Minor code improvements

api/src/main/java/edu/cornell/mannlib/vedit/controller/BaseEditController.java

@@ -178,18 +178,15 @@ public class BaseEditController extends VitroHttpServlet {
 
        List<String> bodyVal = new ArrayList<String>();
        List<Option> options = new ArrayList<Option>();
-       Iterator<Option> itr = optionList.iterator();
+        for (Option option : optionList) {
-        while(itr.hasNext()){
-            Option option = itr.next();
             hashMap.put(option.getBody(), option);
             bodyVal.add(option.getBody());
         }
         
                 
        Collections.sort(bodyVal, new ListComparator(vreq.getCollator()));
-       ListIterator<String> itrStr = bodyVal.listIterator();
+        for (String aBodyVal : bodyVal) {
-       while(itrStr.hasNext()){
+            options.add(hashMap.get(aBodyVal));
-           options.add(hashMap.get(itrStr.next()));
         }
        return options;
    }

api/src/main/java/edu/cornell/mannlib/vedit/tags/DynamicFieldsTag.java

@@ -162,10 +162,9 @@ public class DynamicFieldsTag extends EditTag {
 
                     out.print(preWithVars);
 
-                    Iterator<DynamicFieldRow> rowIt = dynf.getRowList().iterator();
+                    for (DynamicFieldRow dynamicFieldRow : dynf.getRowList()) {
-                     while (rowIt.hasNext()) {
                         ++i;
-                        DynamicFieldRow row = rowIt.next();
+                        DynamicFieldRow row = dynamicFieldRow;
                         if (row.getValue() == null)
                             row.setValue("");
                         if (row.getValue().length() > 0) {

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

@@ -301,9 +301,7 @@ public class IndividualImpl extends BaseResourceBean implements Individual, Comp
     protected void sortEnts2EntsForDisplay(){
         if( getObjectPropertyList() == null ) return;
 
-        Iterator it = getObjectPropertyList().iterator();
+        for (ObjectProperty prop : getObjectPropertyList()) {
-        while(it.hasNext()){
-            ObjectProperty prop = (ObjectProperty)it.next();
             prop.sortObjectPropertyStatementsForDisplay(prop, prop.getObjectPropertyStatements());
         }
     }

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

@@ -144,9 +144,7 @@ public class EntityEditController extends BaseEditController {
         try {
             List<Option> externalIdOptionList = new LinkedList<Option>();
             if (ent.getExternalIds() != null) {
-                Iterator<DataPropertyStatement> externalIdIt = ent.getExternalIds().iterator();
+                for (DataPropertyStatement eid : ent.getExternalIds()) {
-                while (externalIdIt.hasNext()) {
-                    DataPropertyStatement eid = externalIdIt.next();
                     String multiplexedString = "DatapropURI:" + new String(Base64.encodeBase64(eid.getDatapropURI().getBytes())) + ";" + "Data:" + new String(Base64.encodeBase64(eid.getData().getBytes()));
                     externalIdOptionList.add(new Option(multiplexedString, eid.getData()));
                 }
@@ -169,9 +167,7 @@ public class EntityEditController extends BaseEditController {
         try {
             List epiOptionList = new LinkedList();
             Collection<PropertyInstance> epiColl = piDao.getExistingProperties(ent.getURI(),null);
-            Iterator<PropertyInstance> epiIt = epiColl.iterator();
+            for (PropertyInstance pi : epiColl) {
-            while (epiIt.hasNext()) {
-                PropertyInstance pi = epiIt.next();
                 String multiplexedString = "PropertyURI:" + new String(Base64.encodeBase64(pi.getPropertyURI().getBytes())) + ";" + "ObjectEntURI:" + new String(Base64.encodeBase64(pi.getObjectEntURI().getBytes()));
                 epiOptionList.add(new Option(multiplexedString, pi.getDomainPublic() + " " + pi.getObjectName()));
             }

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

@@ -211,10 +211,8 @@ public class EntityRetryController extends BaseEditController {
         Collections.sort(allApplicableDataprops);
         
         if (allApplicableDataprops != null) {
-            Iterator<DataProperty> datapropsIt = allApplicableDataprops.iterator();
 
-            while (datapropsIt.hasNext()){
+            for (DataProperty d : allApplicableDataprops) {
-                DataProperty d = datapropsIt.next();
                 if (!dpMap.containsKey(d.getURI())) {
                     dpMap.put(d.getURI(), d);
                 }
@@ -222,9 +220,7 @@ public class EntityRetryController extends BaseEditController {
             }
 
             if (individualForEditing.getDataPropertyList() != null) {
-                Iterator<DataProperty> existingDps = individualForEditing.getDataPropertyList().iterator();
+                for (DataProperty existingDp : individualForEditing.getDataPropertyList()) {
-                while (existingDps.hasNext()) {
-                    DataProperty existingDp = existingDps.next();
                     // Since the edit form begins with a "name" field, which gets saved as the rdfs:label,
                     // do not want to include the label as well.
                     if (!existingDp.getPublicName().equals("label")) {
@@ -249,9 +245,7 @@ public class EntityRetryController extends BaseEditController {
                 rowTemplate.setParameterMap(parameterMap);
                 dynamo.setRowTemplate(rowTemplate);
                 try {
-                    Iterator<DataPropertyStatement> existingValues = dp.getDataPropertyStatements().iterator();
+                    for (DataPropertyStatement existingValue : dp.getDataPropertyStatements()) {
-                    while (existingValues.hasNext()) {
-                        DataPropertyStatement existingValue = existingValues.next();
                         DynamicFieldRow row = new DynamicFieldRow();
                         //TODO: UGH
                         //row.setId(existingValue.getId());

