Added missing JavaDoc for the iordf module

src/main/org/openscience/cdk/io/rdf/CDKOWLReader.java

@@ -48,14 +48,27 @@ public class CDKOWLReader extends DefaultChemObjectReader {
 
     private Reader input;
 
+    /**
+     * Creates a new CDKOWLReader sending output to the given Writer.
+     *
+     * @param input {@link Reader} from which is OWL input is taken.
+     */
     public CDKOWLReader(Reader input) {
         this.input = input;
     }
 
+    /**
+     * Creates a new CDKOWLReader with an undefined input.
+     */
     public CDKOWLReader() {
         this.input = null;
     }
 
+    /**
+     * Returns the {@link IResourceFormat} for this reader.
+     *
+     * @return returns a {@link CDKOWLFormat}.
+     */
     @TestMethod("testGetFormat")
     public IResourceFormat getFormat() {
         return CDKOWLFormat.getInstance();
@@ -64,17 +77,22 @@ public IResourceFormat getFormat() {
     /**
      * This method must not be used; XML reading requires the use of an
      * {@link InputStream}. Use {@link #setReader(InputStream)} instead.
+     *
+     * @param reader reader to which should be written.
+     * @deprecated 
      */
     @TestMethod("testSetReader_Reader")
     public void setReader(Reader reader) throws CDKException {
         this.input = reader;
     }
 
+    /** {@inheritDoc} */
     @TestMethod("testSetReader_InputStream")
     public void setReader(InputStream input) throws CDKException {
         this.input = new InputStreamReader(input);
     }
 
+    /** {@inheritDoc} */
 	@TestMethod("testAccepts")
     public boolean accepts(Class classObject) {
 		Class[] interfaces = classObject.getInterfaces();
@@ -86,6 +104,7 @@ public boolean accepts(Class classObject) {
 	        return false;
 	}
 
+    /** {@inheritDoc} */
     public IChemObject read(IChemObject object) throws CDKException {
       if (object instanceof IMolecule) {
         return readMolecule((IMolecule)object);
@@ -102,6 +121,7 @@ private IMolecule readMolecule(IMolecule mol) throws CDKException {
         return mol;
     }
 
+    /** {@inheritDoc} */
     @TestMethod("testClose")
     public void close() throws IOException {
         input.close();

src/main/org/openscience/cdk/io/rdf/CDKOWLWriter.java

@@ -61,7 +61,9 @@ public CDKOWLWriter() {
     }
 
     /**
-     * Returns the {@link IResourceFormat} for this writer: {@link CDKOWLFormat}.
+     * Returns the {@link IResourceFormat} for this writer.
+     *
+     * @return returns a {@link CDKOWLFormat}.
      */
     public IResourceFormat getFormat() {
         return CDKOWLFormat.getInstance();

src/main/org/openscience/cdk/libio/jena/CDK.java

@@ -25,9 +25,14 @@
 import com.hp.hpl.jena.rdf.model.Property;
 import com.hp.hpl.jena.rdf.model.Resource;
 import com.hp.hpl.jena.rdf.model.ResourceFactory;
+import com.hp.hpl.jena.vocabulary.RDF;
 
 /**
+ * Helper class to provide a Java API to the CDK OWL ontology, following the design of similar namespace
+ * classes in the Jena library, like {@link RDF}.
+ *
  * @cdk.module iordf
+ * @cdk.githash
  */
 public class CDK {
 

src/main/org/openscience/cdk/libio/jena/Convertor.java

@@ -61,6 +61,12 @@
  */
 public class Convertor {
 
+    /**
+     * Converts a {@link IMolecule} into a {@link Model} representation using the CDK OWL.
+     *
+     * @param molecule {@link IMolecule} to serialize into a RDF graph.
+     * @return the RDF graph representing the {@link IMolecule}.
+     */
     public static Model molecule2Model(IMolecule molecule) {
         Model model = createCDKModel();
         Resource subject = model.createResource(
@@ -276,6 +282,12 @@ private static void deserializeIsotopeFields(Resource rdfObject,
             isotope.setNaturalAbundance(naturalAbundance.getDouble());
     }
 
+    /**
+     * Converts a {@link Resource} object into the matching {@link Order}.
+     *
+     * @param rdfOrder Resource for which the matching {@link Order} should be given.
+     * @return the matching {@link Order}.
+     */
     public static Order resource2Order(Resource rdfOrder) {
         if (rdfOrder.equals(CDK.SINGLEBOND)) {
             return Order.SINGLE;
@@ -289,6 +301,12 @@ public static Order resource2Order(Resource rdfOrder) {
         return null;
     }
 
+    /**
+     * Create the {@link Resource} matching the given {@link Order}.
+     *
+     * @param order bond order to return the matching {@link Resource} for.
+     * @return the matching {@link Resource}.
+     */
     public static Resource order2Resource(Order order) {
         if (order == Order.SINGLE) {
             return CDK.SINGLEBOND;
@@ -319,6 +337,13 @@ private static void deserializeElectronContainerFields(
             bond.setElectronCount(count.getInt());
     }
 
+    /**
+     * Converts a {@link Model} into an {@link IMolecule} using the given {@link IChemObjectBuilder}.
+     *
+     * @param model RDF graph to deserialize into an {@link IMolecule}.
+     * @param builder {@link IChemObjectBuilder} used to create new {@link IChemObject}s.
+     * @return a {@link IMolecule} deserialized from the RDF graph.
+     */
     public static IMolecule model2Molecule(Model model,
         IChemObjectBuilder builder) {
         ResIterator mols =