Class AffymetrixUtil

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

public final class AffymetrixUtil extends Object
Utility class with Affymetrix-related functionality.
Since:
3.0
Author:
Nicklas
Last modified
$Date: 2011-09-02 15:01:58 +0200 (fr, 02 sep 2011) $
  • Constructor Details

    • AffymetrixUtil

      public AffymetrixUtil()
  • Method Details

    • isAffymetrix

      public static boolean isAffymetrix(FileStoreEnabled item)
      Check if the item is using the affymetrix platform.
      Parameters:
      item - Item to check. Null is not allowed.
      Returns:
      TRUE if platform is used, FALSE otherwise.
    • validateCelAndCdf

      public static void validateCelAndCdf(RawBioAssay rawBioAssay, ArrayDesign design, boolean required)
      Check if the CEL file on the raw bioassay matches the CDF file on the array design. If the array design has more than one CDF file only the first one is used. If the raw bioassay has more than one CEL file, each file will be validated against the CDF.
      Parameters:
      rawBioAssay - The raw bioassay
      design - The array design
      required - TRUE if the absense of either a CEL or a CDF file is an error condition
      Throws:
      InvalidDataException - If the raw bioassay or array design are not Affymetrix type, or if the CEL doesn't match the CDF
      Since:
      2.4