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Merge pull request #110 from phenoscape/cleanup-imports
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Clean up imports.
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@balhoff
balhoff authored Jun 18, 2021
2 parents bedcb9e + fccf9ba commit 4b60fc3
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Showing 21 changed files with 65 additions and 215 deletions.
1 change: 1 addition & 0 deletions src/main/scala/org/phenoscape/scowl/example/OWL2PrimerManchester.scala
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package org.phenoscape.scowl.example

import org.phenoscape.scowl._

import scala.language.postfixOps

object OWL2PrimerManchester {
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5 changes: 3 additions & 2 deletions src/main/scala/org/phenoscape/scowl/example/ReadMeExamples.scala
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package org.phenoscape.scowl.example

import org.phenoscape.scowl._
import org.semanticweb.owlapi.model.OWLClassExpression
import org.semanticweb.owlapi.apibinding.OWLManager
import scala.collection.JavaConverters._
import org.semanticweb.owlapi.model.OWLClassExpression
import org.semanticweb.owlapi.model.parameters.Imports

import scala.jdk.CollectionConverters._

object ReadMeExamples {

val factory = OWLManager.getOWLDataFactory
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14 changes: 4 additions & 10 deletions src/main/scala/org/phenoscape/scowl/ofn/AnnotationAxioms.scala
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package org.phenoscape.scowl.ofn

import scala.collection.JavaConverters._
import org.phenoscape.scowl.converters.Annotatable
import org.phenoscape.scowl.converters.AnnotationValuer
import org.semanticweb.owlapi.model.OWLAnnotation
import org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom
import org.semanticweb.owlapi.model.OWLAnnotationProperty
import org.semanticweb.owlapi.model.OWLAnnotationSubject
import org.semanticweb.owlapi.model.OWLAnnotationValue
import org.semanticweb.owlapi.model.OWLDeclarationAxiom
import org.semanticweb.owlapi.model.OWLEntity
import org.phenoscape.scowl.converters.{Annotatable, AnnotationValuer}
import org.semanticweb.owlapi.apibinding.OWLManager
import org.semanticweb.owlapi.model._

import scala.jdk.CollectionConverters._

trait AnnotationAxioms {

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16 changes: 3 additions & 13 deletions src/main/scala/org/phenoscape/scowl/ofn/ClassAxioms.scala
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package org.phenoscape.scowl.ofn

import scala.collection.JavaConverters._
import org.semanticweb.owlapi.model.OWLAnnotation
import org.semanticweb.owlapi.model.OWLClass
import org.semanticweb.owlapi.model.OWLClassExpression
import org.semanticweb.owlapi.model.OWLDataPropertyExpression
import org.semanticweb.owlapi.model.OWLDisjointClassesAxiom
import org.semanticweb.owlapi.model.OWLDisjointUnionAxiom
import org.semanticweb.owlapi.model.OWLEquivalentClassesAxiom
import org.semanticweb.owlapi.model.OWLHasKeyAxiom
import org.semanticweb.owlapi.model.OWLNaryClassAxiom
import org.semanticweb.owlapi.model.OWLObjectPropertyExpression
import org.semanticweb.owlapi.model.OWLPropertyExpression
import org.semanticweb.owlapi.model.OWLSubClassOfAxiom
import org.semanticweb.owlapi.apibinding.OWLManager
import org.semanticweb.owlapi.model._

import scala.jdk.CollectionConverters._

trait ClassAxioms {

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19 changes: 4 additions & 15 deletions src/main/scala/org/phenoscape/scowl/ofn/DataExpressions.scala
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package org.phenoscape.scowl.ofn

