Index

A B C D E F G H I K L M N O P R S T U V W
All Classes and Interfaces|All Packages

A

absorption - Variable in class org.uniprot.uniprot.CommentType

Absorption() - Constructor for class org.uniprot.uniprot.CommentType.Absorption

accession - Variable in class org.uniprot.uniprot.Entry

acronym - Variable in class org.uniprot.uniprot.CommentType.Disease

allergenName - Variable in class org.uniprot.uniprot.ProteinType

allergenName - Variable in class org.uniprot.uniprot.ProteinType.Component

allergenName - Variable in class org.uniprot.uniprot.ProteinType.Domain

alternativeName - Variable in class org.uniprot.uniprot.ProteinType

alternativeName - Variable in class org.uniprot.uniprot.ProteinType.Component

alternativeName - Variable in class org.uniprot.uniprot.ProteinType.Domain

AlternativeName() - Constructor for class org.uniprot.uniprot.ProteinType.AlternativeName

authorList - Variable in class org.uniprot.uniprot.CitationType

Describes the authors of a citation.

B

begin - Variable in class org.uniprot.uniprot.LocationType

biotechName - Variable in class org.uniprot.uniprot.ProteinType

biotechName - Variable in class org.uniprot.uniprot.ProteinType.Component

biotechName - Variable in class org.uniprot.uniprot.ProteinType.Domain

C

cdAntigenName - Variable in class org.uniprot.uniprot.ProteinType

cdAntigenName - Variable in class org.uniprot.uniprot.ProteinType.Component

cdAntigenName - Variable in class org.uniprot.uniprot.ProteinType.Domain

CERTAIN - Enum constant in enum org.dishevelled.bio.protein.uniprot.PositionStatus

Certain position status, =.

checksum - Variable in class org.uniprot.uniprot.SequenceType

citation - Variable in class org.uniprot.uniprot.ReferenceType

CitationType - Class in org.uniprot.uniprot

Describes different types of citations.

CitationType() - Constructor for class org.uniprot.uniprot.CitationType

city - Variable in class org.uniprot.uniprot.CitationType

Describes the city where a book was published.

classifyOrganism(String) - Static method in class org.dishevelled.bio.protein.uniprot.UniprotEntrySummaryReader

Classify an organism type from the specified lineage.

cofactor - Variable in class org.uniprot.uniprot.CommentType

CofactorType - Class in org.uniprot.uniprot

Describes a cofactor.

CofactorType() - Constructor for class org.uniprot.uniprot.CofactorType

comment - Variable in class org.uniprot.uniprot.Entry

CommentType - Class in org.uniprot.uniprot

Describes different types of general annotations.

CommentType() - Constructor for class org.uniprot.uniprot.CommentType

CommentType.Absorption - Class in org.uniprot.uniprot

Java class for anonymous complex type

CommentType.Conflict - Class in org.uniprot.uniprot

Java class for anonymous complex type

CommentType.Conflict.Sequence - Class in org.uniprot.uniprot

Java class for anonymous complex type

CommentType.Disease - Class in org.uniprot.uniprot

Java class for anonymous complex type

CommentType.Kinetics - Class in org.uniprot.uniprot

Java class for anonymous complex type

CommentType.Link - Class in org.uniprot.uniprot

Java class for anonymous complex type

CommentType.PhDependence - Class in org.uniprot.uniprot

Java class for anonymous complex type

CommentType.RedoxPotential - Class in org.uniprot.uniprot

Java class for anonymous complex type

CommentType.TemperatureDependence - Class in org.uniprot.uniprot

Java class for anonymous complex type

component - Variable in class org.uniprot.uniprot.ProteinType

Describes names of processed products.

Component() - Constructor for class org.uniprot.uniprot.ProteinType.Component

conflict - Variable in class org.uniprot.uniprot.CommentType

Used in 'sequence caution' annotations.

Conflict() - Constructor for class org.uniprot.uniprot.CommentType.Conflict

consortiumOrPerson - Variable in class org.uniprot.uniprot.NameListType

ConsortiumType - Class in org.uniprot.uniprot

Describes the authors of a citation when these are represented by a consortium.

ConsortiumType() - Constructor for class org.uniprot.uniprot.ConsortiumType

copyright - Variable in class org.uniprot.uniprot.Uniprot

country - Variable in class org.uniprot.uniprot.CitationType

Describes the country where a thesis was made.

createCitationType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of CitationType

createCofactorType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of CofactorType

createCommentType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of CommentType

createCommentTypeAbsorption() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of CommentType.Absorption

createCommentTypeConflict() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of CommentType.Conflict

createCommentTypeConflictSequence() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of CommentType.Conflict.Sequence

createCommentTypeDisease() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of CommentType.Disease

createCommentTypeKinetics() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of CommentType.Kinetics

createCommentTypeLink() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of CommentType.Link

createCommentTypePhDependence() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of CommentType.PhDependence

createCommentTypeRedoxPotential() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of CommentType.RedoxPotential

createCommentTypeTemperatureDependence() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of CommentType.TemperatureDependence

createConsortiumType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of ConsortiumType

createCopyright(String) - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of JAXBElement<String>

created - Variable in class org.uniprot.uniprot.Entry

createDbReferenceType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of DbReferenceType

createEntry() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of Entry

createEventType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of EventType

createEvidencedStringType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of EvidencedStringType

createEvidenceType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of EvidenceType

createFeatureType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of FeatureType

createGeneLocationType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of GeneLocationType

createGeneNameType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of GeneNameType

createGeneType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of GeneType

createImportedFromType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of ImportedFromType

createInteractantType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of InteractantType

createIsoformType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of IsoformType

createIsoformTypeName() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of IsoformType.Name

createIsoformTypeSequence() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of IsoformType.Sequence

createKeywordType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of KeywordType

createLigandPartType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of LigandPartType

createLigandType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of LigandType

createLocationType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of LocationType

createMoleculeType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of MoleculeType

createNameListType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of NameListType

createOrganismNameType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of OrganismNameType

createOrganismType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of OrganismType

createOrganismTypeLineage() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of OrganismType.Lineage

createPersonType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of PersonType

createPhysiologicalReactionType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of PhysiologicalReactionType

createPositionType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of PositionType

createPropertyType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of PropertyType

createProteinExistenceType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of ProteinExistenceType

createProteinType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of ProteinType

createProteinTypeAlternativeName() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of ProteinType.AlternativeName

createProteinTypeComponent() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of ProteinType.Component

createProteinTypeDomain() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of ProteinType.Domain

createProteinTypeRecommendedName() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of ProteinType.RecommendedName

createProteinTypeSubmittedName() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of ProteinType.SubmittedName

createReactionType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of ReactionType

createReferenceType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of ReferenceType

createSequenceType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of SequenceType

createSourceDataType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of SourceDataType

createSourceDataTypePlasmid() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of SourceDataType.Plasmid

createSourceDataTypeStrain() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of SourceDataType.Strain

createSourceDataTypeTissue() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of SourceDataType.Tissue

createSourceDataTypeTransposon() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of SourceDataType.Transposon

createSourceType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of SourceType

createStatusType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of StatusType

createSubcellularLocationType() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of SubcellularLocationType

createUniprot() - Method in class org.uniprot.uniprot.ObjectFactory

Create an instance of Uniprot

D

dataset - Variable in class org.uniprot.uniprot.Entry

date - Variable in class org.uniprot.uniprot.CitationType

db - Variable in class org.uniprot.uniprot.CitationType

Describes the database name of submissions.

dbReference - Variable in class org.uniprot.uniprot.CitationType

Describes cross-references to bibliography databases (MEDLINE, PubMed, AGRICOLA) or other online resources (DOI).

dbReference - Variable in class org.uniprot.uniprot.CofactorType

dbReference - Variable in class org.uniprot.uniprot.CommentType.Disease

dbReference - Variable in class org.uniprot.uniprot.Entry

dbReference - Variable in class org.uniprot.uniprot.ImportedFromType

dbReference - Variable in class org.uniprot.uniprot.InteractantType

dbReference - Variable in class org.uniprot.uniprot.LigandPartType

dbReference - Variable in class org.uniprot.uniprot.LigandType

dbReference - Variable in class org.uniprot.uniprot.OrganismType

Describes a cross-reference to the NCBI taxonomy database.

dbReference - Variable in class org.uniprot.uniprot.PhysiologicalReactionType

dbReference - Variable in class org.uniprot.uniprot.ReactionType

dbReference - Variable in class org.uniprot.uniprot.SourceType

DbReferenceType - Class in org.uniprot.uniprot

Describes a database cross-reference.

DbReferenceType() - Constructor for class org.uniprot.uniprot.DbReferenceType

description - Variable in class org.uniprot.uniprot.CommentType.Disease

description - Variable in class org.uniprot.uniprot.FeatureType

direction - Variable in class org.uniprot.uniprot.PhysiologicalReactionType

disease - Variable in class org.uniprot.uniprot.CommentType

Used in 'disease' annotations.

Disease() - Constructor for class org.uniprot.uniprot.CommentType.Disease

domain - Variable in class org.uniprot.uniprot.ProteinType

Describes names of "domains".

Domain() - Constructor for class org.uniprot.uniprot.ProteinType.Domain

E

ecNumber - Variable in class org.uniprot.uniprot.ProteinType.AlternativeName

ecNumber - Variable in class org.uniprot.uniprot.ProteinType.RecommendedName

ecNumber - Variable in class org.uniprot.uniprot.ProteinType.SubmittedName

editorList - Variable in class org.uniprot.uniprot.CitationType

Describes the editors of a book (only used for books).

end - Variable in class org.uniprot.uniprot.LocationType

entry - Variable in class org.uniprot.uniprot.Uniprot

Describes a UniProtKB entry.

Entry - Class in org.uniprot.uniprot

Java class for anonymous complex type

Entry() - Constructor for class org.uniprot.uniprot.Entry

entryFeature(EntryFeature) - Method in interface org.dishevelled.bio.protein.uniprot.EntryFeatureListener

Notify this listener of the entry feature has been read.

EntryFeature - Class in org.dishevelled.bio.protein.uniprot

Entry feature.

EntryFeature(String, String, String, String, String, String, String, Location, String, String) - Constructor for class org.dishevelled.bio.protein.uniprot.EntryFeature

Create a new entry feature.

