net.sf.basedb.core
Class Affymetrix

java.lang.Object
  net.sf.basedb.core.Affymetrix

public class Affymetrix
extends Object

Utility class for Affymetrix-specific functionality. Use this class to link CDF files with array designs and CEL and CHP files with raw bioassays.

Version:

2.0

Author:

nicklas

Last modified

$Date: 2008-09-11 22:11:02 +0200 (Thu, 11 Sep 2008) $

Field Summary

static String	CDF_LINK_NAME Deprecated. See DataFileType.AFFYMETRIX_CDF
static String	CEL_LINK_NAME Deprecated. See DataFileType.AFFYMETRIX_CEL
static String	CHP_LINK_NAME Deprecated. See DataFileType

Constructor Summary

Affymetrix()

Method Summary

static int	checkIfReportersExists(affymetrix.fusion.cdf.FusionCDFData cdf, ReporterBatcher batcher, boolean create, ReporterType type, ProgressReporter progress) Verify that probesets in a CDF file exists as reporters and optionally create those that doesn't exists.
static File	getCdfFile(ArrayDesign design) Deprecated. Use FileStoreUtil.getDataFile(DbControl, FileStoreEnabled, String) with a data file type of DataFileType.AFFYMETRIX_CDF instead
static File	getCelFile(RawBioAssay rawBioAssay) Deprecated.
static affymetrix.fusion.cdf.FusionCDFData	loadCdfFile(File cdfFile) Deprecated. Use AffymetrixFileHandler.loadCdfFile(File) instead
static affymetrix.fusion.cel.FusionCELData	loadCelFile(File celFile) Deprecated. Use AffymetrixFileHandler.loadCdfFile(File) instead
static void	setCdfFile(ArrayDesign design, File file) Deprecated. Use FileStoreUtil.setDataFile(DbControl, FileStoreEnabled, String, File) instead with DataFileType.AFFYMETRIX_CDF as the file type
static void	setCelFile(RawBioAssay rawBioAssay, File file) Deprecated. Use FileStoreUtil.setDataFile(DbControl, FileStoreEnabled, String, File) instead with DataFileType.AFFYMETRIX_CEL as the file type
private static void	validateCelAndCdf(affymetrix.fusion.cel.FusionCELData cel, affymetrix.fusion.cdf.FusionCDFData cdf, String cdfChipType)
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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

CDF_LINK_NAME

public static final String CDF_LINK_NAME

Deprecated. See DataFileType.AFFYMETRIX_CDF

The name of the AnyToAny link between an array design and a file that contains the CDF information.

See Also:

Constant Field Values

CEL_LINK_NAME

public static final String CEL_LINK_NAME

Deprecated. See DataFileType.AFFYMETRIX_CEL

The name of the AnyToAny link between a raw bioassay and a file that contains the CEL information.

See Also:

Constant Field Values

CHP_LINK_NAME

public static final String CHP_LINK_NAME

Deprecated. See DataFileType

The name of the AnyToAny link between a raw bioassay and a file that contains the CHP information.

See Also:

Constant Field Values

Constructor Detail

Affymetrix

public Affymetrix()

Method Detail

setCdfFile

public static void setCdfFile(ArrayDesign design,
                              File file)
                       throws PermissionDeniedException,
                              InvalidDataException,
                              BaseException

Deprecated. Use FileStoreUtil.setDataFile(DbControl, FileStoreEnabled, String, File) instead with DataFileType.AFFYMETRIX_CDF as the file type

Attach a CDF file to an array design. When an array design has got a CDF file it counts as if it has features and it can be used for linking with RawBioAssay:s.

Starting with BASE 2.4 this method validates that the specified file is actaully a CDF file. See loadCdfFile(File).

