METADATA
- public class MolecularModelManager<METADATA> extends FileBasedMolecularModelManager<METADATA>
Modifier and Type | Class and Description |
---|---|
static class |
MolecularModelManager.LegoAnnotationType |
protected class |
MolecularModelManager.LegoStringDotRenderer
Deprecated.
|
static class |
MolecularModelManager.UnknownIdentifierException |
Modifier and Type | Field and Description |
---|---|
static ThreadLocal<DateFormat> |
LegoAnnotationTypeDateFormat |
Constructor and Description |
---|
MolecularModelManager(OWLGraphWrapper graph) |
Modifier and Type | Method and Description |
---|---|
void |
addAnnotations(String modelId,
Collection<org.apache.commons.lang3.tuple.Pair<String,String>> pairs,
METADATA metadata) |
org.semanticweb.owlapi.model.OWLNamedIndividual |
addAnnotations(String modelId,
String iid,
Collection<org.apache.commons.lang3.tuple.Pair<String,String>> pairs,
METADATA metadata) |
List<org.semanticweb.owlapi.model.OWLNamedIndividual> |
addAnnotations(String modelId,
String pid,
String iid,
String jid,
Collection<org.apache.commons.lang3.tuple.Pair<String,String>> pairs,
METADATA metadata) |
void |
addEnabledBy(String modelId,
org.semanticweb.owlapi.model.OWLNamedIndividual i,
org.semanticweb.owlapi.model.OWLClassExpression enabler)
Deprecated.
|
void |
addEnabledBy(String modelId,
String iid,
String eid)
Deprecated.
|
List<org.semanticweb.owlapi.model.OWLNamedIndividual> |
addFact(String modelId,
OBOUpperVocabulary vocabElement,
String iid,
String jid,
Collection<org.apache.commons.lang3.tuple.Pair<String,String>> pairs,
METADATA metadata)
|
List<org.semanticweb.owlapi.model.OWLNamedIndividual> |
addFact(String modelId,
String pid,
String iid,
String jid,
Collection<org.apache.commons.lang3.tuple.Pair<String,String>> pairs,
METADATA metadata)
|
List<org.semanticweb.owlapi.model.OWLNamedIndividual> |
addFactNonReasoning(String modelId,
String pid,
String iid,
String jid,
Collection<org.apache.commons.lang3.tuple.Pair<String,String>> pairs,
METADATA metadata)
|
void |
addOccursIn(String modelId,
org.semanticweb.owlapi.model.OWLNamedIndividual i,
org.semanticweb.owlapi.model.OWLClassExpression enabler)
Deprecated.
|
void |
addOccursIn(String modelId,
String iid,
String eid)
Deprecated.
|
void |
addPartOf(String modelId,
org.semanticweb.owlapi.model.OWLNamedIndividual i,
org.semanticweb.owlapi.model.OWLNamedIndividual j,
Set<org.semanticweb.owlapi.model.OWLAnnotation> annotations)
Deprecated.
|
void |
addPartOf(String modelId,
String iid,
String jid,
Collection<org.apache.commons.lang3.tuple.Pair<String,String>> pairs)
Deprecated.
|
void |
addType(String modelId,
String iid,
String cid,
METADATA metadata)
|
void |
addType(String modelId,
String iid,
String pid,
String cid,
METADATA metadata)
|
org.semanticweb.owlapi.model.OWLNamedIndividual |
addTypeNonReasoning(String modelId,
String iid,
org.semanticweb.owlapi.model.OWLClassExpression clsExp,
METADATA metadata) |
org.semanticweb.owlapi.model.OWLNamedIndividual |
addTypeNonReasoning(String modelId,
String iid,
String pid,
org.semanticweb.owlapi.model.OWLClassExpression ce,
METADATA metadata) |
ModelContainer |
checkModelId(String modelId) |
org.apache.commons.lang3.tuple.Pair<String,org.semanticweb.owlapi.model.OWLNamedIndividual> |
createIndividual(String modelId,
String cid,
Collection<org.apache.commons.lang3.tuple.Pair<String,String>> annotations,
METADATA metadata)
|
org.apache.commons.lang3.tuple.Pair<String,org.semanticweb.owlapi.model.OWLNamedIndividual> |
createIndividualNonReasoning(String modelId,
String cid,
Collection<org.apache.commons.lang3.tuple.Pair<String,String>> annotations,
METADATA metadata)
|
void |
deleteIndividual(String modelId,
String iid,
METADATA metadata)
Deletes an individual
|
void |
deleteIndividualNonReasoning(String modelId,
String iid,
METADATA metadata)
Deletes an individual
|
void |
deleteModel(String id) |
String |
exportModel(String modelId)
Export the ABox for the given modelId in the default
OWLOntologyFormat . |
String |
exportModelLegacy(String modelId,
String format)
Export the model (ABox) for the given modelId in a legacy format, such as GAF or GPAD.
