Index (molgenis-data-annotators 1.6.0 API)

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

A

AbstractRepositoryAnnotator - Class in org.molgenis.data.annotation: Created with IntelliJ IDEA.
AbstractRepositoryAnnotator() - Constructor for class org.molgenis.data.annotation.AbstractRepositoryAnnotator
addAnnotatorMetadataToRepositories(EntityMetaData, boolean, DefaultAttributeMetaData) - Method in class org.molgenis.data.annotation.CrudRepositoryAnnotator: Adds a new compound attribute to an existing mysql CrudRepository which is part of the #mysqlRepositoryCollection or an existing CrudRepository which is not part of #mysqlRepositoryCollection.
ALLELEID - Static variable in class org.molgenis.data.annotation.impl.ClinVarServiceAnnotator
ALLELIC_CONDITIONS - Static variable in class org.molgenis.data.annotation.impl.ClinicalGenomicsDatabaseServiceAnnotator
ALT_ALLELES - Static variable in class org.molgenis.data.annotation.impl.CosmicServiceAnnotator
ALTERNATIVE - Static variable in class org.molgenis.data.annotation.VariantAnnotator
annotate(Iterable<Entity>) - Method in class org.molgenis.data.annotation.AbstractRepositoryAnnotator
annotate(List<RepositoryAnnotator>, Repository, boolean) - Method in class org.molgenis.data.annotation.CrudRepositoryAnnotator
annotate(RepositoryAnnotator, Repository, boolean) - Method in class org.molgenis.data.annotation.CrudRepositoryAnnotator
annotate(Iterable<Entity>) - Method in class org.molgenis.data.annotation.impl.SnpEffServiceAnnotator
annotateEntity(Entity) - Method in class org.molgenis.data.annotation.AbstractRepositoryAnnotator
annotateEntity(Entity) - Method in class org.molgenis.data.annotation.impl.CaddServiceAnnotator
annotateEntity(Entity) - Method in class org.molgenis.data.annotation.impl.ClinicalGenomicsDatabaseServiceAnnotator
annotateEntity(Entity) - Method in class org.molgenis.data.annotation.impl.ClinVarServiceAnnotator
annotateEntity(Entity) - Method in class org.molgenis.data.annotation.impl.CosmicServiceAnnotator
annotateEntity(Entity) - Method in class org.molgenis.data.annotation.impl.DbnsfpGeneServiceAnnotator
annotateEntity(Entity) - Method in class org.molgenis.data.annotation.impl.DbnsfpVariantServiceAnnotator
annotateEntity(Entity) - Method in class org.molgenis.data.annotation.impl.EbiServiceAnnotator
annotateEntity(Entity) - Method in class org.molgenis.data.annotation.impl.ExACServiceAnnotator
annotateEntity(Entity) - Method in class org.molgenis.data.annotation.impl.GoNLServiceAnnotator
annotateEntity(Entity) - Method in class org.molgenis.data.annotation.impl.HgncSymbolServiceAnnotator
annotateEntity(Entity) - Method in class org.molgenis.data.annotation.impl.KeggServiceAnnotator
annotateEntity(Entity) - Method in class org.molgenis.data.annotation.impl.OmimHpoAnnotator
annotateEntity(Entity) - Method in class org.molgenis.data.annotation.impl.ThousandGenomesServiceAnnotator
ANNOTATION - Static variable in class org.molgenis.data.annotation.impl.SnpEffServiceAnnotator
annotationDataExists() - Method in class org.molgenis.data.annotation.AbstractRepositoryAnnotator: Checks if folder and files that were set with a runtime property actually exist, or if a webservice can be reached
annotationDataExists() - Method in class org.molgenis.data.annotation.impl.CaddServiceAnnotator
annotationDataExists() - Method in class org.molgenis.data.annotation.impl.ClinicalGenomicsDatabaseServiceAnnotator
annotationDataExists() - Method in class org.molgenis.data.annotation.impl.ClinVarServiceAnnotator
annotationDataExists() - Method in class org.molgenis.data.annotation.impl.CosmicServiceAnnotator
annotationDataExists() - Method in class org.molgenis.data.annotation.impl.DbnsfpGeneServiceAnnotator
annotationDataExists() - Method in class org.molgenis.data.annotation.impl.DbnsfpVariantServiceAnnotator
annotationDataExists() - Method in class org.molgenis.data.annotation.impl.EbiServiceAnnotator
annotationDataExists() - Method in class org.molgenis.data.annotation.impl.ExACServiceAnnotator
annotationDataExists() - Method in class org.molgenis.data.annotation.impl.GoNLServiceAnnotator
annotationDataExists() - Method in class org.molgenis.data.annotation.impl.HgncSymbolServiceAnnotator
annotationDataExists() - Method in class org.molgenis.data.annotation.impl.KeggServiceAnnotator
annotationDataExists() - Method in class org.molgenis.data.annotation.impl.OmimHpoAnnotator
annotationDataExists() - Method in class org.molgenis.data.annotation.impl.ThousandGenomesServiceAnnotator
AnnotatorUtils - Class in org.molgenis.data.annotation: Created by charbonb on 11/03/15.
AnnotatorUtils() - Constructor for class org.molgenis.data.annotation.AnnotatorUtils
ASSEMBLY - Static variable in class org.molgenis.data.annotation.impl.ClinVarServiceAnnotator

