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java.lang.Objectnet.sf.basedb.util.affymetrix.CdfValidator
public class CdfValidator
Helper class for working with Affymetrix CDF files.
Constructor Summary | |
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CdfValidator()
Create a new instance. |
Method Summary | |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public CdfValidator()
Method Detail |
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public affymetrix.fusion.cdf.FusionCDFData loadCdfFile(File cdfFile) throws ItemNotFoundException, InvalidDataException
cdfFile
- The file to load
ItemNotFoundException
- If the actual file is not on the server
InvalidDataException
- If the file is not a CDF filepublic void copyMetadata(affymetrix.fusion.cdf.FusionCDFData cdf, ArrayDesign design)
cdf
- The CDF filedesign
- The array designpublic void resetMetadata(ArrayDesign design)
design
- The array designpublic int checkIfReportersExists(affymetrix.fusion.cdf.FusionCDFData cdf, ReporterBatcher batcher, boolean create, ReporterType type, ProgressReporter progress) throws ItemNotFoundException, BaseException
cdf
- The CDF filebatcher
- A reporter batcher used to check and insert reporterscreate
- TRUE to create non-existing reporters, FALSE to throw
an ItemNotFoundExceptiontype
- The reporter type to assign to new reporters (if create is true)progress
- An optional progress reporter
ItemNotFoundException
- If create is FALSE and a reporter isn't found
BaseException
- If there is another error
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