Package net.sf.basedb.util.affymetrix

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 Summary

Constructors

Constructor	Description
CdfValidator()	Create a new instance.

Method Summary

Modifier and Type	Method	Description
int	checkIfReportersExists(affymetrix.fusion.cdf.FusionCDFData cdf, ReporterBatcher batcher, boolean create, ReporterType type, ProgressReporter progress)	Verify if probesets in a CDF file exists as reporters and optionally create those that doesn't exists.
void	copyMetadata(affymetrix.fusion.cdf.FusionCDFData cdf, ArrayDesign design)	Copy metadata from the CDF file to the array design.
affymetrix.fusion.cdf.FusionCDFData	loadCdfFile(File cdfFile)	Load a CDF file using the Affymetric Fusion SDK.
void	resetMetadata(ArrayDesign design)	Reset metadata on the given array design.

Methods inherited from class java.lang.Object

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

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