METADATA
- object for holding meta data associated with each operationpublic abstract class CoreMolecularModelManager<METADATA> extends Object
Modifier and Type | Class and Description |
---|---|
static class |
CoreMolecularModelManager.DeleteInformation |
Constructor and Description |
---|
CoreMolecularModelManager(OWLGraphWrapper graph) |
Modifier and Type | Method and Description |
---|---|
void |
addAnnotations(String modelId,
ModelContainer model,
org.semanticweb.owlapi.model.OWLNamedIndividual i,
Collection<org.semanticweb.owlapi.model.OWLAnnotation> annotations,
METADATA metadata) |
void |
addAnnotations(String modelId,
org.semanticweb.owlapi.model.OWLObjectPropertyExpression p,
org.semanticweb.owlapi.model.OWLNamedIndividual i,
org.semanticweb.owlapi.model.OWLNamedIndividual j,
Set<org.semanticweb.owlapi.model.OWLAnnotation> annotations,
METADATA metadata) |
void |
addAxiom(String modelId,
ModelContainer model,
org.semanticweb.owlapi.model.OWLAxiom axiom,
boolean flushReasoner,
METADATA metadata) |
void |
addDataProperty(String modelId,
ModelContainer model,
org.semanticweb.owlapi.model.OWLNamedIndividual i,
org.semanticweb.owlapi.model.OWLDataProperty prop,
org.semanticweb.owlapi.model.OWLLiteral literal,
boolean flushReasoner,
METADATA metadata) |
void |
addFact(String modelId,
OBOUpperVocabulary vocabElement,
org.semanticweb.owlapi.model.OWLNamedIndividual i,
org.semanticweb.owlapi.model.OWLNamedIndividual j,
Set<org.semanticweb.owlapi.model.OWLAnnotation> annotations,
METADATA metadata)
|
void |
addFact(String modelId,
org.semanticweb.owlapi.model.OWLObjectPropertyExpression p,
org.semanticweb.owlapi.model.OWLNamedIndividual i,
org.semanticweb.owlapi.model.OWLNamedIndividual j,
Set<org.semanticweb.owlapi.model.OWLAnnotation> annotations,
METADATA metadata)
Adds triple (i,p,j) to specified model
|
void |
addImports(Iterable<String> imports)
Add additional import declarations for any newly generated model.
|
void |
addObsoleteImportIRIs(Collection<org.semanticweb.owlapi.model.IRI> obsoleteImports)
Mark the given imports as obsolete.
|
void |
addObsoleteImports(Iterable<String> obsoletes)
Mark the given imports as obsolete.
|
protected void |
addToHistory(String modelId,
ModelContainer model,
List<org.semanticweb.owlapi.model.OWLOntologyChange> appliedChanges,
METADATA metadata)
Hook for implementing an undo and redo.
|
void |
addType(String modelId,
org.semanticweb.owlapi.model.OWLNamedIndividual i,
org.semanticweb.owlapi.model.OWLClass c,
METADATA metadata)
Adds ClassAssertion(c,i) to specified model
|
void |
addType(String modelId,
org.semanticweb.owlapi.model.OWLNamedIndividual i,
org.semanticweb.owlapi.model.OWLObjectPropertyExpression p,
org.semanticweb.owlapi.model.OWLClassExpression filler,
METADATA metadata)
Adds a ClassAssertion, where the class expression instantiated is an
ObjectSomeValuesFrom expression
Example: Individual: i Type: enabledBy some PRO_123
|
static org.semanticweb.owlapi.model.OWLObjectPropertyAssertionAxiom |
createFact(org.semanticweb.owlapi.model.OWLDataFactory f,
org.semanticweb.owlapi.model.OWLObjectPropertyExpression p,
org.semanticweb.owlapi.model.OWLIndividual i,
org.semanticweb.owlapi.model.OWLIndividual j,
Set<org.semanticweb.owlapi.model.OWLAnnotation> annotations) |
org.semanticweb.owlapi.model.OWLNamedIndividual |
createIndividual(String modelId,
ModelContainer model,
org.semanticweb.owlapi.model.OWLClassExpression ce,
METADATA metadata) |
static org.apache.commons.lang3.tuple.Pair<org.semanticweb.owlapi.model.OWLNamedIndividual,Set<org.semanticweb.owlapi.model.OWLAxiom>> |
createIndividual(String modelId,
org.semanticweb.owlapi.model.OWLOntology abox,
org.semanticweb.owlapi.model.OWLClassExpression ce,
Set<org.semanticweb.owlapi.model.OWLAnnotation> annotations) |
static org.semanticweb.owlapi.model.OWLClassAssertionAxiom |
createType(org.semanticweb.owlapi.model.OWLDataFactory f,
org.semanticweb.owlapi.model.OWLIndividual i,
org.semanticweb.owlapi.model.OWLClassExpression c) |
CoreMolecularModelManager.DeleteInformation |
deleteIndividual(String modelId,
ModelContainer model,
org.semanticweb.owlapi.model.OWLNamedIndividual i,
METADATA metadata)
Deletes an individual and return all IRIs used as an annotation value
|
void |
dispose()
internal method to cleanup this instance
|
String |
exportModel(String modelId,
ModelContainer model,
org.semanticweb.owlapi.model.OWLOntologyFormat ontologyFormat)
Export the ABox, will try to set the ontologyID to the given modelId (to
ensure import assumptions are met)
|
String |
exportModelLegacy(String modelId,
ModelContainer model,
String format)
Export the model (ABox) in a legacy format, such as GAF or GPAD.
