Index (UniProt JAPI 1.3.6 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 Y Z
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

A - Enum constant in enum class uk.ac.ebi.kraken.interfaces.common.MoleculeWeight
AA - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCategory
ABCD - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
Absorption - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
AbsorptionNote - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
AbstractMemberConverter<T extends JsonMember,R extends UniRefMember> - Class in uk.ac.ebi.uniprot.dataservice.client.uniref.converter
AbstractMemberConverter() - Constructor for class uk.ac.ebi.uniprot.dataservice.client.uniref.converter.AbstractMemberConverter
AbstractUniRefEntryConverter - Class in uk.ac.ebi.uniprot.dataservice.client.uniref.converter
AbstractUniRefEntryConverter() - Constructor for class uk.ac.ebi.uniprot.dataservice.client.uniref.converter.AbstractUniRefEntryConverter
accession - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtField.Search
accession(String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcQueryBuilder: Creates a query that searches for entries that contain the given source database accession within their database cross-references.
accession(String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Creates a query on a UniProt primary accession.
accessions(Set<String>) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Create a query using a set of UniProt primary accessions
ACT_SITE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
ACTET_STREAM_MEDIA_TYPE_VALUE - Static variable in class uk.ac.ebi.uniprot.dataservice.client.ClientConstant
ACTIVITY_REGULATION - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType
ActSiteFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features: Encapsulates the ActSiteFeature of a UniProtEntry.
Adaptor<T> - Interface in uk.ac.ebi.uniprot.dataservice.client.service
addAssertedGoAnnotation(AssertedGoAnnotation) - Method in interface uk.ac.ebi.kraken.interfaces.go.toprotein.GoProteinContainer
addDatabase(DatabaseOption) - Method in class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastInput.Builder: Add an extra blast database to blast against.
addDatabaseCrossReference(DatabaseCrossReference) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry
addExtra(T, R) - Method in class uk.ac.ebi.uniprot.dataservice.client.uniref.converter.AbstractMemberConverter
addExtra(JsonRepMember, UniRefRepresentativeMember) - Method in class uk.ac.ebi.uniprot.dataservice.client.uniref.converter.UniRefRepMemberConverter
after(UniProtField.SearchDate, LocalDate) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Creates a query that requires results to have a date that is on or after the specified date.
AGD - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
AGR - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
AGRICOLA - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationXrefType
AgricolaId - Interface in uk.ac.ebi.kraken.interfaces.uniprot.citationsNew
ALIGN - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastParameter
Alignment - Interface in uk.ac.ebi.uniprot.dataservice.client.alignment.blast: Details a blast alignment.
AlignmentCutoffOption - Enum Class in uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input: Maximum number of match alignments reported in the result output.
ALIGNMENTS - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastParameter
ALLERGEN - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType
ALLERGEN - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.description.FieldType
AllergenComment - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
ALLERGOME - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
ALPHAFOLDDB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
ALTERNATIVE_PRODUCTS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType
AlternativeProductsComment - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
AlternativeProductsCommentComment - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
AlternativeProductsEvent - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
AlternativeProductsIsoform - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
ALTNAME - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.description.NameType
and(Query) - Method in interface uk.ac.ebi.uniprot.dataservice.query.Query
and(Query...) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcQueryBuilder: The Query composition of the specified subQueries using 'and'.
and(Query...) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: The Query composition of the specified subQueries using 'and'.
and(Query...) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniref.UniRefQueryBuilder: The Query composition of the specified subQueries using 'and'.
and(Query[]) - Method in interface uk.ac.ebi.uniprot.dataservice.query.QueryFactory: The Query composition of the specified subQueries using 'and'.
AND - Static variable in class uk.ac.ebi.uniprot.dataservice.client.ClientConstant
ANTIBODYPEDIA - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
ANTIFAM - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
anyAccession(String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Creates a query on a UniProt accession, either primary or secondary.
API - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.MassSpectrometryMethod
APICOPLAST_PLASTID - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.GeneEncodingType
apply(T) - Method in class uk.ac.ebi.uniprot.dataservice.client.uniref.converter.AbstractMemberConverter
apply(JsonAbstractUniRefEntry) - Method in class uk.ac.ebi.uniprot.dataservice.client.uniref.converter.AbstractUniRefEntryConverter
apply(JsonUniRefEntry) - Method in class uk.ac.ebi.uniprot.dataservice.client.uniref.converter.UniRefEntryConverter
apply(JsonUniRefEntryLight) - Method in class uk.ac.ebi.uniprot.dataservice.client.uniref.converter.UniRefEntryLightConverter
ARACHNOSERVER - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
ARAPORT - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
ARAPORT - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
ARBA - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
AssertedGoAnnotation - Interface in uk.ac.ebi.kraken.interfaces.go.toprotein: Adds an extra field to the GoAnnotation interface.
Author - Interface in uk.ac.ebi.kraken.interfaces.uniprot.citationsNew: The RA (Reference Author) lines list the authors of the paper (or other work) cited.
AuthoringGroup - Interface in uk.ac.ebi.kraken.interfaces.uniprot.citationsNew: Used in the flatfile either in the RA or the RG line The RG line The Reference Group (RG) line lists the consortium name associated with a given citation.
authors(Set<String>) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Creates a query that matches entries containing references, whose unified author list is a super-set of the specified set of authors.

B

B - Enum constant in enum class uk.ac.ebi.kraken.interfaces.common.MoleculeWeight
before(UniProtField.SearchDate, LocalDate) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Creates a query that requires results to have a date that is on or before the specified date.
between(UniProtField.SearchDate, LocalDate, LocalDate) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Creates a query that requires results to have a date that is in between two specified dates.
betweenStr(UniProtField.SearchDate, String, String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Creates a query that requires results to have a date that is in between two specified dates.
BGEE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
BINARY - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.InteractionType
BINDING - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
BINDINGDB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
BindingFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
BIOCYC - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
BIOGRID - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
BIOGRID_ORCS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
BIOMUTA - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
BIOPHYSICOCHEMICAL_PROPERTIES - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType
BioPhysicoChemicalPropertiesComment - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
BIOTECH - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.description.FieldType
BIOTECHNOLOGY - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType
BiotechnologyComment - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
BlastInput - Class in uk.ac.ebi.uniprot.dataservice.client.alignment.blast: Input parameters to configure a blast request.
BlastInput.Builder - Class in uk.ac.ebi.uniprot.dataservice.client.alignment.blast
BLASTP - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.BlastVersionOption
BlastParameter - Enum Class in uk.ac.ebi.uniprot.dataservice.client.alignment.blast
BlastResult<T extends Hit> - Interface in uk.ac.ebi.uniprot.dataservice.client.alignment.blast: Container that wraps a blast result.
BlastService<T extends Hit> - Interface in uk.ac.ebi.uniprot.dataservice.client.alignment.blast: Base blast service interface.
BlastSummary - Interface in uk.ac.ebi.uniprot.dataservice.client.alignment.blast: Holds a blast result for a given entry.
BlastVersionOption - Enum Class in uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input: The BLAST program to be used for the blast.
BLASTX - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.BlastVersionOption
BLOSUM_45 - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.MatrixOption
BLOSUM_50 - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.MatrixOption
BLOSUM_62 - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.MatrixOption
BLOSUM_80 - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.MatrixOption
BLOSUM_90 - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.MatrixOption
BMRB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
Book - Interface in uk.ac.ebi.kraken.interfaces.uniprot.citationsNew: A variation of the RL line format is used for papers found in books or other types of publication, which are then cited using the following format: RL (In) Editor_1 I.[, Editor_2 I., Editor_X I.] (eds.); RL Book_name, pp.[Volume:]First_page-Last_page, Publisher, City (YYYY).
BOOK - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationTypeEnum
BookName - Interface in uk.ac.ebi.kraken.interfaces.uniprot.citationsNew: A book can in the SwissProt flatfile fromat have besides a title have a name This might be a sub title or other memnomic for a book.
BRENDA - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
build() - Method in class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastInput.Builder: Takes all of the configured parameters and builds a valid BlastInput.
Builder(DatabaseOption, String) - Constructor for class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastInput.Builder
BY_SIMILARITY - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.CommentStatus
BY_SIMILARITY - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureStatus

C

C - Enum constant in enum class uk.ac.ebi.kraken.interfaces.common.MoleculeWeight
C - Enum constant in enum class uk.ac.ebi.kraken.interfaces.go.GoCategory
C - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.OntologyType
calcMolecularWeight(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.common.MoleculeWeight
CARBOHYD - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
CarbohydFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features: Encapsulates the CarbohydFeature of a UniProtEntry.
CARBONYLDB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
CATALYTIC_ACTIVITY - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType
CatalyticActivityComment - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
CatalyticActivityCommentStructured - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
CAUTION - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType
CautionComment - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
CAZY - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
CCDS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
CD_ANTIGEN - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.description.FieldType
CDCODE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
CDD - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.SignatureDBType
CDD - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
CGD - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
CGD - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
CHAIN - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
ChainFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features: Encapsulates the ChainFeature of a UniProtEntry.
CHEBI - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CofactorReferenceType
CHEBI - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.ReactionReferenceType
checksum - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcField.Search
checksum(String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcQueryBuilder: Creates a query that searches for UniParc entries whose sequence checksum is equal to the provided checksum.
CHEMBL - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
CHEMISTRY_DATABSES - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseCategory
CHITARS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
CHLOROPLAST - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.TransitType
CHLOROPLAST_PLASTID - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.GeneEncodingType
CHROMATOPHORE_PLASTID - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.GeneEncodingType
Citation - Interface in uk.ac.ebi.kraken.interfaces.uniprot.citationsNew: The basic type containing the common values that are present in each and every Citation
CitationConflictReport - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
CitationSummary - Interface in uk.ac.ebi.kraken.interfaces.uniprot.citationsNew: Created by IntelliJ IDEA.
CitationTypeEnum - Enum Class in uk.ac.ebi.kraken.interfaces.uniprot.citationsNew: User: Emilio Salazar Date: 27-Oct-2005
citationTypeOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationTypeEnum
CitationXrefs - Interface in uk.ac.ebi.kraken.interfaces.uniprot.citationsNew: Created by IntelliJ IDEA.
CitationXrefType - Enum Class in uk.ac.ebi.kraken.interfaces.uniprot.citationsNew: Created by IntelliJ IDEA.
City - Interface in uk.ac.ebi.kraken.interfaces.uniprot.citationsNew
CLEANEX - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
Client - Class in uk.ac.ebi.uniprot.dataservice.client: Client class is the starting point for JAPI client.
Client() - Constructor for class uk.ac.ebi.uniprot.dataservice.client.Client
ClientConfigurator - Interface in uk.ac.ebi.uniprot.dataservice.client: Specification for configuring a client and used by the Client.
ClientConstant - Class in uk.ac.ebi.uniprot.dataservice.client
ClientConstant() - Constructor for class uk.ac.ebi.uniprot.dataservice.client.ClientConstant
clusterId(String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniref.UniRefQueryBuilder: Creates a query that searches for clusters with the given UniRef identifier
clusterName(String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniref.UniRefQueryBuilder: Creates a query that searches for clusters with the given cluster name
Cofactor - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
COFACTOR - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType
CofactorCommentStructured - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments: Description of A cofactor: any non-protein substance required for an enzyme to be catalytically active
CofactorNote - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
CofactorReference - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
CofactorReferenceType - Enum Class in uk.ac.ebi.kraken.interfaces.uniprot.comments
COILED - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
CoiledFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
COLLECTF - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
Comment - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments: A Comment in the UniProtEntry.

Notes: public void setCommentType(CommentType type);
removed because it causes havoc if textual comments change into structured ones.
CommentFreeText - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments: CommentFreeText is used by TextOnlyComment to support multitext comments
CommentNote - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments: Created by IntelliJ IDEA.
comments(CommentType, String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Creates a query that matches entries whose comment type contains a specified value.
COMMENTS - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtData.ComponentType
CommentStatus - Enum Class in uk.ac.ebi.kraken.interfaces.uniprot: Evidence on how the comment was derived.
commentsType(CommentType) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Creates a query that matches entries whose comment type is of the specified value.
CommentText - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments: Free text comment, has EvidencedValue and hasCommentStatus used in free text comment
CommentType - Enum Class in uk.ac.ebi.kraken.interfaces.uniprot.comments: Enumerates all comment types in UniProt.
COMPBIAS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
CompBiasFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features: COMPBIAS - Extent of a compositionally biased region.
COMPLEXPORTAL - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
COMPSTATS - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastParameter
CONFLICT - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
ConflictFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
ConflictReport - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
ConflictReportDescription - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features: User: mkleen@ebi.ac.uk Date: 18-Nov-2005 Time: 14:17:39
CONOSERVER - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
convert(InputStream) - Method in interface uk.ac.ebi.uniprot.dataservice.client.service.Adaptor
convert(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.MichaelisConstantUnit
convertFromECOCode(String) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceConverter
convertToECOCode(GoEvidenceType) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceConverter
convertToECOCode(GoEvidenceType, String) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceConverter
CORUM - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
Country - Interface in uk.ac.ebi.kraken.interfaces.uniprot.citationsNew
CPTAC - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
CPTC - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
create() - Method in class uk.ac.ebi.uniprot.dataservice.client.uniref.converter.AbstractMemberConverter
create() - Method in class uk.ac.ebi.uniprot.dataservice.client.uniref.converter.UniRefMemberConverter
create() - Method in class uk.ac.ebi.uniprot.dataservice.client.uniref.converter.UniRefRepMemberConverter
createBasicQuery(String, String, boolean) - Method in interface uk.ac.ebi.uniprot.dataservice.query.QueryFactory: Create a basic query
created(LocalDate, LocalDate) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Creates a query to get entries created between fromDate and toDate, It does not allow both fromDate and toDate to be null.
createEmptyQuery() - Method in interface uk.ac.ebi.uniprot.dataservice.query.QueryFactory: Create a Empty query: this query will return no result
createMultiValuePhraseQuery(String, String, boolean, int) - Method in interface uk.ac.ebi.uniprot.dataservice.query.QueryFactory: Create a multi value phrase query
createPhraseQuery(String, String, boolean) - Method in interface uk.ac.ebi.uniprot.dataservice.query.QueryFactory: Create a phrase query
createRangeQuery(String, String, boolean, String, boolean) - Method in interface uk.ac.ebi.uniprot.dataservice.query.QueryFactory: Create a range query
CrosslinkFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
CROSSLNK - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
CTD - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
CTDP - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
CURATION - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCategory
CURATOR - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
CYANELLE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.TransitType
CYANELLE_PLASTID - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.GeneEncodingType

D

D - Enum constant in enum class uk.ac.ebi.kraken.interfaces.common.MoleculeWeight
D2_GEL_DATABASES - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseCategory
D3_STRUCTURE_DATABASES - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseCategory
database - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcField.Search
database - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtField.Search
database(String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcQueryBuilder: Creates a query that searches for UniParc entries that hold reference to at least one cross-reference of the given database type
database(DatabaseType) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcQueryBuilder: Creates a query that searches for UniParc entries that hold reference to at least one cross-reference of the given database type (Uses the DatabaseType enum)
Database - Interface in uk.ac.ebi.kraken.interfaces.common: Created by IntelliJ IDEA.
DATABASE - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastParameter
DatabaseAttribute - Interface in uk.ac.ebi.kraken.interfaces.uniprot.dbx
DatabaseCategory - Enum Class in uk.ac.ebi.kraken.interfaces.uniprot
DatabaseCrossReference - Interface in uk.ac.ebi.kraken.interfaces.uniparc: Created by IntelliJ IDEA.
DatabaseCrossReference - Interface in uk.ac.ebi.kraken.interfaces.uniprot: The DBCrossReference annotation of the UniProtEntry.
DatabaseDefContext - Interface in uk.ac.ebi.kraken.interfaces.uniprot.dbx
DatabaseFTP - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
DatabaseName - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
DatabaseNote - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
DatabaseOption - Enum Class in uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input: The set UniProt of databases one can blast against.
DatabaseType - Enum Class in uk.ac.ebi.kraken.interfaces.uniparc: Created by IntelliJ IDEA.
DatabaseType - Enum Class in uk.ac.ebi.kraken.interfaces.uniprot: A list of all Cross reference databases in UniProt.
DatabaseURL - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
date_created - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtField.SearchDate
date_modified - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtField.SearchDate
DbDisplayOrder - Interface in uk.ac.ebi.kraken.interfaces.uniprot.dbx: Cross Reference database definitions Here is the example of the definition for EMBL and IntAct
dbid - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcField.Search
DBSNP - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
dbTypeOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType
DEFAULT - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureStatus
DEFAULT_PAGE_SIZE - Static variable in class uk.ac.ebi.uniprot.dataservice.client.ClientConstant
DEPOD - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
DESCRIBED - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.IsoformSequenceStatus
DEVELOPMENTAL_STAGE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType
DevelopmentalStageComment - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
DICTYBASE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
DICTYBASE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
DIP - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
Disease - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments: Container used to represent the definition of the disease.
DISEASE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType
DiseaseAcronym - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments: A name by which the disease is also known as.
DiseaseCommentStructured - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments: Description of the disease(s) associated with a deficiency of a protein
DiseaseDescription - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments: Generic description of the disease.
DiseaseId - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments: Identifier of the disease within the disease controlled vocabulary file humdisease.txt.
DiseaseNote - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments: Contains text describing the manifestation of a particular disease on a particular protein.
DiseaseReference - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments: Reference of an external source the best describes the disease
DiseaseReferenceId - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments: The identifier of the disease provided by the external source DiseaseReferenceType
DiseaseReferenceType - Enum Class in uk.ac.ebi.kraken.interfaces.uniprot.comments: Enumeration of the possible external sources that have a references to diseases.
DISGENET - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
DISPLAYED - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.IsoformSequenceStatus
displayValues() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.description.FlagType
DISPROT - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
DISRUPTION_PHENOTYPE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType
DisruptionPhenotypeComment - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
DISULFID - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
DisulfidFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
DMDM - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
DNA - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.SequenceTypeOption
DNA_BIND - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
DnaBindFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
DNASU - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
DOI - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationXrefType
DOI - Interface in uk.ac.ebi.kraken.interfaces.uniprot.citationsNew
Domain - Interface in uk.ac.ebi.kraken.interfaces.uniparc
DOMAIN - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType
DOMAIN - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
DomainComment - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
DomainFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features: DOMAIN - Extent of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.
DOSACCOBS2DPAGE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType: Deprecated.
DROPOFF - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastParameter
DropOffOption - Enum Class in uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input: The amount a score can drop before gapped extension of word hits is halted.
DRUGBANK - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
DRUGCENTRAL - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType

