Modifier and Type | Method and Description |
---|---|
CellBaseDataResult<T> |
CellBaseDataResponse.first()
This method just returns the first DataResult of response, or null if response is null or empty.
|
CellBaseDataResult<T> |
CellBaseDataResponse.response(int m)
Fetch the DataResult of the m-response.
|
Modifier and Type | Method and Description |
---|---|
List<CellBaseDataResult<T>> |
CellBaseDataResponse.getResponses() |
List<CellBaseDataResult<T>> |
CellBaseDataResponse.responses()
Fetch the list of responses.
|
Modifier and Type | Method and Description |
---|---|
CellBaseDataResponse<T> |
CellBaseDataResponse.setResponses(List<CellBaseDataResult<T>> responses) |
Constructor and Description |
---|
CellBaseDataResponse(org.opencb.commons.datastore.core.ObjectMap params,
List<CellBaseDataResult<T>> responses) |
CellBaseDataResponse(String apiVersion,
int time,
List<org.opencb.commons.datastore.core.Event> events,
org.opencb.commons.datastore.core.ObjectMap params,
List<CellBaseDataResult<T>> responses) |
Modifier and Type | Method and Description |
---|---|
CellBaseDataResult |
XRefDBAdaptor.contains(String likeQuery,
org.opencb.commons.datastore.core.QueryOptions options) |
default CellBaseDataResult<Long> |
CellBaseDBAdaptor.count() |
CellBaseDataResult<Long> |
CellBaseDBAdaptor.count(org.opencb.commons.datastore.core.Query query) |
CellBaseDataResult<String> |
CellBaseDBAdaptor.distinct(org.opencb.commons.datastore.core.Query query,
String field) |
default CellBaseDataResult<String> |
CellBaseDBAdaptor.distinct(String field) |
default CellBaseDataResult |
FeatureDBAdaptor.first() |
default CellBaseDataResult |
FeatureDBAdaptor.first(org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult<T> |
CellBaseDBAdaptor.get(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult<String> |
ClinicalDBAdaptor.getAlleleOriginLabels() |
CellBaseDataResult<T> |
VariantAnnotationDBAdaptor.getAnnotationByVariant(org.opencb.biodata.models.variant.Variant variant,
org.opencb.commons.datastore.core.QueryOptions options)
Deprecated.
|
CellBaseDataResult<String> |
GeneDBAdaptor.getBiotypes(org.opencb.commons.datastore.core.Query query) |
default CellBaseDataResult<T> |
FeatureDBAdaptor.getByRegion(org.opencb.biodata.models.core.Region region,
org.opencb.commons.datastore.core.QueryOptions options) |
default CellBaseDataResult<T> |
VariantDBAdaptor.getByVariant(org.opencb.biodata.models.variant.Variant variant,
org.opencb.commons.datastore.core.QueryOptions options) |
default CellBaseDataResult<T> |
FeatureDBAdaptor.getByVariant(org.opencb.biodata.models.variant.Variant variant,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult<String> |
TranscriptDBAdaptor.getCdna(String id) |
CellBaseDataResult |
GenomeDBAdaptor.getChromosomeInfo(String chromosomeId,
org.opencb.commons.datastore.core.QueryOptions queryOptions) |
CellBaseDataResult<String> |
ClinicalDBAdaptor.getClinsigLabels() |
CellBaseDataResult<String> |
VariantDBAdaptor.getConsequenceTypes(org.opencb.commons.datastore.core.Query query) |
CellBaseDataResult<org.opencb.biodata.models.variant.avro.ConsequenceType> |
VariantAnnotationDBAdaptor.getConsequenceTypes(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options)
Deprecated.
|
default CellBaseDataResult<org.opencb.biodata.models.core.GenomicScoreRegion<Float>> |
GenomeDBAdaptor.getConservation(org.opencb.biodata.models.core.Region region,
org.opencb.commons.datastore.core.QueryOptions queryOptions) |
CellBaseDataResult<String> |
ClinicalDBAdaptor.getConsistencyLabels() |
CellBaseDataResult<org.opencb.biodata.models.variant.avro.Cytoband> |
GenomeDBAdaptor.getCytobands(org.opencb.biodata.models.core.Region region,
org.opencb.commons.datastore.core.QueryOptions queryOptions) |
CellBaseDataResult<org.opencb.biodata.models.variant.avro.Score> |
VariantAnnotationDBAdaptor.getFunctionalScore(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options)
Deprecated.
|
CellBaseDataResult<org.opencb.biodata.models.variant.avro.Score> |
VariantAnnotationDBAdaptor.getFunctionalScore(org.opencb.biodata.models.variant.Variant variant,
org.opencb.commons.datastore.core.QueryOptions options)
Deprecated.
|
CellBaseDataResult<org.opencb.biodata.models.variant.avro.Score> |
VariantDBAdaptor.getFunctionalScoreVariant(org.opencb.biodata.models.variant.Variant variant,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
GenomeDBAdaptor.getGenomeInfo(org.opencb.commons.datastore.core.QueryOptions queryOptions) |
CellBaseDataResult<org.opencb.biodata.models.core.GenomeSequenceFeature> |
GenomeDBAdaptor.getGenomicSequence(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions queryOptions)
Deprecated.