|
String |
generateDot(String modelId)
Deprecated.
|
File |
generateImage(String modelId)
Deprecated.
|
String |
generateModel(String pid,
String db,
METADATA metadata)
|
Set<org.semanticweb.owlapi.model.OWLNamedIndividual> |
getIndividualsByQuery(String modelId,
String qs) |
org.semanticweb.owlapi.model.OWLNamedIndividual |
getNamedIndividual(String modelId,
String iid) |
static org.semanticweb.owlapi.model.OWLClassExpression |
parseClassExpression(String expression,
OWLGraphWrapper g)
Deprecated.
|
void |
removeAnnotations(String modelId,
Collection<org.apache.commons.lang3.tuple.Pair<String,String>> pairs,
METADATA metadata) |
org.semanticweb.owlapi.model.OWLNamedIndividual |
removeAnnotations(String modelId,
String iid,
Collection<org.apache.commons.lang3.tuple.Pair<String,String>> pairs,
METADATA metadata) |
List<org.semanticweb.owlapi.model.OWLNamedIndividual> |
removeAnnotations(String modelId,
String pid,
String iid,
String jid,
Collection<org.apache.commons.lang3.tuple.Pair<String,String>> pairs,
METADATA metadata) |
List<org.semanticweb.owlapi.model.OWLNamedIndividual> |
removeFact(String modelId,
String pid,
String iid,
String jid,
METADATA metadata) |
List<org.semanticweb.owlapi.model.OWLNamedIndividual> |
removeFactNonReasoning(String modelId,
String pid,
String iid,
String jid,
METADATA metadata) |
void |
removeType(String modelId,
String iid,
String cid,
METADATA metadata)
|
org.semanticweb.owlapi.model.OWLNamedIndividual |
removeTypeNonReasoning(String modelId,
String iid,
org.semanticweb.owlapi.model.OWLClassExpression clsExp,
METADATA metadata) |
void |
saveModel(String modelId,
Collection<org.apache.commons.lang3.tuple.Pair<String,String>> annotations,
METADATA metadata)
Save a model to disk.
|
Set<String> |
searchModels(Collection<String> ids) |
void |
updateImports(String modelId)
This method will check the given model and update the import declarations.
|
void |
writeLego(org.semanticweb.owlapi.model.OWLOntology ontology,
String output,
String modelId)
Deprecated.
