Uses of Class
ubic.gemma.core.goldenpath.GoldenPathSequenceAnalysis

Packages that use GoldenPathSequenceAnalysis

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

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

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

Modifier and Type	Method	Description
Map<String,Collection<BlatAssociation>>	ProbeMapper.processBlatResults(GoldenPathSequenceAnalysis goldenPathDb, Collection<BlatResult> blatResults)	Given some blat results (possibly for multiple sequences) determine which if any gene products they should be associatd 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>>	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)
Map<String,Collection<BlatAssociation>>	ProbeMapperImpl.processBlatResults(GoldenPathSequenceAnalysis goldenPathDb, Collection<BlatResult> blatResults, ProbeMapperConfig config)
Map<String,Collection<BlatAssociation>>	ProbeMapper.processGbId(GoldenPathSequenceAnalysis goldenPathDb, String genbankId)	Given a genbank accession (for a mRNA or EST), find alignment data from GoldenPath.
Map<String,Collection<BlatAssociation>>	ProbeMapperImpl.processGbId(GoldenPathSequenceAnalysis goldenPathDb, String genbankId)
Map<String,Collection<BlatAssociation>>	ProbeMapper.processGbIds(GoldenPathSequenceAnalysis goldenPathDb, Collection<String[]> genbankIds)
Map<String,Collection<BlatAssociation>>	ProbeMapperImpl.processGbIds(GoldenPathSequenceAnalysis goldenPathDb, Collection<String[]> genbankIds)
Collection<BlatAssociation>	ProbeMapper.processSequence(GoldenPathSequenceAnalysis goldenPath, BioSequence sequence)	Get BlatAssociation results for a single sequence.
Collection<BlatAssociation>	ProbeMapperImpl.processSequence(GoldenPathSequenceAnalysis goldenPath, BioSequence sequence)
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 GoldenPathSequenceAnalysis in ubic.gemma.core.loader.expression.arrayDesign

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

Modifier and Type	Method	Description
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)