Uses of Class
ubic.gemma.core.analysis.sequence.ProbeMapperConfig

Packages that use ProbeMapperConfig

Package	Description
ubic.gemma.core.analysis.sequence
ubic.gemma.core.goldenpath
ubic.gemma.core.loader.expression.arrayDesign

Uses of ProbeMapperConfig in ubic.gemma.core.analysis.sequence

Methods in ubic.gemma.core.analysis.sequence with parameters of type ProbeMapperConfig

Modifier and Type	Method	Description
Map<String,Collection<BlatAssociation>>	ProbeMapper.processBlatResults(GoldenPathSequenceAnalysis goldenPathDb, Collection<BlatResult> blatResults, ProbeMapperConfig config)	Given some blat results (possibly for multiple sequences) determine which if any gene products they should be associated with; if there are multiple results for a single sequence, these are further analyzed for specificity and redundancy, so that there is a single BlatAssociation between any sequence andy andy gene product.
Map<String,Collection<BlatAssociation>>	ProbeMapperImpl.processBlatResults(GoldenPathSequenceAnalysis goldenPathDb, Collection<BlatResult> blatResults, ProbeMapperConfig config)
Map<String,Collection<BlatAssociation>>	ProbeMapper.processSequences(GoldenPathSequenceAnalysis goldenpath, Collection<BioSequence> sequences, ProbeMapperConfig config)	Given a collection of sequences, blat them against the selected genome.
Map<String,Collection<BlatAssociation>>	ProbeMapperImpl.processSequences(GoldenPathSequenceAnalysis goldenpath, Collection<BioSequence> sequences, ProbeMapperConfig config)

Uses of ProbeMapperConfig in ubic.gemma.core.goldenpath

Methods in ubic.gemma.core.goldenpath with parameters of type ProbeMapperConfig

Modifier and Type	Method	Description
Collection<BlatAssociation>	GoldenPathSequenceAnalysis.findAssociations(String chromosome, Long queryStart, Long queryEnd, String starts, String sizes, String strand, ThreePrimeDistanceMethod method, ProbeMapperConfig config)	Given a physical location, identify overlapping genes or predicted genes.

Uses of ProbeMapperConfig in ubic.gemma.core.loader.expression.arrayDesign

Methods in ubic.gemma.core.loader.expression.arrayDesign with parameters of type ProbeMapperConfig

Modifier and Type	Method	Description
void	ArrayDesignProbeMapperService.processArrayDesign(ArrayDesign arrayDesign, ProbeMapperConfig config, boolean useDB)
void	ArrayDesignProbeMapperServiceImpl.processArrayDesign(ArrayDesign arrayDesign, ProbeMapperConfig config, boolean useDB)
Map<String,Collection<BlatAssociation>>	ArrayDesignProbeMapperService.processCompositeSequence(ProbeMapperConfig config, Taxon taxon, GoldenPathSequenceAnalysis goldenPathDb, CompositeSequence compositeSequence)
Map<String,Collection<BlatAssociation>>	ArrayDesignProbeMapperServiceImpl.processCompositeSequence(ProbeMapperConfig config, Taxon taxon, GoldenPathSequenceAnalysis goldenPathDb, CompositeSequence compositeSequence)