|
exportModel, exportModel, generateBlankModel, generateBlankModelWithTaxon, generateDerivedModel, generateModel, getAvailableModelIds, getCurrentModelIds, getGaf, getPathToGafs, getPathToOWLFiles, getStoredModelIds, loadGaf, loadGaf, loadModel, loadModelABox, saveAllModels, saveModel, setPathToGafs, setPathToOWLFiles
addAnnotations, addAnnotations, addFact, addFact, addImports, addObsoleteImportIRIs, addObsoleteImports, addToHistory, addType, addType, createFact, createIndividual, createIndividual, createType, deleteIndividual, dispose, exportModel, exportModelLegacy, getGraph, getImports, getIndividuals, getIndividualsByQuery, getModel, getModelAbox, getModelIds, getOntology, getOWLDataFactory, getOWLOntologyManager, getTboxIRI, importModel, init, isConsistent, loadOntologyIRI, removeAnnotations, removeFact, removeType, removeType, unlinkModel, updateImports
public static final ThreadLocal<DateFormat> LegoAnnotationTypeDateFormat
public MolecularModelManager(OWLGraphWrapper graph) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
graph
- org.semanticweb.owlapi.model.OWLOntologyCreationException
public String generateModel(String pid, String db, METADATA metadata) throws org.semanticweb.owlapi.model.OWLOntologyCreationException, IOException, URISyntaxException, MolecularModelManager.UnknownIdentifierException
pid
- db
- metadata
- org.semanticweb.owlapi.model.OWLOntologyCreationException
IOException
URISyntaxException
MolecularModelManager.UnknownIdentifierException
public Set<org.semanticweb.owlapi.model.OWLNamedIndividual> getIndividualsByQuery(String modelId, String qs) throws MolecularModelManager.UnknownIdentifierException
modelId
- qs
- MolecularModelManager.UnknownIdentifierException
public org.apache.commons.lang3.tuple.Pair<String,org.semanticweb.owlapi.model.OWLNamedIndividual> createIndividual(String modelId, String cid, Collection<org.apache.commons.lang3.tuple.Pair<String,String>> annotations, METADATA metadata) throws MolecularModelManager.UnknownIdentifierException
modelId
- cid
- annotations
- metadata
- MolecularModelManager.UnknownIdentifierException
public org.apache.commons.lang3.tuple.Pair<String,org.semanticweb.owlapi.model.OWLNamedIndividual> createIndividualNonReasoning(String modelId, String cid, Collection<org.apache.commons.lang3.tuple.Pair<String,String>> annotations, METADATA metadata) throws MolecularModelManager.UnknownIdentifierException
modelId
- cid
- annotations
- metadata
- MolecularModelManager.UnknownIdentifierException
public org.semanticweb.owlapi.model.OWLNamedIndividual getNamedIndividual(String modelId, String iid) throws MolecularModelManager.UnknownIdentifierException
public void deleteIndividual(String modelId, String iid, METADATA metadata) throws MolecularModelManager.UnknownIdentifierException
modelId
- iid
- metadata
- MolecularModelManager.UnknownIdentifierException
public void deleteIndividualNonReasoning(String modelId, String iid, METADATA metadata) throws MolecularModelManager.UnknownIdentifierException
modelId
- iid
- metadata
- MolecularModelManager.UnknownIdentifierException
public void addAnnotations(String modelId, Collection<org.apache.commons.lang3.tuple.Pair<String,String>> pairs, METADATA metadata) throws MolecularModelManager.UnknownIdentifierException
public org.semanticweb.owlapi.model.OWLNamedIndividual addAnnotations(String modelId, String iid, Collection<org.apache.commons.lang3.tuple.Pair<String,String>> pairs, METADATA metadata) throws MolecularModelManager.UnknownIdentifierException
public org.semanticweb.owlapi.model.OWLNamedIndividual removeAnnotations(String modelId, String iid, Collection<org.apache.commons.lang3.tuple.Pair<String,String>> pairs, METADATA metadata) throws MolecularModelManager.UnknownIdentifierException
public void removeAnnotations(String modelId, Collection<org.apache.commons.lang3.tuple.Pair<String,String>> pairs, METADATA metadata) throws MolecularModelManager.UnknownIdentifierException
public void deleteModel(String id)
id
- public Set<String> searchModels(Collection<String> ids) throws IOException
IOException
