A B C D E F G H I L M N O P R S T V W X
All Classes All Packages

A

AbstractBasicPropertyValue - Class in org.geneontology.obographs.core.model.meta

A generic PropertyValue that is not explicitly modeled

AbstractBasicPropertyValue() - Constructor for class org.geneontology.obographs.core.model.meta.AbstractBasicPropertyValue

AbstractDefinitionPropertyValue - Class in org.geneontology.obographs.core.model.meta

A PropertyValue that represents a textual definition of an ontology class or property

AbstractDefinitionPropertyValue() - Constructor for class org.geneontology.obographs.core.model.meta.AbstractDefinitionPropertyValue

AbstractDomainRangeAxiom - Class in org.geneontology.obographs.core.model.axiom

This combined ObjectPropertyDomain, ObjectPropertyRange, and some AllValuesFrom expressions into a single convenience structure

AbstractDomainRangeAxiom() - Constructor for class org.geneontology.obographs.core.model.axiom.AbstractDomainRangeAxiom

AbstractEdge - Class in org.geneontology.obographs.core.model

An edge connects two nodes via a predicate

AbstractEdge() - Constructor for class org.geneontology.obographs.core.model.AbstractEdge

AbstractEquivalentNodesSet - Class in org.geneontology.obographs.core.model.axiom

A set of nodes that all stand in a mutual equivalence or identity relationship to one another Corresponds to Node in the OWLAPI

AbstractEquivalentNodesSet() - Constructor for class org.geneontology.obographs.core.model.axiom.AbstractEquivalentNodesSet

AbstractExistentialRestrictionExpression - Class in org.geneontology.obographs.core.model.axiom

Corresponds to an axiom of the form C = X1 and ...

AbstractExistentialRestrictionExpression() - Constructor for class org.geneontology.obographs.core.model.axiom.AbstractExistentialRestrictionExpression

AbstractGraph - Class in org.geneontology.obographs.core.model

A graph object holds a collection of nodes and edges Corresponds to a Named Graph in RDF, and an Ontology in OWL Note: there is no assumption that either nodes or edges are unique to a graph ## Basic OBO Graphs  *

AbstractGraph() - Constructor for class org.geneontology.obographs.core.model.AbstractGraph

AbstractGraphDocument - Class in org.geneontology.obographs.core.model

Holds a collection of graphs, plus document-level metadata ## Model 

AbstractGraphDocument() - Constructor for class org.geneontology.obographs.core.model.AbstractGraphDocument

AbstractLogicalDefinitionAxiom - Class in org.geneontology.obographs.core.model.axiom

Corresponds to an axiom of the form C = X1 and ...

AbstractLogicalDefinitionAxiom() - Constructor for class org.geneontology.obographs.core.model.axiom.AbstractLogicalDefinitionAxiom

AbstractMeta - Class in org.geneontology.obographs.core.model

A holder for metadata The information in a Meta object consists sets of PropertyValue objects, which associate the Meta object holder with some value via some property.

AbstractMeta() - Constructor for class org.geneontology.obographs.core.model.AbstractMeta

AbstractNode - Class in org.geneontology.obographs.core.model

A graph node corresponds to a class, individual or property 

AbstractNode() - Constructor for class org.geneontology.obographs.core.model.AbstractNode

AbstractNode.RDFTYPES - Enum in org.geneontology.obographs.core.model

AbstractPropertyChainAxiom - Class in org.geneontology.obographs.core.model.axiom

P <- P1 ...

AbstractPropertyChainAxiom() - Constructor for class org.geneontology.obographs.core.model.axiom.AbstractPropertyChainAxiom

AbstractSynonymPropertyValue - Class in org.geneontology.obographs.core.model.meta

A PropertyValue that represents a an alternative term for a node

AbstractSynonymPropertyValue() - Constructor for class org.geneontology.obographs.core.model.meta.AbstractSynonymPropertyValue

AbstractSynonymPropertyValue.SCOPES - Enum in org.geneontology.obographs.core.model.meta

OBO-style synonym scopes

AbstractXrefPropertyValue - Class in org.geneontology.obographs.core.model.meta

AbstractXrefPropertyValue() - Constructor for class org.geneontology.obographs.core.model.meta.AbstractXrefPropertyValue

addAllAllValuesFromEdges(Iterable<? extends Edge>) - Method in class org.geneontology.obographs.core.model.axiom.DomainRangeAxiom.Builder

Adds elements to allValuesFromEdges set.

addAllBasicPropertyValues(Iterable<? extends BasicPropertyValue>) - Method in class org.geneontology.obographs.core.model.Meta.Builder

Adds elements to basicPropertyValues list.

addAllChainPredicateIds(Iterable<String>) - Method in class org.geneontology.obographs.core.model.axiom.PropertyChainAxiom.Builder

Adds elements to chainPredicateIds list.

addAllComments(Iterable<String>) - Method in class org.geneontology.obographs.core.model.Meta.Builder

Adds elements to comments list.

addAllDomainClassIds(Iterable<String>) - Method in class org.geneontology.obographs.core.model.axiom.DomainRangeAxiom.Builder

Adds elements to domainClassIds set.

addAllDomainRangeAxioms(Iterable<? extends DomainRangeAxiom>) - Method in class org.geneontology.obographs.core.model.Graph.Builder

Adds elements to domainRangeAxioms list.

addAllEdges(Iterable<? extends Edge>) - Method in class org.geneontology.obographs.core.model.Graph.Builder

Adds elements to edges list.

addAllEquivalentNodesSets(Iterable<? extends EquivalentNodesSet>) - Method in class org.geneontology.obographs.core.model.Graph.Builder

Adds elements to equivalentNodesSets list.

addAllGenusIds(Iterable<String>) - Method in class org.geneontology.obographs.core.model.axiom.LogicalDefinitionAxiom.Builder

Adds elements to genusIds list.

addAllGraphs(Iterable<? extends Graph>) - Method in class org.geneontology.obographs.core.model.GraphDocument.Builder

Adds elements to graphs list.

addAllLogicalDefinitionAxioms(Iterable<? extends LogicalDefinitionAxiom>) - Method in class org.geneontology.obographs.core.model.Graph.Builder

Adds elements to logicalDefinitionAxioms list.

addAllNodeIds(Iterable<String>) - Method in class org.geneontology.obographs.core.model.axiom.EquivalentNodesSet.Builder

Adds elements to nodeIds set.

addAllNodes(Iterable<? extends Node>) - Method in class org.geneontology.obographs.core.model.Graph.Builder

Adds elements to nodes list.

addAllPropertyChainAxioms(Iterable<? extends PropertyChainAxiom>) - Method in class org.geneontology.obographs.core.model.Graph.Builder

Adds elements to propertyChainAxioms list.

addAllRangeClassIds(Iterable<String>) - Method in class org.geneontology.obographs.core.model.axiom.DomainRangeAxiom.Builder

Adds elements to rangeClassIds set.

addAllRestrictions(Iterable<? extends ExistentialRestrictionExpression>) - Method in class org.geneontology.obographs.core.model.axiom.LogicalDefinitionAxiom.Builder

Adds elements to restrictions list.

addAllSubsets(Iterable<String>) - Method in class org.geneontology.obographs.core.model.Meta.Builder

Adds elements to subsets list.

addAllSynonyms(Iterable<? extends SynonymPropertyValue>) - Method in class org.geneontology.obographs.core.model.Meta.Builder

Adds elements to synonyms list.

addAllValuesFromEdge(Edge) - Method in class org.geneontology.obographs.core.model.axiom.DomainRangeAxiom.Builder

Adds one element to allValuesFromEdges set.

addAllValuesFromEdges(Edge...) - Method in class org.geneontology.obographs.core.model.axiom.DomainRangeAxiom.Builder

Adds elements to allValuesFromEdges set.

addAllXrefs(Iterable<? extends XrefPropertyValue>) - Method in class org.geneontology.obographs.core.model.Meta.Builder

Adds elements to xrefs list.

addAllXrefs(Iterable<String>) - Method in class org.geneontology.obographs.core.model.meta.BasicPropertyValue.Builder

Adds elements to xrefs list.

addAllXrefs(Iterable<String>) - Method in class org.geneontology.obographs.core.model.meta.DefinitionPropertyValue.Builder

Adds elements to xrefs list.

addAllXrefs(Iterable<String>) - Method in class org.geneontology.obographs.core.model.meta.SynonymPropertyValue.Builder

Adds elements to xrefs list.

addAllXrefs(Iterable<String>) - Method in class org.geneontology.obographs.core.model.meta.XrefPropertyValue.Builder

Adds elements to xrefs list.

addAllXrefsValues(Iterable<String>) - Method in class org.geneontology.obographs.core.model.Meta.Builder

Adds elements to xrefsValues list.

addBasicPropertyValue(BasicPropertyValue) - Method in class org.geneontology.obographs.core.model.Meta.Builder

Adds one element to basicPropertyValues list.

addBasicPropertyValues(BasicPropertyValue...) - Method in class org.geneontology.obographs.core.model.Meta.Builder

Adds elements to basicPropertyValues list.

addChainPredicateId(String) - Method in class org.geneontology.obographs.core.model.axiom.PropertyChainAxiom.Builder

Adds one element to chainPredicateIds list.

addChainPredicateIds(String...) - Method in class org.geneontology.obographs.core.model.axiom.PropertyChainAxiom.Builder

Adds elements to chainPredicateIds list.

addComment(String) - Method in class org.geneontology.obographs.core.model.Meta.Builder

Adds one element to comments list.

addComments(String...) - Method in class org.geneontology.obographs.core.model.Meta.Builder

Adds elements to comments list.

addDomainClassId(String) - Method in class org.geneontology.obographs.core.model.axiom.DomainRangeAxiom.Builder

Adds one element to domainClassIds set.

addDomainClassIds(String...) - Method in class org.geneontology.obographs.core.model.axiom.DomainRangeAxiom.Builder

Adds elements to domainClassIds set.

