Index (CellBase project 5.0.0-SNAPSHOT API)

A B C D E F G H I J K L M N O P Q R S T U V W X Z

A

A_TO_CODON - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
about() - Method in class org.opencb.cellbase.client.rest.MetaClient
AbstractVariationFile - Class in org.opencb.cellbase.lib.builders.variation: Created by parce on 08/12/15.
AbstractVariationFile(Path, String, String) - Constructor for class org.opencb.cellbase.lib.builders.variation.AbstractVariationFile
AbstractVariationFile(Path, String, String, int) - Constructor for class org.opencb.cellbase.lib.builders.variation.AbstractVariationFile
addCaddValues(float, float, String) - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
addClinvar(ClinvarPublicSet) - Method in class org.opencb.cellbase.lib.model.ClinicalVariation: Deprecated.
addCosmic(Cosmic) - Method in class org.opencb.cellbase.lib.model.ClinicalVariation: Deprecated.
addEvent(Event) - Method in class org.opencb.cellbase.core.CellBaseDataResponse
addExcludeReturnFields(String, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptor: Deprecated.
addGwas(Gwas) - Method in class org.opencb.cellbase.lib.model.ClinicalVariation: Deprecated.
addHaplotypeProperty(List<EvidenceEntry>, List<String>) - Method in class org.opencb.cellbase.lib.builders.clinical.variant.ClinicalIndexer
addIncludeReturnFields(String, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptor: Deprecated.
addNonCodingSOs(boolean) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
addPrivateExcludeOptions(QueryOptions) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptor
addPrivateExcludeOptions(QueryOptions, String) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptor
addSource(String, List<Float>) - Method in class org.opencb.cellbase.lib.builders.formats.ConservedRegionFeature: Deprecated.
addStudies(List<GwasStudy>) - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
addStudy(GwasStudy) - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
addTest(GwasTest) - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasTrait
addTests(List<GwasTest>) - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasTrait
addTrait(GwasTrait) - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasStudy
addTraits(List<GwasTrait>) - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasStudy
addVariantPrivateExcludeOptions(QueryOptions) - Method in class org.opencb.cellbase.lib.impl.VariantMongoDBAdaptor
AdminCliOptionsParser - Class in org.opencb.cellbase.app.cli.admin: Created by imedina on 03/02/15.
AdminCliOptionsParser() - Constructor for class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser
AdminCliOptionsParser.BuildCommandOptions - Class in org.opencb.cellbase.app.cli.admin
AdminCliOptionsParser.DownloadCommandOptions - Class in org.opencb.cellbase.app.cli.admin
AdminCliOptionsParser.IndexCommandOptions - Class in org.opencb.cellbase.app.cli.admin
AdminCliOptionsParser.InstallCommandOptions - Class in org.opencb.cellbase.app.cli.admin
AdminCliOptionsParser.LoadCommandOptions - Class in org.opencb.cellbase.app.cli.admin
AdminCliOptionsParser.ServerCommandOptions - Class in org.opencb.cellbase.app.cli.admin
AdminMain - Class in org.opencb.cellbase.app.cli.admin: Created by imedina on 03/02/15.
AdminMain() - Constructor for class org.opencb.cellbase.app.cli.admin.AdminMain
AdminRestWebService - Class in org.opencb.cellbase.server.rest
AdminRestWebService(String, UriInfo, HttpServletRequest, ServletContext) - Constructor for class org.opencb.cellbase.server.rest.AdminRestWebService
alleleOriginLabels() - Method in class org.opencb.cellbase.client.rest.ClinicalVariantClient
allResults() - Method in class org.opencb.cellbase.core.CellBaseDataResponse: This method flats the two levels (DataResponse and DataResult) into a single list of T.
allResultsSize() - Method in class org.opencb.cellbase.core.CellBaseDataResponse
AMBIGUOUS_ORF - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
annotate(List<Variant>, QueryOptions) - Method in class org.opencb.cellbase.client.rest.VariantClient
annotate(List<Variant>, QueryOptions, boolean) - Method in class org.opencb.cellbase.client.rest.VariantClient
AnnotationBasedPhasedQueryManager<T> - Class in org.opencb.cellbase.core.variant
AnnotationBasedPhasedQueryManager() - Constructor for class org.opencb.cellbase.core.variant.AnnotationBasedPhasedQueryManager
ANSI_BLACK - Static variable in class org.opencb.cellbase.app.cli.CliOptionsParser
ANSI_BLUE - Static variable in class org.opencb.cellbase.app.cli.CliOptionsParser
ANSI_CYAN - Static variable in class org.opencb.cellbase.app.cli.CliOptionsParser
ANSI_GREEN - Static variable in class org.opencb.cellbase.app.cli.CliOptionsParser
ANSI_PURPLE - Static variable in class org.opencb.cellbase.app.cli.CliOptionsParser
ANSI_RED - Static variable in class org.opencb.cellbase.app.cli.CliOptionsParser
ANSI_RESET - Static variable in class org.opencb.cellbase.app.cli.CliOptionsParser
ANSI_WHITE - Static variable in class org.opencb.cellbase.app.cli.CliOptionsParser
ANSI_YELLOW - Static variable in class org.opencb.cellbase.app.cli.CliOptionsParser
ANTISENSE - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
apiVersion - Variable in class org.opencb.cellbase.server.rest.AdminRestWebService
appendChromosome(String, StringBuilder) - Static method in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
appHome - Variable in class org.opencb.cellbase.app.cli.CommandExecutor
ApplicationDetails() - Constructor for class org.opencb.cellbase.core.monitor.HealthStatus.ApplicationDetails
apply(List<VariantAnnotation>) - Method in class org.opencb.cellbase.app.cli.main.annotation.BenchmarkTask
apply(List<String>) - Method in class org.opencb.cellbase.app.cli.main.annotation.JsonStringAnnotatorTask: Deprecated.
apply(List<Variant>) - Method in class org.opencb.cellbase.app.cli.main.annotation.VariantAnnotatorTask
apply(List<String>) - Method in class org.opencb.cellbase.app.cli.main.annotation.VcfStringAnnotatorTask: Deprecated.
assembly - Variable in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.BuildCommandOptions
assembly - Variable in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.IndexCommandOptions
assembly - Variable in class org.opencb.cellbase.app.cli.CliOptionsParser.SpeciesAndAssemblyCommandOptions
assembly - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.QueryCommandOptions
assembly - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.VariantAnnotationCommandOptions
assembly - Variable in class org.opencb.cellbase.client.rest.ParentRestClient
Assembly() - Constructor for class org.opencb.cellbase.core.config.SpeciesConfiguration.Assembly
assembly - Variable in class org.opencb.cellbase.lib.impl.MongoDBAdaptor
assembly - Variable in class org.opencb.cellbase.server.rest.GenericRestWSServer

B

batchSize - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.VariantAnnotationCommandOptions
benchmark - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.VariantAnnotationCommandOptions
BenchmarkDataWriter - Class in org.opencb.cellbase.app.cli.main.annotation: Created by fjlopez on 07/04/16.
BenchmarkDataWriter(String, String, Path) - Constructor for class org.opencb.cellbase.app.cli.main.annotation.BenchmarkDataWriter
BenchmarkTask - Class in org.opencb.cellbase.app.cli.main.annotation: Created by fjlopez on 07/04/16.
BenchmarkTask(VariantAnnotator, FastaIndexManager) - Constructor for class org.opencb.cellbase.app.cli.main.annotation.BenchmarkTask
BIG_VARIANT_SIZE_THRESHOLD - Static variable in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeGenericRegionCalculator
blockingQueue - Variable in class org.opencb.cellbase.core.loader.CellBaseLoader
blockingQueue - Variable in class org.opencb.cellbase.core.loader.LoadRunner
BuildCommandExecutor - Class in org.opencb.cellbase.app.cli.admin.executors: Created by imedina on 03/02/15.
BuildCommandExecutor(AdminCliOptionsParser.BuildCommandOptions) - Constructor for class org.opencb.cellbase.app.cli.admin.executors.BuildCommandExecutor
BuildCommandOptions() - Constructor for class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.BuildCommandOptions
buildParams - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.VariantAnnotationCommandOptions
buildResponse(Response.ResponseBuilder) - Method in class org.opencb.cellbase.server.rest.AdminRestWebService
buildVariantId(String, int, String, String) - Static method in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils

C

CACHE_TRANSCRIPT - Static variable in class org.opencb.cellbase.server.rest.feature.VariationWSServer
Cadd - Class in org.opencb.cellbase.lib.builders.formats
Cadd(String, String, String, Integer, Integer, Float, Float, Float, Float, Float, Integer, Float, Float, Float, Float, Float, Float, Float, Float, Float, Float, Float) - Constructor for class org.opencb.cellbase.lib.builders.formats.Cadd
Cadd() - Constructor for class org.opencb.cellbase.lib.builders.formats.Cadd
Cadd.CaddValues - Class in org.opencb.cellbase.lib.builders.formats
CADD_DATA - Static variable in class org.opencb.cellbase.lib.EtlCommons
CaddAllAnnotationParser - Class in org.opencb.cellbase.lib.builders
CaddAllAnnotationParser(Path, String, CellBaseSerializer) - Constructor for class org.opencb.cellbase.lib.builders.CaddAllAnnotationParser
CaddScoreParser - Class in org.opencb.cellbase.lib.builders: Created by imedina on 06/11/15.
CaddScoreParser(Path, CellBaseSerializer) - Constructor for class org.opencb.cellbase.lib.builders.CaddScoreParser
CaddValues(float, float, String) - Constructor for class org.opencb.cellbase.lib.builders.formats.Cadd.CaddValues
call() - Method in class org.opencb.cellbase.core.loader.CellBaseLoader
call() - Method in class org.opencb.cellbase.lib.loader.MongoDBCellBaseLoader: Deprecated.
category - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.QueryCommandOptions
category - Variable in class org.opencb.cellbase.client.rest.ParentRestClient
CdnaCoord - Class in org.opencb.cellbase.core.variant.annotation.hgvs: Created by fjlopez on 27/01/17.
CdnaCoord() - Constructor for class org.opencb.cellbase.core.variant.annotation.hgvs.CdnaCoord
CdnaCoord.Landmark - Enum in org.opencb.cellbase.core.variant.annotation.hgvs
CDS_END_NF - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
CDS_START_NF - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
CELLBASE_DATABASES_MONGODB_HOST - Static variable in class org.opencb.cellbase.core.config.CellBaseConfiguration
CELLBASE_DATABASES_MONGODB_OPTIONS_PREFIX - Static variable in class org.opencb.cellbase.core.config.CellBaseConfiguration
CELLBASE_DATABASES_MONGODB_PASSWORD - Static variable in class org.opencb.cellbase.core.config.CellBaseConfiguration
CELLBASE_DATABASES_MONGODB_USER - Static variable in class org.opencb.cellbase.core.config.CellBaseConfiguration
CELLBASE_PREFIX - Static variable in class org.opencb.cellbase.core.config.CellBaseConfiguration
cellBaseAnnotation - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.VariantAnnotationCommandOptions
CellBaseClient - Class in org.opencb.cellbase.client.rest: Created by imedina on 12/05/16.
CellBaseClient(ClientConfiguration) - Constructor for class org.opencb.cellbase.client.rest.CellBaseClient
CellBaseClient(String, ClientConfiguration) - Constructor for class org.opencb.cellbase.client.rest.CellBaseClient
CellBaseClient(String, String, ClientConfiguration) - Constructor for class org.opencb.cellbase.client.rest.CellBaseClient
CellBaseCliOptionsParser - Class in org.opencb.cellbase.app.cli.main: Created by imedina on 03/02/15.
CellBaseCliOptionsParser() - Constructor for class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser
CellBaseCliOptionsParser.QueryCommandOptions - Class in org.opencb.cellbase.app.cli.main
CellBaseCliOptionsParser.VariantAnnotationCommandOptions - Class in org.opencb.cellbase.app.cli.main
cellBaseConfiguration - Variable in class org.opencb.cellbase.core.api.DBAdaptorFactory
CellBaseConfiguration - Class in org.opencb.cellbase.core.config
CellBaseConfiguration() - Constructor for class org.opencb.cellbase.core.config.CellBaseConfiguration
cellBaseConfiguration - Variable in class org.opencb.cellbase.core.loader.CellBaseLoader
cellBaseConfiguration - Variable in class org.opencb.cellbase.server.rest.GenericRestWSServer: Loading properties file just one time to be more efficient.
CellBaseConfiguration.ConfigurationFileFormat - Enum in org.opencb.cellbase.core.config
CellBaseDataResponse<T> - Class in org.opencb.cellbase.core
CellBaseDataResponse() - Constructor for class org.opencb.cellbase.core.CellBaseDataResponse
CellBaseDataResponse(ObjectMap, List<CellBaseDataResult<T>>) - Constructor for class org.opencb.cellbase.core.CellBaseDataResponse
CellBaseDataResponse(String, int, List<Event>, ObjectMap, List<CellBaseDataResult<T>>) - Constructor for class org.opencb.cellbase.core.CellBaseDataResponse
CellBaseDataResult<T> - Class in org.opencb.cellbase.core.result
CellBaseDataResult() - Constructor for class org.opencb.cellbase.core.result.CellBaseDataResult
CellBaseDataResult(String) - Constructor for class org.opencb.cellbase.core.result.CellBaseDataResult
CellBaseDataResult(DataResult<T>) - Constructor for class org.opencb.cellbase.core.result.CellBaseDataResult
CellBaseDataResult(String, int, List<Event>, long) - Constructor for class org.opencb.cellbase.core.result.CellBaseDataResult
CellBaseDataResult(String, int, List<Event>, int, List<T>, long) - Constructor for class org.opencb.cellbase.core.result.CellBaseDataResult
CellBaseDataResult(String, int, List<Event>, int, List<T>, long, long, long, long, ObjectMap) - Constructor for class org.opencb.cellbase.core.result.CellBaseDataResult
CellBaseDBAdaptor<T> - Interface in org.opencb.cellbase.core.api: Created by imedina on 25/11/15.
CellbaseException - Exception in org.opencb.cellbase.core.exception
CellbaseException(String) - Constructor for exception org.opencb.cellbase.core.exception.CellbaseException
CellBaseExceptionMapper - Class in org.opencb.cellbase.server.rest: Created by imedina on 02/03/16.
CellBaseExceptionMapper(UriInfo) - Constructor for class org.opencb.cellbase.server.rest.CellBaseExceptionMapper
CellBaseFileSerializer - Interface in org.opencb.cellbase.core.serializer: Created by parce on 9/02/15.
CellBaseJsonFileSerializer - Class in org.opencb.cellbase.core.serializer: Created by parce on 2/6/15.
CellBaseJsonFileSerializer(Path) - Constructor for class org.opencb.cellbase.core.serializer.CellBaseJsonFileSerializer
CellBaseJsonFileSerializer(Path, String) - Constructor for class org.opencb.cellbase.core.serializer.CellBaseJsonFileSerializer
CellBaseJsonFileSerializer(Path, String, boolean) - Constructor for class org.opencb.cellbase.core.serializer.CellBaseJsonFileSerializer
CellBaseJsonFileSerializer(Path, String, boolean, boolean, boolean) - Constructor for class org.opencb.cellbase.core.serializer.CellBaseJsonFileSerializer
CellBaseLoader - Class in org.opencb.cellbase.core.loader: Created by parce on 18/02/15.
CellBaseLoader(BlockingQueue<List<String>>, String, String, String, String[], CellBaseConfiguration) - Constructor for class org.opencb.cellbase.core.loader.CellBaseLoader
CellBaseLocalVariantAnnotator - Class in org.opencb.cellbase.app.cli.main.annotation: Created by fjlopez on 22/09/15.
CellBaseLocalVariantAnnotator(VariantAnnotationCalculator, QueryOptions) - Constructor for class org.opencb.cellbase.app.cli.main.annotation.CellBaseLocalVariantAnnotator
CellBaseMain - Class in org.opencb.cellbase.app.cli.main: Created by imedina on 03/02/15.
CellBaseMain() - Constructor for class org.opencb.cellbase.app.cli.main.CellBaseMain
CellBaseNormalizerSequenceAdaptor - Class in org.opencb.cellbase.core.variant.annotation
CellBaseNormalizerSequenceAdaptor(GenomeDBAdaptor) - Constructor for class org.opencb.cellbase.core.variant.annotation.CellBaseNormalizerSequenceAdaptor
CellBaseParser - Class in org.opencb.cellbase.lib.builders: Created by imedina on 30/08/14.
CellBaseParser(CellBaseSerializer) - Constructor for class org.opencb.cellbase.lib.builders.CellBaseParser
CellBaseSerializer - Interface in org.opencb.cellbase.core.serializer: Created by parce on 9/02/15.
CellBaseTypeConverter<DataModel,StorageSchema> - Interface in org.opencb.cellbase.core.loader: Created by imedina on 17/06/14.
CellBaseWSVariantAnnotator - Class in org.opencb.cellbase.app.cli.main.annotation: Created by fjlopez on 02/03/15.
CellBaseWSVariantAnnotator(VariantClient, QueryOptions) - Constructor for class org.opencb.cellbase.app.cli.main.annotation.CellBaseWSVariantAnnotator
chromosomeList - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.VariantAnnotationCommandOptions
ChromosomeWSServer - Class in org.opencb.cellbase.server.rest.genomic
ChromosomeWSServer(String, String, UriInfo, HttpServletRequest) - Constructor for class org.opencb.cellbase.server.rest.genomic.ChromosomeWSServer
clazz - Variable in class org.opencb.cellbase.client.rest.ParentRestClient
client - Variable in class org.opencb.cellbase.client.rest.ParentRestClient
clientConfiguration - Variable in class org.opencb.cellbase.app.cli.CommandExecutor
ClientConfiguration - Class in org.opencb.cellbase.client.config: Created by imedina on 12/05/16.
ClientConfiguration() - Constructor for class org.opencb.cellbase.client.config.ClientConfiguration
CLINICAL_VARIANTS_ANNOTATED_JSON_FILE - Static variable in class org.opencb.cellbase.lib.EtlCommons
CLINICAL_VARIANTS_DATA - Static variable in class org.opencb.cellbase.lib.EtlCommons
CLINICAL_VARIANTS_FOLDER - Static variable in class org.opencb.cellbase.lib.EtlCommons
CLINICAL_VARIANTS_JSON_FILE - Static variable in class org.opencb.cellbase.lib.EtlCommons
ClinicalDBAdaptor<T> - Interface in org.opencb.cellbase.core.api: Created by imedina on 30/11/15.
ClinicalDBAdaptor.QueryParams - Enum in org.opencb.cellbase.core.api
ClinicalIndexer - Class in org.opencb.cellbase.lib.builders.clinical.variant: Created by fjlopez on 04/10/16.
ClinicalIndexer(Path) - Constructor for class org.opencb.cellbase.lib.builders.clinical.variant.ClinicalIndexer
ClinicalLegacyMongoDBAdaptor - Class in org.opencb.cellbase.lib.impl: Deprecated.
ClinicalLegacyMongoDBAdaptor(String, String, MongoDataStore) - Constructor for class org.opencb.cellbase.lib.impl.ClinicalLegacyMongoDBAdaptor: Deprecated.
ClinicalLegacyWSServer - Class in org.opencb.cellbase.server.rest.feature: Deprecated.
ClinicalLegacyWSServer(String, String, UriInfo, HttpServletRequest) - Constructor for class org.opencb.cellbase.server.rest.feature.ClinicalLegacyWSServer: Deprecated.
ClinicalMongoDBAdaptor - Class in org.opencb.cellbase.lib.impl: Created by fjlopez on 06/12/16.
ClinicalMongoDBAdaptor(String, String, MongoDataStore) - Constructor for class org.opencb.cellbase.lib.impl.ClinicalMongoDBAdaptor
ClinicalPhasedQueryManager - Class in org.opencb.cellbase.core.variant
ClinicalPhasedQueryManager() - Constructor for class org.opencb.cellbase.core.variant.ClinicalPhasedQueryManager
ClinicalVariant - Class in org.opencb.cellbase.core.common.clinical: Created by pol on 20/08/15.
ClinicalVariant(String) - Constructor for class org.opencb.cellbase.core.common.clinical.ClinicalVariant
ClinicalVariant(String, int, int, String, String, String) - Constructor for class org.opencb.cellbase.core.common.clinical.ClinicalVariant
ClinicalVariantClient - Class in org.opencb.cellbase.client.rest: Created by fjlopez on 07/07/17.
ClinicalVariantClient(String, String, ClientConfiguration) - Constructor for class org.opencb.cellbase.client.rest.ClinicalVariantClient
ClinicalVariantParser - Class in org.opencb.cellbase.lib.builders.clinical.variant: Created by fjlopez on 26/09/16.
ClinicalVariantParser(Path, boolean, Path, String, CellBaseSerializer) - Constructor for class org.opencb.cellbase.lib.builders.clinical.variant.ClinicalVariantParser
ClinicalVariantParser(Path, Path, Path, Path, Path, Path, Path, Path, Path, Path, Path, Path, boolean, Path, String, CellBaseSerializer) - Constructor for class org.opencb.cellbase.lib.builders.clinical.variant.ClinicalVariantParser
ClinicalVariation - Class in org.opencb.cellbase.lib.model: Deprecated.
ClinicalVariation(String, int, int, String, String) - Constructor for class org.opencb.cellbase.lib.model.ClinicalVariation: Deprecated.
ClinicalVariation(ClinvarPublicSet) - Constructor for class org.opencb.cellbase.lib.model.ClinicalVariation: Deprecated.
ClinicalVariation(Cosmic) - Constructor for class org.opencb.cellbase.lib.model.ClinicalVariation: Deprecated.
ClinicalVariation(Gwas) - Constructor for class org.opencb.cellbase.lib.model.ClinicalVariation: Deprecated.
ClinicalWSServer - Class in org.opencb.cellbase.server.rest.clinical: Created by fjlopez on 06/12/16.
ClinicalWSServer(String, String, UriInfo, HttpServletRequest) - Constructor for class org.opencb.cellbase.server.rest.clinical.ClinicalWSServer
clinsigLabels() - Method in class org.opencb.cellbase.client.rest.ClinicalVariantClient
CLINVAR_CLINSIG_TO_ACMG - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
CLINVAR_CLINSIG_TO_DRUG_RESPONSE - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
CLINVAR_CLINSIG_TO_TRAIT_ASSOCIATION - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
CLINVAR_DATA - Static variable in class org.opencb.cellbase.lib.EtlCommons
CLINVAR_EFO_FILE - Static variable in class org.opencb.cellbase.lib.EtlCommons
CLINVAR_REVIEW_TO_CONSISTENCY_STATUS - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
CLINVAR_SUMMARY_FILE - Static variable in class org.opencb.cellbase.lib.EtlCommons
CLINVAR_VARIATION_ALLELE_FILE - Static variable in class org.opencb.cellbase.lib.EtlCommons
CLINVAR_XML_FILE - Static variable in class org.opencb.cellbase.lib.EtlCommons
ClinVarIndexer - Class in org.opencb.cellbase.lib.builders.clinical.variant: Created by fjlopez on 28/09/16.
ClinVarIndexer(Path, Path, Path, Path, boolean, Path, String, RocksDB) - Constructor for class org.opencb.cellbase.lib.builders.clinical.variant.ClinVarIndexer
ClinVarParser - Class in org.opencb.cellbase.lib.builders.clinical.variant: Deprecated.
ClinVarParser(Path, Path, Path, String, CellBaseSerializer) - Constructor for class org.opencb.cellbase.lib.builders.clinical.variant.ClinVarParser: Deprecated.
ClinvarPublicSet - Class in org.opencb.cellbase.core.common.clinical: Created by parce on 10/29/14.
ClinvarPublicSet(String, int, int, String, String, PublicSetType) - Constructor for class org.opencb.cellbase.core.common.clinical.ClinvarPublicSet
CliOptionsParser - Class in org.opencb.cellbase.app.cli: Created by imedina on 03/02/15.
CliOptionsParser() - Constructor for class org.opencb.cellbase.app.cli.CliOptionsParser
CliOptionsParser.CommonCommandOptions - Class in org.opencb.cellbase.app.cli
CliOptionsParser.GeneralOptions - Class in org.opencb.cellbase.app.cli
CliOptionsParser.SpeciesAndAssemblyCommandOptions - Class in org.opencb.cellbase.app.cli
close() - Method in class org.opencb.cellbase.app.cli.main.annotation.BenchmarkDataWriter
close() - Method in class org.opencb.cellbase.app.cli.main.annotation.CellBaseLocalVariantAnnotator
close() - Method in class org.opencb.cellbase.app.cli.main.annotation.CellBaseWSVariantAnnotator
close() - Method in class org.opencb.cellbase.app.cli.main.annotation.indexers.VariantIndexer
close() - Method in class org.opencb.cellbase.app.cli.main.annotation.PopulationFrequenciesAnnotator
close() - Method in class org.opencb.cellbase.app.cli.main.annotation.VariationDataReader
close() - Method in class org.opencb.cellbase.app.cli.main.annotation.VcfVariantAnnotator
close() - Method in class org.opencb.cellbase.core.api.DBAdaptorFactory
close() - Method in class org.opencb.cellbase.core.loader.CellBaseLoader
close() - Method in class org.opencb.cellbase.core.serializer.CellBaseJsonFileSerializer
close() - Method in interface org.opencb.cellbase.core.serializer.CellBaseSerializer
close() - Method in interface org.opencb.cellbase.core.variant.annotation.VariantAnnotator
close() - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptorFactory
close() - Method in class org.opencb.cellbase.lib.loader.MongoDBCellBaseLoader: Deprecated.
CNV_EXTRA_PADDING - Static variable in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
cnvExtraPadding - Variable in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
CODING_SEQUENCE_VARIANT - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
CODING_SO_NAMES - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
CODON_TO_A - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
CODON_TO_AMINOACID - Static variable in class org.opencb.cellbase.core.common.DNASequenceUtils
CODON_TO_AMINOACID_SHORT - Static variable in class org.opencb.cellbase.core.common.DNASequenceUtils
CommandExecutor - Class in org.opencb.cellbase.app.cli: Created by imedina on 03/02/15.
CommandExecutor() - Constructor for class org.opencb.cellbase.app.cli.CommandExecutor
CommandExecutor(String, boolean, String) - Constructor for class org.opencb.cellbase.app.cli.CommandExecutor
CommonCommandOptions() - Constructor for class org.opencb.cellbase.app.cli.CliOptionsParser.CommonCommandOptions
commonOptions - Variable in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.BuildCommandOptions
commonOptions - Variable in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.DownloadCommandOptions
commonOptions - Variable in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.IndexCommandOptions
commonOptions - Variable in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.InstallCommandOptions
commonOptions - Variable in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.LoadCommandOptions
commonOptions - Variable in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.ServerCommandOptions
commonOptions - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.QueryCommandOptions
commonOptions - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.VariantAnnotationCommandOptions
COMPLEMENT - Static variable in class org.opencb.cellbase.core.common.DNASequenceUtils
COMPLEMENTARY_NT - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
COMPLEMENTARY_START_CODON - Static variable in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
conf - Variable in class org.opencb.cellbase.app.cli.CliOptionsParser.CommonCommandOptions
conf - Variable in class org.opencb.cellbase.app.cli.CommandExecutor
configFile - Variable in class org.opencb.cellbase.app.cli.CommandExecutor: Deprecated.
configuration - Variable in class org.opencb.cellbase.app.cli.CommandExecutor
configuration - Variable in class org.opencb.cellbase.client.rest.ParentRestClient
consequenceType - Variable in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
ConsequenceTypeBNDCalculator - Class in org.opencb.cellbase.core.variant.annotation: Created by fjlopez on 09/05/17.
ConsequenceTypeBNDCalculator() - Constructor for class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeBNDCalculator
ConsequenceTypeCalculator - Class in org.opencb.cellbase.core.variant.annotation: Created by fjlopez on 19/06/15.
ConsequenceTypeCalculator() - Constructor for class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
ConsequenceTypeCNVGainCalculator - Class in org.opencb.cellbase.core.variant.annotation: Created by fjlopez on 31/05/16.
ConsequenceTypeCNVGainCalculator() - Constructor for class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCNVGainCalculator
ConsequenceTypeDeletionCalculator - Class in org.opencb.cellbase.core.variant.annotation: Created by fjlopez on 05/08/15.
ConsequenceTypeDeletionCalculator(GenomeDBAdaptor) - Constructor for class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeDeletionCalculator
ConsequenceTypeGenericRegionCalculator - Class in org.opencb.cellbase.core.variant.annotation: Created by fjlopez on 29/03/17.
ConsequenceTypeGenericRegionCalculator() - Constructor for class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeGenericRegionCalculator
ConsequenceTypeInsertionCalculator - Class in org.opencb.cellbase.core.variant.annotation: Created by fjlopez on 23/07/15.
ConsequenceTypeInsertionCalculator(GenomeDBAdaptor) - Constructor for class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeInsertionCalculator
ConsequenceTypeMNVCalculator - Class in org.opencb.cellbase.core.variant.annotation: Created by fjlopez on 15/03/17.
ConsequenceTypeMNVCalculator(GenomeDBAdaptor) - Constructor for class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeMNVCalculator
ConsequenceTypeSNVCalculator - Class in org.opencb.cellbase.core.variant.annotation: Created by fjlopez on 22/06/15.
ConsequenceTypeSNVCalculator() - Constructor for class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeSNVCalculator
conservation(String) - Method in class org.opencb.cellbase.server.rest.genomic.RegionWSServer
CONSERVATION_CHUNK_SIZE - Static variable in class org.opencb.cellbase.lib.MongoDBCollectionConfiguration
CONSERVATION_DATA - Static variable in class org.opencb.cellbase.lib.EtlCommons
ConservationDBAdaptor<T> - Interface in org.opencb.cellbase.core.api: Deprecated.
ConservationDBAdaptor.QueryParams - Enum in org.opencb.cellbase.core.api: Deprecated.
ConservationMongoDBAdaptor - Class in org.opencb.cellbase.lib.impl: Deprecated.
ConservationMongoDBAdaptor(String, String, MongoDataStore) - Constructor for class org.opencb.cellbase.lib.impl.ConservationMongoDBAdaptor: Deprecated.
ConservationParser - Class in org.opencb.cellbase.lib.builders
ConservationParser(Path, CellBaseFileSerializer) - Constructor for class org.opencb.cellbase.lib.builders.ConservationParser
ConservationParser(Path, int, CellBaseFileSerializer) - Constructor for class org.opencb.cellbase.lib.builders.ConservationParser
ConservedRegion - Class in org.opencb.cellbase.core.common.regulatory: ConservedRegion generated by hbm2java.
ConservedRegion() - Constructor for class org.opencb.cellbase.core.common.regulatory.ConservedRegion
ConservedRegion(int, String, int, int, String, int, double, double, double, double, double, double, double, double, double, double, double, double, String) - Constructor for class org.opencb.cellbase.core.common.regulatory.ConservedRegion
ConservedRegionFeature - Class in org.opencb.cellbase.lib.builders.formats: Deprecated.
ConservedRegionFeature(String, int, int, int) - Constructor for class org.opencb.cellbase.lib.builders.formats.ConservedRegionFeature: Deprecated.
ConservedRegionFeature.ConservedRegionSource - Class in org.opencb.cellbase.lib.builders.formats: Deprecated.
ConservedRegionSource(String, List<Float>) - Constructor for class org.opencb.cellbase.lib.builders.formats.ConservedRegionFeature.ConservedRegionSource: Deprecated.
consistencyLabels() - Method in class org.opencb.cellbase.client.rest.ClinicalVariantClient
contains(String, QueryOptions) - Method in interface org.opencb.cellbase.core.api.XRefDBAdaptor
contains(String, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.XRefMongoDBAdaptor
convertToDataModel(StorageSchema) - Method in interface org.opencb.cellbase.core.loader.CellBaseTypeConverter
convertToDataModel(Document) - Method in class org.opencb.cellbase.lib.loader.converters.GeneConverter: Deprecated.
convertToDataModel(Document) - Method in class org.opencb.cellbase.lib.loader.converters.VariationConverter: Deprecated.
convertToStorageSchema(DataModel) - Method in interface org.opencb.cellbase.core.loader.CellBaseTypeConverter
convertToStorageSchema(Gene) - Method in class org.opencb.cellbase.lib.loader.converters.GeneConverter: Deprecated.
convertToStorageSchema(Variation) - Method in class org.opencb.cellbase.lib.loader.converters.VariationConverter: Deprecated.
COPY_NUMBER_CHANGE - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
CORSFilter - Class in org.opencb.cellbase.server.rest
CORSFilter() - Constructor for class org.opencb.cellbase.server.rest.CORSFilter
Cosmic - Class in org.opencb.cellbase.core.common.clinical
Cosmic() - Constructor for class org.opencb.cellbase.core.common.clinical.Cosmic
COSMIC_DATA - Static variable in class org.opencb.cellbase.lib.EtlCommons
COSMIC_FILE - Static variable in class org.opencb.cellbase.lib.EtlCommons
COSMIC_SOMATICSTATUS_TO_ALLELE_ORIGIN - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
CosmicIndexer - Class in org.opencb.cellbase.lib.builders.clinical.variant: Created by fjlopez on 04/10/16.
CosmicIndexer(Path, boolean, Path, String, RocksDB) - Constructor for class org.opencb.cellbase.lib.builders.clinical.variant.CosmicIndexer
CosmicParser - Class in org.opencb.cellbase.lib.builders.clinical.variant: Deprecated.
CosmicParser(Path, CellBaseSerializer, String) - Constructor for class org.opencb.cellbase.lib.builders.clinical.variant.CosmicParser: Deprecated.
count - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.QueryCommandOptions
count(Query) - Method in class org.opencb.cellbase.client.rest.ParentRestClient
count() - Method in interface org.opencb.cellbase.core.api.CellBaseDBAdaptor
count(Query) - Method in interface org.opencb.cellbase.core.api.CellBaseDBAdaptor
count(Query) - Method in class org.opencb.cellbase.lib.impl.ClinicalLegacyMongoDBAdaptor: Deprecated.
count(Query) - Method in class org.opencb.cellbase.lib.impl.ClinicalMongoDBAdaptor
count(Query) - Method in class org.opencb.cellbase.lib.impl.ConservationMongoDBAdaptor: Deprecated.
count(Query) - Method in class org.opencb.cellbase.lib.impl.GeneMongoDBAdaptor
count(Query) - Method in class org.opencb.cellbase.lib.impl.GenomeMongoDBAdaptor
count(Query) - Method in class org.opencb.cellbase.lib.impl.MetaMongoDBAdaptor
count(Query) - Method in class org.opencb.cellbase.lib.impl.ProteinMongoDBAdaptor
count(Query) - Method in class org.opencb.cellbase.lib.impl.ProteinProteinInteractionMongoDBAdaptor
count(Query) - Method in class org.opencb.cellbase.lib.impl.RegulationMongoDBAdaptor
count(Query) - Method in class org.opencb.cellbase.lib.impl.RepeatsMongoDBAdaptor
count(Query) - Method in class org.opencb.cellbase.lib.impl.TranscriptMongoDBAdaptor
count(Query) - Method in class org.opencb.cellbase.lib.impl.VariantMongoDBAdaptor
count(Query) - Method in class org.opencb.cellbase.lib.impl.XRefMongoDBAdaptor
count() - Method in class org.opencb.cellbase.server.rest.feature.GeneWSServer
count(String, String, String) - Method in class org.opencb.cellbase.server.rest.feature.TranscriptWSServer
count() - Method in class org.opencb.cellbase.server.rest.feature.VariationWSServer
count - Variable in class org.opencb.cellbase.server.rest.GenericRestWSServer
count() - Method in interface org.opencb.cellbase.server.rest.IWSServer
countFileLines(Path) - Static method in class org.opencb.cellbase.lib.EtlCommons
createBufferedReader() - Method in class org.opencb.cellbase.lib.builders.variation.AbstractVariationFile
createErrorResponse(Exception) - Method in class org.opencb.cellbase.server.rest.GenericRestWSServer
createErrorResponse(String, String) - Method in class org.opencb.cellbase.server.rest.GenericRestWSServer
createGeneGenomicFeature(String) - Method in class org.opencb.cellbase.lib.builders.clinical.variant.ClinicalIndexer
createIndex(String) - Method in class org.opencb.cellbase.core.loader.CellBaseLoader
createIndex(String) - Method in class org.opencb.cellbase.lib.loader.MongoDBCellBaseLoader: Deprecated.
createJsonResponse(CellBaseDataResponse) - Method in class org.opencb.cellbase.server.rest.GenericRestWSServer
createModelResponse(Class) - Method in class org.opencb.cellbase.server.rest.GenericRestWSServer
createMongoDBIndexes(String, String, String, boolean) - Method in class org.opencb.cellbase.lib.indexer.IndexManager: Create indexes.
createMongoDBIndexes(String, String, boolean) - Method in class org.opencb.cellbase.lib.indexer.IndexManager: Create indexes for specified collection.
createOkResponse(Object) - Method in class org.opencb.cellbase.server.rest.AdminRestWebService
createOkResponse(Object) - Method in class org.opencb.cellbase.server.rest.GenericRestWSServer
createOkResponse(Object, MediaType) - Method in class org.opencb.cellbase.server.rest.GenericRestWSServer
createOkResponse(Object, MediaType, String) - Method in class org.opencb.cellbase.server.rest.GenericRestWSServer
createOrQuery(Query, String, String, List<Bson>) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptor
createOrQuery(Query, String, String, List<Bson>, MongoDBAdaptor.QueryValueType) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptor
createOrQuery(List<T>, String, List<Bson>) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptor
createQueries(String, String, String...) - Method in class org.opencb.cellbase.server.rest.GenericRestWSServer
createRegionQuery(Query, String, List<Bson>) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptor
createRegionQuery(Query, String, int, List<Bson>) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptor
createSQLiteRegulatoryFiles(Path) - Method in class org.opencb.cellbase.lib.builders.RegulatoryRegionParser
createSQLiteRegulatoryFiles(Path, String, List<String>, List<String>) - Method in class org.opencb.cellbase.lib.builders.RegulatoryRegionParser
createStringResponse(String) - Method in class org.opencb.cellbase.server.rest.GenericRestWSServer
CustomAnnotationPhasedQueryManager - Class in org.opencb.cellbase.core.variant
CustomAnnotationPhasedQueryManager() - Constructor for class org.opencb.cellbase.core.variant.CustomAnnotationPhasedQueryManager
CustomAnnotationVariantIndexer - Class in org.opencb.cellbase.app.cli.main.annotation.indexers
CustomAnnotationVariantIndexer(VariantReader, int, List<String>) - Constructor for class org.opencb.cellbase.app.cli.main.annotation.indexers.CustomAnnotationVariantIndexer
CustomAnnotationVariantIndexer(VariantReader, int, boolean, List<String>) - Constructor for class org.opencb.cellbase.app.cli.main.annotation.indexers.CustomAnnotationVariantIndexer
customFileFields - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.VariantAnnotationCommandOptions
customFileIds - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.VariantAnnotationCommandOptions
customFiles - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.VariantAnnotationCommandOptions

