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java.lang.Objectorg.obolibrary.obo2owl.Owl2Obo
public class Owl2Obo
Nested Class Summary | |
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static class |
Owl2Obo.UntranslatableAxiomException
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Field Summary | |
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static Map<String,String> |
annotationPropertyMap
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Constructor Summary | |
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Owl2Obo()
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Method Summary | |
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OBODoc |
convert(org.semanticweb.owlapi.model.OWLOntology ont)
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static String |
getDataVersion(org.semanticweb.owlapi.model.OWLOntology ontology)
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static String |
getIdentifier(org.semanticweb.owlapi.model.IRI iriId)
See table 5.9.2. |
static String |
getIdentifier(org.semanticweb.owlapi.model.IRI iriId,
org.semanticweb.owlapi.model.OWLOntology baseOntology)
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String |
getIdentifier(org.semanticweb.owlapi.model.OWLObject obj)
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static String |
getIdentifierFromObject(org.semanticweb.owlapi.model.OWLObject obj,
org.semanticweb.owlapi.model.OWLOntology ont)
Retrieve the identifier for a given OWLObject . |
static String |
getIdentifierFromObject(org.semanticweb.owlapi.model.OWLObject obj,
org.semanticweb.owlapi.model.OWLOntology ont,
String defaultValue)
Retrieve the identifier for a given OWLObject . |
org.semanticweb.owlapi.model.OWLOntologyManager |
getManager()
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OBODoc |
getObodoc()
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static String |
getOntologyId(org.semanticweb.owlapi.model.IRI iriObj)
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static String |
getOntologyId(org.semanticweb.owlapi.model.OWLOntology ontology)
E.g. |
boolean |
getStrictConversion()
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Collection<org.semanticweb.owlapi.model.OWLAxiom> |
getUntranslatableAxioms()
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protected boolean |
handleDuplicateClause(Frame frame,
Clause clause)
Handle a duplicate clause in a frame during translation. |
boolean |
isDiscardUntranslatable()
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static List<Clause> |
normalizeRelationshipClauses(List<Clause> clauses)
Join clauses and its QualifierValue which have the same
relationship type and target. |
static String |
owlObjectToTag(org.semanticweb.owlapi.model.OWLObject obj)
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void |
setDiscardUntranslatable(boolean discardUntranslatable)
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void |
setManager(org.semanticweb.owlapi.model.OWLOntologyManager manager)
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void |
setObodoc(OBODoc obodoc)
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void |
setStrictConversion(boolean b)
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Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static Map<String,String> annotationPropertyMap
Constructor Detail |
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public Owl2Obo()
Method Detail |
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public void setStrictConversion(boolean b)
public boolean getStrictConversion()
public boolean isDiscardUntranslatable()
public void setDiscardUntranslatable(boolean discardUntranslatable)
discardUntranslatable
- the discardUntranslatable to setpublic org.semanticweb.owlapi.model.OWLOntologyManager getManager()
public void setManager(org.semanticweb.owlapi.model.OWLOntologyManager manager)
public OBODoc getObodoc()
public void setObodoc(OBODoc obodoc)
public OBODoc convert(org.semanticweb.owlapi.model.OWLOntology ont) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyCreationException
public Collection<org.semanticweb.owlapi.model.OWLAxiom> getUntranslatableAxioms()
protected boolean handleDuplicateClause(Frame frame, Clause clause)
frame
- clause
-
public static String getOntologyId(org.semanticweb.owlapi.model.OWLOntology ontology)
ontology
-
public static String getOntologyId(org.semanticweb.owlapi.model.IRI iriObj)
public static String getDataVersion(org.semanticweb.owlapi.model.OWLOntology ontology)
public String getIdentifier(org.semanticweb.owlapi.model.OWLObject obj)
public static String getIdentifierFromObject(org.semanticweb.owlapi.model.OWLObject obj, org.semanticweb.owlapi.model.OWLOntology ont, String defaultValue)
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.
obj
- the OWLObject
to resolveont
- the target ontologydefaultValue
- the value to return in case of an error or no id
public static String getIdentifierFromObject(org.semanticweb.owlapi.model.OWLObject obj, org.semanticweb.owlapi.model.OWLOntology ont) throws Owl2Obo.UntranslatableAxiomException
OWLObject
.
This methods uses also shorthand hints to resolve the
identifier.
Should the translation process encounter an unexpected
axiom an Owl2Obo.UntranslatableAxiomException
is thrown.
obj
- the OWLObject
to resolveont
- the target ontology
Owl2Obo.UntranslatableAxiomException
public static String getIdentifier(org.semanticweb.owlapi.model.IRI iriId)
iriId
-
public static String getIdentifier(org.semanticweb.owlapi.model.IRI iriId, org.semanticweb.owlapi.model.OWLOntology baseOntology)
public static String owlObjectToTag(org.semanticweb.owlapi.model.OWLObject obj)
public static List<Clause> normalizeRelationshipClauses(List<Clause> clauses)
QualifierValue
which have the same
relationship type and target. Try to resolve conflicts for multiple
statements. E.g., min=2 and min=3 is resolved to min=2, or max=2 and max=4
is resolved to max=4. It will not merge conflicting exact cardinality statements.
TODO How to merge "all_some", and "all_only"?
clauses
-
Clause
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