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SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectowltools.gaf.lego.MolecularModelManager
public class MolecularModelManager
Manager object for operations on collections of MolecularModels (aka lego diagrams) any number of models can be loaded at any time (todo - impose some limit to avoid using too much memory) each model has a generator, an OWLOntology (containing the set of class assertions) and a reasoner associated with it (todo - test memory requirements) This manager is designed to be used within a web server. Multiple clients can contact the same manager instance through services
Nested Class Summary | |
---|---|
static class |
MolecularModelManager.LegoAnnotationType
|
protected class |
MolecularModelManager.LegoStringDotRenderer
Deprecated. |
class |
MolecularModelManager.OWLOperationResponse
Represents the reponse to a requested translation on an ontology/model |
static class |
MolecularModelManager.UnknownIdentifierException
|
Constructor Summary | |
---|---|
MolecularModelManager(OWLGraphWrapper graph)
|
|
MolecularModelManager(org.semanticweb.owlapi.model.OWLOntology ont)
|
Method Summary | |
---|---|
void |
addAnnotations(String modelId,
Collection<org.apache.commons.lang3.tuple.Pair<String,String>> pairs)
|
void |
addAnnotations(String modelId,
org.semanticweb.owlapi.model.OWLNamedIndividual i,
Collection<org.semanticweb.owlapi.model.OWLAnnotation> annotations)
|
MolecularModelManager.OWLOperationResponse |
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)
|
org.semanticweb.owlapi.model.OWLNamedIndividual |
addAnnotations(String modelId,
String iid,
Collection<org.apache.commons.lang3.tuple.Pair<String,String>> pairs)
|
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)
|
MolecularModelManager.OWLOperationResponse |
addCompositeIndividual(String modelId,
String classId,
String enabledById,
String occursInId)
A simple wrapping function that captures the most basic type of editing. |
MolecularModelManager.OWLOperationResponse |
addEnabledBy(String modelId,
org.semanticweb.owlapi.model.OWLNamedIndividual i,
org.semanticweb.owlapi.model.OWLClassExpression enabler)
Adds a ClassAssertion to the model, connecting an activity instance to the class of molecule that enables the activity. |
MolecularModelManager.OWLOperationResponse |
addEnabledBy(String modelId,
String iid,
String eid)
Convenience wrapper for addEnabledBy(String, OWLNamedIndividual, OWLClassExpression) |
MolecularModelManager.OWLOperationResponse |
addFact(String modelId,
OBOUpperVocabulary vocabElement,
org.semanticweb.owlapi.model.OWLNamedIndividual i,
org.semanticweb.owlapi.model.OWLNamedIndividual j,
Set<org.semanticweb.owlapi.model.OWLAnnotation> annotations)
Convenience wrapper for addFact(String, OWLObjectPropertyExpression, OWLNamedIndividual, OWLNamedIndividual, Set) |
MolecularModelManager.OWLOperationResponse |
addFact(String modelId,
OBOUpperVocabulary vocabElement,
String iid,
String jid,
Collection<org.apache.commons.lang3.tuple.Pair<String,String>> pairs)
Convenience wrapper for addFact(String, OWLObjectPropertyExpression, OWLNamedIndividual, OWLNamedIndividual, Set) |
MolecularModelManager.OWLOperationResponse |
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)
Adds triple (i,p,j) to specified model |
MolecularModelManager.OWLOperationResponse |
addFact(String modelId,
String pid,
String iid,
String jid,
Collection<org.apache.commons.lang3.tuple.Pair<String,String>> pairs)
Convenience wrapper for addFact(String, OWLObjectPropertyExpression, OWLNamedIndividual, OWLNamedIndividual, Set) |
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)
Convenience wrapper for addFact(String, OWLObjectPropertyExpression, OWLNamedIndividual, OWLNamedIndividual, Set) |
void |
addImports(Iterable<String> imports)
Add additional import declarations for any newly generated model. |
MolecularModelManager.OWLOperationResponse |
addOccursIn(String modelId,
org.semanticweb.owlapi.model.OWLNamedIndividual i,
org.semanticweb.owlapi.model.OWLClassExpression enabler)