|
CellBaseDataResult |
FeatureDBAdaptor.getIntervalFrequencies(org.opencb.commons.datastore.core.Query query,
int intervalSize,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult<String> |
ClinicalDBAdaptor.getModeInheritanceLabels() |
CellBaseDataResult |
GeneDBAdaptor.getRegulatoryElements(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions queryOptions) |
CellBaseDataResult<org.opencb.biodata.models.core.GenomeSequenceFeature> |
GenomeDBAdaptor.getSequence(org.opencb.biodata.models.core.Region region,
org.opencb.commons.datastore.core.QueryOptions queryOptions) |
CellBaseDataResult<org.opencb.biodata.models.variant.avro.Score> |
ProteinDBAdaptor.getSubstitutionScores(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
GeneDBAdaptor.getTfbs(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions queryOptions) |
CellBaseDataResult<org.opencb.biodata.models.variant.avro.ProteinVariantAnnotation> |
ProteinDBAdaptor.getVariantAnnotation(String enstranscriptId,
int position,
String aaReference,
String aaAlternate,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult<String> |
ClinicalDBAdaptor.getVariantTypes() |
CellBaseDataResult |
CellBaseDBAdaptor.groupBy(org.opencb.commons.datastore.core.Query query,
List<String> fields,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
CellBaseDBAdaptor.groupBy(org.opencb.commons.datastore.core.Query query,
String field,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
CellBaseDBAdaptor.nativeGet(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
FeatureDBAdaptor.nativeNext(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult<T> |
FeatureDBAdaptor.next(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
CellBaseDBAdaptor.rank(org.opencb.commons.datastore.core.Query query,
String field,
int numResults,
boolean asc) |
CellBaseDataResult |
XRefDBAdaptor.startsWith(String id,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
GeneDBAdaptor.startsWith(String id,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
VariantDBAdaptor.startsWith(String id,
org.opencb.commons.datastore.core.QueryOptions options) |
default CellBaseDataResult |
CellBaseDBAdaptor.stats() |
CellBaseDataResult |
CellBaseDBAdaptor.stats(org.opencb.commons.datastore.core.Query query) |
CellBaseDataResult<Long> |
CellBaseDBAdaptor.update(List objectList,
String field,
String[] innerFields) |
Modifier and Type | Method and Description |
---|---|
default List<CellBaseDataResult<T>> |
CellBaseDBAdaptor.get(List<org.opencb.commons.datastore.core.Query> queries,
org.opencb.commons.datastore.core.QueryOptions options) |
List<CellBaseDataResult> |
ConservationDBAdaptor.getAllByRegionList(List<org.opencb.biodata.models.core.Region> regionList,
org.opencb.commons.datastore.core.QueryOptions options)
Deprecated.
|
List<CellBaseDataResult> |
ConservationDBAdaptor.getAllScoresByRegionList(List<org.opencb.biodata.models.core.Region> regions,
org.opencb.commons.datastore.core.QueryOptions options)
Deprecated.
|
List<CellBaseDataResult<T>> |
VariantAnnotationDBAdaptor.getAnnotationByVariantList(List<org.opencb.biodata.models.variant.Variant> variants,
org.opencb.commons.datastore.core.QueryOptions options)
Deprecated.
|
default List<CellBaseDataResult<T>> |
FeatureDBAdaptor.getByRegion(List<org.opencb.biodata.models.core.Region> regions,
org.opencb.commons.datastore.core.QueryOptions options) |
default List<CellBaseDataResult<T>> |
VariantDBAdaptor.getByVariant(List<org.opencb.biodata.models.variant.Variant> variants,
org.opencb.commons.datastore.core.QueryOptions options) |
default List<CellBaseDataResult<T>> |
FeatureDBAdaptor.getByVariant(List<org.opencb.biodata.models.variant.Variant> variants,
org.opencb.commons.datastore.core.QueryOptions options) |
default List<CellBaseDataResult<String>> |
TranscriptDBAdaptor.getCdna(List<String> idList) |
List<CellBaseDataResult<org.opencb.biodata.models.core.GenomicScoreRegion<Float>>> |
GenomeDBAdaptor.getConservation(List<org.opencb.biodata.models.core.Region> regions,
org.opencb.commons.datastore.core.QueryOptions queryOptions) |
default List<CellBaseDataResult<org.opencb.biodata.models.variant.avro.Cytoband>> |
GenomeDBAdaptor.getCytobands(List<org.opencb.biodata.models.core.Region> regionList)
Deprecated.
|
default List<CellBaseDataResult<org.opencb.biodata.models.variant.avro.Cytoband>> |
GenomeDBAdaptor.getCytobands(List<org.opencb.biodata.models.core.Region> regionList,
org.opencb.commons.datastore.core.QueryOptions queryOptions) |
List<CellBaseDataResult<org.opencb.biodata.models.variant.avro.Score>> |
VariantAnnotationDBAdaptor.getFunctionalScore(List<org.opencb.biodata.models.variant.Variant> variants,
org.opencb.commons.datastore.core.QueryOptions options)
Deprecated.