D

data - Variable in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.BuildCommandOptions
data - Variable in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.DownloadCommandOptions
data - Variable in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.IndexCommandOptions
data - Variable in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.LoadCommandOptions
data - Variable in class org.opencb.cellbase.core.loader.CellBaseLoader
database - Variable in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.LoadCommandOptions
database - Variable in class org.opencb.cellbase.core.loader.CellBaseLoader
DatabaseCredentials - Class in org.opencb.cellbase.core.config: Created by imedina on 19/08/16.
DatabaseCredentials() - Constructor for class org.opencb.cellbase.core.config.DatabaseCredentials
DatabaseCredentials(String, String, String, Map<String, String>) - Constructor for class org.opencb.cellbase.core.config.DatabaseCredentials
Databases - Class in org.opencb.cellbase.core.config: Created by imedina on 16/09/16.
Databases() - Constructor for class org.opencb.cellbase.core.config.Databases
Databases(MongoDBDatabaseCredentials, Map<String, DatabaseCredentials>) - Constructor for class org.opencb.cellbase.core.config.Databases
DatastoreDependenciesStatus() - Constructor for class org.opencb.cellbase.core.monitor.HealthStatus.ApplicationDetails.DependenciesStatus.DatastoreDependenciesStatus
DatastoreStatus() - Constructor for class org.opencb.cellbase.core.monitor.HealthStatus.ApplicationDetails.DependenciesStatus.DatastoreDependenciesStatus.DatastoreStatus
DBAdaptorFactory - Class in org.opencb.cellbase.core.api
DBAdaptorFactory() - Constructor for class org.opencb.cellbase.core.api.DBAdaptorFactory
DBAdaptorFactory(CellBaseConfiguration) - Constructor for class org.opencb.cellbase.core.api.DBAdaptorFactory
dbAdaptorFactory - Variable in class org.opencb.cellbase.server.rest.GenericRestWSServer: DBAdaptorFactory creation, this object can be initialize with an HibernateDBAdaptorFactory or an HBaseDBAdaptorFactory.
dbIndex - Variable in class org.opencb.cellbase.app.cli.main.annotation.indexers.VariantIndexer
DBSNP_FILE - Static variable in class org.opencb.cellbase.lib.EtlCommons
decideStopCodonModificationAnnotation(Set<String>, String, String, boolean) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
DEFAULT_NUM_THREADS - Static variable in class org.opencb.cellbase.client.rest.ParentRestClient
defaultMethod() - Method in class org.opencb.cellbase.server.rest.feature.GeneWSServer
defaultMethod() - Method in class org.opencb.cellbase.server.rest.feature.IdWSServer
defaultMethod() - Method in class org.opencb.cellbase.server.rest.feature.ProteinWSServer
defaultMethod() - Method in class org.opencb.cellbase.server.rest.feature.TranscriptWSServer
defaultMethod() - Method in class org.opencb.cellbase.server.rest.GenericRestWSServer
defaultMethod() - Method in class org.opencb.cellbase.server.rest.genomic.ChromosomeWSServer
defaultMethod() - Method in class org.opencb.cellbase.server.rest.genomic.RegionWSServer
defaultMethod() - Method in class org.opencb.cellbase.server.rest.genomic.VariantWSServer
defaultMethod() - Method in class org.opencb.cellbase.server.rest.network.PathwayWSServer
defaultMethod() - Method in class org.opencb.cellbase.server.rest.regulatory.MiRnaGeneWSServer
defaultMethod() - Method in class org.opencb.cellbase.server.rest.regulatory.TfWSServer
DependenciesStatus() - Constructor for class org.opencb.cellbase.core.monitor.HealthStatus.ApplicationDetails.DependenciesStatus
description() - Method in enum org.opencb.cellbase.core.api.ClinicalDBAdaptor.QueryParams
description() - Method in enum org.opencb.cellbase.core.api.ConservationDBAdaptor.QueryParams: Deprecated.
description() - Method in enum org.opencb.cellbase.core.api.GeneDBAdaptor.QueryParams
description() - Method in enum org.opencb.cellbase.core.api.GenomeDBAdaptor.QueryParams
description() - Method in enum org.opencb.cellbase.core.api.ProteinDBAdaptor.QueryParams
description() - Method in enum org.opencb.cellbase.core.api.ProteinProteinInteractionDBAdaptor.QueryParams
description() - Method in enum org.opencb.cellbase.core.api.RegulationDBAdaptor.QueryParams
description() - Method in enum org.opencb.cellbase.core.api.RepeatsDBAdaptor.QueryParams
description() - Method in enum org.opencb.cellbase.core.api.TranscriptDBAdaptor.QueryParams
description() - Method in enum org.opencb.cellbase.core.api.VariantDBAdaptor.QueryParams
description() - Method in enum org.opencb.cellbase.core.api.XRefDBAdaptor.QueryParams
deserialize(JsonParser, DeserializationContext) - Method in class org.opencb.cellbase.client.rest.models.mixin.DrugResponseClassificationMixIn.Deserializer
deserialize(String) - Method in class org.opencb.cellbase.core.serializer.CellBaseJsonFileSerializer
Deserializer() - Constructor for class org.opencb.cellbase.client.rest.models.mixin.DrugResponseClassificationMixIn.Deserializer
destroy() - Method in class org.opencb.cellbase.server.rest.CORSFilter
DGV_FILE - Static variable in class org.opencb.cellbase.lib.EtlCommons
DGV_VERSION_FILE - Static variable in class org.opencb.cellbase.lib.EtlCommons
DgvParser - Class in org.opencb.cellbase.lib.builders: Created by fjlopez on 08/05/17.
DgvParser(Path, CellBaseSerializer) - Constructor for class org.opencb.cellbase.lib.builders.DgvParser
disconnect() - Method in class org.opencb.cellbase.lib.builders.CellBaseParser
Disgenet - Class in org.opencb.cellbase.core.common.genedisease: Deprecated.
Disgenet(String, String, List<Disease>) - Constructor for class org.opencb.cellbase.core.common.genedisease.Disgenet: Deprecated.
DISGENET_DATA - Static variable in class org.opencb.cellbase.lib.EtlCommons
DisgenetParser - Class in org.opencb.cellbase.lib.builders: Deprecated.
DisgenetParser(Path, CellBaseSerializer) - Constructor for class org.opencb.cellbase.lib.builders.DisgenetParser: Deprecated.
distinct - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.QueryCommandOptions
distinct(String) - Method in interface org.opencb.cellbase.core.api.CellBaseDBAdaptor
distinct(Query, String) - Method in interface org.opencb.cellbase.core.api.CellBaseDBAdaptor
distinct(Query, String) - Method in class org.opencb.cellbase.lib.impl.ClinicalLegacyMongoDBAdaptor: Deprecated.
distinct(Query, String) - Method in class org.opencb.cellbase.lib.impl.ClinicalMongoDBAdaptor
distinct(Query, String) - Method in class org.opencb.cellbase.lib.impl.ConservationMongoDBAdaptor: Deprecated.
distinct(Query, String) - Method in class org.opencb.cellbase.lib.impl.GeneMongoDBAdaptor
distinct(Query, String) - Method in class org.opencb.cellbase.lib.impl.GenomeMongoDBAdaptor
distinct(Query, String) - Method in class org.opencb.cellbase.lib.impl.MetaMongoDBAdaptor
distinct(Query, String) - Method in class org.opencb.cellbase.lib.impl.ProteinMongoDBAdaptor
distinct(Query, String) - Method in class org.opencb.cellbase.lib.impl.ProteinProteinInteractionMongoDBAdaptor
distinct(Query, String) - Method in class org.opencb.cellbase.lib.impl.RegulationMongoDBAdaptor
distinct(Query, String) - Method in class org.opencb.cellbase.lib.impl.RepeatsMongoDBAdaptor
distinct(Query, String) - Method in class org.opencb.cellbase.lib.impl.TranscriptMongoDBAdaptor
distinct(Query, String) - Method in class org.opencb.cellbase.lib.impl.VariantMongoDBAdaptor
distinct(Query, String) - Method in class org.opencb.cellbase.lib.impl.XRefMongoDBAdaptor
DNASequenceUtils - Class in org.opencb.cellbase.core.common
DNASequenceUtils() - Constructor for class org.opencb.cellbase.core.common.DNASequenceUtils
DOCM_DATA - Static variable in class org.opencb.cellbase.lib.EtlCommons
DOCM_FILE - Static variable in class org.opencb.cellbase.lib.EtlCommons
DOCM_NAME - Static variable in class org.opencb.cellbase.lib.EtlCommons
DOCMIndexer - Class in org.opencb.cellbase.lib.builders.clinical.variant: Created by fjlopez on 29/03/17.
DOCMIndexer(Path, boolean, Path, String, RocksDB) - Constructor for class org.opencb.cellbase.lib.builders.clinical.variant.DOCMIndexer
doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class org.opencb.cellbase.server.rest.CORSFilter
DotServer - Class in org.opencb.cellbase.server.rest.network
DotServer() - Constructor for class org.opencb.cellbase.server.rest.network.DotServer
DotServer(String) - Constructor for class org.opencb.cellbase.server.rest.network.DotServer
DOWN_UP_STREAM_GENE_TAG - Static variable in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
downloadCaddScores() - Method in class org.opencb.cellbase.lib.download.DownloadManager
downloadClinical() - Method in class org.opencb.cellbase.lib.download.DownloadManager
DownloadCommandExecutor - Class in org.opencb.cellbase.app.cli.admin.executors: Created by imedina on 03/02/15.
DownloadCommandExecutor(AdminCliOptionsParser.DownloadCommandOptions) - Constructor for class org.opencb.cellbase.app.cli.admin.executors.DownloadCommandExecutor
DownloadCommandOptions() - Constructor for class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.DownloadCommandOptions
downloadConservation() - Method in class org.opencb.cellbase.lib.download.DownloadManager: This method downloads bith PhastCons and PhyloP data from UCSC for Human and Mouse species.
downloadEnsemblGene() - Method in class org.opencb.cellbase.lib.download.DownloadManager
DownloadFile - Class in org.opencb.cellbase.lib.download
DownloadFile(String, String, String) - Constructor for class org.opencb.cellbase.lib.download.DownloadFile
DownloadManager - Class in org.opencb.cellbase.lib.download
DownloadManager(CellBaseConfiguration, Path, SpeciesConfiguration, SpeciesConfiguration.Assembly) - Constructor for class org.opencb.cellbase.lib.download.DownloadManager
DownloadProperties - Class in org.opencb.cellbase.core.config: Created by imedina on 19/08/16.
DownloadProperties() - Constructor for class org.opencb.cellbase.core.config.DownloadProperties
DownloadProperties.EnsemblProperties - Class in org.opencb.cellbase.core.config
DownloadProperties.URLProperties - Class in org.opencb.cellbase.core.config
downloadProtein() - Method in class org.opencb.cellbase.lib.download.DownloadManager: This method downloads UniProt, IntAct and Interpro data from EMBL-EBI.
downloadReferenceGenome() - Method in class org.opencb.cellbase.lib.download.DownloadManager
downloadRegulation() - Method in class org.opencb.cellbase.lib.download.DownloadManager
downloadRepeats() - Method in class org.opencb.cellbase.lib.download.DownloadManager
downloadStructuralVariants() - Method in class org.opencb.cellbase.lib.download.DownloadManager
downloadVariation() - Method in class org.opencb.cellbase.lib.download.DownloadManager
DOWNSTREAM_GENE_VARIANT - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
drain() - Method in class org.opencb.cellbase.app.cli.main.annotation.VcfStringAnnotatorTask: Deprecated.
dropIndexesFirst - Variable in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.IndexCommandOptions
Drug - Class in org.opencb.cellbase.core.common.drug: Created with IntelliJ IDEA.
Drug() - Constructor for class org.opencb.cellbase.core.common.drug.Drug
DRUG_DATA - Static variable in class org.opencb.cellbase.lib.EtlCommons
DrugParser - Class in org.opencb.cellbase.lib.builders: Deprecated.
DrugParser(Path, CellBaseSerializer) - Constructor for class org.opencb.cellbase.lib.builders.DrugParser: Deprecated.
DrugPartnerInteraction - Class in org.opencb.cellbase.core.common.drug: Created with IntelliJ IDEA.
DrugPartnerInteraction() - Constructor for class org.opencb.cellbase.core.common.drug.DrugPartnerInteraction
DrugResponseClassificationMixIn - Interface in org.opencb.cellbase.client.rest.models.mixin: Created on 07/01/19.
DrugResponseClassificationMixIn.Deserializer - Class in org.opencb.cellbase.client.rest.models.mixin

E

EFO_ID - Static variable in class org.opencb.cellbase.lib.builders.clinical.variant.ClinVarParser: Deprecated.
EFO_NAME - Static variable in class org.opencb.cellbase.lib.builders.clinical.variant.ClinVarParser: Deprecated.
EFO_URL - Static variable in class org.opencb.cellbase.lib.builders.clinical.variant.ClinVarParser: Deprecated.
EMPTY_STRING - Static variable in class org.opencb.cellbase.client.rest.ParentRestClient
EnsemblInfo - Class in org.opencb.cellbase.lib.download
EnsemblInfo(String, String, String) - Constructor for class org.opencb.cellbase.lib.download.EnsemblInfo
EnsemblProperties() - Constructor for class org.opencb.cellbase.core.config.DownloadProperties.EnsemblProperties
equals(Object) - Method in class org.opencb.cellbase.app.cli.main.annotation.SequenceOntologyTermComparisonObject
equals(Object) - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasStudy
equals(Object) - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasTrait
equals(Object) - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.CdnaCoord
EtlCommons - Class in org.opencb.cellbase.lib: Created by fjlopez on 03/06/16.
EtlCommons() - Constructor for class org.opencb.cellbase.lib.EtlCommons
exclude - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.QueryCommandOptions
exclude - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.VariantAnnotationCommandOptions
exclude - Variable in class org.opencb.cellbase.server.rest.GenericRestWSServer
execute() - Method in class org.opencb.cellbase.app.cli.admin.executors.BuildCommandExecutor: Parse specific 'build' command options.
execute() - Method in class org.opencb.cellbase.app.cli.admin.executors.DownloadCommandExecutor: Execute specific 'download' command options.
execute() - Method in class org.opencb.cellbase.app.cli.admin.executors.IndexCommandExecutor
execute() - Method in class org.opencb.cellbase.app.cli.admin.executors.InstallCommandExecutor
execute() - Method in class org.opencb.cellbase.app.cli.admin.executors.LoadCommandExecutor: Parse specific 'data' command options.
execute() - Method in class org.opencb.cellbase.app.cli.admin.executors.ServerCommandExecutor
execute() - Method in class org.opencb.cellbase.app.cli.CommandExecutor
execute() - Method in class org.opencb.cellbase.app.cli.main.executors.QueryCommandExecutor
execute() - Method in class org.opencb.cellbase.app.cli.main.executors.VariantAnnotationCommandExecutor
execute(String, Query, QueryOptions, Class) - Method in class org.opencb.cellbase.client.rest.ParentRestClient
execute(String, Query, QueryOptions, Class, boolean) - Method in class org.opencb.cellbase.client.rest.ParentRestClient
execute(String, String, QueryOptions, Class) - Method in class org.opencb.cellbase.client.rest.ParentRestClient
execute(String, String, QueryOptions, Class, boolean) - Method in class org.opencb.cellbase.client.rest.ParentRestClient
execute(List<String>, String, QueryOptions, Class) - Method in class org.opencb.cellbase.client.rest.ParentRestClient
execute(List<String>, String, QueryOptions, Class, boolean) - Method in class org.opencb.cellbase.client.rest.ParentRestClient
executeAggregation2(Object, List<Bson>, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptor
executeAggregationist2(List<? extends Object>, List<List<Bson>>, QueryOptions, MongoDBCollection) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptor
executeAggregationList2(List<? extends Object>, List<List<Bson>>, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptor
executeDistinct(Object, String, Document) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptor
executeQuery(Object, Document, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptor
executeQuery(Object, Document, QueryOptions, MongoDBCollection) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptor
executeQueryList2(List<? extends Object>, List<Document>, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptor
executeQueryList2(List<? extends Object>, List<Document>, QueryOptions, MongoDBCollection) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptor
existsZippedOrUnzippedFile(String) - Method in class org.opencb.cellbase.lib.builders.variation.AbstractVariationFile
existsZippedOrUnzippedFile() - Method in class org.opencb.cellbase.lib.builders.variation.AbstractVariationFile

F

FEATURE_TRUNCATION - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
FEATURE_VARIANT - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
FeatureClient<T> - Class in org.opencb.cellbase.client.rest: Created by swaathi on 20/05/16.
FeatureClient(String, String, ClientConfiguration) - Constructor for class org.opencb.cellbase.client.rest.FeatureClient
FeatureDBAdaptor<T> - Interface in org.opencb.cellbase.core.api: Created by imedina on 25/11/15.
field - Variable in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.LoadCommandOptions
field - Variable in class org.opencb.cellbase.core.loader.CellBaseLoader
fileReader - Variable in class org.opencb.cellbase.lib.builders.variation.AbstractVariationFile
first() - Method in class org.opencb.cellbase.client.rest.ParentRestClient
first() - Method in interface org.opencb.cellbase.core.api.FeatureDBAdaptor
first(QueryOptions) - Method in interface org.opencb.cellbase.core.api.FeatureDBAdaptor
first() - Method in class org.opencb.cellbase.core.CellBaseDataResponse: This method just returns the first DataResult of response, or null if response is null or empty.
first() - Method in class org.opencb.cellbase.server.rest.feature.GeneWSServer
first() - Method in class org.opencb.cellbase.server.rest.feature.TranscriptWSServer
first() - Method in class org.opencb.cellbase.server.rest.feature.VariationWSServer
first() - Method in interface org.opencb.cellbase.server.rest.IWSServer
firstResult() - Method in class org.opencb.cellbase.core.CellBaseDataResponse: This method returns the first result from the first DataResult of response, this is equivalent to response.get(0).getResult.get(0).
FIVE_PRIME_UTR_VARIANT - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
flexibleGTFParsing - Variable in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.BuildCommandOptions
forEach(Consumer) - Method in interface org.opencb.cellbase.core.api.CellBaseDBAdaptor
forEach(Query, Consumer<? super Object>, QueryOptions) - Method in interface org.opencb.cellbase.core.api.CellBaseDBAdaptor
forEach(Query, Consumer<? super Object>, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ClinicalLegacyMongoDBAdaptor: Deprecated.
forEach(Query, Consumer<? super Object>, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ClinicalMongoDBAdaptor
forEach(Query, Consumer, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ConservationMongoDBAdaptor: Deprecated.
forEach(Query, Consumer<? super Object>, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.GeneMongoDBAdaptor
forEach(Query, Consumer, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.GenomeMongoDBAdaptor
forEach(Query, Consumer, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.MetaMongoDBAdaptor
forEach(Query, Consumer<? super Object>, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ProteinMongoDBAdaptor
forEach(Query, Consumer<? super Object>, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ProteinProteinInteractionMongoDBAdaptor
forEach(Query, Consumer<? super Object>, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.RegulationMongoDBAdaptor
forEach(Query, Consumer, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.RepeatsMongoDBAdaptor
forEach(Query, Consumer, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.TranscriptMongoDBAdaptor
forEach(Query, Consumer<? super Object>, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.VariantMongoDBAdaptor
forEach(Query, Consumer<? super Object>, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.XRefMongoDBAdaptor
forEachRemaining(Consumer<? super Variant>) - Method in class org.opencb.cellbase.lib.VariantMongoIterator
format() - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsStringBuilder: Generate a HGVS string.
FRAMESHIFT_VARIANT - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils

