Package net.sf.basedb.util.affymetrix
Class CelValidator
- java.lang.Object
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- net.sf.basedb.util.affymetrix.CelValidator
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public class CelValidator extends Object
Helper class for working with Affymetrix CEL files.- Since:
- 3.0
- Author:
- Nicklas
- Last modified
- $Date: 2011-05-06 14:09:13 +0200 (fr, 06 maj 2011) $
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Constructor Summary
Constructors Constructor Description CelValidator()
Create a new instance.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
copyMetadata(affymetrix.fusion.cel.FusionCELData cel, RawBioAssay rba)
Copy metadata from the CEL file to the raw bioassay.affymetrix.fusion.cel.FusionCELData
loadCelFile(File celFile)
Load a CEL file using the Affymetric Fusion SDK.void
resetMetadata(RawBioAssay rba)
Reset metadata on the given raw bioassay.private void
setHeader(RawBioAssay rba, String name, String value)
void
validateCelAndCdf(affymetrix.fusion.cel.FusionCELData cel, affymetrix.fusion.cdf.FusionCDFData cdf, String cdfChipType)
Check if the loaded CEL and CDF files matches.
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Method Detail
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setHeader
private void setHeader(RawBioAssay rba, String name, String value)
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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 serverInvalidDataException
- If the file is not a CEL file
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copyMetadata
public void copyMetadata(affymetrix.fusion.cel.FusionCELData cel, RawBioAssay rba)
Copy metadata from the CEL file to the raw bioassay. This will set the mumber of spots and headers from the file.- Parameters:
cel
- The CEL filerba
- The raw bioassay
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resetMetadata
public void resetMetadata(RawBioAssay rba)
Reset metadata on the given raw bioassay. This set the number of spots to 0 and remove all headers.- Parameters:
rba
- The raw bioassay
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validateCelAndCdf
public void validateCelAndCdf(affymetrix.fusion.cel.FusionCELData cel, affymetrix.fusion.cdf.FusionCDFData cdf, String cdfChipType) throws InvalidDataException
Check if the loaded CEL and CDF files matches. The chip type is verified. Unfortunately the chip type is not stored inside the CDF file, but has to be given as an extra parameter. Typically, this should be the name of the file. This method also verify that the number rows and columns in the two files matches.- Parameters:
cel
- The CEL fila datacdf
- The CDF file datacdfChipType
- The CDF chip type- Throws:
InvalidDataException
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