A C E G H I N O R S T V

A

addDatattypeProperty(EIEntity, String) - Method in class org.eaglei.model.EIInstance

addEIType(EIEntity) - Method in class org.eaglei.model.EIInstance

addEIType(EIEntity) - Method in class org.eaglei.model.EIInstanceMinimal

addNonOntologyLiteralProperty(EIEntity, String) - Method in class org.eaglei.model.EIInstance

addNonOntologyResourceProperty(EIEntity, EIEntity) - Method in class org.eaglei.model.EIInstance

addObjectProperty(EIEntity, EIEntity) - Method in class org.eaglei.model.EIInstance

C

compareTo(Object) - Method in class org.eaglei.model.EIInstance

compareTo(Object) - Method in class org.eaglei.model.EIInstanceMinimal

create(String, String) - Static method in class org.eaglei.model.EIEntity

create(EIURI, String) - Static method in class org.eaglei.model.EIEntity

create(EIEntity, EIEntity) - Static method in class org.eaglei.model.EIInstance

create(EIClass, EIEntity) - Static method in class org.eaglei.model.EIInstance

create(EIEntity, EIEntity) - Static method in class org.eaglei.model.EIInstanceMinimal

create(EIInstance) - Static method in class org.eaglei.model.EIInstanceMinimal

create(String) - Static method in class org.eaglei.model.EIURI

E

EIClass - Class in org.eaglei.model

EIClass(EIEntity, boolean, boolean, boolean, boolean, boolean, boolean) - Constructor for class org.eaglei.model.EIClass

EIDatatypeProperty - Class in org.eaglei.model

EIDatatypeProperty(EIEntity, String) - Constructor for class org.eaglei.model.EIDatatypeProperty

EIEntity - Class in org.eaglei.model

A class that associates a label string with a URI.

EIEquivalentClass - Class in org.eaglei.model

This data structure represents equivalence information.

EIEquivalentClass(String, List<EIClass>) - Constructor for class org.eaglei.model.EIEquivalentClass

EIInstance - Class in org.eaglei.model

EIInstanceMinimal - Class in org.eaglei.model

EIObjectProperty - Class in org.eaglei.model

EIObjectProperty(EIEntity, EIClass) - Constructor for class org.eaglei.model.EIObjectProperty

EIObjectProperty(EIEntity, List<EIClass>) - Constructor for class org.eaglei.model.EIObjectProperty

EIOntModel - Interface in org.eaglei.model

Provides access to the eagle-i ontology model, a.k.a the data model.

EIOntModel.Visitor - Interface in org.eaglei.model

Interface passed into a call to traverseDataModel.

EIOntResource - Class in org.eaglei.model

EIOntResource() - Constructor for class org.eaglei.model.EIOntResource

EIOntResource(EIEntity) - Constructor for class org.eaglei.model.EIOntResource

EIProperty - Class in org.eaglei.model

EIProperty() - Constructor for class org.eaglei.model.EIProperty

EIProperty(EIEntity) - Constructor for class org.eaglei.model.EIProperty

EIResource - Class in org.eaglei.model

EIResource() - Constructor for class org.eaglei.model.EIResource

EIResource(EIEntity) - Constructor for class org.eaglei.model.EIResource

EIURI - Class in org.eaglei.model

EIValueRestriction - Class in org.eaglei.model

A very simple representation of the restriction constructs we currently support.

EIValueRestriction(EIValueRestriction.Type, String, EIClass) - Constructor for class org.eaglei.model.EIValueRestriction

EIValueRestriction.Type - Enum in org.eaglei.model

equals(Object) - Method in class org.eaglei.model.EIEntity

equals(Object) - Method in class org.eaglei.model.EIResource

equals(Object) - Method in class org.eaglei.model.EIURI

G

generateStackTrace(Deque<String>) - Method in interface org.eaglei.model.EIOntModel

Produces a default display string from the semantic relationship stack generated by data model traversal.

getAllRanges() - Method in class org.eaglei.model.EIInstance

Deprecated.

getAnnotations() - Method in class org.eaglei.model.EIClass

getAnnotations() - Method in class org.eaglei.model.EIProperty

getClass(EIURI) - Method in interface org.eaglei.model.EIOntModel

Returns an EIClass for the given URI.