EntryFeatureListener - Interface in org.dishevelled.bio.protein.uniprot

Entry feature listener.

entrySequence(EntrySequence) - Method in interface org.dishevelled.bio.protein.uniprot.EntrySequenceListener

Notify this listener of the entry sequence has been read.

EntrySequence - Class in org.dishevelled.bio.protein.uniprot

Entry sequence.

EntrySequence(int, int, String, String, int, boolean, String, String) - Constructor for class org.dishevelled.bio.protein.uniprot.EntrySequence

Create a new entry sequence.

EntrySequenceListener - Interface in org.dishevelled.bio.protein.uniprot

Entry sequence listener.

entrySummary(EntrySummary) - Method in interface org.dishevelled.bio.protein.uniprot.EntrySummaryListener

Notify this listener of the entry summary has been read.

EntrySummary - Class in org.dishevelled.bio.protein.uniprot

Entry summary.

EntrySummary(String, String, String, String, boolean, boolean, boolean) - Constructor for class org.dishevelled.bio.protein.uniprot.EntrySummary

Create a new entry summary.

EntrySummaryListener - Interface in org.dishevelled.bio.protein.uniprot

Entry summary listener.

error - Variable in class org.uniprot.uniprot.CommentType

Describes the error of the mass measurement in 'mass spectrometry' annotations.

event - Variable in class org.uniprot.uniprot.CommentType

EventType - Class in org.uniprot.uniprot

Describes the type of events that cause alternative products.

EventType() - Constructor for class org.uniprot.uniprot.EventType

evidence - Variable in class org.uniprot.uniprot.CofactorType

evidence - Variable in class org.uniprot.uniprot.CommentType

evidence - Variable in class org.uniprot.uniprot.DbReferenceType

evidence - Variable in class org.uniprot.uniprot.Entry

evidence - Variable in class org.uniprot.uniprot.EvidencedStringType

evidence - Variable in class org.uniprot.uniprot.FeatureType

evidence - Variable in class org.uniprot.uniprot.GeneLocationType

evidence - Variable in class org.uniprot.uniprot.GeneNameType

evidence - Variable in class org.uniprot.uniprot.IsoformType.Name

evidence - Variable in class org.uniprot.uniprot.KeywordType

evidence - Variable in class org.uniprot.uniprot.OrganismType

evidence - Variable in class org.uniprot.uniprot.PhysiologicalReactionType

evidence - Variable in class org.uniprot.uniprot.PositionType

evidence - Variable in class org.uniprot.uniprot.ReactionType

evidence - Variable in class org.uniprot.uniprot.ReferenceType

evidence - Variable in class org.uniprot.uniprot.SourceDataType.Plasmid

evidence - Variable in class org.uniprot.uniprot.SourceDataType.Strain

evidence - Variable in class org.uniprot.uniprot.SourceDataType.Tissue

evidence - Variable in class org.uniprot.uniprot.SourceDataType.Transposon

EvidencedStringType - Class in org.uniprot.uniprot

Java class for evidencedStringType complex type

EvidencedStringType() - Constructor for class org.uniprot.uniprot.EvidencedStringType

EvidenceType - Class in org.uniprot.uniprot

Describes the evidence for an annotation.

EvidenceType() - Constructor for class org.uniprot.uniprot.EvidenceType

experiments - Variable in class org.uniprot.uniprot.CommentType

F

feature - Variable in class org.uniprot.uniprot.Entry

FeatureType - Class in org.uniprot.uniprot

Describes different types of sequence annotations.

FeatureType() - Constructor for class org.uniprot.uniprot.FeatureType

first - Variable in class org.uniprot.uniprot.CitationType

Describes the first page of an article.

fragment - Variable in class org.uniprot.uniprot.SequenceType

fromDescription(String) - Static method in enum org.dishevelled.bio.protein.uniprot.PositionStatus

Return the position status with the specified description.

fromSymbol(String) - Static method in enum org.dishevelled.bio.protein.uniprot.PositionStatus

Return the position status with the specified symbol.

fullName - Variable in class org.uniprot.uniprot.ProteinType.AlternativeName

fullName - Variable in class org.uniprot.uniprot.ProteinType.RecommendedName

fullName - Variable in class org.uniprot.uniprot.ProteinType.SubmittedName

G

gene - Variable in class org.uniprot.uniprot.Entry

geneLocation - Variable in class org.uniprot.uniprot.Entry

GeneLocationType - Class in org.uniprot.uniprot

Describes non-nuclear gene locations (organelles and plasmids).

GeneLocationType() - Constructor for class org.uniprot.uniprot.GeneLocationType

GeneNameType - Class in org.uniprot.uniprot

Describes different types of gene designations.

GeneNameType() - Constructor for class org.uniprot.uniprot.GeneNameType

GeneType - Class in org.uniprot.uniprot

Describes a gene.

GeneType() - Constructor for class org.uniprot.uniprot.GeneType

getAbsorption() - Method in class org.uniprot.uniprot.CommentType

Gets the value of the absorption property.

getAccession() - Method in class org.dishevelled.bio.protein.uniprot.EntryFeature

Return the accession for this entry feature.

getAccession() - Method in class org.dishevelled.bio.protein.uniprot.EntrySequence

Return the accession for this entry sequence.

getAccession() - Method in class org.uniprot.uniprot.Entry

Gets the value of the accession property.

getAcronym() - Method in class org.uniprot.uniprot.CommentType.Disease

Gets the value of the acronym property.

getAllergenName() - Method in class org.uniprot.uniprot.ProteinType.Component

Gets the value of the allergenName property.

getAllergenName() - Method in class org.uniprot.uniprot.ProteinType.Domain

Gets the value of the allergenName property.

getAllergenName() - Method in class org.uniprot.uniprot.ProteinType

Gets the value of the allergenName property.

getAlternativeName() - Method in class org.uniprot.uniprot.ProteinType.Component

Gets the value of the alternativeName property.

getAlternativeName() - Method in class org.uniprot.uniprot.ProteinType.Domain

Gets the value of the alternativeName property.

getAlternativeName() - Method in class org.uniprot.uniprot.ProteinType

Gets the value of the alternativeName property.

getAuthorList() - Method in class org.uniprot.uniprot.CitationType

Describes the authors of a citation.

getBegin() - Method in class org.dishevelled.bio.protein.uniprot.Location

Return the begin position for this location, may be null.

getBegin() - Method in class org.uniprot.uniprot.LocationType

Gets the value of the begin property.

getBiotechName() - Method in class org.uniprot.uniprot.ProteinType.Component

Gets the value of the biotechName property.

getBiotechName() - Method in class org.uniprot.uniprot.ProteinType.Domain

Gets the value of the biotechName property.

getBiotechName() - Method in class org.uniprot.uniprot.ProteinType

Gets the value of the biotechName property.

getCdAntigenName() - Method in class org.uniprot.uniprot.ProteinType.Component

Gets the value of the cdAntigenName property.

getCdAntigenName() - Method in class org.uniprot.uniprot.ProteinType.Domain

Gets the value of the cdAntigenName property.

getCdAntigenName() - Method in class org.uniprot.uniprot.ProteinType

Gets the value of the cdAntigenName property.

getChecksum() - Method in class org.dishevelled.bio.protein.uniprot.EntrySequence

Return the checksum for this entry sequence.

getChecksum() - Method in class org.uniprot.uniprot.SequenceType

Gets the value of the checksum property.

getCitation() - Method in class org.uniprot.uniprot.ReferenceType

Gets the value of the citation property.

getCity() - Method in class org.uniprot.uniprot.CitationType

Describes the city where a book was published.

getCofactor() - Method in class org.uniprot.uniprot.CommentType

Gets the value of the cofactor property.

getComment() - Method in class org.uniprot.uniprot.Entry

Gets the value of the comment property.

getComponent() - Method in class org.uniprot.uniprot.ProteinType

Describes names of processed products.

getConflict() - Method in class org.uniprot.uniprot.CommentType

Used in 'sequence caution' annotations.

getConsortiumOrPerson() - Method in class org.uniprot.uniprot.NameListType

Gets the value of the consortiumOrPerson property.

getCopyright() - Method in class org.uniprot.uniprot.Uniprot

Gets the value of the copyright property.

getCountry() - Method in class org.uniprot.uniprot.CitationType

Describes the country where a thesis was made.

getCreated() - Method in class org.uniprot.uniprot.Entry

Gets the value of the created property.

getDataset() - Method in class org.uniprot.uniprot.Entry

Gets the value of the dataset property.

getDate() - Method in class org.uniprot.uniprot.CitationType

Gets the value of the date property.

getDb() - Method in class org.uniprot.uniprot.CitationType

Describes the database name of submissions.

getDbReference() - Method in class org.uniprot.uniprot.CitationType

Describes cross-references to bibliography databases (MEDLINE, PubMed, AGRICOLA) or other online resources (DOI).

getDbReference() - Method in class org.uniprot.uniprot.CofactorType

Gets the value of the dbReference property.

getDbReference() - Method in class org.uniprot.uniprot.CommentType.Disease

Gets the value of the dbReference property.

getDbReference() - Method in class org.uniprot.uniprot.Entry

Gets the value of the dbReference property.

getDbReference() - Method in class org.uniprot.uniprot.ImportedFromType

Gets the value of the dbReference property.

getDbReference() - Method in class org.uniprot.uniprot.InteractantType

Gets the value of the dbReference property.

getDbReference() - Method in class org.uniprot.uniprot.LigandPartType

Gets the value of the dbReference property.

getDbReference() - Method in class org.uniprot.uniprot.LigandType

Gets the value of the dbReference property.

getDbReference() - Method in class org.uniprot.uniprot.OrganismType

Describes a cross-reference to the NCBI taxonomy database.

getDbReference() - Method in class org.uniprot.uniprot.PhysiologicalReactionType

Gets the value of the dbReference property.

getDbReference() - Method in class org.uniprot.uniprot.ReactionType

Gets the value of the dbReference property.

getDbReference() - Method in class org.uniprot.uniprot.SourceType

Gets the value of the dbReference property.

getDescription() - Method in class org.dishevelled.bio.protein.uniprot.EntryFeature