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

@@ -122,9 +122,7 @@ public class ObjectPropertyStatementRetryController extends BaseEditController {
         indList.addAll(possIndSet);
         sortForPickList(indList, vreq);
         List objectEntOptionList = new LinkedList();
-        Iterator<Individual> indIt = indList.iterator();
+        for (Individual objInd : indList) {
-        while (indIt.hasNext()) {
-            Individual objInd = indIt.next();
             Option objIndOpt = new Option(objInd.getURI(), objInd.getName());
             if (objectForEditing.getObjectEntURI() != null && objectForEditing.getObjectEntURI().equals(objInd.getURI())) {
                 objIndOpt.setSelected(true);

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

@@ -203,9 +203,7 @@ public class VclassEditController extends BaseEditController {
     
     private List<VClass> getVClassesForURIList(List<String> vclassURIs, VClassDao vcDao) {
         List<VClass> vclasses = new ArrayList<VClass>();
-        Iterator<String> urIt = vclassURIs.iterator();
+        for (String vclassURI : vclassURIs) {
-        while (urIt.hasNext()) {
-            String vclassURI = urIt.next();
             VClass vclass = vcDao.getVClassByURI(vclassURI);
             if (vclass != null) {
                 vclasses.add(vclass);

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/edit/listing/IndividualsListingController.java

@@ -55,7 +55,7 @@ public class IndividualsListingController extends BaseEditController {
         String vclassURI = request.getParameter("VClassURI");
         VClass vc = vcDao.getVClassByURI(vclassURI);
         
-        List inds = dao.getIndividualsByVClassURI(vclassURI);
+        List<Individual> inds = dao.getIndividualsByVClassURI(vclassURI);
         //List inds = dao.getIndividualsByVClassURI(vclassURI,1,MAX_INDIVIDUALS);
 
         ArrayList results = new ArrayList();
@@ -64,10 +64,7 @@ public class IndividualsListingController extends BaseEditController {
         results.add("class");
 
         if (inds != null && inds.size()>0) {
-            Iterator indsIt = inds.iterator();
+            for (Individual ind : inds) {
-            while (indsIt.hasNext()) {
-                Individual ind = (Individual) indsIt.next();
-
                 results.add("XX");
 
                 if (ind.getName() != null) {

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

@@ -146,12 +146,11 @@ public class ListPropertyWebappsController extends FreemarkerHttpServlet {
                 if (props.size()==0) {
                     json = new StringBuilder("{ \"name\": \"" + noResultsMsgStr + "\" }");
                 } else {
-                    Iterator<ObjectProperty> propsIt = props.iterator();
+                    for (ObjectProperty prop1 : props) {
-                    while (propsIt.hasNext()) {
                         if (counter > 0) {
                             json.append(", ");
                         }
-                        ObjectProperty prop = propsIt.next();
+                        ObjectProperty prop = prop1;
 
                         String propNameStr = ShowObjectPropertyHierarchyController.getDisplayLabel(prop);
 

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

@@ -83,12 +83,11 @@ public class ListVClassWebappsController extends FreemarkerHttpServlet {
 
         if (classes != null) {
             sortForPickList(classes, vreq);
-            Iterator<VClass> classesIt = classes.iterator();
+			for (VClass aClass : classes) {
-            while (classesIt.hasNext()) {
 				if (counter > 0) {
 					json.append(", ");
 				}
-                VClass cls = (VClass) classesIt.next();
+				VClass cls = aClass;
 				if ((ontologyURI == null) || ((ontologyURI != null) && (cls.getNamespace() != null) && (ontologyURI.equals(cls.getNamespace())))) {
 					if (cls.getName() != null)
 						try {

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

@@ -134,15 +134,14 @@ public class ShowClassHierarchyController extends FreemarkerHttpServlet {
         List<String> childURIstrs = vcDao.getSubClassURIs(parent.getURI());
         if ((childURIstrs.size()>0) && position<MAXDEPTH) {
             List<VClass> childClasses = new ArrayList<VClass>();
-            Iterator<String> childURIstrIt = childURIstrs.iterator();
+            for (String URIstr : childURIstrs) {
-            while (childURIstrIt.hasNext()) {
-                String URIstr = childURIstrIt.next();
                 try {
                     VClass child = vcDao.getVClassByURI(URIstr);
                     if (!child.getURI().equals(OWL.Nothing.getURI())) {
                         childClasses.add(child);
                     }
-                } catch (Exception e) {}
+                } catch (Exception e) {
+                }
             }
             sortForPickList(childClasses, vreq);
             Iterator<VClass> childClassIt = childClasses.iterator();

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

@@ -147,9 +147,7 @@ public class ShowDataPropertyHierarchyController extends FreemarkerHttpServlet {
         List<String> childURIstrs = dpDao.getSubPropertyURIs(parent.getURI());
         if ( (childURIstrs.size() > 0) && (position < MAXDEPTH) ) {
             List<DataProperty> childProps = new ArrayList<DataProperty>();
-            Iterator<String> childURIstrIt = childURIstrs.iterator();
+            for (String URIstr : childURIstrs) {
-            while (childURIstrIt.hasNext()) {
-                String URIstr = childURIstrIt.next();
                 DataProperty child = dpDao.getDataPropertyByURI(URIstr);
                 childProps.add(child);
             }

