JavaDoc changes required to prevent the release process breaking

api/src/main/java/edu/cornell/mannlib/vedit/util/FormUtils.java

@@ -370,8 +370,7 @@ public class FormUtils {
     /**
      * Decodes a Base-64-encoded String of format 
      * key:value;key2:value2;key3:value, and puts the keys and values in a Map
-     * @param params
+     * @param params Parameters
-     * @return
      */
     public static Map beanParamMapFromString(String params) {
         String[] param = params.split(";");

api/src/main/java/edu/cornell/mannlib/vitro/webapp/auth/policy/specialrelationships/RelationshipChecker.java

@@ -56,7 +56,7 @@ public class RelationshipChecker {
 
 	/**
 	 * Is this resource a member of this type? That is, is there an statement of
-	 * the form: <resourceUri> rdfs:type <typeUri>
+	 * the form: {@code <resourceUri> rdfs:type <typeUri> }
 	 */
 	public boolean isResourceOfType(String resourceUri, String typeUri) {
 		Selector selector = createSelector(resourceUri,
@@ -86,7 +86,7 @@ public class RelationshipChecker {
 	/**
 	 * Get a list of the object URIs that satisfy this statement:
 	 * 
-	 * <resourceUri> <propertyUri> <objectUri>
+	 * {@code <resourceUri> <propertyUri> <objectUri> }
 	 * 
 	 * May return an empty list, but never returns null.
 	 */
@@ -117,9 +117,9 @@ public class RelationshipChecker {
 	/**
 	 * Get a list of the object URIs that satisfy these statements:
 	 * 
-	 * <resourceUri> <linkUri> <contextNodeUri>
+	 * {@code <resourceUri> <linkUri> <contextNodeUri> }
 	 * 
-	 * <contextNodeUri> <propertyUri> <objectUri>
+	 * {@code <contextNodeUri> <propertyUri> <objectUri> }
 	 * 
 	 * May return an empty list, but never returns null.
 	 */
@@ -161,11 +161,11 @@ public class RelationshipChecker {
 	 * 
 	 * So we're looking for object URIs that statisfy these statements:
 	 * 
-	 * <resourceUri> <property1Uri> <linkNodeUri>
+	 * {@code <resourceUri> <property1Uri> <linkNodeUri> }
 	 * 
-	 * <linkNodeUri> rdfs:type <linkNodeTypeUri>
+	 * {@code <linkNodeUri> rdfs:type <linkNodeTypeUri> }
 	 * 
-	 * <linkNodeUri> <property2Uri> <objectUri>
+	 * {@code <linkNodeUri> <property2Uri> <objectUri> }
 	 */
 	public List<String> getObjectsThroughLinkingNode(String resourceUri,
 			String property1Uri, String linkNodeTypeUri, String property2Uri) {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/auth/requestedAction/ifaces/RequiresActions.java

@@ -27,7 +27,7 @@ public interface RequiresActions {
      * calling this method would then have the ability to
      * deny the action if it is not authorized. 
      * 
-     * @param vreq
+     * @param vreq Vitro request
      * @return Should not be null. Return Actions.AUTHORIZED
      * if no authorization is required to do use the object.
      */

api/src/main/java/edu/cornell/mannlib/vitro/webapp/beans/ApplicationBean.java

@@ -182,7 +182,6 @@ public class ApplicationBean {
     /**
      * Directory to find the images.  Subdirectories include css, jsp and site_icons.
      * Example: "themes/enhanced/"
-     * @return
      */
     public String getThemeDir(){
     	if (themeInfo.isValidThemeDir(themeDir)) {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/beans/DataProperty.java

@@ -155,7 +155,7 @@ public class DataProperty extends Property implements Comparable<DataProperty>,
 
     /**
      * adds a single DataPropertyStatement object to a DatatypeProperty's DataPropertyStatements list.
-     * @param dataPropertyStmt
+     * @param dataPropertyStmt  Data property statement
      */
 
     public void addDataPropertyStatement(DataPropertyStatement dataPropertyStmt){

api/src/main/java/edu/cornell/mannlib/vitro/webapp/beans/FauxProperty.java

@@ -43,14 +43,14 @@ public class FauxProperty extends BaseResourceBean implements ResourceBean,
 	private String customListView;
 
 	/**
-	 * Arguments are in this order to mimic the relationship: subject ==>
+	 * Arguments are in this order to mimic the relationship: subject ==>
-	 * property ==> object
+	 * property ==> object
 	 * 
 	 * @param domainURI
 	 *            URI of the subject class. May be null.
 	 * @param baseURI
 	 *            URI of the property. May not be null.
-	 * @param rangeUri
+	 * @param rangeURI
 	 *            URI of the object class. May be null.
 	 */
 	public FauxProperty(String domainURI, String baseURI, String rangeURI) {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/beans/Individual.java

@@ -109,7 +109,7 @@ public interface Individual extends ResourceBean, Comparable<Individual> {
      * This is crap. It was put in so IndividualFiltering could filter object properties properly,
      * but what we really need is either: filters have a reference to a webappDaoFactory, or
      * all ObjectPropertyStatements are resolved when they are created. See VIVO-946 and VIVO-984.
-     * @param list
+     * @param list Object property statements
      */
 	void resolveAsFauxPropertyStatements(List<ObjectPropertyStatement> list);
 }

api/src/main/java/edu/cornell/mannlib/vitro/webapp/beans/IndividualImpl.java

@@ -23,7 +23,7 @@ import edu.cornell.mannlib.vitro.webapp.filestorage.model.ImageInfo;
 public class IndividualImpl extends BaseResourceBean implements Individual, Comparable<Individual> {
 	/**
 	 * This can be used as a "not initialized" indicator for a property that
-	 * could validly be set to <code>null</code>. If <code>get()</code> is
+	 * could validly be set to {@code null}. If {@code get()} is
 	 * called on such a property, and the property has this value, the correct
 	 * value can be fetched and cached.
 	 */

api/src/main/java/edu/cornell/mannlib/vitro/webapp/beans/ObjectProperty.java

@@ -253,7 +253,6 @@ public class ObjectProperty extends Property implements Comparable<ObjectPropert
     
     /**
      * adds a single ObjectPropertyStatement object to Property's object property statements List.
-     * @param e2e
      */
     public final void addObjectPropertyStatement(ObjectPropertyStatement objPropertyStmt){
         if( objPropertyStmt == null ) return;

api/src/main/java/edu/cornell/mannlib/vitro/webapp/beans/PropertyGroup.java

@@ -62,7 +62,6 @@ public class PropertyGroup extends BaseResourceBean implements Comparable<Proper
 
     /**
      * Sorts PropertyGroup objects by group rank, then alphanumeric.
-     * @author bdc34 modified by jc55, bjl23
      */
     public int compareTo(PropertyGroup o2) {
     	Collator collator = Collator.getInstance();

api/src/main/java/edu/cornell/mannlib/vitro/webapp/beans/VClassGroup.java

@@ -152,7 +152,6 @@ public class VClassGroup extends LinkedList <VClass> implements Comparable<VClas
     
     /**
      * Sorts VClassGroup objects by group rank, then alphanumeric.
-     * @author bdc34 modified by jc55, bjl23
      * @return a negative integer, zero, or a positive integer as the
      *         first argument is less than, equal to, or greater than the
      *         second. 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/beans/VClassList.java

@@ -46,7 +46,6 @@ public class VClassList extends VClass {
     }
     /**
      * override this if you want a different sorting.
-     * @return
      */
     public Comparator<Individual> getCompare(){
         return new Comparator<Individual>(){

api/src/main/java/edu/cornell/mannlib/vitro/webapp/config/ConfigurationProperties.java

@@ -125,7 +125,7 @@ public abstract class ConfigurationProperties {
 	// ----------------------------------------------------------------------
 
 	/**
-	 * Get the value of the property, or <code>null</code> if the property has
+	 * Get the value of the property, or {@code null} if the property has
 	 * not been assigned a value.
 	 */
 	public abstract String getProperty(String key);

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/DashboardPropertyListController.java

@@ -48,8 +48,6 @@ public class DashboardPropertyListController extends VitroHttpServlet {
      *
      * Expected Attributes:
      * entity - set to entity to display properties for.
-     *
-     * @author bdc34, then jc55
      */
     
     private static final Log log = LogFactory.getLog(DashboardPropertyListController.class.getName());

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/MailUsersServlet.java

@@ -226,7 +226,7 @@ public class MailUsersServlet extends VitroHttpServlet {
     }
 
     /** Intended to mangle url so it can get through spam filtering
-     *    http://host/dir/servlet?param=value ->  host: dir/servlet?param=value */
+     *    http://host/dir/servlet?param=value ->  host: dir/servlet?param=value */
     public String stripProtocol( String in ){
         if( in == null )
             return "";

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/MultipartRequestWrapper.java

@@ -37,8 +37,8 @@ import org.apache.commons.logging.LogFactory;
  * 
  * The List of FileItems includes both "formField" items and "file" items. As
  * with the usual parameters on a request, we can have more than one value with
- * the same name. So this creates a map of <String, List<String>> to hold the
+ * the same name. So this creates a map of &lt;String, List&lt;String&gt;&gt; to hold the
- * parameters, and a map of <String, List<FileItem>> to hold the files.
+ * parameters, and a map of &lt;String, List&lt;FileItem&gt;&gt; to hold the files.
  * 
  * The parameters will be available to the wrapper through the normal methods.
  * The files will be available as an attribute that holds the map. Also, a

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ContactMailController.java

@@ -197,7 +197,7 @@ public class ContactMailController extends FreemarkerHttpServlet {
 	}
 
     /** Intended to mangle url so it can get through spam filtering
-     *    http://host/dir/servlet?param=value ->  host: dir/servlet?param=value */
+     *    http://host/dir/servlet?param=value ->  host: dir/servlet?param=value */
     public String stripProtocol( String in ){
         if( in == null )
             return "";

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/FreemarkerHttpServlet.java

@@ -429,8 +429,6 @@ public class FreemarkerHttpServlet extends VitroHttpServlet  {
      *  shared variables in the Configuration. (Though we could reset them like other 
      *  shared variables. These variables are not needed outside the page and body templates,
      *  however. If they are needed elsewhere, add to shared variables.
-     *  @param VitroRequest vreq
-     *  @return Map<String, Object>
      */
     // RY This is protected instead of private so FreeMarkerComponentGenerator can access.
     // Once we don't need that (i.e., jsps have been eliminated) it can be made private.