C

C_DNA_POSITION - Static variable in class org.molgenis.data.annotation.impl.SnpEffServiceAnnotator
CADD_ABS - Static variable in class org.molgenis.data.annotation.impl.CaddServiceAnnotator
CADD_FILE_LOCATION_PROPERTY - Static variable in class org.molgenis.data.annotation.impl.CaddServiceAnnotator
CADD_SCALED - Static variable in class org.molgenis.data.annotation.impl.CaddServiceAnnotator
CaddServiceAnnotator - Class in org.molgenis.data.annotation.impl: This class performs a system call to cross reference a chromosome and genomic location with a tabix indexed file.
CaddServiceAnnotator(MolgenisSettings, AnnotationService) - Constructor for class org.molgenis.data.annotation.impl.CaddServiceAnnotator
CaddServiceAnnotator(File, File, File) - Constructor for class org.molgenis.data.annotation.impl.CaddServiceAnnotator
canAnnotate(EntityMetaData) - Method in class org.molgenis.data.annotation.AbstractRepositoryAnnotator
canAnnotate(EntityMetaData) - Method in class org.molgenis.data.annotation.impl.SnpEffServiceAnnotator
CDS_POSITION - Static variable in class org.molgenis.data.annotation.impl.SnpEffServiceAnnotator
CGD_AGE_GROUP - Static variable in class org.molgenis.data.annotation.impl.ClinicalGenomicsDatabaseServiceAnnotator
CGD_CONDITION - Static variable in class org.molgenis.data.annotation.impl.ClinicalGenomicsDatabaseServiceAnnotator
CGD_FILE_LOCATION - Static variable in class org.molgenis.data.annotation.impl.ClinicalGenomicsDatabaseServiceAnnotator
CGD_FILE_LOCATION_PROPERTY - Static variable in class org.molgenis.data.annotation.provider.CgdDataProvider
CGD_GENERALIZED_INHERITANCE - Static variable in class org.molgenis.data.annotation.impl.ClinicalGenomicsDatabaseServiceAnnotator
CGD_INHERITANCE - Static variable in class org.molgenis.data.annotation.impl.ClinicalGenomicsDatabaseServiceAnnotator
CgdData - Class in org.molgenis.data.annotation.impl.datastructures
CgdData(String, String, String, String, String, String, String, String, String, String, String) - Constructor for class org.molgenis.data.annotation.impl.datastructures.CgdData
CgdDataProvider - Class in org.molgenis.data.annotation.provider
CgdDataProvider(MolgenisSettings) - Constructor for class org.molgenis.data.annotation.provider.CgdDataProvider
CgdDataProvider.generalizedInheritance - Enum in org.molgenis.data.annotation.provider
checkPreviouslyAnnotatedAndAddMetadata(File, PrintWriter, List<String>, String) - Static method in class org.molgenis.data.annotation.VcfUtils: Checks for previous annotations
CHROMOSOME - Static variable in class org.molgenis.data.annotation.LocusAnnotator
CHROMOSOME_FILE_LOCATION_PROPERTY - Static variable in class org.molgenis.data.annotation.impl.DbnsfpVariantServiceAnnotator
ClinicalGenomicsDatabaseServiceAnnotator - Class in org.molgenis.data.annotation.impl
ClinicalGenomicsDatabaseServiceAnnotator(MolgenisSettings, AnnotationService, HgncLocationsProvider, CgdDataProvider) - Constructor for class org.molgenis.data.annotation.impl.ClinicalGenomicsDatabaseServiceAnnotator
ClinicalGenomicsDatabaseServiceAnnotator(File, File, File) - Constructor for class org.molgenis.data.annotation.impl.ClinicalGenomicsDatabaseServiceAnnotator
CLINICALSIGNIFICANCE - Static variable in class org.molgenis.data.annotation.impl.ClinVarServiceAnnotator
CLINVAR_CHROMOSOME - Static variable in class org.molgenis.data.annotation.impl.ClinVarServiceAnnotator
CLINVAR_FILE_LOCATION_PROPERTY - Static variable in class org.molgenis.data.annotation.impl.ClinVarServiceAnnotator
CLINVAR_FILE_LOCATION_PROPERTY - Static variable in class org.molgenis.data.annotation.provider.ClinvarDataProvider
ClinvarData - Class in org.molgenis.data.annotation.impl.datastructures
ClinvarData(String, String, String, String, String, String, String, String, String, String, String, String, String, String, String, String, String, String, String, String, String, String, String, String, String) - Constructor for class org.molgenis.data.annotation.impl.datastructures.ClinvarData
ClinvarDataProvider - Class in org.molgenis.data.annotation.provider
ClinvarDataProvider(MolgenisSettings) - Constructor for class org.molgenis.data.annotation.provider.ClinvarDataProvider
ClinVarServiceAnnotator - Class in org.molgenis.data.annotation.impl
ClinVarServiceAnnotator(MolgenisSettings, AnnotationService, ClinvarDataProvider) - Constructor for class org.molgenis.data.annotation.impl.ClinVarServiceAnnotator
CmdLineAnnotator - Class in org.molgenis.data.annotation
CmdLineAnnotator() - Constructor for class org.molgenis.data.annotation.CmdLineAnnotator
COMMENTS - Static variable in class org.molgenis.data.annotation.impl.ClinicalGenomicsDatabaseServiceAnnotator
CONSEQUENCE_TYPE - Static variable in class org.molgenis.data.annotation.impl.CosmicServiceAnnotator
convertToVCF(Entity) - Static method in class org.molgenis.data.annotation.VcfUtils: Convert an vcfEntity to a VCF line
CosmicData - Class in org.molgenis.data.annotation.impl.datastructures: Created with IntelliJ IDEA.
CosmicData() - Constructor for class org.molgenis.data.annotation.impl.datastructures.CosmicData
CosmicServiceAnnotator - Class in org.molgenis.data.annotation.impl: This class calls the Ensembl webservice with a ensemble ID.
CosmicServiceAnnotator() - Constructor for class org.molgenis.data.annotation.impl.CosmicServiceAnnotator
CrudRepositoryAnnotator - Class in org.molgenis.data.annotation
CrudRepositoryAnnotator(DataService, String, PermissionSystemService, UserAccountService) - Constructor for class org.molgenis.data.annotation.CrudRepositoryAnnotator
CYTOGENETIC - Static variable in class org.molgenis.data.annotation.impl.ClinVarServiceAnnotator