|
default List<CellBaseDataResult<org.opencb.biodata.models.variant.avro.Score>> |
VariantDBAdaptor.getFunctionalScoreVariant(List<org.opencb.biodata.models.variant.Variant> variants,
org.opencb.commons.datastore.core.QueryOptions options) |
default List<CellBaseDataResult<org.opencb.biodata.models.core.GenomeSequenceFeature>> |
GenomeDBAdaptor.getGenomicSequence(List<org.opencb.commons.datastore.core.Query> queries,
org.opencb.commons.datastore.core.QueryOptions queryOptions)
Deprecated.
|
default List<CellBaseDataResult> |
FeatureDBAdaptor.getIntervalFrequencies(List<org.opencb.commons.datastore.core.Query> queries,
int intervalSize,
org.opencb.commons.datastore.core.QueryOptions options) |
List<CellBaseDataResult> |
ClinicalDBAdaptor.getPhenotypeGeneRelations(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions queryOptions) |
List<CellBaseDataResult<org.opencb.biodata.models.variant.Variant>> |
VariantDBAdaptor.getPopulationFrequencyByVariant(List<org.opencb.biodata.models.variant.Variant> variants,
org.opencb.commons.datastore.core.QueryOptions queryOptions) |
default List<CellBaseDataResult<org.opencb.biodata.models.core.GenomeSequenceFeature>> |
GenomeDBAdaptor.getSequence(List<org.opencb.biodata.models.core.Region> regions,
org.opencb.commons.datastore.core.QueryOptions queryOptions) |
default List<CellBaseDataResult> |
CellBaseDBAdaptor.nativeGet(List<org.opencb.commons.datastore.core.Query> queries,
org.opencb.commons.datastore.core.QueryOptions options) |
Modifier and Type | Method and Description |
---|---|
CellBaseDataResult<T> |
CellBaseDataResult.setId(String id) |
Modifier and Type | Method and Description |
---|---|
List<CellBaseDataResult<org.opencb.biodata.models.variant.Variant>> |
AnnotationBasedPhasedQueryManager.run(List<org.opencb.biodata.models.variant.Variant> variantList,
List<CellBaseDataResult<org.opencb.biodata.models.variant.Variant>> variantCellBaseDataResultList) |
List<CellBaseDataResult<org.opencb.biodata.models.variant.Variant>> |
CustomAnnotationPhasedQueryManager.run(List<org.opencb.biodata.models.variant.Variant> variantList,
List<CellBaseDataResult<org.opencb.biodata.models.variant.Variant>> variantCellBaseDataResultList) |
Modifier and Type | Method and Description |
---|---|
protected void |
PhasedQueryManager.reset(CellBaseDataResult<org.opencb.biodata.models.variant.Variant> variantCellBaseDataResult) |
Modifier and Type | Method and Description |
---|---|
List<CellBaseDataResult<org.opencb.biodata.models.variant.Variant>> |
AnnotationBasedPhasedQueryManager.run(List<org.opencb.biodata.models.variant.Variant> variantList,
List<CellBaseDataResult<org.opencb.biodata.models.variant.Variant>> variantCellBaseDataResultList) |
List<CellBaseDataResult<org.opencb.biodata.models.variant.Variant>> |
CustomAnnotationPhasedQueryManager.run(List<org.opencb.biodata.models.variant.Variant> variantList,
List<CellBaseDataResult<org.opencb.biodata.models.variant.Variant>> variantCellBaseDataResultList) |
Modifier and Type | Method and Description |
---|---|
CellBaseDataResult |
VariantAnnotationCalculator.getAllConsequenceTypesByVariant(org.opencb.biodata.models.variant.Variant variant,
org.opencb.commons.datastore.core.QueryOptions queryOptions)
Deprecated.
|
CellBaseDataResult |
VariantAnnotationCalculator.getAnnotationByVariant(org.opencb.biodata.models.variant.Variant variant,
org.opencb.commons.datastore.core.QueryOptions queryOptions) |
Modifier and Type | Method and Description |
---|---|
List<CellBaseDataResult<org.opencb.biodata.models.variant.avro.VariantAnnotation>> |
VariantAnnotationCalculator.getAnnotationByVariantList(List<org.opencb.biodata.models.variant.Variant> variantList,
org.opencb.commons.datastore.core.QueryOptions queryOptions) |
Modifier and Type | Method and Description |
---|---|
CellBaseDataResult |
XRefMongoDBAdaptor.contains(String id,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult<Long> |
XRefMongoDBAdaptor.count(org.opencb.commons.datastore.core.Query query) |
CellBaseDataResult<Long> |
ClinicalLegacyMongoDBAdaptor.count(org.opencb.commons.datastore.core.Query query)
Deprecated.