G

gene - Variable in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
GENE_CHUNK_SIZE - Static variable in class org.opencb.cellbase.lib.MongoDBCollectionConfiguration
GENE_DATA - Static variable in class org.opencb.cellbase.lib.EtlCommons
GENE_DISEASE_ASSOCIATION_DATA - Static variable in class org.opencb.cellbase.lib.EtlCommons
GeneClient - Class in org.opencb.cellbase.client.rest: Created by imedina on 12/05/16.
GeneClient(String, String, ClientConfiguration) - Constructor for class org.opencb.cellbase.client.rest.GeneClient
GeneConverter - Class in org.opencb.cellbase.lib.loader.converters: Deprecated.
GeneConverter() - Constructor for class org.opencb.cellbase.lib.loader.converters.GeneConverter: Deprecated.
GeneConverter(int) - Constructor for class org.opencb.cellbase.lib.loader.converters.GeneConverter: Deprecated.
GeneDBAdaptor<T> - Interface in org.opencb.cellbase.core.api: Created by imedina on 25/11/15.
GeneDBAdaptor.QueryParams - Enum in org.opencb.cellbase.core.api
GeneExpressionAtlas - Class in org.opencb.cellbase.lib.builders.formats: Created by antonior on 10/16/14.
GeneExpressionAtlas(String, String, List<GeneExpressionAtlas.Tissue>) - Constructor for class org.opencb.cellbase.lib.builders.formats.GeneExpressionAtlas
GeneExpressionAtlas.Tissue - Class in org.opencb.cellbase.lib.builders.formats
GeneExpressionAtlasParser - Class in org.opencb.cellbase.lib.builders: Created by antonior on 10/16/14.
GeneExpressionAtlasParser(Path, CellBaseSerializer) - Constructor for class org.opencb.cellbase.lib.builders.GeneExpressionAtlasParser
GeneMongoDBAdaptor - Class in org.opencb.cellbase.lib.impl: Created by imedina on 25/11/15.
GeneMongoDBAdaptor(String, String, MongoDataStore) - Constructor for class org.opencb.cellbase.lib.impl.GeneMongoDBAdaptor
GeneParser - Class in org.opencb.cellbase.lib.builders
GeneParser(Path, Path, SpeciesConfiguration, CellBaseSerializer) - Constructor for class org.opencb.cellbase.lib.builders.GeneParser
GeneParser(Path, Path, SpeciesConfiguration, boolean, CellBaseSerializer) - Constructor for class org.opencb.cellbase.lib.builders.GeneParser
GeneParser(Path, Path, Path, Path, Path, Path, Path, Path, Path, Path, Path, SpeciesConfiguration, boolean, CellBaseSerializer) - Constructor for class org.opencb.cellbase.lib.builders.GeneParser
GeneParserUtils - Class in org.opencb.cellbase.lib.builders: Created by imedina on 12/11/15.
GeneParserUtils() - Constructor for class org.opencb.cellbase.lib.builders.GeneParserUtils
generalOptions - Variable in class org.opencb.cellbase.app.cli.CliOptionsParser
GeneralOptions() - Constructor for class org.opencb.cellbase.app.cli.CliOptionsParser.GeneralOptions
generateResponse(String, List) - Method in class org.opencb.cellbase.server.rest.GenericRestWSServer: Deprecated.
generateResponse(String, String, List) - Method in class org.opencb.cellbase.server.rest.GenericRestWSServer: Deprecated.
GenericClient - Class in org.opencb.cellbase.client.rest: Created by fjlopez on 07/07/17.
GenericClient(String, String, ClientConfiguration) - Constructor for class org.opencb.cellbase.client.rest.GenericClient
GenericRestWSServer - Class in org.opencb.cellbase.server.rest
GenericRestWSServer(String, UriInfo, HttpServletRequest) - Constructor for class org.opencb.cellbase.server.rest.GenericRestWSServer
GenericRestWSServer(String, String, UriInfo, HttpServletRequest) - Constructor for class org.opencb.cellbase.server.rest.GenericRestWSServer
GeneWSServer - Class in org.opencb.cellbase.server.rest.feature
GeneWSServer(String, String, UriInfo, HttpServletRequest) - Constructor for class org.opencb.cellbase.server.rest.feature.GeneWSServer
GENOME_DATA - Static variable in class org.opencb.cellbase.lib.EtlCommons
GENOME_INFO_DATA - Static variable in class org.opencb.cellbase.lib.EtlCommons
GENOME_SEQUENCE_CHUNK_SIZE - Static variable in class org.opencb.cellbase.lib.MongoDBCollectionConfiguration
GenomeDBAdaptor - Interface in org.opencb.cellbase.core.api: Created by imedina on 30/11/15.
genomeDBAdaptor - Variable in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
genomeDBAdaptor - Variable in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsCalculator
GenomeDBAdaptor.QueryParams - Enum in org.opencb.cellbase.core.api
GenomeMongoDBAdaptor - Class in org.opencb.cellbase.lib.impl: Created by imedina on 07/12/15.
GenomeMongoDBAdaptor(String, String, MongoDataStore) - Constructor for class org.opencb.cellbase.lib.impl.GenomeMongoDBAdaptor
GenomeSequenceFastaParser - Class in org.opencb.cellbase.lib.builders
GenomeSequenceFastaParser(Path, CellBaseSerializer) - Constructor for class org.opencb.cellbase.lib.builders.GenomeSequenceFastaParser
genomeSequenceFilePath - Variable in class org.opencb.cellbase.lib.builders.clinical.variant.ClinicalIndexer
GenomeSequenceUtils - Class in org.opencb.cellbase.lib.builders.utils: Created with IntelliJ IDEA.
GenomeSequenceUtils() - Constructor for class org.opencb.cellbase.lib.builders.utils.GenomeSequenceUtils
GenomicRegionClient - Class in org.opencb.cellbase.client.rest: Created by imedina on 26/05/16.
GenomicRegionClient(String, String, ClientConfiguration) - Constructor for class org.opencb.cellbase.client.rest.GenomicRegionClient
genomicToCdnaCoord(Transcript, int) - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsCalculator
GENOTYPE_TAG - Static variable in class org.opencb.cellbase.core.variant.PhasedQueryManager
GERP_FILE - Static variable in class org.opencb.cellbase.lib.EtlCommons
GERP_SUBDIRECTORY - Static variable in class org.opencb.cellbase.lib.EtlCommons
get(String, String, QueryOptions, Class<T>) - Method in class org.opencb.cellbase.client.rest.GenericClient
get(String, String, String, String, QueryOptions, Class<T>) - Method in class org.opencb.cellbase.client.rest.GenericClient
get(List<String>, QueryOptions) - Method in class org.opencb.cellbase.client.rest.ParentRestClient
get(Query, QueryOptions) - Method in interface org.opencb.cellbase.core.api.CellBaseDBAdaptor
get(List<Query>, QueryOptions) - Method in interface org.opencb.cellbase.core.api.CellBaseDBAdaptor
get() - Static method in class org.opencb.cellbase.core.common.GitRepositoryState
get(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ClinicalLegacyMongoDBAdaptor: Deprecated.
get(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ClinicalMongoDBAdaptor
get(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ConservationMongoDBAdaptor: Deprecated.
get(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.GeneMongoDBAdaptor
get(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.GenomeMongoDBAdaptor
get(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.MetaMongoDBAdaptor
get(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ProteinMongoDBAdaptor
get(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ProteinProteinInteractionMongoDBAdaptor
get(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.RegulationMongoDBAdaptor
get(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.RepeatsMongoDBAdaptor
get(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.TranscriptMongoDBAdaptor
get(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.VariantMongoDBAdaptor
get(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.XRefMongoDBAdaptor
get_id() - Method in class org.opencb.cellbase.client.rest.models.GroupByFields
get_id() - Method in class org.opencb.cellbase.client.rest.models.GroupCount
getAbout() - Method in class org.opencb.cellbase.server.rest.MetaWSServer
getAbsolute() - Method in class org.opencb.cellbase.core.common.IntervalFeatureFrequency
getAbsorption() - Method in class org.opencb.cellbase.core.common.drug.Drug
getAccession() - Method in class org.opencb.cellbase.app.cli.main.annotation.SequenceOntologyTermComparisonObject
getAccession() - Method in class org.opencb.cellbase.core.common.regulatory.Pwm
getAccessionNumber() - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
getAction() - Method in class org.opencb.cellbase.core.common.drug.DrugPartnerInteraction
getActualFileSize() - Method in class org.opencb.cellbase.lib.download.DownloadFile
getAge() - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
getAll() - Method in class org.opencb.cellbase.server.rest.clinical.ClinicalWSServer
getAll() - Method in class org.opencb.cellbase.server.rest.feature.ClinicalLegacyWSServer: Deprecated.
getAll() - Method in class org.opencb.cellbase.server.rest.feature.GeneWSServer
getAll() - Method in class org.opencb.cellbase.server.rest.feature.ProteinWSServer
getAll() - Method in class org.opencb.cellbase.server.rest.feature.TranscriptWSServer
getAll() - Method in class org.opencb.cellbase.server.rest.regulatory.RegulatoryWSServer
getAllBiotypes() - Method in class org.opencb.cellbase.server.rest.feature.GeneWSServer
getAllByRegionList(List<Region>, QueryOptions) - Method in interface org.opencb.cellbase.core.api.ConservationDBAdaptor: Deprecated.
getAllByRegionList(List, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ConservationMongoDBAdaptor: Deprecated.
getAllByTfbs(String, String) - Method in class org.opencb.cellbase.server.rest.regulatory.TfWSServer
getAllClinicalSignificances() - Method in class org.opencb.cellbase.server.rest.feature.ClinicalLegacyWSServer: Deprecated.
getAllClinvarByGene(String) - Method in class org.opencb.cellbase.server.rest.feature.GeneWSServer: Deprecated.
getAllConsequenceTypes(Query) - Method in class org.opencb.cellbase.client.rest.VariationClient
getAllConsequenceTypes() - Method in class org.opencb.cellbase.server.rest.feature.VariationWSServer
getAllConsequenceTypesByVariant(Variant, QueryOptions) - Method in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationCalculator: Deprecated.
getAlleleOriginLabels() - Method in interface org.opencb.cellbase.core.api.ClinicalDBAdaptor
getAlleleOriginLabels() - Method in class org.opencb.cellbase.lib.impl.ClinicalLegacyMongoDBAdaptor: Deprecated.
getAlleleOriginLabels() - Method in class org.opencb.cellbase.lib.impl.ClinicalMongoDBAdaptor
getAlleleOriginLabels() - Method in class org.opencb.cellbase.server.rest.clinical.ClinicalWSServer
getAlleleOriginList(List<String>) - Method in class org.opencb.cellbase.lib.builders.clinical.variant.ClinicalIndexer
getAllIDs() - Method in class org.opencb.cellbase.server.rest.feature.GeneWSServer
getAllPPI(String, String, String, String, String) - Method in class org.opencb.cellbase.server.rest.network.ProteinProteinInteractionWSServer
getAllRegulatoryElements(String, boolean) - Method in class org.opencb.cellbase.server.rest.feature.GeneWSServer
getAllScoresByRegionList(List<Region>, QueryOptions) - Method in interface org.opencb.cellbase.core.api.ConservationDBAdaptor: Deprecated.
getAllScoresByRegionList(List, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ConservationMongoDBAdaptor: Deprecated.
getAllSpecies() - Method in class org.opencb.cellbase.core.config.CellBaseConfiguration
getAllTfbs(String, boolean) - Method in class org.opencb.cellbase.server.rest.feature.GeneWSServer
getAllXrefsByFeatureId(String, String) - Method in class org.opencb.cellbase.server.rest.feature.IdWSServer
getAlternate() - Method in class org.opencb.cellbase.core.common.clinical.ClinicalVariant
getAlternate() - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsStringBuilder
getAlternate() - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
getAlternate() - Method in class org.opencb.cellbase.lib.model.ClinicalVariation: Deprecated.
getAminoacid(boolean, String) - Static method in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
getAnnotatedFeaturesFields(String) - Static method in class org.opencb.cellbase.lib.builders.RegulatoryRegionParser: Deprecated.
getAnnotation(List<Variant>, QueryOptions) - Method in class org.opencb.cellbase.client.rest.VariantClient
getAnnotation(List<Variant>, QueryOptions, boolean) - Method in class org.opencb.cellbase.client.rest.VariantClient
getAnnotationByVariant(Variant, QueryOptions) - Method in interface org.opencb.cellbase.core.api.VariantAnnotationDBAdaptor: Deprecated.
getAnnotationByVariant(Variant, QueryOptions) - Method in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationCalculator
getAnnotationByVariantIds(String, QueryOptions) - Method in class org.opencb.cellbase.client.rest.VariantClient: Deprecated.
getAnnotationByVariantIds(String, QueryOptions, boolean) - Method in class org.opencb.cellbase.client.rest.VariantClient: Deprecated.
getAnnotationByVariantIds(List<String>, QueryOptions) - Method in class org.opencb.cellbase.client.rest.VariantClient
getAnnotationByVariantIds(List<String>, QueryOptions, boolean) - Method in class org.opencb.cellbase.client.rest.VariantClient
getAnnotationByVariantList(List<Variant>, QueryOptions) - Method in interface org.opencb.cellbase.core.api.VariantAnnotationDBAdaptor: Deprecated.
getAnnotationByVariantList(List<Variant>, QueryOptions) - Method in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationCalculator
getAnnotationByVariantsGET(String, Boolean, Boolean, Boolean, Boolean, Boolean, Integer, Integer) - Method in class org.opencb.cellbase.server.rest.genomic.VariantWSServer
getAnnotationByVariantsPOST(String, Boolean, Boolean, Boolean, Boolean, Boolean, Integer, Integer) - Method in class org.opencb.cellbase.server.rest.genomic.VariantWSServer
getAnnotationObjectList(Variant) - Method in class org.opencb.cellbase.core.variant.AnnotationBasedPhasedQueryManager
getAnnotationObjectList(Variant) - Method in class org.opencb.cellbase.core.variant.ClinicalPhasedQueryManager
getAnnotationObjectList(Variant) - Method in class org.opencb.cellbase.core.variant.PopulationFrequencyPhasedQueryManager
getAPIVersion() - Method in class org.opencb.cellbase.app.cli.CliOptionsParser: Deprecated.
getApiVersion() - Method in class org.opencb.cellbase.core.CellBaseDataResponse
getApiVersion() - Method in class org.opencb.cellbase.core.config.CellBaseConfiguration
getApplication() - Method in class org.opencb.cellbase.core.monitor.HealthStatus
getApplicationTier() - Method in class org.opencb.cellbase.core.monitor.HealthStatus.Service
getAssemblies() - Method in class org.opencb.cellbase.core.config.SpeciesConfiguration
getAssembly(SpeciesConfiguration, String) - Method in class org.opencb.cellbase.core.api.DBAdaptorFactory
getAssembly() - Method in class org.opencb.cellbase.core.common.Species
getAssembly() - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptor
getAssembly(SpeciesConfiguration, String) - Static method in class org.opencb.cellbase.lib.SpeciesUtils: Check given assembly is valid, case insensitve.
getAtcCode() - Method in class org.opencb.cellbase.core.common.drug.Drug
getBacteria() - Method in class org.opencb.cellbase.core.config.SpeciesProperties
getBaseUrl(List<String>, String) - Method in class org.opencb.cellbase.client.rest.GenericClient
getBaseUrl(List<String>, String) - Method in class org.opencb.cellbase.client.rest.MetaClient
getBaseUrl(List<String>, String) - Method in class org.opencb.cellbase.client.rest.ParentRestClient
getBiotypes(Query) - Method in class org.opencb.cellbase.client.rest.GeneClient
getBiotypes(Query) - Method in interface org.opencb.cellbase.core.api.GeneDBAdaptor
getBiotypes(Query) - Method in class org.opencb.cellbase.lib.impl.GeneMongoDBAdaptor
getBranch() - Method in class org.opencb.cellbase.core.common.GitRepositoryState
getBufferedReader(String) - Method in class org.opencb.cellbase.lib.builders.variation.AbstractVariationFile
getBufferedReader() - Method in class org.opencb.cellbase.lib.builders.variation.VariationFile
getBuildCommandOptions() - Method in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser
getBuildHost() - Method in class org.opencb.cellbase.core.common.GitRepositoryState
getBuildTime() - Method in class org.opencb.cellbase.core.common.GitRepositoryState
getBuildUserEmail() - Method in class org.opencb.cellbase.core.common.GitRepositoryState
getBuildUserName() - Method in class org.opencb.cellbase.core.common.GitRepositoryState
getBuildVersion() - Method in class org.opencb.cellbase.core.common.GitRepositoryState
getByContainsQuery(String) - Method in class org.opencb.cellbase.server.rest.feature.IdWSServer
getByEnsemblId(String) - Method in class org.opencb.cellbase.server.rest.feature.GeneWSServer
getByEnsemblId(String) - Method in class org.opencb.cellbase.server.rest.feature.TranscriptWSServer
getByEnsemblId(String) - Method in class org.opencb.cellbase.server.rest.feature.VariationWSServer
getByFeatureIdInfo(String) - Method in class org.opencb.cellbase.server.rest.feature.IdWSServer
getByLikeQuery(String) - Method in class org.opencb.cellbase.server.rest.feature.IdWSServer
getByRegion(Region, QueryOptions) - Method in interface org.opencb.cellbase.core.api.FeatureDBAdaptor
getByRegion(List<Region>, QueryOptions) - Method in interface org.opencb.cellbase.core.api.FeatureDBAdaptor
getByVariant(Variant, QueryOptions) - Method in interface org.opencb.cellbase.core.api.FeatureDBAdaptor
getByVariant(List<Variant>, QueryOptions) - Method in interface org.opencb.cellbase.core.api.FeatureDBAdaptor
getByVariant(Variant, QueryOptions) - Method in interface org.opencb.cellbase.core.api.VariantDBAdaptor
getByVariant(List<Variant>, QueryOptions) - Method in interface org.opencb.cellbase.core.api.VariantDBAdaptor
getByVariant(List<Variant>, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ClinicalMongoDBAdaptor
getCadd() - Method in class org.opencb.cellbase.core.config.DownloadProperties
getCaddScoreByVariant(String) - Method in class org.opencb.cellbase.server.rest.genomic.VariantWSServer
getCaddValues() - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
getCategory() - Method in class org.opencb.cellbase.core.common.drug.Drug
getCategory(String) - Method in class org.opencb.cellbase.server.rest.MetaWSServer
getCdna(String) - Method in interface org.opencb.cellbase.core.api.TranscriptDBAdaptor
getCdna(List<String>) - Method in interface org.opencb.cellbase.core.api.TranscriptDBAdaptor
getCdna(String) - Method in class org.opencb.cellbase.lib.impl.TranscriptMongoDBAdaptor
getCdnaEnd() - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsStringBuilder
getCdnaStart() - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsStringBuilder
getCellBaseConfiguration() - Method in class org.opencb.cellbase.core.api.DBAdaptorFactory
getCellType() - Method in class org.opencb.cellbase.core.common.regulatory.RegulatoryRegion
getCellType() - Method in class org.opencb.cellbase.core.common.regulatory.Tfbs
getCellTypeDescription() - Method in class org.opencb.cellbase.core.common.regulatory.RegulatoryRegion
getCellularLocation() - Method in class org.opencb.cellbase.core.common.drug.Partner
getChromosome() - Method in class org.opencb.cellbase.core.common.clinical.ClinicalVariant
getChromosome() - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
getChromosome() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaTarget
getChromosome() - Method in class org.opencb.cellbase.core.common.regulatory.RegulatoryRegion
getChromosome() - Method in class org.opencb.cellbase.core.common.regulatory.Tfbs
getChromosome() - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsStringBuilder
getChromosome() - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
getChromosome() - Method in class org.opencb.cellbase.lib.builders.formats.ConservedRegionFeature: Deprecated.
getChromosome() - Method in class org.opencb.cellbase.lib.model.ClinicalVariation: Deprecated.
getChromosomeInfo(String, QueryOptions) - Method in interface org.opencb.cellbase.core.api.GenomeDBAdaptor
getChromosomeInfo(String, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.GenomeMongoDBAdaptor
getChromosomes() - Method in class org.opencb.cellbase.server.rest.genomic.ChromosomeWSServer
getChromosomes(String) - Method in class org.opencb.cellbase.server.rest.genomic.ChromosomeWSServer
getChromosomesAll() - Method in class org.opencb.cellbase.server.rest.genomic.ChromosomeWSServer
getChromosomeSequence(String, Path) - Static method in class org.opencb.cellbase.lib.builders.utils.GenomeSequenceUtils
getChromosomeSequenceFromFiles(String, Path) - Static method in class org.opencb.cellbase.lib.builders.utils.GenomeSequenceUtils
getChromosomeSize(String) - Method in class org.opencb.cellbase.server.rest.genomic.ChromosomeWSServer
getChromosomesList(Path, String) - Method in class org.opencb.cellbase.lib.builders.RegulatoryRegionParser
getChunk() - Method in class org.opencb.cellbase.lib.builders.formats.ConservedRegionFeature: Deprecated.
getChunkId(int, int) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptor
getChunkIdPrefix(String, int, int) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptor
getClearance() - Method in class org.opencb.cellbase.core.common.drug.Drug
getClientConfiguration() - Method in class org.opencb.cellbase.client.rest.CellBaseClient
getClinicalByRegion(String) - Method in class org.opencb.cellbase.server.rest.genomic.RegionWSServer
getClinicalClient() - Method in class org.opencb.cellbase.client.rest.CellBaseClient
getClinicalDBAdaptor(String) - Method in class org.opencb.cellbase.core.api.DBAdaptorFactory
getClinicalDBAdaptor(String, String) - Method in class org.opencb.cellbase.core.api.DBAdaptorFactory
getClinicalDBAdaptor(String) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptorFactory
getClinicalDBAdaptor(String, String) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptorFactory
getClinicalLegacyDBAdaptor(String) - Method in class org.opencb.cellbase.core.api.DBAdaptorFactory
getClinicalLegacyDBAdaptor(String, String) - Method in class org.opencb.cellbase.core.api.DBAdaptorFactory
getClinicalLegacyDBAdaptor(String) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptorFactory
getClinicalLegacyDBAdaptor(String, String) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptorFactory
getClinicalSignificanceLabels() - Method in class org.opencb.cellbase.server.rest.clinical.ClinicalWSServer
getClinsigLabels() - Method in interface org.opencb.cellbase.core.api.ClinicalDBAdaptor
getClinsigLabels() - Method in class org.opencb.cellbase.lib.impl.ClinicalLegacyMongoDBAdaptor: Deprecated.
getClinsigLabels() - Method in class org.opencb.cellbase.lib.impl.ClinicalMongoDBAdaptor
getClinvar() - Method in class org.opencb.cellbase.core.config.DownloadProperties
getClinvarEfoTerms() - Method in class org.opencb.cellbase.core.config.DownloadProperties
getClinvarList() - Method in class org.opencb.cellbase.lib.model.ClinicalVariation: Deprecated.
getClinvarSet() - Method in class org.opencb.cellbase.core.common.clinical.ClinvarPublicSet
getClinvarSummary() - Method in class org.opencb.cellbase.core.config.DownloadProperties
getClinvarVariationAllele() - Method in class org.opencb.cellbase.core.config.DownloadProperties
getClosestTagCommitCount() - Method in class org.opencb.cellbase.core.common.GitRepositoryState
getClosestTagName() - Method in class org.opencb.cellbase.core.common.GitRepositoryState
getCnv() - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
getCollection() - Method in class org.opencb.cellbase.core.config.SpeciesConfiguration.ShardConfig
getCommand() - Method in class org.opencb.cellbase.app.cli.CliOptionsParser
getComments() - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
getCommit() - Method in class org.opencb.cellbase.core.monitor.HealthStatus.ApplicationDetails.Version
getCommitId() - Method in class org.opencb.cellbase.core.common.GitRepositoryState
getCommitIdAbbrev() - Method in class org.opencb.cellbase.core.common.GitRepositoryState
getCommitMessageFull() - Method in class org.opencb.cellbase.core.common.GitRepositoryState
getCommitMessageShort() - Method in class org.opencb.cellbase.core.common.GitRepositoryState
getCommitTime() - Method in class org.opencb.cellbase.core.common.GitRepositoryState
getCommitUserEmail() - Method in class org.opencb.cellbase.core.common.GitRepositoryState
getCommitUserName() - Method in class org.opencb.cellbase.core.common.GitRepositoryState
getCommon() - Method in class org.opencb.cellbase.core.common.Species
getCommonCommandOptions() - Method in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser
getCommonCommandOptions() - Method in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser
getCommonName() - Method in class org.opencb.cellbase.core.config.SpeciesConfiguration
getConfigFile() - Method in class org.opencb.cellbase.app.cli.CommandExecutor
getConsequenceTypeByGetMethod(String) - Method in class org.opencb.cellbase.server.rest.feature.VariationWSServer
getConsequenceTypeById(String, QueryOptions) - Method in class org.opencb.cellbase.client.rest.VariationClient
getConsequenceTypeByPostMethod(String) - Method in class org.opencb.cellbase.server.rest.feature.VariationWSServer
getConsequenceTypes(Query, QueryOptions) - Method in interface org.opencb.cellbase.core.api.VariantAnnotationDBAdaptor: Deprecated.
getConsequenceTypes(Query) - Method in interface org.opencb.cellbase.core.api.VariantDBAdaptor
getConsequenceTypes(Query) - Method in class org.opencb.cellbase.lib.impl.VariantMongoDBAdaptor
getConservation(List<String>, QueryOptions) - Method in class org.opencb.cellbase.client.rest.GenomicRegionClient
getConservation(Region, QueryOptions) - Method in interface org.opencb.cellbase.core.api.GenomeDBAdaptor
getConservation(List<Region>, QueryOptions) - Method in interface org.opencb.cellbase.core.api.GenomeDBAdaptor
getConservation() - Method in class org.opencb.cellbase.core.config.DownloadProperties
getConservation(List<Region>, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.GenomeMongoDBAdaptor
getConservationDBAdaptor(String) - Method in class org.opencb.cellbase.core.api.DBAdaptorFactory
getConservationDBAdaptor(String, String) - Method in class org.opencb.cellbase.core.api.DBAdaptorFactory
getConservationDBAdaptor(String) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptorFactory
getConservationDBAdaptor(String, String) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptorFactory
getConservedRegionId() - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
getConsistencyLabels() - Method in interface org.opencb.cellbase.core.api.ClinicalDBAdaptor
getConsistencyLabels() - Method in class org.opencb.cellbase.lib.impl.ClinicalLegacyMongoDBAdaptor: Deprecated.
getConsistencyLabels() - Method in class org.opencb.cellbase.lib.impl.ClinicalMongoDBAdaptor
getConsistencyLabels() - Method in class org.opencb.cellbase.server.rest.clinical.ClinicalWSServer
getConstraints(Path) - Static method in class org.opencb.cellbase.lib.builders.GeneParserUtils
getContext() - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
getCosmicList() - Method in class org.opencb.cellbase.lib.model.ClinicalVariation: Deprecated.
getCount() - Method in class org.opencb.cellbase.client.rest.models.GroupCount
getCscore() - Method in class org.opencb.cellbase.lib.builders.formats.Cadd.CaddValues
getCytobands(List<Region>, QueryOptions) - Method in interface org.opencb.cellbase.core.api.GenomeDBAdaptor
getCytobands(List<Region>) - Method in interface org.opencb.cellbase.core.api.GenomeDBAdaptor: Deprecated.
getCytobands(Region, QueryOptions) - Method in interface org.opencb.cellbase.core.api.GenomeDBAdaptor
getCytobands(Region, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.GenomeMongoDBAdaptor
getData() - Method in class org.opencb.cellbase.core.config.SpeciesConfiguration
getDatabase() - Method in class org.opencb.cellbase.core.config.DownloadProperties.EnsemblProperties
getDatabaseName(String, String) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptorFactory
getDatabases() - Method in class org.opencb.cellbase.core.config.CellBaseConfiguration
getDatabaseStatus(String, String) - Method in class org.opencb.cellbase.core.api.DBAdaptorFactory
getDatabaseStatus(String, String) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptorFactory
getDataRangeMammal() - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
getDataRangePrimate() - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
getDataRangeVertebrate() - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
getDatastores() - Method in class org.opencb.cellbase.core.monitor.HealthStatus.ApplicationDetails.DependenciesStatus
getDate() - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasStudy
getDateAddedToCatalog() - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasTrait
getDbIndex() - Method in class org.opencb.cellbase.app.cli.main.annotation.indexers.VariantIndexer
getDbLocation() - Method in class org.opencb.cellbase.app.cli.main.annotation.indexers.VariantIndexer
getDbName() - Method in class org.opencb.cellbase.core.common.drug.XRef
getDBNames() - Method in class org.opencb.cellbase.server.rest.feature.IdWSServer
getDbsnp() - Method in class org.opencb.cellbase.core.config.DownloadProperties
getDefaultAssembly(SpeciesConfiguration) - Static method in class org.opencb.cellbase.lib.SpeciesUtils: Get the default assembly for species.
getDefaultOutdir() - Method in class org.opencb.cellbase.core.config.CellBaseConfiguration
getDefaultSpecies() - Method in class org.opencb.cellbase.client.config.ClientConfiguration
getDependencies() - Method in class org.opencb.cellbase.core.monitor.HealthStatus.ApplicationDetails
getDescribe() - Method in class org.opencb.cellbase.core.common.GitRepositoryState
getDescribeShort() - Method in class org.opencb.cellbase.core.common.GitRepositoryState
getDescription() - Method in class org.opencb.cellbase.core.common.drug.Drug
getDescription() - Method in class org.opencb.cellbase.core.common.drug.Interactor
getDescription() - Method in class org.opencb.cellbase.core.common.drug.XRef
getDescription() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaDisease
getDescription() - Method in class org.opencb.cellbase.core.common.regulatory.Pwm
getDgidb() - Method in class org.opencb.cellbase.core.config.DownloadProperties
getDgv() - Method in class org.opencb.cellbase.core.config.DownloadProperties
getDirty() - Method in class org.opencb.cellbase.core.common.GitRepositoryState
getDiseaseName() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaDisease
getDiseases() - Method in class org.opencb.cellbase.core.common.genedisease.Disgenet: Deprecated.
getDiseaseTrait() - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasTrait
getDisgenet() - Method in class org.opencb.cellbase.core.config.DownloadProperties
getDisgenetReadme() - Method in class org.opencb.cellbase.core.config.DownloadProperties
getDocm() - Method in class org.opencb.cellbase.core.config.DownloadProperties
getDocmVersion() - Method in class org.opencb.cellbase.core.config.DownloadProperties
getDownload() - Method in class org.opencb.cellbase.core.config.CellBaseConfiguration
getDownloadCommandOptions() - Method in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser
getDownstreamGeneDistance() - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
getDownstreamGeneId() - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
getDrug() - Method in class org.opencb.cellbase.core.common.drug.DrugPartnerInteraction
getDrugInteractor() - Method in class org.opencb.cellbase.core.common.drug.Drug
getElapsedTime() - Method in class org.opencb.cellbase.lib.download.DownloadFile
getEncExp() - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
getEncH3K27Ac() - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
getEncH3K4Me1() - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
getEncH3K4Me3() - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
getEncNucleo() - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
getEncOCC() - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
getEncOCCombPVal() - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
getEncOCctcfPVal() - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
getEncOCctcfSig() - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
getEncOCDNasePVal() - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
getEncOCDNaseSig() - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
getEncOCFairePVal() - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
getEncOCFaireSig() - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
getEncOCmycPVal() - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
getEncOCmycSig() - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
getEncOCpolIIPVal() - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
getEncOCpolIISig() - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
getEnd() - Method in class org.opencb.cellbase.core.common.clinical.ClinicalVariant
getEnd() - Method in class org.opencb.cellbase.core.common.IntervalFeatureFrequency
getEnd() - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
getEnd() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaTarget
getEnd() - Method in class org.opencb.cellbase.core.common.regulatory.RegulatoryRegion
getEnd() - Method in class org.opencb.cellbase.core.common.regulatory.Tfbs
getEnd(int) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
getEnd() - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsStringBuilder
getEnd() - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
getEnd() - Method in class org.opencb.cellbase.lib.builders.formats.ConservedRegionFeature: Deprecated.
getEnd() - Method in class org.opencb.cellbase.lib.model.ClinicalVariation: Deprecated.
getEnd() - Method in class org.opencb.cellbase.server.rest.genomic.Interval: Deprecated.
getEndpointVersion() - Method in class org.opencb.cellbase.core.monitor.HealthStatus.Infrastructure
getEnsembl() - Method in class org.opencb.cellbase.core.config.DownloadProperties
getEnsemblCollection() - Method in class org.opencb.cellbase.core.config.SpeciesConfiguration.Assembly
getEnsemblGenes(String) - Method in class org.opencb.cellbase.server.rest.regulatory.TfWSServer
getEnsemblGenomes() - Method in class org.opencb.cellbase.core.config.DownloadProperties
getEnsemblVersion() - Method in class org.opencb.cellbase.core.config.SpeciesConfiguration.Assembly
getEquivalentAccession() - Method in class org.opencb.cellbase.app.cli.main.annotation.SequenceOntologyTermComparisonObject
getEssentiality() - Method in class org.opencb.cellbase.core.common.drug.Partner
getEvents() - Method in class org.opencb.cellbase.core.CellBaseDataResponse
getExpectedFileSize() - Method in class org.opencb.cellbase.lib.download.DownloadFile
getExperiment() - Method in class org.opencb.cellbase.lib.builders.formats.GeneExpressionAtlas.Tissue
getExperimentalMethod() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaTarget
getExperimentalScore() - Method in class org.opencb.cellbase.core.common.regulatory.RegulatoryRegion
getExpressionValue() - Method in class org.opencb.cellbase.lib.builders.formats.GeneExpressionAtlas.Tissue
getFathmmPrediction() - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
getFeatureClasses() - Method in class org.opencb.cellbase.server.rest.regulatory.RegulatoryWSServer
getFeatureMap(String) - Method in class org.opencb.cellbase.server.rest.genomic.RegionWSServer
getFeatures() - Method in class org.opencb.cellbase.client.rest.models.GroupByFields
getFeatureTypes() - Method in class org.opencb.cellbase.server.rest.regulatory.RegulatoryWSServer
getFields(String, String) - Static method in class org.opencb.cellbase.lib.builders.RegulatoryRegionParser
getFileName() - Method in class org.opencb.cellbase.core.serializer.CellBaseJsonFileSerializer
getFileName() - Method in interface org.opencb.cellbase.core.serializer.CellBaseSerializer
getFiles() - Method in class org.opencb.cellbase.core.config.DownloadProperties.URLProperties
getFirstAuthor() - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasStudy
getFoodInteractor() - Method in class org.opencb.cellbase.core.common.drug.Drug
getFrequencies() - Method in class org.opencb.cellbase.core.common.regulatory.Pwm
getFunctionalScore(Variant, QueryOptions) - Method in interface org.opencb.cellbase.core.api.VariantAnnotationDBAdaptor: Deprecated.
getFunctionalScore(List<Variant>, QueryOptions) - Method in interface org.opencb.cellbase.core.api.VariantAnnotationDBAdaptor: Deprecated.
getFunctionalScore(Query, QueryOptions) - Method in interface org.opencb.cellbase.core.api.VariantAnnotationDBAdaptor: Deprecated.
getFunctionalScoreVariant(Variant, QueryOptions) - Method in interface org.opencb.cellbase.core.api.VariantDBAdaptor
getFunctionalScoreVariant(List<Variant>, QueryOptions) - Method in interface org.opencb.cellbase.core.api.VariantDBAdaptor
getFunctionalScoreVariant(Variant, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.VariantMongoDBAdaptor
getFungi() - Method in class org.opencb.cellbase.core.config.SpeciesProperties
getGene(List<String>, QueryOptions) - Method in class org.opencb.cellbase.client.rest.GenomicRegionClient
getGene(String, QueryOptions) - Method in class org.opencb.cellbase.client.rest.TranscriptClient
getGene() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaTarget
getGene() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaToGene
getGene() - Method in class org.opencb.cellbase.core.common.regulatory.Tfbs
getGene(String) - Method in class org.opencb.cellbase.server.rest.feature.ProteinWSServer
getGeneByEnsemblId(String) - Method in class org.opencb.cellbase.server.rest.feature.IdWSServer
getGeneById(String) - Method in class org.opencb.cellbase.server.rest.feature.TranscriptWSServer
getGeneCDSLength() - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
getGeneClient() - Method in class org.opencb.cellbase.client.rest.CellBaseClient
getGeneDBAdaptor(String) - Method in class org.opencb.cellbase.core.api.DBAdaptorFactory
getGeneDBAdaptor(String, String) - Method in class org.opencb.cellbase.core.api.DBAdaptorFactory
getGeneDBAdaptor(String) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptorFactory
getGeneDBAdaptor(String, String) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptorFactory
getGeneDiseaseAssociationMap(Path, Path) - Static method in class org.opencb.cellbase.lib.builders.GeneParserUtils
getGeneDrugMap(Path) - Static method in class org.opencb.cellbase.lib.builders.GeneParserUtils
getGeneExpressionAtlas() - Method in class org.opencb.cellbase.core.config.DownloadProperties
getGeneExpressionMap(String, Path) - Static method in class org.opencb.cellbase.lib.builders.GeneParserUtils
getGeneId() - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsStringBuilder
getGeneId() - Method in class org.opencb.cellbase.lib.builders.formats.GeneExpressionAtlas
getGeneName() - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
getGeneName() - Method in class org.opencb.cellbase.core.common.genedisease.Disgenet: Deprecated.
getGeneName() - Method in class org.opencb.cellbase.lib.builders.formats.GeneExpressionAtlas
getGeneralFunction() - Method in class org.opencb.cellbase.core.common.drug.Partner
getGeneralOptions() - Method in class org.opencb.cellbase.app.cli.CliOptionsParser
getGenericClient() - Method in class org.opencb.cellbase.client.rest.CellBaseClient
getGenesByRegion(String) - Method in class org.opencb.cellbase.server.rest.genomic.RegionWSServer
getGenesByRegionPost(String) - Method in class org.opencb.cellbase.server.rest.genomic.RegionWSServer
getGeneSymbol() - Method in class org.opencb.cellbase.core.common.genedisease.Disgenet: Deprecated.
getGeneTargetName() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaTarget
getGeneUniprotXref() - Method in class org.opencb.cellbase.core.config.DownloadProperties
getGenomeDBAdaptor(String) - Method in class org.opencb.cellbase.core.api.DBAdaptorFactory
getGenomeDBAdaptor(String, String) - Method in class org.opencb.cellbase.core.api.DBAdaptorFactory
getGenomeDBAdaptor(String) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptorFactory
getGenomeDBAdaptor(String, String) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptorFactory
getGenomeInfo(QueryOptions) - Method in interface org.opencb.cellbase.core.api.GenomeDBAdaptor
getGenomeInfo(QueryOptions) - Method in class org.opencb.cellbase.lib.impl.GenomeMongoDBAdaptor
getGenomeSequence(Path) - Static method in class org.opencb.cellbase.lib.builders.utils.GenomeSequenceUtils
getGenomeSequenceGZipped(Path) - Static method in class org.opencb.cellbase.lib.builders.utils.GenomeSequenceUtils
getGenomeWideScreen() - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
getGenomicFeature() - Method in class org.opencb.cellbase.lib.builders.formats.Cadd.CaddValues
getGenomicRegionClient() - Method in class org.opencb.cellbase.client.rest.CellBaseClient
getGenomicSequence(Query, QueryOptions) - Method in interface org.opencb.cellbase.core.api.GenomeDBAdaptor: Deprecated.
getGenomicSequence(List<Query>, QueryOptions) - Method in interface org.opencb.cellbase.core.api.GenomeDBAdaptor: Deprecated.
getGenomicSequence(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.GenomeMongoDBAdaptor: Deprecated.
getGenomicSuperDups() - Method in class org.opencb.cellbase.core.config.DownloadProperties
getGerp() - Method in class org.opencb.cellbase.core.config.DownloadProperties
getGitRepositoryState() - Static method in class org.opencb.cellbase.core.common.GitRepositoryState
getGnomad() - Method in class org.opencb.cellbase.core.config.DownloadProperties
getGroup() - Method in class org.opencb.cellbase.core.common.drug.Drug
getGwasCatalog() - Method in class org.opencb.cellbase.core.config.DownloadProperties
getGwasList() - Method in class org.opencb.cellbase.lib.model.ClinicalVariation: Deprecated.
getHalfLife() - Method in class org.opencb.cellbase.core.common.drug.Drug
getHaplotype(T, Variant) - Method in class org.opencb.cellbase.core.variant.AnnotationBasedPhasedQueryManager
getHaplotype(EvidenceEntry, Variant) - Method in class org.opencb.cellbase.core.variant.ClinicalPhasedQueryManager
getHaplotype(PopulationFrequency, Variant) - Method in class org.opencb.cellbase.core.variant.PopulationFrequencyPhasedQueryManager
getHgncId() - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
getHistologySubtype() - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
getHost() - Method in class org.opencb.cellbase.core.config.DatabaseCredentials
getHost() - Method in class org.opencb.cellbase.core.config.DownloadProperties.URLProperties
getHosts() - Method in class org.opencb.cellbase.client.config.RestConfig
getHostURL() - Method in class org.opencb.cellbase.lib.download.EnsemblInfo
getHpo() - Method in class org.opencb.cellbase.core.config.DownloadProperties
getIarctp53() - Method in class org.opencb.cellbase.core.config.DownloadProperties
getId() - Method in class org.opencb.cellbase.core.common.drug.Drug
getId() - Method in class org.opencb.cellbase.core.common.drug.Interactor
getId() - Method in class org.opencb.cellbase.core.common.drug.Partner
getId() - Method in class org.opencb.cellbase.core.common.drug.XRef
getId() - Method in class org.opencb.cellbase.core.config.MongoDBDatabaseCredentials.ReplicaSet
getId() - Method in class org.opencb.cellbase.core.config.SpeciesConfiguration
getId() - Method in class org.opencb.cellbase.core.result.CellBaseDataResult
getIdSample() - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
getIdStudy() - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
getIdTumour() - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
getIndexCommandOptions() - Method in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser
getIndication() - Method in class org.opencb.cellbase.core.common.drug.Drug
getInfoByEnsemblId(String) - Method in class org.opencb.cellbase.server.rest.feature.ProteinWSServer
getInfrastructure() - Method in class org.opencb.cellbase.core.monitor.HealthStatus
getInitialSampleSize() - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasStudy
getInstallCommandOptions() - Method in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser
getIntact() - Method in class org.opencb.cellbase.core.config.DownloadProperties
getInteractorsByInteractionId(String, String) - Method in class org.opencb.cellbase.server.rest.network.ProteinProteinInteractionWSServer
getIntergenic() - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
getInterpro() - Method in class org.opencb.cellbase.core.config.DownloadProperties
getInterproRelNotes() - Method in class org.opencb.cellbase.core.config.DownloadProperties
getInterval() - Method in class org.opencb.cellbase.core.common.IntervalFeatureFrequency
getIntervalFeatureFrequencies(Region, int, List<Object[]>, int, double) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptor