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ImageUploadHelper.java

@@ -106,7 +106,7 @@ public class ImageUploadHelper {
 	 * The image must be present and non-empty, and must have a mime-type that
 	 * represents an image we support.
 	 * 
-	 * We rely on the fact that a {@link FileUploadServletRequest} will always
+	 * We rely on the fact that a FileUploadServletRequest will always
 	 * have a map of {@link FileItem}s, even if it is empty. However, that map
 	 * may not contain the field that we want, or that field may contain an
 	 * empty file.

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/grefine/GrefineMqlreadServlet.java

@@ -125,9 +125,9 @@ public class GrefineMqlreadServlet extends VitroHttpServlet {
 
 	/**
 	 * Construct json from query String
-	 * @param query
+	 * @param query Query
-	 * @param subjectUriList
+	 * @param subjectUriList Subject URIs
-	 * @param propertyUriMap
+	 * @param propertyUriMap Property maps
 	 */
 	private void parseQuery(String query, ArrayList<String> subjectUriList, Map<String, JSONArray> propertyUriMap) {
 		try {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/grefine/JSONReconcileServlet.java

@@ -172,9 +172,8 @@ public class JSONReconcileServlet extends VitroHttpServlet {
 	/**
 	 * Returns a default JSON response.
 	 * 
-	 * @param req
+	 * @param req Servlet Request
-	 * @param resp
+	 * @param resp Servlet Response
-	 * @return
 	 * @throws ServletException
 	 */
 	protected JSONObject getMetadata(HttpServletRequest req, HttpServletResponse resp, String defaultNamespace,

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/individual/ExtendedRdfAssembler.java

@@ -78,7 +78,6 @@ public class ExtendedRdfAssembler {
 	}
 
 	/**
-	 * @return
 	 */
 	public ResponseValues assembleRdf() {
 		OntModel ontModel = vreq.getJenaOntModel();

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaXMLFileUpload.java

@@ -229,8 +229,7 @@ public class JenaXMLFileUpload  extends JenaIngestController  {
 
 	/**
 	 * Save files to baseDirectoryForFiles and return a list of File objects.
-	 * @param fileStreams
+	 * @param fileStreams File streams to process
-	 * @return
 	 * @throws ServletException
 	 */
 	private List<File> saveFiles( Map<String, List<FileItem>> fileStreams ) throws ServletException{

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/json/GetEntitiesByVClass.java

@@ -33,13 +33,14 @@ import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
  * If there are more entities the last item on the returned array will be an object
  * with no id property. It will look like this:
  *
+ * {@code
  * {"resultGroup":0,
  *  "resultKey":"2WEK2306",
  *  "nextUrl":"http://caruso.mannlib.cornell.edu:8080/vitro/dataservice?getEntitiesByVClass=1&resultKey=2WEK2306&resultGroup=1&vclassId=null",
  *  "entsInVClass":1752,
  *  "nextResultGroup":1,
  *  "standardReplySize":256}
- *
+ * }
  */
 public class GetEntitiesByVClass extends JsonArrayProducer {
 	private static final Log log = LogFactory.getLog(GetEntitiesByVClass.class);

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/IndividualDao.java

@@ -22,22 +22,21 @@ public interface IndividualDao {
 
     /**
      * Adds the specified Individual to the specified VClass (i.e. adds rdf:type).
-     * @param individualURI
+     * @param individualURI Individual URI
-     * @param vclassURI
+     * @param vclassURI URI for VClass
      */
     public abstract void addVClass(String individualURI, String vclassURI);
     
     /**
      * Removes the specified Individual from the specificed VClass (i.e. retracts rdf:type)
-     * @param individualURI
+     * @param individualURI Individual URI
-     * @param vclassURI
+     * @param vclassURI URI for VCLass
      */
     public abstract void removeVClass(String individualURI, String vclassURI);
     
     /**
      * Returns a list of all the Individuals in the specified VClass.
-     * @param vclass
+     * @param vclass VClass
-     * @return
      */
     public abstract List <Individual> getIndividualsByVClass(VClass vclass);
 
@@ -53,7 +52,7 @@ public interface IndividualDao {
             int quantity);
 
     /**
-     * @returns new individual URI  if success.
+     * @return new individual URI  if success.
      */
     public abstract String insertNewIndividual(Individual individual) throws InsertException;
 
@@ -65,7 +64,7 @@ public interface IndividualDao {
 
     /**
      * deletes a single individual from the knowledge base.
-     * @param id
+     * @param individualURI URI of an individual
      * @return 0 on failed
      */
     public abstract int deleteIndividual(String individualURI);
@@ -78,7 +77,7 @@ public interface IndividualDao {
      * Get a row from the entities table and make an Entity.
      * PropertiesList will not be filled out.
      * VClass will be filled out.
-     * @param entityId
+     * @param individualURI URI for Individual
      * @return an Entity object or null if not found.
      */
     public abstract Individual getIndividualByURI(String individualURI);

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/ObjectPropertyDao.java

@@ -19,10 +19,10 @@ public interface ObjectPropertyDao extends PropertyDao {
      * Use this method to supply a base ObjectProperty whose fields will be updated
      * as necessary to correspond to the configuration for the specified Domain
      * and Range.  
-     * @param objectPropertyURI
+     * @param objectPropertyURI Object Property URI
-     * @param domainURI
+     * @param domainURI Domain URI
-     * @param rangeURI
+     * @param rangeURI Range URI
-     * @param base
+     * @param base Object property
      * @return ObjectProperty
      */
     public ObjectProperty getObjectPropertyByURIs(String objectPropertyURI, String domainURI, String rangeURI, ObjectProperty base);

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/PageDao.java

@@ -10,14 +10,11 @@ public interface PageDao {
     
     /**
      * Returns a list of urlMappings to URIs.
-     * 
-     * @return
      */
     Map<String, String> getPageMappings();
     
     /**
      * Returns URI of home page.
-     * @return
      */
     String getHomePageUri();
    

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/VClassDao.java

@@ -89,15 +89,15 @@ public interface VClassDao {
     void addVClassesToGroups(List <VClassGroup> groups );
     
     /**
-     * @param vc1
+     * @param vc1 VCLass
-     * @param vc2
+     * @param vc2 VClass
      * @return true if vc1 subClassOf vc2
      */
     boolean isSubClassOf(VClass vc1, VClass vc2);
     
     /**
-     * @param vc1
+     * @param vclassURI1 VClass URI
-     * @param vc2
+     * @param vclassURI2 VClass URI
      * @return true if vc1 subClassOf vc2
      */
     boolean isSubClassOf(String vclassURI1, String vclassURI2);

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/VClassGroupDao.java

@@ -13,9 +13,7 @@ public interface VClassGroupDao {
 
     /**
      * Gets all of the ClassGroups as a map ordered by displayRank.
-     * VClassGroup.getPublicName() -> VClassGroup
+     * VClassGroup.getPublicName() -> VClassGroup
-     *
-     * @return
      */
     public abstract LinkedHashMap<String,VClassGroup> getClassGroupMap();
 
@@ -27,24 +25,24 @@ public interface VClassGroupDao {
 
     /**
      * Return a list of VClassGroups with their associated VClasses
-     * @param displayOrder
+     * @param displayOrder  Display order
      * @return List
      */
     public abstract List<VClassGroup> getPublicGroupsWithVClasses(boolean displayOrder);
 
     /**
      * Return a list of VClassGroups with their associated VClasses
-     * @param displayOrder
+     * @param displayOrder Display order
-     * @param includeUninstantiatedClasses
+     * @param includeUninstantiatedClasses Include all classes
      * @return List
      */
     public abstract List<VClassGroup> getPublicGroupsWithVClasses(boolean displayOrder, boolean includeUninstantiatedClasses);
 
     /**
      * Return a list of VClassGroups with their associated VClasses
-     * @param displayOrder
+     * @param displayOrder Display order
-     * @param includeUninstantiatedClasses
+     * @param includeUninstantiatedClasses Include all classes
-     * @param getIndividualCount
+     * @param getIndividualCount Retrieve individual count
      * @return List
      */
     public abstract List<VClassGroup> getPublicGroupsWithVClasses(boolean displayOrder, boolean includeUninstantiatedClasses, boolean getIndividualCount);

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/WebappDaoFactory.java

@@ -32,8 +32,7 @@ public interface WebappDaoFactory {
 	/**
 	 * Check if a given URI string exists in the system:
 	 * checks for the following conditions: URI found as subject in a statement or an object or as a property
-	 * @param uriStr
+	 * @param uriStr URI String
-	 * @return
 	 */
 	public boolean hasExistingURI(String uriStr);
 	
@@ -54,15 +53,13 @@ public interface WebappDaoFactory {
     /**
      * Copy this DAO factory to a new object associated with the specified user 
      * URI, or return the same factory if a user-aware version cannot be used.
-     * @param userURI
+     * @param userURI User URI
-     * @return
      */
     public WebappDaoFactory getUserAwareDaoFactory(String userURI);
 
     /**
      * Return URI of user associated with this WebappDaoFactory, 
      * or null if not applicable.
-     * @return
      */
     public String getUserURI();
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/IndividualDaoSDB.java

@@ -308,7 +308,7 @@ public class IndividualDaoSDB extends IndividualDaoJena {
     /**
      * fills in the Individual objects needed for any ObjectPropertyStatements 
      * attached to the specified individual.
-     * @param entity
+     * @param entity An individual
      */
     private void fillIndividualsForObjectPropertyStatements(Individual entity){
         getOntModel().enterCriticalSection(Lock.READ);

