A C D E G H I M N O P R S T

A

AbstractAssignable - Class in org.dishevelled.vocabulary

Abstract class providing Assignable support.

AbstractAssignable() - Constructor for class org.dishevelled.vocabulary.AbstractAssignable

Create a new abstract assignable entity.

accession - Variable in class org.dishevelled.vocabulary.simple.SimpleConcept

Concept accession.

addAssignment(Assignment) - Method in interface org.dishevelled.vocabulary.Assignable

Add the specified assigment.

addAssignment(Assignment) - Method in class org.dishevelled.vocabulary.AssignableSupport

addAssignment(SimpleAssignment) - Method in class org.dishevelled.vocabulary.simple.SimpleAuthority

Add the specified assignment.

addAssignment(SimpleAssignment) - Method in class org.dishevelled.vocabulary.simple.SimpleConcept

Add the specified assignment.

addConcept(SimpleConcept) - Method in class org.dishevelled.vocabulary.simple.SimpleDomain

Add the specified concept.

addDomain(SimpleDomain) - Method in class org.dishevelled.vocabulary.simple.SimpleAuthority

Add the specified domain.

addEvidence(Evidence) - Method in class org.dishevelled.vocabulary.simple.SimpleAssignment

Add the specified evidence.

addInMapping(SimpleMapping) - Method in class org.dishevelled.vocabulary.simple.SimpleDomain

Add the specified in mapping.

addInProjection(SimpleProjection) - Method in class org.dishevelled.vocabulary.simple.SimpleConcept

Add the specified in projection.

addInRelation(SimpleRelation) - Method in class org.dishevelled.vocabulary.simple.SimpleConcept

Add the specified in relation.

addMapping(SimpleMapping) - Method in class org.dishevelled.vocabulary.simple.SimpleAuthority

Add the specified mapping.

addOutMapping(SimpleMapping) - Method in class org.dishevelled.vocabulary.simple.SimpleDomain

Add the specified out mapping.

addOutProjection(SimpleProjection) - Method in class org.dishevelled.vocabulary.simple.SimpleConcept

Add the specified out projection.

addOutRelation(SimpleRelation) - Method in class org.dishevelled.vocabulary.simple.SimpleConcept

Add the specified out relation.

addProjection(SimpleProjection) - Method in class org.dishevelled.vocabulary.simple.SimpleMapping

Add the specified projection.

addRelation(SimpleRelation) - Method in class org.dishevelled.vocabulary.simple.SimpleDomain

Add the specified relation.

Assignable - Interface in org.dishevelled.vocabulary

Marks an entity as being "assignable," in that it may be assigned to concepts in one or more domains for annotation purposes.

assignable - Variable in class org.dishevelled.vocabulary.AssignableSupport

Assignable entity.

assignable - Variable in class org.dishevelled.vocabulary.simple.SimpleAssignment

Assignable.

AssignableSupport - Class in org.dishevelled.vocabulary

A class that can be used via delegation to provide Assignable support.

AssignableSupport() - Constructor for class org.dishevelled.vocabulary.AssignableSupport

Create a new support class meant to be subclassed.

AssignableSupport(Object) - Constructor for class org.dishevelled.vocabulary.AssignableSupport

Create a new support class that adds Assignable support to the specified entity.

Assignment - Interface in org.dishevelled.vocabulary

An assignment is a binary directional link between a concept and a so-called "assignable" entity, supported by evidence.

assignments - Variable in class org.dishevelled.vocabulary.AssignableSupport

Set of assignments.

assignments - Variable in class org.dishevelled.vocabulary.simple.SimpleAuthority

Set of assignments.

assignments - Variable in class org.dishevelled.vocabulary.simple.SimpleConcept

Set of assignments.

Authority - Interface in org.dishevelled.vocabulary

An authority for a structured vocabulary domain, a mapping between domains, and/or assignments to concepts.

authority - Variable in class org.dishevelled.vocabulary.simple.SimpleAssignment

Authority.

authority - Variable in class org.dishevelled.vocabulary.simple.SimpleDomain

Authority.

authority - Variable in class org.dishevelled.vocabulary.simple.SimpleMapping

Authority.