addDomainRangeAxiom(DomainRangeAxiom) - Method in class org.geneontology.obographs.core.model.Graph.Builder

Adds one element to domainRangeAxioms list.

addDomainRangeAxioms(DomainRangeAxiom...) - Method in class org.geneontology.obographs.core.model.Graph.Builder

Adds elements to domainRangeAxioms list.

addEdge(Edge) - Method in class org.geneontology.obographs.core.model.Graph.Builder

Adds one element to edges list.

addEdges(Edge...) - Method in class org.geneontology.obographs.core.model.Graph.Builder

Adds elements to edges list.

addEquivalentNodesSet(EquivalentNodesSet) - Method in class org.geneontology.obographs.core.model.Graph.Builder

Adds one element to equivalentNodesSets list.

addEquivalentNodesSets(EquivalentNodesSet...) - Method in class org.geneontology.obographs.core.model.Graph.Builder

Adds elements to equivalentNodesSets list.

addGenusId(String) - Method in class org.geneontology.obographs.core.model.axiom.LogicalDefinitionAxiom.Builder

Adds one element to genusIds list.

addGenusIds(String...) - Method in class org.geneontology.obographs.core.model.axiom.LogicalDefinitionAxiom.Builder

Adds elements to genusIds list.

addGraph(Graph) - Method in class org.geneontology.obographs.core.model.GraphDocument.Builder

Adds one element to graphs list.

addGraphs(Graph...) - Method in class org.geneontology.obographs.core.model.GraphDocument.Builder

Adds elements to graphs list.

addLogicalDefinitionAxiom(LogicalDefinitionAxiom) - Method in class org.geneontology.obographs.core.model.Graph.Builder

Adds one element to logicalDefinitionAxioms list.

addLogicalDefinitionAxioms(LogicalDefinitionAxiom...) - Method in class org.geneontology.obographs.core.model.Graph.Builder

Adds elements to logicalDefinitionAxioms list.

addNode(Node) - Method in class org.geneontology.obographs.core.model.Graph.Builder

Adds one element to nodes list.

addNodeId(String) - Method in class org.geneontology.obographs.core.model.axiom.EquivalentNodesSet.Builder

Adds one element to nodeIds set.

addNodeIds(String...) - Method in class org.geneontology.obographs.core.model.axiom.EquivalentNodesSet.Builder

Adds elements to nodeIds set.

addNodes(Node...) - Method in class org.geneontology.obographs.core.model.Graph.Builder

Adds elements to nodes list.

addPropertyChainAxiom(PropertyChainAxiom) - Method in class org.geneontology.obographs.core.model.Graph.Builder

Adds one element to propertyChainAxioms list.

addPropertyChainAxioms(PropertyChainAxiom...) - Method in class org.geneontology.obographs.core.model.Graph.Builder

Adds elements to propertyChainAxioms list.

addRangeClassId(String) - Method in class org.geneontology.obographs.core.model.axiom.DomainRangeAxiom.Builder

Adds one element to rangeClassIds set.

addRangeClassIds(String...) - Method in class org.geneontology.obographs.core.model.axiom.DomainRangeAxiom.Builder

Adds elements to rangeClassIds set.

addRestriction(ExistentialRestrictionExpression) - Method in class org.geneontology.obographs.core.model.axiom.LogicalDefinitionAxiom.Builder

Adds one element to restrictions list.

addRestrictions(ExistentialRestrictionExpression...) - Method in class org.geneontology.obographs.core.model.axiom.LogicalDefinitionAxiom.Builder

Adds elements to restrictions list.

addSubset(String) - Method in class org.geneontology.obographs.core.model.Meta.Builder

Adds one element to subsets list.

addSubsets(String...) - Method in class org.geneontology.obographs.core.model.Meta.Builder

Adds elements to subsets list.

addSynonym(SynonymPropertyValue) - Method in class org.geneontology.obographs.core.model.Meta.Builder

Adds one element to synonyms list.

addSynonyms(SynonymPropertyValue...) - Method in class org.geneontology.obographs.core.model.Meta.Builder

Adds elements to synonyms list.

addXref(String) - Method in class org.geneontology.obographs.core.model.meta.BasicPropertyValue.Builder

Adds one element to xrefs list.

addXref(String) - Method in class org.geneontology.obographs.core.model.meta.DefinitionPropertyValue.Builder

Adds one element to xrefs list.

addXref(String) - Method in class org.geneontology.obographs.core.model.meta.SynonymPropertyValue.Builder

Adds one element to xrefs list.

addXref(String) - Method in class org.geneontology.obographs.core.model.meta.XrefPropertyValue.Builder

Adds one element to xrefs list.

addXref(XrefPropertyValue) - Method in class org.geneontology.obographs.core.model.Meta.Builder

Adds one element to xrefs list.

addXrefs(String...) - Method in class org.geneontology.obographs.core.model.meta.BasicPropertyValue.Builder

Adds elements to xrefs list.

addXrefs(String...) - Method in class org.geneontology.obographs.core.model.meta.DefinitionPropertyValue.Builder

Adds elements to xrefs list.

addXrefs(String...) - Method in class org.geneontology.obographs.core.model.meta.SynonymPropertyValue.Builder

Adds elements to xrefs list.

addXrefs(String...) - Method in class org.geneontology.obographs.core.model.meta.XrefPropertyValue.Builder

Adds elements to xrefs list.

addXrefs(XrefPropertyValue...) - Method in class org.geneontology.obographs.core.model.Meta.Builder

Adds elements to xrefs list.

addXrefsValue(String) - Method in class org.geneontology.obographs.core.model.Meta.Builder

Adds one element to xrefsValues list.

addXrefsValues(String...) - Method in class org.geneontology.obographs.core.model.Meta.Builder

Adds elements to xrefsValues list.

allValuesFromEdges(Iterable<? extends Edge>) - Method in class org.geneontology.obographs.core.model.axiom.DomainRangeAxiom.Builder

Sets or replaces all elements for allValuesFromEdges set.

Axiom - Interface in org.geneontology.obographs.core.model.axiom

B

BasicPropertyValue - Class in org.geneontology.obographs.core.model.meta

A generic PropertyValue that is not explicitly modeled

BasicPropertyValue.Builder - Class in org.geneontology.obographs.core.model.meta

Builds instances of type BasicPropertyValue.

basicPropertyValues(Iterable<? extends BasicPropertyValue>) - Method in class org.geneontology.obographs.core.model.Meta.Builder

Sets or replaces all elements for basicPropertyValues list.

BROAD - org.geneontology.obographs.core.model.meta.AbstractSynonymPropertyValue.SCOPES

build() - Method in class org.geneontology.obographs.core.model.axiom.DomainRangeAxiom.Builder

Builds a new DomainRangeAxiom.

build() - Method in class org.geneontology.obographs.core.model.axiom.EquivalentNodesSet.Builder

Builds a new EquivalentNodesSet.

build() - Method in class org.geneontology.obographs.core.model.axiom.ExistentialRestrictionExpression.Builder

Builds a new ExistentialRestrictionExpression.

build() - Method in class org.geneontology.obographs.core.model.axiom.LogicalDefinitionAxiom.Builder

Builds a new LogicalDefinitionAxiom.

build() - Method in class org.geneontology.obographs.core.model.axiom.PropertyChainAxiom.Builder

Builds a new PropertyChainAxiom.

build() - Method in class org.geneontology.obographs.core.model.Edge.Builder

Builds a new Edge.

build() - Method in class org.geneontology.obographs.core.model.Graph.Builder

Builds a new Graph.

build() - Method in class org.geneontology.obographs.core.model.GraphDocument.Builder

Builds a new GraphDocument.

build() - Method in class org.geneontology.obographs.core.model.meta.BasicPropertyValue.Builder

Builds a new BasicPropertyValue.

build() - Method in class org.geneontology.obographs.core.model.Meta.Builder

Builds a new Meta.

build() - Method in class org.geneontology.obographs.core.model.meta.DefinitionPropertyValue.Builder

Builds a new DefinitionPropertyValue.

build() - Method in class org.geneontology.obographs.core.model.meta.SynonymPropertyValue.Builder

Builds a new SynonymPropertyValue.

build() - Method in class org.geneontology.obographs.core.model.meta.XrefPropertyValue.Builder

Builds a new XrefPropertyValue.

build() - Method in class org.geneontology.obographs.core.model.Node.Builder

Builds a new Node.

Builder() - Constructor for class org.geneontology.obographs.core.model.axiom.DomainRangeAxiom.Builder

Creates a builder for DomainRangeAxiom instances.

Builder() - Constructor for class org.geneontology.obographs.core.model.axiom.EquivalentNodesSet.Builder

Creates a builder for EquivalentNodesSet instances.

Builder() - Constructor for class org.geneontology.obographs.core.model.axiom.ExistentialRestrictionExpression.Builder

Creates a builder for ExistentialRestrictionExpression instances.

Builder() - Constructor for class org.geneontology.obographs.core.model.axiom.LogicalDefinitionAxiom.Builder

Creates a builder for LogicalDefinitionAxiom instances.

Builder() - Constructor for class org.geneontology.obographs.core.model.axiom.PropertyChainAxiom.Builder

Creates a builder for PropertyChainAxiom instances.

Builder() - Constructor for class org.geneontology.obographs.core.model.Edge.Builder

Creates a builder for Edge instances.

Builder() - Constructor for class org.geneontology.obographs.core.model.Graph.Builder

Creates a builder for Graph instances.

Builder() - Constructor for class org.geneontology.obographs.core.model.GraphDocument.Builder

Creates a builder for GraphDocument instances.

Builder() - Constructor for class org.geneontology.obographs.core.model.meta.BasicPropertyValue.Builder

Creates a builder for BasicPropertyValue instances.

Builder() - Constructor for class org.geneontology.obographs.core.model.Meta.Builder

Creates a builder for Meta instances.

Builder() - Constructor for class org.geneontology.obographs.core.model.meta.DefinitionPropertyValue.Builder

Creates a builder for DefinitionPropertyValue instances.

