Uses of Class
ubic.gemma.model.genome.sequenceAnalysis.BlatAssociation

Packages that use BlatAssociation

Package	Description
ubic.gemma.core.analysis.sequence
ubic.gemma.core.goldenpath
ubic.gemma.core.loader.expression.arrayDesign
ubic.gemma.model.genome.sequenceAnalysis
ubic.gemma.persistence.service.genome.sequenceAnalysis

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

Methods in ubic.gemma.core.analysis.sequence that return BlatAssociation

Modifier and Type	Method	Description
static BlatAssociation	BlatAssociationScorer.scoreResults(Collection<BlatAssociation> blatAssociations)	From a collection of BlatAssociations from a single BioSequence, reduce redundancy, fill in the specificity and score and pick the one with the best scoring statistics.

Methods in ubic.gemma.core.analysis.sequence that return types with arguments of type BlatAssociation

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)

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

Modifier and Type	Method	Description
static double	BlatAssociationScorer.computeOverlapFraction(BlatAssociation blatAssociation)	Compute how much the BLAT alignment with the target gene product is as a fraction of the query sequence length.

Method parameters in ubic.gemma.core.analysis.sequence with type arguments of type BlatAssociation

Modifier and Type	Method	Description
static BlatAssociation	BlatAssociationScorer.scoreResults(Collection<BlatAssociation> blatAssociations)	From a collection of BlatAssociations from a single BioSequence, reduce redundancy, fill in the specificity and score and pick the one with the best scoring statistics.

Uses of BlatAssociation in ubic.gemma.core.goldenpath

Methods in ubic.gemma.core.goldenpath that return types with arguments of type BlatAssociation

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 BlatAssociation in ubic.gemma.core.loader.expression.arrayDesign

Methods in ubic.gemma.core.loader.expression.arrayDesign that return types with arguments of type BlatAssociation

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)

Method parameters in ubic.gemma.core.loader.expression.arrayDesign with type arguments of type BlatAssociation

Modifier and Type	Method	Description
void	ArrayDesignProbeMapperService.printResult(CompositeSequence compositeSequence, Collection<BlatAssociation> col)	Print results to STDOUT
void	ArrayDesignProbeMapperServiceImpl.printResult(CompositeSequence compositeSequence, Collection<BlatAssociation> col)

Uses of BlatAssociation in ubic.gemma.model.genome.sequenceAnalysis

Methods in ubic.gemma.model.genome.sequenceAnalysis that return BlatAssociation

Modifier and Type	Method	Description
static BlatAssociation	BlatAssociation.Factory.newInstance()

Uses of BlatAssociation in ubic.gemma.persistence.service.genome.sequenceAnalysis

Methods in ubic.gemma.persistence.service.genome.sequenceAnalysis that return BlatAssociation

Modifier and Type	Method	Description
BlatAssociation	BlatAssociationService.create(BlatAssociation blatAssociation)

Methods in ubic.gemma.persistence.service.genome.sequenceAnalysis that return types with arguments of type BlatAssociation

Modifier and Type	Method	Description
Collection<BlatAssociation>	BlatAssociationDao.find(Collection<GeneProduct> toRemove)
Collection<BlatAssociation>	BlatAssociationDao.find(BioSequence bioSequence)
Collection<BlatAssociation>	BlatAssociationDao.find(Gene gene)
Collection<BlatAssociation>	BlatAssociationDaoImpl.find(Collection<GeneProduct> gps)
Collection<BlatAssociation>	BlatAssociationDaoImpl.find(BioSequence bioSequence)
Collection<BlatAssociation>	BlatAssociationDaoImpl.find(Gene gene)
Collection<BlatAssociation>	BlatAssociationService.find(BioSequence bioSequence)
Collection<BlatAssociation>	BlatAssociationService.find(Gene gene)
Collection<BlatAssociation>	BlatAssociationServiceImpl.find(BioSequence bioSequence)
Collection<BlatAssociation>	BlatAssociationServiceImpl.find(Gene gene)
Collection<BlatAssociation>	BlatAssociationService.findAndThaw(BioSequence bioSequence)
Collection<BlatAssociation>	BlatAssociationServiceImpl.findAndThaw(BioSequence bioSequence)

Methods in ubic.gemma.persistence.service.genome.sequenceAnalysis with parameters of type BlatAssociation

Modifier and Type	Method	Description
BlatAssociation	BlatAssociationService.create(BlatAssociation blatAssociation)
void	BlatAssociationService.remove(BlatAssociation blatAssociation)
void	BlatAssociationDao.thaw(BlatAssociation blatAssociation)
void	BlatAssociationDaoImpl.thaw(BlatAssociation blatAssociation)

Method parameters in ubic.gemma.persistence.service.genome.sequenceAnalysis with type arguments of type BlatAssociation

Modifier and Type	Method	Description
void	BlatAssociationDao.thaw(Collection<BlatAssociation> blatAssociations)
void	BlatAssociationDaoImpl.thaw(Collection<BlatAssociation> blatAssociations)