Package ubic.gemma.persistence.service.expression.arrayDesign

Interface ArrayDesignService

    • Method Detail

      • deleteAlignmentData

        @Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void deleteAlignmentData​(ArrayDesign arrayDesign)
        remove sequence alignment results associated with the bioSequences for this array design. This can indirectly * affect other platforms that use the same sequences.
        Parameters:
        arrayDesign - AD

      • deleteGeneProductAssociations

        @Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void deleteGeneProductAssociations​(ArrayDesign arrayDesign)
        deletes the gene product associations on the specified array design. If you only want to delete alignment-based or annotation-based associations, use deleteGeneProductAlignmentAssociation deleteGeneProductAnnotationAssociations.
        Parameters:
        arrayDesign - AD

      • findByAlternateName

        @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<ArrayDesign> findByAlternateName​(String queryString)

      • findByManufacturer

        @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<ArrayDesign> findByManufacturer​(String searchString)

      • findByName

        @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<ArrayDesign> findByName​(String name)

      • findByShortName

        @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ_QUIET"})
ArrayDesign findByShortName​(String shortName)

      • findByTaxon

        @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<ArrayDesign> findByTaxon​(Taxon taxon)
        Find by the primary taxon.
        Parameters:
        taxon - taxon
        Returns:
        ADs

      • getAlignments

        @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Map<CompositeSequence,​Collection<BlatResult>> getAlignments​(ArrayDesign arrayDesign)
        Retrieves alignments for the platform elements, limited to those which map to a gene product (so not all blat results)
        Parameters:
        arrayDesign - AD
        Returns:
        map of composite sequences to alignments, if available.

      • getAllAssociatedBioAssays

        @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<BioAssay> getAllAssociatedBioAssays​(ArrayDesign arrayDesign)

      • getBioSequences

        @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Map<CompositeSequence,​BioSequence> getBioSequences​(ArrayDesign arrayDesign)
        Return all the (unique) biosequences associated with the array design. Composite sequences that don't have sequences are also returned, so this can be used to do a thawRawAndProcessed, in effect.
        Parameters:
        arrayDesign - AD
        Returns:
        map of composite seqs. to bio seqs.

      • getCompositeSequenceCount

        @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Long getCompositeSequenceCount​(ArrayDesign arrayDesign)

      • getCompositeSequences

        @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<CompositeSequence> getCompositeSequences​(ArrayDesign arrayDesign,
                                                    int limit,
                                                    int offset)

      • getExpressionExperiments

        @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ","AFTER_ACL_COLLECTION_READ"})
Collection<ExpressionExperiment> getExpressionExperiments​(ArrayDesign arrayDesign)

      • getExpressionExperimentsCount

        @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
long getExpressionExperimentsCount​(ArrayDesign arrayDesign)

      • getLastGeneMapping

        Map<Long,​AuditEvent> getLastGeneMapping​(Collection<Long> ids)
        Gets the AuditEvents of the latest gene mapping for the specified array design ids. This returns a map of id -> AuditEvent. If the events do not exist, the map entry will point to null.
        Parameters:
        ids - ids
        Returns:
        map of IDs to events

      • getLastSequenceAnalysis

        Map<Long,​AuditEvent> getLastSequenceAnalysis​(Collection<Long> ids)
        Gets the AuditEvents of the latest sequence analyses for the specified array design ids. This returns a map of id -> AuditEvent. If the events do not exist, the map entry will point to null.
        Parameters:
        ids - ids
        Returns:
        map of IDs to events

      • getLastSequenceUpdate

        Map<Long,​AuditEvent> getLastSequenceUpdate​(Collection<Long> ids)
        Gets the AuditEvents of the latest sequence update for the specified array design ids. This returns a map of id -> AuditEvent. If the events do not exist, the map entry will point to null.
        Parameters:
        ids - ids
        Returns:
        map of IDs to events

      • getSwitchedExperiments

        @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ","AFTER_ACL_COLLECTION_READ"})
Collection<ExpressionExperiment> getSwitchedExperiments​(ArrayDesign id)
        Get the ids of experiments that "originally" used this platform, but which don't any more due to a platform switch. Note that for some old platforms we may not have recorded this information.
        Parameters:
        id - id of the platform
        Returns:
        collection of EE ids

      • getSwitchedExpressionExperimentCount

        @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
long getSwitchedExpressionExperimentCount​(ArrayDesign id)

      • getPerTaxonCount

        Map<Taxon,​Long> getPerTaxonCount()
        Returns:
        a map of taxon -> count of how many array designs there are for that taxon. Taxa with no arrays are excluded.

      • getTaxa

        Collection<Taxon> getTaxa​(ArrayDesign arrayDesign)
        Return the taxa for the array design. This can be multiple, or zero if the array is not processed.
        Parameters:
        arrayDesign - The id of the array design
        Returns:
        The Set of Taxons for array design.

