ubic.gemma.core.loader.expression.simple

Interface SimpleExpressionDataLoaderService

All Known Implementing Classes:

SimpleExpressionDataLoaderServiceImpl

public interface SimpleExpressionDataLoaderService

Load experiment from a flat file. See also DataUpdater for related operations on experiments already in the system.

Author:

paul

Method Summary

Modifier and Type	Method and Description
ExpressionExperiment	convert(SimpleExpressionExperimentMetaData metaData, ubic.basecode.dataStructure.matrix.DoubleMatrix<String,String> matrix)
ExpressionExperiment	create(SimpleExpressionExperimentMetaData metaData, InputStream data) Parses, converts (into Gemma objects), and loads data into the database.
ubic.basecode.dataStructure.matrix.DoubleMatrix<String,String>	getSubMatrixForArrayDesign(ubic.basecode.dataStructure.matrix.DoubleMatrix<String,String> matrix, Collection<Object> usedDesignElements, ArrayDesign design)
ubic.basecode.dataStructure.matrix.DoubleMatrix<String,String>	parse(InputStream data)

Method Detail

convert

ExpressionExperiment convert(SimpleExpressionExperimentMetaData metaData,
                             ubic.basecode.dataStructure.matrix.DoubleMatrix<String,String> matrix)

getSubMatrixForArrayDesign

ubic.basecode.dataStructure.matrix.DoubleMatrix<String,String> getSubMatrixForArrayDesign(ubic.basecode.dataStructure.matrix.DoubleMatrix<String,String> matrix,
                                                                                          Collection<Object> usedDesignElements,
                                                                                          ArrayDesign design)

create

ExpressionExperiment create(SimpleExpressionExperimentMetaData metaData,
                            InputStream data)
                     throws IOException

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

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

ubic.basecode.dataStructure.matrix.DoubleMatrix<String,String> parse(InputStream data)
                                                              throws IOException

Throws:

IOException