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/JenaBaseDao.java

@@ -461,9 +461,10 @@ public class JenaBaseDao extends JenaBaseDaoCon {
 
     /**
      * convenience method
-     * @param ind
+     * @param res Resource
-     * @param dataprop
+     * @param dataprop Datatype property
-     * @param value
+     * @param value Date
+     * @param model Jena Model
      */
     protected synchronized void addPropertyDateValue(Resource res, DatatypeProperty dataprop, Date value, Model model) {
         if (dataprop != null && value != null) {
@@ -916,7 +917,7 @@ public class JenaBaseDao extends JenaBaseDaoCon {
     
     /**
      * Checks a URI for validity.  Jena models can store invalid URIs, but this causes RDF/XML output serialization to fail.
-     * @param uri
+     * @param uri URI
      * @return null if URI is good, otherwise an error message String
      */
     protected String checkURI( String uri ) {
@@ -1047,8 +1048,8 @@ public class JenaBaseDao extends JenaBaseDaoCon {
     
     /**
      * Returns additions and retractions to perform
-     * @param ontRes
+     * @param ontRes Ontology resource
-     * @param ontModel
+     * @param ontModel Ontology model
      * @return Model[] where [0] is retractions and [1] is additions
      */
     protected Model[] getSmartRemoval(OntResource ontRes, OntModel ontModel) {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/JenaModelUtils.java

@@ -60,7 +60,7 @@ public class JenaModelUtils {
      * an ontology.  Also creates annotations to place each root class and all 
      * of its children in the appropriate groups.  In the case of multiple 
      * inheritance, classgroup assignment will be arbitrary.
-     * @param wadf
+     * @param wadf DAO Factory
      * @param tboxModel containing ontology classes
      * @return resultArray of OntModels, where resultArray[0] is the model containing
      * the triples about the classgroups, and resultArray[1] is the model containing

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/PageDaoJena.java

@@ -370,8 +370,7 @@ public class PageDaoJena extends JenaBaseDao implements PageDao {
      * Gets a URI for display:forClassGroup for the specified page.
      * Only one value is expected in the model.
      * This may return null if there is no ClassGroup associated with the page. 
-     * @param pageUri
+     * @param pageUri Page URI
-     * @return
      */
     @Override
     public String getClassGroupPage(String pageUri) {        

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/PropertyDaoJena.java

@@ -412,7 +412,7 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
 
 	/**
 	 * Find named classes to which a restriction "applies"
-	 * @param   resourceURI  identifier of a class
+	 * @param   ontClass Ontology class
 	 * @return  set of class URIs
 	 * 
 	 * Note: this method assumes that the caller holds a read lock on
@@ -461,7 +461,7 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
 
     /**
      * requires SPARQL 1.1 (or ARQ) property path support
-     * @param vclassURI
+     * @param vclassURI VClass URI
      * @return list of property resources with union domains that include the vclass
      */
     protected List<Resource> getPropertiesWithAppropriateDomainFor(String vclassURI) {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/RDFServiceGraph.java

@@ -60,7 +60,7 @@ public class RDFServiceGraph implements GraphWithPerform {
 
     /**
      * Returns a SparqlGraph for the union of named graphs in a remote repository 
-     * @param endpointURI
+     * @param rdfService RDF Service
      */
     public RDFServiceGraph(RDFService rdfService) {
         this(rdfService, null);
@@ -68,8 +68,8 @@ public class RDFServiceGraph implements GraphWithPerform {
     
     /**
      * Returns a SparqlGraph for a particular named graph in a remote repository 
-     * @param endpointURI
+     * @param rdfService RDFService
-     * @param graphURI
+     * @param graphURI Graph URI
      */
     public RDFServiceGraph(RDFService rdfService, String graphURI) {
        this.rdfService = rdfService;

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/RDFServiceGraphBulkUpdater.java

@@ -89,8 +89,7 @@ public class RDFServiceGraphBulkUpdater implements BulkUpdateHandler {
     /**
      * Returns a pair of models.  The first contains any statement containing at 
      * least one blank node.  The second contains all remaining statements.
-     * @param g
+     * @param g Graph
-     * @return
      */
     
     private Model[] separateStatementsWithBlankNodes(Graph g) {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/SparqlGraph.java

@@ -60,7 +60,7 @@ public class SparqlGraph implements GraphWithPerform {
     
     /**
      * Returns a SparqlGraph for the union of named graphs in a remote repository 
-     * @param endpointURI
+     * @param endpointURI Endpoint URI
      */
     public SparqlGraph(String endpointURI) {
         this(endpointURI, null);
@@ -68,8 +68,8 @@ public class SparqlGraph implements GraphWithPerform {
     
     /**
      * Returns a SparqlGraph for a particular named graph in a remote repository 
-     * @param endpointURI
+     * @param endpointURI Endpoint URI
-     * @param graphURI
+     * @param graphURI Graph URI
      */
     public SparqlGraph(String endpointURI, String graphURI) {
        this.endpointURI = endpointURI;

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/SparqlGraphBulkUpdater.java

@@ -82,8 +82,7 @@ public class SparqlGraphBulkUpdater extends SimpleBulkUpdateHandler {
     /**
      * Returns a pair of models.  The first contains any statement containing at 
      * least one blank node.  The second contains all remaining statements.
-     * @param g
+     * @param g Jena Graph
-     * @return
      */
     
     private Model[] separateStatementsWithBlankNodes(Graph g) {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/VClassDaoJena.java

@@ -493,7 +493,6 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
      * of determining whether something is a root class.
      * We also avoid ClassCastExceptions deep in Jena-land by eschewing Jena's 
      * listSuperClasses() method.
-     * @author bjl23
      */
     private Iterator<OntClass> smarterListHierarchyRootClasses(OntModel ontModel, String ontologyURI) {
         List<OntClass> rootClassList = new ArrayList<OntClass>();

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/WebappDaoFactoryJena.java

@@ -451,7 +451,7 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
     
     /**
      * Method for creating a copy - does not pass the same object
-     * @param base
+     * @param base DAO Factory
      */
     public WebappDaoFactoryJena (WebappDaoFactoryJena base) {
     	// Not sure if selector somehow has greater longevity so 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dwr/EntityDWR.java

@@ -33,7 +33,7 @@ public class EntityDWR {
 
     /**
      *  Insets a new entity into the Vitro system.
-     *  @returns < 1 if failed, entityId if success.
+     *  @return &lt; 1 if failed, entityId if success.
      */
     public String insertNewEntity(Individual ent ){
     	try {
@@ -47,8 +47,6 @@ public class EntityDWR {
     /**
      ********************************************************
      * Gets an Entity object for a given entities.id.
-     * @param entityId
-     * @return
      */
     public Individual entityByURI(String entityURI){
         WebContext ctx = WebContextFactory.get();

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dwr/PropertyDWR.java

@@ -49,7 +49,7 @@ public class PropertyDWR {
 
     /**
      * Gets only unhidden properties.
-     * @returns Collection of PropertyInstance objs
+     * @return Collection of PropertyInstance objs
      */
     public Collection getAllPropInstByVClass(String classURI){
         WebContext ctx = WebContextFactory.get();

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dwr/VClassDWR.java

@@ -28,8 +28,8 @@ public class VClassDWR {
      * add proprties form.
      *
      *
-     * @param vclassId - vclass we want to make a property for
+     * @param vclassURI - vclass we want to make a property for
-     * @param propertyId - property we want to use
+     * @param propertyURI - property we want to use
      * @param filterOutUninstanciated - if true filter out any vclasses with zero instances.
      * @return a list of VClass objects, one for each vclass that could be in the
      * relation indicated by the parameters.

api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/VTwo/DateTimeWithPrecisionVTwo.java

@@ -26,7 +26,7 @@ import freemarker.template.Configuration;
 /**
  * This is intended to work in conjunction with a template to create the HTML for a 
  * datetime with precision and to convert the submitted parameters into 
- * varname -> Literal and varname -> URI maps.
+ * varname -> Literal and varname -> URI maps.
  * 
  * The variables that get passed to the template are defined in:
  * DateTimeWithPrecision.getMapForTemplate() 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/VTwo/EditConfigurationUtils.java

@@ -302,7 +302,6 @@ public class EditConfigurationUtils {
         return copyList;
    }        
     
-    /** Make a copy of a Map<String,String> */
     public static Map<String,String> copyMap(Map<String,String> source) {
         HashMap<String, String> map = new HashMap<String, String>();
         Set<String> keys = map.keySet();
@@ -315,7 +314,6 @@ public class EditConfigurationUtils {
         return map;
     }
     
-    /** Make a copy of a Map<String,List<String>> */
     public static Map<String, List<String>> copyListMap(Map<String, List<String>> source) {
         HashMap<String, List<String>> map = new HashMap<String, List<String>>();
         Set<String> keys = map.keySet();
@@ -326,7 +324,6 @@ public class EditConfigurationUtils {
         return map;
     }    
 
-    
     public static EditConfigurationVTwo getEditConfiguration(HttpServletRequest request) {
         HttpSession session = request.getSession();
         EditConfigurationVTwo editConfiguration = EditConfigurationVTwo.getConfigFromSession(session, request);     

api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/VTwo/EditConfigurationVTwo.java

@@ -449,7 +449,6 @@ public class EditConfigurationVTwo {
     }
 
     /** Return a copy of the value so that the configuration is not modified by external code.
-     * @return
      */
     public List<String> getN3Required() {
         return EditConfigurationUtils.copy(n3Required);
@@ -471,7 +470,6 @@ public class EditConfigurationVTwo {
     	 this.n3Required.addAll(Arrays.asList( n3RequiredStrsInput ));  
     }
      /** return a copy of the value so that the configuration is not modified by external code.
-     * @return
      */
     public List<String> getN3Optional() {
          return EditConfigurationUtils.copy( n3Optional );
@@ -600,7 +598,6 @@ public class EditConfigurationVTwo {
     }
 
     /** Return a copy of the value so that the configuration is not modified by external code.
-     * @return
      */
     public Map<String, String> getSparqlForAdditionalUrisInScope() {        
         return copyMap(sparqlForAdditionalUrisInScope);        
@@ -611,7 +608,6 @@ public class EditConfigurationVTwo {
     }
 
