Class CdfValidator


  • public class CdfValidator
    extends Object
    Helper class for working with Affymetrix CDF files.
    Since:
    3.0
    Author:
    Nicklas
    Last modified
    $Date: 2011-05-06 14:09:13 +0200 (fr, 06 maj 2011) $
    • Constructor Detail

      • CdfValidator

        public CdfValidator()
        Create a new instance.
    • Method Detail

      • loadCdfFile

        public affymetrix.fusion.cdf.FusionCDFData loadCdfFile​(File cdfFile)
                                                        throws ItemNotFoundException,
                                                               InvalidDataException
        Load a CDF file using the Affymetric Fusion SDK. This method checks that the file exists, and read all headers.
        Parameters:
        cdfFile - The file to load
        Returns:
        A FusionCDFData object representing the CDF file
        Throws:
        ItemNotFoundException - If the actual file is not on the server
        InvalidDataException - If the file is not a CDF file
      • copyMetadata

        public void copyMetadata​(affymetrix.fusion.cdf.FusionCDFData cdf,
                                 ArrayDesign design)
        Copy metadata from the CDF file to the array design. This sets the number of features to the number of probesets.
        Parameters:
        cdf - The CDF file
        design - The array design
      • resetMetadata

        public void resetMetadata​(ArrayDesign design)
        Reset metadata on the given array design. This set the number of features to 0.
        Parameters:
        design - The array design
      • checkIfReportersExists

        public int checkIfReportersExists​(affymetrix.fusion.cdf.FusionCDFData cdf,
                                          ReporterBatcher batcher,
                                          boolean create,
                                          ReporterType type,
                                          ProgressReporter progress)
                                   throws ItemNotFoundException,
                                          BaseException
        Verify if probesets in a CDF file exists as reporters and optionally create those that doesn't exists. This method will clear the CDF file, read it, and then clear it again. The calling code is responsible for committing the transaction.
        Parameters:
        cdf - The CDF file
        batcher - A reporter batcher used to check and insert reporters
        create - TRUE to create non-existing reporters, FALSE to throw an ItemNotFoundException
        type - The reporter type to assign to new reporters (if create is true)
        progress - An optional progress reporter
        Returns:
        The number of created reporter
        Throws:
        ItemNotFoundException - If create is FALSE and a reporter isn't found
        BaseException - If there is another error
        Since:
        2.4