C

compareTo(Object) - Method in class org.dishevelled.vocabulary.Evidence

Concept - Interface in org.dishevelled.vocabulary

A concept is a vocabulary word defined in a domain that has relations to other concepts present in the same domain, and has projections to other concepts in different domains through a mapping across domains.

concept - Variable in class org.dishevelled.vocabulary.simple.SimpleAssignment

Concept.

concepts - Variable in class org.dishevelled.vocabulary.simple.SimpleDomain

Set of concepts.

confidence - Variable in class org.dishevelled.vocabulary.Evidence

Evidence confidence.

createAssignment(Concept, Assignable, Set<Evidence>) - Method in interface org.dishevelled.vocabulary.Authority

Create a new assignment maintained by this authority of concept to assignable, supported by evidence (optional operation).

createAssignment(Concept, Assignable, Set<Evidence>) - Method in class org.dishevelled.vocabulary.simple.SimpleAuthority

createConcept(String, String, String) - Method in interface org.dishevelled.vocabulary.Domain

Create a new concept in this domain with the specified name, accession, and definition (optional operation).

createConcept(String, String, String) - Method in class org.dishevelled.vocabulary.simple.SimpleDomain

createDomain(String) - Method in interface org.dishevelled.vocabulary.Authority

Create a new domain maintained by this authority with the specified name (optional operation).

createDomain(String) - Method in class org.dishevelled.vocabulary.simple.SimpleAuthority

createMapping(Domain, Domain) - Method in interface org.dishevelled.vocabulary.Authority

Create a new mapping maintained by this authority between the specified domains (optional operation).

createMapping(Domain, Domain) - Method in class org.dishevelled.vocabulary.simple.SimpleAuthority

createProjection(String, Concept, Concept, Set<Evidence>) - Method in interface org.dishevelled.vocabulary.Mapping

Create a new projection in this mapping between concepts source and target with the specified name (optional operation).

createProjection(String, Concept, Concept, Set<Evidence>) - Method in class org.dishevelled.vocabulary.simple.SimpleMapping

createRelation(String, Concept, Concept) - Method in interface org.dishevelled.vocabulary.Domain

Create a new relation in this domain between concepts source and target with the specified name (optional operation).

createRelation(String, Concept, Concept) - Method in class org.dishevelled.vocabulary.simple.SimpleDomain

D

definition - Variable in class org.dishevelled.vocabulary.simple.SimpleConcept

Concept definition.

degree() - Method in interface org.dishevelled.vocabulary.Concept

Return the degree of this concept, that is the total number of relations, projections, and assignments linked to this concept.

degree() - Method in class org.dishevelled.vocabulary.simple.SimpleConcept

Domain - Interface in org.dishevelled.vocabulary

A domain provides a named space in which to define concepts and their relations to each other, and also to project concepts in different domains to each other through a mapping across domains.

domain - Variable in class org.dishevelled.vocabulary.simple.SimpleConcept

Domain.

domain - Variable in class org.dishevelled.vocabulary.simple.SimpleRelation

Domain.

domains - Variable in class org.dishevelled.vocabulary.simple.SimpleAuthority

Set of domains.

E

equals(Object) - Method in class org.dishevelled.vocabulary.Evidence

Evidence - Class in org.dishevelled.vocabulary

Evidence supports an assignment by reflecting the strength of knowledge used to create that assignment.

Evidence(String, double, double) - Constructor for class org.dishevelled.vocabulary.Evidence

Create a new evidence with the specified name, quantitative score, and confidence.

evidence - Variable in class org.dishevelled.vocabulary.simple.SimpleAssignment

Set of evidence.

evidence - Variable in class org.dishevelled.vocabulary.simple.SimpleProjection

Set of evidence.

G

getAccession() - Method in interface org.dishevelled.vocabulary.Concept

Return the accession (an unique identifier) of this concept.

getAccession() - Method in class org.dishevelled.vocabulary.simple.SimpleConcept

getAssignable() - Method in interface org.dishevelled.vocabulary.Assignment

Return the "assignable" entity of this assignment.

getAssignable() - Method in class org.dishevelled.vocabulary.simple.SimpleAssignment

getAssignments() - Method in interface org.dishevelled.vocabulary.Assignable

Return the set of assignments for this entity.

getAssignments() - Method in class org.dishevelled.vocabulary.AssignableSupport

getAssignments() - Method in interface org.dishevelled.vocabulary.Authority

Return the set of assignments maintained by this authority.

getAssignments() - Method in interface org.dishevelled.vocabulary.Concept

Return the set of assignments for this concept.

getAssignments() - Method in class org.dishevelled.vocabulary.simple.SimpleAuthority

getAssignments() - Method in class org.dishevelled.vocabulary.simple.SimpleConcept

getAuthority() - Method in interface org.dishevelled.vocabulary.Assignment

Return the authority for this assignment.

getAuthority() - Method in interface org.dishevelled.vocabulary.Domain

Return the authority for this domain.