      /** Return a copy of the value so that the configuration is not modified by external code.
-     * @return
      */
     public Map<String, String> getSparqlForAdditionalLiteralsInScope() {        
         return copyMap(sparqlForAdditionalLiteralsInScope);        
@@ -650,7 +646,6 @@ public class EditConfigurationVTwo {
     }
 
      /** return a copy of the value so that the configuration is not modified by external code.
-     * @return
      */
     public Map<String, String> getSparqlForExistingLiterals() {
         return copyMap(sparqlForExistingLiterals);        
@@ -661,7 +656,6 @@ public class EditConfigurationVTwo {
     }
 
      /** return a copy of the value so that the configuration is not modified by external code.
-     * @return
      */
     public Map<String, String> getSparqlForExistingUris() {         
         return copyMap(sparqlForExistingUris);        

api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/VTwo/EditN3GeneratorVTwo.java

@@ -34,7 +34,7 @@ public class EditN3GeneratorVTwo {
      * This takes into account multiple values that would be returned from a select list.
      * subInUris should no longer be used.
      * 
-     * It's important that the map contain String to List<String> mapping.  
+     * It's important that the map contain String to List&lt;String&gt; mapping.
      * 
      * Before values are sent in, all of the values for a variable should be placed within an array.
      * 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/VTwo/MultiValueEditSubmission.java

@@ -179,7 +179,7 @@ public class MultiValueEditSubmission {
     }
     /**
      * need to generate something like
-     *  "09:10:11"^^<http://www.w3.org/2001/XMLSchema#time>
+     *  {@code "09:10:11"^^<http://www.w3.org/2001/XMLSchema#time>}
      */ 
     public Literal getTime(Map<String,String[]> queryParameters,String fieldName) {
         List<String> hour = Arrays.asList(queryParameters.get("hour" + fieldName));

api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/VTwo/N3EditUtils.java

@@ -247,8 +247,7 @@ public class N3EditUtils {
 
     /**
      * Strips from a string any characters that are not valid in XML 1.0
-     * @param in
+     * @param in String to strip characters from
-     * @return
      */
     public static String stripInvalidXMLChars(String in) {
         if (in == null) {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/VTwo/ProcessRdfForm.java

@@ -274,7 +274,7 @@ public class ProcessRdfForm {
     /**
      * Parse the n3Strings to a List of RDF Model objects.
      * 
-     * @param n3Strings
+     * @param n3Strings N3 Strings to parse
      * @param parseType if OPTIONAL, then don't throw exceptions on errors
      * If REQUIRED, then throw exceptions on errors.
      * @throws Exception 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/VTwo/RdfLiteralHash.java

@@ -23,7 +23,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
  * RDF literal statement without including the whole literal in the parameters.
  *
  * ex.
- * http://fake.com/delete?sub="http://bob"&pred="http://hasNickName"&stmtHash="23443434"
+ * {@code http://fake.com/delete?sub="http://bob"&pred="http://hasNickName"&stmtHash="23443434"}
  *
  * This could request the deletion of a the statement for Bob's nickname where the 
  * literal matched the hash 23443434.
@@ -39,7 +39,7 @@ public class RdfLiteralHash {
     /**
      * Make a hash based on individual, property, literal and (lang or datatype).
      * 
-     * @param stmt
+     * @param stmt Data statement
      * @return a value between MIN_INTEGER and MAX_INTEGER 
      */
     public static int makeRdfLiteralHash( DataPropertyStatement stmt ){
@@ -72,9 +72,8 @@ public class RdfLiteralHash {
 
 
     /**
-     * @param stmt
+     * @param stmt Data statement
-     * @param hash
+     * @param hash Hash
-     * @return
      */
     public static boolean doesStmtMatchHash( DataPropertyStatement stmt, int hash){ 
         if( stmt == null )
@@ -92,9 +91,9 @@ public class RdfLiteralHash {
     
     /**
      * Forward to either getDataPropertyStmtByHash or getRdfsLabelStatementByHash, depending on the property.
-     * @param subjectUri, 
+     * @param subjectUri  Subject URI
-     * @param predicateUri, 
+     * @param predicateUri  Predicate URI
-     * @param hash
+     * @param hash Hash
      * @param model, may not be null
      * @return a DataPropertyStatement if found or null if not found
      */

api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/VTwo/fields/FieldOptions.java

@@ -20,7 +20,7 @@ public interface FieldOptions {
      * Any object that are needed to get the options should
      * be passed in the constructor of the implementation.
      * 
-     * @return return a map of value->label for the options. 
+     * @return return a map of value->label for the options.
      * Should never return null.
      * 
      * @throws Exception 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/controller/PostEditCleanupController.java

@@ -46,7 +46,6 @@ public class PostEditCleanupController extends FreemarkerHttpServlet{
 	 * Returns a redirect after an edit.
 	 * @param vreq - should have an edit configuration in attributes or session
 	 * @param entityToReturnTo - may be null
-	 * @return
 	 */
     protected static ResponseValues doPostEditRedirect( VitroRequest vreq , String entityToReturnTo){
         EditConfigurationVTwo editConfig = EditConfigurationVTwo.getConfigFromSession(vreq.getSession(), vreq);      

api/src/main/java/edu/cornell/mannlib/vitro/webapp/filestorage/FileServingHelper.java

@@ -106,7 +106,7 @@ public class FileServingHelper {
 	 * replacing the file prefix with the default namespace.
 	 * </p>
 	 * 
-	 * @return the URI, or <code>null</code> if the URL couldn't be translated.
+	 * @return the URI, or {@code null} if the URL couldn't be translated.
 	 */
 	public static String getBytestreamUri(String path, ServletContext ctx) {
 		if (path == null) {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/filestorage/TempFileHolder.java

@@ -31,7 +31,7 @@ public class TempFileHolder implements HttpSessionBindingListener {
 	private static final Log log = LogFactory.getLog(TempFileHolder.class);
 
 	/**
-	 * Create a {@link TempFileHolder} holding the given {@link FileInfo}, and
+	 * Create a  holding the given {@link FileInfo}, and
 	 * attach it to the session with the given attribute name.
 	 * 
 	 * If an attribute with this name already exists, it is replaced.
@@ -52,11 +52,11 @@ public class TempFileHolder implements HttpSessionBindingListener {
 	}
 
 	/**
-	 * Get the {@link TempFileHolder} which is stored as an attribute on this
+	 * Get the  which is stored as an attribute on this
 	 * session, extract the {@link FileInfo} from it, and remove it from the
 	 * session.
 	 * 
-	 * If there is no such attribute, of if it is not a {@link TempFileHolder},
+	 * If there is no such attribute, of if it is not a ,
 	 * return null.
 	 */
 	public static FileInfo remove(HttpSession session, String attributeName) {
@@ -92,8 +92,6 @@ public class TempFileHolder implements HttpSessionBindingListener {
 	/**
 	 * Gets the {@link FileInfo} payload, and removes it so the file won't be
 	 * deleted when the value is unbound.
-	 * 
-	 * @return
 	 */
 	private FileInfo extractFileInfo() {
 		FileInfo result = this.fileInfo;
@@ -104,7 +102,6 @@ public class TempFileHolder implements HttpSessionBindingListener {
 	/**
 	 * When attached to the session, do nothing.
 	 *
-	 * @see HttpSessionBindingListener#valueBound(HttpSessionBindingEvent)
 	 */
 	@Override
 	public void valueBound(HttpSessionBindingEvent event) {
@@ -116,7 +113,6 @@ public class TempFileHolder implements HttpSessionBindingListener {
 	 * delete the file. If you had wanted this file, you should have called
 	 * {@link #remove(HttpSession, String) remove}.
 	 *
-	 * @see HttpSessionBindingListener#valueUnbound(HttpSessionBindingEvent)
 	 */
 	@Override
 	public void valueUnbound(HttpSessionBindingEvent event) {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/filestorage/impl/FileStorageHelper.java

@@ -54,8 +54,6 @@ public class FileStorageHelper {
 
 	/**
 	 * Encode the filename as needed to guard against illegal characters.
-	 * 
-	 * @see edu.cornell.mannlib.vitro.webapp.utils.filestorage
 	 */
 	public static String encodeName(String filename) {
 		String hexed = addHexEncoding(filename);
@@ -149,8 +147,6 @@ public class FileStorageHelper {
 
 	/**
 	 * Restore the filename to its original form, removing the encoding.
-	 * 
-	 * @see edu.cornell.mannlib.vitro.webapp.utils.filestorage
 	 */
 	public static String decodeName(String stored) {
 		String unexcluded = unexcludeWindowsReservedNames(stored);
@@ -228,8 +224,6 @@ public class FileStorageHelper {
 	 * namespace is translated to its prefix, and illegal characters are
 	 * encoded. The resulting string is broken up into 3-character directory
 	 * names (or less). Windows reserved words are prefixed with tilde.
-	 * 
-	 * @see edu.cornell.mannlib.vitro.webapp.utils.filestorage
 	 */
 	public static String id2Path(String id, Map<Character, String> namespacesMap) {
 		char prefix = 0;
@@ -305,8 +299,6 @@ public class FileStorageHelper {
 	/**
 	 * Translate the object ID and the file storage root directory into a full
 	 * path to the directory that would represent that ID.
-	 * 
-	 * @see edu.cornell.mannlib.vitro.webapp.utils.filestorage
 	 */
 	public static File getPathToIdDirectory(String id,
 			Map<Character, String> namespacesMap, File rootDir) {
@@ -316,8 +308,6 @@ public class FileStorageHelper {
 	/**
 	 * Translate the object ID, the file storage root directory and the filename
 	 * into a full path to where the file would be stored.
-	 * 
-	 * @see edu.cornell.mannlib.vitro.webapp.utils.filestorage
 	 */
 	public static File getFullPath(File rootDir, String id, String filename,
 			Map<Character, String> namespacesMap) {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/filestorage/impl/FileStorageImpl.java