Adds a ClassAssertion to the model, connecting an activity instance to the class of molecule that enables the activity. |
MolecularModelManager.OWLOperationResponse |
addOccursIn(String modelId,
String iid,
String eid)
Convenience wrapper for addOccursIn(String, OWLNamedIndividual, OWLClassExpression) |
MolecularModelManager.OWLOperationResponse |
addPartOf(String modelId,
org.semanticweb.owlapi.model.OWLNamedIndividual i,
org.semanticweb.owlapi.model.OWLNamedIndividual j,
Set<org.semanticweb.owlapi.model.OWLAnnotation> annotations)
Adds an OWL ObjectPropertyAssertion connecting i to j via part_of Note that the inverse assertion is entailed, but not asserted |
MolecularModelManager.OWLOperationResponse |
addPartOf(String modelId,
String iid,
String jid,
Collection<org.apache.commons.lang3.tuple.Pair<String,String>> pairs)
Convenience wrapper for addPartOf(String, OWLNamedIndividual, OWLNamedIndividual, Set) |
String |
addProcess(String modelId,
org.semanticweb.owlapi.model.OWLClass processCls)
Adds a process individual (and inferred individuals) to a model |
MolecularModelManager.OWLOperationResponse |
addType(String modelId,
org.semanticweb.owlapi.model.OWLNamedIndividual i,
org.semanticweb.owlapi.model.OWLClass c)
Adds ClassAssertion(c,i) to specified model |
MolecularModelManager.OWLOperationResponse |
addType(String modelId,
org.semanticweb.owlapi.model.OWLNamedIndividual i,
org.semanticweb.owlapi.model.OWLObjectPropertyExpression p,
org.semanticweb.owlapi.model.OWLClassExpression filler)
Adds a ClassAssertion, where the class expression instantiated is an ObjectSomeValuesFrom expression Example: Individual: i Type: enabledBy some PRO_123 |
MolecularModelManager.OWLOperationResponse |
addType(String modelId,
String iid,
String cid)
Convenience wrapper for addType(String, OWLNamedIndividual, OWLClass) |
MolecularModelManager.OWLOperationResponse |
addType(String modelId,
String iid,
String pid,
String cid)
Convenience wrapper for addType(String, OWLNamedIndividual, OWLObjectPropertyExpression, OWLClassExpression) |
org.semanticweb.owlapi.model.OWLNamedIndividual |
addTypeNonReasoning(String modelId,
String iid,
org.semanticweb.owlapi.model.OWLClassExpression clsExp)
|
org.semanticweb.owlapi.model.OWLNamedIndividual |
addTypeNonReasoning(String modelId,
String iid,
String pid,
org.semanticweb.owlapi.model.OWLClassExpression ce)
|
MolecularModelManager.OWLOperationResponse |
createIndividual(String modelId,
org.semanticweb.owlapi.model.OWLClass c)
|
MolecularModelManager.OWLOperationResponse |
createIndividual(String modelId,
String cid,
Collection<org.apache.commons.lang3.tuple.Pair<String,String>> annotations)
Shortcut for createIndividual(String, OWLClass) |
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)
Shortcut for createIndividual(String, OWLClass) |
String |
createMostSpecificClass(String modelId,
String individualId,
String newClassId)
Given an instance, generate the most specific class instance that classifies this instance, and add this as a class to the model ontology |
MolecularModelManager.OWLOperationResponse |
deleteIndividual(String modelId,
org.semanticweb.owlapi.model.OWLNamedIndividual i)
Deletes an individual |
MolecularModelManager.OWLOperationResponse |
deleteIndividual(String modelId,
String iid)
Deletes an individual |
void |
deleteModel(String id)
|
void |
dispose()
internal method to cleanup this instance |
String |
exportModel(String modelId)
Export the ABox for the given modelId in the default OWLOntologyFormat . |
String |
exportModel(String modelId,
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 |
exportModel(String modelId,
String format)
Export the ABox for the given modelId in the given ontology format. Warning: The mapping from String to OWLOntologyFormat does not map every format! |
String |
generateBlankModel(String db)
Generates a new model taking as input a database D. |
String |
generateDot(String modelId)
Deprecated. |
File |
generateImage(String modelId)
Deprecated. |
String |
generateModel(org.semanticweb.owlapi.model.OWLClass processCls,
String db)
Generates a new model taking as input a biological process P and a database D. |
