Package ubic.gemma.core.loader.expression.simple

Class SimpleExpressionDataLoaderServiceImpl

java.lang.Object

ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderServiceImpl

All Implemented Interfaces:

org.springframework.beans.factory.InitializingBean, SimpleExpressionDataLoaderService

@Component
public class SimpleExpressionDataLoaderServiceImpl
extends Object
implements SimpleExpressionDataLoaderService, org.springframework.beans.factory.InitializingBean

Convert a simple matrix and some meta-data into an ExpressionExperiment. Used to handle flat file conversion.

Author:

pavlidis

Constructor Summary

Constructors

Constructor	Description
SimpleExpressionDataLoaderServiceImpl()

Method Summary

Modifier and Type	Method	Description
void	afterPropertiesSet()
ExpressionExperiment	convert(SimpleExpressionExperimentMetadata metaData, DoubleMatrix<String,String> matrix)	Convert simple experiment metadata and data into Gemma objects.
ExpressionExperiment	create(SimpleExpressionExperimentMetadata metaData, DoubleMatrix<String,String> matrix)	Parses, converts (into Gemma objects), and loads data into the database.

Methods inherited from class java.lang.Object

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

Constructor Details

SimpleExpressionDataLoaderServiceImpl

public SimpleExpressionDataLoaderServiceImpl()

Method Details

afterPropertiesSet

public void afterPropertiesSet()
                        throws Exception

Specified by:

afterPropertiesSet in interface org.springframework.beans.factory.InitializingBean

Throws:

Exception

create

public ExpressionExperiment create(SimpleExpressionExperimentMetadata metaData,
 @Nullable
 DoubleMatrix<String,String> matrix)

Description copied from interface: SimpleExpressionDataLoaderService

Parses, converts (into Gemma objects), and loads data into the database.

If data is provided and preferred, post-processing will be triggered.

Specified by:

create in interface SimpleExpressionDataLoaderService

Parameters:

metaData - meta data

matrix - tab-delimited file with row names corresponding to CompositeSequence names and column names corresponding to BioAssay names. Note that if you provide samples in the metadata, all the samples referenced in the data file must be declared.

Returns:

new experiment

convert

public ExpressionExperiment convert(SimpleExpressionExperimentMetadata metaData,
 @Nullable
 DoubleMatrix<String,String> matrix)

Description copied from interface: SimpleExpressionDataLoaderService

Convert simple experiment metadata and data into Gemma objects.

Specified by:

convert in interface SimpleExpressionDataLoaderService