@@ -252,8 +252,6 @@ public class FileStorageImpl {
 	// ----------------------------------------------------------------------
 
 	/**
-	 * {@inheritDoc}
-	 * 
 	 * <p>
 	 * Before creating the file, we may need to create one or more parent
 	 * directories to put it in.
@@ -302,8 +300,6 @@ public class FileStorageImpl {
 	}
 
 	/**
-	 * {@inheritDoc}
-	 * 
 	 * <p>
 	 * If deleting this file leaves its parent directory empty, that directory
 	 * will be deleted. This repeats, up to (but not including) the root
@@ -409,7 +405,6 @@ public class FileStorageImpl {
 	}
 
 	/**
-	 * {@inheritDoc}
 	 */
 	public InputStream getInputStream(String id, String filename)
 			throws IOException {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/filestorage/impl/package-info.java

@@ -6,6 +6,7 @@
  * <h1>Relationship to PairTree</h1>
  * <p>
  * The system incorporates a number of ideas from the PairTree specification,
+ * </p>
  * <ul>
  * <li>
  * The basic pairtree algorithm -
@@ -45,18 +46,17 @@
  * "shorty" directory names may be up to 3 characters long, not 2.
  * </li>
  * </ul>
- * </p>
  * <h1>Directory structure</h1>
  * <p>
  * A typical structure would look like this:
- * <pre>
+ * {@code
  * + basedir
  * |
  * +--+ file_storage_namespaces.properties
  * |
  * +--+ file_storage_root
- * </pre>
+ * }
- * The <code>file_storage_root</code> directory contains the subdirectories
+ * The {@code file_storage_root} directory contains the subdirectories
  * that implement the encoded IDs, and the final directory for each ID will
  * contain a single file that corresponds to that ID.
  * </p>
@@ -71,23 +71,24 @@
  * For example, the sytem might be initialized with a "namespace" of
  * "http://vivo.mydomain.edu/file/". If that is the only namespace, it will
  * be internally assigned a prefix of "a", so a URI like this:
+ * </p>
  * <pre>http://vivo.mydomain.edu/file/n3424/myPhoto.jpg</pre>
  * would be converted to this:
  * <pre>a~n3424/myPhoto.jpg</pre>
- * </p>
  * <p>
  * The namespaces and their assigned prefixes are stored in a properties file
  * when the structure is initialized. When the structure is re-opened, the
  * file is read to find the correct prefixes. The file
  * might look like this:
+ * </p>
  * <pre>
  * a = http://the.first.namespace/
  * b = http://the.second.namespace/
  * </pre>
- * </p>
  * <h1>ID encoding</h1>
  * <p>
  * This is a multi-step process:
+ * </p>
  * <ul>
  * <li>
  * <strong>Namespace recognition</strong> -
@@ -139,17 +140,12 @@
  * </li>
  * </ul>
  * Examples:
- * <br/><code>ark:/13030/xt12t3</code> becomes
+ * {@code ark:/13030/xt12t3} becomes {@code ark/+=1/303/0=x/t12/t3}
- * <code>ark/+=1/303/0=x/t12/t3</code>
+ * {@code http://n2t.info/urn:nbn:se:kb:repos-1} becomes {@code htt/p+=/=n2/t,i/nfo/=ur/n+n/bn+/se+/kb+/rep/os-/1}
- * <br/><code>http://n2t.info/urn:nbn:se:kb:repos-1</code> becomes
+ * {@code what-the-*@?#!^!~?} becomes {@code wha/t-t/he-/^2a/@^3/f#!/^5e/!^7/e^3/f}
- * <code>htt/p+=/=n2/t,i/nfo/=ur/n+n/bn+/se+/kb+/rep/os-/1</code>
+ * {@code http://vivo.myDomain.edu/file/n3424} with namespace
- * <br/><code>what-the-*@?#!^!~?</code> becomes
+ * {@code http://vivo.myDomain.edu/file/} and prefix
- * <code>wha/t-t/he-/^2a/@^3/f#!/^5e/!^7/e^3/f</code>
+ * {@code a} becomes {@code a~n/342/4}
- * <br/><code>http://vivo.myDomain.edu/file/n3424</code> with namespace
- * <code>http://vivo.myDomain.edu/file/</code> and prefix
- * <code>a</code> becomes
- * <code>a~n/342/4</code>
- * </p>
  * <h1>Filename encoding</h1>
  * <p>
  * The name of the file is encoded as needed to guard against illegal
@@ -161,9 +157,6 @@
  * "common character encoding" steps used for ID encoding, except that
  * periods are not encoded.
  * </p>
- * <hr/>
- * <hr/>
- * <hr/>
  * <h2>
  * 	This was summarized in a post to the vivo-dev-all list on 11/29/2010
  * </h2>
@@ -186,19 +179,19 @@
  * </p>
  * <p>
  * 	Let's consider a file with this information:
+ * </p>
  * 	<pre>
  * 		URI = http://vivo.mydomain.edu/individual/n3156
  * 		Filename = lily1.jpg
  * 	</pre>
- * </p>
  * <p>
  * 	We want to turn the URI into the directory path, but the URI contains
  * 	prohibited characters. Using a PairTree-like character substitution,
  * 	we might store it at this path:
+ * </p>
  * 	<pre>
  * 		/usr/local/vivo/uploads/file_storage_root/http+==vivo.mydomain.edu=individual=n3156/lily1.jpg
  * 	</pre>
- * </p>
  * <p>
  * 	Using that scheme would mean that each file sits in its own directory
  * 	under the storage root. At a large institution, there might be hundreds of
@@ -212,15 +205,16 @@
  * 	per directory. In practice, the number will be considerably smaller.
  *
  * 	So then it would look like this:
+ * </p>
  * 	<pre>
  * 		/usr/local/vivo/uploads/file_storage_root/htt/p+=/=vi/vo./myd/oma/in./edu/=in/div/idu/al=/n31/56/lily1.jpg
  * 	</pre>
- * </p>
  * <p>
  * 	But almost all of our URIs will start with the same namespace, so the
  * 	namespace just adds unnecessary and unhelpful depth to the directory tree.
  * 	We assign a single-character prefix to that namespace, using the
  * 	file_storage_namespaces.properties file in the uploads directory, like this:
+ * </p>
  * 	<pre>
  * 		a = http://vivo.mydomain.edu/individual/
  * 	</pre>
@@ -232,9 +226,9 @@
  * 	<pre>
  * 		/usr/local/vivo/uploads/file_storage_root/a~n/315/6/lily1.jpg
  * 	</pre>
- * </p>
  * <p>
  * 	So what we hope we have implemented is a system where:
+ * </p>
  * 	<ul>
  * 		<li>Files are stored by URI and filename.</li>
  * 		<li>File paths are constructed to limit the maximum number of files in a directory.</li>
@@ -244,9 +238,9 @@
  * 		<li>Frequently-used namespaces on the URIs can be collapsed to short prefix sequences.</li>
  * 		<li>URIs with unrecognized namespaces will not cause problems.</li>
  * 	</ul>
- * </p>
  * <p>
  * 	By the way, almost all of this is implemented in
+ * </p>
  * 	<pre>
  * 		edu.cornell.mannlib.vitro.webapp.filestorage.impl.FileStorageHelper
  * 	</pre>
@@ -254,6 +248,5 @@
  * 	<pre>
  * 		edu.cornell.mannlib.vitro.webapp.filestorage.impl.FileStorageHelperTest
  * 	</pre>
- * </p>
  */
 package edu.cornell.mannlib.vitro.webapp.filestorage.impl;

api/src/main/java/edu/cornell/mannlib/vitro/webapp/filestorage/serving/FileServingServlet.java

@@ -32,13 +32,13 @@ import edu.cornell.mannlib.vitro.webapp.modules.fileStorage.FileStorage;
  * <p>
  * The path of the request should be the "alias URL" of the desired file. We
  * need to:
+ * </p>
  * <ul>
  * <li>Use the alias URL to find the URI of the file bytestream object.</li>
  * <li>Find the file surrogate object to get the MIME type of the file, and
  * confirm the filename.</li>
  * <li>Set the MIME type on the output stream and serve the bytes.</li>
  * </ul>
- * </p>
  * <p>
  * If the request is superficially correct, but no such file can be found,
  * return a 404. If there is a break in the data structures within the model or

api/src/main/java/edu/cornell/mannlib/vitro/webapp/filters/CachingResponseFilter.java

@@ -66,8 +66,6 @@ import edu.cornell.mannlib.vitro.webapp.utils.searchengine.SearchResultsParser;
  * 
  * An unconditional request may mean that there is no external cache, or that
  * the cache doesn't have a copy of this particular page.
- * 
- * @see http://tools.ietf.org/pdf/rfc2616
  */
 public class CachingResponseFilter implements Filter {
 	private static final Log log = LogFactory

api/src/main/java/edu/cornell/mannlib/vitro/webapp/filters/JSessionStripFilter.java

@@ -22,6 +22,7 @@ import org.apache.commons.logging.LogFactory;
 
  * Here is what needs to go into the web.xml:
  *
+ * {@code
     <filter>
         <filter-name>JSession Strip Filter</filter-name>
         <filter-class>edu.cornell.mannlib.vitro.filters.JSessionStripFilter</filter-class>
@@ -32,7 +33,7 @@ import org.apache.commons.logging.LogFactory;
         <url-pattern>/*</url-pattern>
         <dispatcher>REQUEST</dispatcher>
     </filter-mapping>
-
+    }
  * some of this code is from URLRewriteFilter
  */
 public class JSessionStripFilter implements Filter {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/filters/VitroURL.java