Builder() - Constructor for class org.geneontology.obographs.core.model.meta.SynonymPropertyValue.Builder

Creates a builder for SynonymPropertyValue instances.

Builder() - Constructor for class org.geneontology.obographs.core.model.meta.XrefPropertyValue.Builder

Creates a builder for XrefPropertyValue instances.

Builder() - Constructor for class org.geneontology.obographs.core.model.Node.Builder

Creates a builder for Node instances.

C

chainPredicateIds(Iterable<String>) - Method in class org.geneontology.obographs.core.model.axiom.PropertyChainAxiom.Builder

Sets or replaces all elements for chainPredicateIds list.

CLASS - org.geneontology.obographs.core.model.AbstractNode.RDFTYPES

comments(Iterable<String>) - Method in class org.geneontology.obographs.core.model.Meta.Builder

Sets or replaces all elements for comments list.

compareTo(AbstractEdge) - Method in class org.geneontology.obographs.core.model.AbstractEdge

compareTo(AbstractNode) - Method in class org.geneontology.obographs.core.model.AbstractNode

compareTo(AbstractDomainRangeAxiom) - Method in class org.geneontology.obographs.core.model.axiom.AbstractDomainRangeAxiom

compareTo(AbstractEquivalentNodesSet) - Method in class org.geneontology.obographs.core.model.axiom.AbstractEquivalentNodesSet

compareTo(AbstractExistentialRestrictionExpression) - Method in class org.geneontology.obographs.core.model.axiom.AbstractExistentialRestrictionExpression

compareTo(AbstractLogicalDefinitionAxiom) - Method in class org.geneontology.obographs.core.model.axiom.AbstractLogicalDefinitionAxiom

compareTo(AbstractPropertyChainAxiom) - Method in class org.geneontology.obographs.core.model.axiom.AbstractPropertyChainAxiom

compareTo(PropertyValue) - Method in interface org.geneontology.obographs.core.model.meta.PropertyValue

context(Object) - Method in class org.geneontology.obographs.core.model.GraphDocument.Builder

Initializes the value for the context attribute.

copyOf(AbstractEdge) - Static method in class org.geneontology.obographs.core.model.Edge

Creates an immutable copy of a AbstractEdge value.

copyOf(AbstractGraph) - Static method in class org.geneontology.obographs.core.model.Graph

Creates an immutable copy of a AbstractGraph value.

copyOf(AbstractGraphDocument) - Static method in class org.geneontology.obographs.core.model.GraphDocument

Creates an immutable copy of a AbstractGraphDocument value.

copyOf(AbstractMeta) - Static method in class org.geneontology.obographs.core.model.Meta

Creates an immutable copy of a AbstractMeta value.

copyOf(AbstractNode) - Static method in class org.geneontology.obographs.core.model.Node

Creates an immutable copy of a AbstractNode value.

copyOf(AbstractDomainRangeAxiom) - Static method in class org.geneontology.obographs.core.model.axiom.DomainRangeAxiom

Creates an immutable copy of a AbstractDomainRangeAxiom value.

copyOf(AbstractEquivalentNodesSet) - Static method in class org.geneontology.obographs.core.model.axiom.EquivalentNodesSet

Creates an immutable copy of a AbstractEquivalentNodesSet value.

copyOf(AbstractExistentialRestrictionExpression) - Static method in class org.geneontology.obographs.core.model.axiom.ExistentialRestrictionExpression

Creates an immutable copy of a AbstractExistentialRestrictionExpression value.

copyOf(AbstractLogicalDefinitionAxiom) - Static method in class org.geneontology.obographs.core.model.axiom.LogicalDefinitionAxiom

Creates an immutable copy of a AbstractLogicalDefinitionAxiom value.

copyOf(AbstractPropertyChainAxiom) - Static method in class org.geneontology.obographs.core.model.axiom.PropertyChainAxiom

Creates an immutable copy of a AbstractPropertyChainAxiom value.

copyOf(AbstractBasicPropertyValue) - Static method in class org.geneontology.obographs.core.model.meta.BasicPropertyValue

Creates an immutable copy of a AbstractBasicPropertyValue value.

copyOf(AbstractDefinitionPropertyValue) - Static method in class org.geneontology.obographs.core.model.meta.DefinitionPropertyValue

Creates an immutable copy of a AbstractDefinitionPropertyValue value.

copyOf(AbstractSynonymPropertyValue) - Static method in class org.geneontology.obographs.core.model.meta.SynonymPropertyValue

Creates an immutable copy of a AbstractSynonymPropertyValue value.

copyOf(AbstractXrefPropertyValue) - Static method in class org.geneontology.obographs.core.model.meta.XrefPropertyValue

Creates an immutable copy of a AbstractXrefPropertyValue value.

D

definedClassId(String) - Method in class org.geneontology.obographs.core.model.axiom.LogicalDefinitionAxiom.Builder

Initializes the value for the definedClassId attribute.

definition(DefinitionPropertyValue) - Method in class org.geneontology.obographs.core.model.Meta.Builder

Initializes the value for the definition attribute.

DefinitionPropertyValue - Class in org.geneontology.obographs.core.model.meta

A PropertyValue that represents a textual definition of an ontology class or property

DefinitionPropertyValue.Builder - Class in org.geneontology.obographs.core.model.meta

Builds instances of type DefinitionPropertyValue.

deprecated(boolean) - Method in class org.geneontology.obographs.core.model.Meta.Builder

Initializes the value for the deprecated attribute.

domainClassIds(Iterable<String>) - Method in class org.geneontology.obographs.core.model.axiom.DomainRangeAxiom.Builder

Sets or replaces all elements for domainClassIds set.

DomainRangeAxiom - Class in org.geneontology.obographs.core.model.axiom

This combined ObjectPropertyDomain, ObjectPropertyRange, and some AllValuesFrom expressions into a single convenience structure

DomainRangeAxiom.Builder - Class in org.geneontology.obographs.core.model.axiom

Builds instances of type DomainRangeAxiom.

domainRangeAxioms(Iterable<? extends DomainRangeAxiom>) - Method in class org.geneontology.obographs.core.model.Graph.Builder

Sets or replaces all elements for domainRangeAxioms list.

E

Edge - Class in org.geneontology.obographs.core.model

An edge connects two nodes via a predicate

Edge.Builder - Class in org.geneontology.obographs.core.model

Builds instances of type Edge.

edges(Iterable<? extends Edge>) - Method in class org.geneontology.obographs.core.model.Graph.Builder

Sets or replaces all elements for edges list.

EMPTY_META - Static variable in interface org.geneontology.obographs.core.model.NodeOrEdge

equals(Object) - Method in class org.geneontology.obographs.core.model.axiom.DomainRangeAxiom

This instance is equal to all instances of DomainRangeAxiom that have equal attribute values.

equals(Object) - Method in class org.geneontology.obographs.core.model.axiom.EquivalentNodesSet

This instance is equal to all instances of EquivalentNodesSet that have equal attribute values.

equals(Object) - Method in class org.geneontology.obographs.core.model.axiom.ExistentialRestrictionExpression

This instance is equal to all instances of ExistentialRestrictionExpression that have equal attribute values.

equals(Object) - Method in class org.geneontology.obographs.core.model.axiom.LogicalDefinitionAxiom

This instance is equal to all instances of LogicalDefinitionAxiom that have equal attribute values.

equals(Object) - Method in class org.geneontology.obographs.core.model.axiom.PropertyChainAxiom

This instance is equal to all instances of PropertyChainAxiom that have equal attribute values.

equals(Object) - Method in class org.geneontology.obographs.core.model.Edge

This instance is equal to all instances of Edge that have equal attribute values.

equals(Object) - Method in class org.geneontology.obographs.core.model.Graph

This instance is equal to all instances of Graph that have equal attribute values.

equals(Object) - Method in class org.geneontology.obographs.core.model.GraphDocument

This instance is equal to all instances of GraphDocument that have equal attribute values.

equals(Object) - Method in class org.geneontology.obographs.core.model.meta.BasicPropertyValue

This instance is equal to all instances of BasicPropertyValue that have equal attribute values.

equals(Object) - Method in class org.geneontology.obographs.core.model.meta.DefinitionPropertyValue

This instance is equal to all instances of DefinitionPropertyValue that have equal attribute values.

equals(Object) - Method in class org.geneontology.obographs.core.model.Meta

This instance is equal to all instances of Meta that have equal attribute values.

equals(Object) - Method in class org.geneontology.obographs.core.model.meta.SynonymPropertyValue

This instance is equal to all instances of SynonymPropertyValue that have equal attribute values.

equals(Object) - Method in class org.geneontology.obographs.core.model.meta.XrefPropertyValue

This instance is equal to all instances of XrefPropertyValue that have equal attribute values.

equals(Object) - Method in class org.geneontology.obographs.core.model.Node

This instance is equal to all instances of Node that have equal attribute values.

EquivalentNodesSet - Class in org.geneontology.obographs.core.model.axiom

A set of nodes that all stand in a mutual equivalence or identity relationship to one another Corresponds to Node in the OWLAPI

EquivalentNodesSet.Builder - Class in org.geneontology.obographs.core.model.axiom

Builds instances of type EquivalentNodesSet.

equivalentNodesSets(Iterable<? extends EquivalentNodesSet>) - Method in class org.geneontology.obographs.core.model.Graph.Builder

Sets or replaces all elements for equivalentNodesSets list.

EXACT - org.geneontology.obographs.core.model.meta.AbstractSynonymPropertyValue.SCOPES

ExistentialRestrictionExpression - Class in org.geneontology.obographs.core.model.axiom

Corresponds to an axiom of the form C = X1 and ...

ExistentialRestrictionExpression.Builder - Class in org.geneontology.obographs.core.model.axiom

Builds instances of type ExistentialRestrictionExpression.

