public class VariantMongoDBAdaptor extends MongoDBAdaptor implements VariantDBAdaptor<org.opencb.biodata.models.variant.Variant>
VariantDBAdaptor.QueryParams
assembly, logger, mongoDataStore, mongoDBCollection, objectMapper, species
MERGE, REGION
Constructor and Description |
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VariantMongoDBAdaptor(String species,
String assembly,
org.opencb.commons.datastore.mongodb.MongoDataStore mongoDataStore) |
Modifier and Type | Method and Description |
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protected org.opencb.commons.datastore.core.QueryOptions |
addVariantPrivateExcludeOptions(org.opencb.commons.datastore.core.QueryOptions options) |
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 inputOptions) |
CellBaseDataResult<String> |
getConsequenceTypes(org.opencb.commons.datastore.core.Query query) |
CellBaseDataResult<org.opencb.biodata.models.variant.avro.Score> |
getFunctionalScoreVariant(org.opencb.biodata.models.variant.Variant variant,
org.opencb.commons.datastore.core.QueryOptions queryOptions) |
CellBaseDataResult |
getIntervalFrequencies(org.opencb.commons.datastore.core.Query query,
int intervalSize,
org.opencb.commons.datastore.core.QueryOptions options) |
List<CellBaseDataResult<org.opencb.biodata.models.variant.Variant>> |
getPopulationFrequencyByVariant(List<org.opencb.biodata.models.variant.Variant> variants,
org.opencb.commons.datastore.core.QueryOptions queryOptions)
Created an specific method for pop freqs here since in this case phase is managed at the Pop.
|
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 inputOptions) |
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 |
startsWith(String id,
org.opencb.commons.datastore.core.QueryOptions options) |
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
getByVariant, getByVariant, getFunctionalScoreVariant
first, first, getByRegion, getByRegion, getIntervalFrequencies
count, distinct, forEach, get, iterator, nativeGet, nativeIterator, stats
spliterator
public CellBaseDataResult startsWith(String id, org.opencb.commons.datastore.core.QueryOptions options)
startsWith
in interface VariantDBAdaptor<org.opencb.biodata.models.variant.Variant>
public CellBaseDataResult<String> getConsequenceTypes(org.opencb.commons.datastore.core.Query query)
getConsequenceTypes
in interface VariantDBAdaptor<org.opencb.biodata.models.variant.Variant>
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 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 inputOptions)
get
in interface CellBaseDBAdaptor<org.opencb.biodata.models.variant.Variant>
protected org.opencb.commons.datastore.core.QueryOptions addVariantPrivateExcludeOptions(org.opencb.commons.datastore.core.QueryOptions options)
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 inputOptions)
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 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<org.opencb.biodata.models.variant.avro.Score> getFunctionalScoreVariant(org.opencb.biodata.models.variant.Variant variant, org.opencb.commons.datastore.core.QueryOptions queryOptions)
getFunctionalScoreVariant
in interface VariantDBAdaptor<org.opencb.biodata.models.variant.Variant>
public List<CellBaseDataResult<org.opencb.biodata.models.variant.Variant>> getPopulationFrequencyByVariant(List<org.opencb.biodata.models.variant.Variant> variants, org.opencb.commons.datastore.core.QueryOptions queryOptions)
getPopulationFrequencyByVariant
in interface VariantDBAdaptor<org.opencb.biodata.models.variant.Variant>
variants
- list of Variant objects to queryqueryOptions
- query options, e.g. phased={true, false}Copyright © 2019. All rights reserved.