String |
generateModel(String pid,
String db)
wrapper for generateModel(OWLClass, String) |
Set<String> |
getAvailableModelIds()
Retrieve a collection of all available model ids. Note: Models may not be loaded at this point. |
Set<String> |
getCurrentModelIds()
Retrieve a collection of all model ids currently in memory. |
Map<String,String> |
getDbToTaxon()
|
GafDocument |
getGaf(String db)
|
OWLGraphWrapper |
getGraph()
|
Collection<org.semanticweb.owlapi.model.IRI> |
getImports()
|
MolecularModelManager.OWLOperationResponse |
getIndividualById(String modelId,
String iid)
Get the individual information for return. |
Set<org.semanticweb.owlapi.model.OWLNamedIndividual> |
getIndividuals(String modelId)
|
Set<org.semanticweb.owlapi.model.OWLNamedIndividual> |
getIndividualsByQuery(String modelId,
org.semanticweb.owlapi.model.OWLClassExpression q)
|
Set<org.semanticweb.owlapi.model.OWLNamedIndividual> |
getIndividualsByQuery(String modelId,
String qs)
|
LegoModelGenerator |
getModel(String id)
Fetches a model by its Id |
Set<String> |
getModelIds()
|
Map<Object,Object> |
getModelObject(String modelId)
|
org.semanticweb.owlapi.model.OWLNamedIndividual |
getNamedIndividual(String modelId,
String iid)
|
org.semanticweb.owlapi.model.OWLOntology |
getOntology()
|
org.semanticweb.owlapi.model.OWLDataFactory |
getOWLDataFactory(String modelId)
|
protected org.semanticweb.owlapi.model.OWLOntologyManager |
getOWLOntologyManager(String modelId)
|
String |
getPathToGafs()
|
String |
getPathToOWLFiles()
Note this may move to an implementation-specific subclass in future |
String |
getPathToProteinFiles()
|
Set<String> |
getStoredModelIds()
Retrieve a collection of all file/stored model ids found in the repo. Note: Models may not be loaded at this point. |
String |
importModel(String modelData)
Try to load (or replace) a model with the given ontology. |
protected void |
init()
|
boolean |
isConsistent(String modelId)
|
GafDocument |
loadGaf(String db)
loads/register a Gaf document |
GafDocument |
loadGaf(String db,
File gafFile)
Loads and caches a GAF document from a specified location |
protected void |
loadModel(String modelId,
boolean isOverride)
|
static org.semanticweb.owlapi.model.OWLClassExpression |
parseClassExpression(String expression,
OWLGraphWrapper g)
|
void |
removeAnnotations(String modelId,
Collection<org.apache.commons.lang3.tuple.Pair<String,String>> pairs)
|
void |
removeAnnotations(String modelId,
org.semanticweb.owlapi.model.OWLNamedIndividual i,
Collection<org.semanticweb.owlapi.model.OWLAnnotation> annotations)
|
org.semanticweb.owlapi.model.OWLNamedIndividual |
removeAnnotations(String modelId,
String iid,
Collection<org.apache.commons.lang3.tuple.Pair<String,String>> pairs)
|
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)
|
MolecularModelManager.OWLOperationResponse |
removeFact(String modelId,
org.semanticweb.owlapi.model.OWLObjectPropertyExpression p,
org.semanticweb.owlapi.model.OWLNamedIndividual i,
org.semanticweb.owlapi.model.OWLNamedIndividual j)
|
MolecularModelManager.OWLOperationResponse |
removeFact(String modelId,
String pid,
String iid,
String jid)
|
List<org.semanticweb.owlapi.model.OWLNamedIndividual> |
removeFactNonReasoning(String modelId,
String pid,
String iid,
String jid)
|
MolecularModelManager.OWLOperationResponse |
removeType(String modelId,
org.semanticweb.owlapi.model.OWLNamedIndividual i,
org.semanticweb.owlapi.model.OWLClass c)
remove ClassAssertion(c,i) to specified model |
MolecularModelManager.OWLOperationResponse |
removeType(String modelId,
org.semanticweb.owlapi.model.OWLNamedIndividual i,
org.semanticweb.owlapi.model.OWLObjectPropertyExpression p,
org.semanticweb.owlapi.model.OWLClassExpression filler)
Removes a ClassAssertion, where the class expression instantiated is an ObjectSomeValuesFrom expression TODO - in future it should be possible to remove multiple assertions by leaving some fields null |
MolecularModelManager.OWLOperationResponse |
removeType(String modelId,
String iid,
String cid)
Convenience wrapper for removeType(String, OWLNamedIndividual, OWLClass) |
