public class MAParser extends Object implements SpotIntensityParser
NOTE! The column names for the M/A values can be redefined by
calling BaseFileParser.setRedefinedColumnName(String, String, String)
.
Modifier and Type | Field and Description |
---|---|
private static String |
aColumn |
private int |
aIndex |
private static String |
mColumn |
private int |
mIndex |
Constructor and Description |
---|
MAParser()
Creates a new MA-parser.
|
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.
|
private int mIndex
private int aIndex
private static final String mColumn
private static final String aColumn
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