getClassAnnotations(List<EIURI>) - Method in interface org.eaglei.model.EIOntModel

Gets the set of class group annotation values for a given list of classes.

getClassDefinition(EIURI) - Method in interface org.eaglei.model.EIOntModel

getClassDefinitions(List<EIURI>) - Method in interface org.eaglei.model.EIOntModel

Gets property annotations for a given class.

getCreationDate() - Method in class org.eaglei.model.EIInstance

getCreationDate() - Method in class org.eaglei.model.EIInstanceMinimal

getDatatypeProperties() - Method in class org.eaglei.model.EIInstance

getDatatypeProperty(EIEntity) - Method in class org.eaglei.model.EIInstance

getDefinition() - Method in class org.eaglei.model.EIOntResource

A class definition string.

getEIClass() - Method in class org.eaglei.model.EIValueRestriction

getEntity() - Method in class org.eaglei.model.EIResource

getEquivalentClasses() - Method in class org.eaglei.model.EIClass

Gets the equivalent classes of this class.

getEquivalentClasses(EIURI) - Method in interface org.eaglei.model.EIOntModel

getEquivalentTo() - Method in class org.eaglei.model.EIEquivalentClass

Gets the List of EIClasses that this data structure expresses equivalence to.

getInstanceClass() - Method in class org.eaglei.model.EIInstance

getInstanceLabel() - Method in class org.eaglei.model.EIInstance

getInstanceLabel() - Method in class org.eaglei.model.EIInstanceMinimal

getInstanceType() - Method in class org.eaglei.model.EIInstance

getInstanceType() - Method in class org.eaglei.model.EIInstanceMinimal

getInstanceURI() - Method in class org.eaglei.model.EIInstance

getInstanceURI() - Method in class org.eaglei.model.EIInstanceMinimal

getLab() - Method in class org.eaglei.model.EIInstanceMinimal

getLabel() - Method in class org.eaglei.model.EIEntity

getLabels(EIURI) - Method in interface org.eaglei.model.EIOntModel

Retrieves all unique labels for the specified resource using the the following priority order http://eagle-i.org/ont/app/1.0/preferredLabel http://purl.obolibrary.org/obo/IAO_0000111 (IAO preferred term) rdfs:label http://purl.obolibrary.org/obo/IAO_0000118 (IAO alternate term)

getNonOntologyLiteralProperties() - Method in class org.eaglei.model.EIInstance

getNonOntologyLiteralProperty(EIEntity) - Method in class org.eaglei.model.EIInstance

getNonOntologyResourceProperties() - Method in class org.eaglei.model.EIInstance

getNonOntologyResourceProperty(EIEntity) - Method in class org.eaglei.model.EIInstance

getNonResourceBaseClasses() - Method in interface org.eaglei.model.EIOntModel

getObjectProperties() - Method in class org.eaglei.model.EIInstance

getObjectProperty(EIEntity) - Method in class org.eaglei.model.EIInstance

getOtherEITypes() - Method in class org.eaglei.model.EIInstance

getOtherEITypes() - Method in class org.eaglei.model.EIInstanceMinimal

getPreferredLabel(EIURI) - Method in interface org.eaglei.model.EIOntModel

Retrieves the preferred label for the specified resource.

getProperties() - Method in class org.eaglei.model.EIClass

Gets the properties of this class.

getProperties(EIURI) - Method in interface org.eaglei.model.EIOntModel

getPropertyDefinition(EIURI) - Method in interface org.eaglei.model.EIOntModel

getPropertyDefinitions(List<EIURI>) - Method in interface org.eaglei.model.EIOntModel

getRange() - Method in class org.eaglei.model.EIObjectProperty

Deprecated. Should call getRangeList() instead.

getRangeList(EIEntity) - Method in class org.eaglei.model.EIInstance

Deprecated.

getRangeList() - Method in class org.eaglei.model.EIObjectProperty

If there are more than one range class, returns the first one.

getReadOnlyLiteralProperties() - Method in class org.eaglei.model.EIInstance

getReadOnlyResourceProperties() - Method in class org.eaglei.model.EIInstance

getSubClasses() - Method in class org.eaglei.model.EIClass

Gets the subclasses of this class.