      • loadValueObjectsForEE

        List<ArrayDesignValueObject> loadValueObjectsForEE​(Long eeId)
        Loads the Value Objects for array designs used by expression experiment with the given ID
        Parameters:
        eeId - the id of an expression experiment
        Returns:
        AD VOs

      • numAllCompositeSequenceWithBioSequences

        long numAllCompositeSequenceWithBioSequences()
        Function to return a count of all compositeSequences with bioSequence associations
        Returns:
        count

      • numAllCompositeSequenceWithBioSequences

        long numAllCompositeSequenceWithBioSequences​(Collection<Long> ids)
        Function to return the count of all composite sequences with biosequences, given a list of array design Ids
        Parameters:
        ids - ids
        Returns:
        count

      • numAllCompositeSequenceWithBlatResults

        long numAllCompositeSequenceWithBlatResults()
        Function to return all composite sequences with blat results
        Returns:
        count

      • numAllCompositeSequenceWithBlatResults

        long numAllCompositeSequenceWithBlatResults​(Collection<Long> ids)
        Function to return the count of all composite sequences with blat results, given a list of array design Ids
        Parameters:
        ids - ids
        Returns:
        count

      • numAllCompositeSequenceWithGenes

        long numAllCompositeSequenceWithGenes()
        Function to return a count of all composite sequences with associated genes.
        Returns:
        count

      • numAllCompositeSequenceWithGenes

        long numAllCompositeSequenceWithGenes​(Collection<Long> ids)
        Function to return the count of all composite sequences with genes, given a list of array design Ids
        Parameters:
        ids - ids
        Returns:
        count

      • numAllGenes

        long numAllGenes()
        Returns a count of the number of genes associated with all arrayDesigns
        Returns:
        count

      • numAllGenes

        long numAllGenes​(Collection<Long> ids)
        Returns the number of unique Genes associated with the collection of ArrayDesign ids.
        Parameters:
        ids - ids
        Returns:
        count

      • numBioSequences

        @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
long numBioSequences​(ArrayDesign arrayDesign)
        returns the number of bioSequences associated with this ArrayDesign id
        Parameters:
        arrayDesign - AD
        Returns:
        count

      • numBlatResults

        @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
long numBlatResults​(ArrayDesign arrayDesign)
        returns the number of BlatResults (BioSequence2GeneProduct) entries associated with this ArrayDesign id.
        Parameters:
        arrayDesign - AD
        Returns:
        count

      • numCompositeSequenceWithBioSequences

        @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
long numCompositeSequenceWithBioSequences​(ArrayDesign arrayDesign)

      • numCompositeSequenceWithBlatResults

        @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
long numCompositeSequenceWithBlatResults​(ArrayDesign arrayDesign)

      • numCompositeSequenceWithGenes

        @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
long numCompositeSequenceWithGenes​(ArrayDesign arrayDesign)

      • numExperiments

        @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
long numExperiments​(ArrayDesign arrayDesign)
        Parameters:
        arrayDesign - AD
        Returns:
        how many experiments use this platform (not including experiment subsets) security filtered

      • numGenes

        @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
long numGenes​(ArrayDesign arrayDesign)
        Returns the number of unique Genes associated with this ArrayDesign id
        Parameters:
        arrayDesign - AD
        Returns:
        count

      • removeBiologicalCharacteristics

        @Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void removeBiologicalCharacteristics​(ArrayDesign arrayDesign)
        Remove all associations that this array design has with BioSequences. This is needed for cases where the original import has associated the probes with the wrong sequences. A common case is for GEO data sets where the actual oligonucleotide is not given. Instead the submitter provides Genbank accessions, which are misleading. This method can be used to clear those until the "right" sequences can be identified and filled in. Note that this does not remove the BioSequences, it just nulls the BiologicalCharacteristics of the CompositeSequences.
        Parameters:
        arrayDesign - AD

      • thawLite

        @CheckReturnValue
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
ArrayDesign thawLite​(ArrayDesign arrayDesign)
        Perform a less intensive thaw of an array design: not the composite sequences.
        Parameters:
        arrayDesign - AD
        Returns:
        AD

      • updateSubsumingStatus

        @Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
Boolean updateSubsumingStatus​(ArrayDesign candidateSubsumer,
                              ArrayDesign candidateSubsumee)
        Test whether the candidateSubsumer subsumes the candidateSubsumee. If so, the array designs are updated to reflect this fact. The boolean value returned indicates whether there was indeed a subsuming relationship found.
        Parameters:
        candidateSubsumee - candidate subsumee
        candidateSubsumer - candidate subsumer
        Returns:
        success

      • isBlackListed

        boolean isBlackListed​(String geoAccession)
        Parameters:
        geoAccession - for a GEO series or platform

      • deleteGeneProductAnnotationAssociations

        @Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void deleteGeneProductAnnotationAssociations​(ArrayDesign arrayDesign)

      • deleteGeneProductAlignmentAssociations

        @Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void deleteGeneProductAlignmentAssociations​(ArrayDesign arrayDesign)