net.sf.basedb.core.filehandler
Class AffymetrixFileHandler

java.lang.Object
  net.sf.basedb.core.filehandler.AbstractDataFileHandler
      net.sf.basedb.core.filehandler.AffymetrixFileHandler

All Implemented Interfaces:

DataFileHandler

Direct Known Subclasses:

CdfFileHandler, CelFileHandler

public abstract class AffymetrixFileHandler
extends AbstractDataFileHandler

This class is used as a superclass for all Affymetrix-based validators and metadata readers. It also has some useful utility methods.

Version:

2.5

Author:

Nicklas

Last modified

$Date: 2010-04-29 12:14:59 +0200 (Thu, 29 Apr 2010) $

Constructor Summary

protected

AffymetrixFileHandler()

Method Summary

boolean	isAffymetrix(FileStoreEnabled item) Check if the item is using the affymetrix platform.
affymetrix.fusion.cdf.FusionCDFData	loadCdfFile(File cdfFile) Load a CDF file using the Affymetric Fusion SDK.
affymetrix.fusion.cel.FusionCELData	loadCelFile(File celFile) Load a CEL file using the Affymetric Fusion SDK.

Methods inherited from class net.sf.basedb.core.filehandler.AbstractDataFileHandler

getItem, getMember, setFile, setItem

Methods inherited from class java.lang.Object

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

Constructor Detail

AffymetrixFileHandler

protected AffymetrixFileHandler()

Method Detail

isAffymetrix

public 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.

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

loadCelFile

public affymetrix.fusion.cel.FusionCELData loadCelFile(File celFile)

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 actual file is not on the server

InvalidDataException - If the file is not a CEL file