Return the description for this entry feature, may be null.

getDescription() - Method in enum org.dishevelled.bio.protein.uniprot.PositionStatus

Return the description for this position status.

getDescription() - Method in class org.uniprot.uniprot.CommentType.Disease

Gets the value of the description property.

getDescription() - Method in class org.uniprot.uniprot.FeatureType

Gets the value of the description property.

getDirection() - Method in class org.uniprot.uniprot.PhysiologicalReactionType

Gets the value of the direction property.

getDisease() - Method in class org.uniprot.uniprot.CommentType

Used in 'disease' annotations.

getDomain() - Method in class org.uniprot.uniprot.ProteinType

Describes names of "domains".

getEcNumber() - Method in class org.uniprot.uniprot.ProteinType.AlternativeName

Gets the value of the ecNumber property.

getEcNumber() - Method in class org.uniprot.uniprot.ProteinType.RecommendedName

Gets the value of the ecNumber property.

getEcNumber() - Method in class org.uniprot.uniprot.ProteinType.SubmittedName

Gets the value of the ecNumber property.

getEditorList() - Method in class org.uniprot.uniprot.CitationType

Describes the editors of a book (only used for books).

getEnd() - Method in class org.dishevelled.bio.protein.uniprot.Location

Return the end position for this location, may be null.

getEnd() - Method in class org.uniprot.uniprot.LocationType

Gets the value of the end property.

getEntry() - Method in class org.uniprot.uniprot.Uniprot

Describes a UniProtKB entry.

getError() - Method in class org.uniprot.uniprot.CommentType

Describes the error of the mass measurement in 'mass spectrometry' annotations.

getEvent() - Method in class org.uniprot.uniprot.CommentType

Gets the value of the event property.

getEvidence() - Method in class org.dishevelled.bio.protein.uniprot.EntryFeature

Return the evidence for this entry feature, may be null.

getEvidence() - Method in class org.uniprot.uniprot.CofactorType

Gets the value of the evidence property.

getEvidence() - Method in class org.uniprot.uniprot.CommentType

Gets the value of the evidence property.

getEvidence() - Method in class org.uniprot.uniprot.DbReferenceType

Gets the value of the evidence property.

getEvidence() - Method in class org.uniprot.uniprot.Entry

Gets the value of the evidence property.

getEvidence() - Method in class org.uniprot.uniprot.EvidencedStringType

Gets the value of the evidence property.

getEvidence() - Method in class org.uniprot.uniprot.FeatureType

Gets the value of the evidence property.

getEvidence() - Method in class org.uniprot.uniprot.GeneLocationType

Gets the value of the evidence property.

getEvidence() - Method in class org.uniprot.uniprot.GeneNameType

Gets the value of the evidence property.

getEvidence() - Method in class org.uniprot.uniprot.IsoformType.Name

Gets the value of the evidence property.

getEvidence() - Method in class org.uniprot.uniprot.KeywordType

Gets the value of the evidence property.

getEvidence() - Method in class org.uniprot.uniprot.OrganismType

Gets the value of the evidence property.

getEvidence() - Method in class org.uniprot.uniprot.PhysiologicalReactionType

Gets the value of the evidence property.

getEvidence() - Method in class org.uniprot.uniprot.PositionType

Gets the value of the evidence property.

getEvidence() - Method in class org.uniprot.uniprot.ReactionType

Gets the value of the evidence property.

getEvidence() - Method in class org.uniprot.uniprot.ReferenceType

Gets the value of the evidence property.

getEvidence() - Method in class org.uniprot.uniprot.SourceDataType.Plasmid

Gets the value of the evidence property.

getEvidence() - Method in class org.uniprot.uniprot.SourceDataType.Strain

Gets the value of the evidence property.

getEvidence() - Method in class org.uniprot.uniprot.SourceDataType.Tissue

Gets the value of the evidence property.

getEvidence() - Method in class org.uniprot.uniprot.SourceDataType.Transposon

Gets the value of the evidence property.

getExperiments() - Method in class org.uniprot.uniprot.CommentType

Gets the value of the experiments property.

getFeature() - Method in class org.uniprot.uniprot.Entry

Gets the value of the feature property.

getFirst() - Method in class org.uniprot.uniprot.CitationType

Describes the first page of an article.

getFragment() - Method in class org.dishevelled.bio.protein.uniprot.EntrySequence

Return the fragment for this entry sequence, may be null.

getFragment() - Method in class org.uniprot.uniprot.SequenceType

Gets the value of the fragment property.

getFullName() - Method in class org.uniprot.uniprot.ProteinType.AlternativeName

Gets the value of the fullName property.

getFullName() - Method in class org.uniprot.uniprot.ProteinType.RecommendedName

Gets the value of the fullName property.

getFullName() - Method in class org.uniprot.uniprot.ProteinType.SubmittedName

Gets the value of the fullName property.

getGene() - Method in class org.uniprot.uniprot.Entry

Gets the value of the gene property.

getGeneLocation() - Method in class org.uniprot.uniprot.Entry

Gets the value of the geneLocation property.

getId() - Method in class org.dishevelled.bio.protein.uniprot.EntryFeature

Return the id for this entry feature, may be null.

getId() - Method in class org.uniprot.uniprot.CommentType.Conflict.Sequence

Gets the value of the id property.

getId() - Method in class org.uniprot.uniprot.CommentType.Disease

Gets the value of the id property.

getId() - Method in class org.uniprot.uniprot.DbReferenceType

Describes a unique database identifier.

getId() - Method in class org.uniprot.uniprot.FeatureType

Gets the value of the id property.

getId() - Method in class org.uniprot.uniprot.InteractantType

Gets the value of the id property.

getId() - Method in class org.uniprot.uniprot.IsoformType

Gets the value of the id property.

getId() - Method in class org.uniprot.uniprot.KeywordType

Gets the value of the id property.

getId() - Method in class org.uniprot.uniprot.MoleculeType

Gets the value of the id property.

getImportedFrom() - Method in class org.uniprot.uniprot.EvidenceType

Gets the value of the importedFrom property.

getInnName() - Method in class org.uniprot.uniprot.ProteinType.Component

Gets the value of the innName property.

getInnName() - Method in class org.uniprot.uniprot.ProteinType.Domain

Gets the value of the innName property.

getInnName() - Method in class org.uniprot.uniprot.ProteinType

Gets the value of the innName property.

getInstitute() - Method in class org.uniprot.uniprot.CitationType

Describes the institute where a thesis was made.

getIntactId() - Method in class org.uniprot.uniprot.InteractantType

Gets the value of the intactId property.

getInteractant() - Method in class org.uniprot.uniprot.CommentType

Gets the value of the interactant property.

getIsoform() - Method in class org.uniprot.uniprot.CommentType

Gets the value of the isoform property.

getKey() - Method in class org.uniprot.uniprot.EvidenceType

A unique key to link annotations (via 'evidence' attributes) to evidences.

getKey() - Method in class org.uniprot.uniprot.ReferenceType

Gets the value of the key property.

getKeyword() - Method in class org.uniprot.uniprot.Entry

Gets the value of the keyword property.

getKinetics() - Method in class org.uniprot.uniprot.CommentType

Gets the value of the kinetics property.

getKM() - Method in class org.uniprot.uniprot.CommentType.Kinetics

Gets the value of the km property.

getLabel() - Method in class org.uniprot.uniprot.InteractantType

Gets the value of the label property.

getLabel() - Method in class org.uniprot.uniprot.LigandPartType

Gets the value of the label property.

getLabel() - Method in class org.uniprot.uniprot.LigandType

Gets the value of the label property.

getLast() - Method in class org.uniprot.uniprot.CitationType

Describes the last page of an article.

getLength() - Method in class org.dishevelled.bio.protein.uniprot.EntrySequence

Return the length for this entry sequence.

getLength() - Method in class org.uniprot.uniprot.SequenceType

Gets the value of the length property.

getLigand() - Method in class org.dishevelled.bio.protein.uniprot.EntryFeature

Return the ligand for this entry feature, may be null.

getLigand() - Method in class org.uniprot.uniprot.FeatureType

Describes the chemical entity that is bound in annotations that describe binding sites.

getLigandPart() - Method in class org.dishevelled.bio.protein.uniprot.EntryFeature

Return the ligand part for this entry feature, may be null.

getLigandPart() - Method in class org.uniprot.uniprot.FeatureType

Describes the specific part of a molecule that is bound in annotations that describe binding sites.

getLineage() - Method in class org.dishevelled.bio.protein.uniprot.EntrySummary

Return the lineage for this entry summary, may be null.

getLineage() - Method in class org.uniprot.uniprot.OrganismType

Describes the lineage of the source organism.

getLink() - Method in class org.uniprot.uniprot.CommentType

Used in 'online information' annotations.

getLocation() - Method in class org.dishevelled.bio.protein.uniprot.EntryFeature

Return the location for this entry feature.

getLocation() - Method in class org.uniprot.uniprot.CommentType

Used in 'mass spectrometry' and 'sequence caution' annotations.

getLocation() - Method in class org.uniprot.uniprot.FeatureType

Describes the sequence coordinates of the annotation.

getLocation() - Method in class org.uniprot.uniprot.SubcellularLocationType

Gets the value of the location property.

getLocationType() - Method in class org.uniprot.uniprot.CommentType

Describes the type of sequence location in 'RNA editing' annotations.

getLocator() - Method in class org.uniprot.uniprot.CitationType

Describes the location (URL) of an online journal article.

getMass() - Method in class org.dishevelled.bio.protein.uniprot.EntrySequence

Return the mass for this entry sequence.

getMass() - Method in class org.uniprot.uniprot.CommentType

Describes the molecular mass in 'mass spectrometry' annotations.

getMass() - Method in class org.uniprot.uniprot.SequenceType

Gets the value of the mass property.

getMax() - Method in class org.uniprot.uniprot.CommentType.Absorption

Gets the value of the max property.

getMethod() - Method in class org.uniprot.uniprot.CommentType

Describes the experimental method in 'mass spectrometry' annotations.

getModified() - Method in class org.dishevelled.bio.protein.uniprot.EntrySequence

Return the last modified date for this entry sequence.

getModified() - Method in class org.uniprot.uniprot.Entry

Gets the value of the modified property.