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

@@ -151,9 +151,7 @@ public class ShowObjectPropertyHierarchyController extends FreemarkerHttpServlet
         List<String> childURIstrs = opDao.getSubPropertyURIs(parent.getURI());
         if ( (childURIstrs.size() > 0) && (position < MAXDEPTH) ) {
             List<ObjectProperty> childProps = new ArrayList<ObjectProperty>();
-            Iterator<String> childURIstrIt = childURIstrs.iterator();
+            for (String URIstr : childURIstrs) {
-            while (childURIstrIt.hasNext()) {
-                String URIstr = childURIstrIt.next();
                 ObjectProperty child = opDao.getObjectPropertyByURI(URIstr);
                 childProps.add(child);
             }

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

@@ -203,9 +203,7 @@ public class GrefinePropertyListServlet extends VitroHttpServlet {
 		List<DataProperty> props = new ArrayList<DataProperty>();
 		VClass topVc = vcDao.getVClassByURI(uri);
 		Collection <DataProperty> dataProps = dao.getDataPropertiesForVClass(uri);
-	        Iterator<DataProperty> dataPropIt = dataProps.iterator();
+		for (DataProperty dp : dataProps) {
-	        while (dataPropIt.hasNext()) {
-	            DataProperty dp = dataPropIt.next();
 			if (!(propURIs.contains(dp.getURI()))) {
 				propURIs.add(dp.getURI());
 				DataProperty prop = dao.getDataPropertyByURI(dp.getURI());
@@ -256,20 +254,19 @@ public class GrefinePropertyListServlet extends VitroHttpServlet {
 	        List childURIstrs = vcDao.getSubClassURIs(parent.getURI());
 	        if ((childURIstrs.size()>0) && position<MAXDEPTH) {
 	            List childClasses = new ArrayList();
-	            Iterator childURIstrIt = childURIstrs.iterator();
+				for (Object childURIstr : childURIstrs) {
-	            while (childURIstrIt.hasNext()) {
+					String URIstr = (String) childURIstr;
-	                String URIstr = (String) childURIstrIt.next();
 					try {
 						VClass child = (VClass) vcDao.getVClassByURI(URIstr);
 						if (!child.getURI().equals(OWL.Nothing.getURI())) {
 							childClasses.add(child);
 						}
-	                } catch (Exception e) {}
+					} catch (Exception e) {
+					}
 				}
 	            Collections.sort(childClasses);
-	            Iterator childClassIt = childClasses.iterator();
+				for (Object childClass : childClasses) {
-	            while (childClassIt.hasNext()) {
+					VClass child = (VClass) childClass;
-	                VClass child = (VClass) childClassIt.next();
 					addChildren(vcDao, wadf, child, list, position + childShift, ontologyUri);
 				}
 

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

@@ -403,9 +403,7 @@ public class JSONReconcileServlet extends VitroHttpServlet {
         query.addFields(VitroSearchTermNames.NAME_RAW, VitroSearchTermNames.URI, "*", "score"); // fields to retrieve
  
 		// if propertiesList has elements, add extra queries to query
-		Iterator<String[]> it = propertiesList.iterator();
+		for (String[] pvPair : propertiesList) {
-		while (it.hasNext()) {
-			String[] pvPair = it.next();
 			query.addFilterQueries(tokenizeNameQuery(pvPair[1]), VitroSearchTermNames.RDFTYPE + ":\"" + pvPair[0] + "\"");
 		}       
 

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

@@ -500,9 +500,7 @@ public class JenaIngestController extends BaseEditController {
         List<Ontology> ontologiesObj = daoObj.getAllOntologies();
         List<String> prefixList = new ArrayList<>();       
         if(ontologiesObj !=null && ontologiesObj.size()>0){
-            Iterator<Ontology> ontItr = ontologiesObj.iterator();
+            for (Ontology ont : ontologiesObj) {
-            while(ontItr.hasNext()){
-                Ontology ont = ontItr.next();
                 prefixList.add(ont.getPrefix() == null ? "(not yet specified)" : ont.getPrefix());
                 prefixList.add(ont.getURI() == null ? "" : ont.getURI());
             }

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

@@ -190,11 +190,9 @@ public class VClassDaoFiltering extends BaseFiltering implements VClassDao{
         }
     }
 
-    public void addVClassesToGroups(List groups) {
+    public void addVClassesToGroups(List<VClassGroup> groups) {
         if ((groups != null) && (groups.size()>0)) {
-            Iterator groupIt = groups.iterator();
+            for (VClassGroup g : groups) {
-            while (groupIt.hasNext()) {
-                VClassGroup g = (VClassGroup) groupIt.next();
                 this.addVClassesToGroup(g);
             }
         } else {

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

@@ -633,9 +633,7 @@ public class DataPropertyDaoJena extends PropertyDaoJena implements
                     		isRoot = true;
                     	} else {
                     		isRoot = true;
-                    	    Iterator<Property> pit = parentList.iterator();
+                            for (Property pt : parentList) {
-                    	    while (pit.hasNext()) {
-                    	    	Property pt = pit.next();
                                 if ((!pt.equals(op)) && (!(ontModel.contains(op, OWL.equivalentProperty, pt)) || (ontModel.contains(pt, OWL.equivalentProperty, op)))) {
                                     isRoot = false;
                                 }

