public class TranscriptMongoDBAdaptor extends MongoDBAdaptor implements TranscriptDBAdaptor<org.opencb.biodata.models.core.Transcript>
TranscriptDBAdaptor.QueryParams
assembly, logger, mongoDataStore, mongoDBCollection, objectMapper, species
MERGE, REGION
Constructor and Description |
---|
TranscriptMongoDBAdaptor(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 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) |
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
getCdna
first, first, getByRegion, getByRegion, getByVariant, getByVariant, getIntervalFrequencies
count, distinct, forEach, get, iterator, nativeGet, nativeIterator, stats
spliterator
public CellBaseDataResult<String> getCdna(String id)
getCdna
in interface TranscriptDBAdaptor<org.opencb.biodata.models.core.Transcript>
public CellBaseDataResult<Long> update(List objectList, String field, String[] innerFields)
update
in interface CellBaseDBAdaptor<org.opencb.biodata.models.core.Transcript>
public CellBaseDataResult<Long> count(org.opencb.commons.datastore.core.Query query)
count
in interface CellBaseDBAdaptor<org.opencb.biodata.models.core.Transcript>
public CellBaseDataResult distinct(org.opencb.commons.datastore.core.Query query, String field)
distinct
in interface CellBaseDBAdaptor<org.opencb.biodata.models.core.Transcript>
public CellBaseDataResult stats(org.opencb.commons.datastore.core.Query query)
stats
in interface CellBaseDBAdaptor<org.opencb.biodata.models.core.Transcript>
public CellBaseDataResult<org.opencb.biodata.models.core.Transcript> get(org.opencb.commons.datastore.core.Query query, org.opencb.commons.datastore.core.QueryOptions options)
get
in interface CellBaseDBAdaptor<org.opencb.biodata.models.core.Transcript>
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.core.Transcript>
public Iterator<org.opencb.biodata.models.core.Transcript> iterator(org.opencb.commons.datastore.core.Query query, org.opencb.commons.datastore.core.QueryOptions options)
iterator
in interface CellBaseDBAdaptor<org.opencb.biodata.models.core.Transcript>
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.core.Transcript>
public void forEach(org.opencb.commons.datastore.core.Query query, Consumer action, org.opencb.commons.datastore.core.QueryOptions options)
forEach
in interface CellBaseDBAdaptor<org.opencb.biodata.models.core.Transcript>
public CellBaseDataResult rank(org.opencb.commons.datastore.core.Query query, String field, int numResults, boolean asc)
rank
in interface CellBaseDBAdaptor<org.opencb.biodata.models.core.Transcript>
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.core.Transcript>
public CellBaseDataResult groupBy(org.opencb.commons.datastore.core.Query query, List fields, org.opencb.commons.datastore.core.QueryOptions options)
groupBy
in interface CellBaseDBAdaptor<org.opencb.biodata.models.core.Transcript>
public CellBaseDataResult next(org.opencb.commons.datastore.core.Query query, org.opencb.commons.datastore.core.QueryOptions options)
next
in interface FeatureDBAdaptor<org.opencb.biodata.models.core.Transcript>
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.core.Transcript>
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.core.Transcript>
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