Package net.sf.basedb.plugins

Class Summary

AbstractFlatFileImporter	An abstract base class for all importers that imports data from one or more flat files.
AnnotationFlatFileImporter	Plug-in for importing annotations from simple text files.
AnnotationFlatFileImporter.AnnotationValue
AnnotationFlatFileImporter.NewAnnotations	Internal cache for storing annotation values from the file for a single item.
Base1PluginExecuter	This plug-in executes a plug-in from the Base1 system.
BaseFileExporterPlugin	Exports bioassay set data as serial or matrix BASEfile:s.
BaseFileExporterPlugin.ExtendedDynamicField
BfsExporterPlugin	Exports bioassay set data to BFS format.
BfsExporterPlugin.ExtendedExportableField
BioAssaySetExporter	Deprecated. In 2.12.
BioAssaySetExporter.QueryItem
BioAssaySetExporter.QueryItemTitleComparator
CdfFileReporterImporter	This plug-in can import probesets from Affymetrix CDF files as reporters.
FormulaFilter	This plugin provides methods to filter a bioassayset based on formulas entered by the user.
GalExporter	Exports an array design with features to a GAL file.
HelpExporter	This plugin exports helptexts stored in the database to a XML-file.
HelpImporter	This plugin imports helptexts into database from a XML-file.
IlluminaRawDataImporter	An importer plug-in for Illumina raw data.
IlluminaRawDataImporter.BatchAndMapHolder	Holds a RawBioAssay and the RawDataBatcher to use for import and the Mapper for all it's data columns.
IntensityCalculatorPlugin	This plugin provides methods to calculate the intensity for a root bioassayset using different formulas.
JepExtraValueCalculator	This plugin caluclates extra values from a bioassayset using mathematical formulas entered by the user.
JepIntensityTransformer	This plugin transform channel intensities using mathematical formulas entered by the user.
LowessNormalization
LowessNormalization.CallableWorker
LowessNormalization.SpotData
ManualTransformCreator	Plug-in that allows a user to manually register an external analysis procedure and to upload files that was generated by it.
MedianRatioNormalization
MedianRatioNormalization.SpotData
PackedFileExporter	Plug-in that packs one or more selected files and directories into a single file.
PlateFlatFileImporter
PlateMappingExporter	Exporter for plate mappings.
PlateMappingImporter	Importer for plate mappings.
PluginConfigurationExporter	This plugin exports parameters of a pluginconfiguration into an XML-file.
PluginConfigurationImporter	This plugin imports pluginconfiguration from an XML-file.
PrintMapFlatFileImporter	A plugin that imports an ArrayDesign from a printmap.
PrintMapFlatFileImporter.MetaBlock
RawDataFlatFileImporter	A plugin that imports rawdata from a flatfile.
ReporterFlatFileImporter	A plugin that imports reporter from a flat file.
ReporterMapFlatFileImporter	A plugin that imports features to an ArrayDesign from a flat file.
SpotImageCreator
TarFileUnpacker	A plugin for unpacking tar, gzipped tar and bzipped tar files to the BASE file system.
ZipFileUnpacker	A plugin for unpacking zip and jar file on the BASE file system.

Enum Summary

Base1PluginExecuter.Base1JobParameterType
PrintMapFlatFileImporter.FormatType
PrintMapFlatFileImporter.Section