|
static Set<org.semanticweb.owlapi.model.IRI> |
extractIRIValues(Set<org.semanticweb.owlapi.model.OWLAnnotation> annotations) |
Set<String> |
getCurrentModelIds()
Retrieve a collection of all model ids currently in memory.
|
OWLGraphWrapper |
getGraph() |
Collection<org.semanticweb.owlapi.model.IRI> |
getImports() |
Set<org.semanticweb.owlapi.model.OWLNamedIndividual> |
getIndividuals(String modelId) |
Set<org.semanticweb.owlapi.model.OWLNamedIndividual> |
getIndividualsByQuery(String modelId,
org.semanticweb.owlapi.model.OWLClassExpression q) |
ModelContainer |
getModel(String id)
Fetches a model by its Id
|
org.semanticweb.owlapi.model.OWLOntology |
getModelAbox(String id)
Retrieve the abox ontology.
|
Set<String> |
getModelIds() |
org.semanticweb.owlapi.model.OWLOntology |
getOntology() |
org.semanticweb.owlapi.model.OWLDataFactory |
getOWLDataFactory(String modelId) |
protected org.semanticweb.owlapi.model.OWLOntologyManager |
getOWLOntologyManager(String modelId) |
protected org.semanticweb.owlapi.model.IRI |
getTboxIRI(OWLGraphWrapper graph)
Executed before the init call
init() . |
String |
importModel(String modelData)
Try to load (or replace) a model with the given ontology.
|
protected void |
init() |
boolean |
isConsistent(String modelId) |
protected abstract void |
loadModel(String modelId,
boolean isOverride) |
protected abstract org.semanticweb.owlapi.model.OWLOntology |
loadModelABox(String modelId) |
protected org.semanticweb.owlapi.model.OWLOntology |
loadOntologyIRI(org.semanticweb.owlapi.model.IRI sourceIRI,
boolean minimal) |
void |
removeAnnotations(String modelId,
ModelContainer model,
org.semanticweb.owlapi.model.OWLNamedIndividual i,
Collection<org.semanticweb.owlapi.model.OWLAnnotation> annotations,
METADATA metadata) |
void |
removeDataProperty(String modelId,
ModelContainer model,
org.semanticweb.owlapi.model.OWLNamedIndividual i,
org.semanticweb.owlapi.model.OWLDataProperty prop,
org.semanticweb.owlapi.model.OWLLiteral literal,
boolean flushReasoner,
METADATA metadata) |
void |
removeFact(String modelId,
org.semanticweb.owlapi.model.OWLObjectPropertyExpression p,
org.semanticweb.owlapi.model.OWLNamedIndividual i,
org.semanticweb.owlapi.model.OWLNamedIndividual j,
METADATA metadata) |
void |
removeType(String modelId,
org.semanticweb.owlapi.model.OWLNamedIndividual i,
org.semanticweb.owlapi.model.OWLClass c,
METADATA metadata)
remove ClassAssertion(c,i) to specified model
|
void |
removeType(String modelId,
org.semanticweb.owlapi.model.OWLNamedIndividual i,
org.semanticweb.owlapi.model.OWLObjectPropertyExpression p,
org.semanticweb.owlapi.model.OWLClassExpression filler,
METADATA metadata)
Removes a ClassAssertion, where the class expression instantiated is an
ObjectSomeValuesFrom expression
|
void |
unlinkModel(String id) |
void |
updateImports(String modelId,
ModelContainer model)
This method will check the given model and update the import declarations.
