Class CelValidator

java.lang.Object
net.sf.basedb.util.affymetrix.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 Details

    • CelValidator

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

    • setHeader

      private void setHeader​(RawBioAssay rba, String name, String value)
    • 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