D

DbnsfpGeneServiceAnnotator - Class in org.molgenis.data.annotation.impl: This class uses a location to retrieve a gene from the ...
DbnsfpGeneServiceAnnotator(MolgenisSettings, AnnotationService, HgncLocationsProvider) - Constructor for class org.molgenis.data.annotation.impl.DbnsfpGeneServiceAnnotator
DbnsfpVariantServiceAnnotator - Class in org.molgenis.data.annotation.impl: This class uses a chromosome to approach a dbNSFP chromosome variant file, it then checks all locations recorded for a chromosome in the data set, for every line, and uses a matching line to add annotation to the data set variant.
DbnsfpVariantServiceAnnotator(MolgenisSettings, AnnotationService) - Constructor for class org.molgenis.data.annotation.impl.DbnsfpVariantServiceAnnotator
DEFAULT_HGNC_LOCATIONS_VALUE - Static variable in class org.molgenis.data.annotation.provider.HgncLocationsProvider
DEFAULT_HPO_MAPPING_VALUE - Static variable in class org.molgenis.data.annotation.provider.HpoMappingProvider
DISTANCE_TO_FEATURE - Static variable in class org.molgenis.data.annotation.impl.SnpEffServiceAnnotator

E

EbiServiceAnnotator - Class in org.molgenis.data.annotation.impl: This class calls the EBI CHeMBL webservice with a uniprot ID.
EbiServiceAnnotator() - Constructor for class org.molgenis.data.annotation.impl.EbiServiceAnnotator
EbiServiceAnnotator(HttpClient) - Constructor for class org.molgenis.data.annotation.impl.EbiServiceAnnotator
END - Static variable in class org.molgenis.data.annotation.impl.CosmicServiceAnnotator
ENSEMBLE_ID - Static variable in class org.molgenis.data.annotation.impl.CosmicServiceAnnotator
ENTREZ_GENE_ID - Static variable in class org.molgenis.data.annotation.impl.ClinicalGenomicsDatabaseServiceAnnotator
equals(Object) - Method in class org.molgenis.data.annotation.impl.datastructures.Locus
ERRORS - Static variable in class org.molgenis.data.annotation.impl.SnpEffServiceAnnotator
EXAC_MAF - Static variable in class org.molgenis.data.annotation.impl.ExACServiceAnnotator
EXAC_VCFGZ_LOCATION - Static variable in class org.molgenis.data.annotation.impl.ExACServiceAnnotator
ExACServiceAnnotator - Class in org.molgenis.data.annotation.impl: ExAC annotator Data @ ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3/ TODO: feature enhancement: match multiple alternatives from SOURCE file to multiple alternatives in ExAC e.g.
ExACServiceAnnotator(MolgenisSettings, AnnotationService) - Constructor for class org.molgenis.data.annotation.impl.ExACServiceAnnotator
ExACServiceAnnotator(File, File, File) - Constructor for class org.molgenis.data.annotation.impl.ExACServiceAnnotator

F

FEATURE_ID - Static variable in class org.molgenis.data.annotation.impl.SnpEffServiceAnnotator
FEATURE_TYPE - Static variable in class org.molgenis.data.annotation.impl.CosmicServiceAnnotator
FEATURE_TYPE - Static variable in class org.molgenis.data.annotation.impl.SnpEffServiceAnnotator

