net.sf.basedb.core.filehandler
Class CelFileHandler

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

All Implemented Interfaces:

DataFileHandler, DataFileMetadataReader, DataFileValidator

public class CelFileHandler
extends AffymetrixFileHandler
implements DataFileValidator, DataFileMetadataReader

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

Version:

2.5

Author:

Nicklas

Last modified

$Date:2007-10-12 12:03:18 +0200 (Fri, 12 Oct 2007) $

Field Summary

private affymetrix.fusion.cel.FusionCELData

celData

Constructor Summary

CelFileHandler()

Method Summary

void	extractMetadata(DbControl dc) Extract metadata from the file(s) and write the metadata to the item passed to the DataFileHandler.setItem(net.sf.basedb.core.FileStoreEnabled) method.
void	resetMetadata(DbControl dc) Reset the number of file spots to 0, and remove all headers.
private void	setHeader(RawBioAssay rba, String name, String value)
void	validate(DbControl dc) Check that the raw bioassay is using the Affymetrix platform (Platform.AFFYMETRIX) and that the file selected as the CEL file really is a CEL file.
private static void	validateCelAndCdf(affymetrix.fusion.cel.FusionCELData cel, affymetrix.fusion.cdf.FusionCDFData cdf, String cdfChipType)

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

celData

private affymetrix.fusion.cel.FusionCELData celData

Constructor Detail

CelFileHandler

public CelFileHandler()

Method Detail

validate

public void validate(DbControl dc)

Check that the raw bioassay is using the Affymetrix platform (Platform.AFFYMETRIX) and that the file selected as the CEL file really is a CEL 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)

Description copied from interface: DataFileMetadataReader

Extract metadata from the file(s) and write the metadata to the item passed to the DataFileHandler.setItem(net.sf.basedb.core.FileStoreEnabled) method.

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 the number of file spots to 0, and remove all headers.

Specified by:

resetMetadata in interface DataFileMetadataReader

Parameters:

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

setHeader

private void setHeader(RawBioAssay rba,
                       String name,
                       String value)

validateCelAndCdf

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

Throws:

InvalidDataException