Reorganize project with Java-like folder structure

16 files changed, 43 insertions, 35 deletions

diff --git a/src/main/scala/rsacomb/CanonicalModel.scala b/src/main/scala/uk/ac/ox/cs/rsacomb/CanonicalModel.scala
index d9e1641..f0f1bf8 100644
--- a/src/main/scala/rsacomb/CanonicalModel.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/CanonicalModel.scala
@@ -1,4 +1,4 @@
-package rsacomb
+package uk.ac.ox.cs.rsacomb
 
 import org.semanticweb.owlapi.model.{OWLObjectInverseOf, OWLObjectProperty}
 import org.semanticweb.owlapi.model.{
@@ -23,8 +23,14 @@ import tech.oxfordsemantic.jrdfox.logic.expression.{
   IRI
 }
 
-import suffix.{Empty, Forward, Backward, Inverse}
-import util.RSA
+import uk.ac.ox.cs.rsacomb.converter.{
+  SkolemStrategy,
+  RDFoxAxiomConverter,
+  RDFoxPropertyExprConverter
+}
+import uk.ac.ox.cs.rsacomb.implicits.RSAAxiom
+import uk.ac.ox.cs.rsacomb.suffix.{Empty, Forward, Backward, Inverse}
+import uk.ac.ox.cs.rsacomb.util.RSA
 
 class CanonicalModel(val ontology: RSAOntology) extends RSAAxiom {
 
diff --git a/src/main/scala/rsacomb/FilteringProgram.scala b/src/main/scala/uk/ac/ox/cs/rsacomb/FilteringProgram.scala
index c82dcb6..b154575 100644
--- a/src/main/scala/rsacomb/FilteringProgram.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/FilteringProgram.scala
@@ -1,4 +1,4 @@
-package rsacomb
+package uk.ac.ox.cs.rsacomb
 
 import tech.oxfordsemantic.jrdfox.logic.Datatype
 import tech.oxfordsemantic.jrdfox.logic.expression.{
@@ -27,9 +27,9 @@ import tech.oxfordsemantic.jrdfox.logic.sparql.pattern.{
 
 import scala.collection.JavaConverters._
 
-import implicits.RSAAtom
-import suffix.{RSASuffix, Forward, Backward}
-import util.RSA
+import uk.ac.ox.cs.rsacomb.implicits.RSAAtom
+import uk.ac.ox.cs.rsacomb.suffix.{RSASuffix, Forward, Backward}
+import uk.ac.ox.cs.rsacomb.util.RSA
 
 class FilteringProgram(query: SelectQuery, constants: List[Term])
     extends RSAAtom {
diff --git a/src/main/scala/rsacomb/Main.scala b/src/main/scala/uk/ac/ox/cs/rsacomb/Main.scala
index 31dd5a0..c3db99d 100644
--- a/src/main/scala/rsacomb/Main.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/Main.scala
@@ -1,4 +1,4 @@
-package rsacomb
+package uk.ac.ox.cs.rsacomb
 
 /* Java imports */
 import java.io.File
diff --git a/src/main/scala/rsacomb/RSAOntology.scala b/src/main/scala/uk/ac/ox/cs/rsacomb/RSAOntology.scala
index 53bc560..ac86e3d 100644
--- a/src/main/scala/rsacomb/RSAOntology.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/RSAOntology.scala
@@ -1,4 +1,4 @@
-package rsacomb
+package uk.ac.ox.cs.rsacomb
 
 /* Java imports */
 import java.util.HashMap
@@ -46,8 +46,10 @@ import org.semanticweb.owlapi.dlsyntax.renderer.DLSyntaxObjectRenderer
 import tech.oxfordsemantic.jrdfox.logic._
 import org.semanticweb.owlapi.model.OWLObjectInverseOf
 
-import suffix.{Empty, Forward, Backward, Inverse}
-import util.{RDFoxHelpers, RSA}
+import uk.ac.ox.cs.rsacomb.converter.{RDFoxAxiomConverter, SkolemStrategy}
+import uk.ac.ox.cs.rsacomb.implicits.RSAAxiom
+import uk.ac.ox.cs.rsacomb.suffix.{Empty, Forward, Backward, Inverse}
+import uk.ac.ox.cs.rsacomb.util.{RDFoxHelpers, RSA}
 
 object RSAOntology {
 
diff --git a/src/main/scala/rsacomb/RDFoxAxiomConverter.scala b/src/main/scala/uk/ac/ox/cs/rsacomb/converter/RDFoxAxiomConverter.scala
index 9b78e8e..a8d1ffd 100644
--- a/src/main/scala/rsacomb/RDFoxAxiomConverter.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/converter/RDFoxAxiomConverter.scala
@@ -1,4 +1,4 @@
-package rsacomb
+package uk.ac.ox.cs.rsacomb.converter
 
 import org.semanticweb.owlapi.model.{
   OWLAxiom,
@@ -23,13 +23,12 @@ import tech.oxfordsemantic.jrdfox.logic.expression.{
 
 import scala.collection.JavaConverters._
 
-import rsacomb.SkolemStrategy
-import rsacomb.RDFoxRuleShards
 import org.semanticweb.owlapi.model.OWLSubObjectPropertyOfAxiom
 import org.semanticweb.owlapi.model.OWLObjectProperty
 import org.semanticweb.owlapi.model.OWLClassAssertionAxiom
 