org.semanticweb.owlapi.model.OWLNamedIndividual |
removeTypeNonReasoning(String modelId,
String iid,
org.semanticweb.owlapi.model.OWLClassExpression clsExp)
|
void |
saveAllModels()
|
void |
saveModel(String modelId)
TODO - locking |
void |
setDbToTaxon(Map<String,String> dbToTaxon)
|
void |
setPathToGafs(String pathToGafs)
Can either be an HTTP prefix, or an absolute file path |
void |
setPathToOWLFiles(String pathToOWLFiles)
|
void |
setPathToProteinFiles(String pathToProteinFiles)
|
void |
setPathToProteinFiles(String pathToProteinFiles,
String catalogXML)
|
MolecularModelManager.OWLOperationResponse |
undo(String modelId,
String changeId)
|
void |
unlinkModel(String id)
|
void |
writeLego(org.semanticweb.owlapi.model.OWLOntology ontology,
String output,
String name)
Deprecated. |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
---|
public MolecularModelManager(OWLGraphWrapper graph) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
graph
-
org.semanticweb.owlapi.model.OWLOntologyCreationException
public MolecularModelManager(org.semanticweb.owlapi.model.OWLOntology ont) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
ont
-
org.semanticweb.owlapi.model.OWLOntologyCreationException
Method Detail |
---|
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 String getPathToGafs()
public void setPathToGafs(String pathToGafs)
pathToGafs
- public String getPathToOWLFiles()
public void setPathToOWLFiles(String pathToOWLFiles)
pathToOWLFiles
- public void setPathToProteinFiles(String pathToProteinFiles) throws IOException
pathToProteinFiles
-
IOException
public void setPathToProteinFiles(String pathToProteinFiles, String catalogXML) throws IOException
pathToProteinFiles
- catalogXML
-
IOException
public String getPathToProteinFiles()
public Map<String,String> getDbToTaxon()
public void setDbToTaxon(Map<String,String> dbToTaxon)
dbToTaxon
- the dbToTaxon to setpublic GafDocument loadGaf(String db) throws IOException, URISyntaxException
db
-
IOException
URISyntaxException
public GafDocument loadGaf(String db, File gafFile) throws IOException, URISyntaxException
db
- gafFile
-
IOException
URISyntaxException
public GafDocument getGaf(String db) throws IOException, URISyntaxException
db
-
IOException
URISyntaxException
public void addImports(Iterable<String> imports)
imports
- public Collection<org.semanticweb.owlapi.model.IRI> getImports()
public String generateModel(org.semanticweb.owlapi.model.OWLClass processCls, String db) throws org.semanticweb.owlapi.model.OWLOntologyCreationException, IOException, URISyntaxException
LegoModelGenerator.buildNetwork(OWLClass, java.util.Collection)
And also https://docs.google.com/document/d/1TV8Eb9sSvFY-weVZaIfzCxF1qbnmkUaiUhTm9Bs3gRE/edit
Note the resulting model is uniquely identified by the modeId, which is currently constructed
as a concatenation of the db and the P id. This means that if there is an existing model by
this ID it will be overwritten
processCls
- db
-
org.semanticweb.owlapi.model.OWLOntologyCreationException
URISyntaxException
IOException
public String generateModel(String pid, String db) throws org.semanticweb.owlapi.model.OWLOntologyCreationException, IOException, URISyntaxException, MolecularModelManager.UnknownIdentifierException
generateModel(OWLClass, String)
pid
- db
-
org.semanticweb.owlapi.model.OWLOntologyCreationException
IOException
URISyntaxException
MolecularModelManager.UnknownIdentifierException
public String generateBlankModel(String db) throws org.semanticweb.owlapi.model.OWLOntologyCreationException, IOException, URISyntaxException
db
-
org.semanticweb.owlapi.model.OWLOntologyCreationException
URISyntaxException
IOException
public String addProcess(String modelId, org.semanticweb.owlapi.model.OWLClass processCls) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
modelId
- processCls
-
org.semanticweb.owlapi.model.OWLOntologyCreationException
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 Set<org.semanticweb.owlapi.model.OWLNamedIndividual> getIndividualsByQuery(String modelId, String qs)
modelId
- qs
-