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

@@ -66,9 +66,7 @@ public class DependentResourceDeleteJena {
 		ListIterator <Statement>removed = removedStmts.listIterator();
 		while( removed.hasNext()){
 			Statement removedStmt = removed.next();
-			ListIterator <Statement>changed = changedStmts.listIterator();			
+			for (Statement changedStmt : changedStmts) {
-			while( changed.hasNext()){
-				Statement changedStmt = changed.next();
 				if (removedStmt.equals(changedStmt)) {
 					removed.remove();
 				}

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

@@ -69,9 +69,7 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao {
         HashSet<String> nonExternalIdPropURISet = new HashSet<String>();
         if (ind != null) {
             Collection<DataPropertyStatement> dpsColl = getWebappDaoFactory().getDataPropertyStatementDao().getDataPropertyStatementsForIndividualByDataPropertyURI(ind, dataPropertyURI);
-            Iterator<DataPropertyStatement> dpsIt = dpsColl.iterator();
+            for (DataPropertyStatement dps : dpsColl) {
-            while (dpsIt.hasNext()) {
-                DataPropertyStatement dps = dpsIt.next();
                 if (externalIdPropURISet.contains(dps.getDatapropURI())) {
                     externalIdStatements.add(dps);
                 } else if (!nonExternalIdPropURISet.contains(dps.getDatapropURI())) {

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

@@ -311,10 +311,7 @@ public class IndividualDaoSDB extends IndividualDaoJena {
     private void fillIndividualsForObjectPropertyStatements(Individual entity){
         getOntModel().enterCriticalSection(Lock.READ);
         try {
-            Iterator e2eIt = entity.getObjectPropertyStatements().iterator();
+            for (ObjectPropertyStatement e2e : entity.getObjectPropertyStatements()) {
-            while (e2eIt.hasNext()) {
-                ObjectPropertyStatement e2e = 
-                		(ObjectPropertyStatement) e2eIt.next();
                 e2e.setSubject(makeIndividual(e2e.getSubjectURI()));
                 e2e.setObject(makeIndividual(e2e.getObjectURI()));
             }

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

@@ -517,9 +517,7 @@ public class IndividualJena extends IndividualImpl implements Individual {
     protected void sortEnts2EntsForDisplay(){
         if( getObjectPropertyList() == null ) return;
 
-        Iterator it = getObjectPropertyList().iterator();
+		for (ObjectProperty prop : getObjectPropertyList()) {
-        while(it.hasNext()){
-            ObjectProperty prop = (ObjectProperty)it.next();
 			/*  if (prop.getObjectIndividualSortPropertyURI()==null) {
             	prop.sortObjectPropertyStatementsForDisplay(prop,prop.getObjectPropertyStatements());
             } else {*/

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

@@ -953,9 +953,7 @@ public class IndividualSDB extends IndividualImpl implements Individual {
     protected void sortEnts2EntsForDisplay(){ 
         if( getObjectPropertyList() == null ) return;
 
-        Iterator it = getObjectPropertyList().iterator();
+		for (ObjectProperty prop : getObjectPropertyList()) {
-        while(it.hasNext()){
-            ObjectProperty prop = (ObjectProperty)it.next();
 			/*  if (prop.getObjectIndividualSortPropertyURI()==null) {
             	prop.sortObjectPropertyStatementsForDisplay(prop,prop.getObjectPropertyStatements());
             } else {*/

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

@@ -771,9 +771,7 @@ public class JenaBaseDao extends JenaBaseDaoCon {
     }
     
     private Literal getLabel(String lang, List<RDFNode>labelList) {
-    	Iterator<RDFNode> labelIt = labelList.iterator();
+        for (RDFNode label : labelList) {
-    	while (labelIt.hasNext()) {
-    		RDFNode label = labelIt.next();
             if (label.isLiteral()) {
                 Literal labelLit = ((Literal) label);
                 String labelLanguage = labelLit.getLanguage();
@@ -1019,9 +1017,7 @@ public class JenaBaseDao extends JenaBaseDaoCon {
     	}
     	// Now for each value, work backwards and see if it has an alternate path to the original resource.
     	// If not, add it to the list of direct values.
-    	Iterator<Resource> possibleValueIt = possibleValueSet.iterator();
+        for (Resource possibleRes : possibleValueSet) {
-    	while (possibleValueIt.hasNext()) {
-    		Resource possibleRes = possibleValueIt.next();
             StmtIterator pStmtIt = getOntModel().listStatements((Resource) null, prop, possibleRes);
             boolean hasAlternatePath = false;
             while (stmtIt.hasNext()) {
@@ -1048,9 +1044,7 @@ public class JenaBaseDao extends JenaBaseDaoCon {
     		possibleSubjectSet.add(stmt.getSubject());
     		
     	}
-    	Iterator<Resource> possibleSubjectIt = possibleSubjectSet.iterator();
+        for (Resource possibleRes : possibleSubjectSet) {
-    	while (possibleSubjectIt.hasNext()) {
-    		Resource possibleRes = possibleSubjectIt.next();
             StmtIterator pStmtIt = getOntModel().listStatements(possibleRes, prop, (RDFNode) null);
             boolean hasAlternatePath = false;
             while (stmtIt.hasNext()) {

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

@@ -497,9 +497,7 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
             }
 