Parameters:

design - The array design

file - The CDF file, or null to remove the file

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission for the design and use permission for the file

InvalidDataException - If the design is null or isn't an Affymetrix chip or if the file is not a CDF file

BaseException - If there is another error

getCdfFile

public static File getCdfFile(ArrayDesign design)
                       throws PermissionDeniedException,
                              InvalidDataException,
                              BaseException

Deprecated. Use FileStoreUtil.getDataFile(DbControl, FileStoreEnabled, String) with a data file type of DataFileType.AFFYMETRIX_CDF instead

Get the file that has been specified as the CDF file for an array design. This method has been deprecated with the implementation of the Platform and DataFileType which solves the problem in a more generic way.

This method is equivalent to:

DataFileType cdfType = 
   DataFileType.getByExternalId(dc, DataFileType.AFFYMETRIX_CDF);
File cdfFile = design.getFileSet().getMember(cdfType.getFile());

Parameters:

design - The design to get the CDF file from, it must be an Affymetrix chip

Returns:

The CDF file or null if no CDF file has been specified

Throws:

PermissionDeniedException - If the logged in user doesn't have read permission for the file

InvalidDataException - If the design is null or isn't an Affymetrix chip

BaseException - If there is another error

setCelFile

public static void setCelFile(RawBioAssay rawBioAssay,
                              File file)
                       throws PermissionDeniedException,
                              InvalidDataException,
                              BaseException

Deprecated. Use FileStoreUtil.setDataFile(DbControl, FileStoreEnabled, String, File) instead with DataFileType.AFFYMETRIX_CEL as the file type

Attach a CEL file to a raw bioassay. When a raw bioassay has got a CEL file it counts as if data has been loaded and it can be used in experiments for analysis. To be able to add a CEL file the array design must also be connected to an array design with a CDF file. See setCdfFile(ArrayDesign, File).

Starting with BASE 2.4 this method validates that the specified file is a CEL file and that it matches the CDF file attached to the array design. The check includes:

• That the CEL chip type mathces the file name of the CDF file.
• That the number of rows and columns are the same in both the CEL and the CDF

This method also sets the number of spots to the number of cells found in the CEL file.

Parameters:

rawBioAssay - The raw bioassay

file - The CEL file, or null to remove the file

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission for the raw bioassay and use permission for the file

InvalidDataException - If the raw bioassay is null or isn't an Affymetrix raw data type

BaseException - If there is another error

getCelFile

public static File getCelFile(RawBioAssay rawBioAssay)
                       throws PermissionDeniedException,
                              InvalidDataException,
                              BaseException

Deprecated.

Get the file that has been specified as the CEL file for a raw bioassay.

Parameters:

rawBioAssay - The raw bioassay to get the CEL file from, it must be a raw bioassay of an Affymetrix raw data type

Returns:

The CEL file or null if no CEL file has been specified

Throws:

PermissionDeniedException - If the logged in user doesn't have read permission for the file

InvalidDataException - If the raw bioassay is null or isn't an Affymetrix raw data type

BaseException - If there is another error

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.

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

validateCelAndCdf

private static void validateCelAndCdf(affymetrix.fusion.cel.FusionCELData cel,
                                      affymetrix.fusion.cdf.FusionCDFData cdf,
                                      String cdfChipType)
                               throws InvalidDataException

Throws:

InvalidDataException

loadCdfFile

public static affymetrix.fusion.cdf.FusionCDFData loadCdfFile(File cdfFile)
                                                       throws ItemNotFoundException,
                                                              InvalidDataException

Deprecated. Use AffymetrixFileHandler.loadCdfFile(File) instead

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 actaul file is not on the server

InvalidDataException - If the file is not a CDF file

Since:

2.4

loadCelFile

public static affymetrix.fusion.cel.FusionCELData loadCelFile(File celFile)
                                                       throws InvalidDataException

Deprecated. Use AffymetrixFileHandler.loadCdfFile(File) instead

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 actaul file is not on the server

InvalidDataException - If the file is not a CEL file

Since:

2.4

checkIfReportersExists

public static int checkIfReportersExists(affymetrix.fusion.cdf.FusionCDFData cdf,
                                         ReporterBatcher batcher,
                                         boolean create,
                                         ReporterType type,
                                         ProgressReporter progress)
                                  throws ItemNotFoundException,
                                         BaseException

Verify that 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