Expression - Interface in org.geneontology.obographs.core.model.axiom

F

fillerId(String) - Method in class org.geneontology.obographs.core.model.axiom.ExistentialRestrictionExpression.Builder

Initializes the value for the fillerId attribute.

from(AbstractEdge) - Method in class org.geneontology.obographs.core.model.Edge.Builder

Fill a builder with attribute values from the provided org.geneontology.obographs.core.model.AbstractEdge instance.

from(AbstractGraph) - Method in class org.geneontology.obographs.core.model.Graph.Builder

Fill a builder with attribute values from the provided AbstractGraph instance.

from(AbstractGraphDocument) - Method in class org.geneontology.obographs.core.model.GraphDocument.Builder

Fill a builder with attribute values from the provided AbstractGraphDocument instance.

from(AbstractMeta) - Method in class org.geneontology.obographs.core.model.Meta.Builder

Fill a builder with attribute values from the provided AbstractMeta instance.

from(AbstractNode) - Method in class org.geneontology.obographs.core.model.Node.Builder

Fill a builder with attribute values from the provided org.geneontology.obographs.core.model.AbstractNode instance.

from(AbstractDomainRangeAxiom) - Method in class org.geneontology.obographs.core.model.axiom.DomainRangeAxiom.Builder

Fill a builder with attribute values from the provided org.geneontology.obographs.core.model.axiom.AbstractDomainRangeAxiom instance.

from(AbstractEquivalentNodesSet) - Method in class org.geneontology.obographs.core.model.axiom.EquivalentNodesSet.Builder

Fill a builder with attribute values from the provided org.geneontology.obographs.core.model.axiom.AbstractEquivalentNodesSet instance.

from(AbstractExistentialRestrictionExpression) - Method in class org.geneontology.obographs.core.model.axiom.ExistentialRestrictionExpression.Builder

Fill a builder with attribute values from the provided AbstractExistentialRestrictionExpression instance.

from(AbstractLogicalDefinitionAxiom) - Method in class org.geneontology.obographs.core.model.axiom.LogicalDefinitionAxiom.Builder

Fill a builder with attribute values from the provided org.geneontology.obographs.core.model.axiom.AbstractLogicalDefinitionAxiom instance.

from(AbstractPropertyChainAxiom) - Method in class org.geneontology.obographs.core.model.axiom.PropertyChainAxiom.Builder

Fill a builder with attribute values from the provided org.geneontology.obographs.core.model.axiom.AbstractPropertyChainAxiom instance.

from(Axiom) - Method in class org.geneontology.obographs.core.model.axiom.DomainRangeAxiom.Builder

Fill a builder with attribute values from the provided org.geneontology.obographs.core.model.axiom.Axiom instance.

from(Axiom) - Method in class org.geneontology.obographs.core.model.axiom.EquivalentNodesSet.Builder

Fill a builder with attribute values from the provided org.geneontology.obographs.core.model.axiom.Axiom instance.

from(Axiom) - Method in class org.geneontology.obographs.core.model.axiom.LogicalDefinitionAxiom.Builder

Fill a builder with attribute values from the provided org.geneontology.obographs.core.model.axiom.Axiom instance.

from(Axiom) - Method in class org.geneontology.obographs.core.model.axiom.PropertyChainAxiom.Builder

Fill a builder with attribute values from the provided org.geneontology.obographs.core.model.axiom.Axiom instance.

from(AbstractBasicPropertyValue) - Method in class org.geneontology.obographs.core.model.meta.BasicPropertyValue.Builder

Fill a builder with attribute values from the provided org.geneontology.obographs.core.model.meta.AbstractBasicPropertyValue instance.

from(AbstractDefinitionPropertyValue) - Method in class org.geneontology.obographs.core.model.meta.DefinitionPropertyValue.Builder

Fill a builder with attribute values from the provided org.geneontology.obographs.core.model.meta.AbstractDefinitionPropertyValue instance.

from(AbstractSynonymPropertyValue) - Method in class org.geneontology.obographs.core.model.meta.SynonymPropertyValue.Builder

Fill a builder with attribute values from the provided org.geneontology.obographs.core.model.meta.AbstractSynonymPropertyValue instance.

from(AbstractXrefPropertyValue) - Method in class org.geneontology.obographs.core.model.meta.XrefPropertyValue.Builder

Fill a builder with attribute values from the provided org.geneontology.obographs.core.model.meta.AbstractXrefPropertyValue instance.

from(PropertyValue) - Method in class org.geneontology.obographs.core.model.meta.BasicPropertyValue.Builder

Fill a builder with attribute values from the provided org.geneontology.obographs.core.model.meta.PropertyValue instance.

from(PropertyValue) - Method in class org.geneontology.obographs.core.model.meta.DefinitionPropertyValue.Builder

Fill a builder with attribute values from the provided org.geneontology.obographs.core.model.meta.PropertyValue instance.

from(PropertyValue) - Method in class org.geneontology.obographs.core.model.meta.SynonymPropertyValue.Builder

Fill a builder with attribute values from the provided org.geneontology.obographs.core.model.meta.PropertyValue instance.

from(PropertyValue) - Method in class org.geneontology.obographs.core.model.meta.XrefPropertyValue.Builder

Fill a builder with attribute values from the provided org.geneontology.obographs.core.model.meta.PropertyValue instance.

from(NodeOrEdge) - Method in class org.geneontology.obographs.core.model.Edge.Builder

Fill a builder with attribute values from the provided org.geneontology.obographs.core.model.NodeOrEdge instance.

from(NodeOrEdge) - Method in class org.geneontology.obographs.core.model.Node.Builder

Fill a builder with attribute values from the provided org.geneontology.obographs.core.model.NodeOrEdge instance.

G

genusIds(Iterable<String>) - Method in class org.geneontology.obographs.core.model.axiom.LogicalDefinitionAxiom.Builder

Sets or replaces all elements for genusIds list.

getAllValuesFromEdges() - Method in class org.geneontology.obographs.core.model.axiom.AbstractDomainRangeAxiom

Set of edges representing `X SubClassOf P only Y` axioms.

getAllValuesFromEdges() - Method in class org.geneontology.obographs.core.model.axiom.DomainRangeAxiom

Set of edges representing `X SubClassOf P only Y` axioms.

getBasicPropertyValues() - Method in class org.geneontology.obographs.core.model.AbstractMeta

getBasicPropertyValues() - Method in class org.geneontology.obographs.core.model.Meta

getChainPredicateIds() - Method in class org.geneontology.obographs.core.model.axiom.AbstractPropertyChainAxiom

getChainPredicateIds() - Method in class org.geneontology.obographs.core.model.axiom.PropertyChainAxiom

getComments() - Method in class org.geneontology.obographs.core.model.AbstractMeta

getComments() - Method in class org.geneontology.obographs.core.model.Meta

getContext() - Method in class org.geneontology.obographs.core.model.AbstractGraphDocument

The JSON-LD context for this document.

getContext() - Method in class org.geneontology.obographs.core.model.GraphDocument

The JSON-LD context for this document.

getDefinedClassId() - Method in class org.geneontology.obographs.core.model.axiom.AbstractLogicalDefinitionAxiom

getDefinedClassId() - Method in class org.geneontology.obographs.core.model.axiom.LogicalDefinitionAxiom

getDefinition() - Method in class org.geneontology.obographs.core.model.AbstractMeta

getDefinition() - Method in class org.geneontology.obographs.core.model.Meta

getDeprecated() - Method in class org.geneontology.obographs.core.model.AbstractMeta

getDeprecated() - Method in class org.geneontology.obographs.core.model.Meta

getDomainClassIds() - Method in class org.geneontology.obographs.core.model.axiom.AbstractDomainRangeAxiom

For multiple domains, this is treated as intersection

getDomainClassIds() - Method in class org.geneontology.obographs.core.model.axiom.DomainRangeAxiom

For multiple domains, this is treated as intersection

getDomainRangeAxioms() - Method in class org.geneontology.obographs.core.model.AbstractGraph

getDomainRangeAxioms() - Method in class org.geneontology.obographs.core.model.Graph

getEdges() - Method in class org.geneontology.obographs.core.model.AbstractGraph

getEdges() - Method in class org.geneontology.obographs.core.model.Graph

getEquivalentNodesSets() - Method in class org.geneontology.obographs.core.model.AbstractGraph

getEquivalentNodesSets() - Method in class org.geneontology.obographs.core.model.Graph

getFillerId() - Method in class org.geneontology.obographs.core.model.axiom.AbstractExistentialRestrictionExpression

getFillerId() - Method in class org.geneontology.obographs.core.model.axiom.ExistentialRestrictionExpression

getGenusIds() - Method in class org.geneontology.obographs.core.model.axiom.AbstractLogicalDefinitionAxiom

getGenusIds() - Method in class org.geneontology.obographs.core.model.axiom.LogicalDefinitionAxiom

getGraphs() - Method in class org.geneontology.obographs.core.model.AbstractGraphDocument

getGraphs() - Method in class org.geneontology.obographs.core.model.GraphDocument

getId() - Method in class org.geneontology.obographs.core.model.AbstractGraph

getId() - Method in class org.geneontology.obographs.core.model.AbstractNode

getId() - Method in class org.geneontology.obographs.core.model.Graph

getId() - Method in class org.geneontology.obographs.core.model.Node

getLabel() - Method in class org.geneontology.obographs.core.model.AbstractNode

getLabel() - Method in class org.geneontology.obographs.core.model.Node

getLbl() - Method in class org.geneontology.obographs.core.model.AbstractGraph

getLbl() - Method in class org.geneontology.obographs.core.model.Graph

getLbl() - Method in class org.geneontology.obographs.core.model.meta.AbstractXrefPropertyValue

getLbl() - Method in class org.geneontology.obographs.core.model.meta.XrefPropertyValue

getLogicalDefinitionAxioms() - Method in class org.geneontology.obographs.core.model.AbstractGraph

getLogicalDefinitionAxioms() - Method in class org.geneontology.obographs.core.model.Graph

getMeta() - Method in class org.geneontology.obographs.core.model.AbstractGraph

getMeta() - Method in class org.geneontology.obographs.core.model.AbstractGraphDocument

getMeta() - Method in interface org.geneontology.obographs.core.model.axiom.Axiom

