net.sf.basedb.core.filehandler
Class CdfFileHandler

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

All Implemented Interfaces:

DataFileHandler, DataFileMetadataReader, DataFileValidator

public class CdfFileHandler
extends AffymetrixFileHandler
implements DataFileValidator, DataFileMetadataReader

File handler that can validate and extract metadata from Affymetrix CDF files.

Version:

2.5

Author:

Nicklas

Last modified

$Date: 2008-09-11 22:09:17 +0200 (Thu, 11 Sep 2008) $

Field Summary

private affymetrix.fusion.cdf.FusionCDFData

cdfData

Constructor Summary

CdfFileHandler()

Method Summary

void	extractMetadata(DbControl dc) Reads the number of probesets in the CDF file and stores it in ArrayDesign.getNumFileFeatures().
void	resetMetadata(DbControl dc) Reset ArrayDesign.getNumFileFeatures() to 0.
void	validate(DbControl dc) Check that the array design is using the Affymetrix platform (Platform.AFFYMETRIX) and that the file selected as the CDF file really is a CDF file.

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

isAffymetrix, loadCdfFile, loadCelFile

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

Methods inherited from interface net.sf.basedb.core.filehandler.DataFileHandler

setFile, setItem

Field Detail

cdfData

private affymetrix.fusion.cdf.FusionCDFData cdfData

Constructor Detail

CdfFileHandler

public CdfFileHandler()

Method Detail

validate

public void validate(DbControl dc)

Check that the array design is using the Affymetrix platform (Platform.AFFYMETRIX) and that the file selected as the CDF file really is a CDF file.

Specified by:

validate in interface DataFileValidator

Parameters:

dc - A DbControl object that can be used for database access

extractMetadata

public void extractMetadata(DbControl dc)

Reads the number of probesets in the CDF file and stores it in ArrayDesign.getNumFileFeatures().

Specified by:

extractMetadata in interface DataFileMetadataReader

Parameters:

dc - A DbControl object that can be used for database access

resetMetadata

public void resetMetadata(DbControl dc)

Reset ArrayDesign.getNumFileFeatures() to 0.

Specified by:

resetMetadata in interface DataFileMetadataReader

Parameters:

dc - A DbControl object that can be used for database access