import scala.collection.JavaConverters._
import org.semanticweb.owlapi.model.OWLDataOneOf
import org.semanticweb.owlapi.model.OWLDatatype
import org.semanticweb.owlapi.model.OWLLiteral
import org.semanticweb.owlapi.model.OWLDataRange
import org.semanticweb.owlapi.model.OWLAnnotation
import org.semanticweb.owlapi.model.OWLDatatypeDefinitionAxiom
import org.semanticweb.owlapi.model.OWLFacetRestriction
import org.semanticweb.owlapi.model.OWLDatatypeRestriction
import org.semanticweb.owlapi.vocab.OWLFacet
import org.semanticweb.owlapi.model.OWLDataIntersectionOf
import org.semanticweb.owlapi.model.OWLDataComplementOf
import org.semanticweb.owlapi.model.OWLDataSomeValuesFrom
import org.semanticweb.owlapi.model.OWLDataPropertyExpression
import org.semanticweb.owlapi.model.OWLDataAllValuesFrom
import org.phenoscape.scowl.converters.Literalable
import org.semanticweb.owlapi.apibinding.OWLManager
import org.semanticweb.owlapi.model._
import org.semanticweb.owlapi.vocab.OWLFacet

import scala.jdk.CollectionConverters._

trait DataExpressions {

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15 changes: 3 additions & 12 deletions src/main/scala/org/phenoscape/scowl/ofn/Entities.scala
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package org.phenoscape.scowl.ofn

import org.semanticweb.owlapi.apibinding.OWLManager
import org.semanticweb.owlapi.model.OWLNamedObject
import org.semanticweb.owlapi.model.OWLAnonymousIndividual
import org.semanticweb.owlapi.model.OWLAnnotationProperty
import org.semanticweb.owlapi.model.IRI
import org.semanticweb.owlapi.model.OWLDataProperty
import org.semanticweb.owlapi.model.OWLNamedIndividual
import org.semanticweb.owlapi.model.OWLObjectProperty
import org.semanticweb.owlapi.model.OWLOntology
import org.semanticweb.owlapi.model.OWLClass
import org.semanticweb.owlapi.model.OWLAxiom
import scala.collection.JavaConverters._
import org.semanticweb.owlapi.model.OWLDatatype
import org.semanticweb.owlapi.model._

import scala.jdk.CollectionConverters._

trait Entities {

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19 changes: 3 additions & 16 deletions src/main/scala/org/phenoscape/scowl/ofn/IndividualAxioms.scala
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package org.phenoscape.scowl.ofn

import scala.collection.JavaConverters._
import org.phenoscape.scowl.converters.Literalable
import org.semanticweb.owlapi.model.OWLAnnotation
import org.semanticweb.owlapi.model.OWLClassAssertionAxiom
import org.semanticweb.owlapi.model.OWLClassExpression
import org.semanticweb.owlapi.model.OWLDataPropertyAssertionAxiom
import org.semanticweb.owlapi.model.OWLDataPropertyExpression
import org.semanticweb.owlapi.model.OWLDifferentIndividualsAxiom
import org.semanticweb.owlapi.model.OWLIndividual
import org.semanticweb.owlapi.model.OWLLiteral
import org.semanticweb.owlapi.model.OWLNaryIndividualAxiom
import org.semanticweb.owlapi.model.OWLNegativeDataPropertyAssertionAxiom
import org.semanticweb.owlapi.model.OWLNegativeObjectPropertyAssertionAxiom
import org.semanticweb.owlapi.model.OWLObjectPropertyAssertionAxiom
import org.semanticweb.owlapi.model.OWLObjectPropertyExpression
import org.semanticweb.owlapi.model.OWLPropertyAssertionAxiom
import org.semanticweb.owlapi.model.OWLSameIndividualAxiom
import org.semanticweb.owlapi.apibinding.OWLManager
import org.semanticweb.owlapi.model._

import scala.jdk.CollectionConverters._

trait IndividualAxioms {

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19 changes: 3 additions & 16 deletions src/main/scala/org/phenoscape/scowl/ofn/ObjectExpressions.scala
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package org.phenoscape.scowl.ofn