getMeta() - Method in class org.geneontology.obographs.core.model.axiom.DomainRangeAxiom

getMeta() - Method in class org.geneontology.obographs.core.model.axiom.EquivalentNodesSet

getMeta() - Method in class org.geneontology.obographs.core.model.axiom.LogicalDefinitionAxiom

getMeta() - Method in class org.geneontology.obographs.core.model.axiom.PropertyChainAxiom

getMeta() - Method in class org.geneontology.obographs.core.model.Edge

getMeta() - Method in class org.geneontology.obographs.core.model.Graph

getMeta() - Method in class org.geneontology.obographs.core.model.GraphDocument

getMeta() - Method in class org.geneontology.obographs.core.model.meta.BasicPropertyValue

getMeta() - Method in class org.geneontology.obographs.core.model.meta.DefinitionPropertyValue

getMeta() - Method in interface org.geneontology.obographs.core.model.meta.PropertyValue

getMeta() - Method in class org.geneontology.obographs.core.model.meta.SynonymPropertyValue

getMeta() - Method in class org.geneontology.obographs.core.model.meta.XrefPropertyValue

getMeta() - Method in class org.geneontology.obographs.core.model.Node

getMeta() - Method in interface org.geneontology.obographs.core.model.NodeOrEdge

getNodeIds() - Method in class org.geneontology.obographs.core.model.axiom.AbstractEquivalentNodesSet

getNodeIds() - Method in class org.geneontology.obographs.core.model.axiom.EquivalentNodesSet

getNodes() - Method in class org.geneontology.obographs.core.model.AbstractGraph

getNodes() - Method in class org.geneontology.obographs.core.model.Graph

getObj() - Method in class org.geneontology.obographs.core.model.AbstractEdge

getObj() - Method in class org.geneontology.obographs.core.model.Edge

getPred() - Method in class org.geneontology.obographs.core.model.AbstractEdge

getPred() - Method in class org.geneontology.obographs.core.model.Edge

getPred() - Method in class org.geneontology.obographs.core.model.meta.BasicPropertyValue

Predicates correspond to OWL properties.

getPred() - Method in class org.geneontology.obographs.core.model.meta.DefinitionPropertyValue

Predicates correspond to OWL properties.

getPred() - Method in interface org.geneontology.obographs.core.model.meta.PropertyValue

Predicates correspond to OWL properties.

getPred() - Method in class org.geneontology.obographs.core.model.meta.SynonymPropertyValue

Predicates correspond to OWL properties.

getPred() - Method in class org.geneontology.obographs.core.model.meta.XrefPropertyValue

Predicates correspond to OWL properties.

getPredicateId() - Method in class org.geneontology.obographs.core.model.axiom.AbstractDomainRangeAxiom

getPredicateId() - Method in class org.geneontology.obographs.core.model.axiom.AbstractPropertyChainAxiom

getPredicateId() - Method in class org.geneontology.obographs.core.model.axiom.DomainRangeAxiom

getPredicateId() - Method in class org.geneontology.obographs.core.model.axiom.PropertyChainAxiom

getPropertyChainAxioms() - Method in class org.geneontology.obographs.core.model.AbstractGraph

getPropertyChainAxioms() - Method in class org.geneontology.obographs.core.model.Graph

getPropertyId() - Method in class org.geneontology.obographs.core.model.axiom.AbstractExistentialRestrictionExpression

getPropertyId() - Method in class org.geneontology.obographs.core.model.axiom.ExistentialRestrictionExpression

getRangeClassIds() - Method in class org.geneontology.obographs.core.model.axiom.AbstractDomainRangeAxiom

For multiple ranges, this is treated as intersection

getRangeClassIds() - Method in class org.geneontology.obographs.core.model.axiom.DomainRangeAxiom

For multiple ranges, this is treated as intersection

getRepresentativeNodeId() - Method in class org.geneontology.obographs.core.model.axiom.AbstractEquivalentNodesSet

getRepresentativeNodeId() - Method in class org.geneontology.obographs.core.model.axiom.EquivalentNodesSet

getRestrictions() - Method in class org.geneontology.obographs.core.model.axiom.AbstractLogicalDefinitionAxiom

getRestrictions() - Method in class org.geneontology.obographs.core.model.axiom.LogicalDefinitionAxiom

getSub() - Method in class org.geneontology.obographs.core.model.AbstractEdge

getSub() - Method in class org.geneontology.obographs.core.model.Edge

getSubsets() - Method in class org.geneontology.obographs.core.model.AbstractMeta

getSubsets() - Method in class org.geneontology.obographs.core.model.Meta

getSynonyms() - Method in class org.geneontology.obographs.core.model.AbstractMeta

getSynonyms() - Method in class org.geneontology.obographs.core.model.Meta

getSynonymType() - Method in class org.geneontology.obographs.core.model.meta.AbstractSynonymPropertyValue

getSynonymType() - Method in class org.geneontology.obographs.core.model.meta.SynonymPropertyValue

getType() - Method in class org.geneontology.obographs.core.model.AbstractNode

getType() - Method in class org.geneontology.obographs.core.model.Node

getTypes() - Method in class org.geneontology.obographs.core.model.meta.AbstractSynonymPropertyValue

getVal() - Method in class org.geneontology.obographs.core.model.meta.BasicPropertyValue

The value of the property-value

getVal() - Method in class org.geneontology.obographs.core.model.meta.DefinitionPropertyValue

The value of the property-value

getVal() - Method in interface org.geneontology.obographs.core.model.meta.PropertyValue

The value of the property-value

getVal() - Method in class org.geneontology.obographs.core.model.meta.SynonymPropertyValue

The value of the property-value

getVal() - Method in class org.geneontology.obographs.core.model.meta.XrefPropertyValue

The value of the property-value

getVersion() - Method in class org.geneontology.obographs.core.model.AbstractMeta

getVersion() - Method in class org.geneontology.obographs.core.model.Meta

getXrefs() - Method in class org.geneontology.obographs.core.model.AbstractMeta

getXrefs() - Method in class org.geneontology.obographs.core.model.meta.BasicPropertyValue

An array denoting objects that support the property value assertion

getXrefs() - Method in class org.geneontology.obographs.core.model.meta.DefinitionPropertyValue

An array denoting objects that support the property value assertion

getXrefs() - Method in class org.geneontology.obographs.core.model.Meta

getXrefs() - Method in interface org.geneontology.obographs.core.model.meta.PropertyValue

An array denoting objects that support the property value assertion

getXrefs() - Method in class org.geneontology.obographs.core.model.meta.SynonymPropertyValue

An array denoting objects that support the property value assertion

getXrefs() - Method in class org.geneontology.obographs.core.model.meta.XrefPropertyValue

An array denoting objects that support the property value assertion

getXrefsValues() - Method in class org.geneontology.obographs.core.model.AbstractMeta

getXrefsValues() - Method in class org.geneontology.obographs.core.model.Meta

Graph - Class in org.geneontology.obographs.core.model

A graph object holds a collection of nodes and edges Corresponds to a Named Graph in RDF, and an Ontology in OWL Note: there is no assumption that either nodes or edges are unique to a graph ## Basic OBO Graphs  *

Graph.Builder - Class in org.geneontology.obographs.core.model

Builds instances of type Graph.

GraphDocument - Class in org.geneontology.obographs.core.model

Holds a collection of graphs, plus document-level metadata ## Model 

GraphDocument.Builder - Class in org.geneontology.obographs.core.model

Builds instances of type GraphDocument.

graphs(Iterable<? extends Graph>) - Method in class org.geneontology.obographs.core.model.GraphDocument.Builder

Sets or replaces all elements for graphs list.

H

hashCode() - Method in class org.geneontology.obographs.core.model.axiom.DomainRangeAxiom

Computes a hash code from attributes: meta, predicateId, domainClassIds, rangeClassIds, allValuesFromEdges.

hashCode() - Method in class org.geneontology.obographs.core.model.axiom.EquivalentNodesSet

Computes a hash code from attributes: meta, representativeNodeId, nodeIds.

hashCode() - Method in class org.geneontology.obographs.core.model.axiom.ExistentialRestrictionExpression

Computes a hash code from attributes: propertyId, fillerId.

hashCode() - Method in class org.geneontology.obographs.core.model.axiom.LogicalDefinitionAxiom

Computes a hash code from attributes: meta, definedClassId, genusIds, restrictions.

hashCode() - Method in class org.geneontology.obographs.core.model.axiom.PropertyChainAxiom

Computes a hash code from attributes: meta, predicateId, chainPredicateIds.

hashCode() - Method in class org.geneontology.obographs.core.model.Edge

Computes a hash code from attributes: meta, sub, pred, obj.

hashCode() - Method in class org.geneontology.obographs.core.model.Graph

Computes a hash code from attributes: id, lbl, meta, nodes, edges, equivalentNodesSets, logicalDefinitionAxioms, domainRangeAxioms, propertyChainAxioms.

hashCode() - Method in class org.geneontology.obographs.core.model.GraphDocument

Computes a hash code from attributes: context, meta, graphs.

hashCode() - Method in class org.geneontology.obographs.core.model.meta.BasicPropertyValue

Computes a hash code from attributes: pred, val, xrefs, meta.

hashCode() - Method in class org.geneontology.obographs.core.model.meta.DefinitionPropertyValue

Computes a hash code from attributes: pred, val, xrefs, meta.

hashCode() - Method in class org.geneontology.obographs.core.model.Meta

Computes a hash code from attributes: definition, comments, subsets, synonyms, xrefs, xrefsValues, basicPropertyValues, version, deprecated.

hashCode() - Method in class org.geneontology.obographs.core.model.meta.SynonymPropertyValue

Computes a hash code from attributes: pred, val, xrefs, meta, synonymType.

hashCode() - Method in class org.geneontology.obographs.core.model.meta.XrefPropertyValue

Computes a hash code from attributes: pred, val, xrefs, meta, lbl.

hashCode() - Method in class org.geneontology.obographs.core.model.Node

Computes a hash code from attributes: meta, id, label, type.