             List<ObjectProperty> props = new ArrayList<ObjectProperty>();
-            Iterator<String> keyIt = hash.keySet().iterator();
+            for (String key : hash.keySet()) {
-            while (keyIt.hasNext()) {
-                Object key = keyIt.next();
                 props.add(hash.get(key));
             }
             return props;

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

@@ -163,9 +163,7 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
 
     private void getAllSubPropertyURIs(String propertyURI, HashSet<String> subtree){
         List<String> directSubproperties = getSubPropertyURIs(propertyURI);
-        Iterator<String> it=directSubproperties.iterator();
+		for (String uri : directSubproperties) {
-        while(it.hasNext()){
-            String uri = it.next();
 			if (!subtree.contains(uri)) {
 				subtree.add(uri);
 				getAllSubPropertyURIs(uri, subtree);
@@ -206,9 +204,7 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
 
     private void getAllSuperPropertyURIs(String propertyURI, HashSet<String> subtree){
         List<String> directSuperproperties = getSuperPropertyURIs(propertyURI,true);
-        Iterator<String> it=directSuperproperties.iterator();
+		for (String uri : directSuperproperties) {
-        while(it.hasNext()){
-            String uri = it.next();
 			if (!subtree.contains(uri)) {
 				subtree.add(uri);
 				getAllSuperPropertyURIs(uri, subtree);
@@ -421,11 +417,7 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
         List<OntClass> classList = ontClass.listEquivalentClasses().toList();
         classList.addAll(ontClass.listSubClasses().toList());
 
-        Iterator<OntClass> it = classList.iterator();
+		for (OntClass oc : classList) {
-		         
-        while (it.hasNext()) {
-        	OntClass oc = it.next();
-        	
 			if (!oc.isAnon()) {
 				classSet.add(oc.getURI());
 			} else {

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

@@ -148,12 +148,8 @@ public class PropertyInstanceDaoJena extends PropertyDaoJena implements
         List existingPropertyInstances = new ArrayList();
         if (ent.getObjectPropertyList()==null)
             return existingPropertyInstances;
-        Iterator objPropertyIter = ent.getObjectPropertyList().iterator();
+        for (edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty op : ent.getObjectPropertyList()) {
-        while (objPropertyIter.hasNext()) {
+            for (ObjectPropertyStatement objPropertyStmt : op.getObjectPropertyStatements()) {
-            edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty op = (edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty) objPropertyIter.next();
-            Iterator objPropertyStmtIter = op.getObjectPropertyStatements().iterator();
-            while (objPropertyStmtIter.hasNext()) {
-                ObjectPropertyStatement objPropertyStmt = (ObjectPropertyStatement) objPropertyStmtIter.next();
                 if (propertyURI == null || objPropertyStmt.getPropertyURI().equals(propertyURI)) {
                     PropertyInstance pi = new PropertyInstance();
                     pi.setSubjectSide(true);

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

@@ -411,9 +411,7 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
 
     public void getAllSubClassURIs(String classURI, HashSet<String> subtree){
         List<String> directSubclasses = getSubClassURIs(classURI);
-        Iterator<String> it=directSubclasses.iterator();
+        for (String uri : directSubclasses) {
-        while(it.hasNext()){
-            String uri = it.next();
             if (!subtree.contains(uri)) {
                 subtree.add(uri);
                 getAllSubClassURIs(uri, subtree);
@@ -450,9 +448,7 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
 
     public void getAllSuperClassURIs(String classURI, HashSet<String> subtree){
         List<String> directSuperclasses = getSuperClassURIs(classURI, true);
-        Iterator<String> it=directSuperclasses.iterator();
+        for (String uri : directSuperclasses) {
-        while(it.hasNext()){
-            String uri = it.next();
             if (!subtree.contains(uri)) {
                 subtree.add(uri);
                 getAllSuperClassURIs(uri, subtree);
@@ -787,9 +783,7 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
 						// if this model infers types based on the taxonomy, adding the subclasses will only
 						// waste time for no benefit
 						if (!isUnderlyingStoreReasoned()) {
-                        	Iterator classURIs = getAllSubClassURIs(getClassURIStr(superclass)).iterator();
+                            for (String classURI : getAllSubClassURIs(getClassURIStr(superclass))) {
-                        	while (classURIs.hasNext()) {
-                            	String classURI = (String) classURIs.next();
                                 VClass vClass = getVClassByURI(classURI);
                                 if (vClass != null)
                                     vClasses.add(vClass);
@@ -919,9 +913,7 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
         getOntModel().enterCriticalSection(Lock.READ);
         try {
             if (groups != null) {
-                Iterator groupIt = groups.iterator();
+                for (VClassGroup g : groups) {
-                while (groupIt.hasNext()) {
-                    VClassGroup g = (VClassGroup) groupIt.next();
                     addVClassesToGroup(g);
                 }
             }

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

@@ -87,9 +87,7 @@ public class VClassGroupDaoJena extends JenaBaseDao implements VClassGroupDao {
                 groupIt.close();
             }
             Collections.sort(groups);
-            Iterator<VClassGroup> groupsIt = groups.iterator();
+            for (VClassGroup group : groups) {
-            while (groupsIt.hasNext()) {
-                VClassGroup group = groupsIt.next();
                 map.put(group.getPublicName(), group);
             }
             return map;

api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/listener/impl/IndividualDataPropertyStatementProcessor.java