@@ -156,8 +156,7 @@ class VitroURL {
      * This seems like a huge problem.  We will only correctly handle odd things 
      * as a query parameter 'uri' in the last position.
      *  
-     * @param queryStr
+     * @param queryStr Querst string
-     * @return
      */
     protected List<String[]> parseQueryParams(String queryStr) {
         List<String[]> queryParamList = new ArrayList<String[]>();

api/src/main/java/edu/cornell/mannlib/vitro/webapp/i18n/VitroResourceBundle.java

@@ -30,7 +30,7 @@ import org.apache.commons.logging.LogFactory;
  * relative to the i18n directory. Again, a file in the theme will override one
  * in the application.
  * 
- * If a property has a value (after overriding) of "@@file <filepath>", the
+ * If a property has a value (after overriding) of "@@file &lt;filepath&gt;", the
  * bundle looks for the file relative to the i18n directory of the theme, then
  * relative to the i18n directory of the application. If the file is not found
  * in either location, a warning is written to the log and the property will

api/src/main/java/edu/cornell/mannlib/vitro/webapp/i18n/freemarker/I18nStringTemplateModel.java

@@ -20,11 +20,11 @@ import freemarker.template.utility.DeepUnwrap;
  * implements TemplateMethodModel, you can pass arguments to it for formatting.
  * 
  * So if the string is "His name is {0}!", then these references could be used:
- * 
+ * {@code
  * ${string} ==> "His name is {0}!"
  * 
  * ${string("Bozo")} ==> "His name is Bozo!"
- * 
+ * }
  * Note that the format of the message is determined by java.text.MessageFormat,
  * so argument indices start at 0 and you can escape a substring by wrapping it
  * in apostrophes.

api/src/main/java/edu/cornell/mannlib/vitro/webapp/i18n/selection/LocaleSelectionController.java

@@ -21,10 +21,11 @@ import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
 import edu.cornell.mannlib.vitro.webapp.i18n.I18n;
 
 /**
+ * {@code
  * Call this at /selectLocale&selection=[locale_string]
  * 
  * For example: /selectLocale&selection=en_US or /selectLocale&selection=es
- * 
+ * }
  * Write an error to the log (and to DisplayMessage) if the selection is not
  * syntactically valid.
  * 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/modules/fileStorage/FileStorage.java

@@ -28,7 +28,7 @@ public interface FileStorage extends Application.Module {
 	 * If a file exists with this ID, get its name.
 	 * 
 	 * @return The name of the file (un-encoded) if it exists, or
-	 *         <code>null</code> if it does not.
+	 *         {@code null} if it does not.
 	 */
 	String getFilename(String id) throws IOException;
 
@@ -47,7 +47,7 @@ public interface FileStorage extends Application.Module {
 	 * If a file exists with this ID, it will be deleted, regardless of the file
 	 * name. If no such file exists, no action is taken, no exception is thrown.
 	 * 
-	 * @return <code>true<code> if a file existed, <code>false</code> otherwise.
+	 * @return {@code true} if a file existed, {@code false} otherwise.
 	 */
 	boolean deleteFile(String id) throws IOException;
 }

api/src/main/java/edu/cornell/mannlib/vitro/webapp/modules/searchEngine/SearchResultDocumentList.java

@@ -22,7 +22,6 @@ public interface SearchResultDocumentList extends
 	 * Retrieve the i'th document, starting with 0.
 	 * 
 	 * @throws ArrayIndexOutOfBoundsException
-	 *             if i < 0 or i >= size()
 	 */
 	SearchResultDocument get(int i);
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/modules/searchIndexer/SearchIndexer.java

@@ -77,7 +77,7 @@ public interface SearchIndexer extends Application.Module {
 	 * If called before startup or while paused, the task will be queued. If
 	 * called after shutdown, this has no effect.
 	 * 
-	 * @param urls
+	 * @param changes
 	 *            if null or empty, this call has no effect.
 	 */
 	void scheduleUpdatesForStatements(List<Statement> changes);

api/src/main/java/edu/cornell/mannlib/vitro/webapp/ontology/update/ABoxUpdater.java

@@ -55,9 +55,7 @@ public class ABoxUpdater {
 	 * 
 	 * Constructor 
 	 *  
-	 * @param   oldTboxModel - previous version of the ontology
+	 * @param   settings     - Update settings
-	 * @param   newTboxModel - new version of the ontology
-	 * @param   aboxModel    - the knowledge base to be updated
 	 * @param   logger       - for writing to the change log
 	 *                         and the error log.
 	 * @param   record       - for writing to the additions model 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/ontology/update/AtomicOntologyChange.java

@@ -40,7 +40,6 @@ public class AtomicOntologyChange {
 	 * Contains the URI of a class or property in the previous version of
 	 * the ontology, or null if a new class or property was introduced
 	 * in the current version of the ontology.
-	 * @return
 	 */
 	public String getSourceURI() {
 		return this.sourceURI;
@@ -54,7 +53,6 @@ public class AtomicOntologyChange {
 	 * Contains the URI of a class or property in the current version of 
 	 * the ontology, or null if a class or property was removed from the
 	 * previous version of the ontology.
-	 * @return
 	 */
 	public String getDestinationURI() {
 		return this.destinationURI;

api/src/main/java/edu/cornell/mannlib/vitro/webapp/ontology/update/KnowledgeBaseUpdater.java

@@ -145,9 +145,8 @@ public class KnowledgeBaseUpdater {
      * data, for changes that cannot be expressed as simple property
      * or class additions, deletions, or renamings.
      * Blank nodes created by the queries are given random URIs.
-     * @param sparqlConstructDir
+     * @param sparqlConstructDir Sparql CONSTRUCT
-     * @param readModel
+	 * @param rdfService RDF Service to use
-     * @param writeModel
 	 * @param add (add = true; retract = false)
 	 */
     private void performSparqlConstructs(String sparqlConstructDir, 
@@ -362,7 +361,7 @@ public class KnowledgeBaseUpdater {
 	
 	/**
 	 * loads a SPARQL ASK query from a text file
-	 * @param filePath
+	 * @param filePath Path of a file
 	 * @return the query string or null if file not found
 	 */
 	public static String loadSparqlQuery(String filePath) throws IOException {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/ontology/update/OntologyChangeParser.java

@@ -34,7 +34,7 @@ public class OntologyChangeParser {
 	}
 		
 	/**
-	 * @param args
+	 * @param diffPath Diff path
 	 * @throws IOException 
 	 */
 	

api/src/main/java/edu/cornell/mannlib/vitro/webapp/ontology/update/TBoxUpdater.java

@@ -61,9 +61,7 @@ public class TBoxUpdater {
      * 
      * Constructor 
      *
-     * @param   oldTboxAnnotationsModel - previous version of the annotations in the ontology
+     * @param   settings     - update settings
-     * @param   newTboxAnnotationsModel - new version of the annotations in the ontology
-     * @param   siteModel    - the knowledge base to be updated
      * @param   logger       - for writing to the change log
      *                         and the error log.
      * @param   record       - for writing to the additions model 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/ChangeSet.java

@@ -33,7 +33,6 @@ public interface ChangeSet {
 	public void setPreconditionQueryType(RDFService.SPARQLQueryType queryType);
 
 	/**   
-	 * @return List<ModelChange> - list of model changes           
 	 */
 	public List<ModelChange> getModelChanges();
 	
@@ -104,16 +103,12 @@ public interface ChangeSet {
     /**
      * Returns a list of events to pass to any change listeners in 
      * advance of the change set additions and retractions being performed.
-     * 
-     * @return List<Object>
      */
 	public List<Object> getPreChangeEvents();
 	
     /**
      * Returns a list of events to pass to any change listeners after 
      * the change set additions and retractions are performed.
-     * 
-     * @return List<Object>
      */
     public List<Object> getPostChangeEvents();
     

api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/RDFService.java

@@ -141,7 +141,7 @@ public interface RDFService {
 	/**
 	 * Returns a list of all the graph URIs in the RDF store.
 	 * 
-	 * @return  List<String> - list of all the named graph URIs in the RDF store. 
+	 * @return  list of all the named graph URIs in the RDF store.
 	 *          Return an empty list of there no named graphs in
 	 *                         the store. 
 	 */

api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/ResultSetConsumer.java

@@ -86,7 +86,7 @@ public abstract class ResultSetConsumer {
 
         /**
          * Helper method that calls the processQuerySolution on an embedded ResultSetConsumer
-         * @param qs
+         * @param qs Query solution
          */
         protected void chainProcessQuerySolution(QuerySolution qs) {
             if (innerConsumer != null) {
@@ -135,7 +135,6 @@ public abstract class ResultSetConsumer {
 
         /**
          * Were any results found
-         * @return
          */
         public boolean hasResult() {
             return hasResult;

api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/RDFServiceImpl.java

@@ -295,8 +295,7 @@ public abstract class RDFServiceImpl implements RDFService {
     /**
      * Returns a pair of models.  The first contains any statement containing at 
      * least one blank node.  The second contains all remaining statements.
-     * @param g
+     * @param gm Jena model
-     * @return
      */
     
     protected Model[] separateStatementsWithBlankNodes(Model gm) {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/jena/model/RDFServiceModel.java

@@ -30,7 +30,7 @@ public class RDFServiceModel extends RDFServiceJena implements RDFService {
     
     /**
      * Create an RDFService to access a single default graph
-     * @param model
+     * @param model Jena Model
      */
     public RDFServiceModel(Model model) {
         this.model = model;
@@ -38,7 +38,7 @@ public class RDFServiceModel extends RDFServiceJena implements RDFService {
     
     /**
      * Create an RDFService to access a Jena Dataset
-     * @param dataset
+     * @param dataset Jena Dataset
      */
     public RDFServiceModel(Dataset dataset) {
         this.dataset = dataset;

api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/sparql/RDFServiceSparql.java

@@ -92,9 +92,9 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
 
 	/**
 	 * Returns an RDFService for a remote repository
-	 * @param String - URI of the read SPARQL endpoint for the knowledge base
+	 * @param readEndpointURI - URI of the read SPARQL endpoint for the knowledge base
-	 * @param String - URI of the update SPARQL endpoint for the knowledge base
+	 * @param updateEndpointURI - URI of the update SPARQL endpoint for the knowledge base
-	 * @param String - URI of the default write graph within the knowledge base.
+	 * @param defaultWriteGraphURI - URI of the default write graph within the knowledge base.
 	 *                   this is the graph that will be written to when a graph
 	 *                   is not explicitly specified.
 	 *
@@ -125,8 +125,8 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
 