|
CellBaseDataResult<Long> |
GeneMongoDBAdaptor.count(org.opencb.commons.datastore.core.Query query) |
CellBaseDataResult<Long> |
RegulationMongoDBAdaptor.count(org.opencb.commons.datastore.core.Query query) |
CellBaseDataResult<Long> |
ClinicalMongoDBAdaptor.count(org.opencb.commons.datastore.core.Query query) |
CellBaseDataResult<Long> |
MetaMongoDBAdaptor.count(org.opencb.commons.datastore.core.Query query) |
CellBaseDataResult<Long> |
ProteinMongoDBAdaptor.count(org.opencb.commons.datastore.core.Query query) |
CellBaseDataResult<Long> |
ConservationMongoDBAdaptor.count(org.opencb.commons.datastore.core.Query query)
Deprecated.
|
CellBaseDataResult<Long> |
TranscriptMongoDBAdaptor.count(org.opencb.commons.datastore.core.Query query) |
CellBaseDataResult<Long> |
GenomeMongoDBAdaptor.count(org.opencb.commons.datastore.core.Query query) |
CellBaseDataResult<Long> |
ProteinProteinInteractionMongoDBAdaptor.count(org.opencb.commons.datastore.core.Query query) |
CellBaseDataResult<Long> |
VariantMongoDBAdaptor.count(org.opencb.commons.datastore.core.Query query) |
CellBaseDataResult<Long> |
RepeatsMongoDBAdaptor.count(org.opencb.commons.datastore.core.Query query) |
CellBaseDataResult |
XRefMongoDBAdaptor.distinct(org.opencb.commons.datastore.core.Query query,
String field) |
CellBaseDataResult |
ClinicalLegacyMongoDBAdaptor.distinct(org.opencb.commons.datastore.core.Query query,
String field)
Deprecated.
|
CellBaseDataResult<String> |
GeneMongoDBAdaptor.distinct(org.opencb.commons.datastore.core.Query query,
String field) |
CellBaseDataResult |
RegulationMongoDBAdaptor.distinct(org.opencb.commons.datastore.core.Query query,
String field) |
CellBaseDataResult |
ClinicalMongoDBAdaptor.distinct(org.opencb.commons.datastore.core.Query query,
String field) |
CellBaseDataResult |
MetaMongoDBAdaptor.distinct(org.opencb.commons.datastore.core.Query query,
String field) |
CellBaseDataResult |
ProteinMongoDBAdaptor.distinct(org.opencb.commons.datastore.core.Query query,
String field) |
CellBaseDataResult |
ConservationMongoDBAdaptor.distinct(org.opencb.commons.datastore.core.Query query,
String field)
Deprecated.
|
CellBaseDataResult |
TranscriptMongoDBAdaptor.distinct(org.opencb.commons.datastore.core.Query query,
String field) |
CellBaseDataResult |
GenomeMongoDBAdaptor.distinct(org.opencb.commons.datastore.core.Query query,
String field) |
CellBaseDataResult |
ProteinProteinInteractionMongoDBAdaptor.distinct(org.opencb.commons.datastore.core.Query query,
String field) |
CellBaseDataResult |
VariantMongoDBAdaptor.distinct(org.opencb.commons.datastore.core.Query query,
String field) |
CellBaseDataResult |
RepeatsMongoDBAdaptor.distinct(org.opencb.commons.datastore.core.Query query,
String field) |
protected CellBaseDataResult |
MongoDBAdaptor.executeAggregation2(Object id,
List<org.bson.conversions.Bson> pipeline,
org.opencb.commons.datastore.core.QueryOptions options) |
protected CellBaseDataResult |
MongoDBAdaptor.executeDistinct(Object id,
String fields,
org.bson.Document query) |
protected CellBaseDataResult |
MongoDBAdaptor.executeQuery(Object id,
org.bson.Document query,
org.opencb.commons.datastore.core.QueryOptions options) |
protected CellBaseDataResult |
MongoDBAdaptor.executeQuery(Object id,
org.bson.Document query,
org.opencb.commons.datastore.core.QueryOptions options,
org.opencb.commons.datastore.mongodb.MongoDBCollection mongoDBCollection2) |
CellBaseDataResult<org.opencb.biodata.models.core.Xref> |
XRefMongoDBAdaptor.get(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult<ClinicalVariant> |
ClinicalLegacyMongoDBAdaptor.get(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options)
Deprecated.
|
CellBaseDataResult<org.opencb.biodata.models.core.Gene> |
GeneMongoDBAdaptor.get(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions inputOptions) |
CellBaseDataResult<org.opencb.biodata.models.core.RegulatoryFeature> |
RegulationMongoDBAdaptor.get(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions inputOptions) |
CellBaseDataResult<org.opencb.biodata.models.variant.Variant> |
ClinicalMongoDBAdaptor.get(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
MetaMongoDBAdaptor.get(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult<org.opencb.biodata.formats.protein.uniprot.v201504jaxb.Entry> |
ProteinMongoDBAdaptor.get(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
ConservationMongoDBAdaptor.get(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options)
Deprecated.
