METADATA
- object for holding meta data associated with each operationpublic abstract class CoreMolecularModelManager<METADATA> extends Object
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 |
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(ModelContainer model,
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) |
static org.apache.commons.lang3.tuple.Pair<org.semanticweb.owlapi.model.OWLNamedIndividual,Set<org.semanticweb.owlapi.model.OWLAxiom>> |
createIndividual(String modelId,
ModelContainer model,
org.semanticweb.owlapi.model.OWLClassExpression ce,
Set<org.semanticweb.owlapi.model.OWLAnnotation> annotations) |
org.semanticweb.owlapi.model.OWLNamedIndividual |
createIndividual(String modelId,
ModelContainer model,
org.semanticweb.owlapi.model.OWLClass c,
METADATA metadata) |
static org.semanticweb.owlapi.model.OWLClassAssertionAxiom |
createType(ModelContainer model,
org.semanticweb.owlapi.model.OWLIndividual i,
org.semanticweb.owlapi.model.OWLClassExpression c) |
void |
deleteIndividual(String modelId,
ModelContainer model,
org.semanticweb.owlapi.model.OWLNamedIndividual i,
METADATA metadata)
Deletes an individual
|
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.
|
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 |
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.OWLClass c, METADATA metadata)
modelId
- model
- c
- metadata
- public static org.apache.commons.lang3.tuple.Pair<org.semanticweb.owlapi.model.OWLNamedIndividual,Set<org.semanticweb.owlapi.model.OWLAxiom>> createIndividual(String modelId, ModelContainer model, org.semanticweb.owlapi.model.OWLClassExpression ce, Set<org.semanticweb.owlapi.model.OWLAnnotation> annotations)
public void deleteIndividual(String modelId, ModelContainer model, org.semanticweb.owlapi.model.OWLNamedIndividual i, METADATA metadata)
modelId
- model
- i
- metadata
- 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 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(ModelContainer model, org.semanticweb.owlapi.model.OWLIndividual i, org.semanticweb.owlapi.model.OWLClassExpression c)
model
- 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(ModelContainer model, 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)
model
- 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)
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)
Copyright © 2010-2014. All Rights Reserved.