net.maizegenetics.plugindef

Class AbstractPlugin

net.maizegenetics.plugindef.AbstractPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

Direct Known Subclasses:

AMatrixPlugin, AbstractDisplayPlugin, AddDistanceMatrixPlugin, AddReferenceAlleleToHDF5Plugin, AddReferenceToGenotypePlugin, AdditiveSiteStorePlugin, AdjustPhasingPlugin, AnnotateTOPMwSAMPlugin, ArchaeopteryxPlugin, AvgPhenotypeByTaxaPlugin, BinaryToTextPlugin, BoxCoxTransformationPlugin, BuildUnfinishedHDF5GenotypesPlugin, CallParentAllelesPlugin, ClusterGenotypesPlugin, ColumnsToBinaryFullGenomeTablePlugin, ColumnsToBinarySNPOnlyTablePlugin, CombineDataSetsPlugin, CompareGenosBetweenHapMapFilesPlugin, ContigPETagCountPlugin, ConvertAlignmentCoordinatesPlugin, ConvertOldFastqToModernFormatPlugin, ConvertTreeNamesPlugin, 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, KeepSpecifiedReadsinFastqPlugin, KeepSpecifiedSitesInTOPMPlugin, KinshipPlugin, KmerCountingPlugin, KmerToTBTPlugin, KmerToTagCountPlugin, LDKNNiImputationHetV2Plugin, LDKNNiImputationHetV3Plugin, LDKNNiImputationPlugin, LIXPlugin, LinkageDisequilibriumPlugin, ListPluginParameters, ListPlugins, LoadRNAContigsToGBSDBPlugin, MLMPlugin, MarkerDNARun_IFLFilePlugin, MaskGenotypePlugin, 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, 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, TagAgainstAnchorPlugin, TagCountToFastqPlugin, TagExportToFastqPlugin, TasselLogging, TextToBinaryPlugin, ThinSitesByPositionPlugin, TransformDataPlugin, UTagCountToTagPairPlugin, UTagPairToTOPMPlugin, UnionAlignmentPlugin, UpdateSNPPositionQualityPlugin, VCAPScanPlugin, ViterbiAlgorithmPlugin, WorkflowPlugin, WritePopulationAlignmentPlugin

public class AbstractPlugin
implements Plugin

Field Detail

DEFAULT_CITATION

public static java.lang.String DEFAULT_CITATION

See Also:

Constant Field Values

POSITION_LIST_NONE

public static java.lang.String POSITION_LIST_NONE

See Also:

Constant Field Values

TAXA_LIST_NONE

public static java.lang.String TAXA_LIST_NONE

See Also:

Constant Field Values

myWasCancelled

protected boolean myWasCancelled

Constructor Detail

AbstractPlugin

public AbstractPlugin()

Creates a new instance of AbstractPlugin

AbstractPlugin

public AbstractPlugin(java.awt.Frame parentFrame,
                      boolean isInteractive)

Creates a new instance of AbstractPlugin

Method Detail

performFunction

public DataSet performFunction(DataSet input)

preProcessParameters

protected void preProcessParameters(DataSet input)

postProcessParameters

protected void postProcessParameters()

processData

public DataSet processData(DataSet input)

getParameterFields

protected java.util.List<java.lang.reflect.Field> getParameterFields()

isPluginParameter

public boolean isPluginParameter(java.lang.String key)

convert

public static <T> T convert(java.lang.String input,
                            java.lang.Class<T> outputClass)

setParameters

public void setParameters(java.lang.String[] args)

setConfigParameters

public void setConfigParameters()

printParameterValues

protected void printParameterValues()

getUsage

public java.lang.String getUsage()

usageParameters

public java.util.Map<java.lang.String,java.util.Map> usageParameters()

pluginParameters

public java.util.Map<java.lang.String,java.lang.String> pluginParameters()

getParameter

public java.lang.Object getParameter(java.lang.Enum key)

getParameter

public java.lang.Object getParameter(java.lang.String key)

setParameter

public Plugin setParameter(PluginParameter<?> param,
                           java.lang.Object value)

setParameter

public Plugin setParameter(java.lang.String key,
                           java.lang.Object value)

setParameter

public Plugin setParameter(java.lang.String key,
                           java.lang.String value)

setParametersToDefault

public void setParametersToDefault()

getUsageHTML

public java.lang.String getUsageHTML()

getMenu

public javax.swing.JMenu getMenu()

Returns menu that can be added to main menu bar.

Returns:

org.jetbrains.dokka.NodeRenderContent@7ea4ef81: menu

receiveInput

public void receiveInput(Plugin input)

Sets up this plugin to receive input from another plugin.

Parameters:

input - input

getPanel

public javax.swing.JPanel getPanel()

GUI Panel for this plugin.

Returns:

org.jetbrains.dokka.NodeRenderContent@778861ed: panel

isInteractive

public boolean isInteractive()

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

Returns:

org.jetbrains.dokka.NodeRenderContent@289aaff4: boolean

getParentFrame

public java.awt.Frame getParentFrame()

Parent Frame for this plugin. Can be null.

Returns:

org.jetbrains.dokka.NodeRenderContent@66477867: frame

addListener

public void addListener(PluginListener listener)

Adds listener to this plugin.

Parameters:

listener - listener to add

getListeners

public java.util.List<net.maizegenetics.plugindef.PluginListener> getListeners()

hasListeners

public boolean hasListeners()

getInputs

public java.util.List<net.maizegenetics.plugindef.Plugin> getInputs()

fireDataSetReturned

protected void fireDataSetReturned(PluginEvent event)

Returns data set after complete.

Parameters:

event - event

fireDataSetReturned

protected void fireDataSetReturned(DataSet data)

Returns data set after complete.

Parameters:

data - data set

fireProgress

protected void fireProgress(PluginEvent event)

Returns progress of execution.

Parameters:

event - event

fireProgress

protected void fireProgress(java.lang.Integer percent)

Returns progress of execution.

Parameters:

percent - percentage between 0 and 100 inclusive.

getCitation

public java.lang.String getCitation()

pluginDescription

public java.lang.String pluginDescription()

pluginUserManualURL

public java.lang.String pluginUserManualURL()

dataSetReturned

public void dataSetReturned(PluginEvent event)

Returns data set after complete.

Parameters:

event - event

progress

public void progress(PluginEvent event)

No operation for this abstract class.

Parameters:

event - event

reverseTrace

public void reverseTrace(int indent)

trace

public void trace(int indent)

setThreaded

public void setThreaded(boolean threaded)

cancel

public boolean cancel()

run

public void run()

progress

public void progress(int percent,
                     java.lang.Object meta)

wasCancelled

public boolean wasCancelled()