Uses of Class
ubic.gemma.model.genome.biosequence.BioSequence

Packages that use BioSequence

Package	Description
ubic.gemma.core.analysis.sequence
ubic.gemma.core.apps
ubic.gemma.core.loader.expression
ubic.gemma.core.loader.expression.arrayDesign
ubic.gemma.core.loader.genome
ubic.gemma.core.search
ubic.gemma.core.search.source
ubic.gemma.model.association
ubic.gemma.model.expression.designElement
ubic.gemma.model.genome
ubic.gemma.model.genome.biosequence
ubic.gemma.model.genome.sequenceAnalysis
ubic.gemma.persistence.persister
ubic.gemma.persistence.service.expression.arrayDesign
ubic.gemma.persistence.service.expression.designElement
ubic.gemma.persistence.service.genome.biosequence
ubic.gemma.persistence.service.genome.sequenceAnalysis
ubic.gemma.persistence.util

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

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

Modifier and Type	Method	Description
static BioSequence	SequenceManipulation.collapse(Collection<Reporter> sequences)	Convert a CompositeSequence's immobilizedCharacteristics into a single sequence, using a simple merge-join strategy.

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

Modifier and Type	Method	Description
Collection<BioSequence>	RepeatScan.processRepeatMaskerOutput(Collection<BioSequence> sequences, String outputSequencePath)
Collection<BioSequence>	RepeatScan.repeatScan(Collection<BioSequence> sequences)	Run repeatmasker on the sequences.

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

Modifier and Type	Method	Description
static String	SequenceWriter.getIdentifier(BioSequence b)	Modify the identifier for the purposes of using in temporary Fasta files.
Collection<BlatAssociation>	ProbeMapper.processSequence(GoldenPathSequenceAnalysis goldenPath, BioSequence sequence)	Get BlatAssociation results for a single sequence.
Collection<BlatAssociation>	ProbeMapperImpl.processSequence(GoldenPathSequenceAnalysis goldenPath, BioSequence sequence)
static int	SequenceManipulation.rightHandOverlap(BioSequence target, BioSequence query)	Compute just any overlap the compare sequence has with the target on the right side.

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

Modifier and Type	Method	Description
Collection<BioSequence>	RepeatScan.processRepeatMaskerOutput(Collection<BioSequence> sequences, String outputSequencePath)
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)
Collection<BioSequence>	RepeatScan.repeatScan(Collection<BioSequence> sequences)	Run repeatmasker on the sequences.
static int	SequenceWriter.writeSequencesToFile(Collection<BioSequence> sequences, File outputFile)	Write a collection of sequences in FASTA format

Uses of BioSequence in ubic.gemma.core.apps

Methods in ubic.gemma.core.apps that return types with arguments of type BioSequence

Modifier and Type	Method	Description
Map<BioSequence,Collection<BlatResult>>	Blat.blatQuery(Collection<BioSequence> sequences, boolean sensitive, Taxon taxon)
Map<BioSequence,Collection<BlatResult>>	Blat.blatQuery(Collection<BioSequence> sequences, Taxon taxon)
Map<BioSequence,Collection<BlatResult>>	ShellDelegatingBlat.blatQuery(Collection<BioSequence> sequences, boolean sensitive, Taxon taxon)
Map<BioSequence,Collection<BlatResult>>	ShellDelegatingBlat.blatQuery(Collection<BioSequence> sequences, Taxon taxon)

Methods in ubic.gemma.core.apps with parameters of type BioSequence

Modifier and Type	Method	Description
Collection<BlatResult>	Blat.blatQuery(BioSequence b)	Run a BLAT search using the gfClient.
Collection<BlatResult>	Blat.blatQuery(BioSequence b, Taxon taxon, boolean sensitive)	Run a BLAT search using the gfClient.
Collection<BlatResult>	ShellDelegatingBlat.blatQuery(BioSequence b)
Collection<BlatResult>	ShellDelegatingBlat.blatQuery(BioSequence b, Taxon taxon, boolean sensitive)

Method parameters in ubic.gemma.core.apps with type arguments of type BioSequence

