Class CdfValidator

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

    • CdfValidator

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

    • 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