Uses of Class
ubic.gemma.model.expression.designElement.CompositeSequenceValueObject

Packages that use CompositeSequenceValueObject

Package	Description
ubic.gemma.model.analysis.sequence
ubic.gemma.model.expression.bioAssayData
ubic.gemma.persistence.service.expression.designElement
ubic.gemma.rest
ubic.gemma.rest.util.args

Uses of CompositeSequenceValueObject in ubic.gemma.model.analysis.sequence

Methods in ubic.gemma.model.analysis.sequence that return CompositeSequenceValueObject

Modifier and Type	Method	Description
CompositeSequenceValueObject	GeneMappingSummary.getCompositeSequence()

Methods in ubic.gemma.model.analysis.sequence with parameters of type CompositeSequenceValueObject

Modifier and Type	Method	Description
void	GeneMappingSummary.setCompositeSequence(CompositeSequenceValueObject compositeSequence)

Uses of CompositeSequenceValueObject in ubic.gemma.model.expression.bioAssayData

Methods in ubic.gemma.model.expression.bioAssayData that return CompositeSequenceValueObject

Modifier and Type	Method	Description
CompositeSequenceValueObject	DataVectorValueObject.getDesignElement()

Methods in ubic.gemma.model.expression.bioAssayData with parameters of type CompositeSequenceValueObject

Modifier and Type	Method	Description
void	DataVectorValueObject.setDesignElement(CompositeSequenceValueObject designElement)

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

Subclasses with type arguments of type CompositeSequenceValueObject in ubic.gemma.persistence.service.expression.designElement

Modifier and Type	Class	Description
class	CompositeSequenceDaoImpl
class	CompositeSequenceServiceImpl

Subinterfaces with type arguments of type CompositeSequenceValueObject in ubic.gemma.persistence.service.expression.designElement

Modifier and Type	Interface	Description
interface	CompositeSequenceDao
interface	CompositeSequenceService

Methods in ubic.gemma.persistence.service.expression.designElement that return CompositeSequenceValueObject

Modifier and Type	Method	Description
protected CompositeSequenceValueObject	CompositeSequenceDaoImpl.doLoadValueObject(CompositeSequence entity)
CompositeSequenceValueObject	CompositeSequenceService.loadValueObjectWithGeneMappingSummary(CompositeSequence cs)	Include gene mapping summary in the CompositeSequenceValueObject.
CompositeSequenceValueObject	CompositeSequenceServiceImpl.loadValueObjectWithGeneMappingSummary(CompositeSequence cs)

Methods in ubic.gemma.persistence.service.expression.designElement that return types with arguments of type CompositeSequenceValueObject

Modifier and Type	Method	Description
Slice<CompositeSequenceValueObject>	CompositeSequenceService.loadValueObjectsForGene(Gene gene, int start, int limit, boolean useGene2Cs)
Slice<CompositeSequenceValueObject>	CompositeSequenceServiceImpl.loadValueObjectsForGene(Gene gene, int start, int limit, boolean useGene2Cs)
CursorPage<CompositeSequenceValueObject>	CompositeSequenceService.loadValueObjectsForGeneByCursor(Gene gene, Cursor cursor, int limit, boolean useGene2Cs)	Cursor-mode counterpart to CompositeSequenceService.loadValueObjectsForGene(Gene, int, int, boolean) — see CURSOR_PAGINATION_STEP1_PLAN.md step 1m.
CursorPage<CompositeSequenceValueObject>	CompositeSequenceServiceImpl.loadValueObjectsForGeneByCursor(Gene gene, Cursor cursor, int limit, boolean useGene2Cs)

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

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

Uses of CompositeSequenceValueObject in ubic.gemma.rest

Methods in ubic.gemma.rest that return CompositeSequenceValueObject

Modifier and Type	Method	Description
CompositeSequenceValueObject	GeneWebService.CompositeSequenceSummaryValueObject.getProbe()

Methods in ubic.gemma.rest that return types with arguments of type CompositeSequenceValueObject

Modifier and Type	Method	Description
ResponseDataObject<CompositeSequenceValueObject>	PlatformsWebService.getPlatformElementMappingSummary(PlatformArg<?> platformArg, CompositeSequenceArg<?> probeArg)	Retrieves the per-probe gene-mapping summary (BLAT alignments + biological-sequence metadata + supported genes) for a single probe on a given platform.

Constructors in ubic.gemma.rest with parameters of type CompositeSequenceValueObject

Modifier	Constructor	Description
	CompositeSequenceSummaryValueObject(CompositeSequenceValueObject probe, List<GeneValueObject> genes, int numGenes, Integer numBlatHits)

Uses of CompositeSequenceValueObject in ubic.gemma.rest.util.args

Methods in ubic.gemma.rest.util.args that return types with arguments of type CompositeSequenceValueObject