Modifier and Type	Method	Description
Map<BioSequence,Collection<BlatResult>>	Blat.blatQuery(Collection<BioSequence> sequences, boolean sensitive, Taxon taxon)
Map<BioSequence,Collection<BlatResult>>	Blat.blatQuery(Collection<BioSequence> sequences, Taxon taxon)
Map<BioSequence,Collection<BlatResult>>	ShellDelegatingBlat.blatQuery(Collection<BioSequence> sequences, boolean sensitive, Taxon taxon)
Map<BioSequence,Collection<BlatResult>>	ShellDelegatingBlat.blatQuery(Collection<BioSequence> sequences, Taxon taxon)

Uses of BioSequence in ubic.gemma.core.loader.expression

Fields in ubic.gemma.core.loader.expression declared as BioSequence

Modifier and Type	Field	Description
static BioSequence	ExpressionExperimentPlatformSwitchService.NULL_BIOSEQUENCE	Used to identify design elements that have no sequence associated with them.

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

Methods in ubic.gemma.core.loader.expression.arrayDesign that return BioSequence

Modifier and Type	Method	Description
BioSequence	Reporter.getImmobilizedCharacteristic()
BioSequence	ArrayDesignSequenceProcessingService.processSingleAccession(String sequenceId, String[] databaseNames, String blastDbHome, boolean force)	Update a single sequence in the system.
BioSequence	ArrayDesignSequenceProcessingServiceImpl.processSingleAccession(String sequenceId, String[] databaseNames, String blastDbHome, boolean force)	Update a single sequence in the system.

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

Modifier and Type	Method	Description
static Collection<BioSequence>	ArrayDesignSequenceAlignmentServiceImpl.getSequences(ArrayDesign ad)
static Collection<BioSequence>	ArrayDesignSequenceAlignmentServiceImpl.getSequences(ArrayDesign ad, Taxon taxon)
Collection<BioSequence>	ArrayDesignSequenceProcessingService.processAffymetrixDesign(ArrayDesign arrayDesign, InputStream probeSequenceFile, Taxon taxon)	Use this to add sequences to an existing Affymetrix design.
Collection<BioSequence>	ArrayDesignSequenceProcessingServiceImpl.processAffymetrixDesign(ArrayDesign arrayDesign, InputStream probeSequenceFile, Taxon taxon)
Collection<BioSequence>	ArrayDesignSequenceProcessingService.processArrayDesign(ArrayDesign arrayDesign, InputStream sequenceFile, InputStream sequenceIdentifierFile, SequenceType sequenceType, Taxon taxon)	Read from FASTA file when the sequence file lacks any way to link the sequences back to the probes.
Collection<BioSequence>	ArrayDesignSequenceProcessingService.processArrayDesign(ArrayDesign arrayDesign, InputStream sequenceIdentifierFile, String[] databaseNames, String blastDbHome, Taxon taxon, boolean force)	Intended for use with array designs that use sequences that are in genbank, but the accessions need to be assigned after the array is already in the system.
Collection<BioSequence>	ArrayDesignSequenceProcessingService.processArrayDesign(ArrayDesign arrayDesign, InputStream sequenceIdentifierFile, String[] databaseNames, String blastDbHome, Taxon taxon, boolean force, FastaCmd fc)
Collection<BioSequence>	ArrayDesignSequenceProcessingService.processArrayDesign(ArrayDesign arrayDesign, InputStream sequenceFile, SequenceType sequenceType)	The sequence file must provide an unambiguous way to associate the sequences with design elements on the array.
Collection<BioSequence>	ArrayDesignSequenceProcessingService.processArrayDesign(ArrayDesign arrayDesign, InputStream sequenceFile, SequenceType sequenceType, Taxon taxon)	The sequence file must provide an unambiguous way to associate the sequences with design elements on the array.
Collection<BioSequence>	ArrayDesignSequenceProcessingService.processArrayDesign(ArrayDesign arrayDesign, String[] databaseNames, boolean force)
Collection<BioSequence>	ArrayDesignSequenceProcessingService.processArrayDesign(ArrayDesign arrayDesign, String[] databaseNames, String blastDbHome, boolean force)	For the case where the sequences are retrieved simply by the Genbank accession.
Collection<BioSequence>	ArrayDesignSequenceProcessingService.processArrayDesign(ArrayDesign arrayDesign, String[] databaseNames, String blastDbHome, boolean force, FastaCmd fc)	Provided primarily for testing.
Collection<BioSequence>	ArrayDesignSequenceProcessingServiceImpl.processArrayDesign(ArrayDesign arrayDesign, InputStream sequenceFile, InputStream sequenceIdentifierFile, SequenceType sequenceType, Taxon taxon)
Collection<BioSequence>	ArrayDesignSequenceProcessingServiceImpl.processArrayDesign(ArrayDesign arrayDesign, InputStream sequenceIdentifierFile, String[] databaseNames, String blastDbHome, Taxon taxon, boolean force)
Collection<BioSequence>	ArrayDesignSequenceProcessingServiceImpl.processArrayDesign(ArrayDesign arrayDesign, InputStream sequenceIdentifierFile, String[] databaseNames, String blastDbHome, Taxon taxon, boolean force, FastaCmd fc)
Collection<BioSequence>	ArrayDesignSequenceProcessingServiceImpl.processArrayDesign(ArrayDesign arrayDesign, InputStream sequenceFile, SequenceType sequenceType)
Collection<BioSequence>	ArrayDesignSequenceProcessingServiceImpl.processArrayDesign(ArrayDesign arrayDesign, InputStream sequenceFile, SequenceType sequenceType, Taxon taxon)
Collection<BioSequence>	ArrayDesignSequenceProcessingServiceImpl.processArrayDesign(ArrayDesign arrayDesign, String[] databaseNames, boolean force)
Collection<BioSequence>	ArrayDesignSequenceProcessingServiceImpl.processArrayDesign(ArrayDesign arrayDesign, String[] databaseNames, String blastDbHome, boolean force)
Collection<BioSequence>	ArrayDesignSequenceProcessingServiceImpl.processArrayDesign(ArrayDesign arrayDesign, String[] databaseNames, String blastDbHome, boolean force, FastaCmd fc)