getIntervalFeatureFrequencies(Region, int, List<Object[]>) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptor
getIntervalFrequencies(Query, int, QueryOptions) - Method in interface org.opencb.cellbase.core.api.FeatureDBAdaptor
getIntervalFrequencies(List<Query>, int, QueryOptions) - Method in interface org.opencb.cellbase.core.api.FeatureDBAdaptor
getIntervalFrequencies(Query, int, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ClinicalLegacyMongoDBAdaptor: Deprecated.
getIntervalFrequencies(Query, int, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ClinicalMongoDBAdaptor
getIntervalFrequencies(Query, int, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.GeneMongoDBAdaptor
getIntervalFrequencies(Bson, Region, int, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptor
getIntervalFrequencies(Query, int, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.RegulationMongoDBAdaptor
getIntervalFrequencies(Query, int, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.RepeatsMongoDBAdaptor
getIntervalFrequencies(Query, int, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.TranscriptMongoDBAdaptor
getIntervalFrequencies(Query, int, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.VariantMongoDBAdaptor
getIntervals() - Method in class org.opencb.cellbase.server.rest.genomic.Histogram: Deprecated.
getJCommander() - Method in class org.opencb.cellbase.app.cli.CliOptionsParser
getJournal() - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasStudy
getKey() - Method in class org.opencb.cellbase.core.config.SpeciesConfiguration.ShardConfig
getKind() - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsStringBuilder
getKnownAction() - Method in class org.opencb.cellbase.core.common.drug.DrugPartnerInteraction
getLandmark() - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.CdnaCoord
getLength() - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
getLength() - Method in class org.opencb.cellbase.core.common.regulatory.Pwm
getLibs() - Method in class org.opencb.cellbase.core.config.DownloadProperties.EnsemblProperties
getLink() - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasStudy
getLoadCommandOptions() - Method in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser
getLogFile() - Method in class org.opencb.cellbase.client.config.ClientConfiguration
getLogger() - Method in class org.opencb.cellbase.app.cli.CommandExecutor
getLogLevel() - Method in class org.opencb.cellbase.app.cli.CommandExecutor
getLogLevel() - Method in class org.opencb.cellbase.client.config.ClientConfiguration
getLowerLimitMammal() - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
getLowerLimitPrimate() - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
getLowerLimitVertebrate() - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
getMaintainer() - Method in class org.opencb.cellbase.core.monitor.HealthStatus.ApplicationDetails
getMaintainerContact() - Method in class org.opencb.cellbase.core.config.CellBaseConfiguration
getMaintenanceFlagFile() - Method in class org.opencb.cellbase.core.config.CellBaseConfiguration
getMappedGene() - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
getMaximum() - Method in class org.opencb.cellbase.core.config.SpeciesConfiguration.ShardRange
getMechanismOfAction() - Method in class org.opencb.cellbase.core.common.drug.Drug
getMerged() - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
getMessage() - Method in class org.opencb.cellbase.lib.download.DownloadFile
getMetaClient() - Method in class org.opencb.cellbase.client.rest.CellBaseClient
getMetaDBAdaptor(String) - Method in class org.opencb.cellbase.core.api.DBAdaptorFactory
getMetaDBAdaptor(String, String) - Method in class org.opencb.cellbase.core.api.DBAdaptorFactory
getMetaDBAdaptor(String) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptorFactory
getMetaDBAdaptor(String, String) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptorFactory
getMetazoa() - Method in class org.opencb.cellbase.core.config.SpeciesProperties
getMethod() - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
getMinimum() - Method in class org.opencb.cellbase.core.config.SpeciesConfiguration.ShardRange
getMirbase() - Method in class org.opencb.cellbase.core.config.DownloadProperties
getMirbaseAcc() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaGene
getMirbaseAcc() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaMature: Deprecated.
getMirbaseId() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaDisease
getMirbaseId() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaGene
getMirbaseId() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaMature: Deprecated.
getMirbaseId() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaTarget
getMirbaseReadme() - Method in class org.opencb.cellbase.core.config.DownloadProperties
getMirnaDiseaseId() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaDisease
getMirnaDiseases() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaGene
getMirnaFeaturesFields(String) - Static method in class org.opencb.cellbase.lib.builders.RegulatoryRegionParser
getMirnaGene() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaDisease
getMirnaGene() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaGeneToMature
getMirnaGene() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaToGene
getMirnaGeneId() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaGene
getMirnaGeneToMatureId() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaGeneToMature
getMirnaGeneToMatures() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaGene
getMirnaGeneToMatures() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaMature: Deprecated.
getMirnaMature() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaGeneToMature
getMirnaMature() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaTarget
getMirnaMatureId() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaMature: Deprecated.
getMirnaTargetId() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaTarget
getMirnaTargets() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaMature: Deprecated.
getMirnaToGeneId() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaToGene
getMirnaToGenes() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaGene
getMiRTarBase() - Method in class org.opencb.cellbase.core.config.DownloadProperties
getModeInheritanceLabels() - Method in interface org.opencb.cellbase.core.api.ClinicalDBAdaptor
getModeInheritanceLabels() - Method in class org.opencb.cellbase.lib.impl.ClinicalLegacyMongoDBAdaptor: Deprecated.
getModeInheritanceLabels() - Method in class org.opencb.cellbase.lib.impl.ClinicalMongoDBAdaptor
getModeInheritanceLabels() - Method in class org.opencb.cellbase.server.rest.clinical.ClinicalWSServer
getModel() - Method in class org.opencb.cellbase.server.rest.feature.GeneWSServer
getModel() - Method in class org.opencb.cellbase.server.rest.feature.IdWSServer
getModel() - Method in class org.opencb.cellbase.server.rest.feature.ProteinWSServer
getModel() - Method in class org.opencb.cellbase.server.rest.feature.TranscriptWSServer
getModel() - Method in class org.opencb.cellbase.server.rest.feature.VariationWSServer
getModel() - Method in class org.opencb.cellbase.server.rest.genomic.ChromosomeWSServer
getModel() - Method in class org.opencb.cellbase.server.rest.genomic.RegionWSServer
getModel() - Method in class org.opencb.cellbase.server.rest.genomic.VariantWSServer
getModel() - Method in class org.opencb.cellbase.server.rest.network.ProteinProteinInteractionWSServer
getMongodb() - Method in class org.opencb.cellbase.core.config.Databases
getMongodb() - Method in class org.opencb.cellbase.core.monitor.HealthStatus.ApplicationDetails.DependenciesStatus.DatastoreDependenciesStatus
getMongoDBDatastore(String, String) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptorFactory: Get database based on species, assembly and version.
getMongoDBDatastore(String) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptorFactory: Get database based on database name.
getMotifFeaturesFields(String) - Static method in class org.opencb.cellbase.lib.builders.RegulatoryRegionParser
getMutationAA() - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
getMutationCDS() - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
getMutationDescription() - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
getMutationGRCh37GenomePosition() - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
getMutationGRCh37Strand() - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
getMutationID() - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
getMutationSomaticStatus() - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
getMutationType() - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsStringBuilder
getMutationZygosity() - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
getName() - Method in class org.opencb.cellbase.app.cli.main.annotation.SequenceOntologyTermComparisonObject
getName() - Method in class org.opencb.cellbase.core.common.drug.Drug
getName() - Method in class org.opencb.cellbase.core.common.drug.Interactor
getName() - Method in class org.opencb.cellbase.core.common.drug.Partner
getName() - Method in class org.opencb.cellbase.core.common.regulatory.RegulatoryRegion
getName() - Method in class org.opencb.cellbase.core.config.SpeciesConfiguration.Assembly
getName() - Method in class org.opencb.cellbase.core.config.SpeciesConfiguration.Zone
getName() - Method in class org.opencb.cellbase.core.monitor.HealthStatus.Service
getNeo4j() - Method in class org.opencb.cellbase.core.config.Databases
getNextByEnsemblId(String) - Method in class org.opencb.cellbase.server.rest.feature.GeneWSServer
getNextById(String) - Method in class org.opencb.cellbase.server.rest.feature.VariationWSServer
getNodes() - Method in class org.opencb.cellbase.core.config.MongoDBDatabaseCredentials.ReplicaSet
getNormalisedVariantString(String, int, String, String) - Method in class org.opencb.cellbase.lib.builders.clinical.variant.ClinicalIndexer
getOffset() - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.CdnaCoord
getOptions() - Method in class org.opencb.cellbase.core.config.DatabaseCredentials
getOrBeta() - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasTest
getOutdir() - Method in class org.opencb.cellbase.core.serializer.CellBaseJsonFileSerializer
getOutdir() - Method in interface org.opencb.cellbase.core.serializer.CellBaseSerializer
getOutputFile() - Method in class org.opencb.cellbase.lib.download.DownloadFile
getParams() - Method in class org.opencb.cellbase.core.CellBaseDataResponse
getPartner() - Method in class org.opencb.cellbase.core.common.drug.DrugPartnerInteraction
getPassword() - Method in class org.opencb.cellbase.core.config.DatabaseCredentials
getPercentCI() - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasTest
getPharmacology() - Method in class org.opencb.cellbase.core.common.drug.Drug
getPhenotype(String, QueryOptions) - Method in class org.opencb.cellbase.client.rest.VariationClient
getPhenotypeGeneRelations(Query, QueryOptions) - Method in interface org.opencb.cellbase.core.api.ClinicalDBAdaptor
getPhenotypeGeneRelations(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ClinicalLegacyMongoDBAdaptor: Deprecated.
getPhenotypeGeneRelations(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ClinicalMongoDBAdaptor
getPhenotypeGeneRelations() - Method in class org.opencb.cellbase.server.rest.feature.ClinicalLegacyWSServer: Deprecated.
getPhred() - Method in class org.opencb.cellbase.lib.builders.formats.Cadd.CaddValues
getPlants() - Method in class org.opencb.cellbase.core.config.SpeciesProperties
getPlatform() - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasStudy
getPopulationFrequency(String, QueryOptions) - Method in class org.opencb.cellbase.client.rest.VariationClient
getPopulationFrequency(String) - Method in class org.opencb.cellbase.server.rest.feature.VariationWSServer
getPopulationFrequencyByVariant(List<Variant>, QueryOptions) - Method in interface org.opencb.cellbase.core.api.VariantDBAdaptor
getPopulationFrequencyByVariant(List<Variant>, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.VariantMongoDBAdaptor: Created an specific method for pop freqs here since in this case phase is managed at the Pop.
getPort() - Method in class org.opencb.cellbase.core.config.Rest
getPPIByEnsemblId(String) - Method in class org.opencb.cellbase.server.rest.feature.GeneWSServer
getPPIByInteractionId(String) - Method in class org.opencb.cellbase.server.rest.network.ProteinProteinInteractionWSServer
getPrefix() - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsStringBuilder
getPrimaryHistology() - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
getPrimarySite() - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
getProtein(String, QueryOptions) - Method in class org.opencb.cellbase.client.rest.GeneClient
getProtein(String, QueryOptions) - Method in class org.opencb.cellbase.client.rest.TranscriptClient
getProtein(String) - Method in class org.opencb.cellbase.server.rest.feature.TranscriptWSServer
getProteinById(String) - Method in class org.opencb.cellbase.server.rest.feature.GeneWSServer
getproteinByName(String) - Method in class org.opencb.cellbase.server.rest.feature.ProteinWSServer: Deprecated.
getProteinClient() - Method in class org.opencb.cellbase.client.rest.CellBaseClient
getProteinDBAdaptor(String) - Method in class org.opencb.cellbase.core.api.DBAdaptorFactory
getProteinDBAdaptor(String, String) - Method in class org.opencb.cellbase.core.api.DBAdaptorFactory
getProteinDBAdaptor(String) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptorFactory
getProteinDBAdaptor(String, String) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptorFactory
getProteinFunctionPrediction(String, QueryOptions) - Method in class org.opencb.cellbase.client.rest.TranscriptClient
getProteinFunctionPredictionByTranscriptId(String) - Method in class org.opencb.cellbase.server.rest.feature.TranscriptWSServer
getProteinProteinInteractionDBAdaptor(String) - Method in class org.opencb.cellbase.core.api.DBAdaptorFactory
getProteinProteinInteractionDBAdaptor(String, String) - Method in class org.opencb.cellbase.core.api.DBAdaptorFactory
getProteinProteinInteractionDBAdaptor(String) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptorFactory
getProteinProteinInteractionDBAdaptor(String, String) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptorFactory
getProtist() - Method in class org.opencb.cellbase.core.config.SpeciesProperties
getPubmedId() - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasStudy
getPubmedId() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaDisease
getPubmedId() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaTarget
getPubmedPMID() - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
getpValue() - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasTest
getpValueMlog() - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasTest
getpValueText() - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasTest
getPwm() - Method in class org.opencb.cellbase.core.common.regulatory.Tfbs
getPwmId() - Method in class org.opencb.cellbase.core.common.regulatory.Pwm
getQueryCommandOptions() - Method in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser
getRangeKey() - Method in class org.opencb.cellbase.core.config.SpeciesConfiguration.ShardConfig
getReactome() - Method in class org.opencb.cellbase.core.config.DownloadProperties
getReference() - Method in class org.opencb.cellbase.core.common.clinical.ClinicalVariant
getReference() - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsStringBuilder
getReference() - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
getReference() - Method in class org.opencb.cellbase.lib.model.ClinicalVariation: Deprecated.
getReference(String) - Method in class org.opencb.cellbase.server.rest.feature.ProteinWSServer: Deprecated.
getReferencePosition() - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.CdnaCoord
getReferences() - Method in class org.opencb.cellbase.core.common.drug.Partner
getRegion() - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
getRegulationDBAdaptor(String) - Method in class org.opencb.cellbase.core.api.DBAdaptorFactory
getRegulationDBAdaptor(String, String) - Method in class org.opencb.cellbase.core.api.DBAdaptorFactory
getRegulationDBAdaptor(String) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptorFactory
getRegulationDBAdaptor(String, String) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptorFactory
getRegulatory(List<String>, QueryOptions) - Method in class org.opencb.cellbase.client.rest.GenomicRegionClient
getRegulatory(String, QueryOptions) - Method in class org.opencb.cellbase.client.rest.VariationClient
getRegulatoryByGetMethod(String) - Method in class org.opencb.cellbase.server.rest.feature.VariationWSServer
getRegulatoryElements(Query, QueryOptions) - Method in interface org.opencb.cellbase.core.api.GeneDBAdaptor
getRegulatoryElements(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.GeneMongoDBAdaptor
getRegulatoryFeaturesFields(String) - Static method in class org.opencb.cellbase.lib.builders.RegulatoryRegionParser
getRegulatoryRegion() - Method in class org.opencb.cellbase.core.common.regulatory.Tfbs
getRegulatoryRegionId() - Method in class org.opencb.cellbase.core.common.regulatory.RegulatoryRegion
getRegulatoryTypeByPostMethod(String) - Method in class org.opencb.cellbase.server.rest.feature.VariationWSServer
getRelativeEnd() - Method in class org.opencb.cellbase.core.common.regulatory.Tfbs
getRelativeStart() - Method in class org.opencb.cellbase.core.common.regulatory.Tfbs
getRelease() - Method in class org.opencb.cellbase.lib.download.EnsemblInfo
getRemoteOriginUrl() - Method in class org.opencb.cellbase.core.common.GitRepositoryState
getRepeat(List<String>, QueryOptions) - Method in class org.opencb.cellbase.client.rest.GenomicRegionClient
getRepeatByRegion(String) - Method in class org.opencb.cellbase.server.rest.genomic.RegionWSServer
getRepeatsDBAdaptor(String, String) - Method in class org.opencb.cellbase.core.api.DBAdaptorFactory
getRepeatsDBAdaptor(String, String) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptorFactory
getReplicationSampleSize() - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasStudy
getReportedGenes() - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
getRepset() - Method in class org.opencb.cellbase.core.monitor.HealthStatus.ApplicationDetails.DependenciesStatus.DatastoreDependenciesStatus.DatastoreStatus
getResponses() - Method in class org.opencb.cellbase.core.CellBaseDataResponse
getResponseTime() - Method in class org.opencb.cellbase.core.monitor.HealthStatus.ApplicationDetails.DependenciesStatus.DatastoreDependenciesStatus.DatastoreStatus
getRest() - Method in class org.opencb.cellbase.client.config.ClientConfiguration
getRest() - Method in class org.opencb.cellbase.core.config.ServerProperties
getReturnFields(QueryOptions) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptor: Deprecated.
getReverseComplementaryCodon(String, int) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
getRiskAlleleFrequency() - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
getRole() - Method in class org.opencb.cellbase.core.monitor.HealthStatus.ApplicationDetails.DependenciesStatus.DatastoreDependenciesStatus.DatastoreStatus
getRouteOfElimination() - Method in class org.opencb.cellbase.core.common.drug.Drug
getSampleAttribute(Variant, String) - Static method in class org.opencb.cellbase.core.variant.PhasedQueryManager
getSampleName() - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
getSampleSource() - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
getScientific() - Method in class org.opencb.cellbase.core.common.Species
getScientificName() - Method in class org.opencb.cellbase.core.config.SpeciesConfiguration
getScore() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaTarget
getScore() - Method in class org.opencb.cellbase.core.common.regulatory.Tfbs
getSequence(List<String>, QueryOptions) - Method in class org.opencb.cellbase.client.rest.GenomicRegionClient
getSequence(String, QueryOptions) - Method in class org.opencb.cellbase.client.rest.ProteinClient
getSequence(String, QueryOptions) - Method in class org.opencb.cellbase.client.rest.TranscriptClient
getSequence(String, QueryOptions) - Method in class org.opencb.cellbase.client.rest.VariationClient
getSequence(Region, QueryOptions) - Method in interface org.opencb.cellbase.core.api.GenomeDBAdaptor
getSequence(List<Region>, QueryOptions) - Method in interface org.opencb.cellbase.core.api.GenomeDBAdaptor
getSequence() - Method in class org.opencb.cellbase.core.common.drug.Partner
getSequence() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaGene
getSequence() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaMature: Deprecated.
getSequence() - Method in class org.opencb.cellbase.core.common.regulatory.Tfbs
getSequence(Region, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.GenomeMongoDBAdaptor
getSequence(String) - Method in class org.opencb.cellbase.server.rest.feature.ProteinWSServer
getSequence(String) - Method in class org.opencb.cellbase.server.rest.feature.VariationWSServer
getSequenceByRegion(String, String) - Method in class org.opencb.cellbase.server.rest.genomic.RegionWSServer
getSequenceOntology() - Method in class org.opencb.cellbase.app.cli.main.annotation.VariantAnnotationDiff
getSequenceOntologyTerms(HashSet<String>) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
getSequenceOntologyTerms(Iterable<String>) - Static method in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
getSequencesByIdList(String) - Method in class org.opencb.cellbase.server.rest.feature.TranscriptWSServer
getServer() - Method in class org.opencb.cellbase.core.config.CellBaseConfiguration
getServer() - Method in class org.opencb.cellbase.core.monitor.HealthStatus.ApplicationDetails
getServer() - Static method in class org.opencb.cellbase.server.rest.AdminRestWebService
getServerCommandOptions() - Method in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser
getService() - Method in class org.opencb.cellbase.core.monitor.HealthStatus
getServiceDiscovery() - Method in class org.opencb.cellbase.core.monitor.HealthStatus.Infrastructure
getShardRanges() - Method in class org.opencb.cellbase.core.config.SpeciesConfiguration.Zone
getShards() - Method in class org.opencb.cellbase.core.config.MongoDBDatabaseCredentials
getShards() - Method in class org.opencb.cellbase.core.config.SpeciesConfiguration
getSimpleRepeats() - Method in class org.opencb.cellbase.core.config.DownloadProperties
getSiteSubtype() - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
getSNPByGeneId(String, boolean) - Method in class org.opencb.cellbase.server.rest.feature.GeneWSServer
getSnpByRegion(String, String, String) - Method in class org.opencb.cellbase.server.rest.genomic.RegionWSServer: Deprecated.
getSnpGeneIds() - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
getSnpId() - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
getSnpIdCurrent() - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
getSource() - Method in class org.opencb.cellbase.core.common.clinical.ClinicalVariant
getSource() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaGene
getSource() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaTarget
getSource() - Method in class org.opencb.cellbase.core.common.regulatory.Pwm
getSource() - Method in class org.opencb.cellbase.core.common.regulatory.RegulatoryRegion
getSource() - Method in class org.opencb.cellbase.core.common.regulatory.Tfbs
getSources() - Method in class org.opencb.cellbase.lib.builders.formats.ConservedRegionFeature: Deprecated.
getSpecies() - Method in class org.opencb.cellbase.client.rest.CellBaseClient
getSpecies(String) - Method in class org.opencb.cellbase.core.api.DBAdaptorFactory
getSpecies() - Method in class org.opencb.cellbase.core.common.Species
getSpecies() - Method in class org.opencb.cellbase.core.config.CellBaseConfiguration
getSpecies() - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptor
getSpecies(CellBaseConfiguration, String, String) - Static method in class org.opencb.cellbase.lib.SpeciesUtils: Return species object based on species name and assembly.
getSpecies() - Method in class org.opencb.cellbase.server.rest.MetaWSServer
getSpeciesConfig(String) - Method in class org.opencb.cellbase.core.config.CellBaseConfiguration: get the config for this species.
getSpeciesConfiguration(CellBaseConfiguration, String) - Static method in class org.opencb.cellbase.lib.SpeciesUtils: Get configuration for the specified species.
getSpeciesInfo() - Method in class org.opencb.cellbase.server.rest.SpeciesWSServer
getSpeciesShortname(SpeciesConfiguration) - Static method in class org.opencb.cellbase.lib.SpeciesUtils: Formats the species name, e.g.
getSpecificFunction() - Method in class org.opencb.cellbase.core.common.drug.Partner
getStart() - Method in class org.opencb.cellbase.core.common.clinical.ClinicalVariant
getStart() - Method in class org.opencb.cellbase.core.common.IntervalFeatureFrequency
getStart() - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
getStart() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaTarget
getStart() - Method in class org.opencb.cellbase.core.common.regulatory.RegulatoryRegion
getStart() - Method in class org.opencb.cellbase.core.common.regulatory.Tfbs
getStart(int) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
getStart() - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsStringBuilder
getStart() - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
getStart() - Method in class org.opencb.cellbase.lib.builders.formats.ConservedRegionFeature: Deprecated.
getStart() - Method in class org.opencb.cellbase.lib.model.ClinicalVariation: Deprecated.
getStart() - Method in class org.opencb.cellbase.server.rest.genomic.Interval: Deprecated.
getStarted() - Method in class org.opencb.cellbase.core.monitor.HealthStatus.ApplicationDetails
getStartTime() - Method in class org.opencb.cellbase.lib.download.DownloadFile
getStatus() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaGene
getStatus() - Method in class org.opencb.cellbase.core.monitor.HealthStatus.Service
getStatus() - Method in class org.opencb.cellbase.lib.download.DownloadFile
getStrand() - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
getStrand() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaTarget
getStrand() - Method in class org.opencb.cellbase.core.common.regulatory.Tfbs
getStrongestSNPRiskAllele() - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
getStudies() - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
getStudy() - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasStudy
getSubcategory(String, String) - Method in class org.opencb.cellbase.server.rest.MetaWSServer
getSubCommand() - Method in class org.opencb.cellbase.app.cli.CliOptionsParser
getSubCommand(JCommander) - Static method in class org.opencb.cellbase.app.cli.CliOptionsParser
getSubstitutionScores(String, QueryOptions) - Method in class org.opencb.cellbase.client.rest.ProteinClient
getSubstitutionScores(Query, QueryOptions) - Method in interface org.opencb.cellbase.core.api.ProteinDBAdaptor
getSubstitutionScores(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ProteinMongoDBAdaptor
getSubstitutionScores(String) - Method in class org.opencb.cellbase.server.rest.feature.ProteinWSServer
getSumDataMammal() - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
getSumDataPrimate() - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
getSumDataVertebrate() - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
getSumSquareMammal() - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
getSumSquarePrimate() - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
getSumSquareVertebrate() - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
getTagName() - Method in class org.opencb.cellbase.core.monitor.HealthStatus.ApplicationDetails.Version
getTags() - Method in class org.opencb.cellbase.core.common.GitRepositoryState
getTargetGeneName() - Method in class org.opencb.cellbase.core.common.regulatory.Tfbs
getTargetScan() - Method in class org.opencb.cellbase.core.config.DownloadProperties
getTests() - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasTrait
getTfbs(String, QueryOptions) - Method in class org.opencb.cellbase.client.rest.GeneClient
getTfbs(List<String>, QueryOptions) - Method in class org.opencb.cellbase.client.rest.GenomicRegionClient
getTfbs(Query, QueryOptions) - Method in interface org.opencb.cellbase.core.api.GeneDBAdaptor
getTfbs(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.GeneMongoDBAdaptor
getTfbses() - Method in class org.opencb.cellbase.core.common.regulatory.Pwm
getTfbses() - Method in class org.opencb.cellbase.core.common.regulatory.RegulatoryRegion
getTfbsId() - Method in class org.opencb.cellbase.core.common.regulatory.Tfbs
getTfbsMap(Path) - Static method in class org.opencb.cellbase.lib.builders.GeneParserUtils
getTfByRegion(String) - Method in class org.opencb.cellbase.server.rest.genomic.RegionWSServer
getTfName() - Method in class org.opencb.cellbase.core.common.regulatory.Pwm
getTfName() - Method in class org.opencb.cellbase.core.common.regulatory.Tfbs
getTime() - Method in class org.opencb.cellbase.core.CellBaseDataResponse
getTimeout() - Method in class org.opencb.cellbase.client.config.RestConfig
getTissueName() - Method in class org.opencb.cellbase.lib.builders.formats.GeneExpressionAtlas.Tissue
getTissues() - Method in class org.opencb.cellbase.lib.builders.formats.GeneExpressionAtlas
getToxicity() - Method in class org.opencb.cellbase.core.common.drug.Drug
getTraits() - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasStudy
getTranscript(String, QueryOptions) - Method in class org.opencb.cellbase.client.rest.GeneClient
getTranscript(List<String>, QueryOptions) - Method in class org.opencb.cellbase.client.rest.GenomicRegionClient
getTranscript() - Method in class org.opencb.cellbase.core.common.regulatory.MirnaToGene
getTranscript() - Method in class org.opencb.cellbase.core.common.regulatory.Tfbs
getTranscript(String) - Method in class org.opencb.cellbase.server.rest.feature.ProteinWSServer
getTranscriptByRegion(String) - Method in class org.opencb.cellbase.server.rest.genomic.RegionWSServer
getTranscriptClient() - Method in class org.opencb.cellbase.client.rest.CellBaseClient
getTranscriptDBAdaptor(String) - Method in class org.opencb.cellbase.core.api.DBAdaptorFactory
getTranscriptDBAdaptor(String, String) - Method in class org.opencb.cellbase.core.api.DBAdaptorFactory
getTranscriptDBAdaptor(String) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptorFactory
getTranscriptDBAdaptor(String, String) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptorFactory
getTranscriptId() - Method in class org.opencb.cellbase.app.cli.main.annotation.SequenceOntologyTermComparisonObject
getTranscriptId() - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsStringBuilder
getTranscriptsByGeneId(String) - Method in class org.opencb.cellbase.server.rest.feature.GeneWSServer
getTumourOrigin() - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
getType() - Method in class org.opencb.cellbase.core.common.drug.Drug
getType() - Method in class org.opencb.cellbase.core.common.drug.DrugPartnerInteraction
getType() - Method in class org.opencb.cellbase.core.common.regulatory.Pwm
getType() - Method in class org.opencb.cellbase.core.common.regulatory.RegulatoryRegion
getType() - Method in class org.opencb.cellbase.lib.builders.formats.ConservedRegionFeature.ConservedRegionSource: Deprecated.
getUniprot() - Method in class org.opencb.cellbase.core.config.DownloadProperties
getUniprotRelNotes() - Method in class org.opencb.cellbase.core.config.DownloadProperties
getUnprocessedFileBufferedReader() - Method in class org.opencb.cellbase.lib.builders.variation.AbstractVariationFile
getUpstreamGeneDistance() - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
getUpstreamGeneId() - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
getUptime() - Method in class org.opencb.cellbase.core.monitor.HealthStatus.ApplicationDetails
getUrl() - Method in class org.opencb.cellbase.core.config.DownloadProperties.EnsemblProperties
getUrl() - Method in class org.opencb.cellbase.core.config.Rest
getUrl() - Method in class org.opencb.cellbase.lib.download.DownloadFile
getUser() - Method in class org.opencb.cellbase.core.config.DatabaseCredentials
getValue() - Method in class org.opencb.cellbase.core.common.IntervalFeatureFrequency
getValue() - Method in class org.opencb.cellbase.server.rest.genomic.Interval: Deprecated.
getValues() - Method in class org.opencb.cellbase.lib.builders.formats.ConservedRegionFeature.ConservedRegionSource: Deprecated.
getVariantAnnotation() - Method in class org.opencb.cellbase.app.cli.main.annotation.VariantAnnotationDiff
getVariantAnnotation(String, int, String, String, QueryOptions) - Method in interface org.opencb.cellbase.core.api.ProteinDBAdaptor
getVariantAnnotation(byte[]) - Method in class org.opencb.cellbase.lib.builders.clinical.variant.ClinicalIndexer
getVariantAnnotation(String, int, String, String, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ProteinMongoDBAdaptor
getVariantAnnotationCommandOptions() - Method in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser
getVariantAnnotationId(Variant, Boolean) - Method in class org.opencb.cellbase.client.rest.VariantClient
getVariantAnnotationIds(List<Variant>, Boolean) - Method in class org.opencb.cellbase.client.rest.VariantClient
getVariantClassification(List<String>) - Method in class org.opencb.cellbase.lib.builders.clinical.variant.ClinicalIndexer
getVariantClient() - Method in class org.opencb.cellbase.client.rest.CellBaseClient
getVariantsByPhenotype(String) - Method in class org.opencb.cellbase.server.rest.genomic.VariantWSServer
getVariantString() - Method in class org.opencb.cellbase.lib.model.ClinicalVariation: Deprecated.
getVariantType(Variant) - Static method in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
getVariantTypes() - Method in interface org.opencb.cellbase.core.api.ClinicalDBAdaptor
getVariantTypes() - Method in class org.opencb.cellbase.lib.impl.ClinicalLegacyMongoDBAdaptor: Deprecated.
getVariantTypes() - Method in class org.opencb.cellbase.lib.impl.ClinicalMongoDBAdaptor
getVariantTypes() - Method in class org.opencb.cellbase.server.rest.clinical.ClinicalWSServer
getVariation(List<String>, QueryOptions) - Method in class org.opencb.cellbase.client.rest.GeneClient
getVariation(List<String>, QueryOptions) - Method in class org.opencb.cellbase.client.rest.GenomicRegionClient
getVariation(String, QueryOptions) - Method in class org.opencb.cellbase.client.rest.TranscriptClient
getVariationByRegion(String) - Method in class org.opencb.cellbase.server.rest.genomic.RegionWSServer
getVariationClient() - Method in class org.opencb.cellbase.client.rest.CellBaseClient
getVariationDBAdaptor(String) - Method in class org.opencb.cellbase.core.api.DBAdaptorFactory
getVariationDBAdaptor(String, String) - Method in class org.opencb.cellbase.core.api.DBAdaptorFactory
getVariationDBAdaptor(String) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptorFactory
getVariationDBAdaptor(String, String) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptorFactory
getVariationRelatedLines(int) - Method in class org.opencb.cellbase.lib.builders.variation.AbstractVariationFile
getVariationsByTranscriptId(String) - Method in class org.opencb.cellbase.server.rest.feature.TranscriptWSServer
getVersion() - Method in class org.opencb.cellbase.client.config.ClientConfiguration
getVersion() - Method in class org.opencb.cellbase.core.config.CellBaseConfiguration
getVersion() - Method in class org.opencb.cellbase.core.config.DownloadProperties.URLProperties
getVersion() - Method in class org.opencb.cellbase.core.monitor.HealthStatus.ApplicationDetails
getVersion() - Method in class org.opencb.cellbase.lib.download.EnsemblInfo
getVersion(String) - Method in class org.opencb.cellbase.server.rest.MetaWSServer
getVertebrates() - Method in class org.opencb.cellbase.core.config.SpeciesProperties
getVirus() - Method in class org.opencb.cellbase.core.config.SpeciesProperties
getVolumeOfDistribution() - Method in class org.opencb.cellbase.core.common.drug.Drug
getWiki() - Method in class org.opencb.cellbase.core.config.CellBaseConfiguration
getWindowMasker() - Method in class org.opencb.cellbase.core.config.DownloadProperties
getXref(String, QueryOptions) - Method in class org.opencb.cellbase.client.rest.VariationClient
getXRefDBAdaptor(String) - Method in class org.opencb.cellbase.core.api.DBAdaptorFactory
getXRefDBAdaptor(String, String) - Method in class org.opencb.cellbase.core.api.DBAdaptorFactory
getXRefDBAdaptor(String) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptorFactory
getXRefDBAdaptor(String, String) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptorFactory
getXrefMap(Path, Path) - Static method in class org.opencb.cellbase.lib.builders.GeneParserUtils
getXrefs() - Method in class org.opencb.cellbase.core.common.drug.Drug
getXrefs() - Method in class org.opencb.cellbase.core.common.drug.Partner
getXrefs(String) - Method in class org.opencb.cellbase.server.rest.feature.VariationWSServer
getZones() - Method in class org.opencb.cellbase.core.config.SpeciesConfiguration.ShardConfig
GitRepositoryState - Class in org.opencb.cellbase.core.common: Created by fjlopez on 26/09/16.
GRCH37_ASSEMBLY - Static variable in class org.opencb.cellbase.lib.builders.clinical.variant.ClinVarParser: Deprecated.
GRCH38_ASSEMBLY - Static variable in class org.opencb.cellbase.lib.builders.clinical.variant.ClinVarParser: Deprecated.
group(Query, QueryOptions) - Method in class org.opencb.cellbase.client.rest.FeatureClient
groupBy - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.QueryCommandOptions
groupBy(Query, String, QueryOptions) - Method in interface org.opencb.cellbase.core.api.CellBaseDBAdaptor
groupBy(Query, List<String>, QueryOptions) - Method in interface org.opencb.cellbase.core.api.CellBaseDBAdaptor
groupBy(Query, String, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ClinicalLegacyMongoDBAdaptor: Deprecated.
groupBy(Query, List<String>, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ClinicalLegacyMongoDBAdaptor: Deprecated.
groupBy(Query, String, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ClinicalMongoDBAdaptor
groupBy(Query, List<String>, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ClinicalMongoDBAdaptor
groupBy(Query, String, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ConservationMongoDBAdaptor: Deprecated.
groupBy(Query, List, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ConservationMongoDBAdaptor: Deprecated.
groupBy(Query, String, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.GeneMongoDBAdaptor
groupBy(Query, List<String>, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.GeneMongoDBAdaptor
groupBy(Query, String, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.GenomeMongoDBAdaptor
groupBy(Query, List, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.GenomeMongoDBAdaptor
groupBy(Query, String, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.MetaMongoDBAdaptor
groupBy(Query, List, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.MetaMongoDBAdaptor
groupBy(Bson, String, String, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptor
groupBy(Bson, List<String>, String, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptor
groupBy(Query, String, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ProteinMongoDBAdaptor
groupBy(Query, List<String>, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ProteinMongoDBAdaptor
groupBy(Query, String, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ProteinProteinInteractionMongoDBAdaptor
groupBy(Query, List<String>, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ProteinProteinInteractionMongoDBAdaptor
groupBy(Query, String, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.RegulationMongoDBAdaptor
groupBy(Query, List<String>, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.RegulationMongoDBAdaptor
groupBy(Query, String, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.RepeatsMongoDBAdaptor
groupBy(Query, List, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.RepeatsMongoDBAdaptor
groupBy(Query, String, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.TranscriptMongoDBAdaptor
groupBy(Query, List, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.TranscriptMongoDBAdaptor
groupBy(Query, String, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.VariantMongoDBAdaptor
groupBy(Query, List<String>, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.VariantMongoDBAdaptor
groupBy(Query, String, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.XRefMongoDBAdaptor
groupBy(Query, List<String>, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.XRefMongoDBAdaptor
groupBy(String) - Method in class org.opencb.cellbase.server.rest.feature.ClinicalLegacyWSServer: Deprecated.
groupBy(String) - Method in class org.opencb.cellbase.server.rest.feature.GeneWSServer
GroupByFields - Class in org.opencb.cellbase.client.rest.models: Created by swaathi on 20/05/16.
GroupByFields() - Constructor for class org.opencb.cellbase.client.rest.models.GroupByFields
GroupByFields(String, List<String>) - Constructor for class org.opencb.cellbase.client.rest.models.GroupByFields
groupCount(Query, QueryOptions) - Method in class org.opencb.cellbase.client.rest.FeatureClient
GroupCount - Class in org.opencb.cellbase.client.rest.models: Created by swaathi on 20/05/16.
GroupCount() - Constructor for class org.opencb.cellbase.client.rest.models.GroupCount
GroupCount(String, int) - Constructor for class org.opencb.cellbase.client.rest.models.GroupCount
GSD_FILE - Static variable in class org.opencb.cellbase.lib.EtlCommons
GSD_VERSION_FILE - Static variable in class org.opencb.cellbase.lib.EtlCommons
gunzip(byte[]) - Static method in class org.opencb.cellbase.lib.builders.utils.StringUtils: Deprecated.
gunzip() - Method in class org.opencb.cellbase.lib.builders.variation.AbstractVariationFile
Gwas - Class in org.opencb.cellbase.core.common.clinical.gwas
Gwas(String, Integer, Integer, String, String, String, String, String, String, String, String, String, String, String, String, String, String, String, String, Float, String) - Constructor for class org.opencb.cellbase.core.common.clinical.gwas.Gwas
Gwas(Gwas) - Constructor for class org.opencb.cellbase.core.common.clinical.gwas.Gwas
GWAS_DATA - Static variable in class org.opencb.cellbase.lib.EtlCommons
GWAS_FILE - Static variable in class org.opencb.cellbase.lib.EtlCommons
GwasParser - Class in org.opencb.cellbase.lib.builders.clinical.variant: Deprecated.
GwasParser(Path, Path, CellBaseSerializer) - Constructor for class org.opencb.cellbase.lib.builders.clinical.variant.GwasParser: Deprecated.
GwasStudy - Class in org.opencb.cellbase.core.common.clinical.gwas: Created by parce on 5/12/14.
GwasStudy() - Constructor for class org.opencb.cellbase.core.common.clinical.gwas.GwasStudy
GwasStudy(String, String, String, String, String, String, String, String, String) - Constructor for class org.opencb.cellbase.core.common.clinical.gwas.GwasStudy
GwasTest - Class in org.opencb.cellbase.core.common.clinical.gwas: Created by parce on 5/12/14.
GwasTest() - Constructor for class org.opencb.cellbase.core.common.clinical.gwas.GwasTest
GwasTest(Float, Float, String, String, String) - Constructor for class org.opencb.cellbase.core.common.clinical.gwas.GwasTest
GwasTrait - Class in org.opencb.cellbase.core.common.clinical.gwas: Created by parce on 5/12/14.
GwasTrait() - Constructor for class org.opencb.cellbase.core.common.clinical.gwas.GwasTrait
GwasTrait(String, String) - Constructor for class org.opencb.cellbase.core.common.clinical.gwas.GwasTrait
gzip - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.VariantAnnotationCommandOptions
gzip(String) - Static method in class org.opencb.cellbase.lib.builders.utils.StringUtils: Deprecated.
gzip() - Method in class org.opencb.cellbase.lib.builders.variation.AbstractVariationFile

