Package ubic.gemma.core.loader.expression.geo

Interface GeoConverter

All Superinterfaces:

Converter<GeoData,Object>

All Known Implementing Classes:

GeoConverterImpl

public interface GeoConverter
extends Converter<GeoData,Object>

Author:

paul

Method Summary

Modifier and Type	Method	Description
void	clear()	Remove old results.
Collection<Object>	convert(Collection<? extends GeoData> geoObjects)
Collection<Object>	convert(Collection<? extends GeoData> geoObjects, boolean skipDataVectors)
Object	convert(GeoData geoObject)
Object	convert(GeoData geoObject, boolean skipDataVectors)
Object[]	convertData(String[] vector, QuantitationType qt)	Convert a vector of data to a vector of the appropriate type for the quantitation type.
void	convertSubsetToExperimentalFactor(ExpressionExperiment expExp, GeoSubset geoSubSet)	Converts Geo subsets to experimental factors.
Taxon	getPrimaryArrayTaxon(Collection<Taxon> platformTaxa, Collection<String> probeTaxa)
void	setElementLimitForStrictness(int i)
void	setForceConvertElements(boolean forceConvertElements)
void	setSplitByPlatform(boolean splitByPlatform)

Method Detail

clear

void clear()

Remove old results. Call this prior to starting conversion of a full dataset.

convert

Collection<Object> convert(Collection<? extends GeoData> geoObjects)

Specified by:

convert in interface Converter<GeoData,Object>

convert

Collection<Object> convert(Collection<? extends GeoData> geoObjects,
                           boolean skipDataVectors)

convert

Object convert(GeoData geoObject)

Specified by:

convert in interface Converter<GeoData,Object>

convert

Object convert(GeoData geoObject,
               boolean skipDataVectors)

convertSubsetToExperimentalFactor

void convertSubsetToExperimentalFactor(ExpressionExperiment expExp,
                                       GeoSubset geoSubSet)

Converts Geo subsets to experimental factors. This adds a new factor value to the experimental factor of an experimental design, and adds the factor value to each BioMaterial of a specific BioAssay.

Parameters:

expExp - experiment

geoSubSet - geo subset

getPrimaryArrayTaxon

Taxon getPrimaryArrayTaxon(Collection<Taxon> platformTaxa,
                           Collection<String> probeTaxa)
                    throws IllegalArgumentException

Throws:

IllegalArgumentException

setSplitByPlatform

void setSplitByPlatform(boolean splitByPlatform)

Parameters:

splitByPlatform - If true, and the series uses more than one platform, split it up. This often isn't necessary/desirable. This is overridden if the series uses more than one species, in which case it is always split up.

convertData

@Nullable
Object[] convertData(String[] vector,
                     QuantitationType qt)

Convert a vector of data to a vector of the appropriate type for the quantitation type.

Returns:

null if all the data is missing

setForceConvertElements

void setForceConvertElements(boolean forceConvertElements)

Parameters:

forceConvertElements - Set the behaviour when a platform that normally would not be loaded in detail is encountered, such as an Exon array.

setElementLimitForStrictness

void setElementLimitForStrictness(int i)

Parameters:

i - this is here for tests only. The default value should be okay otherwise.