@@ -39,11 +39,9 @@ public class IndividualDataPropertyStatementProcessor implements ChangeListener
 
     private void processDataprops (EditProcessObject epo) {
         HashSet<String> deletedDataPropertyURIs = new HashSet<String>();
-        Map dpm = datapropParameterMap(epo.getRequestParameterMap());
+        Map<String, String[]> dpm = datapropParameterMap(epo.getRequestParameterMap());
         DataPropertyStatementDao dataPropertyStatementDao = (DataPropertyStatementDao)epo.getAdditionalDaoMap().get("DataPropertyStatement");
-        Iterator dpmIt = dpm.keySet().iterator();
+        for (String key : dpm.keySet()) {
-        while (dpmIt.hasNext()) {
-            String key = (String) dpmIt.next();
             String[] data = (String[]) dpm.get(key);
             for (String aData : data) {
                 String[] keyArg = key.split("_");
@@ -105,11 +103,9 @@ public class IndividualDataPropertyStatementProcessor implements ChangeListener
     }
 
     // might want to roll this into the other thing
-    private HashMap datapropParameterMap(Map requestParameterMap) {
+    private Map<String, String[]> datapropParameterMap(Map<String, String[]> requestParameterMap) {
-        HashMap dpm = new HashMap();
+        Map<String, String[]> dpm = new HashMap<String, String[]>();
-        Iterator paramIt = requestParameterMap.keySet().iterator();
+        for (String key : requestParameterMap.keySet()) {
-        while (paramIt.hasNext()) {
-            String key = (String) paramIt.next();
             if (key.startsWith("_DataPropertyStatement")) {
                 dpm.put(key, requestParameterMap.get(key));
             }

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

@@ -463,9 +463,7 @@ public class ProcessRdfForm {
 	   Map<String, List<String>> newUris = new HashMap<String, List<String>>();
 	   //Check if any values from the submission have the "force new uri" value
 	   //TODO: Check how to handle multiple new resource values
-	   Iterator<String> keyIterator = urisFromForm.keySet().iterator();
+       for (String key : urisFromForm.keySet()) {
-	   while(keyIterator.hasNext()) {
-		   String key = keyIterator.next();
            if (urisFromForm.get(key).contains(EditConfigurationConstants.NEW_URI_SENTINEL)) {
                String newUri = urisForNewResources.get(key);
                List<String> newUrisForKey = new ArrayList<String>();

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

@@ -91,11 +91,7 @@ public class ABoxUpdater {
 	 */
 	public void processClassChanges(List<AtomicOntologyChange> changes) throws IOException {
 
-		Iterator<AtomicOntologyChange> iter = changes.iterator();
+		for (AtomicOntologyChange change : changes) {
-		
-		while (iter.hasNext()) {
-			AtomicOntologyChange change = iter.next();
-
 			switch (change.getAtomicChangeType()) {
 				case ADD:
 					addClass(change);
@@ -236,11 +232,7 @@ public class ABoxUpdater {
 			namedClassList.add(OWL_THING);
 		}
 
-		Iterator<OntClass> classIter = namedClassList.iterator();
+		for (OntClass parentOfAddedClass : namedClassList) {
-		
-		while (classIter.hasNext()) {
-			OntClass parentOfAddedClass = classIter.next();
-
 			if (!parentOfAddedClass.equals(OWL.Thing)) {
 
 				Iterator<String> graphIt = dataset.listNames();
@@ -415,9 +407,7 @@ public class ABoxUpdater {
 	
 	public void processPropertyChanges(List<AtomicOntologyChange> changes) throws IOException {
 
-		Iterator<AtomicOntologyChange> propItr = changes.iterator();
+		for (AtomicOntologyChange propChangeObj : changes) {
-		while(propItr.hasNext()){
-			AtomicOntologyChange propChangeObj = propItr.next();
 			log.debug("processing " + propChangeObj);
 			try {
 				if (propChangeObj.getAtomicChangeType() == null) {

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

@@ -419,10 +419,7 @@ public class KnowledgeBaseUpdater {
 				List<AtomicOntologyChange> changeList, OntModel newTboxModel,
 				OntModel oldTboxModel) throws IOException {
 
-			Iterator<AtomicOntologyChange> listItr = changeList.iterator();
+			for (AtomicOntologyChange changeObj : changeList) {
-			
-			while(listItr.hasNext()) {
-				AtomicOntologyChange changeObj = listItr.next();
 				if (changeObj.getSourceURI() != null) {
 					log.debug("triaging " + changeObj);
 					if (oldTboxModel.getOntProperty(changeObj.getSourceURI()) != null) {

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

@@ -171,9 +171,7 @@ public class LanguageFilteringRDFService implements RDFService {
                 s.sparqlSelectQuery(query, RDFService.ResultFormat.JSON));
         List<QuerySolution> solnList = getSolutionList(resultSet);
         List<String> vars = resultSet.getResultVars();
-        Iterator<String> varIt = vars.iterator();
+        for (String var : vars) {
-        while (varIt.hasNext()) {
-            String var = varIt.next();           
             for (int i = 0; i < solnList.size(); i++) {
                 QuerySolution s = solnList.get(i);
                 if (s == null) {
@@ -218,9 +216,7 @@ public class LanguageFilteringRDFService implements RDFService {
             }
         }
         List<QuerySolution> compactedList = new ArrayList<QuerySolution>();
-        Iterator<QuerySolution> solIt = solnList.iterator();
+        for (QuerySolution soln : solnList) {
-        while(solIt.hasNext()) {
-            QuerySolution soln = solIt.next();
             if (soln != null) {
                 compactedList.add(soln);
             }
@@ -268,9 +264,7 @@ public class LanguageFilteringRDFService implements RDFService {
             protected void endProcessing() {
                 chainStartProcessing();
 