I

id(String) - Method in class org.geneontology.obographs.core.model.Graph.Builder

Initializes the value for the id attribute.

id(String) - Method in class org.geneontology.obographs.core.model.Node.Builder

Initializes the value for the id attribute.

INDIVIDUAL - org.geneontology.obographs.core.model.AbstractNode.RDFTYPES

isBroad() - Method in class org.geneontology.obographs.core.model.meta.AbstractSynonymPropertyValue

isExact() - Method in class org.geneontology.obographs.core.model.meta.AbstractSynonymPropertyValue

isNarrow() - Method in class org.geneontology.obographs.core.model.meta.AbstractSynonymPropertyValue

isRelated() - Method in class org.geneontology.obographs.core.model.meta.AbstractSynonymPropertyValue

L

label(String) - Method in class org.geneontology.obographs.core.model.Node.Builder

Initializes the value for the label attribute.

lbl(String) - Method in class org.geneontology.obographs.core.model.Graph.Builder

Initializes the value for the lbl attribute.

lbl(String) - Method in class org.geneontology.obographs.core.model.meta.XrefPropertyValue.Builder

Initializes the value for the lbl attribute.

LogicalDefinitionAxiom - Class in org.geneontology.obographs.core.model.axiom

Corresponds to an axiom of the form C = X1 and ...

LogicalDefinitionAxiom.Builder - Class in org.geneontology.obographs.core.model.axiom

Builds instances of type LogicalDefinitionAxiom.

logicalDefinitionAxioms(Iterable<? extends LogicalDefinitionAxiom>) - Method in class org.geneontology.obographs.core.model.Graph.Builder

Sets or replaces all elements for logicalDefinitionAxioms list.

M

makeSchema(Class<?>) - Static method in class org.geneontology.obographs.core.io.OgSchemaGenerator

meta(Meta) - Method in class org.geneontology.obographs.core.model.axiom.DomainRangeAxiom.Builder

Initializes the value for the meta attribute.

meta(Meta) - Method in class org.geneontology.obographs.core.model.axiom.EquivalentNodesSet.Builder

Initializes the value for the meta attribute.

meta(Meta) - Method in class org.geneontology.obographs.core.model.axiom.LogicalDefinitionAxiom.Builder

Initializes the value for the meta attribute.

meta(Meta) - Method in class org.geneontology.obographs.core.model.axiom.PropertyChainAxiom.Builder

Initializes the value for the meta attribute.

meta(Meta) - Method in class org.geneontology.obographs.core.model.Edge.Builder

Initializes the value for the meta attribute.

meta(Meta) - Method in class org.geneontology.obographs.core.model.Graph.Builder

Initializes the value for the meta attribute.

meta(Meta) - Method in class org.geneontology.obographs.core.model.GraphDocument.Builder

Initializes the value for the meta attribute.

meta(Meta) - Method in class org.geneontology.obographs.core.model.meta.BasicPropertyValue.Builder

Initializes the value for the meta attribute.

meta(Meta) - Method in class org.geneontology.obographs.core.model.meta.DefinitionPropertyValue.Builder

Initializes the value for the meta attribute.

meta(Meta) - Method in class org.geneontology.obographs.core.model.meta.SynonymPropertyValue.Builder

Initializes the value for the meta attribute.

meta(Meta) - Method in class org.geneontology.obographs.core.model.meta.XrefPropertyValue.Builder

Initializes the value for the meta attribute.

meta(Meta) - Method in class org.geneontology.obographs.core.model.Node.Builder

Initializes the value for the meta attribute.

Meta - Class in org.geneontology.obographs.core.model

A holder for metadata The information in a Meta object consists sets of PropertyValue objects, which associate the Meta object holder with some value via some property.

Meta.Builder - Class in org.geneontology.obographs.core.model

Builds instances of type Meta.

N

NARROW - org.geneontology.obographs.core.model.meta.AbstractSynonymPropertyValue.SCOPES

Node - Class in org.geneontology.obographs.core.model

A graph node corresponds to a class, individual or property 

Node.Builder - Class in org.geneontology.obographs.core.model

Builds instances of type Node.

nodeIds(Iterable<String>) - Method in class org.geneontology.obographs.core.model.axiom.EquivalentNodesSet.Builder

Sets or replaces all elements for nodeIds set.

NodeOrEdge - Interface in org.geneontology.obographs.core.model

nodes(Iterable<? extends Node>) - Method in class org.geneontology.obographs.core.model.Graph.Builder

Sets or replaces all elements for nodes list.

O

obj(String) - Method in class org.geneontology.obographs.core.model.Edge.Builder

Initializes the value for the obj attribute.

OboGraph - Annotation Type in org.geneontology.obographs.core.model

OgJsonGenerator - Class in org.geneontology.obographs.core.io

OgJsonReader - Class in org.geneontology.obographs.core.io

OgSchemaGenerator - Class in org.geneontology.obographs.core.io

OgYamlGenerator - Class in org.geneontology.obographs.core.io

OgYamlReader - Class in org.geneontology.obographs.core.io

org.geneontology.obographs.core - package org.geneontology.obographs.core

OBO Graphs Useful classes: GraphDocument

org.geneontology.obographs.core.io - package org.geneontology.obographs.core.io

org.geneontology.obographs.core.model - package org.geneontology.obographs.core.model

## Basic Obo Graph Model Corresponds to the subset of OWL consisting of SubClassOf axioms between named classes and either named classes or simple existential restrictions.

org.geneontology.obographs.core.model.axiom - package org.geneontology.obographs.core.model.axiom

Advanced Obo Graph model Represents OWL axioms that do not fit into the Basic Obo Graph model

org.geneontology.obographs.core.model.meta - package org.geneontology.obographs.core.model.meta

Objects that can be associated with a Meta holder

P

pred() - Method in enum org.geneontology.obographs.core.model.meta.AbstractSynonymPropertyValue.SCOPES

pred(String) - Method in class org.geneontology.obographs.core.model.Edge.Builder

Initializes the value for the pred attribute.

pred(String) - Method in class org.geneontology.obographs.core.model.meta.BasicPropertyValue.Builder

Initializes the value for the pred attribute.

pred(String) - Method in class org.geneontology.obographs.core.model.meta.DefinitionPropertyValue.Builder

Initializes the value for the pred attribute.

pred(String) - Method in class org.geneontology.obographs.core.model.meta.SynonymPropertyValue.Builder

Initializes the value for the pred attribute.

pred(String) - Method in class org.geneontology.obographs.core.model.meta.XrefPropertyValue.Builder

Initializes the value for the pred attribute.

predicateId(String) - Method in class org.geneontology.obographs.core.model.axiom.DomainRangeAxiom.Builder

Initializes the value for the predicateId attribute.

predicateId(String) - Method in class org.geneontology.obographs.core.model.axiom.PropertyChainAxiom.Builder

Initializes the value for the predicateId attribute.

PROPERTY - org.geneontology.obographs.core.model.AbstractNode.RDFTYPES

PropertyChainAxiom - Class in org.geneontology.obographs.core.model.axiom

P <- P1 ...

PropertyChainAxiom.Builder - Class in org.geneontology.obographs.core.model.axiom

Builds instances of type PropertyChainAxiom.

propertyChainAxioms(Iterable<? extends PropertyChainAxiom>) - Method in class org.geneontology.obographs.core.model.Graph.Builder

Sets or replaces all elements for propertyChainAxioms list.

propertyId(String) - Method in class org.geneontology.obographs.core.model.axiom.ExistentialRestrictionExpression.Builder

Initializes the value for the propertyId attribute.

PropertyValue - Interface in org.geneontology.obographs.core.model.meta

Associates the container object with a value via a property.

R

rangeClassIds(Iterable<String>) - Method in class org.geneontology.obographs.core.model.axiom.DomainRangeAxiom.Builder

Sets or replaces all elements for rangeClassIds set.

read(Reader) - Static method in class org.geneontology.obographs.core.io.OgJsonReader

read(Reader) - Static method in class org.geneontology.obographs.core.io.OgYamlReader

readFile(File) - Static method in class org.geneontology.obographs.core.io.OgJsonReader

readFile(File) - Static method in class org.geneontology.obographs.core.io.OgYamlReader

readFile(String) - Static method in class org.geneontology.obographs.core.io.OgJsonReader

readFile(String) - Static method in class org.geneontology.obographs.core.io.OgYamlReader

readInputStream(InputStream) - Static method in class org.geneontology.obographs.core.io.OgJsonReader

readInputStream(InputStream) - Static method in class org.geneontology.obographs.core.io.OgYamlReader

RELATED - org.geneontology.obographs.core.model.meta.AbstractSynonymPropertyValue.SCOPES

render(Object) - Static method in class org.geneontology.obographs.core.io.OgJsonGenerator

render(Object) - Static method in class org.geneontology.obographs.core.io.OgYamlGenerator

representativeNodeId(String) - Method in class org.geneontology.obographs.core.model.axiom.EquivalentNodesSet.Builder

Initializes the value for the representativeNodeId attribute.

restrictions(Iterable<? extends ExistentialRestrictionExpression>) - Method in class org.geneontology.obographs.core.model.axiom.LogicalDefinitionAxiom.Builder

Sets or replaces all elements for restrictions list.

S

sub(String) - Method in class org.geneontology.obographs.core.model.Edge.Builder

Initializes the value for the sub attribute.

subsets(Iterable<String>) - Method in class org.geneontology.obographs.core.model.Meta.Builder

Sets or replaces all elements for subsets list.

SynonymPropertyValue - Class in org.geneontology.obographs.core.model.meta

A PropertyValue that represents a an alternative term for a node

SynonymPropertyValue.Builder - Class in org.geneontology.obographs.core.model.meta

Builds instances of type SynonymPropertyValue.

synonyms(Iterable<? extends SynonymPropertyValue>) - Method in class org.geneontology.obographs.core.model.Meta.Builder

Sets or replaces all elements for synonyms list.

synonymType(String) - Method in class org.geneontology.obographs.core.model.meta.SynonymPropertyValue.Builder

Initializes the value for the synonymType attribute.