|
CellBaseDataResult<org.opencb.biodata.models.core.Transcript> |
TranscriptMongoDBAdaptor.get(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
GenomeMongoDBAdaptor.get(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult<org.opencb.biodata.models.protein.Interaction> |
ProteinProteinInteractionMongoDBAdaptor.get(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult<org.opencb.biodata.models.variant.Variant> |
VariantMongoDBAdaptor.get(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions inputOptions) |
CellBaseDataResult |
RepeatsMongoDBAdaptor.get(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions inputOptions) |
CellBaseDataResult<String> |
ClinicalLegacyMongoDBAdaptor.getAlleleOriginLabels()
Deprecated.
|
CellBaseDataResult<String> |
ClinicalMongoDBAdaptor.getAlleleOriginLabels() |
CellBaseDataResult<String> |
GeneMongoDBAdaptor.getBiotypes(org.opencb.commons.datastore.core.Query query) |
CellBaseDataResult<String> |
TranscriptMongoDBAdaptor.getCdna(String id) |
CellBaseDataResult |
GenomeMongoDBAdaptor.getChromosomeInfo(String chromosomeId,
org.opencb.commons.datastore.core.QueryOptions queryOptions) |
CellBaseDataResult<String> |
ClinicalLegacyMongoDBAdaptor.getClinsigLabels()
Deprecated.
|
CellBaseDataResult<String> |
ClinicalMongoDBAdaptor.getClinsigLabels() |
CellBaseDataResult<String> |
VariantMongoDBAdaptor.getConsequenceTypes(org.opencb.commons.datastore.core.Query query) |
CellBaseDataResult<String> |
ClinicalLegacyMongoDBAdaptor.getConsistencyLabels()
Deprecated.
|
CellBaseDataResult<String> |
ClinicalMongoDBAdaptor.getConsistencyLabels() |
CellBaseDataResult<org.opencb.biodata.models.variant.avro.Cytoband> |
GenomeMongoDBAdaptor.getCytobands(org.opencb.biodata.models.core.Region region,
org.opencb.commons.datastore.core.QueryOptions queryOptions) |
CellBaseDataResult<org.opencb.biodata.models.variant.avro.Score> |
VariantMongoDBAdaptor.getFunctionalScoreVariant(org.opencb.biodata.models.variant.Variant variant,
org.opencb.commons.datastore.core.QueryOptions queryOptions) |
CellBaseDataResult |
GenomeMongoDBAdaptor.getGenomeInfo(org.opencb.commons.datastore.core.QueryOptions queryOptions) |
CellBaseDataResult<org.opencb.biodata.models.core.GenomeSequenceFeature> |
GenomeMongoDBAdaptor.getGenomicSequence(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions queryOptions)
Deprecated.
|
CellBaseDataResult |
MongoDBAdaptor.getIntervalFrequencies(org.bson.conversions.Bson query,
org.opencb.biodata.models.core.Region region,
int intervalSize,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
ClinicalLegacyMongoDBAdaptor.getIntervalFrequencies(org.opencb.commons.datastore.core.Query query,
int intervalSize,
org.opencb.commons.datastore.core.QueryOptions options)
Deprecated.
|
CellBaseDataResult |
GeneMongoDBAdaptor.getIntervalFrequencies(org.opencb.commons.datastore.core.Query query,
int intervalSize,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
RegulationMongoDBAdaptor.getIntervalFrequencies(org.opencb.commons.datastore.core.Query query,
int intervalSize,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
ClinicalMongoDBAdaptor.getIntervalFrequencies(org.opencb.commons.datastore.core.Query query,
int intervalSize,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
TranscriptMongoDBAdaptor.getIntervalFrequencies(org.opencb.commons.datastore.core.Query query,
int intervalSize,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
VariantMongoDBAdaptor.getIntervalFrequencies(org.opencb.commons.datastore.core.Query query,
int intervalSize,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
RepeatsMongoDBAdaptor.getIntervalFrequencies(org.opencb.commons.datastore.core.Query query,
int intervalSize,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult<String> |
ClinicalLegacyMongoDBAdaptor.getModeInheritanceLabels()
Deprecated.
|
CellBaseDataResult<String> |
ClinicalMongoDBAdaptor.getModeInheritanceLabels() |
CellBaseDataResult |
GeneMongoDBAdaptor.getRegulatoryElements(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions queryOptions) |
CellBaseDataResult<org.opencb.biodata.models.core.GenomeSequenceFeature> |
GenomeMongoDBAdaptor.getSequence(org.opencb.biodata.models.core.Region region,
org.opencb.commons.datastore.core.QueryOptions queryOptions) |
CellBaseDataResult<org.opencb.biodata.models.variant.avro.Score> |
ProteinMongoDBAdaptor.getSubstitutionScores(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
GeneMongoDBAdaptor.getTfbs(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions queryOptions) |
CellBaseDataResult<org.opencb.biodata.models.variant.avro.ProteinVariantAnnotation> |
ProteinMongoDBAdaptor.getVariantAnnotation(String ensemblTranscriptId,
int position,
String aaReference,
String aaAlternate,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult<String> |
ClinicalLegacyMongoDBAdaptor.getVariantTypes()
Deprecated.