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

Modifier and Type	Method	Description
void	Reporter.setImmobilizedCharacteristic(BioSequence immobilizedCharacteristic)

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

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

Modifier and Type	Method	Description
BioSequence	ProbeSequenceParser.get(String key)
BioSequence	FastaCmd.getByAccession(String accession, String database)
BioSequence	FastaCmd.getByAccession(String accession, String database, String blastHome)
BioSequence	SimpleFastaCmd.getByAccession(String accession, String database)
BioSequence	SimpleFastaCmd.getByAccession(String accession, String database, String blastHome)
BioSequence	FastaCmd.getByIdentifier(int identifier, String database)
BioSequence	FastaCmd.getByIdentifier(int identifier, String database, String blastHome)
BioSequence	SimpleFastaCmd.getByIdentifier(int identifier, String database)
BioSequence	SimpleFastaCmd.getByIdentifier(int identifier, String database, String blastHome)
BioSequence	ProbeSequenceParser.parseOneLine(String line)

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

Modifier and Type	Method	Description
Collection<BioSequence>	FastaCmd.getBatchAccessions(Collection<String> accessions, String database)
Collection<BioSequence>	FastaCmd.getBatchAccessions(Collection<String> accessions, String database, String blastHome)
Collection<BioSequence>	SimpleFastaCmd.getBatchAccessions(Collection<String> accessions, String database)
Collection<BioSequence>	SimpleFastaCmd.getBatchAccessions(Collection<String> accessions, String database, String blastHome)
Collection<BioSequence>	FastaCmd.getBatchIdentifiers(Collection<Integer> identifiers, String database)
Collection<BioSequence>	FastaCmd.getBatchIdentifiers(Collection<Integer> identifiers, String database, String blastHome)
Collection<BioSequence>	SimpleFastaCmd.getBatchIdentifiers(Collection<Integer> identifiers, String database)
Collection<BioSequence>	SimpleFastaCmd.getBatchIdentifiers(Collection<Integer> identifiers, String database, String blastHome)
Collection<BioSequence>	FastaParser.getResults()
Collection<BioSequence>	ProbeSequenceParser.getResults()