|
public CoreMolecularModelManager(OWLGraphWrapper graph) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
graph
- org.semanticweb.owlapi.model.OWLOntologyCreationException
protected org.semanticweb.owlapi.model.IRI getTboxIRI(OWLGraphWrapper graph) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
init()
.graph
- org.semanticweb.owlapi.model.OWLOntologyCreationException
protected void init() throws org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyCreationException
public OWLGraphWrapper getGraph()
public org.semanticweb.owlapi.model.OWLOntology getOntology()
public void addImports(Iterable<String> imports)
imports
- public void addObsoleteImports(Iterable<String> obsoletes)
obsoletes
- public void addObsoleteImportIRIs(Collection<org.semanticweb.owlapi.model.IRI> obsoleteImports)
obsoleteImports
- public Collection<org.semanticweb.owlapi.model.IRI> getImports()
public Set<org.semanticweb.owlapi.model.OWLNamedIndividual> getIndividuals(String modelId)
modelId
- public Set<org.semanticweb.owlapi.model.OWLNamedIndividual> getIndividualsByQuery(String modelId, org.semanticweb.owlapi.model.OWLClassExpression q)
modelId
- q
- public org.semanticweb.owlapi.model.OWLNamedIndividual createIndividual(String modelId, ModelContainer model, org.semanticweb.owlapi.model.OWLClassExpression ce, METADATA metadata)
modelId
- model
- ce
- metadata
- public static org.apache.commons.lang3.tuple.Pair<org.semanticweb.owlapi.model.OWLNamedIndividual,Set<org.semanticweb.owlapi.model.OWLAxiom>> createIndividual(String modelId, org.semanticweb.owlapi.model.OWLOntology abox, org.semanticweb.owlapi.model.OWLClassExpression ce, Set<org.semanticweb.owlapi.model.OWLAnnotation> annotations)
public CoreMolecularModelManager.DeleteInformation deleteIndividual(String modelId, ModelContainer model, org.semanticweb.owlapi.model.OWLNamedIndividual i, METADATA metadata)
modelId
- model
- i
- metadata
- public static Set<org.semanticweb.owlapi.model.IRI> extractIRIValues(Set<org.semanticweb.owlapi.model.OWLAnnotation> annotations)
public void addAnnotations(String modelId, ModelContainer model, org.semanticweb.owlapi.model.OWLNamedIndividual i, Collection<org.semanticweb.owlapi.model.OWLAnnotation> annotations, METADATA metadata)
public void removeAnnotations(String modelId, ModelContainer model, org.semanticweb.owlapi.model.OWLNamedIndividual i, Collection<org.semanticweb.owlapi.model.OWLAnnotation> annotations, METADATA metadata)
public void addDataProperty(String modelId, ModelContainer model, org.semanticweb.owlapi.model.OWLNamedIndividual i, org.semanticweb.owlapi.model.OWLDataProperty prop, org.semanticweb.owlapi.model.OWLLiteral literal, boolean flushReasoner, METADATA metadata)
public void removeDataProperty(String modelId, ModelContainer model, org.semanticweb.owlapi.model.OWLNamedIndividual i, org.semanticweb.owlapi.model.OWLDataProperty prop, org.semanticweb.owlapi.model.OWLLiteral literal, boolean flushReasoner, METADATA metadata)
public ModelContainer getModel(String id)
id
- public org.semanticweb.owlapi.model.OWLOntology getModelAbox(String id)
id
- protected abstract org.semanticweb.owlapi.model.OWLOntology loadModelABox(String modelId) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
modelId
- org.semanticweb.owlapi.model.OWLOntologyCreationException
public void unlinkModel(String id)
id
- public void dispose()
public String exportModelLegacy(String modelId, ModelContainer model, String format) throws IOException
modelId
- model
- format
- format name or null for defaultIOException
public String exportModel(String modelId, ModelContainer model, org.semanticweb.owlapi.model.OWLOntologyFormat ontologyFormat) throws org.semanticweb.owlapi.model.OWLOntologyStorageException
modelId
- model
- ontologyFormat
- org.semanticweb.owlapi.model.OWLOntologyStorageException
public String importModel(String modelData) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
modelData
- org.semanticweb.owlapi.model.OWLOntologyCreationException