public Map<Object,Object> getModelObject(String modelId)
modelId
-
public String createMostSpecificClass(String modelId, String individualId, String newClassId)
modelId
- individualId
- newClassId
-
public MolecularModelManager.OWLOperationResponse createIndividual(String modelId, org.semanticweb.owlapi.model.OWLClass c)
modelId
- c
-
public MolecularModelManager.OWLOperationResponse createIndividual(String modelId, String cid, Collection<org.apache.commons.lang3.tuple.Pair<String,String>> annotations) throws MolecularModelManager.UnknownIdentifierException
createIndividual(String, OWLClass)
modelId
- cid
- annotations
-
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) throws MolecularModelManager.UnknownIdentifierException
createIndividual(String, OWLClass)
modelId
- cid
- annotations
-
MolecularModelManager.UnknownIdentifierException
public MolecularModelManager.OWLOperationResponse getIndividualById(String modelId, String iid) throws MolecularModelManager.UnknownIdentifierException
modelId
- iid
-
MolecularModelManager.UnknownIdentifierException
public org.semanticweb.owlapi.model.OWLNamedIndividual getNamedIndividual(String modelId, String iid) throws MolecularModelManager.UnknownIdentifierException
MolecularModelManager.UnknownIdentifierException
public MolecularModelManager.OWLOperationResponse deleteIndividual(String modelId, String iid) throws MolecularModelManager.UnknownIdentifierException
modelId
- iid
-
MolecularModelManager.UnknownIdentifierException
public MolecularModelManager.OWLOperationResponse deleteIndividual(String modelId, org.semanticweb.owlapi.model.OWLNamedIndividual i)
modelId
- i
-
public void addAnnotations(String modelId, Collection<org.apache.commons.lang3.tuple.Pair<String,String>> pairs) throws MolecularModelManager.UnknownIdentifierException
MolecularModelManager.UnknownIdentifierException
public org.semanticweb.owlapi.model.OWLNamedIndividual addAnnotations(String modelId, String iid, Collection<org.apache.commons.lang3.tuple.Pair<String,String>> pairs) throws MolecularModelManager.UnknownIdentifierException
MolecularModelManager.UnknownIdentifierException
public void addAnnotations(String modelId, org.semanticweb.owlapi.model.OWLNamedIndividual i, Collection<org.semanticweb.owlapi.model.OWLAnnotation> annotations)
public org.semanticweb.owlapi.model.OWLNamedIndividual removeAnnotations(String modelId, String iid, Collection<org.apache.commons.lang3.tuple.Pair<String,String>> pairs) throws MolecularModelManager.UnknownIdentifierException
MolecularModelManager.UnknownIdentifierException
public void removeAnnotations(String modelId, org.semanticweb.owlapi.model.OWLNamedIndividual i, Collection<org.semanticweb.owlapi.model.OWLAnnotation> annotations)
public void removeAnnotations(String modelId, Collection<org.apache.commons.lang3.tuple.Pair<String,String>> pairs) throws MolecularModelManager.UnknownIdentifierException
MolecularModelManager.UnknownIdentifierException
public LegoModelGenerator getModel(String id)
id
-
public void unlinkModel(String id)
id
- public void deleteModel(String id)
id
- public Set<String> getModelIds()
public void dispose()
public void saveModel(String modelId) throws org.semanticweb.owlapi.model.OWLOntologyStorageException, org.semanticweb.owlapi.model.OWLOntologyCreationException, IOException
modelId
-
org.semanticweb.owlapi.model.OWLOntologyStorageException
org.semanticweb.owlapi.model.OWLOntologyCreationException
IOException
public void saveAllModels() throws org.semanticweb.owlapi.model.OWLOntologyStorageException, org.semanticweb.owlapi.model.OWLOntologyCreationException, IOException
org.semanticweb.owlapi.model.OWLOntologyStorageException
org.semanticweb.owlapi.model.OWLOntologyCreationException
IOException
public String exportModel(String modelId) throws org.semanticweb.owlapi.model.OWLOntologyStorageException
OWLOntologyFormat
.
modelId
-
org.semanticweb.owlapi.model.OWLOntologyStorageException
public String exportModel(String modelId, String format) throws org.semanticweb.owlapi.model.OWLOntologyStorageException
OWLOntologyFormat
does not map every format!
