net.sf.basedb.util.importer.spotdata
Interface SpotIntensityParser

All Known Implementing Classes:

GenericIntensityParser, MAParser

public interface SpotIntensityParser

A spot intensity parser is responsible for parsing and extracting spot intensity data on a row-by-row basis from a BASEfile. After parsing the headers of a 'spot' section each registered spot intensity parser will be asked if the section contains all needed data columns hasRequiredAssayFields(BaseFileParser, FlatFileParser, List). The first parser that gives a positive response will be used to parse the spot intensity data for that section.

The actual parsing is done in the second pass.

Version:

2.14

Author:

Nicklas

See Also:

FirstPassSectionSpotsParser.addSpotIntensityParser(SpotIntensityParser)

Last modified

$Date: 2009-09-14 08:29:17 +0200 (Mon, 14 Sep 2009) $

Method Summary

void	beginSection(BaseFileParser parser, FlatFileParser ffp, List<String> assayFields) Prepare for parsing the data section.
boolean	hasRequiredAssayFields(BaseFileParser parser, FlatFileParser ffp, List<String> assayFields) Check the list of assay fields to see if all columns that are required are present or not.
boolean	setIntensities(FlatFileParser.Data data, float[] intensities, int firstIndex) Extract the intensity values from the current data line for a single bioassay.

Method Detail

hasRequiredAssayFields

boolean hasRequiredAssayFields(BaseFileParser parser,
                               FlatFileParser ffp,
                               List<String> assayFields)

Check the list of assay fields to see if all columns that are required are present or not. This method is called in the first pass to decide which spot intensity parser that should be used in the second pass.

Parameters:

parser - The master BASEfile parser

ffp - The flat file parser that parses the current file

assayFields - The list of assay fields

Returns:

TRUE if all required fields are present, FALSE otherwise

beginSection

void beginSection(BaseFileParser parser,
                  FlatFileParser ffp,
                  List<String> assayFields)

Prepare for parsing the data section. Preparations typically include extracting the column indexes of the data columns. This method is called in the second pass before starting to parse data for a 'spot' section. NOTE! The same object instance may be used to parse more than one section in a serial BASEfile.

Parameters:

parser - The master BASEfile parser

ffp - The flat file parser that parses the current file

assayFields - The list of assay fields

setIntensities

boolean setIntensities(FlatFileParser.Data data,
                       float[] intensities,
                       int firstIndex)

Extract the intensity values from the current data line for a single bioassay. If the section contains data for multiple bioassays (eg. a matrix BASEfile) this method is called multiple times (with different 'firstIndex' value) for each row.

Parameters:

data - The current data line

intensities - An array that should be populate with intensity values

firstIndex - The index of the first data column that contains data for the current bioassay

Returns:

TRUE if the values could be set correctly, FALSE otherwise (which means that the spot data will not be inserted)