public class ClinicalMongoDBAdaptor extends MongoDBAdaptor implements ClinicalDBAdaptor<org.opencb.biodata.models.variant.Variant>
ClinicalDBAdaptor.QueryParams
assembly, logger, mongoDataStore, mongoDBCollection, objectMapper, species
MERGE, REGION
Constructor and Description |
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ClinicalMongoDBAdaptor(String species,
String assembly,
org.opencb.commons.datastore.mongodb.MongoDataStore mongoDataStore) |
Modifier and Type | Method and Description |
---|---|
CellBaseDataResult<Long> |
count(org.opencb.commons.datastore.core.Query query) |
CellBaseDataResult |
distinct(org.opencb.commons.datastore.core.Query query,
String field) |
void |
forEach(org.opencb.commons.datastore.core.Query query,
Consumer<? super Object> action,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult<org.opencb.biodata.models.variant.Variant> |
get(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult<String> |
getAlleleOriginLabels() |
List<CellBaseDataResult<org.opencb.biodata.models.variant.Variant>> |
getByVariant(List<org.opencb.biodata.models.variant.Variant> variants,
org.opencb.commons.datastore.core.QueryOptions queryOptions) |
CellBaseDataResult<String> |
getClinsigLabels() |
CellBaseDataResult<String> |
getConsistencyLabels() |
CellBaseDataResult |
getIntervalFrequencies(org.opencb.commons.datastore.core.Query query,
int intervalSize,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult<String> |
getModeInheritanceLabels() |
List<CellBaseDataResult> |
getPhenotypeGeneRelations(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions queryOptions) |
CellBaseDataResult<String> |
getVariantTypes() |
CellBaseDataResult |
groupBy(org.opencb.commons.datastore.core.Query query,
List<String> fields,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
groupBy(org.opencb.commons.datastore.core.Query query,
String field,
org.opencb.commons.datastore.core.QueryOptions options) |
Iterator<org.opencb.biodata.models.variant.Variant> |
iterator(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
nativeGet(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
Iterator |
nativeIterator(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
nativeNext(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult<org.opencb.biodata.models.variant.Variant> |
next(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
rank(org.opencb.commons.datastore.core.Query query,
String field,
int numResults,
boolean asc) |
CellBaseDataResult |
stats(org.opencb.commons.datastore.core.Query query) |
CellBaseDataResult<Long> |
update(List objectList,
String field,
String[] innerFields) |
addExcludeReturnFields, addIncludeReturnFields, addPrivateExcludeOptions, addPrivateExcludeOptions, createOrQuery, createOrQuery, createOrQuery, createRegionQuery, createRegionQuery, executeAggregation2, executeAggregationist2, executeAggregationList2, executeDistinct, executeQuery, executeQuery, executeQueryList2, executeQueryList2, getAssembly, getChunkId, getChunkIdPrefix, getIntervalFeatureFrequencies, getIntervalFeatureFrequencies, getIntervalFrequencies, getReturnFields, getSpecies, groupBy, groupBy, next, setAssembly, setSpecies
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
first, first, getByRegion, getByRegion, getByVariant, getIntervalFrequencies
count, distinct, forEach, get, iterator, nativeGet, nativeIterator, stats
spliterator
public CellBaseDataResult<org.opencb.biodata.models.variant.Variant> next(org.opencb.commons.datastore.core.Query query, org.opencb.commons.datastore.core.QueryOptions options)
next
in interface FeatureDBAdaptor<org.opencb.biodata.models.variant.Variant>
public CellBaseDataResult nativeNext(org.opencb.commons.datastore.core.Query query, org.opencb.commons.datastore.core.QueryOptions options)
nativeNext
in interface FeatureDBAdaptor<org.opencb.biodata.models.variant.Variant>
public CellBaseDataResult rank(org.opencb.commons.datastore.core.Query query, String field, int numResults, boolean asc)
rank
