Plugin

All Superinterfaces:

PluginListener, ProgressListener

All Known Implementing Classes:

AMatrixPlugin, AbstractDisplayPlugin, AbstractPlugin, AddDistanceMatrixPlugin, AddReferenceAlleleToHDF5Plugin, AddReferenceToGenotypePlugin, AdditiveSiteStorePlugin, AdjustPhasingPlugin, AnnotateTOPMwSAMPlugin, ArchaeopteryxPlugin, AvgPhenotypeByTaxaPlugin, BinaryToTextPlugin, BoxCoxTransformationPlugin, BuildUnfinishedHDF5GenotypesPlugin, CallParentAllelesPlugin, ChartDisplayPlugin, ClusterGenotypesPlugin, ColumnsToBinaryFullGenomeTablePlugin, ColumnsToBinarySNPOnlyTablePlugin, CombineDataSetsPlugin, CompareGenosBetweenHapMapFilesPlugin, ContigPETagCountPlugin, ConvertAlignmentCoordinatesPlugin, ConvertOldFastqToModernFormatPlugin, ConvertTreeNamesPlugin, CountAssociationsPlugin, CreateHybridGenotypesPlugin, CreateTreePlugin, DiscoverySNPCallerPlugin, DiscoverySNPCallerPluginV2, DistanceMatrixPlugin, DistanceMatrixRangesPlugin, EqtlAssociationPlugin, ExportMultiplePlugin, ExportPlugin, ExtractHapmapSubsetPlugin, FILLINFindHaplotypesPlugin, FILLINImputationPlugin, FSFHapImputationPlugin, FastMultithreadedAssociationPlugin, FastqToPETagCountPlugin, FastqToTBTPlugin, FastqToTagCountPlugin, FeatureListToPositionsPlugin, FileLoadPlugin, FilterAlignmentPlugin, FilterDataSetPlugin, FilterSiteBuilderPlugin, FilterSiteNamePlugin, FilterSubsetPlugin, FilterTaxaBuilderPlugin, FilterTaxaPropertiesPlugin, FilterTraitsPlugin, FindInversionsPlugin, FindMergeHaplotypesPlugin, FixedEffectLMPlugin, GBSSeqToTagDBPlugin, GOBIIPlugin, GWAS_IFLPlugin, GenomeAnnosDBQueryToPositionListPlugin, GenomicSelectionPlugin, GenosToABHPlugin, GenotypeSummaryPlugin, GenotypeToAdditiveValuesPlugin, GetPhenotypeFromB4RPlugin, GetPositionListPlugin, GetTagSequenceFromDBPlugin, GetTagTaxaDistFromDBPlugin, GetTaxaListPlugin, HDF5SummaryPlugin, HMatrixPlugin, HapBreakpoints_IFLFilePlugin, HetsToUnknownPlugin, IdentityRecognitionPlugin, ImputationAccuracyPlugin, ImputationPlugin, ImputeProgenyStatesPlugin, IndelsToUnknownPlugin, IntersectionAlignmentPlugin, KeepSpecifiedReadsinFastqPlugin, KeepSpecifiedSitesInTOPMPlugin, KinshipPlugin, KmerCountingPlugin, KmerToTBTPlugin, KmerToTagCountPlugin, LDKNNiImputationHetV2Plugin, LDKNNiImputationHetV3Plugin, LDKNNiImputationPlugin, LIXPlugin, LinkageDiseqDisplayPlugin, LinkageDisequilibriumPlugin, ListPluginParameters, ListPlugins, LoadRNAContigsToGBSDBPlugin, MLMPlugin, ManhattanDisplayPlugin, MarkerDNARun_IFLFilePlugin, MaskGenotypePlugin, MeanR2FromLDPlugin, MemoryUsagePlugin, MergeAlignmentsSameSitesPlugin, MergeBreakpointFilesPlugin, MergeDuplicateSNPsPlugin, MergeGenotypeTablesPlugin, MergeGenotypeTablesPluginV2, MergeHDF5GenotypesSameSitesPlugin, MergeMultipleTOPMPlugin, MergeMultipleTagCountPlugin, MergePETagCountPlugin, MergeRenameDeleteTaxaPlugin, MergeTagsByTaxaFilesByRowPlugin, MergeTagsByTaxaFilesPlugin, MergeTreesPlugin, ModifyTBTHDF5Plugin, MonetDB_IFLFilePlugin, MultiDimensionalScalingPlugin, NumericalGenotypePlugin, PanAAddPosToTagMapPlugin, PanABuildPivotTBTPlugin, PanABuildTagBlockPosPlugin, PanABuildTagGWASMapPlugin, PanABuildTrainingSetPlugin, PanAFilteringTagMapPlugin, PanAH5ToAnchorPlugin, PanAMergeMappingResultPlugin, PanAModelTrainingPlugin, PanAPredictionPlugin, PanAReadDigestPlugin, PanAReadToKmerPlugin, PanASamToMultiPositionTOPMPlugin, PanASplitTBTPlugin, PanASplitTagBlockPosPlugin, PanATagGWASMappingPlugin, PanATagMapToFastaPlugin, ParentPhasingPlugin, PassThroughPlugin, PlinkLoadPlugin, PreProcessGOBIIMappingFilePlugin, PreferencesDialog, PrincipalComponentsPlugin, ProductionPipeline, ProductionSNPCallerPlugin, ProductionSNPCallerPluginV2, ProjectPcsAndRunModelSelectionPlugin, ProjectionLoadPlugin, QQDisplayPlugin, QseqToPETagCountPlugin, QseqToTBTPlugin, QseqToTagCountPlugin, RGBSProductionSNPCallerPlugin, RNADeMultiPlexSeqToDBPlugin, RNADeMultiplexProductionPlugin, RampSeqAlignFromBlastTags, RandomGenotypeImputationPlugin, ReImputeUpdatedTaxaByFILLINPlugin, RemoveBranchLengthsPlugin, RemoveIndelsForBeaglePlugin, RemoveNaNFromDistanceMatrixPlugin, RepGenAlignerPlugin, RepGenLDAnalysisPlugin, RepGenLoadSeqToDBPlugin, RepGenPhase2AlignerPlugin, ResamplingGWASPlugin, RidgeRegressionEmmaPlugin, SAMConverterPlugin, SAMToGBSdbPlugin, SAMWGMapConverterPlugin, SNPCutPosTagVerificationPlugin, SNPQualityProfilerPlugin, SeparatePlugin, SeqToTBTHDF5Plugin, SequenceDiversityPlugin, SetLowDepthGenosToMissingPlugin, ShowParameterCachePlugin, SortGenotypeFilePlugin, SortTaxaAlphabeticallyPlugin, SplitFile_IFLFilePlugin, SplitHDF5ByChromosomePlugin, StepwiseAdditiveModelFitterPlugin, StepwiseOLSModelFitterPlugin, SubsetTreePlugin, SubtractDistanceMatrixPlugin, SubtractGenotypesPlugin, SubtractPhenotypeByTaxaPlugin, SynonymizerPlugin, TOPMSummaryPlugin, TableDisplayPlugin, TagAgainstAnchorPlugin, TagCountToFastqPlugin, TagExportToFastqPlugin, TasselLogging, TextToBinaryPlugin, ThinSitesByPositionPlugin, TransformDataPlugin, UTagCountToTagPairPlugin, UTagPairToTOPMPlugin, UnionAlignmentPlugin, UpdateSNPPositionQualityPlugin, VCAPScanPlugin, ViterbiAlgorithmPlugin, WeightedMLMPlugin, WorkflowPlugin, WritePopulationAlignmentPlugin
```
public Plugin
extends PluginListener, ProgressListener
```