G

GENE - Static variable in class org.molgenis.data.annotation.impl.ClinicalGenomicsDatabaseServiceAnnotator
GENE_FILE_LOCATION_PROPERTY - Static variable in class org.molgenis.data.annotation.impl.DbnsfpGeneServiceAnnotator
GENE_ID - Static variable in class org.molgenis.data.annotation.impl.SnpEffServiceAnnotator
GENE_NAME - Static variable in class org.molgenis.data.annotation.impl.ClinVarServiceAnnotator
GENE_NAME - Static variable in class org.molgenis.data.annotation.impl.SnpEffServiceAnnotator
GENEID - Static variable in class org.molgenis.data.annotation.impl.ClinVarServiceAnnotator
GENESYMBOL - Static variable in class org.molgenis.data.annotation.impl.ClinVarServiceAnnotator
getAge_group() - Method in class org.molgenis.data.annotation.impl.datastructures.CgdData
getAlleleid() - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
getAllelic_conditions() - Method in class org.molgenis.data.annotation.impl.datastructures.CgdData
getAlt() - Method in class org.molgenis.data.annotation.impl.datastructures.Variant
getAlt_alleles() - Method in class org.molgenis.data.annotation.impl.datastructures.CosmicData
getAnnotatedEntity(RepositoryAnnotator, Entity, Map<String, Object>) - Static method in class org.molgenis.data.annotation.AnnotatorUtils
getAssembly() - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
getCausedBy() - Method in class org.molgenis.data.annotation.impl.datastructures.OMIMTerm
getCgdData() - Method in class org.molgenis.data.annotation.provider.CgdDataProvider
getChrom() - Method in class org.molgenis.data.annotation.impl.datastructures.HGNCLocations
getChrom() - Method in class org.molgenis.data.annotation.impl.datastructures.Locus
getChromosomePositionReferenceAlternativeInformationFromClinvarLine(String[]) - Method in class org.molgenis.data.annotation.provider.ClinvarDataProvider
getClinicalsignificance() - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
getClinvar_chromosome() - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
getClinvarData() - Method in class org.molgenis.data.annotation.provider.ClinvarDataProvider
getComments() - Method in class org.molgenis.data.annotation.impl.datastructures.CgdData
getCompoundResultAttribute(RepositoryAnnotator, EntityMetaData) - Static method in class org.molgenis.data.annotation.AnnotatorUtils
getCondition() - Method in class org.molgenis.data.annotation.impl.datastructures.CgdData
getConsequence_type() - Method in class org.molgenis.data.annotation.impl.datastructures.CosmicData
getCytogenetic() - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
getCytoLoc() - Method in class org.molgenis.data.annotation.impl.datastructures.OMIMTerm
getDescription() - Method in class org.molgenis.data.annotation.impl.CaddServiceAnnotator
getDescription() - Method in class org.molgenis.data.annotation.impl.datastructures.HPOTerm
getDescription() - Method in class org.molgenis.data.annotation.impl.HgncSymbolServiceAnnotator
getDescription() - Method in class org.molgenis.data.annotation.impl.SnpEffServiceAnnotator
getDiseaseDb() - Method in class org.molgenis.data.annotation.impl.datastructures.HPOTerm
getDiseaseDbEntry() - Method in class org.molgenis.data.annotation.impl.datastructures.HPOTerm
getEnd() - Method in class org.molgenis.data.annotation.impl.datastructures.CosmicData
getEnd() - Method in class org.molgenis.data.annotation.impl.datastructures.HGNCLocations
getEntrez_gene_id() - Method in class org.molgenis.data.annotation.impl.datastructures.CgdData
getEntry() - Method in class org.molgenis.data.annotation.impl.datastructures.OMIMTerm
getFeature_type() - Method in class org.molgenis.data.annotation.impl.datastructures.CosmicData
getFullName() - Method in class org.molgenis.data.annotation.AbstractRepositoryAnnotator
getFullName() - Method in class org.molgenis.data.annotation.impl.SnpEffServiceAnnotator
getGene_name() - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
getGeneEntrezID() - Method in class org.molgenis.data.annotation.impl.datastructures.HPOTerm
getGeneid() - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
getGeneName() - Method in class org.molgenis.data.annotation.impl.datastructures.HPOTerm
getGeneralizedInheritance() - Method in class org.molgenis.data.annotation.impl.datastructures.CgdData
getGenesymbol() - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
getGuidelines() - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
getHgnc() - Method in class org.molgenis.data.annotation.impl.datastructures.HGNCLocations
getHgnc_id() - Method in class org.molgenis.data.annotation.impl.datastructures.CgdData
getHgncIds() - Method in class org.molgenis.data.annotation.impl.datastructures.OMIMTerm
getHgncLocations() - Method in class org.molgenis.data.annotation.provider.HgncLocationsProvider
getHgvs_c() - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
getHgvs_p() - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
getHpoMapping() - Method in class org.molgenis.data.annotation.provider.HpoMappingProvider
getID() - Method in class org.molgenis.data.annotation.impl.datastructures.CosmicData
getId() - Method in class org.molgenis.data.annotation.impl.datastructures.HPOTerm
getId() - Method in class org.molgenis.data.annotation.impl.datastructures.KeggGene
getId() - Method in class org.molgenis.data.annotation.impl.datastructures.Variant
getInfo() - Method in class org.molgenis.data.annotation.impl.datastructures.Variant
getInheritance() - Method in class org.molgenis.data.annotation.impl.datastructures.CgdData
getInputMetaData() - Method in class org.molgenis.data.annotation.impl.CosmicServiceAnnotator
getInputMetaData() - Method in class org.molgenis.data.annotation.impl.EbiServiceAnnotator
getInputMetaData() - Method in class org.molgenis.data.annotation.impl.SnpEffServiceAnnotator
getInputMetaData() - Method in class org.molgenis.data.annotation.LocusAnnotator
getInputMetaData() - Method in class org.molgenis.data.annotation.VariantAnnotator
getInputTempFile(Iterable<Entity>, String) - Method in class org.molgenis.data.annotation.impl.SnpEffServiceAnnotator
getIntervention_categories() - Method in class org.molgenis.data.annotation.impl.datastructures.CgdData
getIntervention_rationale() - Method in class org.molgenis.data.annotation.impl.datastructures.CgdData
getKeggGenePathways(Map<String, ArrayList<String>>) - Static method in class org.molgenis.data.annotation.impl.KeggServiceAnnotator: Convert map of (pathway -> genes) to (gene -> pathways)
getKeggHsaReader() - Method in class org.molgenis.data.annotation.provider.KeggDataProvider
getKeggPathwayHsaReader() - Method in class org.molgenis.data.annotation.provider.KeggDataProvider
getKeggPathwayReader() - Method in class org.molgenis.data.annotation.provider.KeggDataProvider
getLastevaluated() - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
getManifestation_categories() - Method in class org.molgenis.data.annotation.impl.datastructures.CgdData
getName() - Method in class org.molgenis.data.annotation.impl.datastructures.OMIMTerm
getNsv_dbvar() - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
getNumbersubmitters() - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
getOmimMorbidMap() - Method in class org.molgenis.data.annotation.provider.OmimMorbidMapProvider
getOrigin() - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
getOtherids() - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
getOutputMetaData() - Method in class org.molgenis.data.annotation.impl.CaddServiceAnnotator
getOutputMetaData() - Method in class org.molgenis.data.annotation.impl.ClinicalGenomicsDatabaseServiceAnnotator
getOutputMetaData() - Method in class org.molgenis.data.annotation.impl.ClinVarServiceAnnotator
getOutputMetaData() - Method in class org.molgenis.data.annotation.impl.CosmicServiceAnnotator
getOutputMetaData() - Method in class org.molgenis.data.annotation.impl.DbnsfpGeneServiceAnnotator
getOutputMetaData() - Method in class org.molgenis.data.annotation.impl.DbnsfpVariantServiceAnnotator
getOutputMetaData() - Method in class org.molgenis.data.annotation.impl.EbiServiceAnnotator
getOutputMetaData() - Method in class org.molgenis.data.annotation.impl.ExACServiceAnnotator
getOutputMetaData() - Method in class org.molgenis.data.annotation.impl.GoNLServiceAnnotator
getOutputMetaData() - Method in class org.molgenis.data.annotation.impl.HgncSymbolServiceAnnotator
getOutputMetaData() - Method in class org.molgenis.data.annotation.impl.KeggServiceAnnotator
getOutputMetaData() - Method in class org.molgenis.data.annotation.impl.OmimHpoAnnotator
getOutputMetaData() - Method in class org.molgenis.data.annotation.impl.SnpEffServiceAnnotator
getOutputMetaData() - Method in class org.molgenis.data.annotation.impl.ThousandGenomesServiceAnnotator
getPhenotypeids() - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
getPos() - Method in class org.molgenis.data.annotation.impl.datastructures.Locus
getProteins() - Method in class org.molgenis.data.annotation.impl.datastructures.KeggGene
getRcvaccession() - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
getRef() - Method in class org.molgenis.data.annotation.impl.datastructures.Variant
getReferences() - Method in class org.molgenis.data.annotation.impl.datastructures.CgdData
getReviewstatus() - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
getRs_dbsnp() - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
getSeq_region_name() - Method in class org.molgenis.data.annotation.impl.datastructures.CosmicData
getSimpleName() - Method in class org.molgenis.data.annotation.impl.CaddServiceAnnotator
getSimpleName() - Method in class org.molgenis.data.annotation.impl.ClinicalGenomicsDatabaseServiceAnnotator
getSimpleName() - Method in class org.molgenis.data.annotation.impl.ClinVarServiceAnnotator
getSimpleName() - Method in class org.molgenis.data.annotation.impl.CosmicServiceAnnotator
getSimpleName() - Method in class org.molgenis.data.annotation.impl.DbnsfpGeneServiceAnnotator
getSimpleName() - Method in class org.molgenis.data.annotation.impl.DbnsfpVariantServiceAnnotator
getSimpleName() - Method in class org.molgenis.data.annotation.impl.EbiServiceAnnotator
getSimpleName() - Method in class org.molgenis.data.annotation.impl.ExACServiceAnnotator
getSimpleName() - Method in class org.molgenis.data.annotation.impl.GoNLServiceAnnotator
getSimpleName() - Method in class org.molgenis.data.annotation.impl.HgncSymbolServiceAnnotator
getSimpleName() - Method in class org.molgenis.data.annotation.impl.KeggServiceAnnotator
getSimpleName() - Method in class org.molgenis.data.annotation.impl.OmimHpoAnnotator
getSimpleName() - Method in class org.molgenis.data.annotation.impl.SnpEffServiceAnnotator
getSimpleName() - Method in class org.molgenis.data.annotation.impl.ThousandGenomesServiceAnnotator
getStart() - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
getStart() - Method in class org.molgenis.data.annotation.impl.datastructures.CosmicData
getStart() - Method in class org.molgenis.data.annotation.impl.datastructures.HGNCLocations
getStop() - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
getStrand() - Method in class org.molgenis.data.annotation.impl.datastructures.CosmicData
getSymbols() - Method in class org.molgenis.data.annotation.impl.datastructures.KeggGene
getTestedingtr() - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
getType() - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
getType() - Method in class org.molgenis.data.annotation.impl.datastructures.OMIMTerm
getVariantids() - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
GONL_DIRECTORY_LOCATION_PROPERTY - Static variable in class org.molgenis.data.annotation.impl.GoNLServiceAnnotator
GONL_GTC - Static variable in class org.molgenis.data.annotation.impl.GoNLServiceAnnotator
GONL_MAF - Static variable in class org.molgenis.data.annotation.impl.GoNLServiceAnnotator
GoNLServiceAnnotator - Class in org.molgenis.data.annotation.impl: GoNl annotator data: https://molgenis26.target.rug.nl/downloads/gonl_public/variants/release5_with_GTC/ release5_noContam_noChildren_with_AN_AC_GTC_stripped.tgz PLUS chrX from http://molgenis15.target.rug.nl/release4_noContam_noChildren_with_AN_AC_GTC_stripped.tgz GoNL example line: 1 126108 rs146756510 G A .
GoNLServiceAnnotator(MolgenisSettings, AnnotationService) - Constructor for class org.molgenis.data.annotation.impl.GoNLServiceAnnotator
GoNLServiceAnnotator(File, File, File) - Constructor for class org.molgenis.data.annotation.impl.GoNLServiceAnnotator
GUIDELINES - Static variable in class org.molgenis.data.annotation.impl.ClinVarServiceAnnotator

