org.obolibrary.obo2owl
Class Owl2Obo
java.lang.Object
org.obolibrary.obo2owl.Owl2Obo
public class Owl2Obo
- extends Object
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
annotationPropertyMap
public static Map<String,String> annotationPropertyMap
Owl2Obo
public Owl2Obo()
setStrictConversion
public void setStrictConversion(boolean b)
getStrictConversion
public boolean getStrictConversion()
getManager
public org.semanticweb.owlapi.model.OWLOntologyManager getManager()
setManager
public void setManager(org.semanticweb.owlapi.model.OWLOntologyManager manager)
getObodoc
public OBODoc getObodoc()
setObodoc
public void setObodoc(OBODoc obodoc)
convert
public OBODoc convert(org.semanticweb.owlapi.model.OWLOntology ont)
throws org.semanticweb.owlapi.model.OWLOntologyCreationException
- Throws:
org.semanticweb.owlapi.model.OWLOntologyCreationException
getUntranslatableAxioms
public Collection<org.semanticweb.owlapi.model.OWLAxiom> getUntranslatableAxioms()
- Returns:
- the untranslatableAxioms
getOntologyId
public static String getOntologyId(org.semanticweb.owlapi.model.OWLOntology ontology)
- E.g. http://purl.obolibrary.org/obo/go.owl --> "go"
- Parameters:
ontology
-
- Returns:
- The OBO ID of the ontology
getIdentifier
public String getIdentifier(org.semanticweb.owlapi.model.OWLObject obj)
getIdentifierFromObject
public static String getIdentifierFromObject(org.semanticweb.owlapi.model.OWLObject obj,
org.semanticweb.owlapi.model.OWLOntology ont,
String defaultValue)
- Retrieve the identifier for a given
OWLObject
.
This methods uses also shorthand hints to resolve the
identifier.
Should the translation process encounter a problem or
not find an identifier the defaultValue is returned.
- Parameters:
obj
- the OWLObject
to resolveont
- the target ontologydefaultValue
- the value to return in case of an error or no id
- Returns:
- identifier or the default value
getIdentifierFromObject
public static String getIdentifierFromObject(org.semanticweb.owlapi.model.OWLObject obj,
org.semanticweb.owlapi.model.OWLOntology ont)
throws Owl2Obo.UntranslatableAxiomException
- Retrieve the identifier for a given
OWLObject
.
This methods uses also shorthand hints to resolve the
identifier.
Should the translation process encounter an unexpected
axiom an Owl2Obo.UntranslatableAxiomException
is thrown.
- Parameters:
obj
- the OWLObject
to resolveont
- the target ontology
- Returns:
- identifier or null
- Throws:
Owl2Obo.UntranslatableAxiomException
getIdentifier
public static String getIdentifier(org.semanticweb.owlapi.model.IRI iriId)
- See table 5.9.2. Translation of identifiers
- Parameters:
iriId
-
- Returns:
- obo identifier or null
owlObjectToTag
public static String owlObjectToTag(org.semanticweb.owlapi.model.OWLObject obj)
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