import scala.collection.JavaConverters._
import org.phenoscape.scowl.Vocab
import org.semanticweb.owlapi.model.OWLClassExpression
import org.semanticweb.owlapi.model.OWLIndividual
import org.semanticweb.owlapi.model.OWLObjectAllValuesFrom
import org.semanticweb.owlapi.model.OWLObjectComplementOf
import org.semanticweb.owlapi.model.OWLObjectExactCardinality
import org.semanticweb.owlapi.model.OWLObjectHasSelf
import org.semanticweb.owlapi.model.OWLObjectHasValue
import org.semanticweb.owlapi.model.OWLObjectIntersectionOf
import org.semanticweb.owlapi.model.OWLObjectMaxCardinality
import org.semanticweb.owlapi.model.OWLObjectMinCardinality
import org.semanticweb.owlapi.model.OWLObjectOneOf
import org.semanticweb.owlapi.model.OWLObjectPropertyExpression
import org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom
import org.semanticweb.owlapi.model.OWLObjectUnionOf
import org.semanticweb.owlapi.model.OWLObjectInverseOf
import org.semanticweb.owlapi.apibinding.OWLManager
import org.semanticweb.owlapi.model._

import scala.jdk.CollectionConverters._

trait ObjectExpressions extends Vocab {

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32 changes: 3 additions & 29 deletions src/main/scala/org/phenoscape/scowl/ofn/PropertyAxioms.scala
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package org.phenoscape.scowl.ofn

import scala.collection.JavaConverters._

import org.semanticweb.owlapi.apibinding.OWLManager
import org.semanticweb.owlapi.model.OWLAnnotation
import org.semanticweb.owlapi.model.OWLAsymmetricObjectPropertyAxiom
import org.semanticweb.owlapi.model.OWLClassExpression
import org.semanticweb.owlapi.model.OWLDataPropertyDomainAxiom
import org.semanticweb.owlapi.model.OWLDataPropertyExpression
import org.semanticweb.owlapi.model.OWLDataPropertyRangeAxiom
import org.semanticweb.owlapi.model.OWLDataRange
import org.semanticweb.owlapi.model.OWLDisjointDataPropertiesAxiom
import org.semanticweb.owlapi.model.OWLDisjointObjectPropertiesAxiom
import org.semanticweb.owlapi.model.OWLEquivalentDataPropertiesAxiom
import org.semanticweb.owlapi.model.OWLEquivalentObjectPropertiesAxiom
import org.semanticweb.owlapi.model.OWLFunctionalDataPropertyAxiom
import org.semanticweb.owlapi.model.OWLFunctionalObjectPropertyAxiom
import org.semanticweb.owlapi.model.OWLInverseFunctionalObjectPropertyAxiom
import org.semanticweb.owlapi.model.OWLInverseObjectPropertiesAxiom
import org.semanticweb.owlapi.model.OWLIrreflexiveObjectPropertyAxiom
import org.semanticweb.owlapi.model.OWLObjectPropertyDomainAxiom
import org.semanticweb.owlapi.model.OWLObjectPropertyExpression
import org.semanticweb.owlapi.model.OWLObjectPropertyRangeAxiom
import org.semanticweb.owlapi.model.OWLPropertyExpression
import org.semanticweb.owlapi.model.OWLReflexiveObjectPropertyAxiom
import org.semanticweb.owlapi.model.OWLSubDataPropertyOfAxiom
import org.semanticweb.owlapi.model.OWLSubObjectPropertyOfAxiom
import org.semanticweb.owlapi.model.OWLSubPropertyChainOfAxiom
import org.semanticweb.owlapi.model.OWLSymmetricObjectPropertyAxiom
import org.semanticweb.owlapi.model.OWLTransitiveObjectPropertyAxiom
import org.semanticweb.owlapi.model.OWLUnaryPropertyAxiom
import org.semanticweb.owlapi.model._

import scala.jdk.CollectionConverters._

trait PropertyAxioms {

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28 changes: 4 additions & 24 deletions src/main/scala/org/phenoscape/scowl/ofn/SWRL.scala
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package org.phenoscape.scowl.ofn