H

HAPLOTYPE_FIELD_NAME - Static variable in class org.opencb.cellbase.lib.builders.clinical.variant.ClinicalIndexer
HAPLOTYPE_STRING_SEPARATOR - Static variable in class org.opencb.cellbase.lib.builders.clinical.variant.ClinicalIndexer
hashCode() - Method in class org.opencb.cellbase.app.cli.main.annotation.SequenceOntologyTermComparisonObject
hashCode() - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasStudy
hashCode() - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasTrait
hashCode() - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.CdnaCoord
hasNext() - Method in class org.opencb.cellbase.lib.VariantMongoIterator
HealthStatus - Class in org.opencb.cellbase.core.monitor: Created by fjlopez on 20/09/17.
HealthStatus() - Constructor for class org.opencb.cellbase.core.monitor.HealthStatus
HealthStatus.ApplicationDetails - Class in org.opencb.cellbase.core.monitor
HealthStatus.ApplicationDetails.DependenciesStatus - Class in org.opencb.cellbase.core.monitor
HealthStatus.ApplicationDetails.DependenciesStatus.DatastoreDependenciesStatus - Class in org.opencb.cellbase.core.monitor
HealthStatus.ApplicationDetails.DependenciesStatus.DatastoreDependenciesStatus.DatastoreStatus - Class in org.opencb.cellbase.core.monitor
HealthStatus.ApplicationDetails.Version - Class in org.opencb.cellbase.core.monitor
HealthStatus.Infrastructure - Class in org.opencb.cellbase.core.monitor
HealthStatus.Service - Class in org.opencb.cellbase.core.monitor
HealthStatus.ServiceStatus - Enum in org.opencb.cellbase.core.monitor
help - Variable in class org.opencb.cellbase.app.cli.CliOptionsParser.CommonCommandOptions
help - Variable in class org.opencb.cellbase.app.cli.CliOptionsParser.GeneralOptions
help() - Method in class org.opencb.cellbase.server.rest.feature.GeneWSServer
help() - Method in class org.opencb.cellbase.server.rest.feature.IdWSServer
help() - Method in class org.opencb.cellbase.server.rest.feature.ProteinWSServer
help() - Method in class org.opencb.cellbase.server.rest.feature.TranscriptWSServer
help() - Method in class org.opencb.cellbase.server.rest.GenericRestWSServer
help() - Method in class org.opencb.cellbase.server.rest.genomic.ChromosomeWSServer
help() - Method in class org.opencb.cellbase.server.rest.genomic.RegionWSServer
help() - Method in interface org.opencb.cellbase.server.rest.IWSServer
help() - Method in class org.opencb.cellbase.server.rest.network.PathwayWSServer
help() - Method in class org.opencb.cellbase.server.rest.network.PathwayWSServerMongo
help() - Method in class org.opencb.cellbase.server.rest.regulatory.MiRnaGeneWSServer
help() - Method in class org.opencb.cellbase.server.rest.regulatory.MiRnaMatureWSServer
help() - Method in class org.opencb.cellbase.server.rest.regulatory.TfWSServer
HgvsCalculator - Class in org.opencb.cellbase.core.variant.annotation.hgvs: Created by fjlopez on 26/01/17.
HgvsCalculator(GenomeDBAdaptor) - Constructor for class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsCalculator
HgvsDeletionCalculator - Class in org.opencb.cellbase.core.variant.annotation.hgvs: Created by fjlopez on 15/06/17.
HgvsDeletionCalculator(GenomeDBAdaptor) - Constructor for class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsDeletionCalculator
HgvsInsertionCalculator - Class in org.opencb.cellbase.core.variant.annotation.hgvs: Created by fjlopez on 15/06/17.
HgvsInsertionCalculator(GenomeDBAdaptor) - Constructor for class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsInsertionCalculator
HgvsSNVCalculator - Class in org.opencb.cellbase.core.variant.annotation.hgvs: Created by fjlopez on 15/06/17.
HgvsSNVCalculator(GenomeDBAdaptor) - Constructor for class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsSNVCalculator
HgvsStringBuilder - Class in org.opencb.cellbase.core.variant.annotation.hgvs: Builder to get the hgvs identifier properly formatted.
HgvsStringBuilder() - Constructor for class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsStringBuilder
histogram - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.QueryCommandOptions
Histogram - Class in org.opencb.cellbase.server.rest.genomic: Deprecated.
Histogram(List<?>, int) - Constructor for class org.opencb.cellbase.server.rest.genomic.Histogram: Deprecated.
HPO_DATA - Static variable in class org.opencb.cellbase.lib.EtlCommons
httpServletRequest - Variable in class org.opencb.cellbase.server.rest.GenericRestWSServer

I

IARCTP53_FILE - Static variable in class org.opencb.cellbase.lib.EtlCommons
IARCTP53_GERMLINE_FILE - Static variable in class org.opencb.cellbase.lib.EtlCommons
IARCTP53_GERMLINE_REFERENCES_FILE - Static variable in class org.opencb.cellbase.lib.EtlCommons
IARCTP53_SOMATIC_FILE - Static variable in class org.opencb.cellbase.lib.EtlCommons
IARCTP53_SOMATIC_REFERENCES_FILE - Static variable in class org.opencb.cellbase.lib.EtlCommons
IARCTP53Indexer - Class in org.opencb.cellbase.lib.builders.clinical.variant: Created by fjlopez on 21/11/16.
IARCTP53Indexer(Path, Path, Path, Path, boolean, Path, String, RocksDB) - Constructor for class org.opencb.cellbase.lib.builders.clinical.variant.IARCTP53Indexer
id - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.QueryCommandOptions
IdWSServer - Class in org.opencb.cellbase.server.rest.feature
IdWSServer(String, String, UriInfo, HttpServletRequest) - Constructor for class org.opencb.cellbase.server.rest.feature.IdWSServer
IG_C_GENE - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
IG_C_PSEUDOGENE - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
IG_D_GENE - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
IG_J_GENE - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
IG_J_PSEUDOGENE - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
IG_V_GENE - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
IG_V_PSEUDOGENE - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
IGNORE_PHASE - Static variable in interface org.opencb.cellbase.core.variant.annotation.VariantAnnotator
ignorePhase - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.VariantAnnotationCommandOptions
imprecise - Variable in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
IMPRECISE - Static variable in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
include - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.QueryCommandOptions
include - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.VariantAnnotationCommandOptions
include - Variable in class org.opencb.cellbase.server.rest.GenericRestWSServer
INCOMPLETE_TERMINAL_CODON_VARIANT - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
index - Variable in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.LoadCommandOptions
index() - Method in class org.opencb.cellbase.lib.builders.clinical.variant.ClinVarIndexer
index() - Method in class org.opencb.cellbase.lib.builders.clinical.variant.CosmicIndexer
index() - Method in class org.opencb.cellbase.lib.builders.clinical.variant.DOCMIndexer
index() - Method in class org.opencb.cellbase.lib.builders.clinical.variant.IARCTP53Indexer
IndexCommandExecutor - Class in org.opencb.cellbase.app.cli.admin.executors
IndexCommandExecutor(AdminCliOptionsParser.IndexCommandOptions) - Constructor for class org.opencb.cellbase.app.cli.admin.executors.IndexCommandExecutor
IndexCommandOptions() - Constructor for class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.IndexCommandOptions
IndexManager - Class in org.opencb.cellbase.lib.indexer
IndexManager(CellBaseConfiguration) - Constructor for class org.opencb.cellbase.lib.indexer.IndexManager
INFRAME_DELETION - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
INFRAME_INSERTION - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
INFRAME_VARIANT - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
Infrastructure() - Constructor for class org.opencb.cellbase.core.monitor.HealthStatus.Infrastructure
Infrastructure(int, String) - Constructor for class org.opencb.cellbase.core.monitor.HealthStatus.Infrastructure
init() - Method in class org.opencb.cellbase.core.loader.CellBaseLoader
init() - Method in class org.opencb.cellbase.lib.loader.MongoDBCellBaseLoader: Deprecated.
init(FilterConfig) - Method in class org.opencb.cellbase.server.rest.CORSFilter
initialized - Variable in class org.opencb.cellbase.server.rest.GenericRestWSServer
INITIATOR_CODON_VARIANT - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
innerFields - Variable in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.LoadCommandOptions
innerFields - Variable in class org.opencb.cellbase.core.loader.CellBaseLoader
input - Variable in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.LoadCommandOptions
input - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.VariantAnnotationCommandOptions
insertByType(PreparedStatement, List<String>, List<String>) - Static method in class org.opencb.cellbase.lib.builders.RegulatoryRegionParser
install(String, String) - Method in class org.opencb.cellbase.lib.install.InstallManager: Add shard indexes and ranges in Mongo based on config file entries.
InstallCommandExecutor - Class in org.opencb.cellbase.app.cli.admin.executors
InstallCommandExecutor(AdminCliOptionsParser.InstallCommandOptions) - Constructor for class org.opencb.cellbase.app.cli.admin.executors.InstallCommandExecutor
InstallCommandOptions() - Constructor for class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.InstallCommandOptions
InstallManager - Class in org.opencb.cellbase.lib.install
InstallManager(CellBaseConfiguration) - Constructor for class org.opencb.cellbase.lib.install.InstallManager
InteractionParser - Class in org.opencb.cellbase.lib.builders: Created with IntelliJ IDEA.
InteractionParser(Path, String, CellBaseSerializer) - Constructor for class org.opencb.cellbase.lib.builders.InteractionParser
Interactor - Class in org.opencb.cellbase.core.common.drug: Created by mbleda on 1/15/14.
Interactor(String) - Constructor for class org.opencb.cellbase.core.common.drug.Interactor
Interactor(String, String, String) - Constructor for class org.opencb.cellbase.core.common.drug.Interactor
INTERGENIC_VARIANT - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
interval - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.QueryCommandOptions
Interval - Class in org.opencb.cellbase.server.rest.genomic: Deprecated.
Interval(int, int, float) - Constructor for class org.opencb.cellbase.server.rest.genomic.Interval: Deprecated.
IntervalFeatureFrequency - Class in org.opencb.cellbase.core.common
IntervalFeatureFrequency(int, int, int, int, float) - Constructor for class org.opencb.cellbase.core.common.IntervalFeatureFrequency
INTRON_VARIANT - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
IS_SYNONYMOUS_CODON - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
isCoding(Transcript) - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsCalculator
isEmpty() - Method in class org.opencb.cellbase.app.cli.main.annotation.VariantAnnotationDiff
isEmpty() - Method in class org.opencb.cellbase.lib.builders.variation.AbstractVariationFile
isHelp() - Method in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser
isHelp() - Method in class org.opencb.cellbase.app.cli.CliOptionsParser
isHelp() - Method in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser
isMissing(String) - Static method in class org.opencb.cellbase.core.variant.PhasedQueryManager
isMissing(String) - Static method in class org.opencb.cellbase.lib.EtlCommons
isSnp() - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
isStartCodon(boolean, String) - Static method in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
isStopCodon(String) - Static method in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
isStopCodon(boolean, String) - Static method in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
isSynonymousCodon(String, String) - Static method in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
isSynonymousCodon(Boolean, String, String) - Static method in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
isVerbose() - Method in class org.opencb.cellbase.app.cli.CommandExecutor
iterator() - Method in interface org.opencb.cellbase.core.api.CellBaseDBAdaptor
iterator(Query, QueryOptions) - Method in interface org.opencb.cellbase.core.api.CellBaseDBAdaptor
iterator(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ClinicalLegacyMongoDBAdaptor: Deprecated.
iterator(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ClinicalMongoDBAdaptor
iterator(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ConservationMongoDBAdaptor: Deprecated.
iterator(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.GeneMongoDBAdaptor
iterator(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.GenomeMongoDBAdaptor
iterator(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.MetaMongoDBAdaptor
iterator(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ProteinMongoDBAdaptor
iterator(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ProteinProteinInteractionMongoDBAdaptor
iterator(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.RegulationMongoDBAdaptor
iterator(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.RepeatsMongoDBAdaptor
iterator(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.TranscriptMongoDBAdaptor
iterator(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.VariantMongoDBAdaptor
iterator(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.XRefMongoDBAdaptor
IWSServer - Interface in org.opencb.cellbase.server.rest

J

jCommander - Variable in class org.opencb.cellbase.app.cli.CliOptionsParser
jsonObjectMapper - Variable in class org.opencb.cellbase.app.cli.main.annotation.indexers.VariantIndexer
jsonObjectMapper - Static variable in class org.opencb.cellbase.client.rest.ParentRestClient
jsonObjectMapper - Variable in class org.opencb.cellbase.lib.loader.converters.MongoDBTypeConverter
jsonObjectMapper - Variable in class org.opencb.cellbase.server.rest.GenericRestWSServer
jsonObjectWriter - Variable in class org.opencb.cellbase.app.cli.main.annotation.indexers.VariantIndexer
jsonObjectWriter - Static variable in class org.opencb.cellbase.lib.builders.clinical.variant.ClinicalIndexer
jsonObjectWriter - Variable in class org.opencb.cellbase.lib.loader.converters.MongoDBTypeConverter
jsonObjectWriter - Static variable in class org.opencb.cellbase.server.rest.GenericRestWSServer
JsonStringAnnotatorTask - Class in org.opencb.cellbase.app.cli.main.annotation: Deprecated.
JsonStringAnnotatorTask(List<VariantAnnotator>) - Constructor for class org.opencb.cellbase.app.cli.main.annotation.JsonStringAnnotatorTask: Deprecated.
JsonStringAnnotatorTask(List<VariantAnnotator>, boolean, VariantNormalizer.VariantNormalizerConfig) - Constructor for class org.opencb.cellbase.app.cli.main.annotation.JsonStringAnnotatorTask: Deprecated.
justify(Variant, int, int, String, String, String) - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsCalculator: Justify an indel to the left or right along a sequence 'seq'.

K

key() - Method in enum org.opencb.cellbase.core.api.ClinicalDBAdaptor.QueryParams
key() - Method in enum org.opencb.cellbase.core.api.ConservationDBAdaptor.QueryParams: Deprecated.
key() - Method in enum org.opencb.cellbase.core.api.GeneDBAdaptor.QueryParams
key() - Method in enum org.opencb.cellbase.core.api.GenomeDBAdaptor.QueryParams
key() - Method in enum org.opencb.cellbase.core.api.ProteinDBAdaptor.QueryParams
key() - Method in enum org.opencb.cellbase.core.api.ProteinProteinInteractionDBAdaptor.QueryParams
key() - Method in enum org.opencb.cellbase.core.api.RegulationDBAdaptor.QueryParams
key() - Method in enum org.opencb.cellbase.core.api.RepeatsDBAdaptor.QueryParams
key() - Method in enum org.opencb.cellbase.core.api.TranscriptDBAdaptor.QueryParams
key() - Method in enum org.opencb.cellbase.core.api.VariantDBAdaptor.QueryParams
key() - Method in enum org.opencb.cellbase.core.api.XRefDBAdaptor.QueryParams
KNOWN_NCRNA - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils

L

limit - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.QueryCommandOptions
LIMIT - Static variable in class org.opencb.cellbase.client.rest.ParentRestClient
limit - Variable in class org.opencb.cellbase.server.rest.GenericRestWSServer
LINCRNA - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
list(Query) - Method in class org.opencb.cellbase.client.rest.GeneClient: Deprecated.
load(InputStream) - Static method in class org.opencb.cellbase.client.config.ClientConfiguration
load(InputStream, CellBaseConfiguration.ConfigurationFileFormat) - Static method in class org.opencb.cellbase.client.config.ClientConfiguration
load(Path) - Static method in class org.opencb.cellbase.core.config.CellBaseConfiguration
load(InputStream) - Static method in class org.opencb.cellbase.core.config.CellBaseConfiguration
load(InputStream, CellBaseConfiguration.ConfigurationFileFormat) - Static method in class org.opencb.cellbase.core.config.CellBaseConfiguration
load(Path, String) - Method in class org.opencb.cellbase.core.loader.LoadRunner
load(Path, String, String, String[]) - Method in class org.opencb.cellbase.core.loader.LoadRunner
load(List<Document>) - Method in class org.opencb.cellbase.lib.loader.MongoDBCellBaseLoader: Deprecated.
loadCellBaseConfiguration() - Method in class org.opencb.cellbase.app.cli.CommandExecutor
loadClientConfiguration() - Method in class org.opencb.cellbase.app.cli.CommandExecutor: This method attempts to first data configuration from CLI parameter, if not present then uses the configuration from installation directory, if not exists then loads JAR client-configuration.yml.
LoadCommandExecutor - Class in org.opencb.cellbase.app.cli.admin.executors: Created by imedina on 03/02/15.
LoadCommandExecutor(AdminCliOptionsParser.LoadCommandOptions) - Constructor for class org.opencb.cellbase.app.cli.admin.executors.LoadCommandExecutor
LoadCommandOptions() - Constructor for class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.LoadCommandOptions
loader - Variable in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.LoadCommandOptions
LoaderException - Exception in org.opencb.cellbase.core.loader: Created by parce on 27/02/15.
LoaderException(String) - Constructor for exception org.opencb.cellbase.core.loader.LoaderException
LoaderException(Exception) - Constructor for exception org.opencb.cellbase.core.loader.LoaderException
loaderParams - Variable in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.LoadCommandOptions
LoadRunner - Class in org.opencb.cellbase.core.loader: Created by parce on 18/02/15.
LoadRunner(String, String, int, CellBaseConfiguration) - Constructor for class org.opencb.cellbase.core.loader.LoadRunner
local - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.VariantAnnotationCommandOptions
logger - Variable in class org.opencb.cellbase.app.cli.CommandExecutor
logger - Variable in class org.opencb.cellbase.client.rest.ParentRestClient
logger - Variable in class org.opencb.cellbase.core.api.DBAdaptorFactory
logger - Variable in class org.opencb.cellbase.core.loader.CellBaseLoader
logger - Variable in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
logger - Variable in class org.opencb.cellbase.core.variant.AnnotationBasedPhasedQueryManager
logger - Variable in class org.opencb.cellbase.lib.builders.CellBaseParser
logger - Static variable in class org.opencb.cellbase.lib.builders.clinical.variant.ClinicalIndexer
logger - Variable in class org.opencb.cellbase.lib.builders.DrugParser: Deprecated.
logger - Variable in class org.opencb.cellbase.lib.builders.ProteinParser
logger - Variable in class org.opencb.cellbase.lib.builders.variation.AbstractVariationFile
logger - Variable in class org.opencb.cellbase.lib.impl.MongoDBAdaptor
logger - Variable in class org.opencb.cellbase.server.rest.GenericRestWSServer
logLevel - Variable in class org.opencb.cellbase.app.cli.CliOptionsParser.CommonCommandOptions
logLevel - Variable in class org.opencb.cellbase.app.cli.CommandExecutor
logQuery(String) - Method in class org.opencb.cellbase.server.rest.GenericRestWSServer
LRG_GENE - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils

M

main(String[]) - Static method in class org.opencb.cellbase.app.cli.admin.AdminMain
main(String[]) - Static method in class org.opencb.cellbase.app.cli.main.CellBaseMain
makeDir(Path) - Method in class org.opencb.cellbase.app.cli.CommandExecutor
mapper - Static variable in class org.opencb.cellbase.lib.builders.clinical.variant.ClinicalIndexer
MATURE_MIRNA_VARIANT - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
maxOpenFiles - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.VariantAnnotationCommandOptions
MERGE - Static variable in interface org.opencb.cellbase.core.api.FeatureDBAdaptor
META - Static variable in class org.opencb.cellbase.client.rest.ParentRestClient
MetaClient - Class in org.opencb.cellbase.client.rest: Created by fjlopez on 06/07/17.
MetaClient(String, String, ClientConfiguration) - Constructor for class org.opencb.cellbase.client.rest.MetaClient
MetaMongoDBAdaptor - Class in org.opencb.cellbase.lib.impl: Created by fjlopez on 07/06/16.
MetaMongoDBAdaptor(String, String, MongoDataStore) - Constructor for class org.opencb.cellbase.lib.impl.MetaMongoDBAdaptor
MetaWSServer - Class in org.opencb.cellbase.server.rest: Created by imedina on 04/08/15.
MetaWSServer(String, UriInfo, HttpServletRequest) - Constructor for class org.opencb.cellbase.server.rest.MetaWSServer
MIRNA - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
MIRNA_PSEUDOGENE - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
MirnaDisease - Class in org.opencb.cellbase.core.common.regulatory: MirnaDisease generated by hbm2java.
MirnaDisease() - Constructor for class org.opencb.cellbase.core.common.regulatory.MirnaDisease
MirnaDisease(int, MirnaGene, String, String, String, String) - Constructor for class org.opencb.cellbase.core.common.regulatory.MirnaDisease
MirnaGene - Class in org.opencb.cellbase.core.common.regulatory: MirnaGene generated by hbm2java.
MirnaGene() - Constructor for class org.opencb.cellbase.core.common.regulatory.MirnaGene
MirnaGene(int, String, String, String, String, String) - Constructor for class org.opencb.cellbase.core.common.regulatory.MirnaGene
MirnaGene(int, String, String, String, String, String, Set<MirnaDisease>, Set<MirnaGeneToMature>, Set<MirnaToGene>) - Constructor for class org.opencb.cellbase.core.common.regulatory.MirnaGene
MirnaGeneToMature - Class in org.opencb.cellbase.core.common.regulatory: MirnaGeneToMature generated by hbm2java.
MirnaGeneToMature() - Constructor for class org.opencb.cellbase.core.common.regulatory.MirnaGeneToMature
MirnaGeneToMature(int, MirnaGene, MirnaMature) - Constructor for class org.opencb.cellbase.core.common.regulatory.MirnaGeneToMature
MiRnaGeneWSServer - Class in org.opencb.cellbase.server.rest.regulatory
MiRnaGeneWSServer(String, String, UriInfo, HttpServletRequest) - Constructor for class org.opencb.cellbase.server.rest.regulatory.MiRnaGeneWSServer
MirnaMature - Class in org.opencb.cellbase.core.common.regulatory: Deprecated.
MirnaMature() - Constructor for class org.opencb.cellbase.core.common.regulatory.MirnaMature: Deprecated.
MirnaMature(int, String, String, String) - Constructor for class org.opencb.cellbase.core.common.regulatory.MirnaMature: Deprecated.
MirnaMature(int, String, String, String, Set<MirnaTarget>, Set<MirnaGeneToMature>) - Constructor for class org.opencb.cellbase.core.common.regulatory.MirnaMature: Deprecated.
MiRnaMatureWSServer - Class in org.opencb.cellbase.server.rest.regulatory
MiRnaMatureWSServer(String, String, UriInfo, HttpServletRequest) - Constructor for class org.opencb.cellbase.server.rest.regulatory.MiRnaMatureWSServer
MirnaTarget - Class in org.opencb.cellbase.core.common.regulatory: MirnaTarget generated by hbm2java.
MirnaTarget() - Constructor for class org.opencb.cellbase.core.common.regulatory.MirnaTarget
MirnaTarget(int, Gene, MirnaMature, String, String, String, String, int, int, String, double, String, String) - Constructor for class org.opencb.cellbase.core.common.regulatory.MirnaTarget
MirnaToGene - Class in org.opencb.cellbase.core.common.regulatory: MirnaToGene generated by hbm2java.
MirnaToGene() - Constructor for class org.opencb.cellbase.core.common.regulatory.MirnaToGene
MirnaToGene(int, MirnaGene, Transcript, Gene) - Constructor for class org.opencb.cellbase.core.common.regulatory.MirnaToGene
MISC_RNA - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
MISC_RNA_PSEUDOGENE - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
MISSENSE_VARIANT - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
modeInheritanceLabels() - Method in class org.opencb.cellbase.client.rest.ClinicalVariantClient
MODEOFINHERITANCE_MAP - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
mongoDataStore - Variable in class org.opencb.cellbase.lib.impl.MongoDBAdaptor
MongoDBAdaptor - Class in org.opencb.cellbase.lib.impl
MongoDBAdaptor(MongoDataStore) - Constructor for class org.opencb.cellbase.lib.impl.MongoDBAdaptor
MongoDBAdaptor(String, String, MongoDataStore) - Constructor for class org.opencb.cellbase.lib.impl.MongoDBAdaptor
MongoDBAdaptorFactory - Class in org.opencb.cellbase.lib.impl
MongoDBAdaptorFactory(CellBaseConfiguration) - Constructor for class org.opencb.cellbase.lib.impl.MongoDBAdaptorFactory
MongoDBCellBaseLoader - Class in org.opencb.cellbase.lib.loader: Deprecated.
MongoDBCellBaseLoader(BlockingQueue<List<String>>, String, String) - Constructor for class org.opencb.cellbase.lib.loader.MongoDBCellBaseLoader: Deprecated.
MongoDBCellBaseLoader(BlockingQueue<List<String>>, String, String, String, String[], CellBaseConfiguration) - Constructor for class org.opencb.cellbase.lib.loader.MongoDBCellBaseLoader: Deprecated.
mongoDBCollection - Variable in class org.opencb.cellbase.lib.impl.MongoDBAdaptor
MongoDBCollectionConfiguration - Class in org.opencb.cellbase.lib: Created by imedina on 19/03/15.
MongoDBCollectionConfiguration() - Constructor for class org.opencb.cellbase.lib.MongoDBCollectionConfiguration
MongoDBDatabaseCredentials - Class in org.opencb.cellbase.core.config: Created by imedina on 19/08/16.
MongoDBDatabaseCredentials() - Constructor for class org.opencb.cellbase.core.config.MongoDBDatabaseCredentials
MongoDBDatabaseCredentials(String, String, String, List<MongoDBDatabaseCredentials.ReplicaSet>, Map<String, String>) - Constructor for class org.opencb.cellbase.core.config.MongoDBDatabaseCredentials
MongoDBDatabaseCredentials.ReplicaSet - Class in org.opencb.cellbase.core.config
MongoDBShardUtils - Class in org.opencb.cellbase.lib.install
MongoDBShardUtils() - Constructor for class org.opencb.cellbase.lib.install.MongoDBShardUtils
MongoDBTypeConverter<DATAMODEL,STORAGESCHEMA> - Class in org.opencb.cellbase.lib.loader.converters: Created by imedina on 01/09/14.
MongoDBTypeConverter() - Constructor for class org.opencb.cellbase.lib.loader.converters.MongoDBTypeConverter
Monitor - Class in org.opencb.cellbase.core.monitor: Created by fjlopez on 20/09/17.
Monitor(DBAdaptorFactory) - Constructor for class org.opencb.cellbase.core.monitor.Monitor
Monitor(String) - Constructor for class org.opencb.cellbase.core.monitor.Monitor
monitor - Variable in class org.opencb.cellbase.server.rest.GenericRestWSServer
MOTIF_FEATURES_FILE - Static variable in class org.opencb.cellbase.lib.EtlCommons
MT - Static variable in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
MT_A_TO_CODON - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
MT_CODON_TO_A - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
MT_IS_SYNONYMOUS_CODON - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
MT_RRNA - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
MT_TRNA - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils

N

nativeGet(Query, QueryOptions) - Method in interface org.opencb.cellbase.core.api.CellBaseDBAdaptor
nativeGet(List<Query>, QueryOptions) - Method in interface org.opencb.cellbase.core.api.CellBaseDBAdaptor
nativeGet(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ClinicalLegacyMongoDBAdaptor: Deprecated.
nativeGet(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ClinicalMongoDBAdaptor
nativeGet(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ConservationMongoDBAdaptor: Deprecated.
nativeGet(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.GeneMongoDBAdaptor
nativeGet(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.GenomeMongoDBAdaptor
nativeGet(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.MetaMongoDBAdaptor
nativeGet(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ProteinMongoDBAdaptor
nativeGet(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ProteinProteinInteractionMongoDBAdaptor
nativeGet(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.RegulationMongoDBAdaptor
nativeGet(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.RepeatsMongoDBAdaptor
nativeGet(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.TranscriptMongoDBAdaptor
nativeGet(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.VariantMongoDBAdaptor
nativeGet(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.XRefMongoDBAdaptor
nativeIterator() - Method in interface org.opencb.cellbase.core.api.CellBaseDBAdaptor
nativeIterator(Query, QueryOptions) - Method in interface org.opencb.cellbase.core.api.CellBaseDBAdaptor
nativeIterator(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ClinicalLegacyMongoDBAdaptor: Deprecated.
nativeIterator(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ClinicalMongoDBAdaptor
nativeIterator(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ConservationMongoDBAdaptor: Deprecated.
nativeIterator(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.GeneMongoDBAdaptor
nativeIterator(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.GenomeMongoDBAdaptor
nativeIterator(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.MetaMongoDBAdaptor
nativeIterator(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ProteinMongoDBAdaptor
nativeIterator(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ProteinProteinInteractionMongoDBAdaptor
nativeIterator(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.RegulationMongoDBAdaptor
nativeIterator(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.RepeatsMongoDBAdaptor
nativeIterator(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.TranscriptMongoDBAdaptor
nativeIterator(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.VariantMongoDBAdaptor
nativeIterator(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.XRefMongoDBAdaptor
nativeNext(Query, QueryOptions) - Method in interface org.opencb.cellbase.core.api.FeatureDBAdaptor
nativeNext(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ClinicalLegacyMongoDBAdaptor: Deprecated.
nativeNext(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ClinicalMongoDBAdaptor
nativeNext(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.GeneMongoDBAdaptor
nativeNext(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.RegulationMongoDBAdaptor
nativeNext(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.RepeatsMongoDBAdaptor
nativeNext(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.TranscriptMongoDBAdaptor
nativeNext(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.VariantMongoDBAdaptor
NEIGHBOURING_SEQUENCE_SIZE - Static variable in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsCalculator
newSequenceOntologyTerm(String) - Static method in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
next(String) - Method in class org.opencb.cellbase.client.rest.FeatureClient
next(Query, QueryOptions) - Method in interface org.opencb.cellbase.core.api.FeatureDBAdaptor
next(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ClinicalLegacyMongoDBAdaptor: Deprecated.
next(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.ClinicalMongoDBAdaptor
next(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.GeneMongoDBAdaptor
next(String, int, QueryOptions, MongoDBCollection) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptor
next(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.RegulationMongoDBAdaptor
next(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.RepeatsMongoDBAdaptor
next(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.TranscriptMongoDBAdaptor
next(Query, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.VariantMongoDBAdaptor
next() - Method in class org.opencb.cellbase.lib.VariantMongoIterator
NMD_TRANSCRIPT_VARIANT - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
NO_EXON_OVERLAP - Static variable in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
noImprecision - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.VariantAnnotationCommandOptions
NON_CODING - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
NON_CODING_TRANSCRIPT_EXON_VARIANT - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
NON_CODING_TRANSCRIPT_VARIANT - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
NON_STOP_DECAY - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
NONSENSE_MEDIATED_DECAY - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
normalize(Variant, boolean) - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsCalculator
normalize - Variable in class org.opencb.cellbase.lib.builders.clinical.variant.ClinicalIndexer
normalizer - Variable in class org.opencb.cellbase.lib.builders.clinical.variant.ClinicalIndexer
numberIndexedRecords - Variable in class org.opencb.cellbase.lib.builders.clinical.variant.ClinicalIndexer
numberNewVariants - Variable in class org.opencb.cellbase.lib.builders.clinical.variant.ClinicalIndexer
numberVariantUpdates - Variable in class org.opencb.cellbase.lib.builders.clinical.variant.ClinicalIndexer
numThreads - Variable in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.LoadCommandOptions
numThreads - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.VariantAnnotationCommandOptions

