Package ubic.gemma.core.analysis.preprocess

Class PreprocessorServiceImpl

java.lang.Object

ubic.gemma.core.analysis.preprocess.PreprocessorServiceImpl

All Implemented Interfaces:

PreprocessorService

@Service
@Transactional(propagation=NEVER)
public class PreprocessorServiceImpl
extends Object
implements PreprocessorService

Constructor Summary

Constructors

Constructor	Description
PreprocessorServiceImpl()

Method Summary

Modifier and Type	Method	Description
void	process(ExpressionExperiment ee, boolean ignoreQuantitationMismatch, boolean ignoreDiagnosticsFailure)	Preprocess a dataset.
void	processDiagnostics(ExpressionExperiment ee)	Create or update the sample correlation, PCA and M-V data.

Methods inherited from class java.lang.Object

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

Methods inherited from interface ubic.gemma.core.analysis.preprocess.PreprocessorService

process, process

Constructor Details

PreprocessorServiceImpl

public PreprocessorServiceImpl()

Method Details

process

public void process(ExpressionExperiment ee,
 boolean ignoreQuantitationMismatch,
 boolean ignoreDiagnosticsFailure)
             throws PreprocessingException

Description copied from interface: PreprocessorService

Preprocess a dataset.

Specified by:

process in interface PreprocessorService

Parameters:

ee - the expression experiment to process, it must be fully thawed with ExpressionExperimentService.thaw(ExpressionExperiment)

ignoreQuantitationMismatch - ignore quantitation mismatch when generating processed EVs

ignoreDiagnosticsFailure - simply warn if a diagnostic fails instead of interrupting the pre-processing and raising an exception

Throws:

PreprocessingException - if there was a problem during the processing

processDiagnostics

public void processDiagnostics(ExpressionExperiment ee)
                        throws PreprocessingException

Description copied from interface: PreprocessorService

Create or update the sample correlation, PCA and M-V data.

This is also done as part of PreprocessorService.process(ExpressionExperiment, boolean, boolean) so should only be called if only a refresh is needed.

Specified by:

processDiagnostics in interface PreprocessorService

Parameters:

ee - the expression experiment to process, it must be fully thawed with ExpressionExperimentService.thaw(ExpressionExperiment)

Throws:

PreprocessingException