public void saveModel(String modelId, Collection<org.apache.commons.lang3.tuple.Pair<String,String>> annotations, METADATA metadata) throws org.semanticweb.owlapi.model.OWLOntologyStorageException, org.semanticweb.owlapi.model.OWLOntologyCreationException, IOException, MolecularModelManager.UnknownIdentifierException
modelId
- annotations
- metadata
- org.semanticweb.owlapi.model.OWLOntologyStorageException
org.semanticweb.owlapi.model.OWLOntologyCreationException
IOException
MolecularModelManager.UnknownIdentifierException
public String exportModel(String modelId) throws org.semanticweb.owlapi.model.OWLOntologyStorageException, MolecularModelManager.UnknownIdentifierException
OWLOntologyFormat
.modelId
- org.semanticweb.owlapi.model.OWLOntologyStorageException
MolecularModelManager.UnknownIdentifierException
public String exportModelLegacy(String modelId, String format) throws MolecularModelManager.UnknownIdentifierException, IOException
modelId
- format
- name or null for defaultMolecularModelManager.UnknownIdentifierException
IOException
public ModelContainer checkModelId(String modelId) throws MolecularModelManager.UnknownIdentifierException
public void addType(String modelId, String iid, String cid, METADATA metadata) throws MolecularModelManager.UnknownIdentifierException
CoreMolecularModelManager.addType(java.lang.String, org.semanticweb.owlapi.model.OWLNamedIndividual, org.semanticweb.owlapi.model.OWLClass, METADATA)
modelId
- iid
- cid
- metadata
- MolecularModelManager.UnknownIdentifierException
public org.semanticweb.owlapi.model.OWLNamedIndividual addTypeNonReasoning(String modelId, String iid, org.semanticweb.owlapi.model.OWLClassExpression clsExp, METADATA metadata) throws MolecularModelManager.UnknownIdentifierException
modelId
- iid
- clsExp
- metadata
- MolecularModelManager.UnknownIdentifierException
public void addType(String modelId, String iid, String pid, String cid, METADATA metadata) throws MolecularModelManager.UnknownIdentifierException
CoreMolecularModelManager.addType(java.lang.String, org.semanticweb.owlapi.model.OWLNamedIndividual, org.semanticweb.owlapi.model.OWLClass, METADATA)
.modelId
- iid
- pid
- cid
- metadata
- MolecularModelManager.UnknownIdentifierException
public org.semanticweb.owlapi.model.OWLNamedIndividual addTypeNonReasoning(String modelId, String iid, String pid, org.semanticweb.owlapi.model.OWLClassExpression ce, METADATA metadata) throws MolecularModelManager.UnknownIdentifierException
public void removeType(String modelId, String iid, String cid, METADATA metadata) throws MolecularModelManager.UnknownIdentifierException
CoreMolecularModelManager.removeType(java.lang.String, org.semanticweb.owlapi.model.OWLNamedIndividual, org.semanticweb.owlapi.model.OWLClass, METADATA)
modelId
- iid
- cid
- metadata
- MolecularModelManager.UnknownIdentifierException
public org.semanticweb.owlapi.model.OWLNamedIndividual removeTypeNonReasoning(String modelId, String iid, org.semanticweb.owlapi.model.OWLClassExpression clsExp, METADATA metadata) throws MolecularModelManager.UnknownIdentifierException
@Deprecated public void addOccursIn(String modelId, String iid, String eid) throws MolecularModelManager.UnknownIdentifierException
addOccursIn(String, OWLNamedIndividual, OWLClassExpression)
modelId
- iid
- eid
- - e.g. PR:P12345MolecularModelManager.UnknownIdentifierException
@Deprecated public void addOccursIn(String modelId, org.semanticweb.owlapi.model.OWLNamedIndividual i, org.semanticweb.owlapi.model.OWLClassExpression enabler) throws MolecularModelManager.UnknownIdentifierException
modelId
- i
- enabler
- MolecularModelManager.UnknownIdentifierException
@Deprecated public void addEnabledBy(String modelId, String iid, String eid) throws MolecularModelManager.UnknownIdentifierException, org.semanticweb.owlapi.model.OWLException
addEnabledBy(String, OWLNamedIndividual, OWLClassExpression)
modelId
- iid
- eid
- - e.g. PR:P12345MolecularModelManager.UnknownIdentifierException
org.semanticweb.owlapi.model.OWLException
@Deprecated public static org.semanticweb.owlapi.model.OWLClassExpression parseClassExpression(String expression, OWLGraphWrapper g) throws org.semanticweb.owlapi.model.OWLException