E

E - Enum constant in enum class uk.ac.ebi.kraken.interfaces.common.MoleculeWeight
ec - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtField.Search
ec(String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Creates a query on an Enzyme Commission (EC) number.
EC - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.description.FieldType
ECHOBASE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
ECNUMBER - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtData.ComponentType
ECO_0000001 - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCode: Deprecated.
ECO_0000006 - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCode: Deprecated.
ECO_0000028 - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCode: Deprecated.
ECO_0000034 - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCode: Deprecated.
ECO_0000044 - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCode: Deprecated.
ECO_0000203 - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCode: Deprecated.
ECO_0000213 - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCode
ECO_0000244 - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCode
ECO_0000250 - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCode
ECO_0000255 - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCode
ECO_0000256 - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCode
ECO_0000257 - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCode
ECO_0000259 - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCode
ECO_0000269 - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCode
ECO_0000303 - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCode
ECO_0000305 - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCode
ECO_0000312 - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCode
ECO_0000313 - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCode
ECO_0007744 - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCode
ECO_0007829 - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCode
ECO_0008006 - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCode
ECOGENE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
ECOGENE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
Editor - Interface in uk.ac.ebi.kraken.interfaces.uniprot.citationsNew
EGGNOG - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
EIGHT - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.DropOffOption
ELECTRONIC_ARTICLE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationTypeEnum
ElectronicArticle - Interface in uk.ac.ebi.kraken.interfaces.uniprot.citationsNew: The RL line for an electronic publication includes an '(er)' prefix.
ELECTROSPRAY - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.MassSpectrometryMethod
ELM - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
email(String) - Method in class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastInput.Builder
EMAIL - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastParameter
EMBL - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
EMBL - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
EMBL - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
EMBL_ANNCON - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
EMBL_CON - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
EMBL_GENBANK_DDBJ - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.SubmissionDatabase
EMBL_TPA - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
EMBL_TSA - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
EMBLWGS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
EMDB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
Ensembl - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
Ensembl - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
ENSEMBL - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
EnsemblBacteria - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
EnsemblBacteria - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
ENSEMBLBACTERIA - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
EnsemblFungi - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
EnsemblFungi - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
ENSEMBLFUNGI - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
EnsemblMetazoa - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
EnsemblMetazoa - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
ENSEMBLMETAZOA - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
EnsemblPlants - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
EnsemblPlants - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
ENSEMBLPLANTS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
EnsemblProtists - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
EnsemblProtists - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
ENSEMBLPROTISTS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
EnsemblRapid - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
EntryAudit - Interface in uk.ac.ebi.kraken.interfaces.uniprot: An EntryAudit of a UniProtEntry.
EntryId - Interface in uk.ac.ebi.kraken.interfaces.common: Implemented by all entries describing a protein sequence.
Enzyme - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
ENZYME_AND_PATHWAY_DATABASES - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseCategory
EnzymeRegulationComment - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
EPD - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType: Deprecated.
EPD - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
EPO - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
ERRONEOUS_INITIATION - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.SequenceCautionType
ERRONEOUS_PREDICTION - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.SequenceCautionType
ERRONEOUS_TERMIINATION - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.SequenceCautionType
ERRONEOUS_TRANSLATION - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.SequenceCautionType
ESTHER - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
EUHCVDB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
EUPATHDB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
Evidence - Interface in uk.ac.ebi.kraken.interfaces.uniprot.evidences: The Evidence annotation of the UniProtEntry.
EvidenceAttribute - Interface in uk.ac.ebi.kraken.interfaces.uniprot.evidences: The EvidenceAttribute of the Evidence.
EvidenceCategory - Enum Class in uk.ac.ebi.kraken.interfaces.uniprot.evidences: The EvidenceCategory of the Evidence.
EvidenceCode - Enum Class in uk.ac.ebi.kraken.interfaces.uniprot.evidences: The EvidenceCode of the Evidence.
EvidencedValue - Interface in uk.ac.ebi.kraken.interfaces.uniprot: Most of data in uniprot has evidence EvidencedValue is for this type of data This interface extends Value and HasEvidences
EvidenceId - Interface in uk.ac.ebi.kraken.interfaces.uniprot.evidences: The EvidenceId of the Evidence.
EvidenceOriginName - Interface in uk.ac.ebi.kraken.interfaces.uniprot.evidences: The EvidenceOriginName of the Evidence.
EvidenceType - Enum Class in uk.ac.ebi.kraken.interfaces.uniprot.evidences: The EvidenceType of the Evidence.
EVOLUTIONARYTRACE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
EXACT - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureLocationModifier
execute(Request) - Method in interface uk.ac.ebi.uniprot.dataservice.client.service.JapiService
existence - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtField.Search
EXP - Enum constant in enum class uk.ac.ebi.kraken.interfaces.go.GoAnnotationEvidence
EXP - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceType
EXP - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastParameter
ExpectationOption - Enum Class in uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input
EXPERIMENTAL - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.CommentStatus
EXPERIMENTAL - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
EXPERIMENTAL - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureStatus
EXPRESSIONATLAS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
EXTERNAL - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.IsoformSequenceStatus

F

F - Enum constant in enum class uk.ac.ebi.kraken.interfaces.common.MoleculeWeight
F - Enum constant in enum class uk.ac.ebi.kraken.interfaces.go.GoCategory
F - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.OntologyType
FAB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.MassSpectrometryMethod
factory() - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcQueryBuilder
factory() - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder
factory() - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniref.UniRefQueryBuilder
FAMILY_AND_DOMAIN_DATABASES - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseCategory
feature(String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcQueryBuilder: Creates a query that searches for UniParc entries whose ipr is equal to the provided ipr.
Feature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
feature_id - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcField.Search
FeatureDescription - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
FeatureId - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
FeatureLocation - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
FeatureLocationModifier - Enum Class in uk.ac.ebi.kraken.interfaces.uniprot.features
features(FeatureType, String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Creates a query that matches entries containing features of the specified features type, containing the specified value
FEATURES - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtData.ComponentType
FeatureSequence - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
FeatureStatus - Enum Class in uk.ac.ebi.kraken.interfaces.uniprot.features: Defines which status can be assigned to a Swissprot Feature.
featuresType(FeatureType) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Creates a query that matches entries containing features of the specified type.
FeatureType - Enum Class in uk.ac.ebi.kraken.interfaces.uniprot.features
fetchNextPage() - Method in interface uk.ac.ebi.uniprot.dataservice.client.QueryResultPage
Field - Interface in uk.ac.ebi.kraken.interfaces.uniprot.description: Stores the sub category type of a specific category as well as the respective value.
FieldType - Enum Class in uk.ac.ebi.kraken.interfaces.uniprot.description: Defines the set of valid field types Current valid fields are: Full, Short, EC, Allergen, Biotech, CD_antigen, INN.
FIFTY - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.AlignmentCutoffOption
FIFTY - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.ScoreCutoffOption
FILTER - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastParameter
FilterOption - Enum Class in uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input: Filter regions of low sequence complexity.
FIVE - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.AlignmentCutoffOption
FIVE - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.ScoreCutoffOption
FIVE_HUNDRED - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.AlignmentCutoffOption
FIVE_HUNDRED - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.ScoreCutoffOption
Flag - Interface in uk.ac.ebi.kraken.interfaces.uniprot.description: Contains a flag descriptors found within a DE line along with any evidences
FlagType - Enum Class in uk.ac.ebi.kraken.interfaces.uniprot.description: Contains a list of acceptable flag descriptors found within a DE line current valid flags are Precursor, Fragment, Fragments
FlyBase - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
FlyBase - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
FLYBASE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
FORMAT_LIST - Static variable in class uk.ac.ebi.uniprot.dataservice.client.ClientConstant
FORMAT_TXT - Static variable in class uk.ac.ebi.uniprot.dataservice.client.ClientConstant
FORMAT_XML - Static variable in class uk.ac.ebi.uniprot.dataservice.client.ClientConstant
FOUR - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.DropOffOption
fragment - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtField.Search
fragment(boolean) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Creates a query that searches for fragmented or non fragmented proteins, depending on the flag provided in the argument.
FRAGMENT - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.description.FlagType
FRAGMENTS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.description.FlagType
FRAMESHIFT - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.SequenceCautionType
FULL - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.description.FieldType
FUNCTION - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType
FunctionComment - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
FUNFAM - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.SignatureDBType
FUNFAM - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
FusionGDB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType

G

G - Enum constant in enum class uk.ac.ebi.kraken.interfaces.common.MoleculeWeight
GAPALIGN - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastParameter
GAPEXT - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastParameter
GAPOPEN - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastParameter
gene - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcField.Search
gene - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtField.Search
gene(String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcQueryBuilder: Creates a query that searches for UniParc entries that contain within their database cross-references the given gene name.
gene(String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Creates a query that searches for genes such gene names or synonyms
Gene - Interface in uk.ac.ebi.kraken.interfaces.uniprot: About This Data Structure
gene_exact - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtField.Search
GENE_EXPRESSION_DATABASES - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseCategory
GENE3D - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.SignatureDBType
GENE3D - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
GENECARDS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
GeneEncodingType - Enum Class in uk.ac.ebi.kraken.interfaces.uniprot: Created by IntelliJ IDEA.
geneExact(String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Creates a query that searches for genes exact names such names or synonyms
GENEID - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
GeneName - Interface in uk.ac.ebi.kraken.interfaces.uniprot.genename: About This Data Structure
GeneNameSynonym - Interface in uk.ac.ebi.kraken.interfaces.uniprot.genename: About This Data Structure
GENEREVIEWS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
GENES - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtData.ComponentType
GENETIC_VARIATION_DATABASES - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseCategory
GENETREE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
GENEWIKI - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
GENOME_ANNOTATION_DATABASES - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseCategory
GENOMERNAI - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
GENPEPT - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
getAbsorption() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.BioPhysicoChemicalPropertiesComment
getAcceptType() - Method in interface uk.ac.ebi.uniprot.dataservice.client.Request
getAccession() - Method in interface uk.ac.ebi.kraken.interfaces.go.toprotein.GoProteinContainer
getAccession() - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.DatabaseCrossReference
getAccession() - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtComponent
getAccession() - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtData
getAccessions(Query) - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtService: Given a Query, return an QueryResult of type PrimaryUniProtAccession representing the accessions of the entries that match the query.
getAccessions(Query, EnumSet<QuerySpec>) - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtService: Given a Query, return an QueryResult of type PrimaryUniProtAccession representing the accessions of the entries that match the query.
getAcronym() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Disease
getActiveDatabaseCrossReferences() - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.UniParcEntry: An immutable list of active database cross references.
getActiveDatabseCrossReferences() - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.UniParcEntry: Deprecated.
getAgricolaId() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationXrefs
getAlignmentCutoff() - Method in class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastInput: Maximum number of blast alignments to be presented.
getAlignments() - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastSummary: List of sequences that align against the hit
getAllXRefDBDefs() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.dbx.DatabaseDefContext
getAllXrefDBName() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.dbx.DatabaseDefContext
getAlternativeNames() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.ProteinDescription: Retrieves a list of alternate names for the main protein
getAlternativeSequences() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.HasAlternativeSequence
getAssertedGoAnnotations() - Method in interface uk.ac.ebi.kraken.interfaces.go.toprotein.GoProteinContainer
getAttribute() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.evidences.Evidence
getAttribute() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceId
getAuthoringGroup() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Citation
getAuthors() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Citation
getBitScore() - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.Alignment: Bit score (a normalised score) for the alignment.
getBlastDatabases() - Method in class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastInput: The databases that the blast job will be run against.
getBlastVersion() - Method in class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastInput: The blast program to be used for the blast.
getBookName() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Book
getCategory() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
getCategory() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.evidences.Evidence
getChain() - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.DatabaseCrossReference
getCitationsNew() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry
getCitationsNew(CitationTypeEnum) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry
getCitationSummary() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Citation
getCitationType() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Citation
getCitationXrefs() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Citation
getCity() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Book
getCity() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Thesis
getClustrEntries() - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.UniParcEntry: Deprecated.
getCode() - Method in enum class uk.ac.ebi.kraken.interfaces.go.GoAnnotationEvidence
getCodeValue() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCode
getCofactorReference() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Cofactor
getCofactorReferenceType() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.CofactorReference
getCofactors() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.CofactorCommentStructured
getComment() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.AlternativeProductsComment
getComments() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry
getComments(CommentType) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry
getComments(Query) - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtService: Given a Query, return an QueryResult of type UniProtComponent on .uniprot.comments.Comments, which represent the entry comment results.
getCommentStatus() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.HasCommentStatus
getCommentType() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Comment: Returns the type of this comment.
getCommonName() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.Organism: Returns the common name of this Organism.
getComponent() - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtComponent
getComponent() - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniref.UniRefComponent
getComponent(UniProtData.ComponentType) - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtData: The return type depends on UniProtData.ComponentType
type: COMMENTS: return: list of UniProt Comment
type: FEATURES: return: list of UniProt Feature
type: GENES: return: list of UniProt Gene
type: XREFS: return: list of UniProt DatabaseCrossReference
type: ECNUMBER: return: list of UniProt ec number String
type: PROTEIN_NAMES: return: list of UniProt protein name String
type: KEYWORDS: return: list of UniProt Keyword
type: TAXONOMY: return: list of UniProt NcbiTaxon
getComponents() - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcComponent: Contains a list of annotations that compose a UniParc entry
getConflictReports() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.ConflictFeature
getConstant() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.MichaelisConstant
getConstantStr() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.MichaelisConstant
getContains() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.ProteinDescription: Returns a list of proteins described in the contains section of the DE line
getCountry() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Thesis
getCRC64() - Method in interface uk.ac.ebi.kraken.interfaces.common.Sequence: Returns the crc64 hashcode of this sequence.
getCreated() - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.DatabaseCrossReference
getCreationDate() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.EntryAudit: Deprecated.
getCutoff() - Method in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.AlignmentCutoffOption
getCutoff() - Method in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.ScoreCutoffOption
getCvId() - Method in enum class uk.ac.ebi.kraken.interfaces.go.GoAnnotationEvidence
getDatabase() - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.DatabaseCrossReference
getDatabase() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.DatabaseCrossReference: Returns the DATABASE of the DBCrossReference.
getDatabase() - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastSummary: Database the entry belongs to.
getDatabaseCrossReferences() - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.UniParcEntry
getDatabaseCrossReferences() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry: Returns the list of DatabaseCrossReferences annotated in the UniProtEntry.
getDatabaseCrossReferences(String) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry
getDatabaseCrossReferences(DatabaseType) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry
getDatabaseFTP() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.WebResourceComment
getDatabaseName() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.WebResourceComment
getDatabaseNote() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.WebResourceComment
getDatabaseType(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
getDatabaseTypes(DatabaseCategory) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
getDatabaseURL() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.WebResourceComment
getDate() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.evidences.Evidence
getDate() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.HasDate: Returns the Calendar defining the date associated with this Type.
getDbAccession() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.dbx.HasDbAccession
getDbCode() - Method in enum class uk.ac.ebi.kraken.interfaces.go.GoCategory
getDbId() - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.SequenceFeature
getDbName() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.dbx.DbDisplayOrder
getDbName() - Method in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.DatabaseOption
getDescription() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Disease
getDescription() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.DatabaseCrossReference
getDescription() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceType
getDescription() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.OntologyType
getDescription() - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastSummary: A description containing several elements that characterize an entry.
getDirectionType() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.PhysiologicalReaction
getDisease() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.DiseaseCommentStructured
getDiseaseId() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Disease
getDiseaseReferenceId() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.DiseaseReference
getDiseaseReferenceType() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.DiseaseReference
getDisplayName() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationTypeEnum
getDisplayName() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
getDisplayName() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCode
getDisplayName() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
getDisplayName() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.ProteinExistence
getDisplayName() - Method in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.DatabaseOption
getDisplayOrder() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.dbx.DbDisplayOrder
getDisplayString() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.MichaelisConstantUnit: Added for beans - just use this rather than toDisplayNameString?
getDOI() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationXrefs
getDomain() - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.SequenceFeature
getDropOff() - Method in class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastInput: The amount a score can drop before gapped extension of word hits is halted
getECNumber() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Reaction
getEcNumbers() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.ProteinDescription: Retrieves a list of all the EC numbers present in the DE line
getECNumbers(Query) - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtService: Given a Query, return an QueryResult of type UniProtComponent on Strings, which represent the EC results.
getEcoEvidence() - Method in interface uk.ac.ebi.kraken.interfaces.go.GoAnnotation
getEditors() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Book
getEnd() - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.Location
getEnd() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureLocation
getEnd() - Method in interface uk.ac.ebi.kraken.interfaces.uniref.member.OverlapRegion
getEndMatchSeq() - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.Alignment: Represents the position of the last amino acid from the sequence, obtained from #getMatchSeq, in relation to the entry's complete sequence
getEndModifier() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureLocation
getEndQuerySeq() - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.Alignment: Represents the position of the last amino acid from the sequence, obtained from #getQuerySeq, in relation to the entry's complete sequence
getEntries(List<String>) - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcService
getEntries(List<String>) - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtService: Given a list of accessions, returns the corresponding list of UniProtEntry.
getEntries(Query) - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcService
getEntries(Query) - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtService: Given a Query, returns an QueryResult of UniProtEntry.
getEntries(Query) - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniref.UniRefService: Returns an iterable to UniRef entry.
getEntries(Query, int) - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcService
getEntries(Query, int) - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtService: Given a Query, returns an QueryResult of UniProtEntry.
getEntries(Query, int) - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniref.UniRefService: Returns an iterable to UniRef entry.
getEntries(Query, EnumSet<QuerySpec>) - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtService: Given a Query, returns an QueryResult of UniProtEntry.
getEntry() - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.Hit: The entry focused on this particular blast hit
getEntry() - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.UniParcHit: The entry focused on this particular blast hit
getEntry() - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.UniProtHit: The entry focused on this particular blast hit
getEntry() - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.UniRefHit: The entry focused on this particular blast hit
getEntry(String) - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcService
getEntry(String) - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtService: Given an accession, returns the corresponding UniProtEntry.
getEntry(String) - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniref.UniRefService: Returns a UniRef entry from UniRef ID.
getEntryAc() - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.UniProtBlastSummary: The accession of the entry.
getEntryAudit() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry: Returns the Entry Audit Information.
getEntryByUniParcUPI(String, UniRefDatabaseType) - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniref.UniRefService: Returns a UniRef entry from UniParc upi.
getEntryByUniProtAccession(String, UniRefDatabaseType) - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniref.UniRefService: Returns a UniRef entry from UniProt accession.
getEntryFromUniProtAccession(String) - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcService
getEntryId() - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastSummary: The identifier of the entry.
getEntryIdentifier() - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcComponent: Holds a reference to the primary UniParc entry identifier
getEntryVersion() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.EntryAudit
getEnzyme() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.MaximumVelocity
getEvents() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.AlternativeProductsComment
getEvidence() - Method in interface uk.ac.ebi.kraken.interfaces.go.GoAnnotation: Deprecated.
getEvidence(EvidenceId) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry: Numerous elements in the model could contain lists of evidenceId the evidence ids correspond to a item of evidence listed in the getEvidences()
getEvidenceCode() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.evidences.Evidence
getEvidenceCode() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceId
getEvidenceId() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.evidences.Evidence
getEvidenceIds() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Citation
getEvidenceIds() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.HasEvidences: Returns the EvidenceIds of the EvidenceTagable object.
getEvidences() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry: Returns the list of Evidences annotated in the UniProtEntry.
getExpectation() - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.Alignment: Expectation value (E-value) for the alignment.
getExpectation() - Method in class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastInput: The expectation value that limits the number of scores and alignments reported.
getExpectationValue() - Method in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.ExpectationOption
getExtraTaxonomyIds() - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.DatabaseCrossReference
getFeatureDescription() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.HasFeatureDescription
getFeatureId() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.HasFeatureId
getFeatureLocation() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.Feature
getFeatures() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry: The UniProt object is nolonger linked to UniParc this is now available via the ProteinData
getFeatures(FeatureType) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry
getFeatures(Query) - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtService: Given a Query, return an QueryResult of type UniProtComponent on .uniprot.features.Features, which represent the entry feature results.
getFeatureStatus() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.HasFeatureStatus
getFields() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.description.Name: Returns the fields beloning to this name
getFieldsByType(FieldType) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.description.Name: Returns a list of fields of a specific type
getFilter() - Method in class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastInput: The selected filter option.
getFilter() - Method in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.FilterOption
getFirstInteractant() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Interaction
getFirstInteractor() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Interaction
getFirstPage() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Book
getFirstPage() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.JournalArticle
getFirstPublicDate() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.EntryAudit
getFlags() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.ProteinDescription: Retrives the list of flags from the DE line
getFlagType() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.description.Flag
getFourth() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.DatabaseCrossReference
getFullName() - Method in interface uk.ac.ebi.kraken.interfaces.common.Database
getGapExt() - Method in class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastInput: The value of the penalty taken away from the score for each base or residue in the gap.
getGapOpen() - Method in class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastInput: Penalty taken away from the score when a gap is created in sequence.
getGaps() - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.Alignment: Percentage of gaps in the alignment.
getGeneName() - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.DatabaseCrossReference
getGeneName() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.Gene: Returns the Gene Name of this Gene.
getGeneNameSynonyms() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.Gene: Returns the List of Gene Name Synonyms of this Gene.
getGenes() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry: Returns the Genes in which this protein is encoded.
getGenes(Query) - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtService: Given a Query, return an QueryResult of type UniProtComponent on .uniprot.Genes,
getGiNumber() - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.DatabaseCrossReference
getGoCategory() - Method in interface uk.ac.ebi.kraken.interfaces.go.GoTerm
getGoEvidenceSource() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.Go
getGoEvidenceType() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.Go
getGoId() - Method in interface uk.ac.ebi.kraken.interfaces.go.GoDefinition
getGoId() - Method in interface uk.ac.ebi.kraken.interfaces.go.GoTerm
getGoId() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.Go
getGoTerm() - Method in interface uk.ac.ebi.kraken.interfaces.go.GoAnnotation
getGoTerm() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.Go
getGoTermName() - Method in interface uk.ac.ebi.kraken.interfaces.go.GoTerm
getGoTerms() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry
getHexadecimalValue() - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.UniParcId
getHitCount() - Method in interface uk.ac.ebi.uniprot.dataservice.client.Response
getHitNumber() - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastSummary: Position in which the entry appears in the list of last hits.
getId() - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.Domain
getId() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.ReactionReference
getId() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.Ligand
getIdentity() - Method in enum class uk.ac.ebi.kraken.interfaces.uniref.UniRefDatabaseType
getIdentity() - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.Alignment: Percentage of identical bases/residues in the alignment.
getIds() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.AlternativeProductsIsoform
getIncludes() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.ProteinDescription: Returns a list of proteins described in the includes section of the DE line
getInstitute() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Thesis
getInteractionGeneName() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Interaction
getInteractions() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.InteractionComment
getInteractionType() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Interaction
getInternalSection() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry
getInternalVersion() - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.DatabaseCrossReference
getIsoformId() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.DatabaseCrossReference
getIsoforms() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.AlternativeProductsComment
getIsoformSequenceStatus() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.AlternativeProductsIsoform
getJournalName() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.ElectronicArticle
getJournalName() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.JournalArticle
getKeywords() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry: Returns the list of Keywords annotated in the UniProtEntry.
getKeywords(Query) - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtService: Given a Query, return an QueryResult of type UniProtComponent on .uniprot.Keywords, which represent the entry keyword results.
getKineticParameters() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.BioPhysicoChemicalPropertiesComment
getLabel() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.Ligand
getLastAnnotationUpdateDate() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.EntryAudit
getLastPage() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Book
getLastPage() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.JournalArticle
getLastSequenceUpdateDate() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.EntryAudit
getLength() - Method in interface uk.ac.ebi.kraken.interfaces.common.Sequence: Returns the length of this sequence.
getLength() - Method in interface uk.ac.ebi.kraken.interfaces.uniref.member.UniRefMember
getLigand() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.BindingFeature
getLigandPart() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.BindingFeature
getLink() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.InteractionType
getLocation() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.SubcellularLocation
getLocations() - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.SequenceFeature
getLocationType() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.RnaEditingComment: CC -!- RNA EDITING: Modified_positions=x[, y, z][; Note=].
getLocator() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.ElectronicArticle
getMappedClass() - Method in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtData.ComponentType
getMatchSeq() - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.Alignment: Region of the match/target sequence in the alignment
getMatrix() - Method in class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastInput: The similarity matrix to be used on the blast.
getMatrix() - Method in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.MatrixOption
getMax() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Absorption
getMaximumSize() - Method in interface uk.ac.ebi.uniprot.dataservice.client.ClientConfigurator
getMaximumVelocities() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.KineticParameters
getMaxVelocityUnit() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.MaximumVelocity
getMedlineId() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationXrefs: Deprecated.
getMemberId() - Method in interface uk.ac.ebi.kraken.interfaces.uniref.member.UniRefMember
getMembers() - Method in interface uk.ac.ebi.kraken.interfaces.uniref.UniRefEntry: Returns the members of this UniRefEntry.
getMethod() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.MassSpectrometryComment
getMichaelisConstants() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.KineticParameters
getMolecularWeight() - Method in interface uk.ac.ebi.kraken.interfaces.common.Sequence: Returns the molecular weight of this sequence.
getMolecularWeight() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.PAGEDataComment
getMolecule() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Comment
getMolecule() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.RnaEditingComment
getMolWeight() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.MassSpectrometryComment
getMolWeightError() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.MassSpectrometryComment
getMutagenReport() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.MutagenFeature
getName() - Method in interface uk.ac.ebi.kraken.interfaces.common.Database
getName() - Method in enum class uk.ac.ebi.kraken.interfaces.go.GoAnnotationEvidence
getName() - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.Domain
getName() - Method in enum class uk.ac.ebi.kraken.interfaces.uniparc.SignatureDBType
getName() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.AlternativeProductsIsoform
getName() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Cofactor
getName() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.MichaelisConstantUnit
getName() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Reaction
getName() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.CommentStatus
getName() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseCategory
getName() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
getName() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureStatus
getName() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
getName() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.Ligand
getName() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.SplicedIsoform
getName() - Method in interface uk.ac.ebi.kraken.interfaces.uniref.UniRefEntry: Returns the name of this UniRefEntry.
getName() - Method in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastParameter
getNames() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.description.Section: Returns a list of valid name types as well as the associated names
getNamesByType(NameType) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.description.Section: Returns a list of names that map to a specific type of name type (see NameType)
getNameType() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.description.Name: Returns the type of the name being analyzed
getNCBITaxonomy() - Method in interface uk.ac.ebi.kraken.interfaces.uniref.member.UniRefMember
getNcbiTaxonomyId() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.OrganismHost: Returns the NCBI Taxonomy ID of the Organism of this Organism Host.
getNcbiTaxonomyIds() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry
getNextRequest() - Method in interface uk.ac.ebi.uniprot.dataservice.client.Response
getNote() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Absorption
getNote() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.AlternativeProductsIsoform
getNote() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.CofactorCommentStructured
getNote() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.DiseaseCommentStructured
getNote() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.KineticParameters
getNote() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.MassSpectrometryComment
getNote() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.SequenceCautionComment
getNote() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.Ligand
getNote() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.HasCommentNote
getNumberOfAttribute() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
getNumberOfExperiments() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Interaction
getNumberOfHits() - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastResult: Number of entries hit by blast search
getNumberOfHits() - Method in interface uk.ac.ebi.uniprot.dataservice.client.QueryResult
getOntologyType() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.Go
getOrderedLocusNames() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.Gene: Returns the List of Ordered Locus Names of this Gene.
getOrderedValues() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
getORFNames() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.Gene: Returns the List of ORF Names of this Gene.
getOrganelles() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry
getOrganism() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.OrganismHost: Returns the Organism of this Organism Host.
getOrganism() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry: Returns the Organisms in which this protein is found.
getOrganismHosts() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry: Returns the list of organism hosts.
getOrganismNames() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.Organism: Returns the list of all OrganismNames of this Organism.
getOrientation() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.SubcellularLocation
getOriginalSequence() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.HasAlternativeSequence
getOriginName() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.evidences.Evidence
getOverlap() - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.Alignment: Length of the region covered by the alignment.
getOverlapRegion() - Method in interface uk.ac.ebi.kraken.interfaces.uniref.member.UniRefMember
getPagesize() - Method in interface uk.ac.ebi.uniprot.dataservice.client.QueryResultPage
getPatentNumber() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Patent
getPattern() - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.Alignment: Consensus pattern for the alignment.
getPHDependence() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.BioPhysicoChemicalPropertiesComment
getPhysiologicalReactions() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.CatalyticActivityCommentStructured
getPl() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.PAGEDataComment
getPosition() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Position
getPositionsWithEvidences() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.RnaEditingComment
getPositives() - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.Alignment: Percentage of similar bases/residues in the alignment.
getPrimaryId() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.DatabaseCrossReference
getPrimaryUniProtAccession() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry: Returns the Primary UniProtAccessions of the UniProtEntry.
getProbability() - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.Alignment: Probability value (P-value) for the alignment.
getProteinDescription() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry
getProteinExistence() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry
getProteinName() - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.DatabaseCrossReference
getProteinName() - Method in interface uk.ac.ebi.kraken.interfaces.uniref.member.UniRefMember
getProteinNames(Query) - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtService: Given a Query, return an QueryResult of type UniProtComponent on Strings, which represent the protein name results.
getProteome() - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.DatabaseCrossReference
getProteomeComponent() - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.DatabaseCrossReference
getPublicationDate() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Citation
getPublisher() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Book
getPubmedId() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationXrefs
getQuerySeq() - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.Alignment: Region of the query sequence in the alignment.
getQueryString() - Method in interface uk.ac.ebi.uniprot.dataservice.query.Query: Return the string representation that will be send to the server.
getReaction() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.CatalyticActivityCommentStructured
getReactionReference() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.PhysiologicalReaction
getReactionReferences() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Reaction
getRecommendedName() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.ProteinDescription: Retrieves the recommended name of the protein from the DE line
getRedoxPotential() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.BioPhysicoChemicalPropertiesComment
getReference() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Disease
getReferenceId() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.CofactorReference
getReleaseDate() - Method in interface uk.ac.ebi.kraken.interfaces.uniref.UniRefDatabase
getRepresentativeMember() - Method in interface uk.ac.ebi.kraken.interfaces.uniref.UniRefEntry: Returns the representative member of this UniRefEntry.
getRequest() - Method in interface uk.ac.ebi.uniprot.dataservice.client.QueryResult
getRequestUrl() - Method in interface uk.ac.ebi.uniprot.dataservice.client.Request
getResult(int) - Method in interface uk.ac.ebi.uniprot.dataservice.client.QueryResultPage
getResults() - Method in interface uk.ac.ebi.uniprot.dataservice.client.Response
getResults(Query, EnumSet<QuerySpec>, UniProtData.ComponentType...) - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtService: Given a Query, return an QueryResult of type UniProtData.
getResults(Query, UniProtData.ComponentType...) - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtService: Given a Query, return an QueryResult of type UniProtData.
getRnaEditingNote() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.RnaEditingComment: CC -!- RNA EDITING: Modified_positions=x[, y, z][; Note=].
getSampleSources() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Citation
getSampleSources(SampleSourceType) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Citation
getScientificName() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.Organism: Returns the scientific name of this Organism.
getScore() - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.Alignment: The alignment score
getScoreCutoff() - Method in class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastInput: Maximum number of match score summaries to be reported.
getSecondaryOrder() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.dbx.DbDisplayOrder
getSecondaryUniProtAccessions() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry: Returns the list of UniProtAccessions of the UniProtEntry.
getSecondInteractant() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Interaction
getSecondInteractantParent() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Interaction
getSecondInteractor() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Interaction
getSection() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.ProteinDescription: Alternativley to defining the main protein through the getter methods of the recommended, alternative and sub names methods, one can get the main protein as an entire section.
getSeqRange() - Method in class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastInput: The range of the input sequence to use in the blast search.
getSequence() - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.UniParcEntry
getSequence() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.SequenceCautionComment
getSequence() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureLocation
getSequence() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.SplicedIsoform
getSequence() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry: Returns the Sequence annotation in the UniProtEntry.
getSequence() - Method in interface uk.ac.ebi.kraken.interfaces.uniref.member.UniRefRepresentativeMember
getSequence() - Method in class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastInput: The sequence to blast against.
getSequenceFeatures() - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.UniParcEntry
getSequenceIds() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.AlternativeProductsIsoform
getSequenceLength() - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastSummary: The sequence length of the entry.
getSequences(Query) - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcService
getSequenceType() - Method in class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastInput: Indicator of whether the sequence is a protein or RNA/DNA.
getSequenceVersion() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.EntryAudit
getServiceFactoryInstance() - Static method in class uk.ac.ebi.uniprot.dataservice.client.Client: get service factory
getServiceFactoryInstance(Map<String, String>) - Static method in class uk.ac.ebi.uniprot.dataservice.client.Client
getSignatureDBType() - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.SequenceFeature
getSmithWatermanScore() - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.Alignment: Smith-Waterman alignment score.
getSourceOrganism() - Method in interface uk.ac.ebi.kraken.interfaces.uniref.member.UniRefMember
getSources() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.MassSpectrometryComment
getSplicedSequence(String) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry: Returns the actual sequence of the isoform that is passed in as a parameter.
getStart() - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.Location
getStart() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureLocation
getStart() - Method in interface uk.ac.ebi.kraken.interfaces.uniref.member.OverlapRegion
getStartMatchSeq() - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.Alignment: Represents the position of the first amino acid from the sub-sequence, obtained from #getMatchSeq, in relation to the entry's complete sequence
getStartModifier() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureLocation
getStartQuerySeq() - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.Alignment: Represents the position of the first amino acid from the sub-sequence, obtained from #getQuerySeq, in relation to the entry's complete sequence
getStrand() - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.Alignment: Nucleotide sequence strand.
getSubcellularLocationNote() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.SubcellularLocationComment
getSubcellularLocations() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.SubcellularLocationComment
getSubmittedToDatabase() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Submission
getSubNames() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.ProteinDescription: Retrieves a list of sub names for the main protein
getSubstrate() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.MichaelisConstant
getSummary() - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.Hit: The blast related details
getSummary() - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.UniProtHit: The blast related details
getSynonym() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.Organism: Returns the synonym name of this Organism.
getSynonyms() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.AlternativeProductsIsoform
getTaxonomy() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry: Returns the taxonomy annotated in the UniProtEntry.
getTaxonomyId() - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.DatabaseCrossReference
getTemperatureDependence() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.BioPhysicoChemicalPropertiesComment
getTexts() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentFreeText
getTexts() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.HasFreeText
getThird() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.DatabaseCrossReference
getTitle() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Citation
getTopology() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.SubcellularLocation
getType() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.SampleSource
getType() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.ReactionReference
getType() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.SequenceCautionComment
getType() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.description.Field: Returns the type of field
getType() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.evidences.Evidence
getType() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceId
getType() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.Feature
getType() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.Organelle
getType() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry: Returns the type of the UniProtEntry which is UniProtEntryType.SWISSPROT if the entry is annotated as STANDARD in the ID line and UniProtEntryType.TREMBL if it is annotated PRELIMINARY.
getType() - Method in interface uk.ac.ebi.kraken.interfaces.uniref.member.UniRefMember
getType() - Method in interface uk.ac.ebi.kraken.interfaces.uniref.UniRefDatabase
getType() - Method in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.SequenceTypeOption
getType(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniparc.SignatureDBType
getType(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.RnaEditingLocationType
getTypeValue() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceId
getUngaps() - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.Alignment: Percentage of identical bases/residues in the alignment ignoring gaps.
getUniParcAccession() - Method in interface uk.ac.ebi.kraken.interfaces.uniref.member.UniRefMember
getUniParcBlastService() - Method in interface uk.ac.ebi.uniprot.dataservice.client.ServiceFactory
getUniParcId() - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.UniParcEntry
getUniParcQueryService() - Method in interface uk.ac.ebi.uniprot.dataservice.client.ServiceFactory
getUniParcServiceURL() - Method in interface uk.ac.ebi.uniprot.dataservice.client.ClientConfigurator
getUniProtAccession() - Method in interface uk.ac.ebi.kraken.interfaces.go.GoAnnotation
getUniProtAccession() - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.DatabaseCrossReference
getUniProtAccessions() - Method in interface uk.ac.ebi.kraken.interfaces.uniref.member.UniRefMember
getUniProtBlastService() - Method in interface uk.ac.ebi.uniprot.dataservice.client.ServiceFactory
getUniProtDatabaseCrossReferences() - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.UniParcEntry: An immutable list of UniProt (SwissProt or Trembl) database cross references
getUniProtEntries() - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.UniParcEntry: Deprecated.
getUniProtExclusion() - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.UniParcEntry
getUniProtId() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry: Returns the UniProtId of the UniProtEntry.
getUniProtId() - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtData
getUniProtQueryService() - Method in interface uk.ac.ebi.uniprot.dataservice.client.ServiceFactory
getUniProtServiceURL() - Method in interface uk.ac.ebi.uniprot.dataservice.client.ClientConfigurator
getUniRef100EntryId() - Method in interface uk.ac.ebi.kraken.interfaces.uniref.member.UniRefMember
getUniRef50EntryId() - Method in interface uk.ac.ebi.kraken.interfaces.uniref.member.UniRefMember
getUniRef90EntryId() - Method in interface uk.ac.ebi.kraken.interfaces.uniref.member.UniRefMember
getUniRefBlastService() - Method in interface uk.ac.ebi.uniprot.dataservice.client.ServiceFactory
getUniRefDatabase() - Method in interface uk.ac.ebi.kraken.interfaces.uniref.UniRefEntry: Returns the UniRefDatabase.
getUniRefEntryId() - Method in interface uk.ac.ebi.kraken.interfaces.uniref.UniRefEntry: Returns the id of this UniRefEntry.
getUniRefEntryId() - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniref.UniRefComponent
getUniRefEntryName(Query) - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniref.UniRefService: Given a Query, return an QueryResult of type UniRefComponent on UniRefEntryNames, representing the entry name of every UniRef entry hit by the query.
getUniRefQueryService() - Method in interface uk.ac.ebi.uniprot.dataservice.client.ServiceFactory
getUniRefRepresentative(Query) - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniref.UniRefService: Given a Query, return an QueryResult of type UniRefComponent on UniRefRepresentativeMembers, representing the representative member of every UniRef entry hit by the query.
getUniRefServiceURL() - Method in interface uk.ac.ebi.uniprot.dataservice.client.ClientConfigurator
getUniRefVersion() - Method in interface uk.ac.ebi.kraken.interfaces.uniref.UniRefDatabase
getUnit() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.MichaelisConstant
getUpdate() - Method in interface uk.ac.ebi.kraken.interfaces.uniref.UniRefEntry: Returns the last update of this UniRefEntry.
getUpdated() - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.DatabaseCrossReference
getValue() - Method in interface uk.ac.ebi.kraken.interfaces.common.Sequence: Returns the String representation of the amino acid composition of this sequence.
getValue() - Method in interface uk.ac.ebi.kraken.interfaces.common.Value: Get the value of the object (Value)
getValue() - Method in enum class uk.ac.ebi.kraken.interfaces.go.GoCategory
getValue() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationTypeEnum
getValue() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationXrefType
getValue() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.SubmissionDatabase
getValue() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.IsoformSequenceStatus
getValue() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.MassSpectrometryMethod
getValue() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.CommentStatus
getValue() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceType
getValue() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.OntologyType
getValue() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.description.FieldType
getValue() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.description.FlagType
getValue() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.description.NameType
getValue() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCategory
getValue() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
getValue() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureStatus
getValue() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
getValue() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.GeneEncodingType
getValue() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.ProteinExistence
getValue() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntryType
getValue() - Method in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.DropOffOption
getVariantReport() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.VariantFeature
getVariantReports() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.VariantFeature: Deprecated.
getVarsplicIsoforms() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.VarSeqFeature
getVelocity() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.MaximumVelocity
getVelocityStr() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.MaximumVelocity
getVersion() - Method in interface uk.ac.ebi.kraken.interfaces.common.Database
getVersion() - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.DatabaseCrossReference
getVersion() - Method in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.BlastVersionOption
getVolume() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Book
getVolume() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.JournalArticle
getWeight() - Method in enum class uk.ac.ebi.kraken.interfaces.common.MoleculeWeight
getXRefDBDef() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
getXRefDBDef(DatabaseType) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.dbx.DatabaseDefContext
getXrefs(Query) - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtService: Given a Query, return an QueryResult of type UniProtComponent on .uniprot.DatabaseCrossReferences, which represent the results.
getZScore() - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.Alignment: Z-score statistic for the alignment.
GLYCONNECT - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
GLYCOPROTDB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
GLYCOSMOS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
GLYGEN - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
go - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtField.Search
Go - Interface in uk.ac.ebi.kraken.interfaces.uniprot.dbx.go
GO - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
GoAnnotation - Interface in uk.ac.ebi.kraken.interfaces.go
GoAnnotationEvidence - Enum Class in uk.ac.ebi.kraken.interfaces.go
GoCategory - Enum Class in uk.ac.ebi.kraken.interfaces.go
GoDefinition - Interface in uk.ac.ebi.kraken.interfaces.go
GoEcoEvidence - Interface in uk.ac.ebi.kraken.interfaces.go: Represents a GO ECO evidence
GoEvidenceConverter - Interface in uk.ac.ebi.kraken.interfaces.uniprot.dbx.go
GoEvidenceSource - Interface in uk.ac.ebi.kraken.interfaces.uniprot.dbx.go: This code is autogenerated by the class uk.ac.ebi.util.autocode.AutoCoder.
GoEvidenceType - Enum Class in uk.ac.ebi.kraken.interfaces.uniprot.dbx.go
GoId - Interface in uk.ac.ebi.kraken.interfaces.go
GoId - Interface in uk.ac.ebi.kraken.interfaces.uniprot.dbx.go
GOOGLE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
GoProteinContainer - Interface in uk.ac.ebi.kraken.interfaces.go.toprotein: Models the relationship between a UniProt protein and all the GO terms associated to it
goTerm(String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Creates a query to match entries containing the specified Gene Ontology (GO) term.
GoTerm - Interface in uk.ac.ebi.kraken.interfaces.go
GoTerm - Interface in uk.ac.ebi.kraken.interfaces.uniprot.dbx.go
GoTermName - Interface in uk.ac.ebi.kraken.interfaces.go
GRAMENE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
GUIDETOPHARMACOLOGY - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType

H

H - Enum constant in enum class uk.ac.ebi.kraken.interfaces.common.MoleculeWeight
H_InvDB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
h2o - Enum constant in enum class uk.ac.ebi.kraken.interfaces.common.MoleculeWeight
HAMAP - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.SignatureDBType
HAMAP - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
HAMAP_RULE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
hasA(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.description.FlagType: Check whether a value would be a valid value to be turned into FlagType
hasAbsorptionProperty() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.BioPhysicoChemicalPropertiesComment
hasAgricolaId() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationXrefs
hasAlternativeNames() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.ProteinDescription: Verifies whether there exist alternative names for the protein being described
HasAlternativeSequence - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features: Indicates that a Feature in an UniProtEntry can have an alternative sequence (SubSequence).
hasCitationsNew() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry
hasCitationXref() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationXrefs
hasCitationXrefs() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Citation
HasCommentNote - Interface in uk.ac.ebi.kraken.interfaces.uniprot: Created by IntelliJ IDEA.
HasCommentStatus - Interface in uk.ac.ebi.kraken.interfaces.uniprot: Created by IntelliJ IDEA.
hasCommonName() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.Organism: Indicates whether this Organism has a common name.
hasComponent(UniProtData.ComponentType) - Method in interface uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtData
hasDatabaseFTP() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.WebResourceComment
hasDatabaseName() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.WebResourceComment
hasDatabaseNote() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.WebResourceComment
hasDatabaseURL() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.WebResourceComment
HasDate - Interface in uk.ac.ebi.kraken.interfaces.uniprot: This interface is used for all types that have a Date attached.
HasDbAccession - Interface in uk.ac.ebi.kraken.interfaces.uniprot.dbx
hasDefinedDisease() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.DiseaseCommentStructured: Helper method that verifies whether the {link Disease} object has been populated with a defined disease, or if it holds empty state
hasDOI() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationXrefs
HasEvidences - Interface in uk.ac.ebi.kraken.interfaces.uniprot: The superclass of all annotation items in a UniProtEntry, which can be tagged with evidence tags.
HasFeatureDescription - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
hasFeatureId() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.HasFeatureId
HasFeatureId - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features: Indicates that a Feature in an UniProtEntry can have a FeatureId.
HasFeatureStatus - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
hasFourth() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.DatabaseCrossReference
HasFreeText - Interface in uk.ac.ebi.kraken.interfaces.uniprot: HasFreeText interface is for all Free text notes.
hasGapAlign() - Method in class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastInput: Indicator of whether the blast job to perform optimised alignments within regions involving gaps.
hasGeneName() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.Gene: Indicates whether this Gene has a Gene name.
hasGoEvidenceSource() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.Go
hasGoId() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.Go
hasGoTerm() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.Go
hasKineticParameterNote() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.KineticParameters
hasKineticParametersProperty() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.BioPhysicoChemicalPropertiesComment
hasLocation() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.SubcellularLocation
hasMedlineId() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationXrefs: Deprecated.
hasName() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.AlternativeProductsIsoform
hasNextPage() - Method in interface uk.ac.ebi.uniprot.dataservice.client.QueryResultPage
hasNote() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Absorption
hasNote() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.AlternativeProductsIsoform
hasNote() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.MassSpectrometryComment
hasNote() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.SequenceCautionComment
hasOrientation() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.SubcellularLocation
hasPHDependenceProperty() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.BioPhysicoChemicalPropertiesComment
hasPubmedId() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationXrefs
hasRecommendedName() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.ProteinDescription: Verifies whether there exists a recommended name for the protein being described
hasRedoxPotentialProperty() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.BioPhysicoChemicalPropertiesComment
hasSubNames() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.ProteinDescription: Verifies whether there exist sub names for the protein being described
hasSynonym() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.Organism: Indicates whether this Organism has a synonym name.
hasTemperatureDependenceProperty() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.BioPhysicoChemicalPropertiesComment
hasThird() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.DatabaseCrossReference
hasTitle() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Citation
hasTopology() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.SubcellularLocation
hasValue() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.Organelle
HDA - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceType
HELIX - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
HelixFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
HEP - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceType
HGI - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceType
HGNC - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
HGNC - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
Hit<T,S extends BlastSummary> - Interface in uk.ac.ebi.uniprot.dataservice.client.alignment.blast: Container for the blast result of a given entry
hits() - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastResult: An iterable of hits for a given blast request
HMP - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceType
HOGENOM - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
HOMOLOGY - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.ProteinExistence
HPA - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
HSSP - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
HTP - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceType
HYDROGENOSOME - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.GeneEncodingType

I

I - Enum constant in enum class uk.ac.ebi.kraken.interfaces.common.MoleculeWeight
IBA - Enum constant in enum class uk.ac.ebi.kraken.interfaces.go.GoAnnotationEvidence
IBA - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceType
IBD - Enum constant in enum class uk.ac.ebi.kraken.interfaces.go.GoAnnotationEvidence
IBD - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceType
IC - Enum constant in enum class uk.ac.ebi.kraken.interfaces.go.GoAnnotationEvidence
IC - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceType
id - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtField.Search
id - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniref.UniRefField.Search
id(String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcQueryBuilder: Creates a query that searches for entries with the given UniParc identifier
id(String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Creates a query that searches the entry name.
IDA - Enum constant in enum class uk.ac.ebi.kraken.interfaces.go.GoAnnotationEvidence
IDA - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceType
IDEAL - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
identity - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniref.UniRefField.Search
idToChebiReference() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.Ligand
IEA - Enum constant in enum class uk.ac.ebi.kraken.interfaces.go.GoAnnotationEvidence
IEA - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceType
IEP - Enum constant in enum class uk.ac.ebi.kraken.interfaces.go.GoAnnotationEvidence
IEP - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceType
IGC - Enum constant in enum class uk.ac.ebi.kraken.interfaces.go.GoAnnotationEvidence
IGC - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceType
IGI - Enum constant in enum class uk.ac.ebi.kraken.interfaces.go.GoAnnotationEvidence
IGI - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceType
IKR - Enum constant in enum class uk.ac.ebi.kraken.interfaces.go.GoAnnotationEvidence
IKR - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceType
IMGT_GENE_DB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
IMP - Enum constant in enum class uk.ac.ebi.kraken.interfaces.go.GoAnnotationEvidence
IMP - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceType
implementsInterface(Class<?>) - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationTypeEnum
IMPORT - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCategory
IMPORT - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
IMR - Enum constant in enum class uk.ac.ebi.kraken.interfaces.go.GoAnnotationEvidence
INCLUDE_ISOFORM - Static variable in class uk.ac.ebi.uniprot.dataservice.client.ClientConstant
INDUCTION - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType
InductionComment - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
INIT_MET - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType: Enumerates all features types in UniProt.
InitMetFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
INN - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.description.FieldType
INPARANOID - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
Institute - Interface in uk.ac.ebi.kraken.interfaces.uniprot.citationsNew
INTACT - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
Interaction - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
INTERACTION - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType
InteractionComment - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
InteractionGeneName - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
InteractionType - Enum Class in uk.ac.ebi.kraken.interfaces.uniprot.comments
InteractorAccession - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
InteractorUniProtId - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
INTERPRO - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
INTRAMEM - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
IntramemFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
IPI - Enum constant in enum class uk.ac.ebi.kraken.interfaces.go.GoAnnotationEvidence
IPI - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
IPI - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceType
IPTMNET - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
IRD - Enum constant in enum class uk.ac.ebi.kraken.interfaces.go.GoAnnotationEvidence
IRD - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceType
is_isoform - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtField.Search
ISA - Enum constant in enum class uk.ac.ebi.kraken.interfaces.go.GoAnnotationEvidence
ISA - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceType
isActive() - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.DatabaseCrossReference
isAlive() - Method in interface uk.ac.ebi.kraken.interfaces.common.Database
isApproximation() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Absorption
isAsserted() - Method in interface uk.ac.ebi.kraken.interfaces.go.toprotein.AssertedGoAnnotation: Indicates whether the GO annotation belonging to the protein was asserted or inferred
isEmpty() - Method in interface uk.ac.ebi.uniprot.dataservice.query.Query
isEndAvailable() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureLocation
isEverything() - Method in interface uk.ac.ebi.uniprot.dataservice.query.Query
isFragment() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry: This convienience method is used to test to see if the UniProtKB entry is a fragment or fragments.
isIsoform() - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.UniProtBlastSummary: Indicates whether the hit entry is an isoform or not
ISM - Enum constant in enum class uk.ac.ebi.kraken.interfaces.go.GoAnnotationEvidence
ISM - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceType
ISO - Enum constant in enum class uk.ac.ebi.kraken.interfaces.go.GoAnnotationEvidence
ISO - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceType
IsoformId - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
IsoformName - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
IsoformNote - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
isoformOnly() - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Search in the isoform entry only.
IsoformSequenceId - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
IsoformSequenceStatus - Enum Class in uk.ac.ebi.kraken.interfaces.uniprot.comments: User: mkleen@ebi.ac.uk Date: 28-Nov-2005 Time: 11:24:21
IsoformSynonym - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
ISS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.go.GoAnnotationEvidence
ISS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceType
isSeed() - Method in interface uk.ac.ebi.kraken.interfaces.uniref.member.UniRefMember
isStartAvailable() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureLocation
isStarted() - Method in interface uk.ac.ebi.uniprot.dataservice.client.Service: Deprecated.