getSubClasses(EIURI) - Method in interface org.eaglei.model.EIOntModel

getSuperClass() - Method in class org.eaglei.model.EIClass

Gets the superclass of this class.

getSuperClass(EIClass) - Method in interface org.eaglei.model.EIOntModel

getSuperClasses() - Method in class org.eaglei.model.EIClass

Gets the list of superclasses of this class.

getSuperClasses(EIURI) - Method in interface org.eaglei.model.EIOntModel

getTopLevelClasses() - Method in interface org.eaglei.model.EIOntModel

getType() - Method in class org.eaglei.model.EIValueRestriction

getTypeLabel() - Method in class org.eaglei.model.EIDatatypeProperty

getURI() - Method in class org.eaglei.model.EIEntity

getURI() - Method in class org.eaglei.model.EIEquivalentClass

URI of the equivalent class data structure itself.

getURI() - Method in class org.eaglei.model.EIValueRestriction

getValueRestriction() - Method in class org.eaglei.model.EIProperty

getValueRestrictionMap() - Method in class org.eaglei.model.EIClass

getVersion() - Method in interface org.eaglei.model.EIOntModel

Gets the version of the eagle-i ontology.

getWFOwner() - Method in class org.eaglei.model.EIInstance

getWFOwner() - Method in class org.eaglei.model.EIInstanceMinimal

getWFOwnerUri() - Method in class org.eaglei.model.EIInstanceMinimal

getWFState() - Method in class org.eaglei.model.EIInstance

getWFState() - Method in class org.eaglei.model.EIInstanceMinimal

getWFStateUri() - Method in class org.eaglei.model.EIInstanceMinimal

H

hasEquivalentClass() - Method in class org.eaglei.model.EIClass

Is there an EIEquivalentClass for this class.

hashCode() - Method in class org.eaglei.model.EIEntity

hashCode() - Method in class org.eaglei.model.EIResource

hashCode() - Method in class org.eaglei.model.EIURI

hasProperty() - Method in class org.eaglei.model.EIClass

hasSubClass() - Method in class org.eaglei.model.EIClass

hasSuperClass() - Method in class org.eaglei.model.EIClass

Indicates whether this class has a superclass.

I

isEagleIResource() - Method in class org.eaglei.model.EIClass

Returns true if this class is an eagle-i class (a top-level resource class or a subclass of a top-level class).

isInferred() - Method in class org.eaglei.model.EIClass

isModelClassURI(String) - Method in interface org.eaglei.model.EIOntModel

Determines if the given URI is recognized as being an eagle-i data model URI.

N

NO_DEFINITION - Static variable in class org.eaglei.model.EIOntResource

NO_LABEL - Static variable in class org.eaglei.model.EIEntity

NULL_CLASS - Static variable in class org.eaglei.model.EIClass

NULL_EIURI - Static variable in class org.eaglei.model.EIURI

NULL_ENTITY - Static variable in class org.eaglei.model.EIEntity

NULL_INSTANCE - Static variable in class org.eaglei.model.EIInstance

O

org.eaglei.model - package org.eaglei.model

R

replaceDatatypePropertyAllValues(EIEntity, Set<String>) - Method in class org.eaglei.model.EIInstance

replaceDatatypePropertyValue(EIEntity, String, String) - Method in class org.eaglei.model.EIInstance

replaceNonOntologyLiteralProperty(EIEntity, String, String) - Method in class org.eaglei.model.EIInstance

replaceNonOntologyLiteralPropertyAllValues(EIEntity, Set<String>) - Method in class org.eaglei.model.EIInstance

replaceNonOntologyResourcePropertyAllValues(EIEntity, Set<EIEntity>) - Method in class org.eaglei.model.EIInstance

replaceNonOntologyResourcePropertyValue(EIEntity, EIURI, EIEntity) - Method in class org.eaglei.model.EIInstance

replaceObjectPropertyAllValues(EIEntity, Set<EIEntity>) - Method in class org.eaglei.model.EIInstance

replaceObjectPropertyValue(EIEntity, EIURI, EIEntity) - Method in class org.eaglei.model.EIInstance

