Class CelValidator


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

      • CelValidator

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

      • loadCelFile

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

        public void copyMetadata​(affymetrix.fusion.cel.FusionCELData cel,
                                 RawBioAssay rba)
        Copy metadata from the CEL file to the raw bioassay. This will set the mumber of spots and headers from the file.
        Parameters:
        cel - The CEL file
        rba - The raw bioassay
      • resetMetadata

        public void resetMetadata​(RawBioAssay rba)
        Reset metadata on the given raw bioassay. This set the number of spots to 0 and remove all headers.
        Parameters:
        rba - The raw bioassay
      • validateCelAndCdf

        public void validateCelAndCdf​(affymetrix.fusion.cel.FusionCELData cel,
                                      affymetrix.fusion.cdf.FusionCDFData cdf,
                                      String cdfChipType)
                               throws InvalidDataException
        Check if the loaded CEL and CDF files matches. The chip type is verified. Unfortunately the chip type is not stored inside the CDF file, but has to be given as an extra parameter. Typically, this should be the name of the file. This method also verify that the number rows and columns in the two files matches.
        Parameters:
        cel - The CEL fila data
        cdf - The CDF file data
        cdfChipType - The CDF chip type
        Throws:
        InvalidDataException