getAuthority() - Method in interface org.dishevelled.vocabulary.Mapping

Return the authority for this mapping.

getAuthority() - Method in class org.dishevelled.vocabulary.simple.SimpleAssignment

getAuthority() - Method in class org.dishevelled.vocabulary.simple.SimpleDomain

getAuthority() - Method in class org.dishevelled.vocabulary.simple.SimpleMapping

getConcept() - Method in interface org.dishevelled.vocabulary.Assignment

Return the concept of this assignment.

getConcept() - Method in class org.dishevelled.vocabulary.simple.SimpleAssignment

getConcepts() - Method in interface org.dishevelled.vocabulary.Domain

Return the set of all concepts in this domain.

getConcepts() - Method in class org.dishevelled.vocabulary.simple.SimpleDomain

getConfidence() - Method in class org.dishevelled.vocabulary.Evidence

Return a measure of confidence for the quantitative score, a p-value for instance.

getDefinition() - Method in interface org.dishevelled.vocabulary.Concept

Return the definition of this concept.

getDefinition() - Method in class org.dishevelled.vocabulary.simple.SimpleConcept

getDomain() - Method in interface org.dishevelled.vocabulary.Concept

Return the domain of this concept.

getDomain() - Method in interface org.dishevelled.vocabulary.Relation

Return the domain of this relation.

getDomain() - Method in class org.dishevelled.vocabulary.simple.SimpleConcept

getDomain() - Method in class org.dishevelled.vocabulary.simple.SimpleRelation

getDomains() - Method in interface org.dishevelled.vocabulary.Authority

Return the set of domains maintained by this authority.

getDomains() - Method in class org.dishevelled.vocabulary.simple.SimpleAuthority

getEvidence() - Method in interface org.dishevelled.vocabulary.Assignment

Return the set of evidence supporting this assignment.

getEvidence() - Method in interface org.dishevelled.vocabulary.Projection

Return the set of evidence supporting this assignment.

getEvidence() - Method in class org.dishevelled.vocabulary.simple.SimpleAssignment

getEvidence() - Method in class org.dishevelled.vocabulary.simple.SimpleProjection

getMapping() - Method in interface org.dishevelled.vocabulary.Projection

Return the mapping of this projection.

getMapping() - Method in class org.dishevelled.vocabulary.simple.SimpleProjection

getMappings() - Method in interface org.dishevelled.vocabulary.Authority

Return the set of mappings between domains maintained by this authority.

getMappings() - Method in interface org.dishevelled.vocabulary.Domain

Return the set of all mappings for this domain.

getMappings() - Method in class org.dishevelled.vocabulary.simple.SimpleAuthority

getMappings() - Method in class org.dishevelled.vocabulary.simple.SimpleDomain

getName() - Method in interface org.dishevelled.vocabulary.Authority

Return the name of this authority.

getName() - Method in interface org.dishevelled.vocabulary.Concept

Return the name of this concept.

getName() - Method in interface org.dishevelled.vocabulary.Domain

Return the name of this domain.

getName() - Method in class org.dishevelled.vocabulary.Evidence

Return the name of this evidence.

getName() - Method in interface org.dishevelled.vocabulary.Projection

Return the name of this projection.

getName() - Method in interface org.dishevelled.vocabulary.Relation

Return the name of this relation.

getName() - Method in class org.dishevelled.vocabulary.simple.SimpleAssignable

Return the name of this assignable entity.

getName() - Method in class org.dishevelled.vocabulary.simple.SimpleAuthority

getName() - Method in class org.dishevelled.vocabulary.simple.SimpleConcept

getName() - Method in class org.dishevelled.vocabulary.simple.SimpleDomain

getName() - Method in class org.dishevelled.vocabulary.simple.SimpleProjection

getName() - Method in class org.dishevelled.vocabulary.simple.SimpleRelation

getProjections() - Method in interface org.dishevelled.vocabulary.Concept

Return the set of all projections for this concept.

getProjections() - Method in interface org.dishevelled.vocabulary.Mapping

Return the set of all projections in this mapping.

getProjections() - Method in class org.dishevelled.vocabulary.simple.SimpleConcept

getProjections() - Method in class org.dishevelled.vocabulary.simple.SimpleMapping

getRelations() - Method in interface org.dishevelled.vocabulary.Concept

Return the set of all relations for this concept.

getRelations() - Method in interface org.dishevelled.vocabulary.Domain

Return the set of all relations in this domain.

