public interface SpotIntensityParser
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.
FirstPassSectionSpotsParser.addSpotIntensityParser(SpotIntensityParser)
Modifier and Type | Method and Description |
---|---|
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.
|
boolean hasRequiredAssayFields(BaseFileParser parser, FlatFileParser ffp, List<String> assayFields)
parser
- The master BASEfile parserffp
- The flat file parser that parses the current fileassayFields
- The list of assay fieldsvoid beginSection(BaseFileParser parser, FlatFileParser ffp, List<String> assayFields)
parser
- The master BASEfile parserffp
- The flat file parser that parses the current fileassayFields
- The list of assay fieldsboolean setIntensities(FlatFileParser.Data data, float[] intensities, int firstIndex)
data
- The current data lineintensities
- An array that should be populate with intensity valuesfirstIndex
- The index of the first data column that contains data
for the current bioassay