in interface CellBaseDBAdaptor<org.opencb.biodata.models.variant.Variant>
public CellBaseDataResult groupBy(org.opencb.commons.datastore.core.Query query, String field, org.opencb.commons.datastore.core.QueryOptions options)
groupBy
in interface CellBaseDBAdaptor<org.opencb.biodata.models.variant.Variant>
public CellBaseDataResult groupBy(org.opencb.commons.datastore.core.Query query, List<String> fields, org.opencb.commons.datastore.core.QueryOptions options)
groupBy
in interface CellBaseDBAdaptor<org.opencb.biodata.models.variant.Variant>
public CellBaseDataResult getIntervalFrequencies(org.opencb.commons.datastore.core.Query query, int intervalSize, org.opencb.commons.datastore.core.QueryOptions options)
getIntervalFrequencies
in interface FeatureDBAdaptor<org.opencb.biodata.models.variant.Variant>
public CellBaseDataResult<Long> update(List objectList, String field, String[] innerFields)
update
in interface CellBaseDBAdaptor<org.opencb.biodata.models.variant.Variant>
public CellBaseDataResult<Long> count(org.opencb.commons.datastore.core.Query query)
count
in interface CellBaseDBAdaptor<org.opencb.biodata.models.variant.Variant>
public CellBaseDataResult distinct(org.opencb.commons.datastore.core.Query query, String field)
distinct
in interface CellBaseDBAdaptor<org.opencb.biodata.models.variant.Variant>
public CellBaseDataResult stats(org.opencb.commons.datastore.core.Query query)
stats
in interface CellBaseDBAdaptor<org.opencb.biodata.models.variant.Variant>
public CellBaseDataResult<org.opencb.biodata.models.variant.Variant> get(org.opencb.commons.datastore.core.Query query, org.opencb.commons.datastore.core.QueryOptions options)
get
in interface CellBaseDBAdaptor<org.opencb.biodata.models.variant.Variant>
public CellBaseDataResult nativeGet(org.opencb.commons.datastore.core.Query query, org.opencb.commons.datastore.core.QueryOptions options)
nativeGet
in interface CellBaseDBAdaptor<org.opencb.biodata.models.variant.Variant>
public Iterator<org.opencb.biodata.models.variant.Variant> iterator(org.opencb.commons.datastore.core.Query query, org.opencb.commons.datastore.core.QueryOptions options)
iterator
in interface CellBaseDBAdaptor<org.opencb.biodata.models.variant.Variant>
public Iterator nativeIterator(org.opencb.commons.datastore.core.Query query, org.opencb.commons.datastore.core.QueryOptions options)
nativeIterator
in interface CellBaseDBAdaptor<org.opencb.biodata.models.variant.Variant>
public void forEach(org.opencb.commons.datastore.core.Query query, Consumer<? super Object> action, org.opencb.commons.datastore.core.QueryOptions options)
forEach
in interface CellBaseDBAdaptor<org.opencb.biodata.models.variant.Variant>
public List<CellBaseDataResult> getPhenotypeGeneRelations(org.opencb.commons.datastore.core.Query query, org.opencb.commons.datastore.core.QueryOptions queryOptions)
getPhenotypeGeneRelations
in interface ClinicalDBAdaptor<org.opencb.biodata.models.variant.Variant>
public CellBaseDataResult<String> getAlleleOriginLabels()
getAlleleOriginLabels
in interface ClinicalDBAdaptor<org.opencb.biodata.models.variant.Variant>
public CellBaseDataResult<String> getModeInheritanceLabels()
getModeInheritanceLabels
in interface ClinicalDBAdaptor<org.opencb.biodata.models.variant.Variant>
public CellBaseDataResult<String> getClinsigLabels()
getClinsigLabels
in interface ClinicalDBAdaptor<org.opencb.biodata.models.variant.Variant>
public CellBaseDataResult<String> getConsistencyLabels()
getConsistencyLabels
in interface ClinicalDBAdaptor<org.opencb.biodata.models.variant.Variant>
public CellBaseDataResult<String> getVariantTypes()
getVariantTypes
in interface ClinicalDBAdaptor<org.opencb.biodata.models.variant.Variant>
public List<CellBaseDataResult<org.opencb.biodata.models.variant.Variant>> getByVariant(List<org.opencb.biodata.models.variant.Variant> variants, org.opencb.commons.datastore.core.QueryOptions queryOptions)
getByVariant
in interface FeatureDBAdaptor<org.opencb.biodata.models.variant.Variant>
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