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

Modifier and Type	Method	Description
protected String	ProbeSequenceParser.getKey(BioSequence newItem)
protected void	ProbeSequenceParser.put(String key, BioSequence value)

Uses of BioSequence in ubic.gemma.core.search

Methods in ubic.gemma.core.search that return types with arguments of type BioSequence

Modifier and Type	Method	Description
default Collection<SearchResult<BioSequence>>	SearchSource.searchBioSequence(SearchSettings settings)

Uses of BioSequence in ubic.gemma.core.search.source

Methods in ubic.gemma.core.search.source that return types with arguments of type BioSequence

Modifier and Type	Method	Description
Collection<SearchResult<BioSequence>>	CompositeSearchSource.searchBioSequence(SearchSettings settings)
Collection<SearchResult<BioSequence>>	DatabaseSearchSource.searchBioSequence(SearchSettings settings)	A database search for biosequences.
Collection<SearchResult<BioSequence>>	HibernateSearchSource.searchBioSequence(SearchSettings settings)

Uses of BioSequence in ubic.gemma.model.association

Methods in ubic.gemma.model.association that return BioSequence

Modifier and Type	Method	Description
BioSequence	BioSequence2GeneProduct.getBioSequence()

Methods in ubic.gemma.model.association with parameters of type BioSequence

Modifier and Type	Method	Description
void	BioSequence2GeneProduct.setBioSequence(BioSequence bioSequence)

Uses of BioSequence in ubic.gemma.model.expression.designElement

Methods in ubic.gemma.model.expression.designElement that return BioSequence

Modifier and Type	Method	Description
BioSequence	CompositeSequence.getBiologicalCharacteristic()

Methods in ubic.gemma.model.expression.designElement with parameters of type BioSequence

Modifier and Type	Method	Description
void	CompositeSequence.setBiologicalCharacteristic(BioSequence biologicalCharacteristic)

Uses of BioSequence in ubic.gemma.model.genome

Methods in ubic.gemma.model.genome that return BioSequence

Modifier and Type	Method	Description
BioSequence	Chromosome.getSequence()

Constructors in ubic.gemma.model.genome with parameters of type BioSequence

Constructor	Description
Chromosome(String name, ExternalDatabase assemblyDatabase, BioSequence sequence, Taxon taxon)

Uses of BioSequence in ubic.gemma.model.genome.biosequence

Methods in ubic.gemma.model.genome.biosequence that return BioSequence

Modifier and Type	Method	Description
static BioSequence	BioSequence.Factory.newInstance()
static BioSequence	BioSequence.Factory.newInstance(String name, Taxon taxon)
static BioSequence	BioSequence.Factory.newInstance(Taxon taxon)

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

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

Modifier and Type	Method	Description
BioSequence	SequenceSimilaritySearchResult.getQuerySequence()
BioSequence	SequenceSimilaritySearchResult.getTargetSequence()

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

Modifier and Type	Method	Description
static BioSequenceValueObject	BioSequenceValueObject.fromEntity(BioSequence bs)
void	SequenceSimilaritySearchResult.setQuerySequence(BioSequence querySequence)
void	SequenceSimilaritySearchResult.setTargetSequence(BioSequence targetSequence)

Method parameters in ubic.gemma.model.genome.sequenceAnalysis with type arguments of type BioSequence

Modifier and Type	Method	Description
static Collection<BioSequenceValueObject>	BioSequenceValueObject.fromEntities(Collection<BioSequence> bsList)

Uses of BioSequence in ubic.gemma.persistence.persister

Methods in ubic.gemma.persistence.persister that return BioSequence

Modifier and Type	Method	Description
protected BioSequence	GenomePersister.persistBioSequence(BioSequence bioSequence, AbstractPersister.Caches caches)

Methods in ubic.gemma.persistence.persister with parameters of type BioSequence

Modifier and Type	Method	Description
protected BioSequence	GenomePersister.persistBioSequence(BioSequence bioSequence, AbstractPersister.Caches caches)

