org.opencb.cellbase.lib.impl

Class TranscriptMongoDBAdaptor

java.lang.Object

org.opencb.cellbase.lib.impl.MongoDBAdaptor

org.opencb.cellbase.lib.impl.TranscriptMongoDBAdaptor

All Implemented Interfaces:

Iterable<org.opencb.biodata.models.core.Transcript>, CellBaseDBAdaptor<org.opencb.biodata.models.core.Transcript>, FeatureDBAdaptor<org.opencb.biodata.models.core.Transcript>, TranscriptDBAdaptor<org.opencb.biodata.models.core.Transcript>

public class TranscriptMongoDBAdaptor
extends MongoDBAdaptor
implements TranscriptDBAdaptor<org.opencb.biodata.models.core.Transcript>

Created by swaathi on 27/11/15.

Nested Class Summary

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

TranscriptDBAdaptor.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
TranscriptMongoDBAdaptor(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<org.opencb.biodata.models.core.Transcript>	get(org.opencb.commons.datastore.core.Query query, org.opencb.commons.datastore.core.QueryOptions options)
CellBaseDataResult<String>	getCdna(String id)
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<org.opencb.biodata.models.core.Transcript>	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	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.TranscriptDBAdaptor

getCdna

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

TranscriptMongoDBAdaptor

public TranscriptMongoDBAdaptor(String species,
                                String assembly,
                                org.opencb.commons.datastore.mongodb.MongoDataStore mongoDataStore)

Method Detail

getCdna

public CellBaseDataResult<String> getCdna(String id)

Specified by:

getCdna in interface TranscriptDBAdaptor<org.opencb.biodata.models.core.Transcript>

update

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

Specified by:

update in interface CellBaseDBAdaptor<org.opencb.biodata.models.core.Transcript>

count

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

Specified by:

count in interface CellBaseDBAdaptor<org.opencb.biodata.models.core.Transcript>

distinct

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

Specified by:

distinct in interface CellBaseDBAdaptor<org.opencb.biodata.models.core.Transcript>

stats

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

Specified by:

stats in interface CellBaseDBAdaptor<org.opencb.biodata.models.core.Transcript>

get

public CellBaseDataResult<org.opencb.biodata.models.core.Transcript> get(org.opencb.commons.datastore.core.Query query,
                                                                         org.opencb.commons.datastore.core.QueryOptions options)

Specified by:

get in interface CellBaseDBAdaptor<org.opencb.biodata.models.core.Transcript>

nativeGet

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

Specified by:

nativeGet in interface CellBaseDBAdaptor<org.opencb.biodata.models.core.Transcript>

iterator

public Iterator<org.opencb.biodata.models.core.Transcript> iterator(org.opencb.commons.datastore.core.Query query,
                                                                    org.opencb.commons.datastore.core.QueryOptions options)

Specified by:

iterator in interface CellBaseDBAdaptor<org.opencb.biodata.models.core.Transcript>

nativeIterator

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

Specified by:

nativeIterator in interface CellBaseDBAdaptor<org.opencb.biodata.models.core.Transcript>

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<org.opencb.biodata.models.core.Transcript>

rank

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

Specified by:

rank in interface CellBaseDBAdaptor<org.opencb.biodata.models.core.Transcript>

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<org.opencb.biodata.models.core.Transcript>

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<org.opencb.biodata.models.core.Transcript>

next

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

Specified by:

next in interface FeatureDBAdaptor<org.opencb.biodata.models.core.Transcript>

nativeNext

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

Specified by:

nativeNext in interface FeatureDBAdaptor<org.opencb.biodata.models.core.Transcript>

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<org.opencb.biodata.models.core.Transcript>