H

hashCode() - Method in class org.molgenis.data.annotation.impl.datastructures.Locus
HGNC_ID - Static variable in class org.molgenis.data.annotation.impl.ClinicalGenomicsDatabaseServiceAnnotator
HGNCLocations - Class in org.molgenis.data.annotation.impl.datastructures: Created by jvelde on 1/30/14.
HGNCLocations(String, Long, Long, String) - Constructor for class org.molgenis.data.annotation.impl.datastructures.HGNCLocations
HgncLocationsProvider - Class in org.molgenis.data.annotation.provider
HgncLocationsProvider(MolgenisSettings) - Constructor for class org.molgenis.data.annotation.provider.HgncLocationsProvider
HgncLocationsUtils - Class in org.molgenis.data.annotation
HgncLocationsUtils() - Constructor for class org.molgenis.data.annotation.HgncLocationsUtils
HgncSymbolServiceAnnotator - Class in org.molgenis.data.annotation.impl
HgncSymbolServiceAnnotator(AnnotationService, HgncLocationsProvider) - Constructor for class org.molgenis.data.annotation.impl.HgncSymbolServiceAnnotator
HGVS_C - Static variable in class org.molgenis.data.annotation.impl.ClinVarServiceAnnotator
HGVS_C - Static variable in class org.molgenis.data.annotation.impl.SnpEffServiceAnnotator
HGVS_P - Static variable in class org.molgenis.data.annotation.impl.ClinVarServiceAnnotator
HGVS_P - Static variable in class org.molgenis.data.annotation.impl.SnpEffServiceAnnotator
HPO_DESCRIPTIONS - Static variable in class org.molgenis.data.annotation.impl.OmimHpoAnnotator
HPO_DISEASE_DATABASE - Static variable in class org.molgenis.data.annotation.impl.OmimHpoAnnotator
HPO_DISEASE_DATABASE_ENTRY - Static variable in class org.molgenis.data.annotation.impl.OmimHpoAnnotator
HPO_ENTREZ_ID - Static variable in class org.molgenis.data.annotation.impl.OmimHpoAnnotator
HPO_GENE_NAME - Static variable in class org.molgenis.data.annotation.impl.OmimHpoAnnotator
HPO_IDENTIFIERS - Static variable in class org.molgenis.data.annotation.impl.OmimHpoAnnotator
HpoMappingProvider - Class in org.molgenis.data.annotation.provider
HpoMappingProvider(MolgenisSettings) - Constructor for class org.molgenis.data.annotation.provider.HpoMappingProvider
HPOTerm - Class in org.molgenis.data.annotation.impl.datastructures: Created by jvelde on 2/12/14.
HPOTerm(String, String, String, Integer, String, Integer) - Constructor for class org.molgenis.data.annotation.impl.datastructures.HPOTerm