|
CellBaseDataResult<String> |
ClinicalMongoDBAdaptor.getVariantTypes() |
protected CellBaseDataResult |
MongoDBAdaptor.groupBy(org.bson.conversions.Bson query,
List<String> groupByField,
String featureIdField,
org.opencb.commons.datastore.core.QueryOptions options) |
protected CellBaseDataResult |
MongoDBAdaptor.groupBy(org.bson.conversions.Bson query,
String groupByField,
String featureIdField,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
XRefMongoDBAdaptor.groupBy(org.opencb.commons.datastore.core.Query query,
List<String> fields,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
ClinicalLegacyMongoDBAdaptor.groupBy(org.opencb.commons.datastore.core.Query query,
List<String> fields,
org.opencb.commons.datastore.core.QueryOptions options)
Deprecated.
|
CellBaseDataResult |
GeneMongoDBAdaptor.groupBy(org.opencb.commons.datastore.core.Query query,
List<String> fields,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
RegulationMongoDBAdaptor.groupBy(org.opencb.commons.datastore.core.Query query,
List<String> fields,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
ClinicalMongoDBAdaptor.groupBy(org.opencb.commons.datastore.core.Query query,
List<String> fields,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
ProteinMongoDBAdaptor.groupBy(org.opencb.commons.datastore.core.Query query,
List<String> fields,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
ProteinProteinInteractionMongoDBAdaptor.groupBy(org.opencb.commons.datastore.core.Query query,
List<String> fields,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
VariantMongoDBAdaptor.groupBy(org.opencb.commons.datastore.core.Query query,
List<String> fields,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
MetaMongoDBAdaptor.groupBy(org.opencb.commons.datastore.core.Query query,
List fields,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
ConservationMongoDBAdaptor.groupBy(org.opencb.commons.datastore.core.Query query,
List fields,
org.opencb.commons.datastore.core.QueryOptions options)
Deprecated.
|
CellBaseDataResult |
TranscriptMongoDBAdaptor.groupBy(org.opencb.commons.datastore.core.Query query,
List fields,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
GenomeMongoDBAdaptor.groupBy(org.opencb.commons.datastore.core.Query query,
List fields,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
RepeatsMongoDBAdaptor.groupBy(org.opencb.commons.datastore.core.Query query,
List fields,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
XRefMongoDBAdaptor.groupBy(org.opencb.commons.datastore.core.Query query,
String field,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
ClinicalLegacyMongoDBAdaptor.groupBy(org.opencb.commons.datastore.core.Query query,
String field,
org.opencb.commons.datastore.core.QueryOptions options)
Deprecated.
|
CellBaseDataResult |
GeneMongoDBAdaptor.groupBy(org.opencb.commons.datastore.core.Query query,
String field,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
RegulationMongoDBAdaptor.groupBy(org.opencb.commons.datastore.core.Query query,
String field,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
ClinicalMongoDBAdaptor.groupBy(org.opencb.commons.datastore.core.Query query,
String field,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
MetaMongoDBAdaptor.groupBy(org.opencb.commons.datastore.core.Query query,
String field,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
ProteinMongoDBAdaptor.groupBy(org.opencb.commons.datastore.core.Query query,
String field,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
ConservationMongoDBAdaptor.groupBy(org.opencb.commons.datastore.core.Query query,
String field,
org.opencb.commons.datastore.core.QueryOptions options)
Deprecated.
|
CellBaseDataResult |
TranscriptMongoDBAdaptor.groupBy(org.opencb.commons.datastore.core.Query query,
String field,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
GenomeMongoDBAdaptor.groupBy(org.opencb.commons.datastore.core.Query query,
String field,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
ProteinProteinInteractionMongoDBAdaptor.groupBy(org.opencb.commons.datastore.core.Query query,
String field,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
VariantMongoDBAdaptor.groupBy(org.opencb.commons.datastore.core.Query query,
String field,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
RepeatsMongoDBAdaptor.groupBy(org.opencb.commons.datastore.core.Query query,
String field,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
XRefMongoDBAdaptor.nativeGet(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
ClinicalLegacyMongoDBAdaptor.nativeGet(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options)
Deprecated.
|
CellBaseDataResult |
GeneMongoDBAdaptor.nativeGet(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
RegulationMongoDBAdaptor.nativeGet(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
ClinicalMongoDBAdaptor.nativeGet(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
MetaMongoDBAdaptor.nativeGet(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions inputOptions) |
CellBaseDataResult |
ProteinMongoDBAdaptor.nativeGet(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
ConservationMongoDBAdaptor.nativeGet(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options)
Deprecated.
|
CellBaseDataResult |
TranscriptMongoDBAdaptor.nativeGet(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
GenomeMongoDBAdaptor.nativeGet(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
ProteinProteinInteractionMongoDBAdaptor.nativeGet(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
VariantMongoDBAdaptor.nativeGet(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
RepeatsMongoDBAdaptor.nativeGet(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions inputOptions) |
CellBaseDataResult |
ClinicalLegacyMongoDBAdaptor.nativeNext(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options)
Deprecated.
