Uses of Class
org.obolibrary.oboformat.model.Clause

Packages that use Clause

Package	Description
org.obolibrary.obo2owl
org.obolibrary.oboformat.diff
org.obolibrary.oboformat.model
org.obolibrary.oboformat.parser
org.obolibrary.oboformat.writer

Uses of Clause in org.obolibrary.obo2owl

Methods in org.obolibrary.obo2owl that return Clause

Modifier and Type	Method and Description
protected Clause	OWLAPIOwl2Obo.createRelationshipClauseWithCardinality(org.semanticweb.owlapi.model.OWLObjectCardinalityRestriction restriction, String fillerId, Set<QualifierValue> qvs, org.semanticweb.owlapi.model.OWLSubClassOfAxiom ax)
protected Clause	OWLAPIOwl2Obo.createRelationshipClauseWithRestrictions(org.semanticweb.owlapi.model.OWLQuantifiedObjectRestriction r, String fillerId, Set<QualifierValue> qvs, org.semanticweb.owlapi.model.OWLSubClassOfAxiom ax)

Methods in org.obolibrary.obo2owl that return types with arguments of type Clause

Modifier and Type	Method and Description
static List<Clause>	OWLAPIOwl2Obo.normalizeRelationshipClauses(List<Clause> clauses) Join clauses and its QualifierValue which have the same relationship type and target.

Methods in org.obolibrary.obo2owl with parameters of type Clause

Modifier and Type	Method and Description
protected void	OWLAPIOwl2Obo.addQualifiers(Clause c, Set<org.semanticweb.owlapi.model.OWLAnnotation> qualifiers)
protected boolean	OWLAPIOwl2Obo.handleDuplicateClause(Frame frame, Clause clause) Handle a duplicate clause in a frame during translation.
protected void	OWLAPIOwl2Obo.handleSynonym(Set<org.semanticweb.owlapi.model.OWLAnnotation> qualifiers, String scope, Clause clause, Set<org.semanticweb.owlapi.model.OWLAnnotation> unprocessedQualifiers)
protected Set<org.semanticweb.owlapi.model.OWLAnnotation>	OWLAPIObo2Owl.trAnnotations(Clause clause) Tr annotations.
protected void	OWLAPIObo2Owl.trAnnotations(Clause clause, Set<org.semanticweb.owlapi.model.OWLAnnotation> anns) Tr annotations.
protected org.semanticweb.owlapi.model.OWLAxiom	OWLAPIObo2Owl.trGenericClause(org.semanticweb.owlapi.model.OWLAnnotationSubject sub, String tag, Clause clause) Tr generic clause.
protected org.semanticweb.owlapi.model.OWLAxiom	OWLAPIObo2Owl.trGenericClause(org.semanticweb.owlapi.model.OWLNamedObject e, String tag, Clause clause) Tr generic clause.
protected org.semanticweb.owlapi.model.OWLAxiom	OWLAPIObo2Owl.trTermClause(org.semanticweb.owlapi.model.OWLClass cls, String tag, Clause clause) #5.2
protected org.semanticweb.owlapi.model.OWLAxiom	OWLAPIObo2Owl.trTypedefClause(org.semanticweb.owlapi.model.OWLObjectProperty p, String tag, Clause clause) Tr typedef clause.