getModified() - Method in class org.uniprot.uniprot.SequenceType

Gets the value of the modified property.

getMolecule() - Method in class org.uniprot.uniprot.CommentType

Gets the value of the molecule property.

getMolecule() - Method in class org.uniprot.uniprot.DbReferenceType

Gets the value of the molecule property.

getName() - Method in class org.uniprot.uniprot.CitationType

Describes the name of an (online) journal or book.

getName() - Method in class org.uniprot.uniprot.CofactorType

Gets the value of the name property.

getName() - Method in class org.uniprot.uniprot.CommentType.Disease

Gets the value of the name property.

getName() - Method in class org.uniprot.uniprot.CommentType

Describes an optional name for an 'online information'.

getName() - Method in class org.uniprot.uniprot.ConsortiumType

Gets the value of the name property.

getName() - Method in class org.uniprot.uniprot.Entry

Gets the value of the name property.

getName() - Method in class org.uniprot.uniprot.GeneLocationType

Gets the value of the name property.

getName() - Method in class org.uniprot.uniprot.GeneType

Gets the value of the name property.

getName() - Method in class org.uniprot.uniprot.IsoformType

Gets the value of the name property.

getName() - Method in class org.uniprot.uniprot.LigandPartType

Gets the value of the name property.

getName() - Method in class org.uniprot.uniprot.LigandType

Gets the value of the name property.

getName() - Method in class org.uniprot.uniprot.OrganismType

Describes the names of the source organism.

getName() - Method in class org.uniprot.uniprot.PersonType

Gets the value of the name property.

getNote() - Method in class org.uniprot.uniprot.LigandPartType

Gets the value of the note property.

getNote() - Method in class org.uniprot.uniprot.LigandType

Gets the value of the note property.

getNumber() - Method in class org.uniprot.uniprot.CitationType

Describes a patent number.

getOrganism() - Method in class org.dishevelled.bio.protein.uniprot.EntrySummary

Return the organism for this entry summary, may be null.

getOrganism() - Method in class org.uniprot.uniprot.Entry

Gets the value of the organism property.

getOrganismHost() - Method in class org.uniprot.uniprot.Entry

Gets the value of the organismHost property.

getOrganismId() - Method in class org.dishevelled.bio.protein.uniprot.EntrySummary

Return the organism id for this entry summary, may be null.

getOrientation() - Method in class org.uniprot.uniprot.SubcellularLocationType

Gets the value of the orientation property.

getOriginal() - Method in class org.dishevelled.bio.protein.uniprot.EntryFeature

Return the original sequence for this entry feature, may be null.

getOriginal() - Method in class org.uniprot.uniprot.FeatureType

Describes the original sequence in annotations that describe natural or artifical sequence variations.

getPhDependence() - Method in class org.uniprot.uniprot.CommentType

Gets the value of the phDependence property.

getPhysiologicalReaction() - Method in class org.uniprot.uniprot.CommentType

Gets the value of the physiologicalReaction property.

getPosition() - Method in class org.dishevelled.bio.protein.uniprot.Location

Return the position for this location, may be null.

getPosition() - Method in class org.dishevelled.bio.protein.uniprot.Position

Return the position, may be null.

getPosition() - Method in class org.uniprot.uniprot.LocationType

Gets the value of the position property.

getPosition() - Method in class org.uniprot.uniprot.PositionType

Gets the value of the position property.

getProperty() - Method in class org.uniprot.uniprot.DbReferenceType

Gets the value of the property property.

getProtein() - Method in class org.uniprot.uniprot.Entry

Gets the value of the protein property.

getProteinExistence() - Method in class org.uniprot.uniprot.Entry

Gets the value of the proteinExistence property.

getPublisher() - Method in class org.uniprot.uniprot.CitationType

Describes the publisher of a book.

getReaction() - Method in class org.uniprot.uniprot.CommentType

Gets the value of the reaction property.

getRecommendedName() - Method in class org.uniprot.uniprot.ProteinType.Component

Gets the value of the recommendedName property.

getRecommendedName() - Method in class org.uniprot.uniprot.ProteinType.Domain

Gets the value of the recommendedName property.

getRecommendedName() - Method in class org.uniprot.uniprot.ProteinType

Gets the value of the recommendedName property.

getRedoxPotential() - Method in class org.uniprot.uniprot.CommentType

Gets the value of the redoxPotential property.

getRef() - Method in class org.dishevelled.bio.protein.uniprot.EntryFeature

Return the ref for this entry feature, may be null.

getRef() - Method in class org.uniprot.uniprot.CommentType.Conflict

Refers to the 'key' attribute of a 'reference' element.

getRef() - Method in class org.uniprot.uniprot.FeatureType

Gets the value of the ref property.

getRef() - Method in class org.uniprot.uniprot.IsoformType.Sequence

Gets the value of the ref property.

getRef() - Method in class org.uniprot.uniprot.SourceType

Gets the value of the ref property.

getReference() - Method in class org.uniprot.uniprot.Entry

Gets the value of the reference property.

getResource() - Method in class org.uniprot.uniprot.CommentType.Conflict.Sequence

Gets the value of the resource property.

getScope() - Method in class org.uniprot.uniprot.ReferenceType

Describes the scope of a citation.

getSequence() - Method in class org.dishevelled.bio.protein.uniprot.EntrySequence

Return the sequence for this entry sequence.

getSequence() - Method in class org.dishevelled.bio.protein.uniprot.Location

Return the sequence for this location, may be null.

getSequence() - Method in class org.uniprot.uniprot.CommentType.Conflict

Gets the value of the sequence property.

getSequence() - Method in class org.uniprot.uniprot.Entry

Gets the value of the sequence property.

getSequence() - Method in class org.uniprot.uniprot.IsoformType

Gets the value of the sequence property.

getSequence() - Method in class org.uniprot.uniprot.LocationType

Gets the value of the sequence property.

getShortName() - Method in class org.uniprot.uniprot.ProteinType.AlternativeName

Gets the value of the shortName property.

getShortName() - Method in class org.uniprot.uniprot.ProteinType.RecommendedName

Gets the value of the shortName property.

getSource() - Method in class org.uniprot.uniprot.EvidenceType

Gets the value of the source property.

getSource() - Method in class org.uniprot.uniprot.ReferenceType

Gets the value of the source property.

getStatus() - Method in class org.dishevelled.bio.protein.uniprot.Position

Return the status for this position.

getStatus() - Method in class org.uniprot.uniprot.PositionType

Gets the value of the status property.

getStatus() - Method in class org.uniprot.uniprot.StatusType

Gets the value of the status property.

getStrainOrPlasmidOrTransposon() - Method in class org.uniprot.uniprot.SourceDataType

Gets the value of the strainOrPlasmidOrTransposon property.

getSubcellularLocation() - Method in class org.uniprot.uniprot.CommentType

Gets the value of the subcellularLocation property.

getSubmittedName() - Method in class org.uniprot.uniprot.ProteinType.Component

Gets the value of the submittedName property.

getSubmittedName() - Method in class org.uniprot.uniprot.ProteinType.Domain

Gets the value of the submittedName property.

getSubmittedName() - Method in class org.uniprot.uniprot.ProteinType

Gets the value of the submittedName property.

getSymbol() - Method in enum org.dishevelled.bio.protein.uniprot.PositionStatus

Return the symbol for this position status.

getTaxon() - Method in class org.uniprot.uniprot.OrganismType.Lineage

Gets the value of the taxon property.

getTemperatureDependence() - Method in class org.uniprot.uniprot.CommentType

Gets the value of the temperatureDependence property.

getText() - Method in class org.uniprot.uniprot.CommentType.Absorption

Gets the value of the text property.

getText() - Method in class org.uniprot.uniprot.CommentType

Gets the value of the text property.

getText() - Method in class org.uniprot.uniprot.CommentType.Kinetics

Gets the value of the text property.

getText() - Method in class org.uniprot.uniprot.CommentType.PhDependence

Gets the value of the text property.

getText() - Method in class org.uniprot.uniprot.CommentType.RedoxPotential

Gets the value of the text property.

getText() - Method in class org.uniprot.uniprot.CommentType.TemperatureDependence

Gets the value of the text property.

getText() - Method in class org.uniprot.uniprot.IsoformType

Gets the value of the text property.

getText() - Method in class org.uniprot.uniprot.ReactionType

Gets the value of the text property.

getTitle() - Method in class org.uniprot.uniprot.CitationType

Describes the title of a citation.

getTopology() - Method in class org.uniprot.uniprot.SubcellularLocationType

Gets the value of the topology property.

getType() - Method in class org.dishevelled.bio.protein.uniprot.EntryFeature

Return the type for this entry feature.

getType() - Method in class org.dishevelled.bio.protein.uniprot.EntrySummary

Return the type for this entry summary, may be null.

getType() - Method in class org.uniprot.uniprot.CitationType

Describes the type of a citation.

getType() - Method in class org.uniprot.uniprot.CommentType.Conflict

Gets the value of the type property.

getType() - Method in class org.uniprot.uniprot.CommentType

Describes the type of a general annotation.

getType() - Method in class org.uniprot.uniprot.DbReferenceType

Describes the name of the database.

getType() - Method in class org.uniprot.uniprot.EventType

Gets the value of the type property.

getType() - Method in class org.uniprot.uniprot.EvidenceType

Describes the type of an evidence using the Evidence Code Ontology (http://www.obofoundry.org/cgi-bin/detail.cgi?

getType() - Method in class org.uniprot.uniprot.FeatureType

Describes the type of a sequence annotation.

getType() - Method in class org.uniprot.uniprot.GeneLocationType

Gets the value of the type property.

getType() - Method in class org.uniprot.uniprot.GeneNameType

Gets the value of the type property.

getType() - Method in class org.uniprot.uniprot.IsoformType.Sequence

Gets the value of the type property.

getType() - Method in class org.uniprot.uniprot.OrganismNameType

Gets the value of the type property.

getType() - Method in class org.uniprot.uniprot.PropertyType

Gets the value of the type property.

getType() - Method in class org.uniprot.uniprot.ProteinExistenceType

Gets the value of the type property.

getUri() - Method in class org.uniprot.uniprot.CommentType.Link

Gets the value of the uri property.