Modifier and Type	Method	Description
Slice<CompositeSequenceValueObject>	PlatformArgService.getElements(PlatformArg<?> arg, int limit, int offset)	Retrieves the design elements of the platform that this argument represents.
Slice<CompositeSequenceValueObject>	PlatformArgService.getElements(PlatformArg<?> arg, int limit, int offset, boolean withSequence)	Variant that opt-in hydrates the probe-sequence projection (sequence + length) via a single batch HQL after the main page is fetched.
Slice<CompositeSequenceValueObject>	PlatformArgService.getElements(PlatformArg<?> arg, int limit, int offset, boolean withSequence, boolean withGenes, Collection<Long> geneIds)	Full-projection variant: adds the opt-in gene column (withGenes) and the opt-in gene restriction (geneIds).
Slice<CompositeSequenceValueObject>	PlatformArgService.getElements(PlatformArg<?> arg, Filters userFilters, Collection<Long> geneIds, int limit, int offset, boolean withSequence, boolean withGenes)	Widest offset-mode variant: user-supplied filter= conjunct on top of everything else.
Slice<CompositeSequenceValueObject>	PlatformArgService.getElements(PlatformArg<?> arg, CompositeSequenceArrayArg probesArg, int limit, int offset, boolean withSequence)	Offset-mode variant of PlatformArgService.getElementsByCursor(PlatformArg, CompositeSequenceArrayArg, Cursor, int, boolean).
Slice<CompositeSequenceValueObject>	PlatformArgService.getElements(PlatformArg<?> arg, CompositeSequenceArrayArg probesArg, int limit, int offset, boolean withSequence, boolean withGenes)	Probe-set variant with the opt-in gene column.
CursorPage<CompositeSequenceValueObject>	PlatformArgService.getElementsByCursor(PlatformArg<?> arg, Cursor cursor, int limit)	Cursor-mode counterpart to PlatformArgService.getElements(PlatformArg, int, int): keyset pagination over the design elements of a single platform, always sorted by ascending id (the primary key, indexed and unique) — see CURSOR_PAGINATION_STEP1_PLAN.md step 1e.
CursorPage<CompositeSequenceValueObject>	PlatformArgService.getElementsByCursor(PlatformArg<?> arg, Cursor cursor, int limit, boolean withSequence)	Cursor-mode variant of PlatformArgService.getElements(PlatformArg, int, int, boolean).
CursorPage<CompositeSequenceValueObject>	PlatformArgService.getElementsByCursor(PlatformArg<?> arg, Cursor cursor, int limit, boolean withSequence, boolean withGenes, Collection<Long> geneIds)	Cursor-mode variant of PlatformArgService.getElements(PlatformArg, int, int, boolean, boolean, Collection).
CursorPage<CompositeSequenceValueObject>	PlatformArgService.getElementsByCursor(PlatformArg<?> arg, Filters userFilters, Collection<Long> geneIds, Cursor cursor, int limit, boolean withSequence, boolean withGenes)	Widest cursor-mode variant; see PlatformArgService.getElements(PlatformArg, Filters, Collection, int, int, boolean, boolean).
CursorPage<CompositeSequenceValueObject>	PlatformArgService.getElementsByCursor(PlatformArg<?> arg, CompositeSequenceArrayArg probesArg, Cursor cursor, int limit)	Cursor-mode counterpart to FilteringVoEnabledService.loadValueObjects(Filters, Sort, int, int) scoped to a single platform AND a fixed set of probe identifiers (the /{platform}/elements/{probes} endpoint) — see CURSOR_PAGINATION_STEP1_PLAN.md step 1j.
CursorPage<CompositeSequenceValueObject>	PlatformArgService.getElementsByCursor(PlatformArg<?> arg, CompositeSequenceArrayArg probesArg, Cursor cursor, int limit, boolean withSequence)	Cursor-mode + probe-set variant of PlatformArgService.getElements(PlatformArg, int, int, boolean).
CursorPage<CompositeSequenceValueObject>	PlatformArgService.getElementsByCursor(PlatformArg<?> arg, CompositeSequenceArrayArg probesArg, Cursor cursor, int limit, boolean withSequence, boolean withGenes)	Cursor-mode + probe-set variant with the opt-in gene column.
Slice<CompositeSequenceValueObject>	GeneArgService.getGeneProbes(GeneArg<?> geneArg, int offset, int limit)	Obtain probes for the gene across all platforms.
CursorPage<CompositeSequenceValueObject>	GeneArgService.getGeneProbesByCursor(GeneArg<?> geneArg, Cursor cursor, int limit)	Cursor-mode counterpart to GeneArgService.getGeneProbes(GeneArg, int, int): keyset pagination over the probes (composite sequences) mapped to a single gene across all platforms — see CURSOR_PAGINATION_STEP1_PLAN.md step 1m.
Slice<CompositeSequenceValueObject>	GeneArgService.getGeneProbesInTaxon(GeneArg<?> geneArg, Taxon taxon, int offset, int limit)	Obtain probes for the gene in the given taxon across all platforms.
CursorPage<CompositeSequenceValueObject>	GeneArgService.getGeneProbesInTaxonByCursor(GeneArg<?> geneArg, Taxon taxon, Cursor cursor, int limit)	Cursor-mode counterpart to GeneArgService.getGeneProbesInTaxon(GeneArg, Taxon, int, int): keyset pagination over the probes (composite sequences) mapped to a single gene in the given taxon across all platforms — see CURSOR_PAGINATION_STEP1_PLAN.md step 1n.