T

toString() - Method in class org.geneontology.obographs.core.model.axiom.DomainRangeAxiom

Prints the immutable value DomainRangeAxiom with attribute values.

toString() - Method in class org.geneontology.obographs.core.model.axiom.EquivalentNodesSet

Prints the immutable value EquivalentNodesSet with attribute values.

toString() - Method in class org.geneontology.obographs.core.model.axiom.ExistentialRestrictionExpression

Prints the immutable value ExistentialRestrictionExpression with attribute values.

toString() - Method in class org.geneontology.obographs.core.model.axiom.LogicalDefinitionAxiom

Prints the immutable value LogicalDefinitionAxiom with attribute values.

toString() - Method in class org.geneontology.obographs.core.model.axiom.PropertyChainAxiom

Prints the immutable value PropertyChainAxiom with attribute values.

toString() - Method in class org.geneontology.obographs.core.model.Edge

Prints the immutable value Edge with attribute values.

toString() - Method in class org.geneontology.obographs.core.model.Graph

Prints the immutable value Graph with attribute values.

toString() - Method in class org.geneontology.obographs.core.model.GraphDocument

Prints the immutable value GraphDocument with attribute values.

toString() - Method in class org.geneontology.obographs.core.model.meta.BasicPropertyValue

Prints the immutable value BasicPropertyValue with attribute values.

toString() - Method in class org.geneontology.obographs.core.model.meta.DefinitionPropertyValue

Prints the immutable value DefinitionPropertyValue with attribute values.

toString() - Method in class org.geneontology.obographs.core.model.meta.SynonymPropertyValue

Prints the immutable value SynonymPropertyValue with attribute values.

toString() - Method in class org.geneontology.obographs.core.model.Meta

Prints the immutable value Meta with attribute values.

toString() - Method in class org.geneontology.obographs.core.model.meta.XrefPropertyValue

Prints the immutable value XrefPropertyValue with attribute values.

toString() - Method in class org.geneontology.obographs.core.model.Node

Prints the immutable value Node with attribute values.

type(AbstractNode.RDFTYPES) - Method in class org.geneontology.obographs.core.model.Node.Builder

Initializes the value for the type attribute.

V

val(String) - Method in class org.geneontology.obographs.core.model.meta.BasicPropertyValue.Builder

Initializes the value for the val attribute.

val(String) - Method in class org.geneontology.obographs.core.model.meta.DefinitionPropertyValue.Builder

Initializes the value for the val attribute.

val(String) - Method in class org.geneontology.obographs.core.model.meta.SynonymPropertyValue.Builder

Initializes the value for the val attribute.

val(String) - Method in class org.geneontology.obographs.core.model.meta.XrefPropertyValue.Builder

Initializes the value for the val attribute.

valueOf(String) - Static method in enum org.geneontology.obographs.core.model.AbstractNode.RDFTYPES

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.geneontology.obographs.core.model.meta.AbstractSynonymPropertyValue.SCOPES

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.geneontology.obographs.core.model.AbstractNode.RDFTYPES

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.geneontology.obographs.core.model.meta.AbstractSynonymPropertyValue.SCOPES

Returns an array containing the constants of this enum type, in the order they are declared.

version(String) - Method in class org.geneontology.obographs.core.model.Meta.Builder

Initializes the value for the version attribute.

W

withAllValuesFromEdges(Iterable<? extends Edge>) - Method in class org.geneontology.obographs.core.model.axiom.DomainRangeAxiom

Copy the current immutable object with elements that replace the content of allValuesFromEdges.

withAllValuesFromEdges(Edge...) - Method in class org.geneontology.obographs.core.model.axiom.DomainRangeAxiom

Copy the current immutable object with elements that replace the content of allValuesFromEdges.

withBasicPropertyValues(Iterable<? extends BasicPropertyValue>) - Method in class org.geneontology.obographs.core.model.Meta

Copy the current immutable object with elements that replace the content of basicPropertyValues.

withBasicPropertyValues(BasicPropertyValue...) - Method in class org.geneontology.obographs.core.model.Meta

Copy the current immutable object with elements that replace the content of basicPropertyValues.

withChainPredicateIds(Iterable<String>) - Method in class org.geneontology.obographs.core.model.axiom.PropertyChainAxiom

Copy the current immutable object with elements that replace the content of chainPredicateIds.

withChainPredicateIds(String...) - Method in class org.geneontology.obographs.core.model.axiom.PropertyChainAxiom

Copy the current immutable object with elements that replace the content of chainPredicateIds.

withComments(Iterable<String>) - Method in class org.geneontology.obographs.core.model.Meta

Copy the current immutable object with elements that replace the content of comments.

withComments(String...) - Method in class org.geneontology.obographs.core.model.Meta

Copy the current immutable object with elements that replace the content of comments.

withContext(Object) - Method in class org.geneontology.obographs.core.model.GraphDocument

Copy the current immutable object by setting a value for the context attribute.

withDefinedClassId(String) - Method in class org.geneontology.obographs.core.model.axiom.LogicalDefinitionAxiom

Copy the current immutable object by setting a value for the definedClassId attribute.

withDefinition(DefinitionPropertyValue) - Method in class org.geneontology.obographs.core.model.Meta

Copy the current immutable object by setting a value for the definition attribute.

withDeprecated(boolean) - Method in class org.geneontology.obographs.core.model.Meta

Copy the current immutable object by setting a value for the deprecated attribute.

withDomainClassIds(Iterable<String>) - Method in class org.geneontology.obographs.core.model.axiom.DomainRangeAxiom

Copy the current immutable object with elements that replace the content of domainClassIds.

withDomainClassIds(String...) - Method in class org.geneontology.obographs.core.model.axiom.DomainRangeAxiom

Copy the current immutable object with elements that replace the content of domainClassIds.

withDomainRangeAxioms(Iterable<? extends DomainRangeAxiom>) - Method in class org.geneontology.obographs.core.model.Graph

Copy the current immutable object with elements that replace the content of domainRangeAxioms.

withDomainRangeAxioms(DomainRangeAxiom...) - Method in class org.geneontology.obographs.core.model.Graph

Copy the current immutable object with elements that replace the content of domainRangeAxioms.

withEdges(Iterable<? extends Edge>) - Method in class org.geneontology.obographs.core.model.Graph

Copy the current immutable object with elements that replace the content of edges.

withEdges(Edge...) - Method in class org.geneontology.obographs.core.model.Graph

Copy the current immutable object with elements that replace the content of edges.

withEquivalentNodesSets(Iterable<? extends EquivalentNodesSet>) - Method in class org.geneontology.obographs.core.model.Graph

Copy the current immutable object with elements that replace the content of equivalentNodesSets.

withEquivalentNodesSets(EquivalentNodesSet...) - Method in class org.geneontology.obographs.core.model.Graph

Copy the current immutable object with elements that replace the content of equivalentNodesSets.

withFillerId(String) - Method in class org.geneontology.obographs.core.model.axiom.ExistentialRestrictionExpression

Copy the current immutable object by setting a value for the fillerId attribute.

withGenusIds(Iterable<String>) - Method in class org.geneontology.obographs.core.model.axiom.LogicalDefinitionAxiom

Copy the current immutable object with elements that replace the content of genusIds.

withGenusIds(String...) - Method in class org.geneontology.obographs.core.model.axiom.LogicalDefinitionAxiom

Copy the current immutable object with elements that replace the content of genusIds.

withGraphs(Iterable<? extends Graph>) - Method in class org.geneontology.obographs.core.model.GraphDocument

Copy the current immutable object with elements that replace the content of graphs.

withGraphs(Graph...) - Method in class org.geneontology.obographs.core.model.GraphDocument

Copy the current immutable object with elements that replace the content of graphs.

withId(String) - Method in class org.geneontology.obographs.core.model.Graph

Copy the current immutable object by setting a value for the id attribute.

withId(String) - Method in class org.geneontology.obographs.core.model.Node

Copy the current immutable object by setting a value for the id attribute.

withLabel(String) - Method in class org.geneontology.obographs.core.model.Node

Copy the current immutable object by setting a value for the label attribute.

withLbl(String) - Method in class org.geneontology.obographs.core.model.Graph

Copy the current immutable object by setting a value for the lbl attribute.

withLbl(String) - Method in class org.geneontology.obographs.core.model.meta.XrefPropertyValue

Copy the current immutable object by setting a value for the lbl attribute.

withLogicalDefinitionAxioms(Iterable<? extends LogicalDefinitionAxiom>) - Method in class org.geneontology.obographs.core.model.Graph

Copy the current immutable object with elements that replace the content of logicalDefinitionAxioms.

withLogicalDefinitionAxioms(LogicalDefinitionAxiom...) - Method in class org.geneontology.obographs.core.model.Graph

Copy the current immutable object with elements that replace the content of logicalDefinitionAxioms.

withMeta(Meta) - Method in class org.geneontology.obographs.core.model.axiom.DomainRangeAxiom

Copy the current immutable object by setting a value for the meta attribute.

withMeta(Meta) - Method in class org.geneontology.obographs.core.model.axiom.EquivalentNodesSet

Copy the current immutable object by setting a value for the meta attribute.

withMeta(Meta) - Method in class org.geneontology.obographs.core.model.axiom.LogicalDefinitionAxiom

Copy the current immutable object by setting a value for the meta attribute.

withMeta(Meta) - Method in class org.geneontology.obographs.core.model.axiom.PropertyChainAxiom

Copy the current immutable object by setting a value for the meta attribute.

withMeta(Meta) - Method in class org.geneontology.obographs.core.model.Edge

Copy the current immutable object by setting a value for the meta attribute.

withMeta(Meta) - Method in class org.geneontology.obographs.core.model.Graph

Copy the current immutable object by setting a value for the meta attribute.

withMeta(Meta) - Method in class org.geneontology.obographs.core.model.GraphDocument

Copy the current immutable object by setting a value for the meta attribute.