getValue() - Method in class org.uniprot.uniprot.EvidencedStringType

Gets the value of the value property.

getValue() - Method in class org.uniprot.uniprot.GeneNameType

Gets the value of the value property.

getValue() - Method in class org.uniprot.uniprot.IsoformType.Name

Gets the value of the value property.

getValue() - Method in class org.uniprot.uniprot.KeywordType

Gets the value of the value property.

getValue() - Method in class org.uniprot.uniprot.MoleculeType

Gets the value of the value property.

getValue() - Method in class org.uniprot.uniprot.OrganismNameType

Gets the value of the value property.

getValue() - Method in class org.uniprot.uniprot.PropertyType

Gets the value of the value property.

getValue() - Method in class org.uniprot.uniprot.SequenceType

Gets the value of the value property.

getValue() - Method in class org.uniprot.uniprot.SourceDataType.Plasmid

Gets the value of the value property.

getValue() - Method in class org.uniprot.uniprot.SourceDataType.Strain

Gets the value of the value property.

getValue() - Method in class org.uniprot.uniprot.SourceDataType.Tissue

Gets the value of the value property.

getValue() - Method in class org.uniprot.uniprot.SourceDataType.Transposon

Gets the value of the value property.

getValue() - Method in class org.uniprot.uniprot.StatusType

Gets the value of the value property.

getVariation() - Method in class org.uniprot.uniprot.FeatureType

Describes the variant sequence in annotations that describe natural or artifical sequence variations.

getVariations() - Method in class org.dishevelled.bio.protein.uniprot.EntryFeature

Return the sequence variations for this entry feature, may be null.

getVersion() - Method in class org.dishevelled.bio.protein.uniprot.EntrySequence

Return the version for this entry sequence.

getVersion() - Method in class org.uniprot.uniprot.CommentType.Conflict.Sequence

Gets the value of the version property.

getVersion() - Method in class org.uniprot.uniprot.Entry

Gets the value of the version property.

getVersion() - Method in class org.uniprot.uniprot.SequenceType

Gets the value of the version property.

getVmax() - Method in class org.uniprot.uniprot.CommentType.Kinetics

Gets the value of the vmax property.

getVolume() - Method in class org.uniprot.uniprot.CitationType

Describes the volume of a journal or book.

GREATER_THAN - Enum constant in enum org.dishevelled.bio.protein.uniprot.PositionStatus

Greater than position status, >.

H

hasStructure() - Method in class org.dishevelled.bio.protein.uniprot.EntrySummary

Return true if this entry summary has structure.

I

id - Variable in class org.uniprot.uniprot.CommentType.Conflict.Sequence

id - Variable in class org.uniprot.uniprot.CommentType.Disease

id - Variable in class org.uniprot.uniprot.DbReferenceType

Describes a unique database identifier.

id - Variable in class org.uniprot.uniprot.FeatureType

id - Variable in class org.uniprot.uniprot.InteractantType

id - Variable in class org.uniprot.uniprot.IsoformType

id - Variable in class org.uniprot.uniprot.KeywordType

id - Variable in class org.uniprot.uniprot.MoleculeType

importedFrom - Variable in class org.uniprot.uniprot.EvidenceType

ImportedFromType - Class in org.uniprot.uniprot

Describes the source of the evidence, when it is not assigned by UniProt, but imported from an external database.

ImportedFromType() - Constructor for class org.uniprot.uniprot.ImportedFromType

innName - Variable in class org.uniprot.uniprot.ProteinType.Component

innName - Variable in class org.uniprot.uniprot.ProteinType.Domain

innName - Variable in class org.uniprot.uniprot.ProteinType

institute - Variable in class org.uniprot.uniprot.CitationType

Describes the institute where a thesis was made.

intactId - Variable in class org.uniprot.uniprot.InteractantType

interactant - Variable in class org.uniprot.uniprot.CommentType

InteractantType - Class in org.uniprot.uniprot

Java class for interactantType complex type

InteractantType() - Constructor for class org.uniprot.uniprot.InteractantType

isoform - Variable in class org.uniprot.uniprot.CommentType

IsoformType - Class in org.uniprot.uniprot

Describes isoforms in 'alternative products' annotations.

IsoformType() - Constructor for class org.uniprot.uniprot.IsoformType

IsoformType.Name - Class in org.uniprot.uniprot

Java class for anonymous complex type

IsoformType.Sequence - Class in org.uniprot.uniprot

Java class for anonymous complex type

isOrganismsDiffer() - Method in class org.uniprot.uniprot.CommentType

Gets the value of the organismsDiffer property.

isPrecursor() - Method in class org.dishevelled.bio.protein.uniprot.EntrySequence

Return true if this entry sequence is a precursor.

isPrecursor() - Method in class org.uniprot.uniprot.SequenceType

Gets the value of the precursor property.

isReviewed() - Method in class org.dishevelled.bio.protein.uniprot.EntrySummary

Return true if this entry summary is reviewed.

isUnreviewed() - Method in class org.dishevelled.bio.protein.uniprot.EntrySummary

Return true if this entry summary is unreviewed.

K

key - Variable in class org.uniprot.uniprot.EvidenceType

A unique key to link annotations (via 'evidence' attributes) to evidences.

key - Variable in class org.uniprot.uniprot.ReferenceType

keyword - Variable in class org.uniprot.uniprot.Entry

KeywordType - Class in org.uniprot.uniprot

Java class for keywordType complex type

KeywordType() - Constructor for class org.uniprot.uniprot.KeywordType

kinetics - Variable in class org.uniprot.uniprot.CommentType

Kinetics() - Constructor for class org.uniprot.uniprot.CommentType.Kinetics

km - Variable in class org.uniprot.uniprot.CommentType.Kinetics

L

label - Variable in class org.uniprot.uniprot.InteractantType

label - Variable in class org.uniprot.uniprot.LigandPartType

label - Variable in class org.uniprot.uniprot.LigandType

last - Variable in class org.uniprot.uniprot.CitationType

Describes the last page of an article.

length - Variable in class org.uniprot.uniprot.SequenceType

LESS_THAN - Enum constant in enum org.dishevelled.bio.protein.uniprot.PositionStatus

Less than position status, <.

ligand - Variable in class org.uniprot.uniprot.FeatureType

Describes the chemical entity that is bound in annotations that describe binding sites.

ligandPart - Variable in class org.uniprot.uniprot.FeatureType

Describes the specific part of a molecule that is bound in annotations that describe binding sites.

LigandPartType - Class in org.uniprot.uniprot

Describes a ligand part.

LigandPartType() - Constructor for class org.uniprot.uniprot.LigandPartType

LigandType - Class in org.uniprot.uniprot

Describes a ligand.

LigandType() - Constructor for class org.uniprot.uniprot.LigandType

lineage - Variable in class org.uniprot.uniprot.OrganismType

Describes the lineage of the source organism.

Lineage() - Constructor for class org.uniprot.uniprot.OrganismType.Lineage

link - Variable in class org.uniprot.uniprot.CommentType

Used in 'online information' annotations.

Link() - Constructor for class org.uniprot.uniprot.CommentType.Link

location - Variable in class org.uniprot.uniprot.CommentType

Used in 'mass spectrometry' and 'sequence caution' annotations.

location - Variable in class org.uniprot.uniprot.FeatureType

Describes the sequence coordinates of the annotation.

location - Variable in class org.uniprot.uniprot.SubcellularLocationType

Location - Class in org.dishevelled.bio.protein.uniprot

Location.

Location(Position, String) - Constructor for class org.dishevelled.bio.protein.uniprot.Location

Create a new location with the specified position.

Location(Position, Position, String) - Constructor for class org.dishevelled.bio.protein.uniprot.Location

Create a new location with the specified begin and end positions.

locationType - Variable in class org.uniprot.uniprot.CommentType

Describes the type of sequence location in 'RNA editing' annotations.

LocationType - Class in org.uniprot.uniprot

Describes a sequence location as either a range with a begin and end or as a position.

LocationType() - Constructor for class org.uniprot.uniprot.LocationType

locator - Variable in class org.uniprot.uniprot.CitationType

Describes the location (URL) of an online journal article.

M

mass - Variable in class org.uniprot.uniprot.CommentType

Describes the molecular mass in 'mass spectrometry' annotations.

mass - Variable in class org.uniprot.uniprot.SequenceType

max - Variable in class org.uniprot.uniprot.CommentType.Absorption

method - Variable in class org.uniprot.uniprot.CommentType

Describes the experimental method in 'mass spectrometry' annotations.

modified - Variable in class org.uniprot.uniprot.Entry

modified - Variable in class org.uniprot.uniprot.SequenceType

molecule - Variable in class org.uniprot.uniprot.CommentType

molecule - Variable in class org.uniprot.uniprot.DbReferenceType

MoleculeType - Class in org.uniprot.uniprot

Describes a molecule by name or unique identifier.

MoleculeType() - Constructor for class org.uniprot.uniprot.MoleculeType

N

name - Variable in class org.uniprot.uniprot.CitationType

Describes the name of an (online) journal or book.

name - Variable in class org.uniprot.uniprot.CofactorType

name - Variable in class org.uniprot.uniprot.CommentType.Disease

name - Variable in class org.uniprot.uniprot.CommentType

Describes an optional name for an 'online information'.

name - Variable in class org.uniprot.uniprot.ConsortiumType

name - Variable in class org.uniprot.uniprot.Entry

name - Variable in class org.uniprot.uniprot.GeneLocationType

name - Variable in class org.uniprot.uniprot.GeneType

name - Variable in class org.uniprot.uniprot.IsoformType

name - Variable in class org.uniprot.uniprot.LigandPartType

name - Variable in class org.uniprot.uniprot.LigandType

name - Variable in class org.uniprot.uniprot.OrganismType

Describes the names of the source organism.

name - Variable in class org.uniprot.uniprot.PersonType

Name() - Constructor for class org.uniprot.uniprot.IsoformType.Name

NameListType - Class in org.uniprot.uniprot

Java class for nameListType complex type

NameListType() - Constructor for class org.uniprot.uniprot.NameListType

note - Variable in class org.uniprot.uniprot.LigandPartType

note - Variable in class org.uniprot.uniprot.LigandType

number - Variable in class org.uniprot.uniprot.CitationType

Describes a patent number.