org.semanticweb.owlapi.model.OWLException
@Deprecated public void addEnabledBy(String modelId, org.semanticweb.owlapi.model.OWLNamedIndividual i, org.semanticweb.owlapi.model.OWLClassExpression enabler) throws MolecularModelManager.UnknownIdentifierException
modelId
- i
- enabler
- MolecularModelManager.UnknownIdentifierException
public List<org.semanticweb.owlapi.model.OWLNamedIndividual> addFact(String modelId, String pid, String iid, String jid, Collection<org.apache.commons.lang3.tuple.Pair<String,String>> pairs, METADATA metadata) throws MolecularModelManager.UnknownIdentifierException
modelId
- pid
- iid
- jid
- pairs
- metadata
- MolecularModelManager.UnknownIdentifierException
public List<org.semanticweb.owlapi.model.OWLNamedIndividual> addFactNonReasoning(String modelId, String pid, String iid, String jid, Collection<org.apache.commons.lang3.tuple.Pair<String,String>> pairs, METADATA metadata) throws MolecularModelManager.UnknownIdentifierException
modelId
- pid
- iid
- jid
- pairs
- metadata
- MolecularModelManager.UnknownIdentifierException
public List<org.semanticweb.owlapi.model.OWLNamedIndividual> addFact(String modelId, OBOUpperVocabulary vocabElement, String iid, String jid, Collection<org.apache.commons.lang3.tuple.Pair<String,String>> pairs, METADATA metadata) throws MolecularModelManager.UnknownIdentifierException
modelId
- vocabElement
- iid
- jid
- pairs
- metadata
- MolecularModelManager.UnknownIdentifierException
public List<org.semanticweb.owlapi.model.OWLNamedIndividual> removeFact(String modelId, String pid, String iid, String jid, METADATA metadata) throws MolecularModelManager.UnknownIdentifierException
modelId
- pid
- iid
- jid
- metadata
- MolecularModelManager.UnknownIdentifierException
public List<org.semanticweb.owlapi.model.OWLNamedIndividual> removeFactNonReasoning(String modelId, String pid, String iid, String jid, METADATA metadata) throws MolecularModelManager.UnknownIdentifierException
public List<org.semanticweb.owlapi.model.OWLNamedIndividual> addAnnotations(String modelId, String pid, String iid, String jid, Collection<org.apache.commons.lang3.tuple.Pair<String,String>> pairs, METADATA metadata) throws MolecularModelManager.UnknownIdentifierException
public List<org.semanticweb.owlapi.model.OWLNamedIndividual> removeAnnotations(String modelId, String pid, String iid, String jid, Collection<org.apache.commons.lang3.tuple.Pair<String,String>> pairs, METADATA metadata) throws MolecularModelManager.UnknownIdentifierException
@Deprecated public void addPartOf(String modelId, String iid, String jid, Collection<org.apache.commons.lang3.tuple.Pair<String,String>> pairs) throws MolecularModelManager.UnknownIdentifierException
addPartOf(String, OWLNamedIndividual, OWLNamedIndividual, Set)
modelId
- iid
- jid
- pairs
- MolecularModelManager.UnknownIdentifierException
@Deprecated public void addPartOf(String modelId, org.semanticweb.owlapi.model.OWLNamedIndividual i, org.semanticweb.owlapi.model.OWLNamedIndividual j, Set<org.semanticweb.owlapi.model.OWLAnnotation> annotations) throws MolecularModelManager.UnknownIdentifierException
modelId
- i
- j
- annotations
- MolecularModelManager.UnknownIdentifierException
public void updateImports(String modelId) throws MolecularModelManager.UnknownIdentifierException
@Deprecated public String generateDot(String modelId) throws IOException, LegoTools.UnExpectedStructureException, MolecularModelManager.UnknownIdentifierException
modelId
- IOException
LegoTools.UnExpectedStructureException
MolecularModelManager.UnknownIdentifierException
@Deprecated public File generateImage(String modelId) throws IOException, LegoTools.UnExpectedStructureException, InterruptedException, MolecularModelManager.UnknownIdentifierException
modelId
- IOException
LegoTools.UnExpectedStructureException
InterruptedException
MolecularModelManager.UnknownIdentifierException
@Deprecated public void writeLego(org.semanticweb.owlapi.model.OWLOntology ontology, String output, String modelId) throws Exception
ontology
- output
- modelId
- Exception
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