org.opencb.cellbase.lib.impl

Class RepeatsMongoDBAdaptor

java.lang.Object

org.opencb.cellbase.lib.impl.MongoDBAdaptor

org.opencb.cellbase.lib.impl.RepeatsMongoDBAdaptor

All Implemented Interfaces:

Iterable, CellBaseDBAdaptor, FeatureDBAdaptor, RepeatsDBAdaptor

public class RepeatsMongoDBAdaptor
extends MongoDBAdaptor
implements RepeatsDBAdaptor

Created by fjlopez on 10/05/17.

Nested Class Summary

Nested classes/interfaces inherited from interface org.opencb.cellbase.core.api.RepeatsDBAdaptor

RepeatsDBAdaptor.QueryParams

Field Summary

Fields inherited from class org.opencb.cellbase.lib.impl.MongoDBAdaptor

assembly, logger, mongoDataStore, mongoDBCollection, objectMapper, species

Fields inherited from interface org.opencb.cellbase.core.api.FeatureDBAdaptor

MERGE, REGION

Constructor Summary

Constructors

Constructor and Description
RepeatsMongoDBAdaptor(String species, String assembly, org.opencb.commons.datastore.mongodb.MongoDataStore mongoDatastore)

Method Summary

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 action, org.opencb.commons.datastore.core.QueryOptions options)
CellBaseDataResult	get(org.opencb.commons.datastore.core.Query query, org.opencb.commons.datastore.core.QueryOptions inputOptions)
CellBaseDataResult	getIntervalFrequencies(org.opencb.commons.datastore.core.Query query, int intervalSize, org.opencb.commons.datastore.core.QueryOptions options)
CellBaseDataResult	groupBy(org.opencb.commons.datastore.core.Query query, List 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	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 inputOptions)
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	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)

Methods inherited from class org.opencb.cellbase.lib.impl.MongoDBAdaptor

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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.opencb.cellbase.core.api.FeatureDBAdaptor

first, first, getByRegion, getByRegion, getByVariant, getByVariant, getIntervalFrequencies

Methods inherited from interface org.opencb.cellbase.core.api.CellBaseDBAdaptor

count, distinct, forEach, get, iterator, nativeGet, nativeIterator, stats

Methods inherited from interface java.lang.Iterable

spliterator

Constructor Detail

RepeatsMongoDBAdaptor

public RepeatsMongoDBAdaptor(String species,
                             String assembly,
                             org.opencb.commons.datastore.mongodb.MongoDataStore mongoDatastore)

Method Detail

update

public CellBaseDataResult<Long> update(List objectList,
                                       String field,
                                       String[] innerFields)

Specified by:

update in interface CellBaseDBAdaptor

count

public CellBaseDataResult<Long> count(org.opencb.commons.datastore.core.Query query)

Specified by:

count in interface CellBaseDBAdaptor

distinct

public CellBaseDataResult distinct(org.opencb.commons.datastore.core.Query query,
                                   String field)

Specified by:

distinct in interface CellBaseDBAdaptor

stats

public CellBaseDataResult stats(org.opencb.commons.datastore.core.Query query)

Specified by:

stats in interface CellBaseDBAdaptor

get

public CellBaseDataResult get(org.opencb.commons.datastore.core.Query query,
                              org.opencb.commons.datastore.core.QueryOptions inputOptions)

Specified by:

get in interface CellBaseDBAdaptor

nativeGet

public CellBaseDataResult nativeGet(org.opencb.commons.datastore.core.Query query,
                                    org.opencb.commons.datastore.core.QueryOptions inputOptions)

Specified by:

nativeGet in interface CellBaseDBAdaptor

iterator

public Iterator iterator(org.opencb.commons.datastore.core.Query query,
                         org.opencb.commons.datastore.core.QueryOptions options)

Specified by:

iterator in interface CellBaseDBAdaptor

nativeIterator

public Iterator nativeIterator(org.opencb.commons.datastore.core.Query query,
                               org.opencb.commons.datastore.core.QueryOptions options)

Specified by:

nativeIterator in interface CellBaseDBAdaptor

rank

public CellBaseDataResult rank(org.opencb.commons.datastore.core.Query query,
                               String field,
                               int numResults,
                               boolean asc)

Specified by:

rank in interface CellBaseDBAdaptor

groupBy

public CellBaseDataResult groupBy(org.opencb.commons.datastore.core.Query query,
                                  String field,
                                  org.opencb.commons.datastore.core.QueryOptions options)

Specified by:

groupBy in interface CellBaseDBAdaptor

forEach

public void forEach(org.opencb.commons.datastore.core.Query query,
                    Consumer action,
                    org.opencb.commons.datastore.core.QueryOptions options)

Specified by:

forEach in interface CellBaseDBAdaptor

groupBy

public CellBaseDataResult groupBy(org.opencb.commons.datastore.core.Query query,
                                  List fields,
                                  org.opencb.commons.datastore.core.QueryOptions options)

Specified by:

groupBy in interface CellBaseDBAdaptor

next

public CellBaseDataResult next(org.opencb.commons.datastore.core.Query query,
                               org.opencb.commons.datastore.core.QueryOptions options)

Specified by:

next in interface FeatureDBAdaptor

nativeNext

public CellBaseDataResult nativeNext(org.opencb.commons.datastore.core.Query query,
                                     org.opencb.commons.datastore.core.QueryOptions options)

Specified by:

nativeNext in interface FeatureDBAdaptor

getIntervalFrequencies

public CellBaseDataResult getIntervalFrequencies(org.opencb.commons.datastore.core.Query query,
                                                 int intervalSize,
                                                 org.opencb.commons.datastore.core.QueryOptions options)

Specified by:

getIntervalFrequencies in interface FeatureDBAdaptor