O

ObjectFactory - Class in org.uniprot.uniprot

This object contains factory methods for each Java content interface and Java element interface generated in the org.uniprot.uniprot package.

ObjectFactory() - Constructor for class org.uniprot.uniprot.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: org.uniprot.uniprot

org.dishevelled.bio.protein - package org.dishevelled.bio.protein

Protein sequences and metadata.

org.dishevelled.bio.protein.uniprot - package org.dishevelled.bio.protein.uniprot

UniProt protein sequences and metadata.

org.uniprot.uniprot - package org.uniprot.uniprot

organism - Variable in class org.uniprot.uniprot.Entry

organismHost - Variable in class org.uniprot.uniprot.Entry

OrganismNameType - Class in org.uniprot.uniprot

Describes different types of source organism names.

OrganismNameType() - Constructor for class org.uniprot.uniprot.OrganismNameType

organismsDiffer - Variable in class org.uniprot.uniprot.CommentType

OrganismType - Class in org.uniprot.uniprot

Describes the source organism.

OrganismType() - Constructor for class org.uniprot.uniprot.OrganismType

OrganismType.Lineage - Class in org.uniprot.uniprot

Java class for anonymous complex type

orientation - Variable in class org.uniprot.uniprot.SubcellularLocationType

original - Variable in class org.uniprot.uniprot.FeatureType

Describes the original sequence in annotations that describe natural or artifical sequence variations.

P

PersonType - Class in org.uniprot.uniprot

Java class for personType complex type

PersonType() - Constructor for class org.uniprot.uniprot.PersonType

phDependence - Variable in class org.uniprot.uniprot.CommentType

PhDependence() - Constructor for class org.uniprot.uniprot.CommentType.PhDependence

physiologicalReaction - Variable in class org.uniprot.uniprot.CommentType

PhysiologicalReactionType - Class in org.uniprot.uniprot

Describes a physiological reaction.

PhysiologicalReactionType() - Constructor for class org.uniprot.uniprot.PhysiologicalReactionType

Plasmid() - Constructor for class org.uniprot.uniprot.SourceDataType.Plasmid

position - Variable in class org.uniprot.uniprot.LocationType

position - Variable in class org.uniprot.uniprot.PositionType

Position - Class in org.dishevelled.bio.protein.uniprot

Position.

Position(Integer, PositionStatus) - Constructor for class org.dishevelled.bio.protein.uniprot.Position

Create a new position.

PositionStatus - Enum in org.dishevelled.bio.protein.uniprot

Position status.

PositionType - Class in org.uniprot.uniprot

Java class for positionType complex type

PositionType() - Constructor for class org.uniprot.uniprot.PositionType

precursor - Variable in class org.uniprot.uniprot.SequenceType

property - Variable in class org.uniprot.uniprot.DbReferenceType

PropertyType - Class in org.uniprot.uniprot

Java class for propertyType complex type

PropertyType() - Constructor for class org.uniprot.uniprot.PropertyType

protein - Variable in class org.uniprot.uniprot.Entry

proteinExistence - Variable in class org.uniprot.uniprot.Entry

ProteinExistenceType - Class in org.uniprot.uniprot

Describes the evidence for the protein's existence.

ProteinExistenceType() - Constructor for class org.uniprot.uniprot.ProteinExistenceType

ProteinType - Class in org.uniprot.uniprot

Describes the names for the protein and parts thereof.

ProteinType() - Constructor for class org.uniprot.uniprot.ProteinType

ProteinType.AlternativeName - Class in org.uniprot.uniprot

Java class for anonymous complex type

ProteinType.Component - Class in org.uniprot.uniprot

Java class for anonymous complex type

ProteinType.Domain - Class in org.uniprot.uniprot

Java class for anonymous complex type

ProteinType.RecommendedName - Class in org.uniprot.uniprot

Java class for anonymous complex type

ProteinType.SubmittedName - Class in org.uniprot.uniprot

Java class for anonymous complex type

publisher - Variable in class org.uniprot.uniprot.CitationType

Describes the publisher of a book.

R

reaction - Variable in class org.uniprot.uniprot.CommentType

ReactionType - Class in org.uniprot.uniprot

Describes a chemical reaction.

ReactionType() - Constructor for class org.uniprot.uniprot.ReactionType

read(Reader) - Static method in class org.dishevelled.bio.protein.uniprot.UniprotJaxbReader

Read UniProt XML from the specified reader via JAXB.

recommendedName - Variable in class org.uniprot.uniprot.ProteinType.Component

recommendedName - Variable in class org.uniprot.uniprot.ProteinType.Domain

recommendedName - Variable in class org.uniprot.uniprot.ProteinType

RecommendedName() - Constructor for class org.uniprot.uniprot.ProteinType.RecommendedName

redoxPotential - Variable in class org.uniprot.uniprot.CommentType

RedoxPotential() - Constructor for class org.uniprot.uniprot.CommentType.RedoxPotential

ref - Variable in class org.uniprot.uniprot.CommentType.Conflict

Refers to the 'key' attribute of a 'reference' element.

ref - Variable in class org.uniprot.uniprot.FeatureType

ref - Variable in class org.uniprot.uniprot.IsoformType.Sequence

ref - Variable in class org.uniprot.uniprot.SourceType

reference - Variable in class org.uniprot.uniprot.Entry

ReferenceType - Class in org.uniprot.uniprot

Describes a citation and a summary of its content.

ReferenceType() - Constructor for class org.uniprot.uniprot.ReferenceType

resource - Variable in class org.uniprot.uniprot.CommentType.Conflict.Sequence

S

scope - Variable in class org.uniprot.uniprot.ReferenceType

Describes the scope of a citation.

sequence - Variable in class org.uniprot.uniprot.CommentType.Conflict

sequence - Variable in class org.uniprot.uniprot.Entry

sequence - Variable in class org.uniprot.uniprot.IsoformType

sequence - Variable in class org.uniprot.uniprot.LocationType

Sequence() - Constructor for class org.uniprot.uniprot.CommentType.Conflict.Sequence

Sequence() - Constructor for class org.uniprot.uniprot.IsoformType.Sequence

SequenceType - Class in org.uniprot.uniprot

Java class for sequenceType complex type

SequenceType() - Constructor for class org.uniprot.uniprot.SequenceType

setAbsorption(CommentType.Absorption) - Method in class org.uniprot.uniprot.CommentType

Sets the value of the absorption property.

setAcronym(String) - Method in class org.uniprot.uniprot.CommentType.Disease

Sets the value of the acronym property.

setAllergenName(EvidencedStringType) - Method in class org.uniprot.uniprot.ProteinType.Component

Sets the value of the allergenName property.

setAllergenName(EvidencedStringType) - Method in class org.uniprot.uniprot.ProteinType.Domain

Sets the value of the allergenName property.

setAllergenName(EvidencedStringType) - Method in class org.uniprot.uniprot.ProteinType

Sets the value of the allergenName property.

setAuthorList(NameListType) - Method in class org.uniprot.uniprot.CitationType

Sets the value of the authorList property.

setBegin(PositionType) - Method in class org.uniprot.uniprot.LocationType

Sets the value of the begin property.

setBiotechName(EvidencedStringType) - Method in class org.uniprot.uniprot.ProteinType.Component

Sets the value of the biotechName property.

setBiotechName(EvidencedStringType) - Method in class org.uniprot.uniprot.ProteinType.Domain

Sets the value of the biotechName property.

setBiotechName(EvidencedStringType) - Method in class org.uniprot.uniprot.ProteinType

Sets the value of the biotechName property.

setChecksum(String) - Method in class org.uniprot.uniprot.SequenceType

Sets the value of the checksum property.

setCitation(CitationType) - Method in class org.uniprot.uniprot.ReferenceType

Sets the value of the citation property.

setCity(String) - Method in class org.uniprot.uniprot.CitationType

Sets the value of the city property.

setConflict(CommentType.Conflict) - Method in class org.uniprot.uniprot.CommentType

Sets the value of the conflict property.

setCopyright(String) - Method in class org.uniprot.uniprot.Uniprot

Sets the value of the copyright property.

setCountry(String) - Method in class org.uniprot.uniprot.CitationType

Sets the value of the country property.

setCreated(XMLGregorianCalendar) - Method in class org.uniprot.uniprot.Entry

Sets the value of the created property.

setDataset(String) - Method in class org.uniprot.uniprot.Entry

Sets the value of the dataset property.

setDate(String) - Method in class org.uniprot.uniprot.CitationType

Sets the value of the date property.

setDb(String) - Method in class org.uniprot.uniprot.CitationType

Sets the value of the db property.

setDbReference(DbReferenceType) - Method in class org.uniprot.uniprot.CofactorType

Sets the value of the dbReference property.

setDbReference(DbReferenceType) - Method in class org.uniprot.uniprot.CommentType.Disease

Sets the value of the dbReference property.

setDbReference(DbReferenceType) - Method in class org.uniprot.uniprot.ImportedFromType

Sets the value of the dbReference property.

setDbReference(DbReferenceType) - Method in class org.uniprot.uniprot.InteractantType

Sets the value of the dbReference property.

setDbReference(DbReferenceType) - Method in class org.uniprot.uniprot.LigandPartType

Sets the value of the dbReference property.

setDbReference(DbReferenceType) - Method in class org.uniprot.uniprot.LigandType

Sets the value of the dbReference property.

setDbReference(DbReferenceType) - Method in class org.uniprot.uniprot.PhysiologicalReactionType

Sets the value of the dbReference property.

setDbReference(DbReferenceType) - Method in class org.uniprot.uniprot.SourceType

Sets the value of the dbReference property.

setDescription(String) - Method in class org.uniprot.uniprot.CommentType.Disease

Sets the value of the description property.

setDescription(String) - Method in class org.uniprot.uniprot.FeatureType

Sets the value of the description property.

setDirection(String) - Method in class org.uniprot.uniprot.PhysiologicalReactionType

Sets the value of the direction property.

setDisease(CommentType.Disease) - Method in class org.uniprot.uniprot.CommentType

Sets the value of the disease property.

setEditorList(NameListType) - Method in class org.uniprot.uniprot.CitationType

Sets the value of the editorList property.

