ont-api: rename OntGraphModel -> OntModel (issue #4) + minor changes in javadocs

Author: sszuev

src/main/java/com/github/owlcs/ontapi/BaseModel.java

@@ -19,13 +19,14 @@
 import com.github.owlcs.ontapi.internal.InternalModel;
 import com.github.owlcs.ontapi.jena.impl.conf.OntModelConfig;
 import com.github.owlcs.ontapi.jena.impl.conf.OntPersonality;
+import com.github.owlcs.ontapi.jena.model.OntModel;
 import org.apache.jena.graph.Graph;
 import org.semanticweb.owlapi.model.OWLPrimitive;
 
 import java.util.Map;
 
 /**
- * A technical interface-helper that serves as a bridge between {@link com.github.owlcs.ontapi.jena.model.OntGraphModel Jena RDF model} and
+ * A technical interface-helper that serves as a bridge between {@link OntModel Jena RDF model} and
  * {@link org.semanticweb.owlapi.model.OWLOntology OWLAPI ontology} through the {@link InternalModel} on the one hand,
  * and between all these things and {@link org.semanticweb.owlapi.model.OWLOntologyManager OWLAPI manager}
  * through the {@link ModelConfig} on the other hand.

src/main/java/com/github/owlcs/ontapi/ID.java

@@ -68,7 +68,7 @@ public ID() {
     /**
      * Constructs an ontology identifier from the given {@link OntID Ontology Graph Model ID}.
      * The difference between these two IDs ( {@link OntID} and {@link ID this classs}) is
-     * that the former is used in the RDF representation (i.e. in {@link com.github.owlcs.ontapi.jena.model.OntGraphModel}),
+     * that the former is used in the RDF representation (i.e. in {@link com.github.owlcs.ontapi.jena.model.OntModel}),
      * while the other is in the axiomatic view (i.e. in {@link org.semanticweb.owlapi.model.OWLOntology}).
      *
      * @param id {@link OntID}, not {@code null}
@@ -88,8 +88,7 @@ public ID(OntID id) {
      *                               but we have not yet learned about it
      * @throws NullPointerException  if {@code id} is {@code null}
      */
-    protected ID(Node id, String version) throws OntApiException,
-            IllegalStateException, UnsupportedOperationException, NullPointerException {
+    protected ID(Node id, String version) throws OntApiException, IllegalStateException, NullPointerException {
         Optional<String> internalID;
         Optional<IRI> ontologyIRI, versionIRI;
         if (Objects.requireNonNull(id, "Null id node").isBlank()) {

src/main/java/com/github/owlcs/ontapi/OntBaseModelImpl.java

@@ -15,7 +15,7 @@
 package com.github.owlcs.ontapi;
 
 import com.github.owlcs.ontapi.internal.InternalModel;
-import com.github.owlcs.ontapi.jena.model.OntGraphModel;
+import com.github.owlcs.ontapi.jena.model.OntModel;
 import com.github.owlcs.ontapi.owlapi.OWLObjectImpl;
 import org.apache.jena.graph.Graph;
 import org.apache.jena.mem.GraphMem;
@@ -1107,8 +1107,8 @@ public boolean equals(@Nullable Object obj) {
         if (!(obj instanceof Ontology)) {
             return false;
         }
-        OntGraphModel right = ((Ontology) obj).asGraphModel();
-        OntGraphModel left = getBase();
+        OntModel right = ((Ontology) obj).asGraphModel();
+        OntModel left = getBase();
         return left.getID().sameAs(right.getID());
     }
 }

src/main/java/com/github/owlcs/ontapi/OntGraphUtils.java

@@ -16,7 +16,7 @@
 
 import com.github.owlcs.ontapi.config.OntLoaderConfiguration;
 import com.github.owlcs.ontapi.jena.impl.OntIDImpl;
-import com.github.owlcs.ontapi.jena.model.OntGraphModel;
+import com.github.owlcs.ontapi.jena.model.OntModel;
 import com.github.owlcs.ontapi.jena.utils.Graphs;
 import com.github.owlcs.ontapi.jena.utils.Models;
 import com.github.owlcs.ontapi.transforms.GraphTransformers;
@@ -63,7 +63,7 @@
  */
 @SuppressWarnings("WeakerAccess")
 public class OntGraphUtils {
-    private static final Logger LOGGER = LoggerFactory.getLogger(OntGraphModel.class);
+    private static final Logger LOGGER = LoggerFactory.getLogger(OntModel.class);
 
