Package net.sf.basedb.util.affymetrix

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 Summary

Constructors

Constructor	Description
AffymetrixUtil()

Method Summary

Modifier and Type	Method	Description
static boolean	isAffymetrix(FileStoreEnabled item)	Check if the item is using the affymetrix platform.
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

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