modelId
- format
-
org.semanticweb.owlapi.model.OWLOntologyStorageException
public String exportModel(String modelId, org.semanticweb.owlapi.model.OWLOntologyFormat ontologyFormat) throws org.semanticweb.owlapi.model.OWLOntologyStorageException
modelId
- 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> getStoredModelIds() throws IOException
IOException
public Set<String> getCurrentModelIds() throws IOException
IOException
public Set<String> getAvailableModelIds() throws IOException
IOException
protected 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 MolecularModelManager.OWLOperationResponse addType(String modelId, org.semanticweb.owlapi.model.OWLNamedIndividual i, org.semanticweb.owlapi.model.OWLClass c)
modelId
- i
- c
-
public MolecularModelManager.OWLOperationResponse addType(String modelId, String iid, String cid) throws MolecularModelManager.UnknownIdentifierException
addType(String, OWLNamedIndividual, OWLClass)
modelId
- iid
- cid
-
MolecularModelManager.UnknownIdentifierException
public org.semanticweb.owlapi.model.OWLNamedIndividual addTypeNonReasoning(String modelId, String iid, org.semanticweb.owlapi.model.OWLClassExpression clsExp) throws MolecularModelManager.UnknownIdentifierException
modelId
- iid
- clsExp
-
MolecularModelManager.UnknownIdentifierException
public MolecularModelManager.OWLOperationResponse addType(String modelId, org.semanticweb.owlapi.model.OWLNamedIndividual i, org.semanticweb.owlapi.model.OWLObjectPropertyExpression p, org.semanticweb.owlapi.model.OWLClassExpression filler)
modelId
- i
- p
- filler
-
public MolecularModelManager.OWLOperationResponse addType(String modelId, String iid, String pid, String cid) throws MolecularModelManager.UnknownIdentifierException
addType(String, OWLNamedIndividual, OWLObjectPropertyExpression, OWLClassExpression)
modelId
- iid
- pid
- cid
-
MolecularModelManager.UnknownIdentifierException
public org.semanticweb.owlapi.model.OWLNamedIndividual addTypeNonReasoning(String modelId, String iid, String pid, org.semanticweb.owlapi.model.OWLClassExpression ce) throws MolecularModelManager.UnknownIdentifierException
MolecularModelManager.UnknownIdentifierException
public MolecularModelManager.OWLOperationResponse removeType(String modelId, org.semanticweb.owlapi.model.OWLNamedIndividual i, org.semanticweb.owlapi.model.OWLClass c)
modelId
- i
- c
-
public MolecularModelManager.OWLOperationResponse removeType(String modelId, String iid, String cid) throws MolecularModelManager.UnknownIdentifierException
removeType(String, OWLNamedIndividual, OWLClass)
modelId
- iid
- cid
-
MolecularModelManager.UnknownIdentifierException
public org.semanticweb.owlapi.model.OWLNamedIndividual removeTypeNonReasoning(String modelId, String iid, org.semanticweb.owlapi.model.OWLClassExpression clsExp) throws MolecularModelManager.UnknownIdentifierException
MolecularModelManager.UnknownIdentifierException
public MolecularModelManager.OWLOperationResponse removeType(String modelId, org.semanticweb.owlapi.model.OWLNamedIndividual i, org.semanticweb.owlapi.model.OWLObjectPropertyExpression p, org.semanticweb.owlapi.model.OWLClassExpression filler)
modelId
- i
- p
- filler
-
public MolecularModelManager.OWLOperationResponse addOccursIn(String modelId, String iid, String eid) throws MolecularModelManager.UnknownIdentifierException
addOccursIn(String, OWLNamedIndividual, OWLClassExpression)
modelId
- iid
- eid
- - e.g. PR:P12345
MolecularModelManager.UnknownIdentifierException
public MolecularModelManager.OWLOperationResponse addOccursIn(String modelId, org.semanticweb.owlapi.model.OWLNamedIndividual i, org.semanticweb.owlapi.model.OWLClassExpression enabler)
modelId
- i
- enabler
-
public MolecularModelManager.OWLOperationResponse 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:P12345
MolecularModelManager.UnknownIdentifierException
org.semanticweb.owlapi.model.OWLException
public static org.semanticweb.owlapi.model.OWLClassExpression parseClassExpression(String expression, OWLGraphWrapper g) throws org.semanticweb.owlapi.model.OWLException
org.semanticweb.owlapi.model.OWLException
public MolecularModelManager.OWLOperationResponse addEnabledBy(String modelId, org.semanticweb.owlapi.model.OWLNamedIndividual i, org.semanticweb.owlapi.model.OWLClassExpression enabler)