import scala.collection.JavaConverters._
import org.phenoscape.scowl.converters.SWRLArgs
import org.phenoscape.scowl.converters.SWRLDArgish
import org.phenoscape.scowl.converters.SWRLIArgish
import org.phenoscape.scowl.converters.{SWRLArgs, SWRLDArgish, SWRLIArgish}
import org.semanticweb.owlapi.apibinding.OWLManager
import org.semanticweb.owlapi.model.IRI
import org.semanticweb.owlapi.model.OWLAnnotation
import org.semanticweb.owlapi.model.OWLClassExpression
import org.semanticweb.owlapi.model.OWLDataRange
import org.semanticweb.owlapi.model.OWLObjectPropertyExpression
import org.semanticweb.owlapi.model.SWRLAtom
import org.semanticweb.owlapi.model.SWRLClassAtom
import org.semanticweb.owlapi.model.SWRLDArgument
import org.semanticweb.owlapi.model.SWRLDataRangeAtom
import org.semanticweb.owlapi.model.SWRLIArgument
import org.semanticweb.owlapi.model.SWRLObjectPropertyAtom
import org.semanticweb.owlapi.model.SWRLRule
import org.semanticweb.owlapi.model.SWRLVariable
import org.semanticweb.owlapi.model.OWLDataPropertyExpression
import org.semanticweb.owlapi.model.SWRLDataPropertyAtom
import org.phenoscape.scowl.converters.SWRLDArgish
import org.semanticweb.owlapi.model.SWRLBuiltInAtom
import org.phenoscape.scowl.converters.SWRLIArgish
import org.semanticweb.owlapi.model.SWRLSameIndividualAtom
import org.semanticweb.owlapi.model.SWRLDifferentIndividualsAtom
import org.semanticweb.owlapi.model._

import scala.jdk.CollectionConverters._

trait SWRL {

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16 changes: 3 additions & 13 deletions src/main/scala/org/phenoscape/scowl/omn/ClassExpressions.scala
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package org.phenoscape.scowl.omn

import scala.collection.JavaConverters._
import org.phenoscape.scowl.converters.Literalable
import org.semanticweb.owlapi.model.OWLClassExpression
import org.semanticweb.owlapi.model.OWLDataComplementOf
import org.semanticweb.owlapi.model.OWLDataOneOf
import org.semanticweb.owlapi.model.OWLDataPropertyExpression
import org.semanticweb.owlapi.model.OWLDataRange
import org.semanticweb.owlapi.model.OWLIndividual
import org.semanticweb.owlapi.model.OWLLiteral
import org.semanticweb.owlapi.model.OWLNamedIndividual
import org.semanticweb.owlapi.model.OWLObjectComplementOf
import org.semanticweb.owlapi.model.OWLObjectInverseOf
import org.semanticweb.owlapi.model.OWLObjectOneOf
import org.semanticweb.owlapi.model.OWLObjectPropertyExpression
import org.semanticweb.owlapi.apibinding.OWLManager
import org.semanticweb.owlapi.model._

import scala.jdk.CollectionConverters._

trait ClassExpressions {

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2 changes: 1 addition & 1 deletion src/main/scala/org/phenoscape/scowl/omn/Facets.scala
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package org.phenoscape.scowl.omn

import org.phenoscape.scowl.converters.Literalable
import org.semanticweb.owlapi.vocab.OWLFacet
import org.semanticweb.owlapi.apibinding.OWLManager
import org.semanticweb.owlapi.vocab.OWLFacet

trait Facets {

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18 changes: 1 addition & 17 deletions src/main/scala/org/phenoscape/scowl/omn/PropertyCharacteristics.scala
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package org.phenoscape.scowl.omn

