returns:
    
    frame
  - addListener
```
public void addListener(PluginListener listener)
```
    Adds listener to this plugin.
    
    Specified by:
    
    addListener in interface Plugin
    
    Parameters:
    
    listener - listener to add
  - getInputs
```
public List<Plugin> getInputs()
```
  - getCitation
```
public String getCitation()
```
    Description copied from interface: Plugin
    
    Returns Citation for this plugin.
    
    Specified by:
    
    getCitation in interface Plugin
    
    Returns:
    
    Citation
  - pluginDescription
```
public String pluginDescription()
```
    Description copied from interface: Plugin
    
    Returns description of the plugin.
    
    Specified by:
    
    pluginDescription in interface Plugin
    
    Returns:
    
    description
  - pluginUserManualURL
```
public String pluginUserManualURL()
```
    Description copied from interface: Plugin
    
    Returns URL to User Manual.
    
    Specified by:
    
    pluginUserManualURL in interface Plugin
    
    Returns:
    
    URL
  - dataSetReturned
```
public void dataSetReturned(PluginEvent event)
```
    Returns data set after complete.
    
    Specified by:
    
    dataSetReturned in interface PluginListener
    
    Parameters:
    
    event - event
  - progress
```
public void progress(PluginEvent event)
```
    No operation for this abstract class.
    
    Specified by:
    
    progress in interface PluginListener
    
    Parameters:
    
    event - event
  - reverseTrace
```
public void reverseTrace(int indent)
```
  - trace
```
public void trace(int indent)
```
  - setThreaded
```
public void setThreaded(boolean threaded)
```
    Description copied from interface: Plugin
    
    Set whether this plugin is threaded.
    
    Specified by:
    
    setThreaded in interface Plugin
    
    Parameters:
    
    threaded - whether to be threaded.
  - cancel
```
public boolean cancel()
```
    Description copied from interface: Plugin
    
    Attempt to cancel processing.
    
    Specified by:
    
    cancel in interface Plugin
    
    Returns:
    
    true if plugin will cancel itself.
  - run
```
public void run()
```
    Specified by:
    
    run in interface Runnable
  - progress
```
public void progress(int percent,
                     Object meta)
```
    Description copied from interface: ProgressListener
    
    Returns progress of execution.
    
    Specified by:
    
    progress in interface ProgressListener
    
    Parameters:
    
    percent - percent complete
    
    meta - meta data
  - wasCancelled
```
public boolean wasCancelled()
```
    Specified by:
    
    wasCancelled in interface Plugin

Class AbstractPlugin

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface net.maizegenetics.plugindef.Plugin

Field Detail

DEFAULT_CITATION

POSITION_LIST_NONE

TAXA_LIST_NONE

Constructor Detail

AbstractPlugin

AbstractPlugin

Method Detail

performFunction

processData

convert

setParameters

setConfigParameters

getUsage

getParameter

getParameter

setParameter

setParameter

setParameter

setParametersToDefault

getUsageHTML

getMenu

receiveInput

getPanel

isInteractive

getParentFrame

addListener

getInputs

getCitation

pluginDescription

pluginUserManualURL

dataSetReturned

progress

reverseTrace

trace

setThreaded

cancel

run

progress

wasCancelled