I

ID - Static variable in class org.molgenis.data.annotation.impl.CosmicServiceAnnotator
INTERVENTION_CATEGORIES - Static variable in class org.molgenis.data.annotation.impl.ClinicalGenomicsDatabaseServiceAnnotator
INTERVENTION_RATIONALE - Static variable in class org.molgenis.data.annotation.impl.ClinicalGenomicsDatabaseServiceAnnotator
Iterator(int, int, int, TabixReader.TPair64[]) - Constructor for class org.molgenis.data.annotation.TabixReader.Iterator

K

KEGG_GENE_ID - Static variable in class org.molgenis.data.annotation.impl.KeggServiceAnnotator
KEGG_PATHWAYS_IDS - Static variable in class org.molgenis.data.annotation.impl.KeggServiceAnnotator
KEGG_PATHWAYS_NAMES - Static variable in class org.molgenis.data.annotation.impl.KeggServiceAnnotator
KeggDataProvider - Class in org.molgenis.data.annotation.provider
KeggDataProvider(MolgenisSettings) - Constructor for class org.molgenis.data.annotation.provider.KeggDataProvider
KeggGene - Class in org.molgenis.data.annotation.impl.datastructures: Created by jvelde on 1/30/14.
KeggGene(String, List<String>, List<String>) - Constructor for class org.molgenis.data.annotation.impl.datastructures.KeggGene
KeggServiceAnnotator - Class in org.molgenis.data.annotation.impl
KeggServiceAnnotator(AnnotationService, HgncLocationsProvider, KeggDataProvider) - Constructor for class org.molgenis.data.annotation.impl.KeggServiceAnnotator
KEY_HGNC_LOCATIONS_VALUE - Static variable in class org.molgenis.data.annotation.provider.HgncLocationsProvider
KEY_HPO_MAPPING - Static variable in class org.molgenis.data.annotation.provider.HpoMappingProvider

L

LASTEVALUATED - Static variable in class org.molgenis.data.annotation.impl.ClinVarServiceAnnotator
locationToHgcn(Map<String, HGNCLocations>, Locus) - Static method in class org.molgenis.data.annotation.HgncLocationsUtils
Locus - Class in org.molgenis.data.annotation.impl.datastructures: Created by jvelde on 2/13/14.
Locus(String, Long) - Constructor for class org.molgenis.data.annotation.impl.datastructures.Locus
LocusAnnotator - Class in org.molgenis.data.annotation: Created by jvelde on 2/13/14.
LocusAnnotator() - Constructor for class org.molgenis.data.annotation.LocusAnnotator
LOF - Static variable in class org.molgenis.data.annotation.impl.SnpEffServiceAnnotator

M

main(String[]) - Static method in class org.molgenis.data.annotation.CmdLineAnnotator
MANIFESTATION_CATEGORIES - Static variable in class org.molgenis.data.annotation.impl.ClinicalGenomicsDatabaseServiceAnnotator
mChr2tid - Variable in class org.molgenis.data.annotation.TabixReader
mFn - Variable in class org.molgenis.data.annotation.TabixReader
mFp - Variable in class org.molgenis.data.annotation.TabixReader

N

NAME - Static variable in class org.molgenis.data.annotation.impl.CosmicServiceAnnotator
NAME - Static variable in class org.molgenis.data.annotation.impl.EbiServiceAnnotator
next() - Method in class org.molgenis.data.annotation.TabixReader.Iterator
NMD - Static variable in class org.molgenis.data.annotation.impl.SnpEffServiceAnnotator
NSV_DBVAR - Static variable in class org.molgenis.data.annotation.impl.ClinVarServiceAnnotator
NUMBERSUBMITTERS - Static variable in class org.molgenis.data.annotation.impl.ClinVarServiceAnnotator

O

OMIM_CAUSAL_IDENTIFIER - Static variable in class org.molgenis.data.annotation.impl.OmimHpoAnnotator
OMIM_CYTOGENIC_LOCATION - Static variable in class org.molgenis.data.annotation.impl.OmimHpoAnnotator
OMIM_DISORDERS - Static variable in class org.molgenis.data.annotation.impl.OmimHpoAnnotator
OMIM_ENTRY - Static variable in class org.molgenis.data.annotation.impl.OmimHpoAnnotator
OMIM_HGNC_IDENTIFIERS - Static variable in class org.molgenis.data.annotation.impl.OmimHpoAnnotator
OMIM_IDENTIFIERS - Static variable in class org.molgenis.data.annotation.impl.OmimHpoAnnotator
OMIM_TYPE - Static variable in class org.molgenis.data.annotation.impl.OmimHpoAnnotator
OmimHpoAnnotator - Class in org.molgenis.data.annotation.impl: Created by jvelde on 2/12/14.
OmimHpoAnnotator(AnnotationService, OmimMorbidMapProvider, HgncLocationsProvider, HpoMappingProvider, MolgenisSettings, UrlPinger) - Constructor for class org.molgenis.data.annotation.impl.OmimHpoAnnotator
OmimMorbidMapProvider - Class in org.molgenis.data.annotation.provider
OmimMorbidMapProvider(MolgenisSettings) - Constructor for class org.molgenis.data.annotation.provider.OmimMorbidMapProvider
OMIMTerm - Class in org.molgenis.data.annotation.impl.datastructures: Created by jvelde on 2/12/14.
OMIMTerm(int, String, int, int, String, List<String>) - Constructor for class org.molgenis.data.annotation.impl.datastructures.OMIMTerm
onApplicationEvent(ContextRefreshedEvent) - Method in class org.molgenis.data.annotation.AbstractRepositoryAnnotator
onApplicationEvent(ContextRefreshedEvent) - Method in class org.molgenis.data.annotation.impl.CaddServiceAnnotator
onApplicationEvent(ContextRefreshedEvent) - Method in class org.molgenis.data.annotation.impl.ClinicalGenomicsDatabaseServiceAnnotator
onApplicationEvent(ContextRefreshedEvent) - Method in class org.molgenis.data.annotation.impl.ClinVarServiceAnnotator
onApplicationEvent(ContextRefreshedEvent) - Method in class org.molgenis.data.annotation.impl.DbnsfpGeneServiceAnnotator
onApplicationEvent(ContextRefreshedEvent) - Method in class org.molgenis.data.annotation.impl.DbnsfpVariantServiceAnnotator
onApplicationEvent(ContextRefreshedEvent) - Method in class org.molgenis.data.annotation.impl.ExACServiceAnnotator
onApplicationEvent(ContextRefreshedEvent) - Method in class org.molgenis.data.annotation.impl.GoNLServiceAnnotator
onApplicationEvent(ContextRefreshedEvent) - Method in class org.molgenis.data.annotation.impl.KeggServiceAnnotator
onApplicationEvent(ContextRefreshedEvent) - Method in class org.molgenis.data.annotation.impl.OmimHpoAnnotator
onApplicationEvent(ContextRefreshedEvent) - Method in class org.molgenis.data.annotation.impl.SnpEffServiceAnnotator
onApplicationEvent(ContextRefreshedEvent) - Method in class org.molgenis.data.annotation.impl.ThousandGenomesServiceAnnotator
org.molgenis.data.annotation - package org.molgenis.data.annotation
org.molgenis.data.annotation.impl - package org.molgenis.data.annotation.impl
org.molgenis.data.annotation.impl.datastructures - package org.molgenis.data.annotation.impl.datastructures
org.molgenis.data.annotation.provider - package org.molgenis.data.annotation.provider
ORIGIN - Static variable in class org.molgenis.data.annotation.impl.ClinVarServiceAnnotator
OTHERIDS - Static variable in class org.molgenis.data.annotation.impl.ClinVarServiceAnnotator

