Uses of Class
ubic.gemma.model.genome.sequenceAnalysis.BlatAssociation
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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 BlatAssociationBlatAssociationScorer. 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 doubleBlatAssociationScorer. 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 BlatAssociationBlatAssociationScorer. 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 voidArrayDesignProbeMapperService. printResult(CompositeSequence compositeSequence, Collection<BlatAssociation> col)Print results to STDOUTvoidArrayDesignProbeMapperServiceImpl. 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 BlatAssociationBlatAssociation.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 BlatAssociationBlatAssociationService. 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 BlatAssociationBlatAssociationService. create(BlatAssociation blatAssociation)voidBlatAssociationService. remove(BlatAssociation blatAssociation)voidBlatAssociationDao. thaw(BlatAssociation blatAssociation)voidBlatAssociationDaoImpl. thaw(BlatAssociation blatAssociation)Method parameters in ubic.gemma.persistence.service.genome.sequenceAnalysis with type arguments of type BlatAssociation Modifier and Type Method Description voidBlatAssociationDao. thaw(Collection<BlatAssociation> blatAssociations)voidBlatAssociationDaoImpl. thaw(Collection<BlatAssociation> blatAssociations)
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