modelId
- i
- enabler
-
public MolecularModelManager.OWLOperationResponse 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)
modelId
- p
- i
- j
- annotations
-
public MolecularModelManager.OWLOperationResponse addFact(String modelId, OBOUpperVocabulary vocabElement, org.semanticweb.owlapi.model.OWLNamedIndividual i, org.semanticweb.owlapi.model.OWLNamedIndividual j, Set<org.semanticweb.owlapi.model.OWLAnnotation> annotations)
addFact(String, OWLObjectPropertyExpression, OWLNamedIndividual, OWLNamedIndividual, Set)
modelId
- vocabElement
- i
- j
- annotations
-
public MolecularModelManager.OWLOperationResponse addFact(String modelId, String pid, String iid, String jid, Collection<org.apache.commons.lang3.tuple.Pair<String,String>> pairs) throws MolecularModelManager.UnknownIdentifierException
addFact(String, OWLObjectPropertyExpression, OWLNamedIndividual, OWLNamedIndividual, Set)
modelId
- pid
- iid
- jid
- pairs
-
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) throws MolecularModelManager.UnknownIdentifierException
addFact(String, OWLObjectPropertyExpression, OWLNamedIndividual, OWLNamedIndividual, Set)
modelId
- pid
- iid
- jid
- pairs
-
MolecularModelManager.UnknownIdentifierException
public MolecularModelManager.OWLOperationResponse addFact(String modelId, OBOUpperVocabulary vocabElement, String iid, String jid, Collection<org.apache.commons.lang3.tuple.Pair<String,String>> pairs) throws MolecularModelManager.UnknownIdentifierException
addFact(String, OWLObjectPropertyExpression, OWLNamedIndividual, OWLNamedIndividual, Set)
modelId
- vocabElement
- iid
- jid
- pairs
-
MolecularModelManager.UnknownIdentifierException
public MolecularModelManager.OWLOperationResponse removeFact(String modelId, org.semanticweb.owlapi.model.OWLObjectPropertyExpression p, org.semanticweb.owlapi.model.OWLNamedIndividual i, org.semanticweb.owlapi.model.OWLNamedIndividual j)
modelId
- p
- i
- j
-
public MolecularModelManager.OWLOperationResponse removeFact(String modelId, String pid, String iid, String jid) throws MolecularModelManager.UnknownIdentifierException
modelId
- pid
- iid
- jid
-
MolecularModelManager.UnknownIdentifierException
public List<org.semanticweb.owlapi.model.OWLNamedIndividual> removeFactNonReasoning(String modelId, String pid, String iid, String jid) throws MolecularModelManager.UnknownIdentifierException
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) throws MolecularModelManager.UnknownIdentifierException
MolecularModelManager.UnknownIdentifierException
public MolecularModelManager.OWLOperationResponse 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)
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) throws MolecularModelManager.UnknownIdentifierException
MolecularModelManager.UnknownIdentifierException
public MolecularModelManager.OWLOperationResponse 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
public MolecularModelManager.OWLOperationResponse addPartOf(String modelId, org.semanticweb.owlapi.model.OWLNamedIndividual i, org.semanticweb.owlapi.model.OWLNamedIndividual j, Set<org.semanticweb.owlapi.model.OWLAnnotation> annotations)
modelId
- i
- j
- annotations
-
public MolecularModelManager.OWLOperationResponse undo(String modelId, String changeId)
@Deprecated public String generateDot(String modelId) throws IOException, LegoTools.UnExpectedStructureException
modelId
-
IOException
LegoTools.UnExpectedStructureException
@Deprecated public File generateImage(String modelId) throws IOException, LegoTools.UnExpectedStructureException, InterruptedException
modelId
-
IOException
LegoTools.UnExpectedStructureException
InterruptedException
@Deprecated public void writeLego(org.semanticweb.owlapi.model.OWLOntology ontology, String output, String name) throws Exception
ontology
- output
- name
-
Exception
public MolecularModelManager.OWLOperationResponse addCompositeIndividual(String modelId, String classId, String enabledById, String occursInId) throws MolecularModelManager.UnknownIdentifierException
modelId
- classId
- enabledById
- occursInId
-
MolecularModelManager.UnknownIdentifierException
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