Package net.sf.basedb.util.importer.spotdata

Interface Summary

SpotIntensityParser

A spot intensity parser is responsible for parsing and extracting spot intensity data on a row-by-row basis from a BASEfile.

Class Summary

BaseFileImporter	Imports spot data from a serial or matrix BASEfile.
BaseFileImporter.RawDataProxy
BaseFileImporter.ReporterProxy
BaseFileInfo	Collects information about a BASEfile as it gets parsed by a BaseFileImporter.
BaseFileInfo.ChildBioAssay	Keeps information about a new child bioassay from the 'assays' section or 'spot' sections.
BaseFileInfo.SpotSectionInfo	Keeps information about headers and more in a 'spot' section.
BfsImporter	Imports spot data from a serial or matrix BFS.
BfsImporter.ProgressEventHandler
ExtraFloatParser	Parser that is responsible for extracting extra float values from the 'spot' section in a BASEfile.
FirstPassSectionSpotsParser	Parses a 'spots' section of a BASEfile with bioassay set spot data.
GenericIntensityParser	Generic spot intensity parser implementation that looks for 'intensity1', ..., 'intensityN' data columns for any number of channels.
MAParser	Spot intensity parser implementation for 2-channel data that looks for M/A values in the spot data and converts them to ch1/ch2 intensity values.
MatrixSpotIntensityEventHandler	Event handler that extracts spot intensity information from matrix BFS data files and inserts the values to a spot batcher.
PositionEventHandler	Event handler implementation intended to be used with a SynchronizedSpotDataParser to extract the position number from the parsed data.
SecondPassSectionSpotsParser	The second pass of the 'spots' section extracts spot and extra value data.
SectionAssaysParser	Parses the 'assays' section of a BASEfile with bioassay set spot data.
SectionReporterListParser	Parses the 'reporterlist' section of a BASEfile.
SerialSpotIntensityEventHandler	Event handler that extracts spot intensity information from serial BFS data files and inserts the values to a spot batcher.
SynchronizedSpotDataParser	A parser that synchronizes the parsing of multiple underlying data parsers and a master reporter annotations parser.
SynchronizedSpotDataParser.SynchronizedData	This class holds information that is sent to the event handler when SynchronizedSpotDataParser.DATA_EVENT:s are sent.