public Set<String> getCurrentModelIds() throws IOException
IOException
protected abstract void loadModel(String modelId, boolean isOverride) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyCreationException
public boolean isConsistent(String modelId)
modelId
- public org.semanticweb.owlapi.model.OWLDataFactory getOWLDataFactory(String modelId)
modelId
- protected org.semanticweb.owlapi.model.OWLOntologyManager getOWLOntologyManager(String modelId)
public void addType(String modelId, org.semanticweb.owlapi.model.OWLNamedIndividual i, org.semanticweb.owlapi.model.OWLClass c, METADATA metadata)
modelId
- i
- c
- metadata
- public static org.semanticweb.owlapi.model.OWLClassAssertionAxiom createType(org.semanticweb.owlapi.model.OWLDataFactory f, org.semanticweb.owlapi.model.OWLIndividual i, org.semanticweb.owlapi.model.OWLClassExpression c)
f
- i
- c
- public void addType(String modelId, org.semanticweb.owlapi.model.OWLNamedIndividual i, org.semanticweb.owlapi.model.OWLObjectPropertyExpression p, org.semanticweb.owlapi.model.OWLClassExpression filler, METADATA metadata)
modelId
- i
- p
- filler
- metadata
- public void removeType(String modelId, org.semanticweb.owlapi.model.OWLNamedIndividual i, org.semanticweb.owlapi.model.OWLClass c, METADATA metadata)
modelId
- i
- c
- metadata
- public void removeType(String modelId, org.semanticweb.owlapi.model.OWLNamedIndividual i, org.semanticweb.owlapi.model.OWLObjectPropertyExpression p, org.semanticweb.owlapi.model.OWLClassExpression filler, METADATA metadata)
modelId
- i
- p
- filler
- metadata
- public void addFact(String modelId, org.semanticweb.owlapi.model.OWLObjectPropertyExpression p, org.semanticweb.owlapi.model.OWLNamedIndividual i, org.semanticweb.owlapi.model.OWLNamedIndividual j, Set<org.semanticweb.owlapi.model.OWLAnnotation> annotations, METADATA metadata)
modelId
- p
- i
- j
- annotations
- metadata
- public void addFact(String modelId, OBOUpperVocabulary vocabElement, org.semanticweb.owlapi.model.OWLNamedIndividual i, org.semanticweb.owlapi.model.OWLNamedIndividual j, Set<org.semanticweb.owlapi.model.OWLAnnotation> annotations, METADATA metadata)
addFact(String, OWLObjectPropertyExpression, OWLNamedIndividual, OWLNamedIndividual, Set, Object)
modelId
- vocabElement
- i
- j
- annotations
- metadata
- public static org.semanticweb.owlapi.model.OWLObjectPropertyAssertionAxiom createFact(org.semanticweb.owlapi.model.OWLDataFactory f, org.semanticweb.owlapi.model.OWLObjectPropertyExpression p, org.semanticweb.owlapi.model.OWLIndividual i, org.semanticweb.owlapi.model.OWLIndividual j, Set<org.semanticweb.owlapi.model.OWLAnnotation> annotations)
f
- p
- i
- j
- annotations
- public void removeFact(String modelId, org.semanticweb.owlapi.model.OWLObjectPropertyExpression p, org.semanticweb.owlapi.model.OWLNamedIndividual i, org.semanticweb.owlapi.model.OWLNamedIndividual j, METADATA metadata)
public void addAnnotations(String modelId, org.semanticweb.owlapi.model.OWLObjectPropertyExpression p, org.semanticweb.owlapi.model.OWLNamedIndividual i, org.semanticweb.owlapi.model.OWLNamedIndividual j, Set<org.semanticweb.owlapi.model.OWLAnnotation> annotations, METADATA metadata)
public void addAxiom(String modelId, ModelContainer model, org.semanticweb.owlapi.model.OWLAxiom axiom, boolean flushReasoner, METADATA metadata)
protected void addToHistory(String modelId, ModelContainer model, List<org.semanticweb.owlapi.model.OWLOntologyChange> appliedChanges, METADATA metadata)
modelId
- model
- appliedChanges
- metadata
- protected org.semanticweb.owlapi.model.OWLOntology loadOntologyIRI(org.semanticweb.owlapi.model.IRI sourceIRI, boolean minimal) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyCreationException
public void updateImports(String modelId, ModelContainer model)
modelId
- model
- additionalImports
,
addImports(Iterable)
,
obsoleteOntologies
,
addObsoleteImports(Iterable)
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