O

objectMapper - Variable in class org.opencb.cellbase.lib.impl.MongoDBAdaptor
open() - Method in class org.opencb.cellbase.app.cli.main.annotation.BenchmarkDataWriter
open() - Method in class org.opencb.cellbase.app.cli.main.annotation.CellBaseLocalVariantAnnotator
open() - Method in class org.opencb.cellbase.app.cli.main.annotation.CellBaseWSVariantAnnotator
open() - Method in class org.opencb.cellbase.app.cli.main.annotation.indexers.VariantIndexer
open() - Method in class org.opencb.cellbase.app.cli.main.annotation.PopulationFrequenciesAnnotator
open() - Method in class org.opencb.cellbase.app.cli.main.annotation.VariationDataReader
open() - Method in class org.opencb.cellbase.app.cli.main.annotation.VcfVariantAnnotator
open(String, String) - Method in class org.opencb.cellbase.core.api.DBAdaptorFactory
open() - Method in interface org.opencb.cellbase.core.variant.annotation.VariantAnnotator
open(String, String) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptorFactory
options - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.QueryCommandOptions
org.opencb.cellbase.app.cli - package org.opencb.cellbase.app.cli
org.opencb.cellbase.app.cli.admin - package org.opencb.cellbase.app.cli.admin
org.opencb.cellbase.app.cli.admin.executors - package org.opencb.cellbase.app.cli.admin.executors
org.opencb.cellbase.app.cli.main - package org.opencb.cellbase.app.cli.main
org.opencb.cellbase.app.cli.main.annotation - package org.opencb.cellbase.app.cli.main.annotation
org.opencb.cellbase.app.cli.main.annotation.indexers - package org.opencb.cellbase.app.cli.main.annotation.indexers
org.opencb.cellbase.app.cli.main.executors - package org.opencb.cellbase.app.cli.main.executors
org.opencb.cellbase.client.config - package org.opencb.cellbase.client.config
org.opencb.cellbase.client.rest - package org.opencb.cellbase.client.rest
org.opencb.cellbase.client.rest.models - package org.opencb.cellbase.client.rest.models
org.opencb.cellbase.client.rest.models.mixin - package org.opencb.cellbase.client.rest.models.mixin
org.opencb.cellbase.core - package org.opencb.cellbase.core
org.opencb.cellbase.core.api - package org.opencb.cellbase.core.api
org.opencb.cellbase.core.common - package org.opencb.cellbase.core.common
org.opencb.cellbase.core.common.clinical - package org.opencb.cellbase.core.common.clinical
org.opencb.cellbase.core.common.clinical.gwas - package org.opencb.cellbase.core.common.clinical.gwas
org.opencb.cellbase.core.common.drug - package org.opencb.cellbase.core.common.drug
org.opencb.cellbase.core.common.genedisease - package org.opencb.cellbase.core.common.genedisease
org.opencb.cellbase.core.common.regulatory - package org.opencb.cellbase.core.common.regulatory
org.opencb.cellbase.core.config - package org.opencb.cellbase.core.config
org.opencb.cellbase.core.exception - package org.opencb.cellbase.core.exception
org.opencb.cellbase.core.loader - package org.opencb.cellbase.core.loader
org.opencb.cellbase.core.monitor - package org.opencb.cellbase.core.monitor
org.opencb.cellbase.core.result - package org.opencb.cellbase.core.result
org.opencb.cellbase.core.serializer - package org.opencb.cellbase.core.serializer
org.opencb.cellbase.core.variant - package org.opencb.cellbase.core.variant
org.opencb.cellbase.core.variant.annotation - package org.opencb.cellbase.core.variant.annotation
org.opencb.cellbase.core.variant.annotation.hgvs - package org.opencb.cellbase.core.variant.annotation.hgvs
org.opencb.cellbase.lib - package org.opencb.cellbase.lib
org.opencb.cellbase.lib.builders - package org.opencb.cellbase.lib.builders
org.opencb.cellbase.lib.builders.clinical.variant - package org.opencb.cellbase.lib.builders.clinical.variant
org.opencb.cellbase.lib.builders.formats - package org.opencb.cellbase.lib.builders.formats
org.opencb.cellbase.lib.builders.utils - package org.opencb.cellbase.lib.builders.utils
org.opencb.cellbase.lib.builders.variation - package org.opencb.cellbase.lib.builders.variation
org.opencb.cellbase.lib.download - package org.opencb.cellbase.lib.download
org.opencb.cellbase.lib.impl - package org.opencb.cellbase.lib.impl
org.opencb.cellbase.lib.indexer - package org.opencb.cellbase.lib.indexer
org.opencb.cellbase.lib.install - package org.opencb.cellbase.lib.install
org.opencb.cellbase.lib.loader - package org.opencb.cellbase.lib.loader
org.opencb.cellbase.lib.loader.converters - package org.opencb.cellbase.lib.loader.converters
org.opencb.cellbase.lib.model - package org.opencb.cellbase.lib.model
org.opencb.cellbase.server - package org.opencb.cellbase.server
org.opencb.cellbase.server.exception - package org.opencb.cellbase.server.exception
org.opencb.cellbase.server.rest - package org.opencb.cellbase.server.rest
org.opencb.cellbase.server.rest.clinical - package org.opencb.cellbase.server.rest.clinical
org.opencb.cellbase.server.rest.feature - package org.opencb.cellbase.server.rest.feature
org.opencb.cellbase.server.rest.genomic - package org.opencb.cellbase.server.rest.genomic
org.opencb.cellbase.server.rest.network - package org.opencb.cellbase.server.rest.network
org.opencb.cellbase.server.rest.phenotype - package org.opencb.cellbase.server.rest.phenotype
org.opencb.cellbase.server.rest.regulatory - package org.opencb.cellbase.server.rest.regulatory
org.opencb.cellbase.server.rest.utils - package org.opencb.cellbase.server.rest.utils
ORIGIN_STRING_TO_ALLELE_ORIGIN - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
output - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.QueryCommandOptions
output - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.VariantAnnotationCommandOptions
outputFormat - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.VariantAnnotationCommandOptions
outputFormat - Variable in class org.opencb.cellbase.server.rest.GenericRestWSServer
overwriteEnvVariables(CellBaseConfiguration) - Static method in class org.opencb.cellbase.core.config.CellBaseConfiguration
overwriteEnvVariables(CellBaseConfiguration, Map<String, String>) - Static method in class org.opencb.cellbase.core.config.CellBaseConfiguration

P

params - Variable in class org.opencb.cellbase.server.rest.GenericRestWSServer
ParentRestClient<T> - Class in org.opencb.cellbase.client.rest: Created by imedina on 12/05/16.
ParentRestClient(ClientConfiguration) - Constructor for class org.opencb.cellbase.client.rest.ParentRestClient: Deprecated.
ParentRestClient(String, String, ClientConfiguration) - Constructor for class org.opencb.cellbase.client.rest.ParentRestClient
parse(String[]) - Method in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser
parse(String[]) - Method in class org.opencb.cellbase.app.cli.CliOptionsParser
parse(String[]) - Method in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser
parse() - Method in class org.opencb.cellbase.lib.builders.CaddAllAnnotationParser
parse() - Method in class org.opencb.cellbase.lib.builders.CaddScoreParser
parse() - Method in class org.opencb.cellbase.lib.builders.CellBaseParser
parse() - Method in class org.opencb.cellbase.lib.builders.clinical.variant.ClinicalVariantParser
parse() - Method in class org.opencb.cellbase.lib.builders.clinical.variant.ClinVarParser: Deprecated.
parse() - Method in class org.opencb.cellbase.lib.builders.clinical.variant.CosmicParser: Deprecated.
parse() - Method in class org.opencb.cellbase.lib.builders.clinical.variant.GwasParser: Deprecated.
parse() - Method in class org.opencb.cellbase.lib.builders.ConservationParser
parse() - Method in class org.opencb.cellbase.lib.builders.DgvParser
parse() - Method in class org.opencb.cellbase.lib.builders.DisgenetParser: Deprecated.

Parses a Disgenet file ad the one that can be downloaded from http://www.disgenet.org/ds/DisGeNET/results/all_gene_disease_associations.tar.gz and writes corresponding json objects.
parse() - Method in class org.opencb.cellbase.lib.builders.GeneExpressionAtlasParser
parse() - Method in class org.opencb.cellbase.lib.builders.GeneParser
parse() - Method in class org.opencb.cellbase.lib.builders.GenomeSequenceFastaParser
parse() - Method in class org.opencb.cellbase.lib.builders.InteractionParser
parse() - Method in class org.opencb.cellbase.lib.builders.ProteinParser
parse() - Method in class org.opencb.cellbase.lib.builders.RegulatoryRegionParser
parse() - Method in class org.opencb.cellbase.lib.builders.RepeatsParser
parse() - Method in class org.opencb.cellbase.lib.builders.variation.VariationParser
parse() - Method in class org.opencb.cellbase.lib.builders.VariationPhenotypeAnnotationParser
parseAttribTypeToMap(Path) - Static method in class org.opencb.cellbase.lib.builders.utils.VariationUtils
parseChromosomeStartAndEnd(Cosmic) - Method in class org.opencb.cellbase.lib.builders.clinical.variant.CosmicParser: Deprecated.
parsePhenotypeToMap(Path) - Static method in class org.opencb.cellbase.lib.builders.utils.VariationUtils
parsePosition(ClinicalIndexer.SequenceLocation, String) - Method in class org.opencb.cellbase.lib.builders.clinical.variant.CosmicIndexer
parsePosition(String[], boolean) - Method in class org.opencb.cellbase.lib.builders.clinical.variant.IARCTP53Indexer
parseQueryParam(QueryOptions) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
parseQueryParams() - Method in class org.opencb.cellbase.server.rest.GenericRestWSServer
parseQueryParams() - Method in interface org.opencb.cellbase.server.rest.IWSServer
parseSeqRegionToMap(Path) - Static method in class org.opencb.cellbase.lib.builders.utils.VariationUtils
parseSourceToMap(Path) - Static method in class org.opencb.cellbase.lib.builders.utils.VariationUtils
parseStudyToMap(Path) - Static method in class org.opencb.cellbase.lib.builders.utils.VariationUtils
Partner - Class in org.opencb.cellbase.core.common.drug: Created by mbleda on 12/12/13.
Partner() - Constructor for class org.opencb.cellbase.core.common.drug.Partner
PathwayDBAdaptor<T> - Interface in org.opencb.cellbase.core.api: Created by imedina on 09/02/16.
PathwayWSServer - Class in org.opencb.cellbase.server.rest.network
PathwayWSServer(String, String, UriInfo, HttpServletRequest) - Constructor for class org.opencb.cellbase.server.rest.network.PathwayWSServer
PathwayWSServerMongo - Class in org.opencb.cellbase.server.rest.network
PathwayWSServerMongo(String, String, UriInfo, HttpServletRequest) - Constructor for class org.opencb.cellbase.server.rest.network.PathwayWSServerMongo
PHASE_SET_TAG - Static variable in class org.opencb.cellbase.core.variant.PhasedQueryManager
phased - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.VariantAnnotationCommandOptions: Deprecated.
PHASED_GENOTYPE_SEPARATOR - Static variable in class org.opencb.cellbase.core.variant.PhasedQueryManager
PhasedQueryManager - Class in org.opencb.cellbase.core.variant
PhasedQueryManager() - Constructor for class org.opencb.cellbase.core.variant.PhasedQueryManager
PhenotypeWSServer - Class in org.opencb.cellbase.server.rest.phenotype: Created by imedina on 20/01/14.
PhenotypeWSServer(String, String, UriInfo, HttpServletRequest) - Constructor for class org.opencb.cellbase.server.rest.phenotype.PhenotypeWSServer
ping() - Method in class org.opencb.cellbase.server.rest.MetaWSServer
POISON_PILL - Static variable in class org.opencb.cellbase.core.loader.LoadRunner
POLYMORPHIC_PSEUDOGENE - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
POLYPHEN_DESCRIPTIONS - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
PopulationFrequenciesAnnotator - Class in org.opencb.cellbase.app.cli.main.annotation: Created by fjlopez on 18/07/16.
PopulationFrequenciesAnnotator(String, RocksDB, QueryOptions) - Constructor for class org.opencb.cellbase.app.cli.main.annotation.PopulationFrequenciesAnnotator
PopulationFrequencyPhasedQueryManager - Class in org.opencb.cellbase.core.variant
PopulationFrequencyPhasedQueryManager() - Constructor for class org.opencb.cellbase.core.variant.PopulationFrequencyPhasedQueryManager
PopulationFrequencyVariantIndexer - Class in org.opencb.cellbase.app.cli.main.annotation.indexers
PopulationFrequencyVariantIndexer(VariantReader, int, boolean) - Constructor for class org.opencb.cellbase.app.cli.main.annotation.indexers.PopulationFrequencyVariantIndexer
port - Variable in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.ServerCommandOptions
post() - Method in class org.opencb.cellbase.app.cli.main.annotation.BenchmarkDataWriter
post() - Method in class org.opencb.cellbase.app.cli.main.annotation.BenchmarkTask
post() - Method in class org.opencb.cellbase.app.cli.main.annotation.JsonStringAnnotatorTask: Deprecated.
post() - Method in class org.opencb.cellbase.app.cli.main.annotation.VariantAnnotatorTask
post() - Method in class org.opencb.cellbase.app.cli.main.annotation.VariationDataReader
post() - Method in class org.opencb.cellbase.app.cli.main.annotation.VcfStringAnnotatorTask: Deprecated.
PPI_DATA - Static variable in class org.opencb.cellbase.lib.EtlCommons
pre() - Method in class org.opencb.cellbase.app.cli.main.annotation.BenchmarkDataWriter
pre() - Method in class org.opencb.cellbase.app.cli.main.annotation.BenchmarkTask
pre() - Method in class org.opencb.cellbase.app.cli.main.annotation.JsonStringAnnotatorTask: Deprecated.
pre() - Method in class org.opencb.cellbase.app.cli.main.annotation.VariantAnnotatorTask
pre() - Method in class org.opencb.cellbase.app.cli.main.annotation.VariationDataReader
pre() - Method in class org.opencb.cellbase.app.cli.main.annotation.VcfStringAnnotatorTask: Deprecated.
preprocess(VariationFeatureFile) - Method in class org.opencb.cellbase.lib.builders.variation.VariationTranscriptFile
PREPROCESSED_TRANSCRIPT_VARIATION_FILENAME - Static variable in class org.opencb.cellbase.lib.builders.variation.VariationTranscriptFile
PREPROCESSED_VARIATION_FEATURE_FILENAME - Static variable in class org.opencb.cellbase.lib.builders.variation.VariationFeatureFile
PREPROCESSED_VARIATION_FILENAME - Static variable in class org.opencb.cellbase.lib.builders.variation.VariationFile
PREPROCESSED_VARIATION_FILENAME - Static variable in class org.opencb.cellbase.lib.builders.variation.VariationParser
PREPROCESSED_VARIATION_SYNONYM_FILENAME - Static variable in class org.opencb.cellbase.lib.builders.variation.VariationSynonymFile
preprocessedFileName - Variable in class org.opencb.cellbase.lib.builders.variation.AbstractVariationFile
printCommands(JCommander) - Method in class org.opencb.cellbase.app.cli.CliOptionsParser
printMainUsage() - Method in class org.opencb.cellbase.app.cli.CliOptionsParser
printUsage() - Method in class org.opencb.cellbase.app.cli.CliOptionsParser
printVersion() - Method in class org.opencb.cellbase.app.cli.CliOptionsParser
PROCESSED_PSEUDOGENE - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
PROCESSED_TRANSCRIPT - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
processExons(Transcript, Exon, int, int, Gtf) - Method in class org.opencb.cellbase.lib.builders.GeneParser
PROTEIN_CODING - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
PROTEIN_DATA - Static variable in class org.opencb.cellbase.lib.EtlCommons
PROTEIN_FUNCTIONAL_PREDICTION_DATA - Static variable in class org.opencb.cellbase.lib.EtlCommons
ProteinClient - Class in org.opencb.cellbase.client.rest: Created by swaathi on 25/05/16.
ProteinClient(String, String, ClientConfiguration) - Constructor for class org.opencb.cellbase.client.rest.ProteinClient
ProteinDBAdaptor<T> - Interface in org.opencb.cellbase.core.api: Created by imedina on 30/11/15.
ProteinDBAdaptor.QueryParams - Enum in org.opencb.cellbase.core.api
ProteinMongoDBAdaptor - Class in org.opencb.cellbase.lib.impl: Created by imedina on 01/12/15.
ProteinMongoDBAdaptor(String, String, MongoDataStore) - Constructor for class org.opencb.cellbase.lib.impl.ProteinMongoDBAdaptor
ProteinParser - Class in org.opencb.cellbase.lib.builders
ProteinParser(Path, String, CellBaseSerializer) - Constructor for class org.opencb.cellbase.lib.builders.ProteinParser
ProteinParser(Path, Path, String, CellBaseSerializer) - Constructor for class org.opencb.cellbase.lib.builders.ProteinParser
ProteinProteinInteractionDBAdaptor<PPI> - Interface in org.opencb.cellbase.core.api: Created by imedina on 13/12/15.
ProteinProteinInteractionDBAdaptor.QueryParams - Enum in org.opencb.cellbase.core.api
ProteinProteinInteractionMongoDBAdaptor - Class in org.opencb.cellbase.lib.impl: Created by imedina on 13/12/15.
ProteinProteinInteractionMongoDBAdaptor(String, String, MongoDataStore) - Constructor for class org.opencb.cellbase.lib.impl.ProteinProteinInteractionMongoDBAdaptor
ProteinProteinInteractionWSServer - Class in org.opencb.cellbase.server.rest.network: Created with IntelliJ IDEA.
ProteinProteinInteractionWSServer(String, String, UriInfo, HttpServletRequest) - Constructor for class org.opencb.cellbase.server.rest.network.ProteinProteinInteractionWSServer
ProteinWSServer - Class in org.opencb.cellbase.server.rest.feature
ProteinWSServer(String, String, UriInfo, HttpServletRequest) - Constructor for class org.opencb.cellbase.server.rest.feature.ProteinWSServer
PSEUDOGENE - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
Pwm - Class in org.opencb.cellbase.core.common.regulatory: Pwm generated by hbm2java.
Pwm() - Constructor for class org.opencb.cellbase.core.common.regulatory.Pwm
Pwm(int, String, String, String, String, String, int, String) - Constructor for class org.opencb.cellbase.core.common.regulatory.Pwm
Pwm(int, String, String, String, String, String, int, String, Set<Tfbs>) - Constructor for class org.opencb.cellbase.core.common.regulatory.Pwm

Q

query(String, int, int) - Method in class org.opencb.cellbase.core.variant.annotation.CellBaseNormalizerSequenceAdaptor: Returns sequence from contig "contig" in the range [start, end] (1-based, both inclusive).
query - Variable in class org.opencb.cellbase.server.rest.GenericRestWSServer
queryByVariationId(int, Path) - Method in class org.opencb.cellbase.lib.builders.VariationPhenotypeAnnotationParser
queryChromosomesRegulatoryDB(Path, String, String) - Method in class org.opencb.cellbase.lib.builders.RegulatoryRegionParser
QueryCommandExecutor - Class in org.opencb.cellbase.app.cli.main.executors: Created by imedina on 20/02/15.
QueryCommandExecutor(CellBaseCliOptionsParser.QueryCommandOptions) - Constructor for class org.opencb.cellbase.app.cli.main.executors.QueryCommandExecutor
QueryCommandOptions() - Constructor for class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.QueryCommandOptions
queryOptions - Variable in class org.opencb.cellbase.server.rest.GenericRestWSServer
queryRegulatoryDB(Path, String, String, int, int) - Static method in class org.opencb.cellbase.lib.builders.RegulatoryRegionParser

R

rank - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.QueryCommandOptions
rank(Query, String, int, boolean) - Method in interface org.opencb.cellbase.core.api.CellBaseDBAdaptor
rank(Query, String, int, boolean) - Method in class org.opencb.cellbase.lib.impl.ClinicalLegacyMongoDBAdaptor: Deprecated.
rank(Query, String, int, boolean) - Method in class org.opencb.cellbase.lib.impl.ClinicalMongoDBAdaptor
rank(Query, String, int, boolean) - Method in class org.opencb.cellbase.lib.impl.ConservationMongoDBAdaptor: Deprecated.
rank(Query, String, int, boolean) - Method in class org.opencb.cellbase.lib.impl.GeneMongoDBAdaptor
rank(Query, String, int, boolean) - Method in class org.opencb.cellbase.lib.impl.GenomeMongoDBAdaptor
rank(Query, String, int, boolean) - Method in class org.opencb.cellbase.lib.impl.MetaMongoDBAdaptor
rank(Query, String, int, boolean) - Method in class org.opencb.cellbase.lib.impl.ProteinMongoDBAdaptor
rank(Query, String, int, boolean) - Method in class org.opencb.cellbase.lib.impl.ProteinProteinInteractionMongoDBAdaptor
rank(Query, String, int, boolean) - Method in class org.opencb.cellbase.lib.impl.RegulationMongoDBAdaptor
rank(Query, String, int, boolean) - Method in class org.opencb.cellbase.lib.impl.RepeatsMongoDBAdaptor
rank(Query, String, int, boolean) - Method in class org.opencb.cellbase.lib.impl.TranscriptMongoDBAdaptor
rank(Query, String, int, boolean) - Method in class org.opencb.cellbase.lib.impl.VariantMongoDBAdaptor
rank(Query, String, int, boolean) - Method in class org.opencb.cellbase.lib.impl.XRefMongoDBAdaptor
rdb - Variable in class org.opencb.cellbase.lib.builders.clinical.variant.ClinicalIndexer
read() - Method in class org.opencb.cellbase.app.cli.main.annotation.VariationDataReader: Performs one read of from a CellBase variation collection.
read(int) - Method in class org.opencb.cellbase.app.cli.main.annotation.VariationDataReader
referenceFasta - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.VariantAnnotationCommandOptions
region - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.QueryCommandOptions
REGION - Static variable in interface org.opencb.cellbase.core.api.FeatureDBAdaptor
regionsOverlap(Integer, Integer, Integer, Integer) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
RegionWSServer - Class in org.opencb.cellbase.server.rest.genomic
RegionWSServer(String, String, UriInfo, HttpServletRequest) - Constructor for class org.opencb.cellbase.server.rest.genomic.RegionWSServer
REGULATION_DATA - Static variable in class org.opencb.cellbase.lib.EtlCommons
RegulationDBAdaptor<T> - Interface in org.opencb.cellbase.core.api: Created by imedina on 07/12/15.
RegulationDBAdaptor.FeatureType - Enum in org.opencb.cellbase.core.api
RegulationDBAdaptor.QueryParams - Enum in org.opencb.cellbase.core.api
RegulationMongoDBAdaptor - Class in org.opencb.cellbase.lib.impl: Created by imedina on 07/12/15.
RegulationMongoDBAdaptor(String, String, MongoDataStore) - Constructor for class org.opencb.cellbase.lib.impl.RegulationMongoDBAdaptor
REGULATORY_FEATURES_FILE - Static variable in class org.opencb.cellbase.lib.EtlCommons
REGULATORY_REGION_CHUNK_SIZE - Static variable in class org.opencb.cellbase.lib.MongoDBCollectionConfiguration
REGULATORY_REGION_VARIANT - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
RegulatoryRegion - Class in org.opencb.cellbase.core.common.regulatory: RegulatoryRegion generated by hbm2java.
RegulatoryRegion() - Constructor for class org.opencb.cellbase.core.common.regulatory.RegulatoryRegion
RegulatoryRegion(int, String, String, String, int, int, double, String, String, String) - Constructor for class org.opencb.cellbase.core.common.regulatory.RegulatoryRegion
RegulatoryRegion(int, String, String, String, int, int, double, String, String, String, Set<Tfbs>) - Constructor for class org.opencb.cellbase.core.common.regulatory.RegulatoryRegion
RegulatoryRegionParser - Class in org.opencb.cellbase.lib.builders: User: fsalavert.
RegulatoryRegionParser(Path, CellBaseSerializer) - Constructor for class org.opencb.cellbase.lib.builders.RegulatoryRegionParser
RegulatoryWSServer - Class in org.opencb.cellbase.server.rest.regulatory
RegulatoryWSServer(String, String, UriInfo, HttpServletRequest) - Constructor for class org.opencb.cellbase.server.rest.regulatory.RegulatoryWSServer
remove() - Method in class org.opencb.cellbase.lib.VariantMongoIterator
repeat(String, int) - Method in class org.opencb.cellbase.lib.builders.RegulatoryRegionParser
REPEATS_CHUNK_SIZE - Static variable in class org.opencb.cellbase.lib.MongoDBCollectionConfiguration
REPEATS_DATA - Static variable in class org.opencb.cellbase.lib.EtlCommons
REPEATS_FOLDER - Static variable in class org.opencb.cellbase.lib.EtlCommons
REPEATS_JSON - Static variable in class org.opencb.cellbase.lib.EtlCommons
RepeatsDBAdaptor<T> - Interface in org.opencb.cellbase.core.api: Created by fjlopez on 10/05/17.
RepeatsDBAdaptor.QueryParams - Enum in org.opencb.cellbase.core.api
RepeatsMongoDBAdaptor - Class in org.opencb.cellbase.lib.impl: Created by fjlopez on 10/05/17.
RepeatsMongoDBAdaptor(String, String, MongoDataStore) - Constructor for class org.opencb.cellbase.lib.impl.RepeatsMongoDBAdaptor
RepeatsParser - Class in org.opencb.cellbase.lib.builders: Created by fjlopez on 05/05/17.
RepeatsParser(Path, CellBaseFileSerializer) - Constructor for class org.opencb.cellbase.lib.builders.RepeatsParser
ReplicaSet() - Constructor for class org.opencb.cellbase.core.config.MongoDBDatabaseCredentials.ReplicaSet
reset(CellBaseDataResult<Variant>) - Method in class org.opencb.cellbase.core.variant.PhasedQueryManager
resource - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.QueryCommandOptions
response(int) - Method in class org.opencb.cellbase.core.CellBaseDataResponse: Fetch the DataResult of the m-response.
responses() - Method in class org.opencb.cellbase.core.CellBaseDataResponse: Fetch the list of responses.
REST - Static variable in class org.opencb.cellbase.client.rest.ParentRestClient
Rest - Class in org.opencb.cellbase.core.config
Rest() - Constructor for class org.opencb.cellbase.core.config.Rest
REST_CALL_BATCH_SIZE - Static variable in class org.opencb.cellbase.client.rest.ParentRestClient
RestConfig - Class in org.opencb.cellbase.client.config: Created by imedina on 04/05/16.
RestConfig() - Constructor for class org.opencb.cellbase.client.config.RestConfig
RestConfig(List<String>, int) - Constructor for class org.opencb.cellbase.client.config.RestConfig
RestServer - Class in org.opencb.cellbase.server
RestServer(Path) - Constructor for class org.opencb.cellbase.server.RestServer
RestServer(Path, int) - Constructor for class org.opencb.cellbase.server.RestServer
result(int) - Method in class org.opencb.cellbase.core.CellBaseDataResponse: Fetch the m-result of the first response.
result(int, int) - Method in class org.opencb.cellbase.core.CellBaseDataResponse: Fetch the m-result of the n-response.
results(int) - Method in class org.opencb.cellbase.core.CellBaseDataResponse: Fetch the list of results of the m-response.
resume - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.VariantAnnotationCommandOptions
RETAINED_INTRON - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
RETROTRANSPOSED - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
reverseComplement(String) - Static method in class org.opencb.cellbase.core.common.DNASequenceUtils
RRNA - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
RRNA_PSEUDOGENE - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
RS_COLUMN_INDEX - Static variable in class org.opencb.cellbase.lib.builders.variation.VariationFile
run(List<Variant>) - Method in class org.opencb.cellbase.app.cli.main.annotation.CellBaseLocalVariantAnnotator
run(List<Variant>) - Method in class org.opencb.cellbase.app.cli.main.annotation.CellBaseWSVariantAnnotator
run() - Method in class org.opencb.cellbase.app.cli.main.annotation.indexers.VariantIndexer
run(List<Variant>) - Method in class org.opencb.cellbase.app.cli.main.annotation.PopulationFrequenciesAnnotator: Updates VariantAnnotation objects in variantAnnotationList.
run(List<Variant>) - Method in class org.opencb.cellbase.app.cli.main.annotation.VcfVariantAnnotator: Updates VariantAnnotation objects in variantAnnotationList.
run(String, String) - Method in class org.opencb.cellbase.core.monitor.Monitor
run(Variant, List<Gene>, boolean[], QueryOptions) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeBNDCalculator
run(Variant, List<Gene>, boolean[], QueryOptions) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
run(Variant, List<Gene>, boolean[], QueryOptions) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCNVGainCalculator
run(Variant, List<Gene>, boolean[], QueryOptions) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeDeletionCalculator
run(Variant, List<Gene>, boolean[], QueryOptions) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeGenericRegionCalculator
run(Variant, List<Gene>, boolean[], QueryOptions) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeInsertionCalculator
run(Variant, List<Gene>, boolean[], QueryOptions) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeMNVCalculator
run(Variant, List<Gene>, boolean[], QueryOptions) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeSNVCalculator
run(Variant, List<Gene>) - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsCalculator
run(Variant, List<Gene>, boolean) - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsCalculator
run(Variant, Gene) - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsCalculator
run(Variant, Gene, boolean) - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsCalculator
run(Variant, Transcript, String, boolean) - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsCalculator
run(Variant, Transcript, String, boolean) - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsDeletionCalculator
run(Variant, Transcript, String, boolean) - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsInsertionCalculator
run(Variant, Transcript, String, boolean) - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsSNVCalculator
run(List<Variant>) - Method in interface org.opencb.cellbase.core.variant.annotation.VariantAnnotator
run(List<Variant>, List<CellBaseDataResult<Variant>>) - Method in class org.opencb.cellbase.core.variant.AnnotationBasedPhasedQueryManager
run(List<Variant>, List<CellBaseDataResult<Variant>>) - Method in class org.opencb.cellbase.core.variant.CustomAnnotationPhasedQueryManager
runCommandLineProcess(File, String, List<String>, String) - Static method in class org.opencb.cellbase.lib.EtlCommons
runCreateIndexProcess(Path) - Method in class org.opencb.cellbase.lib.loader.MongoDBCellBaseLoader: Deprecated.