 	/**
 	 * Returns an RDFService for a remote repository
-	 * @param String - URI of the read SPARQL endpoint for the knowledge base
+	 * @param readEndpointURI - URI of the read SPARQL endpoint for the knowledge base
-	 * @param String - URI of the update SPARQL endpoint for the knowledge base
+	 * @param updateEndpointURI - URI of the update SPARQL endpoint for the knowledge base
 	 *
 	 * The default read graph is the union of all graphs in the
 	 * knowledge base
@@ -137,7 +137,7 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
 
 	/**
 	 * Returns an RDFService for a remote repository
-	 * @param String - URI of the read and update SPARQL endpoint for the knowledge base
+	 * @param endpointURI - URI of the read and update SPARQL endpoint for the knowledge base
 	 *
 	 * The default read graph is the union of all graphs in the
 	 * knowledge base
@@ -157,7 +157,7 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
 	 * If the precondition query returns a non-empty result no updates
 	 * will be made.
 	 *
-	 * @param ChangeSet - a set of changes to be performed on the RDF store.
+	 * @param changeSet - a set of changes to be performed on the RDF store.
 	 *
 	 * @return boolean - indicates whether the precondition was satisfied
 	 */
@@ -208,10 +208,8 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
 	 * Performs a SPARQL construct query against the knowledge base. The query may have
 	 * an embedded graph identifier.
 	 *
-	 * @param String query - the SPARQL query to be executed against the RDF store
+	 * @param queryStr - the SPARQL query to be executed against the RDF store
-	 * @param RDFService.ModelSerializationFormat resultFormat - type of serialization for RDF result of the SPARQL query
+	 * @param resultFormat - type of serialization for RDF result of the SPARQL query
-	 * @param OutputStream outputStream - the result of the query
-	 *
 	 */
 	@Override
 	public InputStream sparqlConstructQuery(String queryStr,
@@ -253,8 +251,8 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
 	 * Performs a SPARQL describe query against the knowledge base. The query may have
 	 * an embedded graph identifier.
 	 *
-	 * @param String query - the SPARQL query to be executed against the RDF store
+	 * @param queryStr - the SPARQL query to be executed against the RDF store
-	 * @param RDFService.ModelSerializationFormat resultFormat - type of serialization for RDF result of the SPARQL query
+	 * @param resultFormat - type of serialization for RDF result of the SPARQL query
 	 *
 	 * @return InputStream - the result of the query
 	 *
@@ -283,8 +281,8 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
 	 * Performs a SPARQL select query against the knowledge base. The query may have
 	 * an embedded graph identifier.
 	 *
-	 * @param String query - the SPARQL query to be executed against the RDF store
+	 * @param queryStr - the SPARQL query to be executed against the RDF store
-	 * @param RDFService.ResultFormat resultFormat - format for the result of the Select query
+	 * @param resultFormat - format for the result of the Select query
 	 *
 	 * @return InputStream - the result of the query
 	 *
@@ -374,7 +372,7 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
 	 * Performs a SPARQL ASK query against the knowledge base. The query may have
 	 * an embedded graph identifier.
 	 *
-	 * @param String query - the SPARQL query to be executed against the RDF store
+	 * @param queryStr - the SPARQL query to be executed against the RDF store
 	 *
 	 * @return  boolean - the result of the SPARQL query
 	 */
@@ -393,8 +391,6 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
 
 	/**
 	 * Get a list of all the graph URIs in the RDF store.
-	 *
-	 * @return  List<String> - list of all the graph URIs in the RDF store
 	 */
 	@Override
 	public List<String> getGraphURIs() throws RDFServiceException {
@@ -442,8 +438,6 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
 	}
 
 	/**
-	 * TODO - what is the definition of this method?
-	 * @return
 	 */
 	@Override
 	public void getGraphMetadata() throws RDFServiceException {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/sparql/RDFServiceSparqlHttp.java

@@ -48,10 +48,8 @@ public class RDFServiceSparqlHttp extends RDFServiceSparql {
 	 * Performs a SPARQL construct query against the knowledge base. The query may have
 	 * an embedded graph identifier.
 	 * 
-	 * @param String query - the SPARQL query to be executed against the RDF store
+	 * @param queryStr - the SPARQL query to be executed against the RDF store
-	 * @param RDFService.ModelSerializationFormat resultFormat - type of serialization for RDF result of the SPARQL query
+	 * @param resultFormat - type of serialization for RDF result of the SPARQL query
-	 * @param OutputStream outputStream - the result of the query
-	 * 
 	 */
 	@Override
 	public InputStream sparqlConstructQuery(String queryStr,
@@ -89,8 +87,8 @@ public class RDFServiceSparqlHttp extends RDFServiceSparql {
 	 * Performs a SPARQL describe query against the knowledge base. The query may have
 	 * an embedded graph identifier.
 	 * 
-	 * @param String query - the SPARQL query to be executed against the RDF store
+	 * @param queryStr - the SPARQL query to be executed against the RDF store
-	 * @param RDFService.ModelSerializationFormat resultFormat - type of serialization for RDF result of the SPARQL query
+	 * @param resultFormat - type of serialization for RDF result of the SPARQL query
 	 * 
 	 * @return InputStream - the result of the query
 	 * 
@@ -118,8 +116,8 @@ public class RDFServiceSparqlHttp extends RDFServiceSparql {
 	 * Performs a SPARQL select query against the knowledge base. The query may have
 	 * an embedded graph identifier.
 	 * 
-	 * @param String query - the SPARQL query to be executed against the RDF store
+	 * @param queryStr - the SPARQL query to be executed against the RDF store
-	 * @param RDFService.ResultFormat resultFormat - format for the result of the Select query
+	 * @param resultFormat - format for the result of the Select query
 	 * 
 	 * @return InputStream - the result of the query
 	 * 
@@ -174,7 +172,7 @@ public class RDFServiceSparqlHttp extends RDFServiceSparql {
 	 * Performs a SPARQL ASK query against the knowledge base. The query may have
 	 * an embedded graph identifier.
 	 * 
-	 * @param String query - the SPARQL query to be executed against the RDF store
+	 * @param queryStr - the SPARQL query to be executed against the RDF store
 	 * 
 	 * @return  boolean - the result of the SPARQL query 
 	 */

api/src/main/java/edu/cornell/mannlib/vitro/webapp/reasoner/ABoxRecomputer.java

@@ -249,8 +249,8 @@ public class ABoxRecomputer {
 
     /**
      * Adds inferences to temporary rebuildmodel
-     * @param individualURI
+     * @param individualURI The individual
-     * @param rebuildModel
+     * @param rebuildModel The rebuild model
      * @return any additional inferences produced by plugins that affect other 
      *         individuals
      */

api/src/main/java/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasoner.java

@@ -82,12 +82,12 @@ public class SimpleReasoner extends StatementListener
 
 	/**
 	 * @param tboxModel - input.  This model contains both asserted and inferred TBox axioms
-	 * @param aboxModel - input.  This model contains asserted ABox statements
+	 * @param rdfService - input.  An RDF Service
 	 * @param inferenceModel - output. This is the model in which inferred (materialized) 
      *  ABox statements are maintained (added or retracted).
 	 * @param inferenceRebuildModel - output. This the model is temporarily used when the 
      *  whole ABox inference model is rebuilt
-	 * @param inferenceScratchpadModel - output. This the model is temporarily used when 
+	 * @param scratchpadModel - output. This the model is temporarily used when
      *  the whole ABox inference model is rebuilt
      * @param searchIndexer - output. If not null, the indexer will be paused before the 
      *  ABox inference model is rebuilt and unpaused when the rebuild is complete.

api/src/main/java/edu/cornell/mannlib/vitro/webapp/reasoner/plugin/SimpleBridgingRule.java

@@ -26,7 +26,7 @@ import edu.cornell.mannlib.vitro.webapp.reasoner.SimpleReasoner;
 
 /**
  * handles rules of the form
- * assertedProp1(?x, ?y) ^ assertedProp2(?y, ?z) -> inferredProp(?x, ?z)
+ * assertedProp1(?x, ?y) ^ assertedProp2(?y, ?z) -> inferredProp(?x, ?z)
  * 
  */
 public abstract class SimpleBridgingRule implements ReasonerPlugin {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/reasoner/plugin/SimplePropertyAndTypeRule.java

@@ -18,7 +18,7 @@ import edu.cornell.mannlib.vitro.webapp.reasoner.SimpleReasoner;
 
 /**
  * handles rules of the form
- * assertedProp(?x, ?y) ^ type(?x) -> inferredProp(?x, ?y)
+ * assertedProp(?x, ?y) ^ type(?x) -> inferredProp(?x, ?y)
  *	
  * @author bjl23
  *

api/src/main/java/edu/cornell/mannlib/vitro/webapp/search/controller/PagedSearchController.java

@@ -347,7 +347,6 @@ public class PagedSearchController extends FreemarkerHttpServlet {
 
     /**
      * Get the class groups represented for the individuals in the documents.
-     * @param qtxt 
      */
     private List<VClassGroupSearchLink> getClassGroupsLinks(VitroRequest vreq, VClassGroupDao grpDao, SearchResultDocumentList docs, SearchResponse rsp, String qtxt) {                                 
         Map<String,Long> cgURItoCount = new HashMap<String,Long>();
@@ -604,8 +603,6 @@ public class PagedSearchController extends FreemarkerHttpServlet {
 
     /**
      * Makes a message to display to user for a bad search term.
-     * @param queryText
-     * @param exceptionMsg
      */
     private String makeBadSearchMessage(String querytext, String exceptionMsg, VitroRequest vreq){
         String rv = "";

api/src/main/java/edu/cornell/mannlib/vitro/webapp/sparql/GetAllPrefix.java

@@ -85,7 +85,7 @@ public class GetAllPrefix extends BaseEditController {
 	 * Returns a map of prefixes for use in building queries.  Will manufacture a 
 	 * prefix for any namespace that doesn't have an associated owl:Ontology resource
 	 * with a prefix annotation  
-	 * @param wadf
+	 * @param wadf DAO Factory
 	 * @return map of prefix strings to namespace URIs
 	 */
 	private Map<String, String> getPrefixMap(WebappDaoFactory wadf) {
@@ -135,8 +135,8 @@ public class GetAllPrefix extends BaseEditController {
 	