P

parseOutputLineToEntity(String, String) - Method in class org.molgenis.data.annotation.impl.SnpEffServiceAnnotator
parseReg(String) - Method in class org.molgenis.data.annotation.TabixReader: Parse a region in the format of "chr1", "chr1:100" or "chr1:100-1000"
PHENOTYPEIDS - Static variable in class org.molgenis.data.annotation.impl.ClinVarServiceAnnotator
ping(String, int) - Method in interface org.molgenis.data.annotation.provider.Pinger
ping(String, int) - Method in class org.molgenis.data.annotation.provider.UrlPinger: Pings a HTTP URL.
Pinger - Interface in org.molgenis.data.annotation.provider
POSITION - Static variable in class org.molgenis.data.annotation.LocusAnnotator
PROTEIN_POSITION - Static variable in class org.molgenis.data.annotation.impl.SnpEffServiceAnnotator
PUTATIVE_IMPACT - Static variable in class org.molgenis.data.annotation.impl.SnpEffServiceAnnotator

Q

query(int, int, int) - Method in class org.molgenis.data.annotation.TabixReader
query(String) - Method in class org.molgenis.data.annotation.TabixReader

R

RANK_TOTAL - Static variable in class org.molgenis.data.annotation.impl.SnpEffServiceAnnotator
RCVACCESSION - Static variable in class org.molgenis.data.annotation.impl.ClinVarServiceAnnotator
readIndex(File) - Method in class org.molgenis.data.annotation.TabixReader: Read the Tabix index from a file
readIndex() - Method in class org.molgenis.data.annotation.TabixReader: Read the Tabix index from the default file.
readInt(InputStream) - Static method in class org.molgenis.data.annotation.TabixReader
readLine(InputStream) - Static method in class org.molgenis.data.annotation.TabixReader
readLine() - Method in class org.molgenis.data.annotation.TabixReader: Read one line from the data file.
readLong(InputStream) - Static method in class org.molgenis.data.annotation.TabixReader
REFERENCE - Static variable in class org.molgenis.data.annotation.VariantAnnotator
REFERENCES - Static variable in class org.molgenis.data.annotation.impl.ClinicalGenomicsDatabaseServiceAnnotator
REVIEWSTATUS - Static variable in class org.molgenis.data.annotation.impl.ClinVarServiceAnnotator
RS_DBSNP - Static variable in class org.molgenis.data.annotation.impl.ClinVarServiceAnnotator
runSnpEff(File, File) - Method in class org.molgenis.data.annotation.impl.SnpEffServiceAnnotator