J

JapiService<T> - Interface in uk.ac.ebi.uniprot.dataservice.client.service
JAPONICUSDB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
JAPONICUSDB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
JOURNAL_ARTICLE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationTypeEnum
JournalArticle - Interface in uk.ac.ebi.kraken.interfaces.uniprot.citationsNew: The RL line for a journal citation includes the journal abbreviation, the volume number, the page range and the year.
JournalName - Interface in uk.ac.ebi.kraken.interfaces.uniprot.citationsNew
JPO - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
JPOST - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
JSON_MEDIA_TYPE_VALUE - Static variable in class uk.ac.ebi.uniprot.dataservice.client.ClientConstant
JsonAbstractUniRefEntry - Class in uk.ac.ebi.uniprot.dataservice.client.uniref
JsonAbstractUniRefEntry() - Constructor for class uk.ac.ebi.uniprot.dataservice.client.uniref.JsonAbstractUniRefEntry
JsonMember - Class in uk.ac.ebi.uniprot.dataservice.client.uniref
JsonMember() - Constructor for class uk.ac.ebi.uniprot.dataservice.client.uniref.JsonMember
JsonOverlapRegion - Class in uk.ac.ebi.uniprot.dataservice.client.uniref
JsonOverlapRegion() - Constructor for class uk.ac.ebi.uniprot.dataservice.client.uniref.JsonOverlapRegion
JsonRepMember - Class in uk.ac.ebi.uniprot.dataservice.client.uniref
JsonRepMember() - Constructor for class uk.ac.ebi.uniprot.dataservice.client.uniref.JsonRepMember
JsonSequence - Class in uk.ac.ebi.uniprot.dataservice.client.uniref
JsonSequence() - Constructor for class uk.ac.ebi.uniprot.dataservice.client.uniref.JsonSequence
JsonTaxonomy - Class in uk.ac.ebi.uniprot.dataservice.client.uniref
JsonTaxonomy() - Constructor for class uk.ac.ebi.uniprot.dataservice.client.uniref.JsonTaxonomy
JsonUniRefEntry - Class in uk.ac.ebi.uniprot.dataservice.client.uniref
JsonUniRefEntry() - Constructor for class uk.ac.ebi.uniprot.dataservice.client.uniref.JsonUniRefEntry
JsonUniRefEntryLight - Class in uk.ac.ebi.uniprot.dataservice.client.uniref
JsonUniRefEntryLight() - Constructor for class uk.ac.ebi.uniprot.dataservice.client.uniref.JsonUniRefEntryLight
JsonUniRefEntryLightResult - Class in uk.ac.ebi.uniprot.dataservice.client.uniref
JsonUniRefEntryLightResult() - Constructor for class uk.ac.ebi.uniprot.dataservice.client.uniref.JsonUniRefEntryLightResult

K

K - Enum constant in enum class uk.ac.ebi.kraken.interfaces.common.MoleculeWeight
KEGG - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
keyword - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtField.Search
keyword(String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Creates a query that matches entries containing the specified keyword, e.g., "kinase".
Keyword - Interface in uk.ac.ebi.kraken.interfaces.uniprot: A single Keyword in the Keyword annotation of the UniProtEntry.
KEYWORDS - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtData.ComponentType
KineticParameterNote - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
KineticParameters - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
KIPO - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
Known - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.RnaEditingLocationType
KO - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType

L

L - Enum constant in enum class uk.ac.ebi.kraken.interfaces.common.MoleculeWeight
LEFT_TO_RIGHT - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.PhysiologicalDirectionType
LEGIOLIST - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
length - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcField.Search
length - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtField.Search
LEPROMA - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
Ligand - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
LigandPart - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
LIPID - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
LipidFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
lit_author - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtField.Search
lit_pubdate - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtField.SearchDate
lit_pubmed - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtField.Search
lit_title - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtField.Search
Location - Interface in uk.ac.ebi.kraken.interfaces.uniparc
Locator - Interface in uk.ac.ebi.kraken.interfaces.uniprot.citationsNew
LSI - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.MassSpectrometryMethod

M

M - Enum constant in enum class uk.ac.ebi.kraken.interfaces.common.MoleculeWeight
MAIZEGDB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
MAIZEGDB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
MALACARDS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
MALDI - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.MassSpectrometryMethod
MANE_SELECT - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
mass - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtField.Search
MASS_SPECTROMETRY - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType
MASSIVE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
MassSpectrometryComment - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
MassSpectrometryCommentNote - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
MassSpectrometryCommentSource - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments: Created by mkleen@ebi.ac.uk Date: 14-Sep-2007 Time: 15:02:43
MassSpectrometryMethod - Enum Class in uk.ac.ebi.kraken.interfaces.uniprot.comments
MassSpectrometryRangeNote - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
MATCH_SCORES - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastParameter
MATRIX - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastParameter
MatrixOption - Enum Class in uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input: Enumeration for all possible selections for similarity matrizes used for the BLAST service.
MAXIMUM_SIZE - Static variable in class uk.ac.ebi.uniprot.dataservice.client.ClientConstant
MAXIMUM_SIZE_NAME - Static variable in class uk.ac.ebi.uniprot.dataservice.client.ClientConstant
MaximumVelocity - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
MaxQB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
MAXQB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType: Deprecated.
MaxVelocityUnit - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
MEDLINE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationXrefType
MedlineId - Interface in uk.ac.ebi.kraken.interfaces.uniprot.citationsNew
MemberId - Interface in uk.ac.ebi.kraken.interfaces.uniref.member: Created by IntelliJ IDEA.
memberTaxonId(int) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniref.UniRefQueryBuilder
MEROPS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
METOSITE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
MG_ML - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.MichaelisConstantUnit
MG_ML_2 - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.MichaelisConstantUnit
MGI - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
MGI - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
MGNIFY - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
MGNIFY - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
MichaelisConstant - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
MichaelisConstantUnit - Enum Class in uk.ac.ebi.kraken.interfaces.uniprot.comments
MICRO_MOL - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.MichaelisConstantUnit
MICROBODY - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.TransitType
MILLI_MOL - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.MichaelisConstantUnit
MIM - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.DiseaseReferenceType
MIM - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
MIM - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
MINT - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
MISCELLANEOUS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType
MISCELLANEOUS_DATABASES - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseCategory
MISCELLANEOUS_DISCREPANCY - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.SequenceCautionType
MiscellaneousComment - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
MITOCHONDRION - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.TransitType
MITOCHONDRION - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.GeneEncodingType
MobiDB_lite - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
MOBIDB_LITE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
MOD_RES - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
ModResFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features: MOD_RES - Posttranslational modification of a residue.
MOL - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.MichaelisConstantUnit
MoleculeWeight - Enum Class in uk.ac.ebi.kraken.interfaces.common
MOONDB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
MOONPROT - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
MOTIF - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
MotifFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
MUTAGEN - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
MutagenFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features: MUTAGEN - Site which has been experimentally altered.
MutagenReport - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
MYCOCLAP - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType: Deprecated.

N

N - Enum constant in enum class uk.ac.ebi.kraken.interfaces.common.MoleculeWeight
name - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniref.UniRefField.Search
Name - Interface in uk.ac.ebi.kraken.interfaces.uniprot.description: Maps the Names of a protein in a DE line : RecName, AltName, SubName

As an example:
NameType - Enum Class in uk.ac.ebi.kraken.interfaces.uniprot.description: Conatins a list of acceptable values for the categories expressed in a DE line
NANO_MOL - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.MichaelisConstantUnit
NAS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.go.GoAnnotationEvidence
NAS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceType
NCBIFAM - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
NCBIFAM - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.SignatureDBType
NCBIFAM - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
NCBIFAM - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
NCBIFAM_RULE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
NcbiTaxon - Interface in uk.ac.ebi.kraken.interfaces.uniprot: Encapsulates a single taxon in the taxonomy annotation of the UniProtEntry.
NCBITaxonomy - Interface in uk.ac.ebi.kraken.interfaces.uniref.member
NcbiTaxonomyId - Interface in uk.ac.ebi.kraken.interfaces.uniprot
ND - Enum constant in enum class uk.ac.ebi.kraken.interfaces.go.GoAnnotationEvidence
ND - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceType
NewtTaxon - Interface in uk.ac.ebi.kraken.interfaces.common: Defines a Taxon as represented in the NEWT database.
NEXTPROT - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
NIAGADS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
NO - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.FilterOption
NON_CONS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
NON_PHOTOSYNTHETIC_PLASTID - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.GeneEncodingType
NON_STD - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
NON_TER - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
NonConsFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
NONE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CofactorReferenceType
NONE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.DiseaseReferenceType
NONE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.CommentStatus
NONE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureStatus
NonStandardAAFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
NonTerFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features: NON_TER - The residue at an extremity of the sequence is not the terminal residue.
NORMALIZED_UNIT - Static variable in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.MichaelisConstant
not() - Method in interface uk.ac.ebi.uniprot.dataservice.query.Query
not(UniParcField.Search, String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcQueryBuilder: Creates a query where the search field does not match the value specification.
not(UniProtField.Search, String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Creates a query where the search field does not match the value specification.
not(UniRefField.Search, String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniref.UniRefQueryBuilder: Creates a query where the search field does not match the value specification.
Not_applicable - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.RnaEditingLocationType
NOT_DESCRIBED - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.IsoformSequenceStatus
NOT_SPECIFIED - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCategory
NOT_SPECIFIED - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCode
NOT_SPECIFIED - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
NR - Enum constant in enum class uk.ac.ebi.kraken.interfaces.go.GoAnnotationEvidence
NUCLEOMORPH - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.GeneEncodingType

O

O - Enum constant in enum class uk.ac.ebi.kraken.interfaces.common.MoleculeWeight
OGP - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
OMA - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
ONE - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.ExpectationOption
ONE_EXPONENT_MINUS_FIFTY - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.ExpectationOption
ONE_EXPONENT_MINUS_FIVE - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.ExpectationOption
ONE_EXPONENT_MINUS_FOUR - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.ExpectationOption
ONE_EXPONENT_MINUS_ONE - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.ExpectationOption
ONE_EXPONENT_MINUS_ONE_HUNDRED - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.ExpectationOption
ONE_EXPONENT_MINUS_TEN - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.ExpectationOption
ONE_EXPONENT_MINUS_THREE - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.ExpectationOption
ONE_EXPONENT_MINUS_TWO - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.ExpectationOption
ONE_EXPONENT_MINUS_TWO_HUNDRED - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.ExpectationOption
ONE_HUNDRED - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.AlignmentCutoffOption
ONE_HUNDRED - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.ExpectationOption
ONE_HUNDRED - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.ScoreCutoffOption
ONE_HUNDRED_FIFTY - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.AlignmentCutoffOption
ONE_HUNDRED_FIFTY - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.ScoreCutoffOption
ONE_THOUSAND - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.AlignmentCutoffOption
ONE_THOUSAND - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.ExpectationOption
ONE_THOUSAND - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.ScoreCutoffOption
ONLINE_INFORMATION_XMLTAG - Static variable in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.WebResourceComment
OntologyType - Enum Class in uk.ac.ebi.kraken.interfaces.uniprot.dbx.go
OPENTARGETS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
OPINION - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
or(Query) - Method in interface uk.ac.ebi.uniprot.dataservice.query.Query
or(Query...) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcQueryBuilder: The Query composition of the specified subQueries using 'or'.
or(Query...) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: The Query composition of the specified subQueries using 'or'.
or(Query...) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniref.UniRefQueryBuilder: The Query composition of the specified subQueries using 'or'.
or(Query[]) - Method in interface uk.ac.ebi.uniprot.dataservice.query.QueryFactory: The Query composition of the specified subQueries using 'or'.
OrderedLocusName - Interface in uk.ac.ebi.kraken.interfaces.uniprot.genename: About This Data Structure
ORFName - Interface in uk.ac.ebi.kraken.interfaces.uniprot.genename: About This Data Structure
organelle - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtField.Search
organelle(String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Creates an organelle based query that will return proteins whose organelle line matches the search terms
Organelle - Interface in uk.ac.ebi.kraken.interfaces.uniprot: Encapsulates a single gene coding of the UniProtEntry.
Organism - Interface in uk.ac.ebi.kraken.interfaces.uniprot: About This Data Structure
organism_id - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtField.Search
organism_name - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtField.Search
ORGANISM_SPECIFIC_DATABASES - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseCategory
OrganismCommonName - Interface in uk.ac.ebi.kraken.interfaces.uniprot.organism: About This Data Structure
OrganismHost - Interface in uk.ac.ebi.kraken.interfaces.uniprot: Interface to an Organism Host used in an UniProtKB entry.
organismHostName(String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Creates a search query that will look for virus proteins that are present in the host being searched.
organismName(String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcQueryBuilder: Creates a query that searches for UniParc entries that contain within their database cross-references the given organism name.
organismName(String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Create a query that returns proteins related to a species that contains the given organism name.
organismName(String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniref.UniRefQueryBuilder: Creates a query that searches for UniRef clusters holding members that contain the given organism name.
OrganismName - Interface in uk.ac.ebi.kraken.interfaces.uniprot.organism: About This Data Structure
OrganismScientificName - Interface in uk.ac.ebi.kraken.interfaces.uniprot.organism: About This Data Structure
OrganismSynonym - Interface in uk.ac.ebi.kraken.interfaces.uniprot.organism: About This Data Structure
ORPHANET - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
ORTHODB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
OTHER - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.CommentStatus
OTHER - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureStatus
OUTSIDE_KNOWN_SEQUENCE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureLocationModifier
OverlapRegion - Interface in uk.ac.ebi.kraken.interfaces.uniref.member

P

P - Enum constant in enum class uk.ac.ebi.kraken.interfaces.common.MoleculeWeight
P - Enum constant in enum class uk.ac.ebi.kraken.interfaces.go.GoCategory
P - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.OntologyType
Page - Interface in uk.ac.ebi.kraken.interfaces.uniprot.citationsNew
PAGE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType: Deprecated.
PAGE_BEGINNING - Static variable in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.PAGEDataComment: Constants for the miscellaneous comment representing the PAGE data string
PAGE_END - Static variable in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.PAGEDataComment
PAGE_MIDDLE - Static variable in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.PAGEDataComment
PAGEDataComment - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments: Created by IntelliJ IDEA.
PAGEDataMolecularWeight - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
PAGEDataPl - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
PAM_250 - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.MatrixOption
PAM_30 - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.MatrixOption
PAM_70 - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.MatrixOption
PANTHER - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.SignatureDBType
PANTHER - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
parseGoEvidenceType(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceType
parseOntologyType(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.OntologyType
Patent - Interface in uk.ac.ebi.kraken.interfaces.uniprot.citationsNew: Created by IntelliJ IDEA.
PATENT - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationTypeEnum
PatentNumber - Interface in uk.ac.ebi.kraken.interfaces.uniprot.citationsNew
PATHWAY - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType
PathwayComment - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
PATHWAYCOMMONS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
PATRIC - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
PATRIC - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
PAXDB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
PCDDB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
PDB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
PDB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.SubmissionDatabase
PDB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
PDB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
PDBSUM - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
PEPTIDE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
PeptideAtlas - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
PEPTIDEATLAS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
PeptideFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
PEROXIBASE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
PFAM - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.SignatureDBType
PFAM - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
PFAM - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
PHARMACEUTICAL - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType
PharmaceuticalComment - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
PHARMGKB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
PHAROS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
PHDependence - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
PHI_BASE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
PHOSPHOSITEPLUS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
PHYLOGENOMIC_DATABASES - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseCategory
PHYLOMEDB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
PhysiologicalDirectionType - Enum Class in uk.ac.ebi.kraken.interfaces.uniprot.comments
PhysiologicalReaction - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
PIR - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
PIR - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.SubmissionDatabase
PIR - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
PIR - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
PIRARC - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
PIRNR - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
PIRSF - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.SignatureDBType
PIRSF - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
PIRSR - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
PLANTREACTOME - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
PLASMA_DESORPTION - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.MassSpectrometryMethod
PLASMID - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.SampleSourceType
PLASMID - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.GeneEncodingType
PLASTID - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.GeneEncodingType
PMAPCUTDB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
POLYMORPHISM - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType
PolymorphismComment - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
PomBase - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
POMBASE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
POMBASE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
Position - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments: Created by IntelliJ IDEA.
POSITIONS_PREFIX - Static variable in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.RnaEditingComment
POTENTIAL - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.CommentStatus
POTENTIAL - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureStatus
PRECURSOR - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.description.FlagType
PREDICTED - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.ProteinExistence
PRF - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
PRIDE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
PrimaryUniProtAccession - Interface in uk.ac.ebi.kraken.interfaces.uniprot: The primary UniProtAccession of a UniProtEntry.
PRINTS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.SignatureDBType
PRINTS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
PRO - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
PROBABLE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.CommentStatus
PROBABLE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureStatus
PRODOM - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.SignatureDBType
PRODOM - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
PROGRAM - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastParameter
PROGRAMME - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCategory
PROMEX - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
PROPEP - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
ProPepFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
PROSITE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.SignatureDBType
PROSITE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
PROSITE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
PROSITE_PRORULE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
PROTCHANGE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
PROTCLUSTDB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
protein - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcField.Search
PROTEIN - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.SequenceTypeOption
PROTEIN_FAMILY_GROUP_DATABASES - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseCategory
PROTEIN_LEVEL - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.ProteinExistence
protein_name - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtField.Search
PROTEIN_NAMES - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtData.ComponentType
PROTEIN_PROTEIN_INTERACTION_DATABASES - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseCategory
ProteinDescription - Interface in uk.ac.ebi.kraken.interfaces.uniprot: The description annotation of the UniProtEntry.
proteinExistence(ProteinExistence) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Creates a query that matches entries containing the specified protein existence.
ProteinExistence - Enum Class in uk.ac.ebi.kraken.interfaces.uniprot: User: Emilio Salazar Date: 25-Jun-2007
PROTEINMODELPORTAL - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
proteinName(String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcQueryBuilder: Creates a query that searches for UniParc entries that contain within their database cross-references the given protein name.
proteinName(String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Creates a query that searches for the given name within the protein name block.
ProteinName - Interface in uk.ac.ebi.kraken.interfaces.uniref.member
proteomecomponent - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcField.Search
PROTEOMES - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
PROTEOMES - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
PROTEOMIC_DATABASES - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseCategory
Proteomics - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
ProteomicsDB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
PROTEOMICSDB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
PROTIMP - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
PROTOCOLS_AND_MATERIALS_DATABASES - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseCategory
PSEUDOCAP - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
PSEUDOCAP - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
PTM - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType
PTM_DATABASES - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseCategory
PtmComment - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
PublicationDate - Interface in uk.ac.ebi.kraken.interfaces.uniprot.citationsNew
Publisher - Interface in uk.ac.ebi.kraken.interfaces.uniprot.citationsNew
pubmed(String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Creates a query that matches entries containing a reference with the specified PubMed ID
PUBMED - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationXrefType
PUBMED - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
PubMedId - Interface in uk.ac.ebi.kraken.interfaces.uniprot.citationsNew
PUMBA - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType

Q

Q - Enum constant in enum class uk.ac.ebi.kraken.interfaces.common.MoleculeWeight
query(UniParcField.Search, String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcQueryBuilder: Creates a simple query on the specified search field, based on some input text.
query(UniProtField.Search, String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Creates a simple query on the specified search field, based on some input text.
query(UniRefField.Search, String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniref.UniRefQueryBuilder: Creates a simple query on the specified search field, based on some input text.
Query - Interface in uk.ac.ebi.uniprot.dataservice.query: Basic interface specifying the creation of logical queries.
QUERY - Static variable in class uk.ac.ebi.uniprot.dataservice.client.ClientConstant
QueryFactory - Interface in uk.ac.ebi.uniprot.dataservice.query: The factory provide a set of interfaces to create Query
QueryResult<T> - Interface in uk.ac.ebi.uniprot.dataservice.client
QueryResultPage<T> - Interface in uk.ac.ebi.uniprot.dataservice.client
QuerySpec - Enum Class in uk.ac.ebi.uniprot.dataservice.client.uniprot: Created 12/01/2016
QueryUtil - Class in uk.ac.ebi.uniprot.dataservice.query
QueryUtil() - Constructor for class uk.ac.ebi.uniprot.dataservice.query.QueryUtil

R

R - Enum constant in enum class uk.ac.ebi.kraken.interfaces.common.MoleculeWeight
R - Enum constant in enum class uk.ac.ebi.kraken.interfaces.go.GoCategory
RCA - Enum constant in enum class uk.ac.ebi.kraken.interfaces.go.GoAnnotationEvidence
RCA - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceType
Reaction - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
ReactionReference - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
ReactionReferenceType - Enum Class in uk.ac.ebi.kraken.interfaces.uniprot.comments
REACTOME - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
readEntry(InputStream) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniref.converter.RefSeqJsonReader
readEntryLight(InputStream) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniref.converter.RefSeqJsonReader
REBASE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
RECNAME - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.description.NameType
RedoxPotential - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
REFERENCE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
RefSeq - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
REFSEQ - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
REFSEQ - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
RefSeqJsonReader - Class in uk.ac.ebi.uniprot.dataservice.client.uniref.converter
RefSeqJsonReader() - Constructor for class uk.ac.ebi.uniprot.dataservice.client.uniref.converter.RefSeqJsonReader
REGION - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
RegionFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
REMTREMBL - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
REPEAT - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
RepeatFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
ReportFromCitation - Class in uk.ac.ebi.kraken.interfaces.uniprot.features
ReportFromCitation() - Constructor for class uk.ac.ebi.kraken.interfaces.uniprot.features.ReportFromCitation
representativeAccession(String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniref.UniRefQueryBuilder
representativeId(String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniref.UniRefQueryBuilder
REPRODUCTION2DPAGE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
Request - Interface in uk.ac.ebi.uniprot.dataservice.client
Response<T> - Interface in uk.ac.ebi.uniprot.dataservice.client
reviewed - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtField.Search
reviewed(Query, boolean) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Create a query that further refines an existing query to contained only SwissProt entries or TrEMBL entries.
RGD - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
RGD - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
RHEA - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.ReactionReferenceType
RIGHT_TO_LEFT - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.PhysiologicalDirectionType
RNA_EDITING - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType
RNACT - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
RnaEditingComment - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments: CC -!- RNA EDITING: Modified_positions=x[, y, z][; Note=].
RnaEditingLocationType - Enum Class in uk.ac.ebi.kraken.interfaces.uniprot.comments: Created by IntelliJ IDEA.
RnaEditingNote - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments: Created by mkleen@ebi.ac.uk Date: 22-Oct-2007 Time: 17:02:33
RULEBASE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
runBlast(BlastInput) - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastService: Returns the jobId for a job that has been submitted.
runBlast(BlastInput) - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.UniParcBlastService: Returns the jobId for a job that has been submitted.
runBlast(BlastInput) - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.UniProtBlastService: Returns the jobId for a job that has been submitted.
runBlast(BlastInput) - Method in interface uk.ac.ebi.uniprot.dataservice.client.alignment.blast.UniRefBlastService: Returns the jobId for a job that has been submitted.

