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)
ExpressionExperiment	create(SimpleExpressionExperimentMetaData metaData, InputStream data)	Parses, converts (into Gemma objects), and loads data into the database.
DoubleMatrix<String,String>	getSubMatrixForArrayDesign(DoubleMatrix<String,String> matrix, Collection<Object> usedDesignElements, ArrayDesign design)
DoubleMatrix<String,String>	parse(InputStream data)

Methods inherited from class java.lang.Object

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

Constructor Detail

SimpleExpressionDataLoaderServiceImpl

public SimpleExpressionDataLoaderServiceImpl()

Method Detail

afterPropertiesSet

public void afterPropertiesSet()
                        throws Exception

Specified by:

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

Throws:

Exception

convert

public ExpressionExperiment convert(SimpleExpressionExperimentMetaData metaData,
                                    DoubleMatrix<String,String> matrix)

Specified by:

convert in interface SimpleExpressionDataLoaderService

getSubMatrixForArrayDesign

public DoubleMatrix<String,String> getSubMatrixForArrayDesign(DoubleMatrix<String,String> matrix,
                                                                    Collection<Object> usedDesignElements,
                                                                    ArrayDesign design)

Specified by:

getSubMatrixForArrayDesign in interface SimpleExpressionDataLoaderService

create

public ExpressionExperiment create(SimpleExpressionExperimentMetaData metaData,
                                   InputStream data)
                            throws IOException

Description copied from interface: SimpleExpressionDataLoaderService

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

Specified by:

create in interface SimpleExpressionDataLoaderService

Parameters:

metaData - meta data

data - tab-delimited file with row names corresponding to CompositeSequence names and column names corresponding to BioAssay names.

Returns:

new experiment

Throws:

IOException - when IO problems occur.

parse

public DoubleMatrix<String,String> parse(InputStream data)
                                        throws IOException

Specified by:

parse in interface SimpleExpressionDataLoaderService

Throws:

IOException