org.opencb.cellbase.client.rest

Class VariantClient

java.lang.Object

org.opencb.cellbase.client.rest.ParentRestClient<T>

org.opencb.cellbase.client.rest.FeatureClient<org.opencb.biodata.models.variant.Variant>

org.opencb.cellbase.client.rest.VariantClient

public final class VariantClient
extends FeatureClient<org.opencb.biodata.models.variant.Variant>

Field Summary

Fields inherited from class org.opencb.cellbase.client.rest.ParentRestClient

assembly, category, clazz, client, configuration, DEFAULT_NUM_THREADS, EMPTY_STRING, jsonObjectMapper, LIMIT, logger, META, REST, REST_CALL_BATCH_SIZE, species, subcategory, WEBSERVICES

Constructor Summary

Constructors

Constructor and Description
VariantClient(String species, String assembly, ClientConfiguration configuration)

Method Summary

Modifier and Type	Method and Description
CellBaseDataResponse<org.opencb.biodata.models.variant.Variant>	annotate(List<org.opencb.biodata.models.variant.Variant> variants, org.opencb.commons.datastore.core.QueryOptions options)
CellBaseDataResponse<org.opencb.biodata.models.variant.Variant>	annotate(List<org.opencb.biodata.models.variant.Variant> variants, org.opencb.commons.datastore.core.QueryOptions options, boolean post)
CellBaseDataResponse<org.opencb.biodata.models.variant.avro.VariantAnnotation>	getAnnotation(List<org.opencb.biodata.models.variant.Variant> variants, org.opencb.commons.datastore.core.QueryOptions options)
CellBaseDataResponse<org.opencb.biodata.models.variant.avro.VariantAnnotation>	getAnnotation(List<org.opencb.biodata.models.variant.Variant> variants, org.opencb.commons.datastore.core.QueryOptions options, boolean post)
CellBaseDataResponse<org.opencb.biodata.models.variant.avro.VariantAnnotation>	getAnnotationByVariantIds(List<String> ids, org.opencb.commons.datastore.core.QueryOptions options)
CellBaseDataResponse<org.opencb.biodata.models.variant.avro.VariantAnnotation>	getAnnotationByVariantIds(List<String> ids, org.opencb.commons.datastore.core.QueryOptions options, boolean post)
CellBaseDataResponse<org.opencb.biodata.models.variant.avro.VariantAnnotation>	getAnnotationByVariantIds(String id, org.opencb.commons.datastore.core.QueryOptions options) Deprecated.
CellBaseDataResponse<org.opencb.biodata.models.variant.avro.VariantAnnotation>	getAnnotationByVariantIds(String id, org.opencb.commons.datastore.core.QueryOptions options, boolean post) Deprecated.
String	getVariantAnnotationId(org.opencb.biodata.models.variant.Variant variant, Boolean ignorePhase)
List<String>	getVariantAnnotationIds(List<org.opencb.biodata.models.variant.Variant> variants, Boolean ignorePhase)

Methods inherited from class org.opencb.cellbase.client.rest.FeatureClient

group, groupCount, next, search

Methods inherited from class org.opencb.cellbase.client.rest.ParentRestClient

count, execute, execute, execute, execute, execute, execute, first, get, getBaseUrl

Methods inherited from class java.lang.Object

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

Constructor Detail

VariantClient

public VariantClient(String species,
                     String assembly,
                     ClientConfiguration configuration)

Method Detail

getAnnotationByVariantIds

@Deprecated
public CellBaseDataResponse<org.opencb.biodata.models.variant.avro.VariantAnnotation> getAnnotationByVariantIds(String id,
                                                                                                                            org.opencb.commons.datastore.core.QueryOptions options)
                                                                                                                     throws IOException

Deprecated.

Throws:

IOException

getAnnotationByVariantIds

@Deprecated
public CellBaseDataResponse<org.opencb.biodata.models.variant.avro.VariantAnnotation> getAnnotationByVariantIds(String id,
                                                                                                                            org.opencb.commons.datastore.core.QueryOptions options,
                                                                                                                            boolean post)
                                                                                                                     throws IOException

Deprecated.

Throws:

IOException

getAnnotationByVariantIds

public CellBaseDataResponse<org.opencb.biodata.models.variant.avro.VariantAnnotation> getAnnotationByVariantIds(List<String> ids,
                                                                                                                org.opencb.commons.datastore.core.QueryOptions options)
                                                                                                         throws IOException

Throws:

IOException

getAnnotationByVariantIds

public CellBaseDataResponse<org.opencb.biodata.models.variant.avro.VariantAnnotation> getAnnotationByVariantIds(List<String> ids,
                                                                                                                org.opencb.commons.datastore.core.QueryOptions options,
                                                                                                                boolean post)
                                                                                                         throws IOException

Throws:

IOException

annotate

public CellBaseDataResponse<org.opencb.biodata.models.variant.Variant> annotate(List<org.opencb.biodata.models.variant.Variant> variants,
                                                                                org.opencb.commons.datastore.core.QueryOptions options)
                                                                         throws IOException

Throws:

IOException

annotate

public CellBaseDataResponse<org.opencb.biodata.models.variant.Variant> annotate(List<org.opencb.biodata.models.variant.Variant> variants,
                                                                                org.opencb.commons.datastore.core.QueryOptions options,
                                                                                boolean post)
                                                                         throws IOException

Throws:

IOException

getAnnotation

public CellBaseDataResponse<org.opencb.biodata.models.variant.avro.VariantAnnotation> getAnnotation(List<org.opencb.biodata.models.variant.Variant> variants,
                                                                                                    org.opencb.commons.datastore.core.QueryOptions options)
                                                                                             throws IOException

Throws:

IOException

getAnnotation

public CellBaseDataResponse<org.opencb.biodata.models.variant.avro.VariantAnnotation> getAnnotation(List<org.opencb.biodata.models.variant.Variant> variants,
                                                                                                    org.opencb.commons.datastore.core.QueryOptions options,
                                                                                                    boolean post)
                                                                                             throws IOException

Throws:

IOException

getVariantAnnotationId

public String getVariantAnnotationId(org.opencb.biodata.models.variant.Variant variant,
                                     Boolean ignorePhase)

getVariantAnnotationIds

public List<String> getVariantAnnotationIds(List<org.opencb.biodata.models.variant.Variant> variants,
                                            Boolean ignorePhase)