- Field Detail
  - myLogger
```
static org.apache.log4j.Logger myLogger
```
- Method Detail
  - getMenu
```
javax.swing.JMenu getMenu()
```
    Returns menu that can be added to main menu bar.
    
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@7211431a: menu
  - performFunction
```
DataSet performFunction(DataSet input)
```
    Performs function of this plugin.
    
    Parameters:
    
    input - input
    
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@22def284: 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:
    
    org.jetbrains.dokka.NodeRenderContent@47912d83: resulting data set or null.
  - getParameter
```
java.lang.Object getParameter(java.lang.Enum key)
```
    Returns parameter value for given parameter key.
    
    Parameters:
    
    key - key
    
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@3e7d67b2: value
  - getParameter
```
java.lang.Object getParameter(java.lang.String key)
```
    Returns parameter value for given parameter key.
    
    Parameters:
    
    key - key
    
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@460cfaf4: value
  - setParameter
```
Plugin setParameter(PluginParameter<?> param,
                    java.lang.Object value)
```
    Sets parameter value for a given plugin
    
    Parameters:
    
    param - parameter
    
    value - value
    
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@13136a63: this plugin
  - setParameter
```
Plugin setParameter(java.lang.String key,
                    java.lang.Object value)
```
    Sets parameter value for given parameter key.
    
    Parameters:
    
    key - key
    
    value - value
    
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@5d20a0b7: this plugin
  - setParameter
```
Plugin setParameter(java.lang.String key,
                    java.lang.String value)
```
    Sets parameter value for given parameter key.
    
    Parameters:
    
    key - key
    
    value - value
    
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@8b50c56: this plugin
  - setParametersToDefault
```
void setParametersToDefault()
```
    Sets all parameter values to default.
  - pluginParameters
```
java.util.Map<java.lang.String,java.lang.String> pluginParameters()
```
    Get map of plugin parameters. Key is command line name and value is current value.
    
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@294f8cee: map of parameter values
  - receiveInput
```
void receiveInput(Plugin input)
```
    Sets up this plugin to receive input from another plugin.
    
    Parameters:
    
    input - input
  - getPanel
```
javax.swing.JPanel getPanel()
```
    GUI Panel for this plugin.
    
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@2187bbd6: panel
  - isInteractive
```
boolean isInteractive()
```
    If interactive = true, the plugin will create dialogs and panels to interacts with the user
    
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@797a9249: boolean
  - getParentFrame
```
java.awt.Frame getParentFrame()
```
    Parent Frame for this plugin. Can be null.
    
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@590df68c: frame
  - getIcon
```
javax.swing.ImageIcon getIcon()
```
    Icon for this plugin to be used in buttons, etc.
    
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@c7039bf: ImageIcon
  - getButtonName
```
java.lang.String getButtonName()
```
    Button name for this plugin to be used in buttons, etc.
    
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@10b57aec: String
  - getToolTipText
```
java.lang.String getToolTipText()
```
    Tool Tip Text for this plugin
    
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@3df04a69: 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:
    
    org.jetbrains.dokka.NodeRenderContent@bff72cd: true if plugin will cancel itself.
  - setParameters
```
void setParameters(java.lang.String[] args)
```
    Allows self-describing Plugins to use args to set parameters specific to itself.
    
    Parameters:
    
    args - arguments
  - getCitation
```
java.lang.String getCitation()
```
    Returns Citation for this plugin.
    
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@64f0fcc: Citation
  - pluginDescription
```
java.lang.String pluginDescription()
```
    Returns description of the plugin.
    
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@3d9677f3: description
  - pluginUserManualURL
```
java.lang.String pluginUserManualURL()
```
    Returns URL to User Manual.
    
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@20ac12a: URL
  - getUsage
```
java.lang.String getUsage()
```
    Gets the Usage Statement for this Plugin.
    
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@7293a2bc: Usage Statement
  - wasCancelled
```
boolean wasCancelled()
```
  - getPluginInstance
```
static Plugin getPluginInstance(java.lang.String className,
                                java.awt.Frame frame)
```
  - getPluginInstance
```
static Plugin getPluginInstance(java.lang.String className,
                                java.awt.Frame frame,
                                boolean isInteractive)
```
    Gets instance of Plugin
    
    Parameters:
    
    className - class name
    
    frame - frame (can be null)
    
    isInteractive - is interactive
    
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@cdcf24d: Plugin
  - isPlugin
```
static boolean isPlugin(java.lang.String className)
```
    Returns whether given class name is Plugin.
    
    Parameters:
    
    className - class name
    
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@2fb35ca: true if class is Plugin

Interface Plugin

Field Detail

myLogger

Method Detail

getMenu

performFunction

processData

getParameter

getParameter

setParameter

setParameter

setParameter

setParametersToDefault

pluginParameters

receiveInput

getPanel

isInteractive

getParentFrame

getIcon

getButtonName

getToolTipText

addListener

setThreaded

cancel

setParameters

getCitation

pluginDescription

pluginUserManualURL

getUsage

wasCancelled

getPluginInstance

getPluginInstance

isPlugin