S

S - Enum constant in enum class uk.ac.ebi.kraken.interfaces.common.MoleculeWeight
SAAS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
SABIORK - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
SAM - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
SampleSource - Interface in uk.ac.ebi.kraken.interfaces.uniprot.citationsNew: Created by IntelliJ IDEA.
SampleSourceType - Enum Class in uk.ac.ebi.kraken.interfaces.uniprot.citationsNew: Created by IntelliJ IDEA.
SASBDB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
ScoreCutoffOption - Enum Class in uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input: Maximum number of match alignments reported in the result output.
SCORES - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastParameter
SEARCH - Static variable in class uk.ac.ebi.uniprot.dataservice.client.ClientConstant
sec_acc - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtField.Search
secondaryAccession(String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Creates a query on a UniProt seocnd accession.
SecondaryUniProtAccession - Interface in uk.ac.ebi.kraken.interfaces.uniprot: A secondary UniProtAccession of a UniProtEntry.
Section - Interface in uk.ac.ebi.kraken.interfaces.uniprot.description: Contains a list of all names, and respective fields, that compose a protein within the DE line.
SEED - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
SELDI - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.MassSpectrometryMethod
SELF - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.InteractionType
seqLength(int) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcQueryBuilder
seqLength(int) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder
seqLengthRange(int, int) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcQueryBuilder
seqLengthRange(int, int) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder
SEQRANGE - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastParameter
Sequence - Interface in uk.ac.ebi.kraken.interfaces.common: Encapsulates a protein sequence, in particular the sequence annotation in the UniProtEntry and UniParcEntry.
SEQUENCE - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastParameter
SEQUENCE_ANALAYSIS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
SEQUENCE_CAUTION - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType
SEQUENCE_DATABASES - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseCategory
SequenceCautionComment - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments: User: Emilio Salazar Date: 14-May-2007
SequenceCautionCommentNote - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments: User: Emilio Salazar Date: 14-May-2007
SequenceCautionType - Enum Class in uk.ac.ebi.kraken.interfaces.uniprot.comments: User: Emilio Salazar Date: 14-May-2007
SequenceFeature - Interface in uk.ac.ebi.kraken.interfaces.uniparc
SequenceTypeOption - Enum Class in uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input: Indicate whether the sequence to blast is from DNA/RNA or a protein.
SERVER_URL_BASE - Static variable in class uk.ac.ebi.uniprot.dataservice.client.ClientConstant
Service - Interface in uk.ac.ebi.uniprot.dataservice.client: Basic service specification.
ServiceException - Exception in uk.ac.ebi.uniprot.dataservice.client.exception
ServiceException() - Constructor for exception uk.ac.ebi.uniprot.dataservice.client.exception.ServiceException
ServiceException(String) - Constructor for exception uk.ac.ebi.uniprot.dataservice.client.exception.ServiceException
ServiceException(String, Throwable) - Constructor for exception uk.ac.ebi.uniprot.dataservice.client.exception.ServiceException
ServiceException(Throwable) - Constructor for exception uk.ac.ebi.uniprot.dataservice.client.exception.ServiceException
ServiceFactory - Interface in uk.ac.ebi.uniprot.dataservice.client: Factory specification for creating the different UniProtKB services.
setAbsorption(Absorption) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.BioPhysicoChemicalPropertiesComment
setAccession(String) - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.DatabaseCrossReference
setActive(boolean) - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.DatabaseCrossReference
setAgricolaId(String) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationXrefs
setAgricolaId(AgricolaId) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationXrefs
setAlive(boolean) - Method in interface uk.ac.ebi.kraken.interfaces.common.Database
setAlternativeNames(List<Name>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.ProteinDescription: Sets the alternative names of the main protein within the DE line
setAlternativeSequences(List<FeatureSequence>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.HasAlternativeSequence
setApproximation(boolean) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Absorption
setAttribute(EvidenceAttribute) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.evidences.Evidence
setAuthoringGroup(List<AuthoringGroup>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Citation
setAuthors(List<Author>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Citation
setBookName(BookName) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Book
setCategory(EvidenceCategory) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.evidences.Evidence
setChain(String) - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.DatabaseCrossReference
setCitationsNew(List<Citation>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry
setCitationSummary(List<CitationSummary>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Citation
setCitationSummary(CitationSummary) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Citation
setCitationsXrefs(CitationXrefs) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Citation
setCity(City) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Book
setCity(City) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Thesis
setClustrEntries(Set<ClustrEntry>) - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.UniParcEntry: Deprecated.
setCofactorReference(CofactorReference) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Cofactor
setCofactorReferenceType(CofactorReferenceType) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.CofactorReference
setCofactors(List<Cofactor>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.CofactorCommentStructured
setComment(AlternativeProductsCommentComment) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.AlternativeProductsComment
setComments(Collection<Comment>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry
setCommentStatus(CommentStatus) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.HasCommentStatus
setCommentType(CommentType) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Comment
setCommonName(OrganismCommonName) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.Organism: Sets the common name of this Organism.
setConflictReports(List<ConflictReport>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.ConflictFeature
setConstant(float) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.MichaelisConstant
setConstantStr(String) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.MichaelisConstant
setContains(List<Section>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.ProteinDescription: Sets a list of proteins for the contains section of the DE line
setCountry(Country) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Thesis
setCRC64(String) - Method in interface uk.ac.ebi.kraken.interfaces.common.Sequence: Sets the crc64 hashcode of this sequence to a given value.
setCreated(Date) - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.DatabaseCrossReference
setCreationDate(Date) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.EntryAudit: Deprecated.
setDatabase(Database) - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.DatabaseCrossReference
setDatabaseCrossReferences(List<DatabaseCrossReference>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry: Sets the DatabaseCrossReference annotation of the UniProtEntry to a given list of DatabaseCrossReference values.
setDatabaseCrossReferences(Set<DatabaseCrossReference>) - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.UniParcEntry
setDatabaseFTP(DatabaseFTP) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.WebResourceComment
setDatabaseName(DatabaseName) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.WebResourceComment
setDatabaseNote(DatabaseNote) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.WebResourceComment
setDatabaseURL(DatabaseURL) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.WebResourceComment
setDate(Calendar) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.HasDate: Sets the date associated to the type to the one defined in a given Calendar.
setDate(Date) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.evidences.Evidence
setDbId(String) - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.SequenceFeature
setDescription(DatabaseAttribute) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.DatabaseCrossReference
setDirectionType(PhysiologicalDirectionType) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.PhysiologicalReaction
setDisease(Disease) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.DiseaseCommentStructured
setDiseaseAcronym(DiseaseAcronym) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Disease
setDiseaseDescription(DiseaseDescription) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Disease
setDiseaseId(DiseaseId) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Disease
setDiseaseReference(DiseaseReference) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Disease
setDiseaseReferenceId(DiseaseReferenceId) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.DiseaseReference
setDiseaseReferenceType(DiseaseReferenceType) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.DiseaseReference
setDOI(String) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationXrefs
setDOI(DOI) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationXrefs
setDomain(Domain) - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.SequenceFeature
setECNumber(String) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Reaction
setEditors(List<Editor>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Book
setEnd(int) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureLocation
setEndModifier(FeatureLocationModifier) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureLocation
setEntryAudit(EntryAudit) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry
setEntryVersion(int) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.EntryAudit
setEnzyme(Enzyme) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.MaximumVelocity
setEvents(List<AlternativeProductsEvent>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.AlternativeProductsComment
setEvidence(GoAnnotationEvidence) - Method in interface uk.ac.ebi.kraken.interfaces.go.GoAnnotation: Deprecated.
setEvidenceCode(EvidenceCode) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.evidences.Evidence
setEvidenceId(EvidenceId) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.evidences.Evidence
setEvidenceIds(List<EvidenceId>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Citation
setEvidenceIds(List<EvidenceId>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.HasEvidences: Sets the EvidenceIds of the EvidenceTagable object to a given list of values.
setEvidences(List<Evidence>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry: Sets the Evidence annotation of the UniProtEntry to a given list of Evidences.
setExtraTaxonomyIds(List<Integer>) - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.DatabaseCrossReference
setFeatureDescription(FeatureDescription) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.HasFeatureDescription
setFeatureId(FeatureId) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.HasFeatureId
setFeatureLocation(FeatureLocation) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.Feature
setFeatures(Collection<Feature>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry
setFeatures(List<Feature>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry
setFeatureStatus(FeatureStatus) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.HasFeatureStatus
setFields(List<Field>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.description.Name: Set the fields for the current name
setFirstInteractant(InteractorUniProtId) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Interaction
setFirstInteractor(InteractorAccession) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Interaction
setFirstPage(Page) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Book
setFirstPage(Page) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.JournalArticle
setFirstPublicDate(Date) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.EntryAudit
setFlags(List<Flag>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.ProteinDescription: Sets the list of flags for the current DE line
setFlagType(FlagType) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.description.Flag
setFourth(DatabaseAttribute) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.DatabaseCrossReference
setFullName(String) - Method in interface uk.ac.ebi.kraken.interfaces.common.Database
setGeneName(String) - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.DatabaseCrossReference
setGeneName(GeneName) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.Gene: Sets the Gene Name of this Gene.
setGeneNameSynonyms(List<GeneNameSynonym>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.Gene: Sets the List of Gene Name Synonyms of this Gene.
setGenes(List<Gene>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry: Sets the Genes in which this protein is encoded.
setGiNumber(String) - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.DatabaseCrossReference
setGoCategory(GoCategory) - Method in interface uk.ac.ebi.kraken.interfaces.go.GoTerm
setGoEcoEvidence(GoEcoEvidence) - Method in interface uk.ac.ebi.kraken.interfaces.go.GoAnnotation
setGoId(GoId) - Method in interface uk.ac.ebi.kraken.interfaces.go.GoDefinition
setGoId(GoId) - Method in interface uk.ac.ebi.kraken.interfaces.go.GoTerm
setGoTerm(GoTerm) - Method in interface uk.ac.ebi.kraken.interfaces.go.GoAnnotation
setGoTermName(GoTermName) - Method in interface uk.ac.ebi.kraken.interfaces.go.GoTerm
setHexadecimalValue(int) - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.UniParcId
setId(String) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.ReactionReference
setId(String) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.Ligand
setIds(List<IsoformId>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.AlternativeProductsIsoform
setIncludes(List<Section>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.ProteinDescription: Sets a list of proteins for the includes section of the DE line
setInstitute(Institute) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Thesis
setInteractionGeneName(InteractionGeneName) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Interaction
setInteractions(List<Interaction>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.InteractionComment
setInteractionType(InteractionType) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Interaction
setInternalSection(InternalSection) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry
setInternalVersion(int) - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.DatabaseCrossReference
setIsoformId(UniProtIsoformId) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.DatabaseCrossReference: If it is set, it means the cross reference is only related to the isoform
setIsoforms(List<AlternativeProductsIsoform>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.AlternativeProductsComment
setIsoformSequenceStatus(IsoformSequenceStatus) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.AlternativeProductsIsoform
setJournalName(JournalName) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.ElectronicArticle
setJournalName(JournalName) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.JournalArticle
setKeywords(List<Keyword>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry: Sets the Keyword annotation of the UniProtEntry to a given list of Keyword values.
setKineticParameters(KineticParameters) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.BioPhysicoChemicalPropertiesComment
setLabel(String) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.Ligand
setLastAnnotationUpdateDate(Date) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.EntryAudit
setLastPage(Page) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Book
setLastPage(Page) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.JournalArticle
setLastSequenceUpdateDate(Date) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.EntryAudit
setLength(int) - Method in interface uk.ac.ebi.kraken.interfaces.uniref.member.UniRefMember
setLigand(Ligand) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.BindingFeature
setLigandPart(LigandPart) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.BindingFeature
setLocation(SubcellularLocationValue) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.SubcellularLocation
setLocations(List<Location>) - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.SequenceFeature
setLocationType(RnaEditingLocationType) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.RnaEditingComment
setLocator(Locator) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.ElectronicArticle
setMax(int) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Absorption
setMaximumVelocities(List<MaximumVelocity>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.KineticParameters
setMaxVelocityUnit(MaxVelocityUnit) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.MaximumVelocity
setMedlineId(String) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationXrefs: Deprecated.
setMedlineId(MedlineId) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationXrefs: Deprecated.
setMemberId(MemberId) - Method in interface uk.ac.ebi.kraken.interfaces.uniref.member.UniRefMember
setMembers(List<UniRefMember>) - Method in interface uk.ac.ebi.kraken.interfaces.uniref.UniRefEntry: Sets the members of this UniRefEntry to a given list.
setMethod(MassSpectrometryMethod) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.MassSpectrometryComment
setMichaelisConstants(List<MichaelisConstant>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.KineticParameters
setMolecularWeight(int) - Method in interface uk.ac.ebi.kraken.interfaces.common.Sequence: Sets the molecular weight of this sequence to a given value.
setMolecularWeight(PAGEDataMolecularWeight) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.PAGEDataComment
setMolecule(String) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Comment
setMolecule(String) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.RnaEditingComment
setMolWeight(float) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.MassSpectrometryComment
setMolWeightError(float) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.MassSpectrometryComment
setMutagenReport(MutagenReport) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.MutagenFeature
setName(String) - Method in interface uk.ac.ebi.kraken.interfaces.common.Database
setName(String) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Cofactor
setName(String) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Reaction
setName(String) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.Ligand
setName(IsoformName) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.AlternativeProductsIsoform
setName(UniRefEntryName) - Method in interface uk.ac.ebi.kraken.interfaces.uniref.UniRefEntry: Sets the name of this UniRefEntry to a given value.
setNames(List<Name>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.description.Section: Set the names of a protein
setNameType(NameType) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.description.Name: Sets the name type for the current name
setNCBITaxonomy(NCBITaxonomy) - Method in interface uk.ac.ebi.kraken.interfaces.uniref.member.UniRefMember
setNcbiTaxonomyId(NcbiTaxonomyId) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.OrganismHost: Sets the NCBI Taxonomy ID of the Organism of this Organism Host.
setNcbiTaxonomyIds(List<NcbiTaxonomyId>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry
setNote(String) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.Ligand
setNote(AbsorptionNote) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Absorption
setNote(CofactorNote) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.CofactorCommentStructured
setNote(CommentNote) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.HasCommentNote
setNote(DiseaseNote) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.DiseaseCommentStructured
setNote(IsoformNote) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.AlternativeProductsIsoform
setNote(KineticParameterNote) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.KineticParameters
setNote(MassSpectrometryCommentNote) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.MassSpectrometryComment
setNote(SequenceCautionCommentNote) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.SequenceCautionComment
setNumberOfExperiments(int) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Interaction
setOrderedLocusNames(List<OrderedLocusName>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.Gene: Sets the List of Ordered Locus Names of this Gene.
setORFNames(List<ORFName>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.Gene: Sets the List of ORF Names of this Gene.
setOrganelles(List<Organelle>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry
setOrganism(Organism) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.OrganismHost: Sets the Organism of this Organism Host.
setOrganism(Organism) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry: Sets the Organisms in which this protein is found.
setOrganismHosts(List<OrganismHost>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry: Sets the list of organism hosts.
setOrientation(SubcellularLocationValue) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.SubcellularLocation
setOriginalSequence(FeatureSequence) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.HasAlternativeSequence
setOriginName(EvidenceOriginName) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.evidences.Evidence
setOverlapRegion(OverlapRegion) - Method in interface uk.ac.ebi.kraken.interfaces.uniref.member.UniRefMember
setPatentNumber(PatentNumber) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Patent
setPHDepencence(PHDependence) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.BioPhysicoChemicalPropertiesComment
setPhysiologicalReactions(List<PhysiologicalReaction>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.CatalyticActivityCommentStructured
setPl(PAGEDataPl) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.PAGEDataComment
setPosition(int, int) - Method in interface uk.ac.ebi.kraken.interfaces.uniref.member.OverlapRegion
setPosition(String) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Position
setPositions(List<Position>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.RnaEditingComment
setPrimaryId(DatabaseAttribute) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.DatabaseCrossReference
setPrimaryUniProtAccession(PrimaryUniProtAccession) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry
setProteinDescription(ProteinDescription) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry
setProteinExistence(ProteinExistence) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry
setProteinName(String) - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.DatabaseCrossReference
setProteinName(ProteinName) - Method in interface uk.ac.ebi.kraken.interfaces.uniref.member.UniRefMember
setProteome(String) - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.DatabaseCrossReference
setProteomeComponent(String) - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.DatabaseCrossReference
setPublicationDate(PublicationDate) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Citation
setPublisher(Publisher) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Book
setPubMedId(String) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationXrefs
setPubMedId(PubMedId) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationXrefs
setReaction(Reaction) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.CatalyticActivityCommentStructured
setReactionReference(ReactionReference) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.PhysiologicalReaction
setReactionReferences(List<ReactionReference>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Reaction
setRecommendedName(Name) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.ProteinDescription: Sets the recommended name of the main protein within the DE line
setRedoxPotential(RedoxPotential) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.BioPhysicoChemicalPropertiesComment
setReferenceId(String) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.CofactorReference
setReleaseDate(Date) - Method in interface uk.ac.ebi.kraken.interfaces.uniref.UniRefDatabase
setRepresentativeMember(UniRefRepresentativeMember) - Method in interface uk.ac.ebi.kraken.interfaces.uniref.UniRefEntry: Sets the representative representativeMember of this UniRefEntry to a given value.
setRnaEditingNote(RnaEditingNote) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.RnaEditingComment
setSampleSources(List<SampleSource>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Citation
setScientificName(OrganismScientificName) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.Organism: Sets the scientific name of this Organism.
setSecondaryUniProtAccessions(List<SecondaryUniProtAccession>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry: Sets the UniProtAccessions of the UniProtEntry to a given list of UniProtAccession values.
setSecondInteractant(InteractorUniProtId) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Interaction
setSecondInteractantParent(InteractorUniProtId) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Interaction
setSecondInteractor(InteractorAccession) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.Interaction
setSection(Section) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.ProteinDescription: Alternativley to defining the main protein through the setter methods of the recommended, alternative and sub names methods, one can set the main protein as an entire section.
setSeed(boolean) - Method in interface uk.ac.ebi.kraken.interfaces.uniref.member.UniRefMember
setSequence(String) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.SequenceCautionComment
setSequence(String) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureLocation
setSequence(Sequence) - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.UniParcEntry
setSequence(Sequence) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry: Sets the Sequence annotation in the UniProtEntry to a given value.
setSequence(Sequence) - Method in interface uk.ac.ebi.kraken.interfaces.uniref.member.UniRefRepresentativeMember
setSequenceFeatures(List<SequenceFeature>) - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.UniParcEntry
setSequenceIds(List<IsoformSequenceId>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.AlternativeProductsIsoform
setSequenceVersion(int) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.EntryAudit
setSignatureDBType(SignatureDBType) - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.SequenceFeature
setSourceOrganism(SourceOrganism) - Method in interface uk.ac.ebi.kraken.interfaces.uniref.member.UniRefMember
setSources(List<MassSpectrometryCommentSource>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.MassSpectrometryComment
setStart(int) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureLocation
setStartModifier(FeatureLocationModifier) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureLocation
setSubcellularLocationNote(SubcellularLocationNote) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.SubcellularLocationComment
setSubcellularLocations(List<SubcellularLocation>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.SubcellularLocationComment
setSubmittedToDatabase(SubmissionDatabase) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Submission
setSubNames(List<Name>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.ProteinDescription: Sets the sub names of the main protein within the DE line
setSubstrate(Substrate) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.MichaelisConstant
setSynonym(OrganismSynonym) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.Organism: Sets the synonym name this Organism.
setSynonyms(List<IsoformSynonym>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.AlternativeProductsIsoform
setTaxonomy(List<NcbiTaxon>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry: Sets the taxonomy annotation of the UniProtEntry to a given list of Keyword values.
setTaxonomyId(int) - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.DatabaseCrossReference
setTemperatureDependence(TemperatureDependence) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.BioPhysicoChemicalPropertiesComment
setTexts(List<CommentText>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentFreeText
setTexts(List<EvidencedValue>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.HasFreeText
setThird(DatabaseAttribute) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.DatabaseCrossReference
setTitle(String) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Citation
setTitle(Title) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Citation
setTopology(SubcellularLocationValue) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.SubcellularLocation
setType(ReactionReferenceType) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.ReactionReference
setType(SequenceCautionType) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.SequenceCautionComment
setType(FieldType) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.description.Field: Sets the field to a valid type
setType(EvidenceType) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.evidences.Evidence
setType(GeneEncodingType) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.Organelle
setType(UniProtEntryType) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry: Sets the type of the UniProtEntry which is UniProtEntryType.SWISSPROT if the entry is annotated as STANDARD in the ID line and UniProtEntryType.TREMBL if it is annotated PRELIMINARY.
setType(Type) - Method in interface uk.ac.ebi.kraken.interfaces.uniref.member.UniRefMember
setType(UniRefDatabaseType) - Method in interface uk.ac.ebi.kraken.interfaces.uniref.UniRefDatabase
setUniParcAccession(UniParcAccession) - Method in interface uk.ac.ebi.kraken.interfaces.uniref.member.UniRefMember
setUniParcId(UniParcId) - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.UniParcEntry
setUniProtAccession(String) - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.DatabaseCrossReference
setUniProtAccession(UniProtAccession) - Method in interface uk.ac.ebi.kraken.interfaces.go.GoAnnotation
setUniProtAccessions(List<UniProtAccession>) - Method in interface uk.ac.ebi.kraken.interfaces.uniref.member.UniRefMember
setUniProtEntries(Set<UniProtEntry>) - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.UniParcEntry: Deprecated.
setUniProtExclusion(UniProtAccession) - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.UniParcEntry
setUniProtId(String) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry
setUniProtId(UniProtId) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry: Sets the UniProtId of the UniProtEntry to a given value.
setUniRef100EntryId(UniRefEntryId) - Method in interface uk.ac.ebi.kraken.interfaces.uniref.member.UniRefMember
setUniRef50EntryId(UniRefEntryId) - Method in interface uk.ac.ebi.kraken.interfaces.uniref.member.UniRefMember
setUniRef90EntryId(UniRefEntryId) - Method in interface uk.ac.ebi.kraken.interfaces.uniref.member.UniRefMember
setUniRefDatabase(UniRefDatabase) - Method in interface uk.ac.ebi.kraken.interfaces.uniref.UniRefEntry: Sets the UniRefDatabase.
setUniRefEntryId(UniRefEntryId) - Method in interface uk.ac.ebi.kraken.interfaces.uniref.UniRefEntry: Sets the id of this UniRefEntry to a given value.
setUnit(MichaelisConstantUnit) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.MichaelisConstant
setUpdate(Date) - Method in interface uk.ac.ebi.kraken.interfaces.uniref.UniRefEntry: Sets the last update of this UniRefEntry to a given value.
setUpdated(Date) - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.DatabaseCrossReference
setUri(String) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.WebResourceComment
setValue(String) - Method in interface uk.ac.ebi.kraken.interfaces.common.Sequence: Sets the String representation of the amino acid composition of this sequence to a given value.
setValue(String) - Method in interface uk.ac.ebi.kraken.interfaces.common.Value: Set the value in the object
setValue(String) - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceType
setValue(String) - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.OntologyType
setVariantReport(VariantReport) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.VariantFeature
setVariantReports(List<VariantReport>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.VariantFeature: Deprecated.
setVarsplicIsoforms(List<VarsplicIsoform>) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.features.VarSeqFeature
setVelocity(float) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.MaximumVelocity
setVelocityStr(String) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.MaximumVelocity
setVersion(int) - Method in interface uk.ac.ebi.kraken.interfaces.common.Database
setVersion(int) - Method in interface uk.ac.ebi.kraken.interfaces.uniparc.DatabaseCrossReference
setVersion(UniRefDatabaseVersion) - Method in interface uk.ac.ebi.kraken.interfaces.uniref.UniRefDatabase
setVolume(Volume) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.Book
setVolume(Volume) - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.JournalArticle
SEVEN_HUNDRED_FIFTY - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.AlignmentCutoffOption
SEVEN_HUNDRED_FIFTY - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.ScoreCutoffOption
SFLD - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.SignatureDBType
SFLD - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
SGD - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
SGD - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
SGD - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
SHORT - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.description.FieldType
shortName() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureStatus
SIGNAL - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
SignalFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
SIGNALINK - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
SignatureDBType - Enum Class in uk.ac.ebi.kraken.interfaces.uniparc
SIGNOR - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
SIMILARITY - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType
SIMILARITY - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
SimilarityComment - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
SITE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
SiteFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
SIX - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.DropOffOption
SMART - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.SignatureDBType
SMART - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
SMART - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
SMR - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
SourceOrganism - Interface in uk.ac.ebi.kraken.interfaces.uniref.member
specialCharEncode(String) - Static method in class uk.ac.ebi.uniprot.dataservice.query.QueryUtil
SplicedIsoform - Interface in uk.ac.ebi.kraken.interfaces.uniprot
start() - Method in interface uk.ac.ebi.uniprot.dataservice.client.Service: Deprecated.
stop() - Method in interface uk.ac.ebi.uniprot.dataservice.client.Service: Deprecated.
STRAIN - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.SampleSourceType
STRAND - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
StrandFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
STRENDA_DB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
STRINGXREF - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
STYPE - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastParameter
SUBCELLULAR_LOCATION - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType
SubcellularLocation - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments: Created by IntelliJ IDEA.
SubcellularLocationComment - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
SubcellularLocationNote - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments: User: Emilio Salazar Date: 06-Jun-2007
SubcellularLocationValue - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments: Created by IntelliJ IDEA.
Submission - Interface in uk.ac.ebi.kraken.interfaces.uniprot.citationsNew
SUBMISSION - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationTypeEnum
SubmissionDatabase - Enum Class in uk.ac.ebi.kraken.interfaces.uniprot.citationsNew
SUBNAME - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.description.NameType
subSequence(int, int) - Method in interface uk.ac.ebi.kraken.interfaces.common.Sequence
Substrate - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
SUBUNIT - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType
SubunitComment - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
SUPERFAMILY - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.SignatureDBType
SUPFAM - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
SWISS_PROT - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.SubmissionDatabase
SWISS2DPAGE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
SWISSLIPIDS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
SWISSPALM - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
swissprot() - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Creates a query that searches for just Swiss-Prot entries, equivalent to reviewed(true)
SWISSPROT - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
SWISSPROT - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntryType
SWISSPROT - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.DatabaseOption
SWISSPROT_VARSPLIC - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType

T

T - Enum constant in enum class uk.ac.ebi.kraken.interfaces.common.MoleculeWeight
TAIR - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
TAIR - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
TAIR - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
TAS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.go.GoAnnotationEvidence
TAS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceType
taxonId(int) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcQueryBuilder: Creates a query that searches for UniParc entries that contain within their database cross-references the given taxonomic identifier.
taxonId(int) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniref.UniRefQueryBuilder: Creates a query that searches for UniRef clusters holding members that contain the given NCBI taxonomic identifier.
taxonID(int) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Creates a query that uses the NCBI taxonomy identifiers as a search term.
taxonName(String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Create a query based on an NCBI taxonomy name.
TAXONOMY - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtData.ComponentType
taxonomy_id - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcField.Search
taxonomy_id - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtField.Search
taxonomy_id - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniref.UniRefField.Search
taxonomy_name - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcField.Search
taxonomy_name - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtField.Search
taxonomy_name - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniref.UniRefField.Search
TCDB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
TemperatureDependence - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
TEN - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.AlignmentCutoffOption
TEN - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.DropOffOption
TEN - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.ExpectationOption
TEN - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.ScoreCutoffOption
TextOnlyComment - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments: User: Emilio Salazar Date: 17-Nov-2005
Thesis - Interface in uk.ac.ebi.kraken.interfaces.uniprot.citationsNew
THESIS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationTypeEnum
THYLAKOID - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.TransitType
TISSUE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.SampleSourceType
TISSUE_SPECIFICITY - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType
TissueSpecificityComment - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
title(String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Creates a query that matches entries containing a reference with the specified title
Title - Interface in uk.ac.ebi.kraken.interfaces.uniprot.citationsNew
TITLE - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastParameter
toDisplayName() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CofactorReferenceType: String representation of the external source
toDisplayName() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType: Returns the name of this enum constant, as contained in the declaration.
toDisplayName() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.DiseaseReferenceType: String representation of the external source
toDisplayName() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.PhysiologicalDirectionType: String representation of the external source
toDisplayName() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.ReactionReferenceType: String representation of the external source
toDisplayName() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.SequenceCautionType: Returns the name of this enum constant, as contained in the declaration.
toDisplayNameString() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.MichaelisConstantUnit
TOPO_DOM - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
TopoDomFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
toString() - Method in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType: Returns the name of this enum constant, as contained in the declaration.
toString() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.description.FieldType
toString() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.description.NameType
toString() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.ProteinExistence
toString() - Method in class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastInput
toType(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.MassSpectrometryMethod
toType(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.CommentStatus: Lawrence added this for convienence, like in MassSpectrometryMethod - think this is a bit neater though as it uses the same string values as passed into the enum constructor - less need to maintain.....
toValue() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.comments.SubcellularLocation: Deprecated.
toWebServiceInput() - Method in class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastInput
TOXIC_DOSE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType
ToxicDoseComment - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
toXmlDisplayName() - Method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType: Return the comment type as found in the uniprot.xsd i.e.
TRANSCRIPT_LEVEL - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.ProteinExistence
TRANSIT - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
TransitFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
TransitType - Enum Class in uk.ac.ebi.kraken.interfaces.uniprot.features
TRANSLTABLE - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastParameter
TRANSMEM - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
TransmemFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
TRANSPOSON - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.SampleSourceType
TREEFAM - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
trembl() - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Creates a query that searches for just TrEMBL entries equivalent to reviewed(false)
TrEMBL - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
TREMBL - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
TREMBL - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntryType
TREMBL - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.DatabaseOption
TREMBL_VARSPLIC - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
TREMBLNEW - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
TROME - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
TUBERCULIST - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
TUBERCULIST - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
TURN - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
TurnFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
TWENTY - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.AlignmentCutoffOption
TWENTY - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.ScoreCutoffOption
TWO - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.DropOffOption
TWO_HUNDRED - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.AlignmentCutoffOption
TWO_HUNDRED - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.ScoreCutoffOption
TWO_HUNDRED_FIFTY - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.AlignmentCutoffOption
TWO_HUNDRED_FIFTY - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.ScoreCutoffOption
TXT_MEDIA_TYPE_VALUE - Static variable in class uk.ac.ebi.uniprot.dataservice.client.ClientConstant
Type - Interface in uk.ac.ebi.kraken.interfaces.uniref.member
typeOf(char) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCategory
typeOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.go.GoAnnotationEvidence
typeOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.go.GoCategory
typeOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
typeOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationTypeEnum
typeOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationXrefType
typeOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.SampleSourceType
typeOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.SubmissionDatabase
typeOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CofactorReferenceType: Provided a string representation of a source, return the enum type.
typeOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType
typeOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.DiseaseReferenceType: Provided a string representation of a source, return the enum type.
typeOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.IsoformSequenceStatus
typeOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.PhysiologicalDirectionType: Provided a string representation of a source, return the enum type.
typeOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.ReactionReferenceType: Provided a string representation of a source, return the enum type.
typeOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.SequenceCautionType
typeOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.description.FieldType
typeOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.description.FlagType
typeOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.description.NameType
typeOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCode
typeOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
typeOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureStatus
typeOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
typeOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.GeneEncodingType
typeOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.ProteinExistence
typeOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntryType
typeOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniref.UniRefDatabaseType
typeOf(String) - Static method in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.DatabaseOption
typeOfcvId(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.go.GoAnnotationEvidence: Finds the corresponding GoAnnotationEvidence constant for the given ECO code.

