Class MAParser

  • All Implemented Interfaces:
    SpotIntensityParser

    public class MAParser
    extends Object
    implements SpotIntensityParser
    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. The required assay fields are: l2ratio1_2 (M) and l10intgmean1_2 (A).

    NOTE! The column names for the M/A values can be redefined by calling BaseFileParser.setRedefinedColumnName(String, String, String).

    Version:
    2.14
    Author:
    Nicklas
    Last modified
    $Date: 2019-03-20 14:31:03 +0100 (ons, 20 mars 2019) $
    • Constructor Detail

      • MAParser

        public MAParser()
        Creates a new MA-parser.
    • Method Detail

      • hasRequiredAssayFields

        public boolean hasRequiredAssayFields​(BaseFileParser parser,
                                              FlatFileParser ffp,
                                              List<String> assayFields)
        Description copied from interface: SpotIntensityParser
        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.
        Specified by:
        hasRequiredAssayFields in interface SpotIntensityParser
        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

        public void beginSection​(BaseFileParser parser,
                                 FlatFileParser ffp,
                                 List<String> assayFields)
        Description copied from interface: SpotIntensityParser
        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.
        Specified by:
        beginSection in interface SpotIntensityParser
        Parameters:
        parser - The master BASEfile parser
        ffp - The flat file parser that parses the current file
        assayFields - The list of assay fields
      • setIntensities

        public boolean setIntensities​(FlatFileParser.Data data,
                                      float[] intensities,
                                      int firstIndex)
        Description copied from interface: SpotIntensityParser
        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.
        Specified by:
        setIntensities in interface SpotIntensityParser
        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)