S

serialVersionUID - Static variable in class org.eaglei.model.EIEntity

serialVersionUID - Static variable in class org.eaglei.model.EIURI

setAnnotations(Set<String>) - Method in class org.eaglei.model.EIClass

setAnnotations(Set<String>) - Method in class org.eaglei.model.EIProperty

setCreationDate(String) - Method in class org.eaglei.model.EIInstance

setCreationDate(String) - Method in class org.eaglei.model.EIInstanceMinimal

setDefinition(String) - Method in class org.eaglei.model.EIOntResource

Sets a definition string for this class.

setEquivalentClasses(List<EIEquivalentClass>) - Method in class org.eaglei.model.EIClass

setEquivalentTo(List<EIClass>) - Method in class org.eaglei.model.EIEquivalentClass

setInstanceClass(EIClass) - Method in class org.eaglei.model.EIInstance

setInstanceType(EIEntity) - Method in class org.eaglei.model.EIInstance

setInstanceType(EIEntity) - Method in class org.eaglei.model.EIInstanceMinimal

setLab(EIEntity) - Method in class org.eaglei.model.EIInstanceMinimal

setLabel(String) - Method in class org.eaglei.model.EIEntity

setLabel(String) - Method in class org.eaglei.model.EIResource

setOtherEITypes(List<EIEntity>) - Method in class org.eaglei.model.EIInstance

setOtherEITypes(List<EIEntity>) - Method in class org.eaglei.model.EIInstanceMinimal

setProperties(List<EIProperty>) - Method in class org.eaglei.model.EIClass

setRange(EIClass) - Method in class org.eaglei.model.EIObjectProperty

This method is only here to support cache unmarshalling of this class.

setRange(List<EIClass>) - Method in class org.eaglei.model.EIObjectProperty

This method is only here to support cache unmarshalling of this class.

setRangeList(EIEntity, List<EIClass>) - Method in class org.eaglei.model.EIInstance

Deprecated.

setReadOnlyLiteralProperties(Map<EIEntity, String>) - Method in class org.eaglei.model.EIInstance

setReadOnlyLiteralProperty(EIEntity, String) - Method in class org.eaglei.model.EIInstance

setReadOnlyResourceProperty(EIEntity, EIEntity) - Method in class org.eaglei.model.EIInstance

setSubClasses(List<EIClass>) - Method in class org.eaglei.model.EIClass

setSuperClass(EIClass) - Method in class org.eaglei.model.EIClass

setSuperClasses(List<EIClass>) - Method in class org.eaglei.model.EIClass

setURI(String) - Method in class org.eaglei.model.EIEquivalentClass

setValueRestriction(EIValueRestriction) - Method in class org.eaglei.model.EIProperty

setValueRestrictionMap(Map<String, EIValueRestriction>) - Method in class org.eaglei.model.EIClass

setWFOwner(EIEntity) - Method in class org.eaglei.model.EIInstance

setWFOwner(EIEntity) - Method in class org.eaglei.model.EIInstanceMinimal

setWFState(EIEntity) - Method in class org.eaglei.model.EIInstance

setWFState(EIEntity) - Method in class org.eaglei.model.EIInstanceMinimal

T

toString() - Method in class org.eaglei.model.EIEntity

toString() - Method in class org.eaglei.model.EIInstance

toString() - Method in class org.eaglei.model.EIInstanceMinimal

toString() - Method in class org.eaglei.model.EIResource

toString() - Method in class org.eaglei.model.EIURI

traverseDataModel(List<EIOntModel.Visitor>) - Method in interface org.eaglei.model.EIOntModel

Walks the entire eagle-i data model by starting with the set of "root resource" (top-level resource) classes and traversing through object property relationships and subclass relationships until every class and property in the data model has been visited.

V

valueOf(String) - Static method in enum org.eaglei.model.EIValueRestriction.Type

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

values() - Static method in enum org.eaglei.model.EIValueRestriction.Type

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

visit(EIClass, Deque<String>) - Method in interface org.eaglei.model.EIOntModel.Visitor

visit(EIProperty, Deque<String>) - Method in interface org.eaglei.model.EIOntModel.Visitor

A C E G H I N O R S T V