Add OntologyStatement and remove unused classes

Author: arteymix

src/ubic/basecode/ontology/jena/AnnotationPropertyImpl.java

@@ -99,27 +99,28 @@ public boolean isObsolete() {
     @Override
     public boolean equals( @Nullable Object obj ) {
         if ( this == obj ) return true;
-        if ( obj == null ) return false;
-        if ( obj instanceof AnnotationPropertyImpl ) {
-            final AnnotationPropertyImpl other = ( AnnotationPropertyImpl ) obj;
+        if ( !( obj instanceof AnnotationProperty ) ) {
+            return false;
+        }
+        final AnnotationProperty other = ( AnnotationProperty ) obj;
+        if ( other instanceof AnnotationPropertyImpl ) {
             return super.equals( other )
-                && Objects.equals( object, other.object );
-        } else if ( obj instanceof AnnotationProperty ) {
-            final AnnotationProperty other = ( AnnotationProperty ) obj;
+                && Objects.equals( property, ( ( AnnotationPropertyImpl ) other ).property )
+                && Objects.equals( object, ( ( AnnotationPropertyImpl ) other ).object );
+        } else {
             return super.equals( other )
+                && Objects.equals( getProperty(), other.getProperty() )
                 && Objects.equals( getContents(), other.getContents() );
         }
-        return false;
     }
 
     @Override
     public int hashCode() {
-        return Objects.hash( super.hashCode(), object );
+        return Objects.hash( super.hashCode(), property, object );
     }
 
     @Override
     public String toString() {
         return property.getLocalName() + " " + object;
     }
-
 }

src/ubic/basecode/ontology/model/ChainedStatement.java

@@ -1,8 +1,8 @@
 /*
  * The basecode project
- * 
+ *
  * Copyright (c) 2007-2019 University of British Columbia
- * 
+ *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
@@ -18,16 +18,19 @@
  */
 package ubic.basecode.ontology.model;
 
+import javax.annotation.Nullable;
+
 /**
  * @author pavlidis
  */
 public interface OntologyIndividual extends OntologyResource {
 
     /**
      * Return the term that this is an instance of.
-     * 
+     *
      * @return
      */
+    @Nullable
     public OntologyTerm getInstanceOf();
 
 }

src/ubic/basecode/ontology/model/ChainedStatementObject.java

@@ -34,6 +34,7 @@ public interface OntologyResource {
     /**
      * A local name for this resource.
      */
+    @Nullable
     String getLocalName();
 
     /**

src/ubic/basecode/ontology/model/CharacteristicStatement.java

@@ -0,0 +1,14 @@
+package ubic.basecode.ontology.model;
+
+/**
+ * Represents a statement triplet in an ontology.
+ * @author poirigui
+ */
+public interface OntologyStatement {
+
+    OntologyResource getSubject();
+
+    OntologyProperty getPredicate();
+
+    OntologyResource getObject();
+}