U

U - Enum constant in enum class uk.ac.ebi.kraken.interfaces.common.MoleculeWeight
UCSC - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
uk.ac.ebi.kraken.interfaces.common - package uk.ac.ebi.kraken.interfaces.common: Common Interfaces
uk.ac.ebi.kraken.interfaces.go - package uk.ac.ebi.kraken.interfaces.go
uk.ac.ebi.kraken.interfaces.go.toprotein - package uk.ac.ebi.kraken.interfaces.go.toprotein
uk.ac.ebi.kraken.interfaces.uniparc - package uk.ac.ebi.kraken.interfaces.uniparc
uk.ac.ebi.kraken.interfaces.uniprot - package uk.ac.ebi.kraken.interfaces.uniprot: UniProt
uk.ac.ebi.kraken.interfaces.uniprot.citationsNew - package uk.ac.ebi.kraken.interfaces.uniprot.citationsNew
uk.ac.ebi.kraken.interfaces.uniprot.comments - package uk.ac.ebi.kraken.interfaces.uniprot.comments
uk.ac.ebi.kraken.interfaces.uniprot.dbx - package uk.ac.ebi.kraken.interfaces.uniprot.dbx
uk.ac.ebi.kraken.interfaces.uniprot.dbx.go - package uk.ac.ebi.kraken.interfaces.uniprot.dbx.go
uk.ac.ebi.kraken.interfaces.uniprot.description - package uk.ac.ebi.kraken.interfaces.uniprot.description
uk.ac.ebi.kraken.interfaces.uniprot.evidences - package uk.ac.ebi.kraken.interfaces.uniprot.evidences
uk.ac.ebi.kraken.interfaces.uniprot.features - package uk.ac.ebi.kraken.interfaces.uniprot.features
uk.ac.ebi.kraken.interfaces.uniprot.genename - package uk.ac.ebi.kraken.interfaces.uniprot.genename
uk.ac.ebi.kraken.interfaces.uniprot.organism - package uk.ac.ebi.kraken.interfaces.uniprot.organism
uk.ac.ebi.kraken.interfaces.uniref - package uk.ac.ebi.kraken.interfaces.uniref
uk.ac.ebi.kraken.interfaces.uniref.member - package uk.ac.ebi.kraken.interfaces.uniref.member
uk.ac.ebi.uniprot.dataservice.client - package uk.ac.ebi.uniprot.dataservice.client
uk.ac.ebi.uniprot.dataservice.client.alignment.blast - package uk.ac.ebi.uniprot.dataservice.client.alignment.blast
uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input - package uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input
uk.ac.ebi.uniprot.dataservice.client.exception - package uk.ac.ebi.uniprot.dataservice.client.exception
uk.ac.ebi.uniprot.dataservice.client.service - package uk.ac.ebi.uniprot.dataservice.client.service
uk.ac.ebi.uniprot.dataservice.client.uniparc - package uk.ac.ebi.uniprot.dataservice.client.uniparc
uk.ac.ebi.uniprot.dataservice.client.uniprot - package uk.ac.ebi.uniprot.dataservice.client.uniprot
uk.ac.ebi.uniprot.dataservice.client.uniref - package uk.ac.ebi.uniprot.dataservice.client.uniref
uk.ac.ebi.uniprot.dataservice.client.uniref.converter - package uk.ac.ebi.uniprot.dataservice.client.uniref.converter
uk.ac.ebi.uniprot.dataservice.query - package uk.ac.ebi.uniprot.dataservice.query
UNCERTAIN - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.ProteinExistence
Undetermined - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.RnaEditingLocationType
UNICARBKB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
UNILECTIN - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
UNIMES - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
UNIPARC - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.DatabaseOption
UNIPARC_REMOTE_SERVER_URL - Static variable in class uk.ac.ebi.uniprot.dataservice.client.ClientConstant
UniParcAccession - Interface in uk.ac.ebi.kraken.interfaces.uniref.member
UniParcBlastService - Interface in uk.ac.ebi.uniprot.dataservice.client.alignment.blast: Blast service geared specifically towards the UniParc blast databases.
UniParcComponent<T> - Interface in uk.ac.ebi.uniprot.dataservice.client.uniparc: Component used to store the most informative elements of a UniParc entry.
UniParcEntry - Interface in uk.ac.ebi.kraken.interfaces.uniparc: Created by IntelliJ IDEA.
UniParcField - Interface in uk.ac.ebi.uniprot.dataservice.client.uniparc
UniParcField.Search - Enum Class in uk.ac.ebi.uniprot.dataservice.client.uniparc
UniParcHit - Interface in uk.ac.ebi.uniprot.dataservice.client.alignment.blast: Represents a UniParc based blast hit.
uniparcId(String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniref.UniRefQueryBuilder: Creates a query that searches for UniRef clusters holding members that contain uniparc id
UniParcId - Interface in uk.ac.ebi.kraken.interfaces.uniparc: Created by IntelliJ IDEA.
UniParcQueryBuilder - Class in uk.ac.ebi.uniprot.dataservice.client.uniparc
UniParcQueryBuilder() - Constructor for class uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcQueryBuilder
UniParcService - Interface in uk.ac.ebi.uniprot.dataservice.client.uniparc
UNIPATHWAY - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
UNIPROT - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
UNIPROT_ARCHAEA - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.DatabaseOption
UNIPROT_ARTHROPODA - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.DatabaseOption
UNIPROT_BACTERIA - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.DatabaseOption
UNIPROT_COMPLETE_MICROBIAL_PROTEOMES - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.DatabaseOption
UNIPROT_EUKARYOTA - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.DatabaseOption
UNIPROT_FUNGI - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.DatabaseOption
UNIPROT_HUMAN - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.DatabaseOption
uniprot_id - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniref.UniRefField.Search
UNIPROT_MAMMALS - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.DatabaseOption
UNIPROT_NEMATODA - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.DatabaseOption
UNIPROT_PDB - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.DatabaseOption
UNIPROT_REMOTE_SERVER_URL - Static variable in class uk.ac.ebi.uniprot.dataservice.client.ClientConstant
UNIPROT_RODENTS - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.DatabaseOption
UNIPROT_VERTEBRATES - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.DatabaseOption
UNIPROT_VIRIDIPLANTAE - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.DatabaseOption
UNIPROT_VIRUSES - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.DatabaseOption
uniProtAccession(String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcQueryBuilder: Creates a query that searches for entries that contain an active UniProtKB cross-reference with the given UniProt accession.
UniProtAccession - Interface in uk.ac.ebi.kraken.interfaces.uniprot: One UniProtAccession of a UniProtEntry.
UniProtAccession - Interface in uk.ac.ebi.kraken.interfaces.uniref.member
UniProtBlastService - Interface in uk.ac.ebi.uniprot.dataservice.client.alignment.blast: Blast service geared specifically towards the UniProt blast databases.
UniProtBlastSummary - Interface in uk.ac.ebi.uniprot.dataservice.client.alignment.blast: Has extra properties specific to the UniProt entry blast summary.
UniProtComponent<T> - Interface in uk.ac.ebi.uniprot.dataservice.client.uniprot: UniProt Component interface, returned from query component
the component types are defined in UniProtData.ComponentType
UniProtData - Interface in uk.ac.ebi.uniprot.dataservice.client.uniprot: UniProt query result interfaces
UniProtData.ComponentType - Enum Class in uk.ac.ebi.uniprot.dataservice.client.uniprot: Supported return component types
UniProtEntry - Interface in uk.ac.ebi.kraken.interfaces.uniprot: This is the Interface to the contents of a UniProt entry.
UniProtEntryType - Enum Class in uk.ac.ebi.kraken.interfaces.uniprot
UniProtField - Class in uk.ac.ebi.uniprot.dataservice.client.uniprot: All UniProt related search fields that can be used in a query.
UniProtField() - Constructor for class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtField
UniProtField.Search - Enum Class in uk.ac.ebi.uniprot.dataservice.client.uniprot
UniProtField.SearchDate - Enum Class in uk.ac.ebi.uniprot.dataservice.client.uniprot
UniProtHit - Interface in uk.ac.ebi.uniprot.dataservice.client.alignment.blast: Represents a UniProt based blast hit.
uniprotId(String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniref.UniRefQueryBuilder: Creates a query that searches for UniRef clusters holding members that contain uniprot id
UniProtId - Interface in uk.ac.ebi.kraken.interfaces.uniprot: About This Data Structure
UniProtIsoformId - Interface in uk.ac.ebi.kraken.interfaces.uniprot
uniprotkb - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcField.Search
UNIPROTKB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.SubmissionDatabase
UNIPROTKB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
UNIPROTKB - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.DatabaseOption
UniProtQueryBuilder - Class in uk.ac.ebi.uniprot.dataservice.client.uniprot: The query builder for UniProt Service.
UniProtQueryBuilder() - Constructor for class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder
UniProtService - Interface in uk.ac.ebi.uniprot.dataservice.client.uniprot: The main service used to query the UniProt data through Query objects.
UNIREF_100 - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.DatabaseOption
UNIREF_50 - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.DatabaseOption
UNIREF_90 - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.DatabaseOption
UNIREF_REMOTE_SERVER_URL - Static variable in class uk.ac.ebi.uniprot.dataservice.client.ClientConstant
UniRef100 - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniref.UniRefDatabaseType
UniRef50 - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniref.UniRefDatabaseType
UniRef90 - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniref.UniRefDatabaseType
UniRefBlastService - Interface in uk.ac.ebi.uniprot.dataservice.client.alignment.blast: Blast service geared specifically towards the UniRef blast databases.
uniRefClusterDatabase(UniRefDatabaseType) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniref.UniRefQueryBuilder: Creates a query that searches for UniRef clusters within the given UniRef cluster database.
UniRefComponent<T> - Interface in uk.ac.ebi.uniprot.dataservice.client.uniref: Interface of the UniRef Component returned from query component
UniRefDatabase - Interface in uk.ac.ebi.kraken.interfaces.uniref
UniRefDatabaseType - Enum Class in uk.ac.ebi.kraken.interfaces.uniref: Created by IntelliJ IDEA.
UniRefDatabaseVersion - Interface in uk.ac.ebi.kraken.interfaces.uniref
UniRefEntry - Interface in uk.ac.ebi.kraken.interfaces.uniref: Encapsulates the data found in all UniRef entries.
UniRefEntryConverter - Class in uk.ac.ebi.uniprot.dataservice.client.uniref.converter
UniRefEntryConverter() - Constructor for class uk.ac.ebi.uniprot.dataservice.client.uniref.converter.UniRefEntryConverter
UniRefEntryId - Interface in uk.ac.ebi.kraken.interfaces.uniref
UniRefEntryLightConverter - Class in uk.ac.ebi.uniprot.dataservice.client.uniref.converter
UniRefEntryLightConverter() - Constructor for class uk.ac.ebi.uniprot.dataservice.client.uniref.converter.UniRefEntryLightConverter
UniRefEntryName - Interface in uk.ac.ebi.kraken.interfaces.uniref
UniRefField - Interface in uk.ac.ebi.uniprot.dataservice.client.uniref
UniRefField.Search - Enum Class in uk.ac.ebi.uniprot.dataservice.client.uniref
UniRefHit - Interface in uk.ac.ebi.uniprot.dataservice.client.alignment.blast: Represents a UniRef based blast hit.
UniRefMember - Interface in uk.ac.ebi.kraken.interfaces.uniref.member: Created by IntelliJ IDEA.
UniRefMemberConverter - Class in uk.ac.ebi.uniprot.dataservice.client.uniref.converter
UniRefMemberConverter() - Constructor for class uk.ac.ebi.uniprot.dataservice.client.uniref.converter.UniRefMemberConverter
UniRefQueryBuilder - Class in uk.ac.ebi.uniprot.dataservice.client.uniref: UniRefQueryBuilder class is for building a UniRef query for UniRef Services
UniRefQueryBuilder() - Constructor for class uk.ac.ebi.uniprot.dataservice.client.uniref.UniRefQueryBuilder
UniRefRepMemberConverter - Class in uk.ac.ebi.uniprot.dataservice.client.uniref.converter
UniRefRepMemberConverter() - Constructor for class uk.ac.ebi.uniprot.dataservice.client.uniref.converter.UniRefRepMemberConverter
UniRefRepresentativeMember - Interface in uk.ac.ebi.kraken.interfaces.uniref.member
UniRefService - Interface in uk.ac.ebi.uniprot.dataservice.client.uniref: Service to query UniRef data using a text indexed with Solr.
UniRule - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
Unknown - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.RnaEditingLocationType
UNKNOWN - Enum constant in enum class uk.ac.ebi.kraken.interfaces.go.GoAnnotationEvidence
UNKNOWN - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationTypeEnum
UNKNOWN - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.SubmissionDatabase
UNKNOWN - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType
UNKNOWN - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.InteractionType
UNKNOWN - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.MassSpectrometryMethod
UNKNOWN - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.ReactionReferenceType
UNKNOWN - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.SequenceCautionType
UNKNOWN - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseCategory
UNKNOWN - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
UNKNOWN - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceType
UNKNOWN - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.OntologyType
UNKNOWN - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.description.FieldType
UNKNOWN - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.description.NameType
UNKNOWN - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.TransitType
UNKNOWN - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.ProteinExistence
UNKNOWN - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntryType
UNKOWN - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureLocationModifier
UNKOWN - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.GeneEncodingType
UNPUBLISHED_JOURNAL_ARTICLE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationTypeEnum
UNPUBLISHED_OBSERVATIONS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationTypeEnum
UnpublishedJournalArticle - Interface in uk.ac.ebi.kraken.interfaces.uniprot.citationsNew
UnpublishedObservations - Interface in uk.ac.ebi.kraken.interfaces.uniprot.citationsNew: For unpublished observations the format of the RL line is: RL Unpublished observations (MMM-YYYY).
UnspecifiedConflictReport - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
UNSURE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureLocationModifier
UNSURE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
UnsureFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
updated(LocalDate, LocalDate) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Creates a query to get entries updated between fromDate and toDate, It does not allow both fromDate and toDate to be null.
upi - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcField.Search
upi - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniref.UniRefField.Search
upid - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcField.Search
upid(String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcQueryBuilder: Creates a query that searches for UniParc entries whose proteome upid is equal to the provided proteome upid.
useECOCode() - Method in interface uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceId
usingBlastVersion(BlastVersionOption) - Method in class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastInput.Builder: The BLAST program to be used for the blast.
USPTO - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType

V

V - Enum constant in enum class uk.ac.ebi.kraken.interfaces.common.MoleculeWeight
Value - Interface in uk.ac.ebi.kraken.interfaces.common: A common interface used to describe object values that can be mapped to a single String
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.common.MoleculeWeight: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.go.GoAnnotationEvidence: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.go.GoCategory: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniparc.SignatureDBType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationTypeEnum: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationXrefType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.SampleSourceType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.SubmissionDatabase: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CofactorReferenceType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.DiseaseReferenceType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.InteractionType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.IsoformSequenceStatus: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.MassSpectrometryMethod: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.MichaelisConstantUnit: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.PhysiologicalDirectionType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.ReactionReferenceType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.RnaEditingLocationType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.SequenceCautionType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.CommentStatus: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseCategory: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.OntologyType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.description.FieldType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.description.FlagType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.description.NameType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCategory: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureLocationModifier: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureStatus: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.TransitType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.GeneEncodingType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.ProteinExistence: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntryType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.kraken.interfaces.uniref.UniRefDatabaseType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastParameter: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.AlignmentCutoffOption: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.BlastVersionOption: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.DatabaseOption: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.DropOffOption: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.ExpectationOption: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.FilterOption: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.MatrixOption: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.ScoreCutoffOption: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.SequenceTypeOption: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcField.Search: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.QuerySpec: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtData.ComponentType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtField.Search: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtField.SearchDate: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class uk.ac.ebi.uniprot.dataservice.client.uniref.UniRefField.Search: Returns the enum constant of this class with the specified name.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.common.MoleculeWeight: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.go.GoAnnotationEvidence: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.go.GoCategory: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniparc.SignatureDBType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationTypeEnum: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.CitationXrefType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.SampleSourceType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.citationsNew.SubmissionDatabase: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CofactorReferenceType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.DiseaseReferenceType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.InteractionType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.IsoformSequenceStatus: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.MassSpectrometryMethod: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.MichaelisConstantUnit: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.PhysiologicalDirectionType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.ReactionReferenceType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.RnaEditingLocationType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.SequenceCautionType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.CommentStatus: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseCategory: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.GoEvidenceType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.dbx.go.OntologyType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.description.FieldType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.description.FlagType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.description.NameType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCategory: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceCode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureLocationModifier: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureStatus: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.TransitType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.GeneEncodingType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.ProteinExistence: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntryType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.kraken.interfaces.uniref.UniRefDatabaseType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastParameter: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.AlignmentCutoffOption: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.BlastVersionOption: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.DatabaseOption: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.DropOffOption: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.ExpectationOption: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.FilterOption: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.MatrixOption: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.ScoreCutoffOption: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.SequenceTypeOption: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.uniprot.dataservice.client.uniparc.UniParcField.Search: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.QuerySpec: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtData.ComponentType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtField.Search: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtField.SearchDate: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class uk.ac.ebi.uniprot.dataservice.client.uniref.UniRefField.Search: Returns an array containing the constants of this enum class, in the order they are declared.
VAR_SEQ - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
VARIANT - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
VariantFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features: Encapsulates the Variant Feature of a UniProtEntry.
VariantReport - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
VarSeqFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
VarsplicIsoform - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features
VectorBase - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
VECTORBASE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
VECTORBASE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
VEGA - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
VEUPATHDB - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
VGNC - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
VGNC - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
virus_host_name - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtField.Search
Volume - Interface in uk.ac.ebi.kraken.interfaces.uniprot.citationsNew

W

W - Enum constant in enum class uk.ac.ebi.kraken.interfaces.common.MoleculeWeight
WBParaSite - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
WBParaSite - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
WBPARASITE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
WEBRESOURCE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.CommentType
WebResourceComment - Interface in uk.ac.ebi.kraken.interfaces.uniprot.comments
withDropOff(DropOffOption) - Method in class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastInput.Builder: The amount a score can drop before gapped extension of word hits is halted.
withExpectation(ExpectationOption) - Method in class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastInput.Builder: Limits the number of scores and alignments reported based on the expectation value.
withFilter(FilterOption) - Method in class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastInput.Builder: Filter regions of low sequence complexity.
withGapAlign(boolean) - Method in class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastInput.Builder: This is a true/false setting that tells the program the perform optimised alignments within regions involving gaps.
withGapExt(int) - Method in class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastInput.Builder: Penalty taken away from the score for each base or residue in the gap.
withGapOpen(int) - Method in class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastInput.Builder: Penalty taken away from the score when a gap is created in sequence.
WithIsoform - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.QuerySpec
withMatrix(MatrixOption) - Method in class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastInput.Builder: Enumeration for all possible selections for similarity matrizes used for the BLAST service.
withMaximumNumberOfAlignments(AlignmentCutoffOption) - Method in class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastInput.Builder: Maximum number of match alignments reported in the result output.
withMaximumNumberOfScores(ScoreCutoffOption) - Method in class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastInput.Builder: Maximum number of match alignments reported in the result output.
withSequenceRange(int, int) - Method in class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastInput.Builder: Specify a range or section of the input sequence to use in the search.
withSequenceType(SequenceTypeOption) - Method in class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.BlastInput.Builder: Indicate whether the sequence to blast is from DNA/RNA or a protein.
WormBase - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniparc.DatabaseType
WormBase - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
WORMBASE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
WormPep - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType

X

X - Enum constant in enum class uk.ac.ebi.kraken.interfaces.common.MoleculeWeight
Xenbase - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
XENBASE - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
XENO - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.comments.InteractionType
XML_MEDIA_TYPE_VALUE - Static variable in class uk.ac.ebi.uniprot.dataservice.client.ClientConstant
xref - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtField.Search
xref(String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Creates a query that matches entries whose database cross-reference entities contain the specified value.
xref(DatabaseType) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Creates a query that matches entries containing the specified database cross-reference.
xref(DatabaseType, String) - Static method in class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtQueryBuilder: Creates a query that matches entries containing a specified database cross-reference type, with the specified cross-reference value.
XREFS - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtData.ComponentType

Y

Y - Enum constant in enum class uk.ac.ebi.kraken.interfaces.common.MoleculeWeight
YCHAROS - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
YES - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.FilterOption

Z

Z - Enum constant in enum class uk.ac.ebi.kraken.interfaces.common.MoleculeWeight
ZERO - Enum constant in enum class uk.ac.ebi.uniprot.dataservice.client.alignment.blast.input.DropOffOption
ZFIN - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType
ZFIN - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.evidences.EvidenceType
ZN_FING - Enum constant in enum class uk.ac.ebi.kraken.interfaces.uniprot.features.FeatureType
ZnFingFeature - Interface in uk.ac.ebi.kraken.interfaces.uniprot.features

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