import org.semanticweb.owlapi.model.OWLAsymmetricObjectPropertyAxiom
import org.semanticweb.owlapi.model.OWLClassExpression
import org.semanticweb.owlapi.model.OWLFunctionalObjectPropertyAxiom
import org.semanticweb.owlapi.model.OWLInverseFunctionalObjectPropertyAxiom
import org.semanticweb.owlapi.model.OWLIrreflexiveObjectPropertyAxiom
import org.semanticweb.owlapi.model.OWLObjectPropertyCharacteristicAxiom
import org.semanticweb.owlapi.model.OWLObjectPropertyExpression
import org.semanticweb.owlapi.model.OWLPropertyAxiom
import org.semanticweb.owlapi.model.OWLPropertyExpression
import org.semanticweb.owlapi.model.OWLPropertyRange
import org.semanticweb.owlapi.model.OWLReflexiveObjectPropertyAxiom
import org.semanticweb.owlapi.model.OWLSymmetricObjectPropertyAxiom
import org.semanticweb.owlapi.model.OWLTransitiveObjectPropertyAxiom
import org.semanticweb.owlapi.model.OWLProperty
import org.semanticweb.owlapi.model.OWLFunctionalDataPropertyAxiom
import org.semanticweb.owlapi.model.OWLDataPropertyCharacteristicAxiom
import org.semanticweb.owlapi.model.OWLDataPropertyExpression
import org.semanticweb.owlapi.apibinding.OWLManager
import org.semanticweb.owlapi.model._

sealed trait PropertyCharacteristic[T <: OWLObjectPropertyCharacteristicAxiom, U <: OWLDataPropertyCharacteristicAxiom] {

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14 changes: 5 additions & 9 deletions src/main/scala/org/phenoscape/scowl/omn/SWRLAtoms.scala
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package org.phenoscape.scowl.omn

import scala.collection.JavaConverters._
import org.phenoscape.scowl.converters.SWRLDArgish
import org.phenoscape.scowl.converters.SWRLIArgish
import org.phenoscape.scowl.converters.{SWRLDArgish, SWRLIArgish}
import org.semanticweb.owlapi.apibinding.OWLManager
import org.semanticweb.owlapi.model.IRI
import org.semanticweb.owlapi.model.SWRLBuiltInAtom
import org.semanticweb.owlapi.model.SWRLDifferentIndividualsAtom
import org.semanticweb.owlapi.model.SWRLSameIndividualAtom
import org.semanticweb.owlapi.vocab.SWRLVocabulary
import org.semanticweb.owlapi.vocab.SWRLBuiltInsVocabulary
import org.semanticweb.owlapi.model.{IRI, SWRLBuiltInAtom, SWRLDifferentIndividualsAtom, SWRLSameIndividualAtom}
import org.semanticweb.owlapi.vocab.{SWRLBuiltInsVocabulary, SWRLVocabulary}

import scala.jdk.CollectionConverters._

trait SWRLAtoms {

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4 changes: 1 addition & 3 deletions src/main/scala/org/phenoscape/scowl/omn/ScowlNegativeDataPropertyValue.scala
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package org.phenoscape.scowl.omn

import org.phenoscape.scowl.converters.Literalable

import org.semanticweb.owlapi.model.OWLDataPropertyExpression
import org.semanticweb.owlapi.model.OWLLiteral
import org.semanticweb.owlapi.model.{OWLDataPropertyExpression, OWLLiteral}

case class ScowlNegativeDataPropertyValue[T: Literalable](property: OWLDataPropertyExpression, value: T) {

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3 changes: 1 addition & 2 deletions src/main/scala/org/phenoscape/scowl/omn/ScowlNegativeObjectPropertyValue.scala
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package org.phenoscape.scowl.omn

import org.semanticweb.owlapi.model.OWLObjectPropertyExpression
import org.semanticweb.owlapi.model.OWLIndividual
import org.semanticweb.owlapi.model.{OWLIndividual, OWLObjectPropertyExpression}

case class ScowlNegativeObjectPropertyValue(property: OWLObjectPropertyExpression, value: OWLIndividual)
6 changes: 3 additions & 3 deletions src/main/scala/org/phenoscape/scowl/omn/ScowlSWRLConjunction.scala
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package org.phenoscape.scowl.omn

import org.semanticweb.owlapi.model.SWRLAtom
import org.semanticweb.owlapi.model.SWRLRule
import org.semanticweb.owlapi.apibinding.OWLManager
import scala.collection.JavaConverters._
import org.semanticweb.owlapi.model.{SWRLAtom, SWRLRule}

import scala.jdk.CollectionConverters._

case class ScowlSWRLConjunction(atoms: Set[SWRLAtom]) {

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16 changes: 5 additions & 11 deletions src/main/scala/org/phenoscape/scowl/package.scala
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package org.phenoscape

