clear up code, javadoc

src/joanakey/persistence/JsonHelper.java

@@ -11,16 +11,35 @@ package joanakey.persistence;
  */
 public class JsonHelper {
 
+	/**
+	 * generate a key value pair and append it to the given stringBuilder object. The value is appended with quotes as String ("value").
+	 * @param stringBuilder object to which you want append the key, value pair
+	 * @param key json key 
+	 * @param value as string
+	 */
     public static void addJsonStringToStringBuilder(StringBuilder stringBuilder,
                                                     String key, String value) {
         stringBuilder.append("\"" + key + "\" : " + "\"" + value + "\"");
     }
 
+    /**
+	 * generate a key value pair and append it to the given stringBuilder object. The value is appended without quotes.
+	 * @param stringBuilder object to which you want append the key, value pair
+	 * @param key json key 
+	 * @param value as string
+     */
     public static void addKeyValueToJsonStringbuilder(StringBuilder stringBuilder,
                                                       String key, String value) {
         stringBuilder.append("\"" + key + "\" : " + value);
     }
 
+
+    /**
+     * generate a key value pair and append it to the given stringBuilder object. The value is appended with curly brackets.
+     * @param stringBuilder object to which you want to append the key, value pair.
+     * @param key json key
+     * @param value as string
+     */
     public static void addJsonObjValueToStringBuiler(StringBuilder stringBuilder,
                                                      String key, String value) {
         stringBuilder.append("\"" + key + "\" : {\n");

src/joanakey/persistence/PersistentCGNode.java

@@ -12,6 +12,8 @@ import org.json.JSONObject;
 import com.ibm.wala.ipa.callgraph.CGNode;
 import com.ibm.wala.ipa.callgraph.propagation.LocalPointerKey;
 
+import net.bytebuddy.asm.Advice.This;
+
 /**
  *
  * @author hklein
@@ -25,6 +27,11 @@ public class PersistentCGNode {
     private static final String CG_NODE_ID ="cg_node_id";
     private static final String IR ="ir";
     
+    /**
+     * generate a {@link PersistentCGNode} object from the given jsonObj
+     * @param jsonObj which contains the call graph node information
+     * @return {@link PersistentCGNode}
+     */
     public static PersistentCGNode generateFromJsonObj(JSONObject jsonObj) {
         PersistentCGNode node =
                 new PersistentCGNode(jsonObj.getInt(ID), jsonObj.getInt(CG_NODE_ID));
@@ -46,6 +53,10 @@ public class PersistentCGNode {
         persistentIR = new PersistentIR(localPointerKeys, n, uniqueId);
     }
     
+    /**
+     * generate a string which contain the information of this {@link PersistentCGNode}.
+     * @return String containing information about this object (ID, CG Node ID, IR)
+     */
     public String generateSaveString() { 
         return "\"" + ID + "\" : " + uniqueId + ", "
                 + "\""+ CG_NODE_ID + "\" :" + cgNodeId + ", " +

src/joanakey/persistence/PersistentIR.java

@@ -25,6 +25,11 @@ public class PersistentIR {
     private Map<Integer, String> vnsToLocalNames = new HashMap<>();
     private int containingNodeId;
 
+    /**
+     * generate a {@link PersistentIR} object from the given jsonObj
+     * @param jsonObj which contains needed information
+     * @return {@link PersistentIR}
+     */
     public static PersistentIR generateFromJsonObj(JSONObject jsonObject, int nodeId) {
         PersistentIR persistentIR = new PersistentIR();
         persistentIR.containingNodeId = nodeId;
@@ -57,7 +62,11 @@ public class PersistentIR {
             }
         }
     }
-
+    
+    /**
+     * generate a string which contain the information of this {@link PersistentIR} object.
+     * @return String containing information about this object.
+     */
     public String generateSaveString() {
         StringBuilder sb = new StringBuilder();
         vnsToLocalNames.forEach((i, s) -> {

src/joanakey/persistence/PersistentLocalPointerKey.java

@@ -26,6 +26,12 @@ public class PersistentLocalPointerKey {
     private PersistentCGNode persistentCGNode;
     private int id;
 
+    /**
+     * generate a {@link PersistentLocalPointerKey} object from the given jsonObj
+     * @param jsonObj which contains needed information
+     * @param cgNodes, list of {@link PersistentCGNode}
+     * @return {@link PersistentCGNode}
+     */
     public static PersistentLocalPointerKey generateFromJsonObj(JSONObject jsonObj,
                                                                 List<PersistentCGNode> cgNodes) {
         int nodeIndex = jsonObj.getInt(NODE);
@@ -42,6 +48,7 @@ public class PersistentLocalPointerKey {
     private PersistentLocalPointerKey() {
     }
 
+
     public PersistentLocalPointerKey(LocalPointerKey localPointerKey, PersistentCGNode persistentCGNode,
                                      int uniqueId) {
         valueNumber = localPointerKey.getValueNumber();
@@ -61,6 +68,10 @@ public class PersistentLocalPointerKey {
         return id;
     }
 
+    /**
+     * generate a string which contain the information of this {@link PersistentLocalPointerKey} object.
+     * @return String containing information about this object.
+     */
     public String generateSaveString() {
         return "\"" + ID + "\" : " + id
                 + ", \"" + VALUE_NUMBER + "\" : " + String.valueOf(valueNumber)

src/joanakey/persistence/ViolationsSaverLoader.java

@@ -32,6 +32,11 @@ public class ViolationsSaverLoader {
     private static final String VIOL_PATHS = "violpaths";
     private static final String NODE_IDS = "node_ids";
 
+    /**
+     * generate a string which contain information of the given {@link IViolation} objects.
+     * @param violations you want to generate the String for.
+     * @return String
+     */
     public static String generateSaveString(Collection<? extends IViolation<SecurityNode>> violations) {
         StringBuilder created = new StringBuilder();
 
@@ -76,6 +81,12 @@ public class ViolationsSaverLoader {
         return created.toString();
     }
 
+    /**
+     * generate a collection of {@link ClassifiedViolation}s from the given {@link JSONArray}
+     * @param violationsArr, containg multiple {@link JSONObjects} with violation informations.
+     * @param sdg Graph, used to get the corresponding sdg nodes
+     * @return 
+     */
     public static Collection<ClassifiedViolation> generateFromJSON(JSONArray violationsArr, SDG sdg) {
         Collection<ClassifiedViolation> created = new ArrayList<>();