-import suffix.{RSASuffix, Empty}
+import uk.ac.ox.cs.rsacomb.RSAOntology
+import uk.ac.ox.cs.rsacomb.suffix.{RSASuffix, Empty}
 
 object RDFoxAxiomConverter {
 
diff --git a/src/main/scala/rsacomb/RDFoxClassExprConverter.scala b/src/main/scala/uk/ac/ox/cs/rsacomb/converter/RDFoxClassExprConverter.scala
index f4187ed..c151c9a 100644
--- a/src/main/scala/rsacomb/RDFoxClassExprConverter.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/converter/RDFoxClassExprConverter.scala
@@ -1,4 +1,4 @@
-package rsacomb
+package uk.ac.ox.cs.rsacomb.converter
 
 import scala.collection.JavaConverters._
 import java.util.stream.{Stream, Collectors}
@@ -29,8 +29,9 @@ import tech.oxfordsemantic.jrdfox.logic.expression.{
 import org.semanticweb.owlapi.model.OWLObjectPropertyExpression
 import org.semanticweb.owlapi.model.OWLObjectProperty
 
-import suffix.{RSASuffix, Empty}
-import util.RSA
+import uk.ac.ox.cs.rsacomb.RSAOntology
+import uk.ac.ox.cs.rsacomb.suffix.{RSASuffix, Empty}
+import uk.ac.ox.cs.rsacomb.util.RSA
 
 object RDFoxClassExprConverter {
 
@@ -60,7 +61,7 @@ class RDFoxClassExprConverter(
     suffix: RSASuffix
 ) extends OWLClassExpressionVisitorEx[RDFoxRuleShards] {
 
-  import implicits.RDFox._
+  import uk.ac.ox.cs.rsacomb.implicits.RDFox._
 
   // OWLClass
   override def visit(expr: OWLClass): RDFoxRuleShards = {
diff --git a/src/main/scala/rsacomb/RDFoxPropertyExprConverter.scala b/src/main/scala/uk/ac/ox/cs/rsacomb/converter/RDFoxPropertyExprConverter.scala
index 826e965..94c7887 100644
--- a/src/main/scala/rsacomb/RDFoxPropertyExprConverter.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/converter/RDFoxPropertyExprConverter.scala
@@ -1,4 +1,4 @@
-package rsacomb
+package uk.ac.ox.cs.rsacomb.converter
 
 import org.semanticweb.owlapi.model.{OWLPropertyExpression, OWLObjectProperty}
 import org.semanticweb.owlapi.model.OWLPropertyExpressionVisitorEx
@@ -8,7 +8,7 @@ import tech.oxfordsemantic.jrdfox.logic.expression.{Term, IRI, Literal}
 
 import org.semanticweb.owlapi.model.OWLObjectInverseOf
 
-import suffix.{RSASuffix, Inverse}
+import uk.ac.ox.cs.rsacomb.suffix.{RSASuffix, Inverse}
 
 class RDFoxPropertyExprConverter(
     term1: Term,
@@ -17,7 +17,7 @@ class RDFoxPropertyExprConverter(
 ) extends OWLPropertyExpressionVisitorEx[List[TupleTableAtom]] {
 
   // Automatically converts OWLAPI types into RDFox equivalent types.
-  import implicits.RDFox._
+  import uk.ac.ox.cs.rsacomb.implicits.RDFox._
 
   override def visit(expr: OWLObjectProperty): List[TupleTableAtom] = {
     val base = expr.getIRI.getIRIString
diff --git a/src/main/scala/rsacomb/RDFoxRuleShards.scala b/src/main/scala/uk/ac/ox/cs/rsacomb/converter/RDFoxRuleShards.scala
index b61cc38..c88cf3c 100644
--- a/src/main/scala/rsacomb/RDFoxRuleShards.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/converter/RDFoxRuleShards.scala
@@ -1,4 +1,4 @@
-package rsacomb
+package uk.ac.ox.cs.rsacomb.converter
 
 import tech.oxfordsemantic.jrdfox.logic.datalog.{TupleTableAtom, BodyFormula}
 
diff --git a/src/main/scala/rsacomb/SkolemStrategy.scala b/src/main/scala/uk/ac/ox/cs/rsacomb/converter/SkolemStrategy.scala
index a2ad0a1..0d72226 100644
--- a/src/main/scala/rsacomb/SkolemStrategy.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/converter/SkolemStrategy.scala
@@ -1,4 +1,4 @@
-package rsacomb
+package uk.ac.ox.cs.rsacomb.converter
 