|
CellBaseDataResult |
GeneMongoDBAdaptor.nativeNext(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
RegulationMongoDBAdaptor.nativeNext(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
ClinicalMongoDBAdaptor.nativeNext(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
TranscriptMongoDBAdaptor.nativeNext(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
VariantMongoDBAdaptor.nativeNext(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
RepeatsMongoDBAdaptor.nativeNext(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult<ClinicalVariant> |
ClinicalLegacyMongoDBAdaptor.next(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options)
Deprecated.
|
CellBaseDataResult<org.opencb.biodata.models.core.Gene> |
GeneMongoDBAdaptor.next(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult<org.opencb.biodata.models.core.RegulatoryFeature> |
RegulationMongoDBAdaptor.next(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult<org.opencb.biodata.models.variant.Variant> |
ClinicalMongoDBAdaptor.next(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
TranscriptMongoDBAdaptor.next(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult<org.opencb.biodata.models.variant.Variant> |
VariantMongoDBAdaptor.next(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
RepeatsMongoDBAdaptor.next(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
MongoDBAdaptor.next(String chromosome,
int position,
org.opencb.commons.datastore.core.QueryOptions options,
org.opencb.commons.datastore.mongodb.MongoDBCollection mongoDBCollection) |
CellBaseDataResult |
XRefMongoDBAdaptor.rank(org.opencb.commons.datastore.core.Query query,
String field,
int numResults,
boolean asc) |
CellBaseDataResult |
ClinicalLegacyMongoDBAdaptor.rank(org.opencb.commons.datastore.core.Query query,
String field,
int numResults,
boolean asc)
Deprecated.
|
CellBaseDataResult |
GeneMongoDBAdaptor.rank(org.opencb.commons.datastore.core.Query query,
String field,
int numResults,
boolean asc) |
CellBaseDataResult |
RegulationMongoDBAdaptor.rank(org.opencb.commons.datastore.core.Query query,
String field,
int numResults,
boolean asc) |
CellBaseDataResult |
ClinicalMongoDBAdaptor.rank(org.opencb.commons.datastore.core.Query query,
String field,
int numResults,
boolean asc) |
CellBaseDataResult |
MetaMongoDBAdaptor.rank(org.opencb.commons.datastore.core.Query query,
String field,
int numResults,
boolean asc) |
CellBaseDataResult |
ProteinMongoDBAdaptor.rank(org.opencb.commons.datastore.core.Query query,
String field,
int numResults,
boolean asc) |
CellBaseDataResult |
ConservationMongoDBAdaptor.rank(org.opencb.commons.datastore.core.Query query,
String field,
int numResults,
boolean asc)
Deprecated.
|
CellBaseDataResult |
TranscriptMongoDBAdaptor.rank(org.opencb.commons.datastore.core.Query query,
String field,
int numResults,
boolean asc) |
CellBaseDataResult |
GenomeMongoDBAdaptor.rank(org.opencb.commons.datastore.core.Query query,
String field,
int numResults,
boolean asc) |
CellBaseDataResult |
ProteinProteinInteractionMongoDBAdaptor.rank(org.opencb.commons.datastore.core.Query query,
String field,
int numResults,
boolean asc) |
CellBaseDataResult |
VariantMongoDBAdaptor.rank(org.opencb.commons.datastore.core.Query query,
String field,
int numResults,
boolean asc) |
CellBaseDataResult |
RepeatsMongoDBAdaptor.rank(org.opencb.commons.datastore.core.Query query,
String field,
int numResults,
boolean asc) |
CellBaseDataResult |
XRefMongoDBAdaptor.startsWith(String id,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
GeneMongoDBAdaptor.startsWith(String id,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
VariantMongoDBAdaptor.startsWith(String id,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
XRefMongoDBAdaptor.stats(org.opencb.commons.datastore.core.Query query) |
CellBaseDataResult |
ClinicalLegacyMongoDBAdaptor.stats(org.opencb.commons.datastore.core.Query query)
Deprecated.
|
CellBaseDataResult |
GeneMongoDBAdaptor.stats(org.opencb.commons.datastore.core.Query query) |
CellBaseDataResult |
RegulationMongoDBAdaptor.stats(org.opencb.commons.datastore.core.Query query) |
CellBaseDataResult |
ClinicalMongoDBAdaptor.stats(org.opencb.commons.datastore.core.Query query) |
CellBaseDataResult |
MetaMongoDBAdaptor.stats(org.opencb.commons.datastore.core.Query query) |
CellBaseDataResult |
ProteinMongoDBAdaptor.stats(org.opencb.commons.datastore.core.Query query) |
CellBaseDataResult |
ConservationMongoDBAdaptor.stats(org.opencb.commons.datastore.core.Query query)
Deprecated.