 	/**
 	 * Makes the markup for a prefix option
-	 * @param prefix
+	 * @param prefix Prefix
-	 * @param URI
+	 * @param URI URI
 	 * @return option string
 	 */
 	private String makeOption(String prefix, String URI) {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/sparql/GetClazzAllProperties.java

@@ -33,9 +33,6 @@ import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
 
 /**
  * This servlet gets all the properties for a given subject.
- * 
- * @param vClassURI
- * @author yuysun
  */
 
 public class GetClazzAllProperties extends BaseEditController {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/sparql/GetClazzDataProperties.java

@@ -22,9 +22,6 @@ import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyDao;
 
 /**
  * This servlet gets all the data properties for a given subject.
- * 
- * @param vClassURI
- * @author yuysun
  */
 
 public class GetClazzDataProperties extends BaseEditController {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/sparql/GetClazzObjectProperties.java

@@ -30,9 +30,6 @@ import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
 
 /**
  * This servlet gets all the object properties for a given subject.
- * 
- * @param vClassURI
- * @author yuysun
  */
 
 public class GetClazzObjectProperties extends BaseEditController {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/sparql/GetObjectClasses.java

@@ -24,9 +24,6 @@ import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
 
 /**
  * This servlet gets all the range classes for a given predicate.
- * 
- * @param predicate
- * @author yuysun
  */
 
 public class GetObjectClasses extends BaseEditController {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/utils/JsonToFmModel.java

@@ -52,7 +52,7 @@ public final class JsonToFmModel
     /**
      * Convert JSON Object string to Freemarker-compatible data model
      * 
-     * @param jsonString
+     * @param jsonString JSON string
      * @return model
      * @throws JSONException
      */
@@ -63,7 +63,7 @@ public final class JsonToFmModel
     }
     
     /**
-     * JSONObject is an unordered collection of name/value pairs -> convert to Map (equivalent to Freemarker "hash")
+     * JSONObject is an unordered collection of name/value pairs -> convert to Map (equivalent to Freemarker "hash")
      */
     @SuppressWarnings("unchecked")
     public static Map<String, Object> convertJSONObjectToMap(JSONObject jo) throws JSONException
@@ -105,7 +105,7 @@ public final class JsonToFmModel
     /**
      * Convert JSON Array string to Freemarker-compatible data model
      * 
-     * @param jsonString
+     * @param jsonString JSON String
      * @return model
      * @throws JSONException
      */
@@ -118,7 +118,7 @@ public final class JsonToFmModel
     }
     
     /**
-     * JSONArray is an ordered sequence of values -> convert to List (equivalent to Freemarker "sequence")
+     * JSONArray is an ordered sequence of values -&gt; convert to List (equivalent to Freemarker "sequence")
      */
     public static List<Object> convertJSONArrayToList(JSONArray ja) throws JSONException
     {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/utils/MakeTidy.java

@@ -81,7 +81,7 @@ public class MakeTidy {
 		}
 
 		/**
-		 * We don't want to log a partial line, so {@link #flush()} does
+		 * We don't want to log a partial line, so does
 		 * nothing.
 		 */
 		@Override

api/src/main/java/edu/cornell/mannlib/vitro/webapp/utils/NamespaceMapper.java

@@ -11,24 +11,21 @@ public interface NamespaceMapper extends ModelChangedListener {
 	/**
 	 * Returns the current abbreviation to use for a given namespace,
 	 * or null if undefined.
-	 * @param namespace
+	 * @param namespace Namespace
-	 * @return
 	 */
 	public String getPrefixForNamespace(String namespace);
 	
 	/**
 	 * Returns a list of abbreviations that have been used to
 	 * represent a given namespace.
-	 * @param namespace
+	 * @param namespace Namespace
-	 * @return
 	 */
 	public List<String> getPrefixesForNamespace(String namespace);
 	
 	/**
 	 * Returns the full namespace URI represented by a given
 	 * abbreviation, or null if not found.
-	 * @param namespace
+	 * @param prefix Prefix
-	 * @return
 	 */
 	public String getNamespaceForPrefix(String prefix);
 	

api/src/main/java/edu/cornell/mannlib/vitro/webapp/utils/SparqlQueryUtils.java

@@ -58,7 +58,7 @@ public class SparqlQueryUtils {
 	
 	/**
 	 * A convenience method to attempt parsing a query string with various syntaxes
-	 * @param queryString
+	 * @param queryString Query String
 	 * @return Query
 	 */
 	public static Query create(String queryString) {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/utils/dataGetter/BrowseDataGetter.java

@@ -143,7 +143,9 @@ public class BrowseDataGetter extends DataGetterBase implements DataGetter {
    
     /**
      * Gets a list of all VClassGroups with vclasses with individual counts.
-     * @param params2 
+     * @param request current VitroRequest
+     * @param params a parameter map
+     * @param context current servlet context
      */
     protected Map<String,Object> getAllClassGroupData(VitroRequest request, Map params, ServletContext context){
         Map<String,Object> map = new HashMap<String,Object>();                  

api/src/main/java/edu/cornell/mannlib/vitro/webapp/utils/dataGetter/DataGetterUtils.java

@@ -352,9 +352,6 @@ public class DataGetterUtils {
     
     /***
      * For the page, get the actual Data Getters to be employed.
-     * @throws ClassNotFoundException 
-     * @throws IllegalAccessException 
-     * @throws InstantiationException 
      */
     /*
     public static List<PageDataGetter> DataGetterObjects(VitroRequest vreq, String pageUri) throws InstantiationException, IllegalAccessException, ClassNotFoundException {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/utils/jena/DedupAndExtract.java

@@ -19,9 +19,8 @@ public class DedupAndExtract {
 	/**
 	 * Returns a model where redundant individuals that are sameAs one another are smushed
 	 * using URIs in preferred namespaces where possible.
-	 * @param model
+	 * @param model Jena Model
-	 * @param preferredIndividualNamespace
+	 * @param preferredNamespace Preferred namespace
-	 * @return
 	 */
 	public Model dedupAndExtract( Model model, String preferredNamespace ) {
 		

api/src/main/java/edu/cornell/mannlib/vitro/webapp/utils/jena/JenaIngestUtils.java

@@ -51,8 +51,8 @@ public class JenaIngestUtils {
 
     /**
      * Returns a new copy of the input model with blank nodes renamed with namespaceEtc plus a random int.
-     * @param namespaceEtc
+     * @param inModel input Jena Model
-     * @return
+     * @param namespaceEtc Namespace
      */
     public Model renameBNodes(Model inModel, String namespaceEtc) {    
         return renameBNodes(inModel, namespaceEtc, null);
@@ -61,8 +61,8 @@ public class JenaIngestUtils {
     /**
      * Returns a new copy of the input model with blank nodes renamed with namespaceEtc plus a random int.
      * Will prevent URI collisions with supplied dedupModel 
-     * @param namespaceEtc
+     * @param inModel input Jena Model
-     * @return
+     * @param namespaceEtc Namespace
      */
     public Model renameBNodes(Model inModel, String namespaceEtc, Model dedupModel) {
         Model outModel = ModelFactory.createDefaultModel();
@@ -361,11 +361,11 @@ public class JenaIngestUtils {
      * Splits values for a given data property URI on a supplied regex and 
      * asserts each value using newPropertyURI.  New statements returned in
      * a Jena Model.  Split values may be optionally trim()ed.
-     * @param inModel
+     * @param inModel Input Jena model
-     * @param propertyURI
+     * @param propertyURI URI for property
-     * @param splitRegex
+     * @param splitRegex Regex for split
-     * @param newPropertyURI
+     * @param newPropertyURI URI for new property
-     * @param trim
+     * @param trim Flag to trim property
      * @return outModel
      */
     public Model splitPropertyValues(Model inModel, String propertyURI, String splitRegex, String newPropertyURI, boolean trim) {
@@ -418,9 +418,8 @@ public class JenaIngestUtils {
     /**
      * A simple resource smusher based on a supplied inverse-functional property.  
      * A new model containing only resources about the smushed statements is returned.
-     * @param inModel
+     * @param inModel Input Jena model
-     * @param prop
+     * @param prop Property
-     * @return
      */
     public Model smushResources(Model inModel, Property prop) { 
         Model outModel = ModelFactory.createDefaultModel();
@@ -480,9 +479,8 @@ public class JenaIngestUtils {
     /**
      * Returns a model where redundant individuals that are sameAs one another are smushed
      * using URIs in preferred namespaces where possible.
-     * @param model
+     * @param model Jena Model
-     * @param preferredIndividualNamespace
+     * @param preferredNamespace Preferred Namespace
-     * @return
      */
     public Model dedupAndExtract( Model model, String preferredNamespace ) {
         Model extractsModel = ModelFactory.createDefaultModel();
@@ -622,7 +620,6 @@ public class JenaIngestUtils {
      * @param baseOntModel The model containing the relevant statements
      * @param tboxOntModel The model containing class and property data
      * @param usePrimaryLabelOnly If true, discard rdfs:labels from uri2.  Otherwise retain.
-     * @return
      */
     public MergeResult doMerge(String uri1, String uri2, OntModel baseOntModel, 
             OntModel tboxOntModel, boolean usePrimaryLabelOnly){

api/src/main/java/edu/cornell/mannlib/vitro/webapp/utils/logging/StackTraceLayout.java

@@ -48,7 +48,7 @@ public class StackTraceLayout extends Layout {
 
 	/**
 	 * The StackTraceLayout does not handle the throwable contained within
-	 * LoggingEvents. Thus, it returns <code>true</code>.
+	 * LoggingEvents. Thus, it returns {@code true}.
 	 */
 	@Override
 	public boolean ignoresThrowable() {