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

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

Modifier and Type	Method	Description
Map<CompositeSequence,BioSequence>	ArrayDesignDao.getBioSequences(ArrayDesign arrayDesign)
Map<CompositeSequence,BioSequence>	ArrayDesignDaoImpl.getBioSequences(ArrayDesign arrayDesign)
Map<CompositeSequence,BioSequence>	ArrayDesignService.getBioSequences(ArrayDesign arrayDesign)	Return all the (unique) biosequences associated with the array design.
Map<CompositeSequence,BioSequence>	ArrayDesignServiceImpl.getBioSequences(ArrayDesign arrayDesign)

Uses of BioSequence in ubic.gemma.persistence.service.expression.designElement

Methods in ubic.gemma.persistence.service.expression.designElement with parameters of type BioSequence

Modifier and Type	Method	Description
Collection<CompositeSequence>	CompositeSequenceDao.findByBioSequence(BioSequence bioSequence)
Collection<CompositeSequence>	CompositeSequenceDaoImpl.findByBioSequence(BioSequence bioSequence)
Collection<CompositeSequence>	CompositeSequenceService.findByBioSequence(BioSequence bioSequence)
Collection<CompositeSequence>	CompositeSequenceServiceImpl.findByBioSequence(BioSequence bioSequence)
Collection<GeneMappingSummary>	CompositeSequenceService.getGeneMappingSummary(BioSequence biologicalCharacteristic, CompositeSequenceValueObject cs)
Collection<GeneMappingSummary>	CompositeSequenceServiceImpl.getGeneMappingSummary(BioSequence biologicalCharacteristic, CompositeSequenceValueObject cs)

Uses of BioSequence in ubic.gemma.persistence.service.genome.biosequence

Methods in ubic.gemma.persistence.service.genome.biosequence that return BioSequence

Modifier and Type	Method	Description
BioSequence	BioSequenceService.create(BioSequence bioSequence)
BioSequence	BioSequenceDaoImpl.find(BioSequence bioSequence)
BioSequence	BioSequenceDao.findByAccession(DatabaseEntry accession)
BioSequence	BioSequenceDaoImpl.findByAccession(DatabaseEntry databaseEntry)
BioSequence	BioSequenceService.findByAccession(DatabaseEntry accession)
BioSequence	BioSequenceServiceImpl.findByAccession(DatabaseEntry accession)
BioSequence	BioSequenceDao.findByCompositeSequence(CompositeSequence compositeSequence)
BioSequence	BioSequenceDaoImpl.findByCompositeSequence(CompositeSequence compositeSequence)
BioSequence	BioSequenceService.findByCompositeSequence(CompositeSequence compositeSequence)
BioSequence	BioSequenceServiceImpl.findByCompositeSequence(CompositeSequence compositeSequence)
BioSequence	BioSequenceService.findOrCreate(BioSequence bioSequence)
BioSequence	BioSequenceDao.thaw(BioSequence bioSequence)
BioSequence	BioSequenceDaoImpl.thaw(BioSequence bioSequence)
BioSequence	BioSequenceService.thaw(BioSequence bs)
BioSequence	BioSequenceServiceImpl.thaw(BioSequence bioSequence)

Methods in ubic.gemma.persistence.service.genome.biosequence that return types with arguments of type BioSequence

Modifier and Type	Method	Description
Map<Gene,Collection<BioSequence>>	BioSequenceDao.findByGenes(Collection<Gene> genes)	Returns matching biosequences for the given genes in a Map (gene to biosequences).
Map<Gene,Collection<BioSequence>>	BioSequenceDaoImpl.findByGenes(Collection<Gene> genes)
Map<Gene,Collection<BioSequence>>	BioSequenceService.findByGenes(Collection<Gene> genes)
Map<Gene,Collection<BioSequence>>	BioSequenceServiceImpl.findByGenes(Collection<Gene> genes)
Collection<BioSequence>	BioSequenceDao.findByName(String name)
Collection<BioSequence>	BioSequenceDaoImpl.findByName(String name)
Collection<BioSequence>	BioSequenceService.findByName(String name)
Collection<BioSequence>	BioSequenceServiceImpl.findByName(String name)
Collection<BioSequence>	BioSequenceService.findOrCreate(Collection<BioSequence> bioSequences)
Collection<BioSequence>	BioSequenceServiceImpl.findOrCreate(Collection<BioSequence> bioSequences)
Collection<BioSequence>	BioSequenceDao.thaw(Collection<BioSequence> bioSequences)
Collection<BioSequence>	BioSequenceDaoImpl.thaw(Collection<BioSequence> bioSequences)
Collection<BioSequence>	BioSequenceService.thaw(Collection<BioSequence> bioSequences)
Collection<BioSequence>	BioSequenceServiceImpl.thaw(Collection<BioSequence> bioSequences)