getRelations() - Method in class org.dishevelled.vocabulary.simple.SimpleConcept

getRelations() - Method in class org.dishevelled.vocabulary.simple.SimpleDomain

getScore() - Method in class org.dishevelled.vocabulary.Evidence

Return a quantitative score reflecting the strength of this evidence.

getSource() - Method in interface org.dishevelled.vocabulary.Mapping

Return the source domain of this mapping.

getSource() - Method in interface org.dishevelled.vocabulary.Projection

Return the source concept of this projection.

getSource() - Method in interface org.dishevelled.vocabulary.Relation

Return the source concept of this relation.

getSource() - Method in class org.dishevelled.vocabulary.simple.SimpleMapping

getSource() - Method in class org.dishevelled.vocabulary.simple.SimpleProjection

getSource() - Method in class org.dishevelled.vocabulary.simple.SimpleRelation

getTarget() - Method in interface org.dishevelled.vocabulary.Mapping

Return the target domain of this mapping.

getTarget() - Method in interface org.dishevelled.vocabulary.Projection

Return the target concept of this projection.

getTarget() - Method in interface org.dishevelled.vocabulary.Relation

Return the target concept of this relation.

getTarget() - Method in class org.dishevelled.vocabulary.simple.SimpleMapping

getTarget() - Method in class org.dishevelled.vocabulary.simple.SimpleProjection

getTarget() - Method in class org.dishevelled.vocabulary.simple.SimpleRelation

H

hashCode() - Method in class org.dishevelled.vocabulary.Evidence

I

inMappings() - Method in interface org.dishevelled.vocabulary.Domain

Return the set of in mappings for this domain, that is those mappings that have this domain as the target.

inMappings - Variable in class org.dishevelled.vocabulary.simple.SimpleDomain

Set of in mappings.

inMappings() - Method in class org.dishevelled.vocabulary.simple.SimpleDomain

inProjections() - Method in interface org.dishevelled.vocabulary.Concept

Return the set of in projections for this concept, that is those projections that have this concept as the target.

inProjections - Variable in class org.dishevelled.vocabulary.simple.SimpleConcept

Set of in projections.

inProjections() - Method in class org.dishevelled.vocabulary.simple.SimpleConcept

inRelations() - Method in interface org.dishevelled.vocabulary.Concept

Return the set of in relations for this concept, that is those relations that have this concept as the target.

inRelations - Variable in class org.dishevelled.vocabulary.simple.SimpleConcept

Set of in relations.

inRelations() - Method in class org.dishevelled.vocabulary.simple.SimpleConcept

M

Mapping - Interface in org.dishevelled.vocabulary

A mapping is a binary directional link between a source and a target domain containing projections of concepts from the source domain to concepts in the target domain.

mapping - Variable in class org.dishevelled.vocabulary.simple.SimpleProjection

Mapping.

mappings - Variable in class org.dishevelled.vocabulary.simple.SimpleAuthority

Set of mappings.

N

name - Variable in class org.dishevelled.vocabulary.Evidence

Evidence name.

name - Variable in class org.dishevelled.vocabulary.simple.SimpleAssignable

Name of this assignable entity.

name - Variable in class org.dishevelled.vocabulary.simple.SimpleAuthority

Authority name.

name - Variable in class org.dishevelled.vocabulary.simple.SimpleConcept

Concept name.

name - Variable in class org.dishevelled.vocabulary.simple.SimpleDomain

Domain name.

name - Variable in class org.dishevelled.vocabulary.simple.SimpleProjection

Projection name.

name - Variable in class org.dishevelled.vocabulary.simple.SimpleRelation

Relation name.

O

org.dishevelled.vocabulary - package org.dishevelled.vocabulary

A structured vocabulary is a description of concepts and their relations in a domain.

org.dishevelled.vocabulary.simple - package org.dishevelled.vocabulary.simple

Simple implementation of the vocabulary interfaces.

outMappings() - Method in interface org.dishevelled.vocabulary.Domain

Return the set of out mappings for this domain, that is those mappings that have this domain as the source.

outMappings - Variable in class org.dishevelled.vocabulary.simple.SimpleDomain

Set of out mappings.

outMappings() - Method in class org.dishevelled.vocabulary.simple.SimpleDomain

outProjections() - Method in interface org.dishevelled.vocabulary.Concept

Return the set of out projections for this concept, that is those projections that have this concept as the source.

outProjections - Variable in class org.dishevelled.vocabulary.simple.SimpleConcept

Set of out projections.

outProjections() - Method in class org.dishevelled.vocabulary.simple.SimpleConcept

outRelations() - Method in interface org.dishevelled.vocabulary.Concept

Return the set of out relations for this concept, that is those relations that have this concept as the source.

outRelations - Variable in class org.dishevelled.vocabulary.simple.SimpleConcept

Set of out relations.

outRelations() - Method in class org.dishevelled.vocabulary.simple.SimpleConcept

P

Projection - Interface in org.dishevelled.vocabulary

A projection is a binary directional link between a source and a target concept from different domains linked together through a mapping, supported by evidence.

projections - Variable in class org.dishevelled.vocabulary.simple.SimpleMapping

Set of projections.