     // following constants are copy-pasted from org.semanticweb.owlapi.io.DocumentSource:
     public static final String TEXT_PLAIN_REQUEST_TYPE = ", text/plain; q=0.1";

src/main/java/com/github/owlcs/ontapi/OntManagers.java

@@ -65,7 +65,7 @@ public class OntManagers implements OWLOntologyManagerFactory {
      * derived from the {@link DataFactory OWL Data Factory}.
      * <p>
      * Alternative way to assembly ontology is direct working with the {@link org.apache.jena.graph.Graph Graph}
-     * through the {@link com.github.owlcs.ontapi.jena.model.OntGraphModel} view of the ontology,
+     * through the {@link com.github.owlcs.ontapi.jena.model.OntModel} view of the ontology,
      * that can be obtained using the method {@link Ontology#asGraphModel()}.
      * The first way of ontology editing is native for OWL-API,
      * the second way is native for Apache Jena and provided by ONT-API as a feature,

src/main/java/com/github/owlcs/ontapi/Ontology.java

@@ -15,16 +15,26 @@
 package com.github.owlcs.ontapi;
 
 import com.github.owlcs.ontapi.config.AxiomsSettings;
-import com.github.owlcs.ontapi.jena.model.OntGraphModel;
+import com.github.owlcs.ontapi.jena.model.OntModel;
 import org.semanticweb.owlapi.model.OWLOntology;
 
 /**
  * A Structural Ontological Model, that is an extended {@link OWLOntology OWL-API Ontology}.
  * It represents an <a href="http://www.w3.org/TR/owl2-syntax/#Ontologies">Ontology</a> in the OWL2 specification.
- * This interface provides a wide range of methods inherited from OWL-API
- * for working with structural (OWL Axioms and Annotations) representation of data
- * stored in the form of {@link org.apache.jena.graph.Graph RDF Graph}.
- * In addition to this range, there are also two new methods: {@link #asGraphModel()} and {@link #clearCache()}.
+ * <p>
+ * This interface provides access to a wide range of methods inherited from OWL-API
+ * to work with the structural representation of data
+ * (i.e. with OWL {@link org.semanticweb.owlapi.model.OWLAxiom Axiom}s
+ * and Ontology Header {@link org.semanticweb.owlapi.model.OWLAnnotation Annotation}s).
+ * Please note, in ONT-API all data is actually stored in the very {@link org.apache.jena.graph.Graph RDF Graph},
+ * and any {@link org.semanticweb.owlapi.model.OWLAxiom Axiom} returned by this interface
+ * is really just a special reading of the same {@link org.apache.jena.graph.Triple RDF Triple}s.
+ * To work directly with triples-view there is the method {@link #asGraphModel()}
+ * returning the {@link OntModel Ont[Graph]Model} view,
+ * that is a {@link org.apache.jena.rdf.model.Model Jena Model} for OWL2.
+ * Also, please note that although ONT-API supports the ability to change data simultaneously through both interfaces,
+ * this is not always correct: an {@link Ontology} impls use caches,
+ * and switching back and forth could flush these caches, which may degrade performance.
  * <p>
  * Created by szuev on 24.10.2016.
  */
@@ -33,7 +43,7 @@ public interface Ontology extends OWLOntology {
     /**
      * Returns the jena model shadow,
      * that is an interface to work with the {@link org.apache.jena.graph.Graph RDF Graph} directly.
-     * The {@code OntGraphModel} is backed by the {@code OntologyModel},
+     * The {@code OntModel} is backed by the {@code Ontology},
      * so changes to the graph model are reflected in the structural model, and vice-versa.
      * <p>
      * Note: synchronisation is performed via different caches and graphs listeners
@@ -46,10 +56,10 @@ public interface Ontology extends OWLOntology {
      * Also note: any changes in the RDF-view will reset the internal cache,
      * that means next attempt to retrieve data from axiomatic view (i.e. list axioms) will take the same time as the very first one.
      *
-     * @return {@link OntGraphModel Ontology RDF Graph Model}, not {@code null}
+     * @return {@link OntModel Ontology RDF Graph Model}, not {@code null}
      * @see org.apache.jena.graph.Graph
      */
-    OntGraphModel asGraphModel();
+    OntModel asGraphModel();
 
     /**
      * Clears the axioms and entities cache.
@@ -79,5 +89,4 @@ public interface Ontology extends OWLOntology {
      * @return {@link OntologyManager} the manager for this ontology
      */
     OntologyManager getOWLOntologyManager();
-
 }

src/main/java/com/github/owlcs/ontapi/OntologyCollectionImpl.java

@@ -14,9 +14,9 @@
 
 package com.github.owlcs.ontapi;
 
+import com.github.owlcs.ontapi.jena.utils.Iter;
 import org.semanticweb.owlapi.model.HasOntologyID;
 import org.semanticweb.owlapi.model.OWLOntologyID;
-import com.github.owlcs.ontapi.jena.utils.Iter;
 
 import java.io.Serializable;
 import java.util.*;
@@ -33,7 +33,7 @@
  * Currently it is not possible to use directly different {@code Map}s with {@link OWLOntologyID Ontology ID} as keys
  * like in the original OWL-API implementation,
  * since anything, including that ID, can be changed externally (e.g. directly from the jena graph
- * using shadow {@link com.github.owlcs.ontapi.jena.model.OntGraphModel} interface or something else).
+ * using shadow {@link com.github.owlcs.ontapi.jena.model.OntModel} interface or something else).
  * On the other hand, it is not expected that this collection will hold a large number of elements,
  * so using reordering operation in every method is OK.
  * <p>