|
CellBaseDataResult |
TranscriptMongoDBAdaptor.stats(org.opencb.commons.datastore.core.Query query) |
CellBaseDataResult |
GenomeMongoDBAdaptor.stats(org.opencb.commons.datastore.core.Query query) |
CellBaseDataResult |
ProteinProteinInteractionMongoDBAdaptor.stats(org.opencb.commons.datastore.core.Query query) |
CellBaseDataResult |
VariantMongoDBAdaptor.stats(org.opencb.commons.datastore.core.Query query) |
CellBaseDataResult |
RepeatsMongoDBAdaptor.stats(org.opencb.commons.datastore.core.Query query) |
CellBaseDataResult<Long> |
XRefMongoDBAdaptor.update(List objectList,
String field,
String[] innerFields) |
CellBaseDataResult<Long> |
ClinicalLegacyMongoDBAdaptor.update(List objectList,
String field,
String[] innerFields)
Deprecated.
|
CellBaseDataResult<Long> |
GeneMongoDBAdaptor.update(List objectList,
String field,
String[] innerFields) |
CellBaseDataResult<Long> |
RegulationMongoDBAdaptor.update(List objectList,
String field,
String[] innerFields) |
CellBaseDataResult<Long> |
ClinicalMongoDBAdaptor.update(List objectList,
String field,
String[] innerFields) |
CellBaseDataResult<Long> |
MetaMongoDBAdaptor.update(List objectList,
String field,
String[] innerFields) |
CellBaseDataResult<Long> |
ProteinMongoDBAdaptor.update(List objectList,
String field,
String[] innerFields) |
CellBaseDataResult<Long> |
ConservationMongoDBAdaptor.update(List objectList,
String field,
String[] innerFields)
Deprecated.
|
CellBaseDataResult<Long> |
TranscriptMongoDBAdaptor.update(List objectList,
String field,
String[] innerFields) |
CellBaseDataResult<Long> |
GenomeMongoDBAdaptor.update(List objectList,
String field,
String[] innerFields) |
CellBaseDataResult<Long> |
ProteinProteinInteractionMongoDBAdaptor.update(List objectList,
String field,
String[] innerFields) |
CellBaseDataResult<Long> |
VariantMongoDBAdaptor.update(List objectList,
String field,
String[] innerFields) |
CellBaseDataResult<Long> |
RepeatsMongoDBAdaptor.update(List objectList,
String field,
String[] innerFields) |
Modifier and Type | Method and Description |
---|---|
protected List<CellBaseDataResult> |
MongoDBAdaptor.executeAggregationist2(List<? extends Object> ids,
List<List<org.bson.conversions.Bson>> pipelines,
org.opencb.commons.datastore.core.QueryOptions options,
org.opencb.commons.datastore.mongodb.MongoDBCollection mongoDBCollection2) |
protected List<CellBaseDataResult> |
MongoDBAdaptor.executeAggregationList2(List<? extends Object> ids,
List<List<org.bson.conversions.Bson>> queries,
org.opencb.commons.datastore.core.QueryOptions options) |
protected List<CellBaseDataResult> |
MongoDBAdaptor.executeQueryList2(List<? extends Object> ids,
List<org.bson.Document> queries,
org.opencb.commons.datastore.core.QueryOptions options) |
protected List<CellBaseDataResult> |
MongoDBAdaptor.executeQueryList2(List<? extends Object> ids,
List<org.bson.Document> queries,
org.opencb.commons.datastore.core.QueryOptions options,
org.opencb.commons.datastore.mongodb.MongoDBCollection mongoDBCollection2) |
List<CellBaseDataResult> |
ConservationMongoDBAdaptor.getAllByRegionList(List regionList,
org.opencb.commons.datastore.core.QueryOptions options)
Deprecated.
|
List<CellBaseDataResult> |
ConservationMongoDBAdaptor.getAllScoresByRegionList(List regionList,
org.opencb.commons.datastore.core.QueryOptions options)
Deprecated.
|
List<CellBaseDataResult<org.opencb.biodata.models.variant.Variant>> |
ClinicalMongoDBAdaptor.getByVariant(List<org.opencb.biodata.models.variant.Variant> variants,
org.opencb.commons.datastore.core.QueryOptions queryOptions) |
List<CellBaseDataResult<org.opencb.biodata.models.core.GenomicScoreRegion<Float>>> |
GenomeMongoDBAdaptor.getConservation(List<org.opencb.biodata.models.core.Region> regionList,
org.opencb.commons.datastore.core.QueryOptions options) |
List<CellBaseDataResult> |
ClinicalLegacyMongoDBAdaptor.getPhenotypeGeneRelations(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions queryOptions)
Deprecated.
|
List<CellBaseDataResult> |
ClinicalMongoDBAdaptor.getPhenotypeGeneRelations(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions queryOptions) |
List<CellBaseDataResult<org.opencb.biodata.models.variant.Variant>> |
VariantMongoDBAdaptor.getPopulationFrequencyByVariant(List<org.opencb.biodata.models.variant.Variant> variants,
org.opencb.commons.datastore.core.QueryOptions queryOptions)
Created an specific method for pop freqs here since in this case phase is managed at the Pop.
|
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