R

Relation - Interface in org.dishevelled.vocabulary

A relation is a binary directional link between a source and a target concept present in the same domain.

relations - Variable in class org.dishevelled.vocabulary.simple.SimpleDomain

Set of relations.

S

score - Variable in class org.dishevelled.vocabulary.Evidence

Evidence quantitative score.

setAssignable(Object) - Method in class org.dishevelled.vocabulary.AssignableSupport

Set the assignable entity for this support class to assignable.

SimpleAssignable - Class in org.dishevelled.vocabulary.simple

Simple implementation of the Assignable interface.

SimpleAssignable(String) - Constructor for class org.dishevelled.vocabulary.simple.SimpleAssignable

Create a new assignable entity with the specified name.

SimpleAssignment - Class in org.dishevelled.vocabulary.simple

Simple implementation of the Assignment interface.

SimpleAssignment(Authority, SimpleConcept, Assignable, Set<Evidence>) - Constructor for class org.dishevelled.vocabulary.simple.SimpleAssignment

Create a new assignment maintained by the specified authority of concept to assignable, supported by evidence.

SimpleAuthority - Class in org.dishevelled.vocabulary.simple

Simple implementation of the Authority interface.

SimpleAuthority(String) - Constructor for class org.dishevelled.vocabulary.simple.SimpleAuthority

Create a new authority with the specified name.

SimpleConcept - Class in org.dishevelled.vocabulary.simple

Simple implementation of the Concept interface.

SimpleConcept(Domain, String, String, String) - Constructor for class org.dishevelled.vocabulary.simple.SimpleConcept

Create a new concept with the specified name, accession, and definition in the specified domain.

SimpleDomain - Class in org.dishevelled.vocabulary.simple

Simple implementation of the Domain interface.

SimpleDomain(Authority, String) - Constructor for class org.dishevelled.vocabulary.simple.SimpleDomain

Create a new domain with the specified authority and name.

SimpleMapping - Class in org.dishevelled.vocabulary.simple

Simple implementation of the Mapping interface.

SimpleMapping(Authority, SimpleDomain, SimpleDomain) - Constructor for class org.dishevelled.vocabulary.simple.SimpleMapping

Create a new mapping with the specified authority, source domain, and target domain.

SimpleProjection - Class in org.dishevelled.vocabulary.simple

Simple implementation of the Projection interface.

SimpleProjection(Mapping, String, SimpleConcept, SimpleConcept, Set<Evidence>) - Constructor for class org.dishevelled.vocabulary.simple.SimpleProjection

Create a new projection in the specified mapping between concepts source and target with the specified name.

SimpleRelation - Class in org.dishevelled.vocabulary.simple

Simple implementation of the Relation interface.

SimpleRelation(Domain, String, SimpleConcept, SimpleConcept) - Constructor for class org.dishevelled.vocabulary.simple.SimpleRelation

Create a new relation in the specified domain between concepts source and target with the specified name.

source - Variable in class org.dishevelled.vocabulary.simple.SimpleMapping

Source domain.

source - Variable in class org.dishevelled.vocabulary.simple.SimpleProjection

Source concept.

source - Variable in class org.dishevelled.vocabulary.simple.SimpleRelation

Source concept.

T

target - Variable in class org.dishevelled.vocabulary.simple.SimpleMapping

Target domain.

target - Variable in class org.dishevelled.vocabulary.simple.SimpleProjection

Source target.

target - Variable in class org.dishevelled.vocabulary.simple.SimpleRelation

Target concept.

toString() - Method in class org.dishevelled.vocabulary.Evidence

toString() - Method in class org.dishevelled.vocabulary.simple.SimpleAssignment

toString() - Method in class org.dishevelled.vocabulary.simple.SimpleAuthority

toString() - Method in class org.dishevelled.vocabulary.simple.SimpleConcept

toString() - Method in class org.dishevelled.vocabulary.simple.SimpleRelation

A C D E G H I M N O P R S T