-                Iterator<String> varIt = vars.iterator();
+                for (String var : vars) {
-                while (varIt.hasNext()) {
-                    String var = varIt.next();
                     for (int i = 0; i < solnList.size(); i++) {
                         QuerySolution s = solnList.get(i);
                         if (s == null) {
@@ -315,9 +309,7 @@ public class LanguageFilteringRDFService implements RDFService {
                     }
                 }
 
-                Iterator<QuerySolution> solIt = solnList.iterator();
+                for (QuerySolution soln : solnList) {
-                while(solIt.hasNext()) {
-                    QuerySolution soln = solIt.next();
                     if (soln != null) {
                         chainProcessQuerySolution(soln);
                     }

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

@@ -142,9 +142,7 @@ public abstract class RDFServiceImpl implements RDFService {
 	
     protected void notifyListeners(ModelChange modelChange) throws IOException {
         modelChange.getSerializedModel().reset();
-        Iterator<ChangeListener> iter = registeredListeners.iterator();
+        for (ChangeListener listener : registeredListeners) {
-        while (iter.hasNext()) {
-            ChangeListener listener = iter.next();
             listener.notifyModelChange(modelChange);
         }
         log.debug(registeredJenaListeners.size() + " registered Jena listeners");
@@ -174,15 +172,11 @@ public abstract class RDFServiceImpl implements RDFService {
     }
     
     public void notifyListenersOfEvent(Object event) {
-        Iterator<ChangeListener> iter = registeredListeners.iterator();
+        for (ChangeListener listener : registeredListeners) {
-        while (iter.hasNext()) {
-            ChangeListener listener = iter.next();
             // TODO what is the graphURI parameter for?
             listener.notifyEvent(null, event);
         }
-        Iterator<ModelChangedListener> jenaIter = registeredJenaListeners.iterator();
+        for (ModelChangedListener listener : registeredJenaListeners) {
-        while (jenaIter.hasNext()) {
-            ModelChangedListener listener = jenaIter.next();
             listener.notifyEvent(null, event);
         }
     }    

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

@@ -79,9 +79,7 @@ public class RDFServiceModel extends RDFServiceJena implements RDFService {
                 this.notifyListenersOfEvent(o);
             }
 
-            Iterator<ModelChange> csIt = changeSet.getModelChanges().iterator();
+            for (ModelChange modelChange : changeSet.getModelChanges()) {
-            while (csIt.hasNext()) {
-                ModelChange modelChange = csIt.next();
                 if (!modelChange.getSerializedModel().markSupported()) {
                     byte[] bytes = IOUtils.toByteArray(modelChange.getSerializedModel());
                     modelChange.setSerializedModel(new ByteArrayInputStream(bytes));

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

@@ -178,9 +178,7 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
 		        this.notifyListenersOfEvent(o);
 			}
 
-			Iterator<ModelChange> csIt = changeSet.getModelChanges().iterator();
+			for (ModelChange modelChange : changeSet.getModelChanges()) {
-			while (csIt.hasNext()) {
-				ModelChange modelChange = csIt.next();
 				if (!modelChange.getSerializedModel().markSupported()) {
 					byte[] bytes = IOUtils.toByteArray(modelChange.getSerializedModel());
 					modelChange.setSerializedModel(new ByteArrayInputStream(bytes));

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

@@ -73,9 +73,7 @@ public class IndividualURIQueue<E> implements Queue<E> {
     @Override
     public synchronized boolean retainAll(Collection<?> c) {
         boolean changed = false;
-        Iterator<E> it = m.keySet().iterator();
+        for (E e : m.keySet()) {
-        while(it.hasNext()) {
-            E e = it.next();
             if (!c.contains(e)) {
                 m.remove(e);
                 q.remove(e);

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

@@ -563,9 +563,7 @@ public class SimpleReasoner extends StatementListener
 
 	    aboxModel.enterCriticalSection(Lock.READ);
 	    try {
-	        Iterator<Resource> sameIter = sameIndividuals.iterator();
+			for (Resource res : sameIndividuals) {
-	        while (sameIter.hasNext()) {
-	            Resource res = sameIter.next();
 				StmtIterator typeIt = aboxModel.listStatements(res, RDF.type, (RDFNode) null);
 				while (typeIt.hasNext()) {
 					Statement stmt = typeIt.nextStatement();
@@ -802,10 +800,7 @@ public class SimpleReasoner extends StatementListener
 				if (handleSameAs) {
 					List<Resource> sameIndividuals = 
                         getSameIndividuals(infStmt.getSubject().asResource(), inferenceModel);
-					Iterator<Resource> sameIter = sameIndividuals.iterator();
+					for (Resource subject : sameIndividuals) {
-					while (sameIter.hasNext()) {
-						Resource subject = sameIter.next();
-						
 						Statement sameStmt =
 								ResourceFactory.createStatement(subject, infStmt.getPredicate(),
 										infStmt.getObject());
@@ -860,10 +855,9 @@ public class SimpleReasoner extends StatementListener
 			    List<Resource> sameIndividuals = 
                     getSameIndividuals(infStmt.getSubject().asResource(), inferenceModel);
 
