public class GenomeMongoDBAdaptor extends MongoDBAdaptor implements GenomeDBAdaptor
GenomeDBAdaptor.QueryParams
assembly, logger, mongoDataStore, mongoDBCollection, objectMapper, species
Constructor and Description |
---|
GenomeMongoDBAdaptor(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 |
get(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult |
getChromosomeInfo(String chromosomeId,
org.opencb.commons.datastore.core.QueryOptions queryOptions) |
List<CellBaseDataResult<org.opencb.biodata.models.core.GenomicScoreRegion<Float>>> |
getConservation(List<org.opencb.biodata.models.core.Region> regionList,
org.opencb.commons.datastore.core.QueryOptions options) |
CellBaseDataResult<org.opencb.biodata.models.variant.avro.Cytoband> |
getCytobands(org.opencb.biodata.models.core.Region region,
org.opencb.commons.datastore.core.QueryOptions queryOptions) |
CellBaseDataResult |
getGenomeInfo(org.opencb.commons.datastore.core.QueryOptions queryOptions) |
CellBaseDataResult<org.opencb.biodata.models.core.GenomeSequenceFeature> |
getGenomicSequence(org.opencb.commons.datastore.core.Query query,
org.opencb.commons.datastore.core.QueryOptions queryOptions)
Deprecated.
|
CellBaseDataResult<org.opencb.biodata.models.core.GenomeSequenceFeature> |
getSequence(org.opencb.biodata.models.core.Region region,
org.opencb.commons.datastore.core.QueryOptions queryOptions) |
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 options) |
Iterator |
nativeIterator(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
getConservation, getCytobands, getCytobands, getGenomicSequence, getSequence
count, distinct, forEach, get, iterator, nativeGet, nativeIterator, stats
spliterator
public CellBaseDataResult getGenomeInfo(org.opencb.commons.datastore.core.QueryOptions queryOptions)
getGenomeInfo
in interface GenomeDBAdaptor
public CellBaseDataResult getChromosomeInfo(String chromosomeId, org.opencb.commons.datastore.core.QueryOptions queryOptions)
getChromosomeInfo
in interface GenomeDBAdaptor
public CellBaseDataResult<org.opencb.biodata.models.variant.avro.Cytoband> getCytobands(org.opencb.biodata.models.core.Region region, org.opencb.commons.datastore.core.QueryOptions queryOptions)
getCytobands
in interface GenomeDBAdaptor
@Deprecated public CellBaseDataResult<org.opencb.biodata.models.core.GenomeSequenceFeature> getGenomicSequence(org.opencb.commons.datastore.core.Query query, org.opencb.commons.datastore.core.QueryOptions queryOptions)
getGenomicSequence
in interface GenomeDBAdaptor
public CellBaseDataResult<org.opencb.biodata.models.core.GenomeSequenceFeature> getSequence(org.opencb.biodata.models.core.Region region, org.opencb.commons.datastore.core.QueryOptions queryOptions)
getSequence
in interface GenomeDBAdaptor
public List<CellBaseDataResult<org.opencb.biodata.models.core.GenomicScoreRegion<Float>>> getConservation(List<org.opencb.biodata.models.core.Region> regionList, org.opencb.commons.datastore.core.QueryOptions options)
getConservation
in interface GenomeDBAdaptor
public CellBaseDataResult<Long> update(List objectList, String field, String[] innerFields)
update
in interface CellBaseDBAdaptor
public CellBaseDataResult<Long> count(org.opencb.commons.datastore.core.Query query)
count
in interface CellBaseDBAdaptor
public CellBaseDataResult distinct(org.opencb.commons.datastore.core.Query query, String field)
distinct
in interface CellBaseDBAdaptor
public CellBaseDataResult stats(org.opencb.commons.datastore.core.Query query)
stats
in interface CellBaseDBAdaptor
public CellBaseDataResult get(org.opencb.commons.datastore.core.Query query, org.opencb.commons.datastore.core.QueryOptions options)
get
in interface CellBaseDBAdaptor
public CellBaseDataResult nativeGet(org.opencb.commons.datastore.core.Query query, org.opencb.commons.datastore.core.QueryOptions options)
nativeGet
in interface CellBaseDBAdaptor
public Iterator iterator(org.opencb.commons.datastore.core.Query query, org.opencb.commons.datastore.core.QueryOptions options)
iterator
in interface CellBaseDBAdaptor
public Iterator nativeIterator(org.opencb.commons.datastore.core.Query query, org.opencb.commons.datastore.core.QueryOptions options)
nativeIterator
in interface CellBaseDBAdaptor
public CellBaseDataResult rank(org.opencb.commons.datastore.core.Query query, String field, int numResults, boolean asc)
rank
in interface CellBaseDBAdaptor
public CellBaseDataResult groupBy(org.opencb.commons.datastore.core.Query query, String field, org.opencb.commons.datastore.core.QueryOptions options)
groupBy
in interface CellBaseDBAdaptor
public CellBaseDataResult groupBy(org.opencb.commons.datastore.core.Query query, List fields, org.opencb.commons.datastore.core.QueryOptions options)
groupBy
in interface CellBaseDBAdaptor
public void forEach(org.opencb.commons.datastore.core.Query query, Consumer action, org.opencb.commons.datastore.core.QueryOptions options)
forEach
in interface CellBaseDBAdaptor
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