Method parameters in org.obolibrary.obo2owl with type arguments of type Clause

Modifier and Type	Method and Description
protected void	OWLAPIObo2Owl.addPropertyValueHeaders(Collection<Clause> clauses) Adds the property value headers.
static List<Clause>	OWLAPIOwl2Obo.normalizeRelationshipClauses(List<Clause> clauses) Join clauses and its QualifierValue which have the same relationship type and target.
protected Set<? extends org.semanticweb.owlapi.model.OWLAnnotation>	OWLAPIObo2Owl.trAnnotations(Collection<Clause> clauses) Tr annotations.
protected Set<org.semanticweb.owlapi.model.OWLAxiom>	OWLAPIObo2Owl.translateAltIds(Collection<Clause> clauses, org.semanticweb.owlapi.model.IRI replacedBy, boolean isClass) Generate axioms for the alternate identifiers of an OWLClass or OWLObjectProperty.
protected org.semanticweb.owlapi.model.OWLAxiom	OWLAPIObo2Owl.trIntersectionOf(org.semanticweb.owlapi.model.OWLClass cls, Collection<Clause> clauses) Tr intersection of.
protected static org.semanticweb.owlapi.model.OWLAxiom	OWLAPIObo2Owl.trRelationIntersectionOf(String id, org.semanticweb.owlapi.model.OWLProperty p, Collection<Clause> clauses) Tr relation intersection of.
protected static org.semanticweb.owlapi.model.OWLAxiom	OWLAPIObo2Owl.trRelationUnionOf(String id, org.semanticweb.owlapi.model.OWLProperty p, Collection<Clause> clauses) Tr relation union of.
Set<org.semanticweb.owlapi.model.OWLAxiom>	OWLAPIObo2Owl.trTermFrameClauses(org.semanticweb.owlapi.model.OWLClass cls, Collection<Clause> clauses, String t) Tr term frame clauses.
protected org.semanticweb.owlapi.model.OWLAxiom	OWLAPIObo2Owl.trUnionOf(org.semanticweb.owlapi.model.OWLClass cls, Collection<Clause> clauses) Tr union of.

Uses of Clause in org.obolibrary.oboformat.diff

Methods in org.obolibrary.oboformat.diff that return Clause

Modifier and Type	Method and Description
Clause	Diff.getClause1()
Clause	Diff.getClause2()

Methods in org.obolibrary.oboformat.diff with parameters of type Clause

Modifier and Type	Method and Description
void	Diff.setClause1(Clause clause1)
void	Diff.setClause2(Clause clause2)

Constructors in org.obolibrary.oboformat.diff with parameters of type Clause

Constructor and Description
Diff(String ftype, String type, Frame f1, Frame f2, Clause c, int n)

Uses of Clause in org.obolibrary.oboformat.model

Fields in org.obolibrary.oboformat.model with type parameters of type Clause

Modifier and Type	Field and Description
protected Collection<Clause>	Frame.clauses The clauses.

Methods in org.obolibrary.oboformat.model that return Clause

Modifier and Type	Method and Description
Clause	Frame.getClause(OBOFormatConstants.OboFormatTag tag)
Clause	Frame.getClause(String tag)

Methods in org.obolibrary.oboformat.model that return types with arguments of type Clause

Modifier and Type	Method and Description
Collection<Clause>	Frame.getClauses()
Collection<Clause>	Frame.getClauses(OBOFormatConstants.OboFormatTag tag)
Collection<Clause>	Frame.getClauses(String tag)

Methods in org.obolibrary.oboformat.model with parameters of type Clause

Modifier and Type	Method and Description
void	Frame.addClause(Clause cl)

Method parameters in org.obolibrary.oboformat.model with type arguments of type Clause

Modifier and Type	Method and Description
void	Frame.setClauses(Collection<Clause> clauses)

Uses of Clause in org.obolibrary.oboformat.parser

Methods in org.obolibrary.oboformat.parser that return Clause

Modifier and Type	Method and Description
Clause	OBOFormatParser.parseTermFrameClause()
Clause	OBOFormatParser.parseTypedefFrameClause()

Methods in org.obolibrary.oboformat.parser with parameters of type Clause

Modifier and Type	Method and Description
void	OBOFormatParser.parseEOL(Clause cl)
protected void	OBOFormatParser.parseUnquotedString(Clause cl)

Uses of Clause in org.obolibrary.oboformat.writer

Methods in org.obolibrary.oboformat.writer with parameters of type Clause

Modifier and Type	Method and Description
void	OBOFormatWriter.write(Clause clause, BufferedWriter writer, OBOFormatWriter.NameProvider nameProvider) Write.
void	OBOFormatWriter.writeDef(Clause clause, BufferedWriter writer) Write def.
void	OBOFormatWriter.writePropertyValue(Clause clause, BufferedWriter writer) Write property value.
void	OBOFormatWriter.writeSynonym(Clause clause, BufferedWriter writer) Write synonym.

Method parameters in org.obolibrary.oboformat.writer with type arguments of type Clause

Modifier and Type	Method and Description
static void	OBOFormatWriter.sortTermClauses(List<Clause> clauses) Sort a list of term frame clauses according to in the OBO format specified tag and value order.