-			    Iterator<Resource> sameIter = sameIndividuals.iterator();	 
+				for (Resource sameIndividual : sameIndividuals) {
-			    while (sameIter.hasNext()) {
 					Statement infStmtSame =
-                      ResourceFactory.createStatement(sameIter.next(), 
+							ResourceFactory.createStatement(sameIndividual,
 									infStmt.getPredicate(), infStmt.getObject());
 					if ((!checkEntailment
 							|| !entailedStatement(infStmtSame))
@@ -936,16 +930,9 @@ public class SimpleReasoner extends StatementListener
 			List<OntClass> types2 = new ArrayList<OntClass>();
 			types2.addAll(types);
 
-			Iterator<OntClass> typeIter = types.iterator();
+			for (OntClass type : types) {
-			
-			while (typeIter.hasNext()) {
-			    OntClass type = typeIter.next();
-			    			    
 				boolean add = true;
-			    Iterator<OntClass> typeIter2 = types2.iterator();
+				for (OntClass type2 : types2) {
-			    while (typeIter2.hasNext()) {
-			    	OntClass type2 = typeIter2.next();
-			    				    	
 					if (type.equals(type2)) {
 						continue;
 					}
@@ -971,10 +958,7 @@ public class SimpleReasoner extends StatementListener
 						equivalentClasses.add(res);
 					}
 
-		            Iterator<Resource> eIter = equivalentClasses.iterator();
+					for (Resource equivClass : equivalentClasses) {
-		                
-		            while (eIter.hasNext()) {
-		                Resource equivClass = eIter.next();
 						if (equivClass.isAnon()) continue;
 						typeURIs.add(equivClass.getURI());
 					}
@@ -1019,9 +1003,7 @@ public class SimpleReasoner extends StatementListener
 			removeInference(rIter.next(), inferenceModel, true, false);
 		}
 
-		Iterator<String> typeIter = typeURIs.iterator();		
+		for (String typeURI : typeURIs) {
-		while (typeIter.hasNext()) {
-			String typeURI = typeIter.next();
 			Statement mstStmt = ResourceFactory.createStatement(individual, mostSpecificType, ResourceFactory.createResource(typeURI));
 			addInference(mstStmt, inferenceModel, true);
 		}

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

@@ -174,10 +174,8 @@ public abstract class SimpleBridgingRule implements ReasonerPlugin {
         } else if (stmt.getPredicate().equals(assertedProp2)) {
             z = stmt.getObject();
         }
-        Iterator<Statement> sit = aboxInferencesModel.listStatements(x, this.inferredProp, z).toList().iterator();
 
-        while(sit.hasNext()) {
+		for (Statement s : aboxInferencesModel.listStatements(x, this.inferredProp, z).toList()) {
-        	Statement s = sit.next();
 			Query ask = createQuery(this.retractionTestString, stmt, s);
 			QueryExecution qe = QueryExecutionFactory.create(ask, aboxAssertionsModel);
 			try {

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

@@ -197,10 +197,8 @@ public class PagedSearchController extends FreemarkerHttpServlet {
             }            
             
             List<Individual> individuals = new ArrayList<Individual>(docs.size());
-            Iterator<SearchResultDocument> docIter = docs.iterator();
+            for (SearchResultDocument doc : docs) {
-            while( docIter.hasNext() ){
                 try {
-                    SearchResultDocument doc = docIter.next();
                     String uri = doc.getStringValue(VitroSearchTermNames.URI);
                     Individual ind = iDao.getIndividualByURI(uri);
                     if (ind != null) {

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

@@ -77,10 +77,8 @@ public class GetAllClasses extends BaseEditController {
 
 		while (classGroupIt.hasNext()) {
 			VClassGroup group = (VClassGroup) classGroupIt.next();
-			List classes = group.getVitroClassList();
+			List<VClass> classes = group.getVitroClassList();
-			Iterator classIt = classes.iterator();
+			for (VClass clazz : classes) {
-			while (classIt.hasNext()) {
-				VClass clazz = (VClass) classIt.next();
 				respo.append("<option>" + "<key>").append(clazz.getPickListName()).append("</key>").append("<value>").append(clazz.getURI()).append("</value>").append("</option>");
 			}
 		}

api/src/main/java/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/GroupedPropertyList.java

@@ -644,9 +644,7 @@ public class GroupedPropertyList extends BaseTemplateModel {
     }
     
     public PropertyGroupTemplateModel pullPropertyGroup(String groupName) {
-        Iterator<PropertyGroupTemplateModel> groupIt = groups.iterator();
+        for (PropertyGroupTemplateModel group : groups) {
-        while (groupIt.hasNext()) {
-            PropertyGroupTemplateModel group = groupIt.next();
             if (groupName.equals(group.getName())) {
                 groups.remove(group);
                 return group;

api/src/test/java/edu/cornell/mannlib/vitro/webapp/dao/jena/VClassJenaTest.java

@@ -426,9 +426,7 @@ public class VClassJenaTest {
     }
     
     private String getLabel2(String lang, List<RDFNode>labelList) {
-    	Iterator<RDFNode> labelIt = labelList.iterator();
+		for (RDFNode label : labelList) {
-    	while (labelIt.hasNext()) {
-    		RDFNode label = labelIt.next();
 			if (label.isLiteral()) {
 				Literal labelLit = ((Literal) label);
 				String labelLanguage = labelLit.getLanguage();