Make get/set additional property URIs public and update docs

Author: arteymix

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

@@ -168,11 +168,7 @@ public void setSearchEnabled( boolean searchEnabled ) {
         this.nextSearchEnabled = searchEnabled;
     }
 
-    /**
-     * The set of properties relation to use when inferring parents and children.
-     * <p>
-     * The default is to use {@link BFO#partOf} and {@link RO#properPartOf}.
-     */
+    @Override
     public Set<String> getAdditionalPropertyUris() {
         Lock lock = rwLock.readLock();
         try {
@@ -183,6 +179,7 @@ public Set<String> getAdditionalPropertyUris() {
         }
     }
 
+    @Override
     public void setAdditionalPropertyUris( Set<String> additionalPropertyUris ) {
         this.nextAdditionalPropertyUris = additionalPropertyUris;
     }

src/ubic/basecode/ontology/providers/OntologyService.java

@@ -12,8 +12,18 @@
 
 public interface OntologyService {
 
+    /**
+     * Check if this ontology will process imports.
+     * <p>
+     * If disabled, ontologies imported by this ontology will not be loaded.
+     */
     boolean getProcessImports();
 
+    /**
+     * Allow of forbid this ontology to process imports.
+     * <p>
+     * Changes are applicable only if the service is re-initialized.
+     */
     void setProcessImports( boolean processImports );
 
     enum LanguageLevel {
@@ -31,8 +41,18 @@ enum LanguageLevel {
         LITE
     }
 
+    /**
+     * Obtain the OWL language level supported by this ontology.
+     * <p>
+     * The default is to use {@link LanguageLevel#FULL}.
+     */
     LanguageLevel getLanguageLevel();
 
+    /**
+     * Set the OWL language level supported by this ontology.
+     * <p>
+     * Changes are applicable only if the service is re-initialized.
+     */
     void setLanguageLevel( LanguageLevel languageLevel );
 
     enum InferenceMode {
@@ -41,7 +61,7 @@ enum InferenceMode {
          */
         NONE,
         /**
-         * Only basic inference is supported for {@code subClassOf} and {@code subPropertyOf}.
+         * Only basic inference is supported for {@code rdfs:subClassOf} and {@code rdfs:subPropertyOf}.
          * <p>
          * This is the fastest inference mode.
          */
@@ -64,6 +84,8 @@ enum InferenceMode {
 
     /**
      * Obtain the inference mode used for this ontology.
+     * <p>
+     * The default is {@link InferenceMode#TRANSITIVE}.
      */
     InferenceMode getInferenceMode();
 
@@ -74,10 +96,43 @@ enum InferenceMode {
      */
     void setInferenceMode( InferenceMode inferenceMode );
 
+    /**
+     * Check if this ontology has full-text search enabled.
+     * <p>
+     * This is necessary for finding term using full-text queries. If enabled, an index will be generated in during
+     * initialization by {@link #initialize(boolean, boolean)}.
+     * <p>
+     * Search is enabled by default.
+     * @see #findTerm(String, boolean)
+     * @see #findIndividuals(String, boolean)
+     * @see #findResources(String, boolean)
+     */
     boolean isSearchEnabled();
 
+    /**
+     * Enable or disable search for this ontology.
+     * <p>
+     * Changes are only applicable if the service is re-initialized.
+     */
     void setSearchEnabled( boolean searchEnabled );
 
+    /**
+     * Obtain the URIs used as additional properties when inferring parents and children.
+     * <p>
+     * The default is to use <a href="http://purl.obolibrary.org/obo/BFO_0000050">part of</a>, <a href="http://www.obofoundry.org/ro/ro.owl#proper_part_of">proper part of</a>
+     * and all of their sub-properties if inference is enabled.
+     * @see #getParents(Collection, boolean, boolean, boolean)
+     * @see #getChildren(Collection, boolean, boolean, boolean)
+     */
+    Set<String> getAdditionalPropertyUris();
+
+    /**
+     * Set the URIs to be used as additional properties when inferring parents and children.
+     * <p>
+     * Changes are applicable only if the service is re-initialized.
+     */
+    void setAdditionalPropertyUris( Set<String> additionalPropertyUris );
+
     /**
      * Initialize this ontology service.
      *