Methods in ubic.gemma.persistence.service.genome.biosequence with parameters of type BioSequence

Modifier and Type	Method	Description
BioSequence	BioSequenceService.create(BioSequence bioSequence)
protected BioSequenceValueObject	BioSequenceDaoImpl.doLoadValueObject(BioSequence entity)
BioSequence	BioSequenceDaoImpl.find(BioSequence bioSequence)
BioSequence	BioSequenceService.findOrCreate(BioSequence bioSequence)
void	BioSequenceService.remove(BioSequence bioSequence)
BioSequence	BioSequenceDao.thaw(BioSequence bioSequence)
BioSequence	BioSequenceDaoImpl.thaw(BioSequence bioSequence)
BioSequence	BioSequenceService.thaw(BioSequence bs)
BioSequence	BioSequenceServiceImpl.thaw(BioSequence bioSequence)
void	BioSequenceService.update(BioSequence bioSequence)

Method parameters in ubic.gemma.persistence.service.genome.biosequence with type arguments of type BioSequence

Modifier and Type	Method	Description
Collection<BioSequence>	BioSequenceService.findOrCreate(Collection<BioSequence> bioSequences)
Collection<BioSequence>	BioSequenceServiceImpl.findOrCreate(Collection<BioSequence> bioSequences)
Collection<BioSequence>	BioSequenceDao.thaw(Collection<BioSequence> bioSequences)
Collection<BioSequence>	BioSequenceDaoImpl.thaw(Collection<BioSequence> bioSequences)
Collection<BioSequence>	BioSequenceService.thaw(Collection<BioSequence> bioSequences)
Collection<BioSequence>	BioSequenceServiceImpl.thaw(Collection<BioSequence> bioSequences)

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

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

Modifier and Type	Method	Description
Collection<AnnotationAssociation>	AnnotationAssociationDao.find(BioSequence bioSequence)
Collection<AnnotationAssociation>	AnnotationAssociationDaoImpl.find(BioSequence bioSequence)
Collection<AnnotationAssociation>	AnnotationAssociationService.find(BioSequence bioSequence)
Collection<AnnotationAssociation>	AnnotationAssociationServiceImpl.find(BioSequence bioSequence)
Collection<BlatAssociation>	BlatAssociationDao.find(BioSequence bioSequence)
Collection<BlatAssociation>	BlatAssociationDaoImpl.find(BioSequence bioSequence)
Collection<BlatAssociation>	BlatAssociationService.find(BioSequence bioSequence)
Collection<BlatAssociation>	BlatAssociationServiceImpl.find(BioSequence bioSequence)
Collection<BlatAssociation>	BlatAssociationService.findAndThaw(BioSequence bioSequence)
Collection<BlatAssociation>	BlatAssociationServiceImpl.findAndThaw(BioSequence bioSequence)
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)

Uses of BioSequence in ubic.gemma.persistence.util

Methods in ubic.gemma.persistence.util with parameters of type BioSequence

Modifier and Type	Method	Description
static void	BusinessKey.addRestrictions(Criteria queryObject, BioSequence bioSequence)	Note: The finder has to do the additional checking for equality of sequence and/or database entry - we don't know until we get the sequences.
static void	BusinessKey.attachCriteria(Criteria queryObject, BioSequence bioSequence, String propertyName)	Restricts the query to the provided BioSequence.
static void	BusinessKey.checkValidKey(BioSequence bioSequence)
static Criteria	BusinessKey.createQueryObject(Session session, BioSequence bioSequence)

Method parameters in ubic.gemma.persistence.util with type arguments of type BioSequence

Modifier and Type	Method	Description
void	ArrayDesignsForExperimentCache.add(ArrayDesign arrayDesign, Map<CompositeSequence,BioSequence> sequences)