 import tech.oxfordsemantic.jrdfox.logic.Datatype
 import tech.oxfordsemantic.jrdfox.logic.expression.{Literal, IRI}
diff --git a/src/main/scala/rsacomb/implicits/JavaCollections.scala b/src/main/scala/uk/ac/ox/cs/rsacomb/implicits/JavaCollections.scala
index 69e825b..3b621f4 100644
--- a/src/main/scala/rsacomb/implicits/JavaCollections.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/implicits/JavaCollections.scala
@@ -1,4 +1,4 @@
-package rsacomb.implicits
+package uk.ac.ox.cs.rsacomb.implicits
 
 import scala.collection.JavaConverters._
 
diff --git a/src/main/scala/rsacomb/implicits/RDFox.scala b/src/main/scala/uk/ac/ox/cs/rsacomb/implicits/RDFox.scala
index 44b7c01..0462a47 100644
--- a/src/main/scala/rsacomb/implicits/RDFox.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/implicits/RDFox.scala
@@ -1,4 +1,4 @@
-package rsacomb.implicits
+package uk.ac.ox.cs.rsacomb.implicits
 
 import tech.oxfordsemantic.jrdfox.logic.expression.{IRI => RDFoxIRI}
 import org.semanticweb.owlapi.model.{IRI => OWLIRI}
diff --git a/src/main/scala/rsacomb/RSAAtom.scala b/src/main/scala/uk/ac/ox/cs/rsacomb/implicits/RSAAtom.scala
index 8832226..a8afc72 100644
--- a/src/main/scala/rsacomb/RSAAtom.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/implicits/RSAAtom.scala
@@ -1,4 +1,4 @@
-package rsacomb.implicits
+package uk.ac.ox.cs.rsacomb.implicits
 
 import tech.oxfordsemantic.jrdfox.logic.Datatype
 import tech.oxfordsemantic.jrdfox.logic.expression.{Literal, FunctionCall}
@@ -10,8 +10,8 @@ import tech.oxfordsemantic.jrdfox.logic.datalog.{
 import tech.oxfordsemantic.jrdfox.logic.expression.{IRI}
 import scala.collection.JavaConverters._
 
-import rsacomb.suffix.{RSASuffix, Nth}
-import rsacomb.RSAOntology
+import uk.ac.ox.cs.rsacomb.suffix.{RSASuffix, Nth}
+import uk.ac.ox.cs.rsacomb.RSAOntology
 
 /* Is this the best way to determine if an atom is an RDF triple?
  * Note that we can't use `getNumberOfArguments()` because is not
diff --git a/src/main/scala/rsacomb/RSAAxiom.scala b/src/main/scala/uk/ac/ox/cs/rsacomb/implicits/RSAAxiom.scala
index 08de5b7..e39d5b2 100644
--- a/src/main/scala/rsacomb/RSAAxiom.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/implicits/RSAAxiom.scala
@@ -1,4 +1,4 @@
-package rsacomb
+package uk.ac.ox.cs.rsacomb.implicits
 
 /* Java imports */
 import org.semanticweb.owlapi.model.{
diff --git a/src/main/scala/rsacomb/RSASuffix.scala b/src/main/scala/uk/ac/ox/cs/rsacomb/suffix/RSASuffix.scala
index ce36b10..b22910b 100644
--- a/src/main/scala/rsacomb/RSASuffix.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/suffix/RSASuffix.scala
@@ -1,4 +1,4 @@
-package rsacomb.suffix
+package uk.ac.ox.cs.rsacomb.suffix
 
 import org.semanticweb.owlapi.model.{
   OWLPropertyExpression,
diff --git a/src/main/scala/rsacomb/util/RDFoxHelpers.scala b/src/main/scala/uk/ac/ox/cs/rsacomb/util/RDFoxHelpers.scala
index 9856e27..fd9e1c5 100644
--- a/src/main/scala/rsacomb/util/RDFoxHelpers.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/util/RDFoxHelpers.scala
@@ -1,4 +1,4 @@
-package rsacomb.util
+package uk.ac.ox.cs.rsacomb.util
 
 import java.util.{Map => JMap, HashMap => JHashMap}
 import java.io.StringReader
@@ -12,7 +12,7 @@ import tech.oxfordsemantic.jrdfox.formats.SPARQLParser
 import tech.oxfordsemantic.jrdfox.logic.expression.Resource
 import tech.oxfordsemantic.jrdfox.logic.sparql.statement.SelectQuery
 
-import rsacomb.suffix.Nth
+import uk.ac.ox.cs.rsacomb.suffix.Nth
 
 object RDFoxHelpers {
 
diff --git a/src/main/scala/rsacomb/RSA.scala b/src/main/scala/uk/ac/ox/cs/rsacomb/util/RSA.scala
index ab4f539..f9ff59b 100644
--- a/src/main/scala/rsacomb/RSA.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/util/RSA.scala
@@ -1,4 +1,4 @@
-package rsacomb.util
+package uk.ac.ox.cs.rsacomb.util
 
 /* Java imports */
 import java.util.Map
@@ -18,7 +18,7 @@ import org.semanticweb.owlapi.model.{
   OWLObjectPropertyExpression
 }
 
-import rsacomb.suffix.RSASuffix
+import uk.ac.ox.cs.rsacomb.suffix.RSASuffix
 
 // Debug only
 import scala.collection.JavaConverters._