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

Packages that use BlatResult

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

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

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

Modifier and Type	Method	Description
Map<BioSequence,List<BlatResult>>	Blat.blatQuery(Collection<BioSequence> sequences, boolean sensitive, Taxon taxon)
Map<BioSequence,List<BlatResult>>	Blat.blatQuery(Collection<BioSequence> sequences, Taxon taxon)
List<BlatResult>	Blat.blatQuery(BioSequence b)	Run a BLAT search using the gfClient.
List<BlatResult>	Blat.blatQuery(BioSequence b, Taxon taxon, boolean sensitive)	Run a BLAT search using the gfClient.
Map<BioSequence,List<BlatResult>>	ShellDelegatingBlat.blatQuery(Collection<BioSequence> sequences, boolean sensitive, Taxon taxon)
Map<BioSequence,List<BlatResult>>	ShellDelegatingBlat.blatQuery(Collection<BioSequence> sequences, Taxon taxon)
List<BlatResult>	ShellDelegatingBlat.blatQuery(BioSequence b)
List<BlatResult>	ShellDelegatingBlat.blatQuery(BioSequence b, Taxon taxon, boolean sensitive)
Collection<BlatResult>	CompositeSequenceMapSummary.getBlatResults()
List<BlatResult>	ShellDelegatingBlat.processPsl(InputStream inputStream, Taxon taxon)	Process the output of a BLAT search in psl format.

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

Modifier and Type	Method	Description
static String	BlatResult2Psl.blatResult2PslTrack(BlatResult blatResult)	Creates text that can be displayed directly as a track in UCSC, using their hgTracks program.
static Integer	ProbeMapUtils.hashBlatResult(BlatResult br)	Compute a hash for the result based only on the characteristics of the alignment (that is, not the Id)
static Double	BlatAssociationScorer.identity(BlatResult blatResult)	Fraction identity computation, as in psl.c.
static Double	BlatAssociationScorer.score(BlatResult blatResult)	Based on the JKSrc method in psl.c, but without double-penalizing for mismatches.

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

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)
static void	ProbeMapUtils.removeDuplicates(Collection<BlatResult> blatResults)	Prune a set of results that have the same coordinates and query.
void	CompositeSequenceMapSummary.setBlatResults(Collection<BlatResult> blatResults)

Uses of BlatResult in ubic.gemma.core.goldenpath

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

Modifier and Type	Method	Description
Collection<BlatResult>	GoldenPathQuery.findAlignments(String accession)	Locate the alignment for the given sequence, if it exists in the goldenpath database.
Collection<BlatResult>	GoldenPathSequenceAnalysis.findSequenceLocations(String identifier)

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

Modifier and Type	Method	Description
Collection<? extends BioSequence2GeneProduct>	GoldenPathSequenceAnalysis.getThreePrimeDistances(BlatResult br, ThreePrimeDistanceMethod method)	Given a physical location, find how close it is to the 3' end of a gene it is in, using default mapping settings.

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

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

Modifier and Type	Method	Description
Collection<BlatResult>	ArrayDesignSequenceAlignmentService.processArrayDesign(ArrayDesign design)
Collection<BlatResult>	ArrayDesignSequenceAlignmentService.processArrayDesign(ArrayDesign ad, boolean sensitive)	Run blat on all sequences on the array design.
Collection<BlatResult>	ArrayDesignSequenceAlignmentService.processArrayDesign(ArrayDesign ad, Blat blat)
Collection<BlatResult>	ArrayDesignSequenceAlignmentService.processArrayDesign(ArrayDesign ad, Taxon taxon, Collection<BlatResult> rawBlatResults)
Collection<BlatResult>	ArrayDesignSequenceAlignmentServiceImpl.processArrayDesign(ArrayDesign design)
Collection<BlatResult>	ArrayDesignSequenceAlignmentServiceImpl.processArrayDesign(ArrayDesign design, boolean sensitive)
Collection<BlatResult>	ArrayDesignSequenceAlignmentServiceImpl.processArrayDesign(ArrayDesign design, Blat blat)
Collection<BlatResult>	ArrayDesignSequenceAlignmentServiceImpl.processArrayDesign(ArrayDesign ad, Taxon taxon, Collection<BlatResult> rawBlatResults)

