public class GenericIntensityParser extends Object implements SpotIntensityParser
Modifier and Type | Field and Description |
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private int |
channels |
private int[] |
index |
Constructor and Description |
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GenericIntensityParser(int channels)
Creates a new parser for the specified number of channels.
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Modifier and Type | Method and Description |
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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.
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boolean |
setIntensities(FlatFileParser.Data data,
float[] intensities,
int firstIndex)
Extract the intensity values from the current data line for a single
bioassay.
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public GenericIntensityParser(int channels)
public boolean hasRequiredAssayFields(BaseFileParser parser, FlatFileParser ffp, List<String> assayFields)
SpotIntensityParser
hasRequiredAssayFields
in interface SpotIntensityParser
parser
- The master BASEfile parserffp
- The flat file parser that parses the current fileassayFields
- The list of assay fieldspublic void beginSection(BaseFileParser parser, FlatFileParser ffp, List<String> assayFields)
SpotIntensityParser
beginSection
in interface SpotIntensityParser
parser
- The master BASEfile parserffp
- The flat file parser that parses the current fileassayFields
- The list of assay fieldspublic boolean setIntensities(FlatFileParser.Data data, float[] intensities, int firstIndex)
SpotIntensityParser
setIntensities
in interface SpotIntensityParser
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