setEnd(PositionType) - Method in class org.uniprot.uniprot.LocationType

Sets the value of the end property.

setError(String) - Method in class org.uniprot.uniprot.CommentType

Sets the value of the error property.

setExperiments(Integer) - Method in class org.uniprot.uniprot.CommentType

Sets the value of the experiments property.

setFirst(String) - Method in class org.uniprot.uniprot.CitationType

Sets the value of the first property.

setFragment(String) - Method in class org.uniprot.uniprot.SequenceType

Sets the value of the fragment property.

setFullName(EvidencedStringType) - Method in class org.uniprot.uniprot.ProteinType.AlternativeName

Sets the value of the fullName property.

setFullName(EvidencedStringType) - Method in class org.uniprot.uniprot.ProteinType.RecommendedName

Sets the value of the fullName property.

setFullName(EvidencedStringType) - Method in class org.uniprot.uniprot.ProteinType.SubmittedName

Sets the value of the fullName property.

setId(String) - Method in class org.uniprot.uniprot.CommentType.Conflict.Sequence

Sets the value of the id property.

setId(String) - Method in class org.uniprot.uniprot.CommentType.Disease

Sets the value of the id property.

setId(String) - Method in class org.uniprot.uniprot.DbReferenceType

Sets the value of the id property.

setId(String) - Method in class org.uniprot.uniprot.FeatureType

Sets the value of the id property.

setId(String) - Method in class org.uniprot.uniprot.InteractantType

Sets the value of the id property.

setId(String) - Method in class org.uniprot.uniprot.KeywordType

Sets the value of the id property.

setId(String) - Method in class org.uniprot.uniprot.MoleculeType

Sets the value of the id property.

setImportedFrom(ImportedFromType) - Method in class org.uniprot.uniprot.EvidenceType

Sets the value of the importedFrom property.

setInstitute(String) - Method in class org.uniprot.uniprot.CitationType

Sets the value of the institute property.

setIntactId(String) - Method in class org.uniprot.uniprot.InteractantType

Sets the value of the intactId property.

setKey(String) - Method in class org.uniprot.uniprot.ReferenceType

Sets the value of the key property.

setKey(BigInteger) - Method in class org.uniprot.uniprot.EvidenceType

Sets the value of the key property.

setKinetics(CommentType.Kinetics) - Method in class org.uniprot.uniprot.CommentType

Sets the value of the kinetics property.

setLabel(String) - Method in class org.uniprot.uniprot.InteractantType

Sets the value of the label property.

setLabel(String) - Method in class org.uniprot.uniprot.LigandPartType

Sets the value of the label property.

setLabel(String) - Method in class org.uniprot.uniprot.LigandType

Sets the value of the label property.

setLast(String) - Method in class org.uniprot.uniprot.CitationType

Sets the value of the last property.

setLength(int) - Method in class org.uniprot.uniprot.SequenceType

Sets the value of the length property.

setLigand(LigandType) - Method in class org.uniprot.uniprot.FeatureType

Sets the value of the ligand property.

setLigandPart(LigandPartType) - Method in class org.uniprot.uniprot.FeatureType

Sets the value of the ligandPart property.

setLineage(OrganismType.Lineage) - Method in class org.uniprot.uniprot.OrganismType

Sets the value of the lineage property.

setLocation(LocationType) - Method in class org.uniprot.uniprot.FeatureType

Sets the value of the location property.

setLocationType(String) - Method in class org.uniprot.uniprot.CommentType

Sets the value of the locationType property.

setLocator(String) - Method in class org.uniprot.uniprot.CitationType

Sets the value of the locator property.

setMass(int) - Method in class org.uniprot.uniprot.SequenceType

Sets the value of the mass property.

setMass(Float) - Method in class org.uniprot.uniprot.CommentType

Sets the value of the mass property.

setMax(EvidencedStringType) - Method in class org.uniprot.uniprot.CommentType.Absorption

Sets the value of the max property.

setMethod(String) - Method in class org.uniprot.uniprot.CommentType

Sets the value of the method property.

setModified(XMLGregorianCalendar) - Method in class org.uniprot.uniprot.Entry

Sets the value of the modified property.

setModified(XMLGregorianCalendar) - Method in class org.uniprot.uniprot.SequenceType

Sets the value of the modified property.

setMolecule(MoleculeType) - Method in class org.uniprot.uniprot.CommentType

Sets the value of the molecule property.

setMolecule(MoleculeType) - Method in class org.uniprot.uniprot.DbReferenceType

Sets the value of the molecule property.

setName(String) - Method in class org.uniprot.uniprot.CitationType

Sets the value of the name property.

setName(String) - Method in class org.uniprot.uniprot.CofactorType

Sets the value of the name property.

setName(String) - Method in class org.uniprot.uniprot.CommentType.Disease

Sets the value of the name property.

setName(String) - Method in class org.uniprot.uniprot.CommentType

Sets the value of the name property.

setName(String) - Method in class org.uniprot.uniprot.ConsortiumType

Sets the value of the name property.

setName(String) - Method in class org.uniprot.uniprot.LigandPartType

Sets the value of the name property.

setName(String) - Method in class org.uniprot.uniprot.LigandType

Sets the value of the name property.

setName(String) - Method in class org.uniprot.uniprot.PersonType

Sets the value of the name property.

setNote(String) - Method in class org.uniprot.uniprot.LigandPartType

Sets the value of the note property.

setNote(String) - Method in class org.uniprot.uniprot.LigandType

Sets the value of the note property.

setNumber(String) - Method in class org.uniprot.uniprot.CitationType

Sets the value of the number property.

setOrganism(OrganismType) - Method in class org.uniprot.uniprot.Entry

Sets the value of the organism property.

setOrganismsDiffer(Boolean) - Method in class org.uniprot.uniprot.CommentType

Sets the value of the organismsDiffer property.

setOriginal(String) - Method in class org.uniprot.uniprot.FeatureType

Sets the value of the original property.

setPhDependence(CommentType.PhDependence) - Method in class org.uniprot.uniprot.CommentType

Sets the value of the phDependence property.

setPosition(BigInteger) - Method in class org.uniprot.uniprot.PositionType

Sets the value of the position property.

setPosition(PositionType) - Method in class org.uniprot.uniprot.LocationType

Sets the value of the position property.

setPrecursor(Boolean) - Method in class org.uniprot.uniprot.SequenceType

Sets the value of the precursor property.

setProtein(ProteinType) - Method in class org.uniprot.uniprot.Entry

Sets the value of the protein property.

setProteinExistence(ProteinExistenceType) - Method in class org.uniprot.uniprot.Entry

Sets the value of the proteinExistence property.

setPublisher(String) - Method in class org.uniprot.uniprot.CitationType

Sets the value of the publisher property.

setReaction(ReactionType) - Method in class org.uniprot.uniprot.CommentType

Sets the value of the reaction property.

setRecommendedName(ProteinType.RecommendedName) - Method in class org.uniprot.uniprot.ProteinType.Component

Sets the value of the recommendedName property.

setRecommendedName(ProteinType.RecommendedName) - Method in class org.uniprot.uniprot.ProteinType.Domain

Sets the value of the recommendedName property.

setRecommendedName(ProteinType.RecommendedName) - Method in class org.uniprot.uniprot.ProteinType

Sets the value of the recommendedName property.

setRedoxPotential(CommentType.RedoxPotential) - Method in class org.uniprot.uniprot.CommentType

Sets the value of the redoxPotential property.

setRef(String) - Method in class org.uniprot.uniprot.CommentType.Conflict

Sets the value of the ref property.

setRef(String) - Method in class org.uniprot.uniprot.FeatureType

Sets the value of the ref property.

setRef(String) - Method in class org.uniprot.uniprot.IsoformType.Sequence

Sets the value of the ref property.

setRef(BigInteger) - Method in class org.uniprot.uniprot.SourceType

Sets the value of the ref property.

setResource(String) - Method in class org.uniprot.uniprot.CommentType.Conflict.Sequence

Sets the value of the resource property.

setSequence(String) - Method in class org.uniprot.uniprot.LocationType

Sets the value of the sequence property.

setSequence(CommentType.Conflict.Sequence) - Method in class org.uniprot.uniprot.CommentType.Conflict

Sets the value of the sequence property.

setSequence(IsoformType.Sequence) - Method in class org.uniprot.uniprot.IsoformType

Sets the value of the sequence property.

setSequence(SequenceType) - Method in class org.uniprot.uniprot.Entry

Sets the value of the sequence property.

setSource(SourceDataType) - Method in class org.uniprot.uniprot.ReferenceType

Sets the value of the source property.

setSource(SourceType) - Method in class org.uniprot.uniprot.EvidenceType

Sets the value of the source property.

setStatus(String) - Method in class org.uniprot.uniprot.PositionType

Sets the value of the status property.

setStatus(String) - Method in class org.uniprot.uniprot.StatusType

Sets the value of the status property.

setTemperatureDependence(CommentType.TemperatureDependence) - Method in class org.uniprot.uniprot.CommentType

Sets the value of the temperatureDependence property.

setText(String) - Method in class org.uniprot.uniprot.ReactionType

Sets the value of the text property.

setTitle(String) - Method in class org.uniprot.uniprot.CitationType

Sets the value of the title property.

setType(String) - Method in class org.uniprot.uniprot.CitationType

Sets the value of the type property.

setType(String) - Method in class org.uniprot.uniprot.CommentType.Conflict

Sets the value of the type property.

setType(String) - Method in class org.uniprot.uniprot.CommentType

Sets the value of the type property.

setType(String) - Method in class org.uniprot.uniprot.DbReferenceType

Sets the value of the type property.

setType(String) - Method in class org.uniprot.uniprot.EventType

Sets the value of the type property.

setType(String) - Method in class org.uniprot.uniprot.EvidenceType

Sets the value of the type property.

setType(String) - Method in class org.uniprot.uniprot.FeatureType

Sets the value of the type property.

setType(String) - Method in class org.uniprot.uniprot.GeneLocationType

Sets the value of the type property.

setType(String) - Method in class org.uniprot.uniprot.GeneNameType

Sets the value of the type property.

setType(String) - Method in class org.uniprot.uniprot.IsoformType.Sequence

Sets the value of the type property.