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

Modifier and Type	Method	Description
Collection<BlatResult>	ArrayDesignSequenceAlignmentService.processArrayDesign(ArrayDesign ad, Taxon taxon, Collection<BlatResult> rawBlatResults)
Collection<BlatResult>	ArrayDesignSequenceAlignmentServiceImpl.processArrayDesign(ArrayDesign ad, Taxon taxon, Collection<BlatResult> rawBlatResults)

Uses of BlatResult in ubic.gemma.core.loader.genome

Methods in ubic.gemma.core.loader.genome that return BlatResult

Modifier and Type	Method	Description
BlatResult	BlatResultParser.parseOneLine(String line)

Methods in ubic.gemma.core.loader.genome that return types with arguments of type BlatResult

Modifier and Type	Method	Description
List<BlatResult>	BlatResultParser.getResults()

Methods in ubic.gemma.core.loader.genome with parameters of type BlatResult

Modifier and Type	Method	Description
protected void	BlatResultParser.addResult(BlatResult obj)

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

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

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

Methods in ubic.gemma.model.genome.sequenceAnalysis with parameters of type BlatResult

Modifier and Type	Method	Description
void	BlatAssociation.setBlatResult(BlatResult blatResult)

Constructors in ubic.gemma.model.genome.sequenceAnalysis with parameters of type BlatResult

Modifier	Constructor	Description
	BlatResultValueObject(BlatResult br, Double score, Double identity)

Uses of BlatResult in ubic.gemma.persistence.service.expression.arrayDesign

Methods in ubic.gemma.persistence.service.expression.arrayDesign that return types with arguments of type BlatResult

Modifier and Type	Method	Description
Map<CompositeSequence,Collection<BlatResult>>	ArrayDesignService.getAlignments(ArrayDesign arrayDesign)	Retrieves alignments for the platform elements, limited to those which map to a gene product (so not all blat results)
Map<CompositeSequence,Collection<BlatResult>>	ArrayDesignServiceImpl.getAlignments(ArrayDesign arrayDesign)
Map<CompositeSequence,Collection<BlatResult>>	ArrayDesignDao.loadAlignments(ArrayDesign arrayDesign)
Map<CompositeSequence,Collection<BlatResult>>	ArrayDesignDaoImpl.loadAlignments(ArrayDesign arrayDesign)

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

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

Modifier and Type	Method	Description
BlatResult	BlatResultDao.thaw(BlatResult blatResult)
BlatResult	BlatResultDaoImpl.thaw(BlatResult blatResult)
BlatResult	BlatResultService.thaw(BlatResult blatResult)
BlatResult	BlatResultServiceImpl.thaw(BlatResult blatResult)

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

Modifier and Type	Method	Description
Collection<BlatResult>	BlatResultDao.findByBioSequence(BioSequence bioSequence)	Find BLAT results for the given sequence
Collection<BlatResult>	BlatResultDaoImpl.findByBioSequence(BioSequence bioSequence)
Collection<BlatResult>	BlatResultService.findByBioSequence(BioSequence bioSequence)
Collection<BlatResult>	BlatResultServiceImpl.findByBioSequence(BioSequence bioSequence)
Collection<BlatResult>	BlatResultDao.thaw(Collection<BlatResult> blatResults)
Collection<BlatResult>	BlatResultDaoImpl.thaw(Collection<BlatResult> blatResults)
Collection<BlatResult>	BlatResultService.thaw(Collection<BlatResult> blatResults)
Collection<BlatResult>	BlatResultServiceImpl.thaw(Collection<BlatResult> blatResults)

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

Modifier and Type	Method	Description
protected BlatResultValueObject	BlatResultDaoImpl.doLoadValueObject(BlatResult entity)
void	BlatResultService.remove(BlatResult blatResult)
BlatResult	BlatResultDao.thaw(BlatResult blatResult)
BlatResult	BlatResultDaoImpl.thaw(BlatResult blatResult)
BlatResult	BlatResultService.thaw(BlatResult blatResult)
BlatResult	BlatResultServiceImpl.thaw(BlatResult blatResult)
void	BlatResultService.update(BlatResult blatResult)

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

Modifier and Type	Method	Description
Collection<BlatResult>	BlatResultDao.thaw(Collection<BlatResult> blatResults)
Collection<BlatResult>	BlatResultDaoImpl.thaw(Collection<BlatResult> blatResults)
Collection<BlatResult>	BlatResultService.thaw(Collection<BlatResult> blatResults)
Collection<BlatResult>	BlatResultServiceImpl.thaw(Collection<BlatResult> blatResults)