import scala.collection.JavaConverters._
import org.phenoscape.scowl.converters.AnnotationValuer
import org.phenoscape.scowl.converters.Literalable
import org.phenoscape.scowl.converters.SWRLDArgish
import org.phenoscape.scowl.converters.SWRLIArgish
import org.phenoscape.scowl.omn.PropertyCharacteristic
import org.phenoscape.scowl.omn.ScowlNegativeDataPropertyValue
import org.phenoscape.scowl.omn.ScowlNegativeObjectPropertyValue
import org.phenoscape.scowl.omn.ScowlPropertyChain
import org.phenoscape.scowl.omn.ScowlSWRLConjunction
import org.phenoscape.scowl.converters.{AnnotationValuer, Literalable, SWRLDArgish, SWRLIArgish}
import org.phenoscape.scowl.omn._
import org.semanticweb.owlapi.apibinding.OWLManager
import org.semanticweb.owlapi.model.{IRI, OWLAnnotation, OWLAnnotationAssertionAxiom, OWLAnnotationProperty, OWLAnnotationSubject, OWLAnnotationValue, OWLAxiom, OWLClassAssertionAxiom, OWLClassExpression, OWLDataAllValuesFrom, OWLDataExactCardinality, OWLDataHasValue, OWLDataIntersectionOf, OWLDataMaxCardinality, OWLDataMinCardinality, OWLDataOneOf, OWLDataPropertyAssertionAxiom, OWLDataPropertyCharacteristicAxiom, OWLDataPropertyDomainAxiom, OWLDataPropertyExpression, OWLDataPropertyRangeAxiom, OWLDataRange, OWLDataSomeValuesFrom, OWLDataUnionOf, OWLDatatype, OWLDatatypeDefinitionAxiom, OWLDatatypeRestriction, OWLDifferentIndividualsAxiom, OWLDisjointClassesAxiom, OWLDisjointDataPropertiesAxiom, OWLDisjointObjectPropertiesAxiom, OWLEquivalentClassesAxiom, OWLEquivalentDataPropertiesAxiom, OWLEquivalentObjectPropertiesAxiom, OWLFacetRestriction, OWLHasKeyAxiom, OWLIndividual, OWLInverseObjectPropertiesAxiom, OWLLiteral, OWLNamedObject, OWLNegativeDataPropertyAssertionAxiom, OWLNegativeObjectPropertyAssertionAxiom, OWLObjectAllValuesFrom, OWLObjectExactCardinality, OWLObjectHasSelf, OWLObjectHasValue, OWLObjectIntersectionOf, OWLObjectMaxCardinality, OWLObjectMinCardinality, OWLObjectOneOf, OWLObjectPropertyAssertionAxiom, OWLObjectPropertyCharacteristicAxiom, OWLObjectPropertyDomainAxiom, OWLObjectPropertyExpression, OWLObjectPropertyRangeAxiom, OWLObjectSomeValuesFrom, OWLObjectUnionOf, OWLPropertyExpression, OWLSameIndividualAxiom, OWLSubClassOfAxiom, OWLSubDataPropertyOfAxiom, OWLSubObjectPropertyOfAxiom, OWLSubPropertyChainOfAxiom, SWRLAtom, SWRLClassAtom, SWRLDataPropertyAtom, SWRLDataRangeAtom, SWRLObjectPropertyAtom, SWRLRule, SWRLVariable}
import org.semanticweb.owlapi.model._

import scala.jdk.CollectionConverters._

package object scowl extends Vocab
with ofn.Entities
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1 change: 1 addition & 0 deletions src/test/scala/org/phenoscape/scowl/example/AnatomyOntology.scala
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Expand Up @@ -3,6 +3,7 @@ package org.phenoscape.scowl.example
import org.phenoscape.scowl._
import org.semanticweb.owlapi.apibinding.OWLManager
import org.semanticweb.owlapi.model.IRI

import java.io.File

object AnatomyOntology extends App {
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