setType(String) - Method in class org.uniprot.uniprot.OrganismNameType

Sets the value of the type property.

setType(String) - Method in class org.uniprot.uniprot.PropertyType

Sets the value of the type property.

setType(String) - Method in class org.uniprot.uniprot.ProteinExistenceType

Sets the value of the type property.

setUri(String) - Method in class org.uniprot.uniprot.CommentType.Link

Sets the value of the uri property.

setValue(String) - Method in class org.uniprot.uniprot.EvidencedStringType

Sets the value of the value property.

setValue(String) - Method in class org.uniprot.uniprot.GeneNameType

Sets the value of the value property.

setValue(String) - Method in class org.uniprot.uniprot.IsoformType.Name

Sets the value of the value property.

setValue(String) - Method in class org.uniprot.uniprot.KeywordType

Sets the value of the value property.

setValue(String) - Method in class org.uniprot.uniprot.MoleculeType

Sets the value of the value property.

setValue(String) - Method in class org.uniprot.uniprot.OrganismNameType

Sets the value of the value property.

setValue(String) - Method in class org.uniprot.uniprot.PropertyType

Sets the value of the value property.

setValue(String) - Method in class org.uniprot.uniprot.SequenceType

Sets the value of the value property.

setValue(String) - Method in class org.uniprot.uniprot.SourceDataType.Plasmid

Sets the value of the value property.

setValue(String) - Method in class org.uniprot.uniprot.SourceDataType.Strain

Sets the value of the value property.

setValue(String) - Method in class org.uniprot.uniprot.SourceDataType.Tissue

Sets the value of the value property.

setValue(String) - Method in class org.uniprot.uniprot.SourceDataType.Transposon

Sets the value of the value property.

setValue(String) - Method in class org.uniprot.uniprot.StatusType

Sets the value of the value property.

setVersion(int) - Method in class org.uniprot.uniprot.Entry

Sets the value of the version property.

setVersion(int) - Method in class org.uniprot.uniprot.SequenceType

Sets the value of the version property.

setVersion(Integer) - Method in class org.uniprot.uniprot.CommentType.Conflict.Sequence

Sets the value of the version property.

setVolume(String) - Method in class org.uniprot.uniprot.CitationType

Sets the value of the volume property.

shortName - Variable in class org.uniprot.uniprot.ProteinType.AlternativeName

shortName - Variable in class org.uniprot.uniprot.ProteinType.RecommendedName

source - Variable in class org.uniprot.uniprot.EvidenceType

source - Variable in class org.uniprot.uniprot.ReferenceType

SourceDataType - Class in org.uniprot.uniprot

Describes the source of the sequence according to the citation.

SourceDataType() - Constructor for class org.uniprot.uniprot.SourceDataType

SourceDataType.Plasmid - Class in org.uniprot.uniprot

Java class for anonymous complex type

SourceDataType.Strain - Class in org.uniprot.uniprot

Java class for anonymous complex type

SourceDataType.Tissue - Class in org.uniprot.uniprot

Java class for anonymous complex type

SourceDataType.Transposon - Class in org.uniprot.uniprot

Java class for anonymous complex type

SourceType - Class in org.uniprot.uniprot

Describes the source of the data using a database cross-reference (or a 'ref' attribute when the source cannot be found in a public data source, such as PubMed, and is cited only within the UniProtKB entry).

SourceType() - Constructor for class org.uniprot.uniprot.SourceType

status - Variable in class org.uniprot.uniprot.PositionType

status - Variable in class org.uniprot.uniprot.StatusType

StatusType - Class in org.uniprot.uniprot

Indicates whether the name of a plasmid is known or unknown.

StatusType() - Constructor for class org.uniprot.uniprot.StatusType

Strain() - Constructor for class org.uniprot.uniprot.SourceDataType.Strain

strainOrPlasmidOrTransposon - Variable in class org.uniprot.uniprot.SourceDataType

stream(Reader, EntryFeatureListener) - Static method in class org.dishevelled.bio.protein.uniprot.UniprotEntryFeatureReader

Stream UniProt XML from the specified reader and extract entry features.

stream(Reader, EntrySequenceListener) - Static method in class org.dishevelled.bio.protein.uniprot.UniprotEntrySequenceReader

Stream UniProt XML from the specified reader and extract entry sequences.

stream(Reader, EntrySummaryListener) - Static method in class org.dishevelled.bio.protein.uniprot.UniprotEntrySummaryReader

Stream UniProt XML from the specified reader and extract entry summaries.

subcellularLocation - Variable in class org.uniprot.uniprot.CommentType

SubcellularLocationType - Class in org.uniprot.uniprot

Describes the subcellular location and optionally the topology and orientation of a molecule.

SubcellularLocationType() - Constructor for class org.uniprot.uniprot.SubcellularLocationType

submittedName - Variable in class org.uniprot.uniprot.ProteinType.Component

submittedName - Variable in class org.uniprot.uniprot.ProteinType.Domain

submittedName - Variable in class org.uniprot.uniprot.ProteinType

SubmittedName() - Constructor for class org.uniprot.uniprot.ProteinType.SubmittedName

T

taxon - Variable in class org.uniprot.uniprot.OrganismType.Lineage

temperatureDependence - Variable in class org.uniprot.uniprot.CommentType

TemperatureDependence() - Constructor for class org.uniprot.uniprot.CommentType.TemperatureDependence

text - Variable in class org.uniprot.uniprot.CommentType.Absorption

text - Variable in class org.uniprot.uniprot.CommentType.Kinetics

text - Variable in class org.uniprot.uniprot.CommentType.PhDependence

text - Variable in class org.uniprot.uniprot.CommentType.RedoxPotential

text - Variable in class org.uniprot.uniprot.CommentType.TemperatureDependence

text - Variable in class org.uniprot.uniprot.CommentType

text - Variable in class org.uniprot.uniprot.IsoformType

text - Variable in class org.uniprot.uniprot.ReactionType

Tissue() - Constructor for class org.uniprot.uniprot.SourceDataType.Tissue

title - Variable in class org.uniprot.uniprot.CitationType

Describes the title of a citation.

topology - Variable in class org.uniprot.uniprot.SubcellularLocationType

Transposon() - Constructor for class org.uniprot.uniprot.SourceDataType.Transposon

type - Variable in class org.uniprot.uniprot.CitationType

Describes the type of a citation.

type - Variable in class org.uniprot.uniprot.CommentType.Conflict

type - Variable in class org.uniprot.uniprot.CommentType

Describes the type of a general annotation.

type - Variable in class org.uniprot.uniprot.DbReferenceType

Describes the name of the database.

type - Variable in class org.uniprot.uniprot.EventType

type - Variable in class org.uniprot.uniprot.EvidenceType

Describes the type of an evidence using the Evidence Code Ontology (http://www.obofoundry.org/cgi-bin/detail.cgi?

type - Variable in class org.uniprot.uniprot.FeatureType

Describes the type of a sequence annotation.

type - Variable in class org.uniprot.uniprot.GeneLocationType

type - Variable in class org.uniprot.uniprot.GeneNameType

type - Variable in class org.uniprot.uniprot.IsoformType.Sequence

type - Variable in class org.uniprot.uniprot.OrganismNameType

type - Variable in class org.uniprot.uniprot.PropertyType

type - Variable in class org.uniprot.uniprot.ProteinExistenceType

U

UNCERTAIN - Enum constant in enum org.dishevelled.bio.protein.uniprot.PositionStatus

Uncertain position status, ~.

Uniprot - Class in org.uniprot.uniprot

Java class for anonymous complex type

Uniprot() - Constructor for class org.uniprot.uniprot.Uniprot

UniprotEntryFeatureReader - Class in org.dishevelled.bio.protein.uniprot

Streaming UniProt XML reader that extracts entry features.

UniprotEntrySequenceReader - Class in org.dishevelled.bio.protein.uniprot

Streaming UniProt XML reader that extracts entry sequences.

UniprotEntrySummaryReader - Class in org.dishevelled.bio.protein.uniprot

Streaming UniProt XML reader that extracts entry summaries.

UniprotJaxbReader - Class in org.dishevelled.bio.protein.uniprot

UniProt XML JAXB reader.

UNKNOWN - Enum constant in enum org.dishevelled.bio.protein.uniprot.PositionStatus

Unknown position status, ?

uri - Variable in class org.uniprot.uniprot.CommentType.Link

V

value - Variable in class org.uniprot.uniprot.EvidencedStringType

value - Variable in class org.uniprot.uniprot.GeneNameType

value - Variable in class org.uniprot.uniprot.IsoformType.Name

value - Variable in class org.uniprot.uniprot.KeywordType

value - Variable in class org.uniprot.uniprot.MoleculeType

value - Variable in class org.uniprot.uniprot.OrganismNameType

value - Variable in class org.uniprot.uniprot.PropertyType

value - Variable in class org.uniprot.uniprot.SequenceType

value - Variable in class org.uniprot.uniprot.SourceDataType.Plasmid

value - Variable in class org.uniprot.uniprot.SourceDataType.Strain

value - Variable in class org.uniprot.uniprot.SourceDataType.Tissue

value - Variable in class org.uniprot.uniprot.SourceDataType.Transposon

value - Variable in class org.uniprot.uniprot.StatusType

valueOf(String) - Static method in enum org.dishevelled.bio.protein.uniprot.PositionStatus

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.dishevelled.bio.protein.uniprot.PositionStatus

Returns an array containing the constants of this enum type, in the order they are declared.

variation - Variable in class org.uniprot.uniprot.FeatureType

Describes the variant sequence in annotations that describe natural or artifical sequence variations.

version - Variable in class org.uniprot.uniprot.CommentType.Conflict.Sequence

version - Variable in class org.uniprot.uniprot.Entry

version - Variable in class org.uniprot.uniprot.SequenceType

vmax - Variable in class org.uniprot.uniprot.CommentType.Kinetics

volume - Variable in class org.uniprot.uniprot.CitationType

Describes the volume of a journal or book.

W

withAccession(String) - Method in class org.dishevelled.bio.protein.uniprot.EntryFeature

Return this entry feature with the specified accession.

withAccession(String) - Method in class org.dishevelled.bio.protein.uniprot.EntrySequence

Return this entry sequence with the specified accession.

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