withMeta(Meta) - Method in class org.geneontology.obographs.core.model.meta.BasicPropertyValue

Copy the current immutable object by setting a value for the meta attribute.

withMeta(Meta) - Method in class org.geneontology.obographs.core.model.meta.DefinitionPropertyValue

Copy the current immutable object by setting a value for the meta attribute.

withMeta(Meta) - Method in class org.geneontology.obographs.core.model.meta.SynonymPropertyValue

Copy the current immutable object by setting a value for the meta attribute.

withMeta(Meta) - Method in class org.geneontology.obographs.core.model.meta.XrefPropertyValue

Copy the current immutable object by setting a value for the meta attribute.

withMeta(Meta) - Method in class org.geneontology.obographs.core.model.Node

Copy the current immutable object by setting a value for the meta attribute.

withNodeIds(Iterable<String>) - Method in class org.geneontology.obographs.core.model.axiom.EquivalentNodesSet

Copy the current immutable object with elements that replace the content of nodeIds.

withNodeIds(String...) - Method in class org.geneontology.obographs.core.model.axiom.EquivalentNodesSet

Copy the current immutable object with elements that replace the content of nodeIds.

withNodes(Iterable<? extends Node>) - Method in class org.geneontology.obographs.core.model.Graph

Copy the current immutable object with elements that replace the content of nodes.

withNodes(Node...) - Method in class org.geneontology.obographs.core.model.Graph

Copy the current immutable object with elements that replace the content of nodes.

withObj(String) - Method in class org.geneontology.obographs.core.model.Edge

Copy the current immutable object by setting a value for the obj attribute.

withPred(String) - Method in class org.geneontology.obographs.core.model.Edge

Copy the current immutable object by setting a value for the pred attribute.

withPred(String) - Method in class org.geneontology.obographs.core.model.meta.BasicPropertyValue

Copy the current immutable object by setting a value for the pred attribute.

withPred(String) - Method in class org.geneontology.obographs.core.model.meta.DefinitionPropertyValue

Copy the current immutable object by setting a value for the pred attribute.

withPred(String) - Method in class org.geneontology.obographs.core.model.meta.SynonymPropertyValue

Copy the current immutable object by setting a value for the pred attribute.

withPred(String) - Method in class org.geneontology.obographs.core.model.meta.XrefPropertyValue

Copy the current immutable object by setting a value for the pred attribute.

withPredicateId(String) - Method in class org.geneontology.obographs.core.model.axiom.DomainRangeAxiom

Copy the current immutable object by setting a value for the predicateId attribute.

withPredicateId(String) - Method in class org.geneontology.obographs.core.model.axiom.PropertyChainAxiom

Copy the current immutable object by setting a value for the predicateId attribute.

withPropertyChainAxioms(Iterable<? extends PropertyChainAxiom>) - Method in class org.geneontology.obographs.core.model.Graph

Copy the current immutable object with elements that replace the content of propertyChainAxioms.

withPropertyChainAxioms(PropertyChainAxiom...) - Method in class org.geneontology.obographs.core.model.Graph

Copy the current immutable object with elements that replace the content of propertyChainAxioms.

withPropertyId(String) - Method in class org.geneontology.obographs.core.model.axiom.ExistentialRestrictionExpression

Copy the current immutable object by setting a value for the propertyId attribute.

withRangeClassIds(Iterable<String>) - Method in class org.geneontology.obographs.core.model.axiom.DomainRangeAxiom

Copy the current immutable object with elements that replace the content of rangeClassIds.

withRangeClassIds(String...) - Method in class org.geneontology.obographs.core.model.axiom.DomainRangeAxiom

Copy the current immutable object with elements that replace the content of rangeClassIds.

withRepresentativeNodeId(String) - Method in class org.geneontology.obographs.core.model.axiom.EquivalentNodesSet

Copy the current immutable object by setting a value for the representativeNodeId attribute.

withRestrictions(Iterable<? extends ExistentialRestrictionExpression>) - Method in class org.geneontology.obographs.core.model.axiom.LogicalDefinitionAxiom

Copy the current immutable object with elements that replace the content of restrictions.

withRestrictions(ExistentialRestrictionExpression...) - Method in class org.geneontology.obographs.core.model.axiom.LogicalDefinitionAxiom

Copy the current immutable object with elements that replace the content of restrictions.

withSub(String) - Method in class org.geneontology.obographs.core.model.Edge

Copy the current immutable object by setting a value for the sub attribute.

withSubsets(Iterable<String>) - Method in class org.geneontology.obographs.core.model.Meta

Copy the current immutable object with elements that replace the content of subsets.

withSubsets(String...) - Method in class org.geneontology.obographs.core.model.Meta

Copy the current immutable object with elements that replace the content of subsets.

withSynonyms(Iterable<? extends SynonymPropertyValue>) - Method in class org.geneontology.obographs.core.model.Meta

Copy the current immutable object with elements that replace the content of synonyms.

withSynonyms(SynonymPropertyValue...) - Method in class org.geneontology.obographs.core.model.Meta

Copy the current immutable object with elements that replace the content of synonyms.

withSynonymType(String) - Method in class org.geneontology.obographs.core.model.meta.SynonymPropertyValue

Copy the current immutable object by setting a value for the synonymType attribute.

withType(AbstractNode.RDFTYPES) - Method in class org.geneontology.obographs.core.model.Node

Copy the current immutable object by setting a value for the type attribute.

withVal(String) - Method in class org.geneontology.obographs.core.model.meta.BasicPropertyValue

Copy the current immutable object by setting a value for the val attribute.

withVal(String) - Method in class org.geneontology.obographs.core.model.meta.DefinitionPropertyValue

Copy the current immutable object by setting a value for the val attribute.

withVal(String) - Method in class org.geneontology.obographs.core.model.meta.SynonymPropertyValue

Copy the current immutable object by setting a value for the val attribute.

withVal(String) - Method in class org.geneontology.obographs.core.model.meta.XrefPropertyValue

Copy the current immutable object by setting a value for the val attribute.

withVersion(String) - Method in class org.geneontology.obographs.core.model.Meta

Copy the current immutable object by setting a value for the version attribute.

withXrefs(Iterable<? extends XrefPropertyValue>) - Method in class org.geneontology.obographs.core.model.Meta

Copy the current immutable object with elements that replace the content of xrefs.

withXrefs(Iterable<String>) - Method in class org.geneontology.obographs.core.model.meta.BasicPropertyValue

Copy the current immutable object with elements that replace the content of xrefs.

withXrefs(Iterable<String>) - Method in class org.geneontology.obographs.core.model.meta.DefinitionPropertyValue

Copy the current immutable object with elements that replace the content of xrefs.

withXrefs(Iterable<String>) - Method in class org.geneontology.obographs.core.model.meta.SynonymPropertyValue

Copy the current immutable object with elements that replace the content of xrefs.

withXrefs(Iterable<String>) - Method in class org.geneontology.obographs.core.model.meta.XrefPropertyValue

Copy the current immutable object with elements that replace the content of xrefs.

withXrefs(String...) - Method in class org.geneontology.obographs.core.model.meta.BasicPropertyValue

Copy the current immutable object with elements that replace the content of xrefs.

withXrefs(String...) - Method in class org.geneontology.obographs.core.model.meta.DefinitionPropertyValue

Copy the current immutable object with elements that replace the content of xrefs.

withXrefs(String...) - Method in class org.geneontology.obographs.core.model.meta.SynonymPropertyValue

Copy the current immutable object with elements that replace the content of xrefs.

withXrefs(String...) - Method in class org.geneontology.obographs.core.model.meta.XrefPropertyValue

Copy the current immutable object with elements that replace the content of xrefs.

withXrefs(XrefPropertyValue...) - Method in class org.geneontology.obographs.core.model.Meta

Copy the current immutable object with elements that replace the content of xrefs.

withXrefsValues(Iterable<String>) - Method in class org.geneontology.obographs.core.model.Meta

Copy the current immutable object with elements that replace the content of xrefsValues.

withXrefsValues(String...) - Method in class org.geneontology.obographs.core.model.Meta

Copy the current immutable object with elements that replace the content of xrefsValues.

write(File, Object) - Static method in class org.geneontology.obographs.core.io.OgJsonGenerator

write(File, Object) - Static method in class org.geneontology.obographs.core.io.OgYamlGenerator

write(OutputStream, Object) - Static method in class org.geneontology.obographs.core.io.OgJsonGenerator

write(OutputStream, Object) - Static method in class org.geneontology.obographs.core.io.OgYamlGenerator

write(Writer, Object) - Static method in class org.geneontology.obographs.core.io.OgJsonGenerator

write(Writer, Object) - Static method in class org.geneontology.obographs.core.io.OgYamlGenerator

X

XrefPropertyValue - Class in org.geneontology.obographs.core.model.meta

Immutable implementation of AbstractXrefPropertyValue.

XrefPropertyValue.Builder - Class in org.geneontology.obographs.core.model.meta

Builds instances of type XrefPropertyValue.

xrefs(Iterable<? extends XrefPropertyValue>) - Method in class org.geneontology.obographs.core.model.Meta.Builder

Sets or replaces all elements for xrefs list.

xrefs(Iterable<String>) - Method in class org.geneontology.obographs.core.model.meta.BasicPropertyValue.Builder

Sets or replaces all elements for xrefs list.

xrefs(Iterable<String>) - Method in class org.geneontology.obographs.core.model.meta.DefinitionPropertyValue.Builder

Sets or replaces all elements for xrefs list.

xrefs(Iterable<String>) - Method in class org.geneontology.obographs.core.model.meta.SynonymPropertyValue.Builder

Sets or replaces all elements for xrefs list.

xrefs(Iterable<String>) - Method in class org.geneontology.obographs.core.model.meta.XrefPropertyValue.Builder

Sets or replaces all elements for xrefs list.

xrefsValues(Iterable<String>) - Method in class org.geneontology.obographs.core.model.Meta.Builder

Sets or replaces all elements for xrefsValues list.

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