S

SEQ_REGION_NAME - Static variable in class org.molgenis.data.annotation.impl.CosmicServiceAnnotator
setAge_group(String) - Method in class org.molgenis.data.annotation.impl.datastructures.CgdData
setAlleleid(String) - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
setAllelic_conditions(String) - Method in class org.molgenis.data.annotation.impl.datastructures.CgdData
setAlt_alleles(String[]) - Method in class org.molgenis.data.annotation.impl.datastructures.CosmicData
setAssembly(String) - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
setClinicalsignificance(String) - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
setClinvar_chromosome(String) - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
setComments(String) - Method in class org.molgenis.data.annotation.impl.datastructures.CgdData
setCondition(String) - Method in class org.molgenis.data.annotation.impl.datastructures.CgdData
setConsequence_type(String) - Method in class org.molgenis.data.annotation.impl.datastructures.CosmicData
setCytogenetic(String) - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
setEnd(Integer) - Method in class org.molgenis.data.annotation.impl.datastructures.CosmicData
setEntrez_gene_id(String) - Method in class org.molgenis.data.annotation.impl.datastructures.CgdData
setFeature_type(String) - Method in class org.molgenis.data.annotation.impl.datastructures.CosmicData
setGene_name(String) - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
setGeneid(String) - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
setGeneralizedInheritance(CgdDataProvider.generalizedInheritance) - Method in class org.molgenis.data.annotation.impl.datastructures.CgdData
setGenesymbol(String) - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
setGuidelines(String) - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
setHgnc_id(String) - Method in class org.molgenis.data.annotation.impl.datastructures.CgdData
setHgvs_c(String) - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
setHgvs_p(String) - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
setID(String) - Method in class org.molgenis.data.annotation.impl.datastructures.CosmicData
setId(String) - Method in class org.molgenis.data.annotation.impl.datastructures.KeggGene
setInheritance(String) - Method in class org.molgenis.data.annotation.impl.datastructures.CgdData
setIntervention_categories(String) - Method in class org.molgenis.data.annotation.impl.datastructures.CgdData
setIntervention_rationale(String) - Method in class org.molgenis.data.annotation.impl.datastructures.CgdData
setLastevaluated(String) - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
setManifestation_categories(String) - Method in class org.molgenis.data.annotation.impl.datastructures.CgdData
setNsv_dbvar(String) - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
setNumbersubmitters(String) - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
setOrigin(String) - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
setOtherids(String) - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
setPhenotypeids(String) - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
setProteins(List<String>) - Method in class org.molgenis.data.annotation.impl.datastructures.KeggGene
setRcvaccession(String) - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
setReferences(String) - Method in class org.molgenis.data.annotation.impl.datastructures.CgdData
setReviewstatus(String) - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
setRs_dbsnp(String) - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
setSeq_region_name(String) - Method in class org.molgenis.data.annotation.impl.datastructures.CosmicData
setStart(String) - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
setStart(Integer) - Method in class org.molgenis.data.annotation.impl.datastructures.CosmicData
setStop(String) - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
setStrand(int) - Method in class org.molgenis.data.annotation.impl.datastructures.CosmicData
setSymbols(List<String>) - Method in class org.molgenis.data.annotation.impl.datastructures.KeggGene
setTestedingtr(String) - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
setType(String) - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
setVariantids(String) - Method in class org.molgenis.data.annotation.impl.datastructures.ClinvarData
SNPEFF_JAR_LOCATION_PROPERTY - Static variable in class org.molgenis.data.annotation.impl.SnpEffServiceAnnotator
snpEffPath - Static variable in class org.molgenis.data.annotation.impl.SnpEffServiceAnnotator
SnpEffServiceAnnotator - Class in org.molgenis.data.annotation.impl: new ANN field replacing EFF: ANN=A|missense_variant|MODERATE|NEXN|NEXN|transcript|NM_144573.3|Coding|8/13|c.733G>A|p.Gly245Arg|1030/3389|733/2028| 245/675|| -lof doesnt seem to work? would be great...
SnpEffServiceAnnotator(MolgenisSettings, AnnotationService, DataService) - Constructor for class org.molgenis.data.annotation.impl.SnpEffServiceAnnotator
SnpEffServiceAnnotator(File, File, File) - Constructor for class org.molgenis.data.annotation.impl.SnpEffServiceAnnotator
SnpEffServiceAnnotator.impact - Enum in org.molgenis.data.annotation.impl
START - Static variable in class org.molgenis.data.annotation.impl.ClinVarServiceAnnotator
START - Static variable in class org.molgenis.data.annotation.impl.CosmicServiceAnnotator
STOP - Static variable in class org.molgenis.data.annotation.impl.ClinVarServiceAnnotator
STRAND - Static variable in class org.molgenis.data.annotation.impl.CosmicServiceAnnotator

T

TAB - Static variable in class org.molgenis.data.annotation.VcfUtils
TabixReader - Class in org.molgenis.data.annotation
TabixReader(String) - Constructor for class org.molgenis.data.annotation.TabixReader: The constructor
TabixReader.Iterator - Class in org.molgenis.data.annotation
TESTEDINGTR - Static variable in class org.molgenis.data.annotation.impl.ClinVarServiceAnnotator
THGEN_DIRECTORY_LOCATION_PROPERTY - Static variable in class org.molgenis.data.annotation.impl.ThousandGenomesServiceAnnotator
THGEN_MAF - Static variable in class org.molgenis.data.annotation.impl.ThousandGenomesServiceAnnotator
ThousandGenomesServiceAnnotator - Class in org.molgenis.data.annotation.impl: 1000G annotator Data @ http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ TODO: feature enhancement: match multiple alternatives from SOURCE file to multiple alternatives in 1000G e.g.
ThousandGenomesServiceAnnotator(MolgenisSettings, AnnotationService) - Constructor for class org.molgenis.data.annotation.impl.ThousandGenomesServiceAnnotator
ThousandGenomesServiceAnnotator(File, File, File) - Constructor for class org.molgenis.data.annotation.impl.ThousandGenomesServiceAnnotator
toString() - Method in class org.molgenis.data.annotation.impl.datastructures.HGNCLocations
toString() - Method in class org.molgenis.data.annotation.impl.datastructures.HPOTerm
toString() - Method in class org.molgenis.data.annotation.impl.datastructures.KeggGene
toString() - Method in class org.molgenis.data.annotation.impl.datastructures.Locus
toString() - Method in class org.molgenis.data.annotation.impl.datastructures.OMIMTerm
toString() - Method in class org.molgenis.data.annotation.impl.datastructures.Variant
TRANSCRIPT_BIOTYPE - Static variable in class org.molgenis.data.annotation.impl.SnpEffServiceAnnotator
TYPE - Static variable in class org.molgenis.data.annotation.impl.ClinVarServiceAnnotator

U

UNIPROT_ID - Static variable in class org.molgenis.data.annotation.impl.EbiServiceAnnotator
UrlPinger - Class in org.molgenis.data.annotation.provider
UrlPinger() - Constructor for class org.molgenis.data.annotation.provider.UrlPinger

V

valueOf(String) - Static method in enum org.molgenis.data.annotation.impl.SnpEffServiceAnnotator.impact: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.molgenis.data.annotation.provider.CgdDataProvider.generalizedInheritance: Returns the enum constant of this type with the specified name.
values() - Static method in enum org.molgenis.data.annotation.impl.SnpEffServiceAnnotator.impact: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.molgenis.data.annotation.provider.CgdDataProvider.generalizedInheritance: Returns an array containing the constants of this enum type, in the order they are declared.
Variant - Class in org.molgenis.data.annotation.impl.datastructures: Created by jvelde on 1/30/14.
Variant(String, Long, String, String, String, String) - Constructor for class org.molgenis.data.annotation.impl.datastructures.Variant
VariantAnnotator - Class in org.molgenis.data.annotation
VariantAnnotator() - Constructor for class org.molgenis.data.annotation.VariantAnnotator
VARIANTIDS - Static variable in class org.molgenis.data.annotation.impl.ClinVarServiceAnnotator
VcfUtils - Class in org.molgenis.data.annotation
VcfUtils() - Constructor for class org.molgenis.data.annotation.VcfUtils

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