S

sameHaplotype(Variant, List<Variant>, List<Variant>) - Method in class org.opencb.cellbase.core.variant.PhasedQueryManager
sameSomaticDocument(EvidenceEntry, EvidenceEntry) - Method in class org.opencb.cellbase.lib.builders.clinical.variant.CosmicIndexer
SCRNA_PSEUDOGENE - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
search(Query, QueryOptions) - Method in class org.opencb.cellbase.client.rest.ClinicalVariantClient
search(Query, QueryOptions) - Method in class org.opencb.cellbase.client.rest.FeatureClient
search() - Method in class org.opencb.cellbase.server.rest.feature.VariationWSServer
SENSE_INTRONIC - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
SENSE_OVERLAPPING - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
SEPARATOR_CHAR - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
SequenceOntologyTermComparisonObject - Class in org.opencb.cellbase.app.cli.main.annotation: Created by fjlopez on 08/04/16.
SequenceOntologyTermComparisonObject(String, SequenceOntologyTerm) - Constructor for class org.opencb.cellbase.app.cli.main.annotation.SequenceOntologyTermComparisonObject
serialize(OutputStream) - Method in class org.opencb.cellbase.client.config.ClientConfiguration
serialize(OutputStream) - Method in class org.opencb.cellbase.core.config.CellBaseConfiguration
serialize(Object, String) - Method in interface org.opencb.cellbase.core.serializer.CellBaseFileSerializer
serialize(Object) - Method in class org.opencb.cellbase.core.serializer.CellBaseJsonFileSerializer
serialize(Object, String) - Method in class org.opencb.cellbase.core.serializer.CellBaseJsonFileSerializer
serialize(Object) - Method in interface org.opencb.cellbase.core.serializer.CellBaseSerializer
serializer - Variable in class org.opencb.cellbase.lib.builders.CellBaseParser
ServerCommandExecutor - Class in org.opencb.cellbase.app.cli.admin.executors
ServerCommandExecutor(AdminCliOptionsParser.ServerCommandOptions) - Constructor for class org.opencb.cellbase.app.cli.admin.executors.ServerCommandExecutor
ServerCommandOptions() - Constructor for class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.ServerCommandOptions
ServerProperties - Class in org.opencb.cellbase.core.config
ServerProperties() - Constructor for class org.opencb.cellbase.core.config.ServerProperties
Service() - Constructor for class org.opencb.cellbase.core.monitor.HealthStatus.Service
SERVICE_START_DATE - Variable in class org.opencb.cellbase.server.rest.GenericRestWSServer
set_id(String) - Method in class org.opencb.cellbase.client.rest.models.GroupByFields
set_id(String) - Method in class org.opencb.cellbase.client.rest.models.GroupCount
setAbsolute(int) - Method in class org.opencb.cellbase.core.common.IntervalFeatureFrequency
setAbsorption(String) - Method in class org.opencb.cellbase.core.common.drug.Drug
setAccession(String) - Method in class org.opencb.cellbase.app.cli.main.annotation.SequenceOntologyTermComparisonObject
setAccession(String) - Method in class org.opencb.cellbase.core.common.regulatory.Pwm
setAccessionNumber(String) - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
setAction(List<String>) - Method in class org.opencb.cellbase.core.common.drug.DrugPartnerInteraction
setActualFileSize(int) - Method in class org.opencb.cellbase.lib.download.DownloadFile
setAge(Float) - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
setAlternate(String) - Method in class org.opencb.cellbase.core.common.clinical.ClinicalVariant
setAlternate(String) - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsStringBuilder
setAlternate(String) - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
setAlternate(String) - Method in class org.opencb.cellbase.lib.model.ClinicalVariation: Deprecated.
setApiVersion(String) - Method in class org.opencb.cellbase.core.CellBaseDataResponse
setApiVersion(String) - Method in class org.opencb.cellbase.core.config.CellBaseConfiguration
setApplication(HealthStatus.ApplicationDetails) - Method in class org.opencb.cellbase.core.monitor.HealthStatus
setApplicationTier(String) - Method in class org.opencb.cellbase.core.monitor.HealthStatus.Service
setAssemblies(List<SpeciesConfiguration.Assembly>) - Method in class org.opencb.cellbase.core.config.SpeciesConfiguration
setAssembly(String) - Method in class org.opencb.cellbase.core.common.Species
setAssembly(String) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptor
setAtcCode(List<String>) - Method in class org.opencb.cellbase.core.common.drug.Drug
setBacteria(List<SpeciesConfiguration>) - Method in class org.opencb.cellbase.core.config.SpeciesProperties
setCadd(DownloadProperties.URLProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties
setCaddValues(List<Cadd.CaddValues>) - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
setCategory(List<String>) - Method in class org.opencb.cellbase.core.common.drug.Drug
setCdnaEnd(CdnaCoord) - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsStringBuilder
setCdnaStart(CdnaCoord) - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsStringBuilder
setCdsAndProteinPosition(int, int, int) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
setCellType(String) - Method in class org.opencb.cellbase.core.common.regulatory.RegulatoryRegion
setCellType(String) - Method in class org.opencb.cellbase.core.common.regulatory.Tfbs
setCellTypeDescription(String) - Method in class org.opencb.cellbase.core.common.regulatory.RegulatoryRegion
setCellularLocation(String) - Method in class org.opencb.cellbase.core.common.drug.Partner
setChromosome(String) - Method in class org.opencb.cellbase.core.common.clinical.ClinicalVariant
setChromosome(String) - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
setChromosome(String) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaTarget
setChromosome(String) - Method in class org.opencb.cellbase.core.common.regulatory.RegulatoryRegion
setChromosome(String) - Method in class org.opencb.cellbase.core.common.regulatory.Tfbs
setChromosome(String) - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsStringBuilder
setChromosome(String) - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
setChromosome(String) - Method in class org.opencb.cellbase.lib.builders.formats.ConservedRegionFeature: Deprecated.
setChromosome(String) - Method in class org.opencb.cellbase.lib.model.ClinicalVariation: Deprecated.
setChunk(int) - Method in class org.opencb.cellbase.lib.builders.formats.ConservedRegionFeature: Deprecated.
setClearance(String) - Method in class org.opencb.cellbase.core.common.drug.Drug
setClientConfiguration(ClientConfiguration) - Method in class org.opencb.cellbase.client.rest.CellBaseClient
setClinvar(DownloadProperties.URLProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties
setClinvarEfoTerms(DownloadProperties.URLProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties
setClinvarList(List<ClinvarPublicSet>) - Method in class org.opencb.cellbase.lib.model.ClinicalVariation: Deprecated.
setClinvarSet(PublicSetType) - Method in class org.opencb.cellbase.core.common.clinical.ClinvarPublicSet
setClinvarSummary(DownloadProperties.URLProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties
setClinvarVariationAllele(DownloadProperties.URLProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties
setCnv(String) - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
setCollection(String) - Method in class org.opencb.cellbase.core.config.SpeciesConfiguration.ShardConfig
setComments(String) - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
setCommit(String) - Method in class org.opencb.cellbase.core.monitor.HealthStatus.ApplicationDetails.Version
setCommon(String) - Method in class org.opencb.cellbase.core.common.Species
setCommonName(String) - Method in class org.opencb.cellbase.core.config.SpeciesConfiguration
setConfigFile(String) - Method in class org.opencb.cellbase.app.cli.CommandExecutor
setConfiguration(CellBaseConfiguration) - Method in class org.opencb.cellbase.core.api.DBAdaptorFactory
setConservation(DownloadProperties.URLProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties
setConservedRegionId(int) - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
setContext(String) - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
setCosmicList(List<Cosmic>) - Method in class org.opencb.cellbase.lib.model.ClinicalVariation: Deprecated.
setCount(int) - Method in class org.opencb.cellbase.client.rest.models.GroupCount
setCscore(float) - Method in class org.opencb.cellbase.lib.builders.formats.Cadd.CaddValues
setData(List<String>) - Method in class org.opencb.cellbase.core.config.SpeciesConfiguration
setDatabase(DatabaseCredentials) - Method in class org.opencb.cellbase.core.config.DownloadProperties.EnsemblProperties
setDatabases(Databases) - Method in class org.opencb.cellbase.core.config.CellBaseConfiguration
setDataRangeMammal(double) - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
setDataRangePrimate(double) - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
setDataRangeVertebrate(double) - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
setDatastores(HealthStatus.ApplicationDetails.DependenciesStatus.DatastoreDependenciesStatus) - Method in class org.opencb.cellbase.core.monitor.HealthStatus.ApplicationDetails.DependenciesStatus
setDate(String) - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasStudy
setDateAddedToCatalog(String) - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasTrait
setDbName(String) - Method in class org.opencb.cellbase.core.common.drug.XRef
setDbsnp(DownloadProperties.URLProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties
setDefaultOutdir(String) - Method in class org.opencb.cellbase.core.config.CellBaseConfiguration
setDefaultSpecies(String) - Method in class org.opencb.cellbase.client.config.ClientConfiguration
setDependencies(HealthStatus.ApplicationDetails.DependenciesStatus) - Method in class org.opencb.cellbase.core.monitor.HealthStatus.ApplicationDetails
setDescription(String) - Method in class org.opencb.cellbase.core.common.drug.Drug
setDescription(String) - Method in class org.opencb.cellbase.core.common.drug.Interactor
setDescription(String) - Method in class org.opencb.cellbase.core.common.drug.XRef
setDescription(String) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaDisease
setDescription(String) - Method in class org.opencb.cellbase.core.common.regulatory.Pwm
setDgidb(DownloadProperties.URLProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties
setDgv(DownloadProperties.URLProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties
setDiseaseName(String) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaDisease
setDiseases(List<Disease>) - Method in class org.opencb.cellbase.core.common.genedisease.Disgenet: Deprecated.
setDiseaseTrait(String) - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasTrait
setDisgenet(DownloadProperties.URLProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties
setDisgenetReadme(DownloadProperties.URLProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties
setDocm(DownloadProperties.URLProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties
setDocmVersion(DownloadProperties.URLProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties
setDownload(DownloadProperties) - Method in class org.opencb.cellbase.core.config.CellBaseConfiguration
setDownstreamGeneDistance(String) - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
setDownstreamGeneId(String) - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
setDrug(Drug) - Method in class org.opencb.cellbase.core.common.drug.DrugPartnerInteraction
setDrugInteractor(List<Interactor>) - Method in class org.opencb.cellbase.core.common.drug.Drug
setElapsedTime(Long, Long) - Method in class org.opencb.cellbase.lib.download.DownloadFile
setEncExp(Float) - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
setEncH3K27Ac(Float) - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
setEncH3K4Me1(Float) - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
setEncH3K4Me3(Float) - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
setEncNucleo(Float) - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
setEncOCC(Integer) - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
setEncOCCombPVal(Float) - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
setEncOCctcfPVal(Float) - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
setEncOCctcfSig(Float) - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
setEncOCDNasePVal(Float) - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
setEncOCDNaseSig(Float) - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
setEncOCFairePVal(Float) - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
setEncOCFaireSig(Float) - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
setEncOCmycPVal(Float) - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
setEncOCmycSig(Float) - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
setEncOCpolIIPVal(Float) - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
setEncOCpolIISig(Float) - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
setEnd(int) - Method in class org.opencb.cellbase.core.common.clinical.ClinicalVariant
setEnd(int) - Method in class org.opencb.cellbase.core.common.IntervalFeatureFrequency
setEnd(int) - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
setEnd(int) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaTarget
setEnd(int) - Method in class org.opencb.cellbase.core.common.regulatory.RegulatoryRegion
setEnd(int) - Method in class org.opencb.cellbase.core.common.regulatory.Tfbs
setEnd(int) - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsStringBuilder
setEnd(Integer) - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
setEnd(int) - Method in class org.opencb.cellbase.lib.builders.formats.ConservedRegionFeature: Deprecated.
setEnd(int) - Method in class org.opencb.cellbase.lib.model.ClinicalVariation: Deprecated.
setEnd(int) - Method in class org.opencb.cellbase.server.rest.genomic.Interval: Deprecated.
setEndpointVersion(int) - Method in class org.opencb.cellbase.core.monitor.HealthStatus.Infrastructure
setEnsembl(DownloadProperties.EnsemblProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties
setEnsemblCollection(String) - Method in class org.opencb.cellbase.core.config.SpeciesConfiguration.Assembly
setEnsemblGenomes(DownloadProperties.EnsemblProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties
setEnsemblVersion(String) - Method in class org.opencb.cellbase.core.config.SpeciesConfiguration.Assembly
setEssentiality(String) - Method in class org.opencb.cellbase.core.common.drug.Partner
setEvents(List<Event>) - Method in class org.opencb.cellbase.core.CellBaseDataResponse
setExpectedFileSize(int) - Method in class org.opencb.cellbase.lib.download.DownloadFile
setExperiment(String) - Method in class org.opencb.cellbase.lib.builders.formats.GeneExpressionAtlas.Tissue
setExperimentalMethod(String) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaTarget
setExperimentalScore(double) - Method in class org.opencb.cellbase.core.common.regulatory.RegulatoryRegion
setExpressionValue(float) - Method in class org.opencb.cellbase.lib.builders.formats.GeneExpressionAtlas.Tissue
setFathmmPrediction(String) - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
setFeatures(List<String>) - Method in class org.opencb.cellbase.client.rest.models.GroupByFields
setFiles(List<String>) - Method in class org.opencb.cellbase.core.config.DownloadProperties.URLProperties
setFirstAuthor(String) - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasStudy
setFoodInteractor(List<Interactor>) - Method in class org.opencb.cellbase.core.common.drug.Drug
setFrequencies(String) - Method in class org.opencb.cellbase.core.common.regulatory.Pwm
setFungi(List<SpeciesConfiguration>) - Method in class org.opencb.cellbase.core.config.SpeciesProperties
setGene(Gene) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaTarget
setGene(Gene) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaToGene
setGene(Gene) - Method in class org.opencb.cellbase.core.common.regulatory.Tfbs
setGeneCDSLength(int) - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
setGeneExpressionAtlas(DownloadProperties.URLProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties
setGeneId(String) - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsStringBuilder
setGeneId(String) - Method in class org.opencb.cellbase.lib.builders.formats.GeneExpressionAtlas
setGeneName(String) - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
setGeneName(String) - Method in class org.opencb.cellbase.core.common.genedisease.Disgenet: Deprecated.
setGeneName(String) - Method in class org.opencb.cellbase.lib.builders.formats.GeneExpressionAtlas
setGeneralFunction(String) - Method in class org.opencb.cellbase.core.common.drug.Partner
setGeneSymbol(String) - Method in class org.opencb.cellbase.core.common.genedisease.Disgenet: Deprecated.
setGeneTargetName(String) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaTarget
setGeneUniprotXref(DownloadProperties.URLProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties
setGenomeWideScreen(String) - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
setGenomicFeature(String) - Method in class org.opencb.cellbase.lib.builders.formats.Cadd.CaddValues
setGenomicSuperDups(DownloadProperties.URLProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties
setGerp(DownloadProperties.URLProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties
setGnomad(DownloadProperties.URLProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties
setGroup(List<String>) - Method in class org.opencb.cellbase.core.common.drug.Drug
setGwasCatalog(DownloadProperties.URLProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties
setGwasList(List<Gwas>) - Method in class org.opencb.cellbase.lib.model.ClinicalVariation: Deprecated.
setHalfLife(String) - Method in class org.opencb.cellbase.core.common.drug.Drug
setHgncId(String) - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
setHistologySubtype(String) - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
setHost(String) - Method in class org.opencb.cellbase.core.config.DatabaseCredentials
setHost(String) - Method in class org.opencb.cellbase.core.config.DownloadProperties.URLProperties
setHosts(List<String>) - Method in class org.opencb.cellbase.client.config.RestConfig
setHpo(DownloadProperties.URLProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties
setIarctp53(DownloadProperties.URLProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties
setId(String) - Method in class org.opencb.cellbase.core.common.drug.Drug
setId(String) - Method in class org.opencb.cellbase.core.common.drug.Interactor
setId(String) - Method in class org.opencb.cellbase.core.common.drug.Partner
setId(String) - Method in class org.opencb.cellbase.core.common.drug.XRef
setId(String) - Method in class org.opencb.cellbase.core.config.MongoDBDatabaseCredentials.ReplicaSet
setId(String) - Method in class org.opencb.cellbase.core.config.SpeciesConfiguration
setId(String) - Method in class org.opencb.cellbase.core.result.CellBaseDataResult
setIdSample(String) - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
setIdStudy(Integer) - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
setIdTumour(String) - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
setIndication(String) - Method in class org.opencb.cellbase.core.common.drug.Drug
setInfrastructure(HealthStatus.Infrastructure) - Method in class org.opencb.cellbase.core.monitor.HealthStatus
setInitialSampleSize(String) - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasStudy
setInsertionAlleleAminoacidChange(String, char[], char[], char[], boolean, boolean) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
setIntact(DownloadProperties.URLProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties
setIntergenic(String) - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
setInterpro(DownloadProperties.URLProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties
setInterproRelNotes(DownloadProperties.URLProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties
setInterval(int) - Method in class org.opencb.cellbase.core.common.IntervalFeatureFrequency
setJournal(String) - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasStudy
setKey(List<String>) - Method in class org.opencb.cellbase.core.config.SpeciesConfiguration.ShardConfig
setKind(HgvsStringBuilder.Kind) - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsStringBuilder
setKnownAction(String) - Method in class org.opencb.cellbase.core.common.drug.DrugPartnerInteraction
setLandmark(CdnaCoord.Landmark) - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.CdnaCoord
setLength(int) - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
setLength(int) - Method in class org.opencb.cellbase.core.common.regulatory.Pwm
setLibs(String) - Method in class org.opencb.cellbase.core.config.DownloadProperties.EnsemblProperties
setLink(String) - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasStudy
setLogFile(String) - Method in class org.opencb.cellbase.client.config.ClientConfiguration
setLogLevel(String) - Method in class org.opencb.cellbase.app.cli.CommandExecutor
setLogLevel(String) - Method in class org.opencb.cellbase.client.config.ClientConfiguration
setLowerLimitMammal(double) - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
setLowerLimitPrimate(double) - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
setLowerLimitVertebrate(double) - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
setMaintainer(String) - Method in class org.opencb.cellbase.core.monitor.HealthStatus.ApplicationDetails
setMaintainerContact(String) - Method in class org.opencb.cellbase.core.config.CellBaseConfiguration
setMaintenanceFlagFile(String) - Method in class org.opencb.cellbase.core.config.CellBaseConfiguration
setMappedGene(String) - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
setMaximum(String) - Method in class org.opencb.cellbase.core.config.SpeciesConfiguration.ShardRange
setMechanismOfAction(String) - Method in class org.opencb.cellbase.core.common.drug.Drug
setMerged(String) - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
setMessage(String) - Method in class org.opencb.cellbase.lib.download.DownloadFile
setMetazoa(List<SpeciesConfiguration>) - Method in class org.opencb.cellbase.core.config.SpeciesProperties
setMethod(String) - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
setMinimum(String) - Method in class org.opencb.cellbase.core.config.SpeciesConfiguration.ShardRange
setMirbase(DownloadProperties.URLProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties
setMirbaseAcc(String) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaGene
setMirbaseAcc(String) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaMature: Deprecated.
setMirbaseId(String) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaDisease
setMirbaseId(String) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaGene
setMirbaseId(String) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaMature: Deprecated.
setMirbaseId(String) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaTarget
setMirbaseReadme(DownloadProperties.URLProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties
setMirnaDiseaseId(int) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaDisease
setMirnaDiseases(Set<MirnaDisease>) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaGene
setMirnaGene(MirnaGene) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaDisease
setMirnaGene(MirnaGene) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaGeneToMature
setMirnaGene(MirnaGene) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaToGene
setMirnaGeneId(int) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaGene
setMirnaGeneToMatureId(int) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaGeneToMature
setMirnaGeneToMatures(Set<MirnaGeneToMature>) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaGene
setMirnaGeneToMatures(Set<MirnaGeneToMature>) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaMature: Deprecated.
setMirnaMature(MirnaMature) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaGeneToMature
setMirnaMature(MirnaMature) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaTarget
setMirnaMatureId(int) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaMature: Deprecated.
setMirnaTargetId(int) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaTarget
setMirnaTargets(Set<MirnaTarget>) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaMature: Deprecated.
setMirnaToGeneId(int) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaToGene
setMirnaToGenes(Set<MirnaToGene>) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaGene
setMiRTarBase(DownloadProperties.URLProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties
setMongodb(MongoDBDatabaseCredentials) - Method in class org.opencb.cellbase.core.config.Databases
setMongodb(Map<String, HealthStatus.ApplicationDetails.DependenciesStatus.DatastoreDependenciesStatus.DatastoreStatus>) - Method in class org.opencb.cellbase.core.monitor.HealthStatus.ApplicationDetails.DependenciesStatus.DatastoreDependenciesStatus
setMutationAA(String) - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
setMutationCDS(String) - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
setMutationDescription(String) - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
setMutationGRCh37GenomePosition(String) - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
setMutationGRCh37Strand(String) - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
setMutationID(String) - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
setMutationSomaticStatus(String) - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
setMutationType(String) - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsStringBuilder
setMutationZygosity(String) - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
setName(String) - Method in class org.opencb.cellbase.app.cli.main.annotation.SequenceOntologyTermComparisonObject
setName(String) - Method in class org.opencb.cellbase.core.common.drug.Drug
setName(String) - Method in class org.opencb.cellbase.core.common.drug.Interactor
setName(String) - Method in class org.opencb.cellbase.core.common.drug.Partner
setName(String) - Method in class org.opencb.cellbase.core.common.regulatory.RegulatoryRegion
setName(String) - Method in class org.opencb.cellbase.core.config.SpeciesConfiguration.Assembly
setName(String) - Method in class org.opencb.cellbase.core.config.SpeciesConfiguration.Zone
setName(String) - Method in class org.opencb.cellbase.core.monitor.HealthStatus.Service
setNeo4j(Map<String, DatabaseCredentials>) - Method in class org.opencb.cellbase.core.config.Databases
setNodes(String) - Method in class org.opencb.cellbase.core.config.MongoDBDatabaseCredentials.ReplicaSet
setOffset(int) - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.CdnaCoord
setOptions(Map<String, String>) - Method in class org.opencb.cellbase.core.config.DatabaseCredentials
setOrBeta(String) - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasTest
setParams(ObjectMap) - Method in class org.opencb.cellbase.core.CellBaseDataResponse
setPartner(Partner) - Method in class org.opencb.cellbase.core.common.drug.DrugPartnerInteraction
setPassword(String) - Method in class org.opencb.cellbase.core.config.DatabaseCredentials
setPercentCI(String) - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasTest
setPharmacology(String) - Method in class org.opencb.cellbase.core.common.drug.Drug
setPhred(float) - Method in class org.opencb.cellbase.lib.builders.formats.Cadd.CaddValues
setPlants(List<SpeciesConfiguration>) - Method in class org.opencb.cellbase.core.config.SpeciesProperties
setPlatform(String) - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasStudy
setPort(int) - Method in class org.opencb.cellbase.core.config.Rest
setPrefix(String) - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsStringBuilder
setPrimaryHistology(String) - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
setPrimarySite(String) - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
setProtist(List<SpeciesConfiguration>) - Method in class org.opencb.cellbase.core.config.SpeciesProperties
setPubmedId(String) - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasStudy
setPubmedId(String) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaDisease
setPubmedId(String) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaTarget
setPubmedPMID(String) - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
setpValue(Float) - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasTest
setpValueMlog(Float) - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasTest
setpValueText(String) - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasTest
setPwm(Pwm) - Method in class org.opencb.cellbase.core.common.regulatory.Tfbs
setPwmId(int) - Method in class org.opencb.cellbase.core.common.regulatory.Pwm
setRangeCoordsAndAlleles(int, int, String, String, Transcript, HgvsStringBuilder) - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsCalculator
setRangeKey(String) - Method in class org.opencb.cellbase.core.config.SpeciesConfiguration.ShardConfig
setReactome(DownloadProperties.URLProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties
setReference(String) - Method in class org.opencb.cellbase.core.common.clinical.ClinicalVariant
setReference(String) - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsStringBuilder
setReference(String) - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
setReference(String) - Method in class org.opencb.cellbase.lib.model.ClinicalVariation: Deprecated.
setReferencePosition(int) - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.CdnaCoord
setReferences(String) - Method in class org.opencb.cellbase.core.common.drug.Partner
setRegion(String) - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
setRegulatoryRegion(RegulatoryRegion) - Method in class org.opencb.cellbase.core.common.regulatory.Tfbs
setRegulatoryRegionId(int) - Method in class org.opencb.cellbase.core.common.regulatory.RegulatoryRegion
setRelativeEnd(int) - Method in class org.opencb.cellbase.core.common.regulatory.Tfbs
setRelativeStart(int) - Method in class org.opencb.cellbase.core.common.regulatory.Tfbs
setReplicationSampleSize(String) - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasStudy
setReportedGenes(String) - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
setRepset(String) - Method in class org.opencb.cellbase.core.monitor.HealthStatus.ApplicationDetails.DependenciesStatus.DatastoreDependenciesStatus.DatastoreStatus
setResponses(List<CellBaseDataResult<T>>) - Method in class org.opencb.cellbase.core.CellBaseDataResponse
setResponseTime(String) - Method in class org.opencb.cellbase.core.monitor.HealthStatus.ApplicationDetails.DependenciesStatus.DatastoreDependenciesStatus.DatastoreStatus
setRest(RestConfig) - Method in class org.opencb.cellbase.client.config.ClientConfiguration
setRest(Rest) - Method in class org.opencb.cellbase.core.config.ServerProperties
setRiskAlleleFrequency(Float) - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
setRole(String) - Method in class org.opencb.cellbase.core.monitor.HealthStatus.ApplicationDetails.DependenciesStatus.DatastoreDependenciesStatus.DatastoreStatus
setRouteOfElimination(String) - Method in class org.opencb.cellbase.core.common.drug.Drug
setSampleName(String) - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
setSampleSource(String) - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
setScientific(String) - Method in class org.opencb.cellbase.core.common.Species
setScientificName(String) - Method in class org.opencb.cellbase.core.config.SpeciesConfiguration
setScore(double) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaTarget
setScore(double) - Method in class org.opencb.cellbase.core.common.regulatory.Tfbs
setSequence(String) - Method in class org.opencb.cellbase.core.common.drug.Partner
setSequence(String) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaGene
setSequence(String) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaMature: Deprecated.
setSequence(String) - Method in class org.opencb.cellbase.core.common.regulatory.Tfbs
setSequenceOntology(List<SequenceOntologyTermComparisonObject>) - Method in class org.opencb.cellbase.app.cli.main.annotation.VariantAnnotationDiff
setServer(ServerProperties) - Method in class org.opencb.cellbase.core.config.CellBaseConfiguration
setServer(String) - Method in class org.opencb.cellbase.core.monitor.HealthStatus.ApplicationDetails
setServer(RestServer) - Static method in class org.opencb.cellbase.server.rest.AdminRestWebService
setService(HealthStatus.Service) - Method in class org.opencb.cellbase.core.monitor.HealthStatus
setServiceDiscovery(String) - Method in class org.opencb.cellbase.core.monitor.HealthStatus.Infrastructure
setShardRanges(List<SpeciesConfiguration.ShardRange>) - Method in class org.opencb.cellbase.core.config.SpeciesConfiguration.Zone
setShards(List<MongoDBDatabaseCredentials.ReplicaSet>) - Method in class org.opencb.cellbase.core.config.MongoDBDatabaseCredentials
setShards(List<SpeciesConfiguration.ShardConfig>) - Method in class org.opencb.cellbase.core.config.SpeciesConfiguration
setSimpleRepeats(DownloadProperties.URLProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties
setSiteSubtype(String) - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
setSnp(boolean) - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
setSnpGeneIds(String) - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
setSnpId(String) - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
setSnpIdCurrent(String) - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
setSource(String) - Method in class org.opencb.cellbase.core.common.clinical.ClinicalVariant
setSource(String) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaGene
setSource(String) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaTarget
setSource(String) - Method in class org.opencb.cellbase.core.common.regulatory.Pwm
setSource(String) - Method in class org.opencb.cellbase.core.common.regulatory.RegulatoryRegion
setSource(String) - Method in class org.opencb.cellbase.core.common.regulatory.Tfbs
setSources(List<ConservedRegionFeature.ConservedRegionSource>) - Method in class org.opencb.cellbase.lib.builders.formats.ConservedRegionFeature: Deprecated.
setSpecies(String) - Method in class org.opencb.cellbase.client.rest.CellBaseClient
setSpecies(String) - Method in class org.opencb.cellbase.core.common.Species
setSpecies(SpeciesProperties) - Method in class org.opencb.cellbase.core.config.CellBaseConfiguration
setSpecies(String) - Method in class org.opencb.cellbase.lib.impl.MongoDBAdaptor
setSpecificFunction(String) - Method in class org.opencb.cellbase.core.common.drug.Partner
setStart(int) - Method in class org.opencb.cellbase.core.common.clinical.ClinicalVariant
setStart(int) - Method in class org.opencb.cellbase.core.common.IntervalFeatureFrequency
setStart(int) - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
setStart(int) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaTarget
setStart(int) - Method in class org.opencb.cellbase.core.common.regulatory.RegulatoryRegion
setStart(int) - Method in class org.opencb.cellbase.core.common.regulatory.Tfbs
setStart(int) - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsStringBuilder
setStart(Integer) - Method in class org.opencb.cellbase.lib.builders.formats.Cadd
setStart(int) - Method in class org.opencb.cellbase.lib.builders.formats.ConservedRegionFeature: Deprecated.
setStart(int) - Method in class org.opencb.cellbase.lib.model.ClinicalVariation: Deprecated.
setStart(int) - Method in class org.opencb.cellbase.server.rest.genomic.Interval: Deprecated.
setStarted(String) - Method in class org.opencb.cellbase.core.monitor.HealthStatus.ApplicationDetails
setStatus(String) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaGene
setStatus(HealthStatus.ServiceStatus) - Method in class org.opencb.cellbase.core.monitor.HealthStatus.Service
setStatus(DownloadFile.Status) - Method in class org.opencb.cellbase.lib.download.DownloadFile
setStrand(String) - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
setStrand(String) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaTarget
setStrand(String) - Method in class org.opencb.cellbase.core.common.regulatory.Tfbs
setStrongestSNPRiskAllele(String) - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
setStudies(List<GwasStudy>) - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
setStudy(String) - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasStudy
setSumDataMammal(double) - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
setSumDataPrimate(double) - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
setSumDataVertebrate(double) - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
setSumSquareMammal(double) - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
setSumSquarePrimate(double) - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
setSumSquareVertebrate(double) - Method in class org.opencb.cellbase.core.common.regulatory.ConservedRegion
setTagName(String) - Method in class org.opencb.cellbase.core.monitor.HealthStatus.ApplicationDetails.Version
setTargetGeneName(String) - Method in class org.opencb.cellbase.core.common.regulatory.Tfbs
setTargetScan(DownloadProperties.URLProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties
setTests(List<GwasTest>) - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasTrait
setTfbses(Set<Tfbs>) - Method in class org.opencb.cellbase.core.common.regulatory.Pwm
setTfbses(Set<Tfbs>) - Method in class org.opencb.cellbase.core.common.regulatory.RegulatoryRegion
setTfbsId(int) - Method in class org.opencb.cellbase.core.common.regulatory.Tfbs
setTfName(String) - Method in class org.opencb.cellbase.core.common.regulatory.Pwm
setTfName(String) - Method in class org.opencb.cellbase.core.common.regulatory.Tfbs
setTime(int) - Method in class org.opencb.cellbase.core.CellBaseDataResponse
setTimeout(int) - Method in class org.opencb.cellbase.client.config.RestConfig
setTissueName(String) - Method in class org.opencb.cellbase.lib.builders.formats.GeneExpressionAtlas.Tissue
setTissues(List<GeneExpressionAtlas.Tissue>) - Method in class org.opencb.cellbase.lib.builders.formats.GeneExpressionAtlas
setToxicity(String) - Method in class org.opencb.cellbase.core.common.drug.Drug
setTraits(List<GwasTrait>) - Method in class org.opencb.cellbase.core.common.clinical.gwas.GwasStudy
setTranscript(Transcript) - Method in class org.opencb.cellbase.core.common.regulatory.MirnaToGene
setTranscript(Transcript) - Method in class org.opencb.cellbase.core.common.regulatory.Tfbs
setTranscriptId(String) - Method in class org.opencb.cellbase.app.cli.main.annotation.SequenceOntologyTermComparisonObject
setTranscriptId(String) - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsStringBuilder
setTumourOrigin(String) - Method in class org.opencb.cellbase.core.common.clinical.Cosmic
setType(String) - Method in class org.opencb.cellbase.core.common.drug.Drug
setType(String) - Method in class org.opencb.cellbase.core.common.drug.DrugPartnerInteraction
setType(String) - Method in class org.opencb.cellbase.core.common.regulatory.Pwm
setType(String) - Method in class org.opencb.cellbase.core.common.regulatory.RegulatoryRegion
setType(String) - Method in class org.opencb.cellbase.lib.builders.formats.ConservedRegionFeature.ConservedRegionSource: Deprecated.
setUniprot(DownloadProperties.URLProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties
setUniprotRelNotes(DownloadProperties.URLProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties
setUpstreamGeneDistance(String) - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
setUpstreamGeneId(String) - Method in class org.opencb.cellbase.core.common.clinical.gwas.Gwas
setUptime(String) - Method in class org.opencb.cellbase.core.monitor.HealthStatus.ApplicationDetails
setUrl(DownloadProperties.URLProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties.EnsemblProperties
setUrl(String) - Method in class org.opencb.cellbase.core.config.Rest
setUser(String) - Method in class org.opencb.cellbase.core.config.DatabaseCredentials
setValue(float) - Method in class org.opencb.cellbase.core.common.IntervalFeatureFrequency
setValue(float) - Method in class org.opencb.cellbase.server.rest.genomic.Interval: Deprecated.
setValues(List<Float>) - Method in class org.opencb.cellbase.lib.builders.formats.ConservedRegionFeature.ConservedRegionSource: Deprecated.
setVariantAnnotation(VariantAnnotation) - Method in class org.opencb.cellbase.app.cli.main.annotation.VariantAnnotationDiff
setVerbose(boolean) - Method in class org.opencb.cellbase.app.cli.CommandExecutor
setVersion(String) - Method in class org.opencb.cellbase.client.config.ClientConfiguration
setVersion(String) - Method in class org.opencb.cellbase.core.config.CellBaseConfiguration
setVersion(String) - Method in class org.opencb.cellbase.core.config.DownloadProperties.URLProperties
setVersion(HealthStatus.ApplicationDetails.Version) - Method in class org.opencb.cellbase.core.monitor.HealthStatus.ApplicationDetails
setVertebrates(List<SpeciesConfiguration>) - Method in class org.opencb.cellbase.core.config.SpeciesProperties
setVirus(List<SpeciesConfiguration>) - Method in class org.opencb.cellbase.core.config.SpeciesProperties
setVolumeOfDistribution(String) - Method in class org.opencb.cellbase.core.common.drug.Drug
setWiki(String) - Method in class org.opencb.cellbase.core.config.CellBaseConfiguration
setWindowMasker(DownloadProperties.URLProperties) - Method in class org.opencb.cellbase.core.config.DownloadProperties
setXrefs(List<XRef>) - Method in class org.opencb.cellbase.core.common.drug.Drug
setXrefs(List<XRef>) - Method in class org.opencb.cellbase.core.common.drug.Partner
setZones(List<SpeciesConfiguration.Zone>) - Method in class org.opencb.cellbase.core.config.SpeciesConfiguration.ShardConfig
shard(MongoDataStore, CellBaseConfiguration, Species) - Static method in class org.opencb.cellbase.lib.install.MongoDBShardUtils: Add shards.
ShardConfig() - Constructor for class org.opencb.cellbase.core.config.SpeciesConfiguration.ShardConfig
ShardRange() - Constructor for class org.opencb.cellbase.core.config.SpeciesConfiguration.ShardRange
SharedContext(int) - Constructor for class org.opencb.cellbase.app.cli.main.annotation.VcfStringAnnotatorTask.SharedContext: Deprecated.
SIFT_DESCRIPTIONS - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
skip - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.QueryCommandOptions
skip - Variable in class org.opencb.cellbase.server.rest.GenericRestWSServer
skipCount - Variable in class org.opencb.cellbase.server.rest.GenericRestWSServer
skipDecompose - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.VariantAnnotationCommandOptions
skipLeftAlign - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.VariantAnnotationCommandOptions
skipNormalize - Variable in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.BuildCommandOptions
skipNormalize - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.VariantAnnotationCommandOptions
SNORNA - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
SNORNA_PSEUDOGENE - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
SNRNA - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
SNRNA_PSEUDOGENE - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
SO_NAMES_CORRECTIONS - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
SO_SEVERITY - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
solveCodingExonVariantInNegativeTranscript(boolean, String, int, int, int) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeDeletionCalculator
solveCodingExonVariantInNegativeTranscript(boolean, String, int, int, int) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeGenericRegionCalculator
solveCodingExonVariantInNegativeTranscript(boolean, String, int, int, int) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeMNVCalculator
solveCodingExonVariantInPositiveTranscript(boolean, String, int, int, int) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeDeletionCalculator
solveCodingExonVariantInPositiveTranscript(boolean, String, int, int, int) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeGenericRegionCalculator
solveCodingExonVariantInPositiveTranscript(boolean, String, int, int, int) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeMNVCalculator
solveCodingNegativeTranscript() - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
solveCodingNegativeTranscript() - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeGenericRegionCalculator
solveCodingNegativeTranscript() - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeInsertionCalculator
solveCodingNegativeTranscript() - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeSNVCalculator
solveCodingPositiveTranscript() - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
solveCodingPositiveTranscript() - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeGenericRegionCalculator
solveCodingPositiveTranscript() - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeInsertionCalculator
solveCodingPositiveTranscript() - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeSNVCalculator
solveExonVariantInNegativeTranscript(boolean, String, int, int, int) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeDeletionCalculator
solveExonVariantInNegativeTranscript(boolean, String, int, int, int) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeGenericRegionCalculator
solveExonVariantInPositiveTranscript(boolean, String, int, int, int) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeDeletionCalculator
solveExonVariantInPositiveTranscript(boolean, String, int, int, int) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeGenericRegionCalculator
solveIntergenic(List<ConsequenceType>, boolean) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
solveJunction(Integer, Integer, String, String, boolean[]) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeGenericRegionCalculator
solveJunction(Integer, Integer, String, String, boolean[]) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeMNVCalculator
solveMiRNA(int, int, boolean) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
solveNegativeTranscript(List<ConsequenceType>) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
solveNonCodingNegativeTranscript() - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
solveNonCodingNegativeTranscript() - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeGenericRegionCalculator
solveNonCodingNegativeTranscript() - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeInsertionCalculator
solveNonCodingNegativeTranscript() - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeSNVCalculator
solveNonCodingPositiveTranscript() - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
solveNonCodingPositiveTranscript() - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeGenericRegionCalculator
solveNonCodingPositiveTranscript() - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeInsertionCalculator
solveNonCodingPositiveTranscript() - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeSNVCalculator
solvePositiveTranscript(List<ConsequenceType>) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
solveRegulatoryRegions(boolean[], List<ConsequenceType>) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
solveStopCodonNegativeVariant(String, int, int, int) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeDeletionCalculator
solveStopCodonNegativeVariant(String, int, int, int) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeGenericRegionCalculator
solveStopCodonPositiveVariant(String, int, int, int) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeDeletionCalculator
solveStopCodonPositiveVariant(String, int, int, int) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeGenericRegionCalculator
solveTranscriptFlankingRegions(String, String) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeGenericRegionCalculator
SoNames - Variable in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
sort() - Method in class org.opencb.cellbase.lib.builders.variation.AbstractVariationFile
sort - Variable in class org.opencb.cellbase.server.rest.GenericRestWSServer
sortFileByNumericColumn(Path, Path, int) - Method in class org.opencb.cellbase.lib.builders.variation.AbstractVariationFile
species - Variable in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.BuildCommandOptions
species - Variable in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.IndexCommandOptions
species - Variable in class org.opencb.cellbase.app.cli.CliOptionsParser.SpeciesAndAssemblyCommandOptions
species - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.QueryCommandOptions
species - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.VariantAnnotationCommandOptions
species() - Method in class org.opencb.cellbase.client.rest.MetaClient
species(String) - Method in class org.opencb.cellbase.client.rest.MetaClient
species - Variable in class org.opencb.cellbase.client.rest.ParentRestClient
Species - Class in org.opencb.cellbase.core.common
Species(String, String, String) - Constructor for class org.opencb.cellbase.core.common.Species
Species(String, String, String, String) - Constructor for class org.opencb.cellbase.core.common.Species
species - Variable in class org.opencb.cellbase.lib.impl.MongoDBAdaptor
species - Variable in class org.opencb.cellbase.server.rest.GenericRestWSServer
SpeciesAndAssemblyCommandOptions() - Constructor for class org.opencb.cellbase.app.cli.CliOptionsParser.SpeciesAndAssemblyCommandOptions
speciesAndAssemblyOptions - Variable in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.DownloadCommandOptions
speciesAndAssemblyOptions - Variable in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.InstallCommandOptions
SpeciesConfiguration - Class in org.opencb.cellbase.core.config: Created by imedina on 19/08/16.
SpeciesConfiguration() - Constructor for class org.opencb.cellbase.core.config.SpeciesConfiguration
SpeciesConfiguration(String, String, String, List<SpeciesConfiguration.Assembly>, List<String>, List<SpeciesConfiguration.ShardConfig>) - Constructor for class org.opencb.cellbase.core.config.SpeciesConfiguration
SpeciesConfiguration.Assembly - Class in org.opencb.cellbase.core.config
SpeciesConfiguration.ShardConfig - Class in org.opencb.cellbase.core.config
SpeciesConfiguration.ShardRange - Class in org.opencb.cellbase.core.config
SpeciesConfiguration.Zone - Class in org.opencb.cellbase.core.config
SpeciesException - Exception in org.opencb.cellbase.server.exception
SpeciesException(String) - Constructor for exception org.opencb.cellbase.server.exception.SpeciesException
SpeciesProperties - Class in org.opencb.cellbase.core.config: Created by imedina on 19/08/16.
SpeciesProperties() - Constructor for class org.opencb.cellbase.core.config.SpeciesProperties
SpeciesProperties(List<SpeciesConfiguration>, List<SpeciesConfiguration>, List<SpeciesConfiguration>, List<SpeciesConfiguration>, List<SpeciesConfiguration>, List<SpeciesConfiguration>, List<SpeciesConfiguration>) - Constructor for class org.opencb.cellbase.core.config.SpeciesProperties
SpeciesUtils - Class in org.opencb.cellbase.lib
SpeciesUtils() - Constructor for class org.opencb.cellbase.lib.SpeciesUtils
SpeciesWSServer - Class in org.opencb.cellbase.server.rest: Created by imedina on 04/08/15.
SpeciesWSServer(String, String, UriInfo, HttpServletRequest) - Constructor for class org.opencb.cellbase.server.rest.SpeciesWSServer
SPLICE_ACCEPTOR_VARIANT - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
SPLICE_DONOR_VARIANT - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
SPLICE_REGION_VARIANT - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
start - Variable in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.ServerCommandOptions
start() - Method in class org.opencb.cellbase.server.RestServer
START_CODON - Static variable in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
START_LOST - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
START_RETAINED_VARIANT - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
startsWith(String, QueryOptions) - Method in interface org.opencb.cellbase.core.api.GeneDBAdaptor
startsWith(String, QueryOptions) - Method in interface org.opencb.cellbase.core.api.VariantDBAdaptor
startsWith(String, QueryOptions) - Method in interface org.opencb.cellbase.core.api.XRefDBAdaptor
startsWith(String, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.GeneMongoDBAdaptor
startsWith(String, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.VariantMongoDBAdaptor
startsWith(String, QueryOptions) - Method in class org.opencb.cellbase.lib.impl.XRefMongoDBAdaptor
startTime - Variable in class org.opencb.cellbase.server.rest.GenericRestWSServer
stats() - Method in interface org.opencb.cellbase.core.api.CellBaseDBAdaptor
stats(Query) - Method in interface org.opencb.cellbase.core.api.CellBaseDBAdaptor
stats(Query) - Method in class org.opencb.cellbase.lib.impl.ClinicalLegacyMongoDBAdaptor: Deprecated.
stats(Query) - Method in class org.opencb.cellbase.lib.impl.ClinicalMongoDBAdaptor
stats(Query) - Method in class org.opencb.cellbase.lib.impl.ConservationMongoDBAdaptor: Deprecated.
stats(Query) - Method in class org.opencb.cellbase.lib.impl.GeneMongoDBAdaptor
stats(Query) - Method in class org.opencb.cellbase.lib.impl.GenomeMongoDBAdaptor
stats(Query) - Method in class org.opencb.cellbase.lib.impl.MetaMongoDBAdaptor
stats(Query) - Method in class org.opencb.cellbase.lib.impl.ProteinMongoDBAdaptor
stats(Query) - Method in class org.opencb.cellbase.lib.impl.ProteinProteinInteractionMongoDBAdaptor
stats(Query) - Method in class org.opencb.cellbase.lib.impl.RegulationMongoDBAdaptor
stats(Query) - Method in class org.opencb.cellbase.lib.impl.RepeatsMongoDBAdaptor
stats(Query) - Method in class org.opencb.cellbase.lib.impl.TranscriptMongoDBAdaptor
stats(Query) - Method in class org.opencb.cellbase.lib.impl.VariantMongoDBAdaptor
stats(Query) - Method in class org.opencb.cellbase.lib.impl.XRefMongoDBAdaptor
stats() - Method in class org.opencb.cellbase.server.rest.feature.GeneWSServer
stats() - Method in class org.opencb.cellbase.server.rest.feature.TranscriptWSServer
stats() - Method in class org.opencb.cellbase.server.rest.feature.VariationWSServer
stats() - Method in interface org.opencb.cellbase.server.rest.IWSServer
status(String) - Method in class org.opencb.cellbase.server.rest.MetaWSServer
stop - Variable in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.ServerCommandOptions
stop() - Method in class org.opencb.cellbase.server.rest.AdminRestWebService
stop() - Method in class org.opencb.cellbase.server.RestServer
STOP_GAINED - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
STOP_LOST - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
STOP_RETAINED_VARIANT - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
StringUtils - Class in org.opencb.cellbase.lib.builders.utils: Deprecated.
StringUtils() - Constructor for class org.opencb.cellbase.lib.builders.utils.StringUtils: Deprecated.
STRUCTURAL_VARIANT - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
STRUCTURAL_VARIANTS_DATA - Static variable in class org.opencb.cellbase.lib.EtlCommons
STRUCTURAL_VARIANTS_FOLDER - Static variable in class org.opencb.cellbase.lib.EtlCommons
STRUCTURAL_VARIANTS_JSON - Static variable in class org.opencb.cellbase.lib.EtlCommons
subcategory - Variable in class org.opencb.cellbase.client.rest.ParentRestClient
SV_EXTRA_PADDING - Static variable in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
svExtraPadding - Variable in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
SYNONYMOUS_VARIANT - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils

T

targetDirectory - Variable in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.BuildCommandOptions
targetDirectory - Variable in class org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser.DownloadCommandOptions
TERMINATOR_CODON_VARIANT - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
TF_BINDING_SITE_VARIANT - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
Tfbs - Class in org.opencb.cellbase.core.common.regulatory: Tfbs generated by hbm2java.
Tfbs() - Constructor for class org.opencb.cellbase.core.common.regulatory.Tfbs
Tfbs(int, Pwm, Transcript, RegulatoryRegion, Gene, String, String, String, int, int, String, int, int, double, String, String, String) - Constructor for class org.opencb.cellbase.core.common.regulatory.Tfbs
TfWSServer - Class in org.opencb.cellbase.server.rest.regulatory
TfWSServer(String, String, UriInfo, HttpServletRequest) - Constructor for class org.opencb.cellbase.server.rest.regulatory.TfWSServer
THREE_PRIME_UTR_VARIANT - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
THREEPRIME_OVERLAPPING_NCRNA - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
Tissue(String, String, Float) - Constructor for class org.opencb.cellbase.lib.builders.formats.GeneExpressionAtlas.Tissue
toResponse(Exception) - Method in class org.opencb.cellbase.server.rest.CellBaseExceptionMapper
toString() - Method in class org.opencb.cellbase.client.config.ClientConfiguration
toString() - Method in class org.opencb.cellbase.client.config.RestConfig
toString() - Method in class org.opencb.cellbase.client.rest.CellBaseClient
toString() - Method in class org.opencb.cellbase.core.CellBaseDataResponse
toString() - Method in class org.opencb.cellbase.core.common.GitRepositoryState
toString() - Method in class org.opencb.cellbase.core.common.IntervalFeatureFrequency
toString() - Method in class org.opencb.cellbase.core.common.Species
toString() - Method in class org.opencb.cellbase.core.config.DatabaseCredentials
toString() - Method in class org.opencb.cellbase.core.config.Databases
toString() - Method in class org.opencb.cellbase.core.config.MongoDBDatabaseCredentials
toString() - Method in class org.opencb.cellbase.core.config.SpeciesConfiguration
toString() - Method in class org.opencb.cellbase.core.config.SpeciesProperties
toString() - Method in class org.opencb.cellbase.core.result.CellBaseDataResult
toString() - Method in class org.opencb.cellbase.core.variant.annotation.hgvs.CdnaCoord
toString() - Method in class org.opencb.cellbase.lib.download.DownloadFile
toString() - Method in class org.opencb.cellbase.lib.download.EnsemblInfo
totalNumberRecords - Variable in class org.opencb.cellbase.lib.builders.clinical.variant.ClinicalIndexer
TR_C_GENE - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
TR_D_GENE - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
TR_J_GENE - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
TR_J_PSEUDOGENE - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
TR_V_GENE - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
TR_V_PSEUDOGENE - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
TRANSCRIBED_PROCESSED_PSEUDOGENE - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
TRANSCRIBED_UNITARY_PSEUDOGENE - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
TRANSCRIBED_UNPROCESSED_PSEUDGENE - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
transcript - Variable in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
TRANSCRIPT_ABLATION - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
TRANSCRIPT_AMPLIFICATION - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
TRANSCRIPT_VARIATION_FILENAME - Static variable in class org.opencb.cellbase.lib.builders.variation.VariationTranscriptFile
TranscriptClient - Class in org.opencb.cellbase.client.rest: Created by swaathi on 20/05/16.
TranscriptClient(String, String, ClientConfiguration) - Constructor for class org.opencb.cellbase.client.rest.TranscriptClient
TranscriptDBAdaptor<Transcript> - Interface in org.opencb.cellbase.core.api: Created by imedina on 30/11/15.
TranscriptDBAdaptor.QueryParams - Enum in org.opencb.cellbase.core.api
TranscriptMongoDBAdaptor - Class in org.opencb.cellbase.lib.impl: Created by swaathi on 27/11/15.
TranscriptMongoDBAdaptor(String, String, MongoDataStore) - Constructor for class org.opencb.cellbase.lib.impl.TranscriptMongoDBAdaptor
TranscriptWSServer - Class in org.opencb.cellbase.server.rest.feature
TranscriptWSServer(String, String, String, UriInfo, HttpServletRequest) - Constructor for class org.opencb.cellbase.server.rest.feature.TranscriptWSServer
translate(String) - Static method in class org.opencb.cellbase.core.common.DNASequenceUtils
translate(String, String) - Static method in class org.opencb.cellbase.core.common.DNASequenceUtils
TRANSLATED_PROCESSED_PSEUDOGENE - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
TRANSLATED_UNPROCESSED_PSEUDOGENE - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
TRF_FILE - Static variable in class org.opencb.cellbase.lib.EtlCommons
TRF_VERSION_FILE - Static variable in class org.opencb.cellbase.lib.EtlCommons
TRNA_PSEUDOGENE - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
TWOKB_DOWNSTREAM_VARIANT - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
TWOKB_UPSTREAM_VARIANT - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
type() - Method in enum org.opencb.cellbase.core.api.ClinicalDBAdaptor.QueryParams
type() - Method in enum org.opencb.cellbase.core.api.ConservationDBAdaptor.QueryParams: Deprecated.
type() - Method in enum org.opencb.cellbase.core.api.GeneDBAdaptor.QueryParams
type() - Method in enum org.opencb.cellbase.core.api.GenomeDBAdaptor.QueryParams
type() - Method in enum org.opencb.cellbase.core.api.ProteinDBAdaptor.QueryParams
type() - Method in enum org.opencb.cellbase.core.api.ProteinProteinInteractionDBAdaptor.QueryParams
type() - Method in enum org.opencb.cellbase.core.api.RegulationDBAdaptor.QueryParams
type() - Method in enum org.opencb.cellbase.core.api.RepeatsDBAdaptor.QueryParams
type() - Method in enum org.opencb.cellbase.core.api.TranscriptDBAdaptor.QueryParams
type() - Method in enum org.opencb.cellbase.core.api.VariantDBAdaptor.QueryParams
type() - Method in enum org.opencb.cellbase.core.api.XRefDBAdaptor.QueryParams

U

UNITARY_PSEUDOGENE - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
UNPHASED_GENOTYPE_SEPARATOR - Static variable in class org.opencb.cellbase.core.variant.PhasedQueryManager
UNPROCESSED_PSEUDOGENE - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
unprocessedFileName - Variable in class org.opencb.cellbase.lib.builders.variation.AbstractVariationFile
UnsupportedURLVariantFormat - Exception in org.opencb.cellbase.core.variant.annotation: Created by fjlopez on 30/06/15.
UnsupportedURLVariantFormat() - Constructor for exception org.opencb.cellbase.core.variant.annotation.UnsupportedURLVariantFormat: Constructs an instance of UnsupportedURLVariantFormat for a field, and with the specified detail message.
UnsupportedURLVariantFormat(String) - Constructor for exception org.opencb.cellbase.core.variant.annotation.UnsupportedURLVariantFormat: Constructs an instance of UnsupportedURLVariantFormat for a field, and with the specified detail message.
update(List, String, String[]) - Method in interface org.opencb.cellbase.core.api.CellBaseDBAdaptor
update(List, String, String[]) - Method in class org.opencb.cellbase.lib.impl.ClinicalLegacyMongoDBAdaptor: Deprecated.
update(List, String, String[]) - Method in class org.opencb.cellbase.lib.impl.ClinicalMongoDBAdaptor
update(List, String, String[]) - Method in class org.opencb.cellbase.lib.impl.ConservationMongoDBAdaptor: Deprecated.
update(List, String, String[]) - Method in class org.opencb.cellbase.lib.impl.GeneMongoDBAdaptor
update(List, String, String[]) - Method in class org.opencb.cellbase.lib.impl.GenomeMongoDBAdaptor
update(List, String, String[]) - Method in class org.opencb.cellbase.lib.impl.MetaMongoDBAdaptor
update(List, String, String[]) - Method in class org.opencb.cellbase.lib.impl.ProteinMongoDBAdaptor
update(List, String, String[]) - Method in class org.opencb.cellbase.lib.impl.ProteinProteinInteractionMongoDBAdaptor
update(List, String, String[]) - Method in class org.opencb.cellbase.lib.impl.RegulationMongoDBAdaptor
update(List, String, String[]) - Method in class org.opencb.cellbase.lib.impl.RepeatsMongoDBAdaptor
update(List, String, String[]) - Method in class org.opencb.cellbase.lib.impl.TranscriptMongoDBAdaptor
update(List, String, String[]) - Method in class org.opencb.cellbase.lib.impl.VariantMongoDBAdaptor
update(List, String, String[]) - Method in class org.opencb.cellbase.lib.impl.XRefMongoDBAdaptor
updateIndex(List<Variant>) - Method in class org.opencb.cellbase.app.cli.main.annotation.indexers.CustomAnnotationVariantIndexer
updateIndex(List<Variant>) - Method in class org.opencb.cellbase.app.cli.main.annotation.indexers.PopulationFrequencyVariantIndexer
updateIndex(List<Variant>) - Method in class org.opencb.cellbase.app.cli.main.annotation.indexers.VariantIndexer
updateNegativeInsertionCodonArrays(String, char[], int, int, char[], char[]) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
updatePositiveInsertionCodonArrays(String, char[], int, int, char[], char[]) - Method in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
UPSTREAM_GENE_VARIANT - Static variable in class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
uriInfo - Variable in class org.opencb.cellbase.server.rest.GenericRestWSServer
url - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.VariantAnnotationCommandOptions
URLProperties() - Constructor for class org.opencb.cellbase.core.config.DownloadProperties.URLProperties
UtilsWSServer - Class in org.opencb.cellbase.server.rest.utils
UtilsWSServer(String, String, UriInfo, HttpServletRequest) - Constructor for class org.opencb.cellbase.server.rest.utils.UtilsWSServer

V

valueOf(String) - Static method in enum org.opencb.cellbase.app.cli.main.executors.VariantAnnotationCommandExecutor.FileFormat: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.opencb.cellbase.core.api.ClinicalDBAdaptor.QueryParams: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.opencb.cellbase.core.api.ConservationDBAdaptor.QueryParams: Deprecated.

Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.opencb.cellbase.core.api.GeneDBAdaptor.QueryParams: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.opencb.cellbase.core.api.GenomeDBAdaptor.QueryParams: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.opencb.cellbase.core.api.ProteinDBAdaptor.QueryParams: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.opencb.cellbase.core.api.ProteinProteinInteractionDBAdaptor.QueryParams: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.opencb.cellbase.core.api.RegulationDBAdaptor.FeatureType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.opencb.cellbase.core.api.RegulationDBAdaptor.QueryParams: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.opencb.cellbase.core.api.RepeatsDBAdaptor.QueryParams: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.opencb.cellbase.core.api.TranscriptDBAdaptor.QueryParams: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.opencb.cellbase.core.api.VariantDBAdaptor.QueryParams: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.opencb.cellbase.core.api.XRefDBAdaptor.QueryParams: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.opencb.cellbase.core.config.CellBaseConfiguration.ConfigurationFileFormat: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.opencb.cellbase.core.monitor.HealthStatus.ServiceStatus: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.opencb.cellbase.core.variant.annotation.hgvs.CdnaCoord.Landmark: Returns the enum constant of this type with the specified name.
values() - Static method in enum org.opencb.cellbase.app.cli.main.executors.VariantAnnotationCommandExecutor.FileFormat: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.opencb.cellbase.core.api.ClinicalDBAdaptor.QueryParams: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.opencb.cellbase.core.api.ConservationDBAdaptor.QueryParams: Deprecated.

Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.opencb.cellbase.core.api.GeneDBAdaptor.QueryParams: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.opencb.cellbase.core.api.GenomeDBAdaptor.QueryParams: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.opencb.cellbase.core.api.ProteinDBAdaptor.QueryParams: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.opencb.cellbase.core.api.ProteinProteinInteractionDBAdaptor.QueryParams: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.opencb.cellbase.core.api.RegulationDBAdaptor.FeatureType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.opencb.cellbase.core.api.RegulationDBAdaptor.QueryParams: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.opencb.cellbase.core.api.RepeatsDBAdaptor.QueryParams: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.opencb.cellbase.core.api.TranscriptDBAdaptor.QueryParams: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.opencb.cellbase.core.api.VariantDBAdaptor.QueryParams: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.opencb.cellbase.core.api.XRefDBAdaptor.QueryParams: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.opencb.cellbase.core.config.CellBaseConfiguration.ConfigurationFileFormat: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.opencb.cellbase.core.monitor.HealthStatus.ServiceStatus: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.opencb.cellbase.core.variant.annotation.hgvs.CdnaCoord.Landmark: Returns an array containing the constants of this enum type, in the order they are declared.
variant - Variable in class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.VariantAnnotationCommandOptions
variant - Variable in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator
VariantAnnotationCalculator - Class in org.opencb.cellbase.core.variant.annotation: Created by imedina on 11/07/14.
VariantAnnotationCalculator(String, String, DBAdaptorFactory) - Constructor for class org.opencb.cellbase.core.variant.annotation.VariantAnnotationCalculator
VariantAnnotationCommandExecutor - Class in org.opencb.cellbase.app.cli.main.executors: Created by fjlopez on 18/03/15.
VariantAnnotationCommandExecutor(CellBaseCliOptionsParser.VariantAnnotationCommandOptions) - Constructor for class org.opencb.cellbase.app.cli.main.executors.VariantAnnotationCommandExecutor
VariantAnnotationCommandExecutor.FileFormat - Enum in org.opencb.cellbase.app.cli.main.executors
VariantAnnotationCommandOptions() - Constructor for class org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.VariantAnnotationCommandOptions
VariantAnnotationDBAdaptor<T> - Interface in org.opencb.cellbase.core.api: Deprecated.
VariantAnnotationDiff - Class in org.opencb.cellbase.app.cli.main.annotation: Created by fjlopez on 07/04/16.
VariantAnnotationDiff() - Constructor for class org.opencb.cellbase.app.cli.main.annotation.VariantAnnotationDiff
VariantAnnotationUtils - Class in org.opencb.cellbase.core.variant.annotation: Created by fjlopez on 22/06/15.
VariantAnnotationUtils() - Constructor for class org.opencb.cellbase.core.variant.annotation.VariantAnnotationUtils
VariantAnnotator - Interface in org.opencb.cellbase.core.variant.annotation: Created by fjlopez on 28/04/15.
VariantAnnotatorTask - Class in org.opencb.cellbase.app.cli.main.annotation: Created by fjlopez on 11/02/16.
VariantAnnotatorTask(List<VariantAnnotator>) - Constructor for class org.opencb.cellbase.app.cli.main.annotation.VariantAnnotatorTask
VariantClient - Class in org.opencb.cellbase.client.rest
VariantClient(String, String, ClientConfiguration) - Constructor for class org.opencb.cellbase.client.rest.VariantClient
VariantDBAdaptor<T> - Interface in org.opencb.cellbase.core.api: Created by imedina on 26/11/15.
VariantDBAdaptor.QueryParams - Enum in org.opencb.cellbase.core.api
variantEnd - Variable in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeGenericRegionCalculator
VariantIndexer - Class in org.opencb.cellbase.app.cli.main.annotation.indexers
VariantIndexer(VariantReader, int, boolean) - Constructor for class org.opencb.cellbase.app.cli.main.annotation.indexers.VariantIndexer
VariantMongoDBAdaptor - Class in org.opencb.cellbase.lib.impl: Created by imedina on 26/11/15.
VariantMongoDBAdaptor(String, String, MongoDataStore) - Constructor for class org.opencb.cellbase.lib.impl.VariantMongoDBAdaptor
VariantMongoIterator - Class in org.opencb.cellbase.lib: Created by fjlopez on 11/02/16.
VariantMongoIterator(Iterator<Document>) - Constructor for class org.opencb.cellbase.lib.VariantMongoIterator
variantStart - Variable in class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeGenericRegionCalculator
variantTypes() - Method in class org.opencb.cellbase.client.rest.ClinicalVariantClient
VariantWSServer - Class in org.opencb.cellbase.server.rest.genomic
VariantWSServer(String, String, UriInfo, HttpServletRequest) - Constructor for class org.opencb.cellbase.server.rest.genomic.VariantWSServer
VARIATION_CHUNK_SIZE - Static variable in class org.opencb.cellbase.lib.MongoDBCollectionConfiguration
VARIATION_DATA - Static variable in class org.opencb.cellbase.lib.EtlCommons
VARIATION_FEATURE_FILENAME - Static variable in class org.opencb.cellbase.lib.builders.variation.VariationFeatureFile
VARIATION_FILENAME - Static variable in class org.opencb.cellbase.lib.builders.variation.VariationFile
VARIATION_FUNCTIONAL_SCORE_CHUNK_SIZE - Static variable in class org.opencb.cellbase.lib.MongoDBCollectionConfiguration
VARIATION_FUNCTIONAL_SCORE_DATA - Static variable in class org.opencb.cellbase.lib.EtlCommons
VARIATION_ID_COLUMN_INDEX - Static variable in class org.opencb.cellbase.lib.builders.variation.VariationFile
VARIATION_ID_COLUMN_INDEX_IN_VARIATION_FEATURE_FILE - Static variable in class org.opencb.cellbase.lib.builders.variation.VariationFeatureFile
VARIATION_SYNONYM_FILENAME - Static variable in class org.opencb.cellbase.lib.builders.variation.VariationSynonymFile
VariationClient - Class in org.opencb.cellbase.client.rest: Created by swaathi on 23/05/16.
VariationClient(String, String, ClientConfiguration) - Constructor for class org.opencb.cellbase.client.rest.VariationClient
VariationConverter - Class in org.opencb.cellbase.lib.loader.converters: Deprecated.
VariationConverter() - Constructor for class org.opencb.cellbase.lib.loader.converters.VariationConverter: Deprecated.
VariationConverter(int) - Constructor for class org.opencb.cellbase.lib.loader.converters.VariationConverter: Deprecated.
VariationDataReader - Class in org.opencb.cellbase.app.cli.main.annotation: Created by fjlopez on 11/02/16.
VariationDataReader(VariantDBAdaptor, Query, QueryOptions) - Constructor for class org.opencb.cellbase.app.cli.main.annotation.VariationDataReader
variationDirectory - Variable in class org.opencb.cellbase.lib.builders.variation.AbstractVariationFile
VariationFeatureFile - Class in org.opencb.cellbase.lib.builders.variation: Created by parce on 09/12/15.
VariationFeatureFile(Path) - Constructor for class org.opencb.cellbase.lib.builders.variation.VariationFeatureFile
VariationFile - Class in org.opencb.cellbase.lib.builders.variation: Created by parce on 09/12/15.
VariationFile(Path) - Constructor for class org.opencb.cellbase.lib.builders.variation.VariationFile
variationIdColumnIndex - Variable in class org.opencb.cellbase.lib.builders.variation.AbstractVariationFile
VariationParser - Class in org.opencb.cellbase.lib.builders.variation
VariationParser(Path, CellBaseFileSerializer) - Constructor for class org.opencb.cellbase.lib.builders.variation.VariationParser
VariationPhenotypeAnnotationParser - Class in org.opencb.cellbase.lib.builders: Created by imedina on 12/01/14.
VariationPhenotypeAnnotationParser(Path, CellBaseSerializer) - Constructor for class org.opencb.cellbase.lib.builders.VariationPhenotypeAnnotationParser
VariationSynonymFile - Class in org.opencb.cellbase.lib.builders.variation: Created by parce on 09/12/15.
VariationSynonymFile(Path) - Constructor for class org.opencb.cellbase.lib.builders.variation.VariationSynonymFile
VariationTranscriptFile - Class in org.opencb.cellbase.lib.builders.variation: Created by parce on 09/12/15.
VariationTranscriptFile(Path) - Constructor for class org.opencb.cellbase.lib.builders.variation.VariationTranscriptFile
VariationUtils - Class in org.opencb.cellbase.lib.builders.utils: Created by imedina on 11/12/13.
VariationUtils() - Constructor for class org.opencb.cellbase.lib.builders.utils.VariationUtils
VariationWSServer - Class in org.opencb.cellbase.server.rest.feature: Created by fjlopez on 29/04/16.
VariationWSServer(String, String, UriInfo, HttpServletRequest) - Constructor for class org.opencb.cellbase.server.rest.feature.VariationWSServer
VcfStringAnnotatorTask - Class in org.opencb.cellbase.app.cli.main.annotation: Deprecated.
VcfStringAnnotatorTask(VCFHeader, VCFHeaderVersion, List<VariantAnnotator>, VcfStringAnnotatorTask.SharedContext) - Constructor for class org.opencb.cellbase.app.cli.main.annotation.VcfStringAnnotatorTask: Deprecated.
VcfStringAnnotatorTask(VCFHeader, VCFHeaderVersion, List<VariantAnnotator>, VcfStringAnnotatorTask.SharedContext, boolean, VariantNormalizer.VariantNormalizerConfig) - Constructor for class org.opencb.cellbase.app.cli.main.annotation.VcfStringAnnotatorTask: Deprecated.
VcfStringAnnotatorTask.SharedContext - Class in org.opencb.cellbase.app.cli.main.annotation: Deprecated.
VcfVariantAnnotator - Class in org.opencb.cellbase.app.cli.main.annotation: Created by fjlopez on 28/04/15.
VcfVariantAnnotator(String, RocksDB, String, QueryOptions) - Constructor for class org.opencb.cellbase.app.cli.main.annotation.VcfVariantAnnotator
verbose - Variable in class org.opencb.cellbase.app.cli.CliOptionsParser.CommonCommandOptions: Deprecated.
verbose - Variable in class org.opencb.cellbase.app.cli.CommandExecutor
version - Variable in class org.opencb.cellbase.app.cli.CliOptionsParser.GeneralOptions
Version() - Constructor for class org.opencb.cellbase.core.monitor.HealthStatus.ApplicationDetails.Version
Version(String, String) - Constructor for class org.opencb.cellbase.core.monitor.HealthStatus.ApplicationDetails.Version
version - Variable in class org.opencb.cellbase.server.rest.GenericRestWSServer
VersionException - Exception in org.opencb.cellbase.server.exception
VersionException(String) - Constructor for exception org.opencb.cellbase.server.exception.VersionException
versions() - Method in class org.opencb.cellbase.client.rest.MetaClient
versions(String) - Method in class org.opencb.cellbase.client.rest.MetaClient

W

WATCH - Variable in class org.opencb.cellbase.server.rest.GenericRestWSServer
WEBSERVICES - Static variable in class org.opencb.cellbase.client.rest.ParentRestClient
WM_FILE - Static variable in class org.opencb.cellbase.lib.EtlCommons
WM_VERSION_FILE - Static variable in class org.opencb.cellbase.lib.EtlCommons
write(Pair<VariantAnnotationDiff, VariantAnnotationDiff>) - Method in class org.opencb.cellbase.app.cli.main.annotation.BenchmarkDataWriter
write(List<Pair<VariantAnnotationDiff, VariantAnnotationDiff>>) - Method in class org.opencb.cellbase.app.cli.main.annotation.BenchmarkDataWriter
writeDownloadLogFile() - Method in class org.opencb.cellbase.lib.download.DownloadManager

X

XRef - Class in org.opencb.cellbase.core.common.drug: Created with IntelliJ IDEA.
XRef() - Constructor for class org.opencb.cellbase.core.common.drug.XRef
XRef(String, String) - Constructor for class org.opencb.cellbase.core.common.drug.XRef
XRef(String, String, String) - Constructor for class org.opencb.cellbase.core.common.drug.XRef
XRefDBAdaptor<XRef> - Interface in org.opencb.cellbase.core.api: Created by imedina on 30/11/15.
XRefDBAdaptor.QueryParams - Enum in org.opencb.cellbase.core.api
XRefMongoDBAdaptor - Class in org.opencb.cellbase.lib.impl: Created by imedina on 07/12/15.
XRefMongoDBAdaptor(String, String, MongoDataStore) - Constructor for class org.opencb.cellbase.lib.impl.XRefMongoDBAdaptor

Z

Zone() - Constructor for class org.opencb.cellbase.core.config.SpeciesConfiguration.Zone

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