clear up code, javadoc

src/gui/asynctaskhandler/AsyncAutoRunner.java

@@ -36,7 +36,7 @@ import joanakey.violations.ViolationsWrapper;
 
 /**
  *
- * @author holger
+ * @author holger,joachim
  */
 public class AsyncAutoRunner implements Runnable {
 
@@ -180,7 +180,7 @@ public class AsyncAutoRunner implements Runnable {
 			NumberFormat formatter = new DecimalFormat("#0.000");
 			Platform.runLater(() -> {
 				if (!violationsWrapper.allDisproved()) {
-					violationsWrapper.resetCheckedEdges();
+					violationsWrapper.resetCheckedEdges(); //TODO: correct to reset checked edges ? 
 					actionLogger.endProgressWithMessage("Run Auto finished attempt in "
 							+ formatter.format((endTime - startTime) / 1000d) + " seconds");
 				} else {

src/joanakey/AutomationHelper.java

@@ -377,13 +377,13 @@ public class AutomationHelper {
                 + LINE_SEP
                 + "[SMTSettings]SelectedTaclets="
                 + LINE_SEP
-                + "[StrategyProperty]METHOD_OPTIONS_KEY="+METHOD_SETTING//METHOD_EXPAND" //TODO: The user should be able to choose from the GUI if he wants expand or contract
+                + "[StrategyProperty]METHOD_OPTIONS_KEY="+METHOD_SETTING
                 + LINE_SEP
                 + "[StrategyProperty]USER_TACLETS_OPTIONS_KEY3=USER_TACLETS_OFF"
                 + LINE_SEP
                 + "[StrategyProperty]SYMBOLIC_EXECUTION_ALIAS_CHECK_OPTIONS_KEY=SYMBOLIC_EXECUTION_ALIAS_CHECK_NEVER"
                 + LINE_SEP
-                + "[StrategyProperty]LOOP_OPTIONS_KEY="+LOOP_SETTING//LOOP_EXPAND" //TODO: The user should be able to choose from the GUI if he want to use the option LOOP_INVARANT instead
+                + "[StrategyProperty]LOOP_OPTIONS_KEY="+LOOP_SETTING
                 + LINE_SEP
                 + "[StrategyProperty]USER_TACLETS_OPTIONS_KEY2=USER_TACLETS_OFF"
                 + LINE_SEP

src/joanakey/CombinedApproach.java

@@ -46,6 +46,13 @@ import joanakey.annotations.SDGAnnotationAdder;
 import joanakey.annotations.SingleAnnotationAdder;
 import joanakey.violations.ViolationsDisproverSemantic;
 
+/**
+ * Entry of the combined approach. 
+ * This class can parse a given .joak file, which is generated by the spec gui and perform a {@link IFCAnalysis} with Joana.
+ * The result of the {@link IFCAnalysis} and the information of the .joak file are used to generate a {@link JoanaAndKeYCheckData}.
+ * @author joachim,..
+ *
+ */
 public class CombinedApproach {
 
     public static final String PATH_KeY = "pathKeY";
@@ -140,6 +147,15 @@ public class CombinedApproach {
         return completeString.toString();
     }
 
+    /**
+     * parse a .joak file and generate {@link JoanaAndKeYCheckData}.
+     * @param filetoload the .joak file you want to parse.
+     * @return {@link JoanaAndKeYCheckData} 
+     * @throws IOException
+     * @throws ClassHierarchyException
+     * @throws UnsoundGraphException
+     * @throws CancelException
+     */
     public static JoanaAndKeYCheckData parseInputFile(File filetoload)
             throws IOException, ClassHierarchyException,
                    UnsoundGraphException, CancelException {
@@ -164,7 +180,7 @@ public class CombinedApproach {
 
         StateSaverCGConsumerBuilder stateSaverBuilder = new StateSaverCGConsumerBuilder();
 
-        SDGAnalysis analysis = (SDGAnalysis) runJoanaCreateSDGAndIFCAnalyis(pathToJar, pathToSDG, entryMethod, stateSaverBuilder); //TODO restore !
+        SDGAnalysis analysis = (SDGAnalysis) runJoanaCreateSDGAndIFCAnalyis(pathToJar, pathToSDG, entryMethod, stateSaverBuilder);
         StateSaver stateSaver;
         if (pathToSDG.isEmpty() && pathToStateSaver.isEmpty()) {
             stateSaver = stateSaverBuilder.buildStateSaver(analysis.getProgram().getSDG(), pathToJar, entryMethod.toString());
@@ -234,17 +250,13 @@ public class CombinedApproach {
         } else if (securityLevelString.equals(LOW_SECURITY)) {
             securityLevelLattice = BuiltinLattices.STD_SECLEVEL_LOW;
         }
-
-
-        Collection<SDGProgramPart> allProgramParts =
-                analysis.getProgram().getAllProgramParts();
-
+        //Collection<SDGProgramPart> allProgramParts =
+        //        analysis.getProgram().getAllProgramParts();
         JSONObject description = jsonObj.getJSONObject(DESCR_CAT);
-        String from = description.getString(FROM);
+        //String from = description.getString(FROM);
         Supplier<Collection<SDGNode>> nodeSupplier = null;
-        Supplier<Collection<SDGNode>> partSupplier = null;
-        
-        String sdgNodeString = description.getString(SDG_NODE);
+        //Supplier<Collection<SDGNode>> partSupplier = null;
+        //String sdgNodeString = description.getString(SDG_NODE);
         int sdgNodeId = description.getInt(SDG_NODE_ID);
         nodeSupplier  = () -> {
                 SDGNode node = analysis.getProgram().getSDG().getNode(sdgNodeId);
@@ -320,6 +332,23 @@ public class CombinedApproach {
         return new SingleAnnotationAdder(partSupplier, annoAddMethod,
                                          securityLevelLattice);
     }
+    
+    /**
+     * perform an IFCAnalysis with the sdg graph given in pathToSDG. 
+     * If this sdg file does not exists, a new {@link SDGProgram}, with a new {@link SDG} is generated. 
+     * If a new {@link SDGProgram} is generated, because of the missing file, the node id's of the new graph can be different from 
+     * the node id's of the sdg graph generated in the spec gui ! 
+     * This can be a problem if you have used the annotation with sdg nodes, in the spec gui.
+     * @param pathToJar String path to the jar file, created by the spec gui.
+     * @param pathToSDG String path to the SDG file, created by the spec gui.
+     * @param entryMethod 
+     * @param stateSaverBuilder
+     * @return
+     * @throws ClassHierarchyException
+     * @throws IOException
+     * @throws UnsoundGraphException
+     * @throws CancelException
+     */
     public static IFCAnalysis
                 runJoanaCreateSDGAndIFCAnalyis(String pathToJar, String pathToSDG,
                                                JavaMethodSignature entryMethod,
@@ -334,30 +363,26 @@ public class CombinedApproach {
         //TODO: write new methods for the two branches and catch empty sdg/saver files
         if (sdg == null || !sdg.exists() || pathToSDG.isEmpty()) { 
             SDGConfig config =
-                    new SDGConfig(pathToJar, entryMethod.toBCString(), Stubs.JRE_15);//TODO: does jre_15 works ?
+                    new SDGConfig(pathToJar, entryMethod.toBCString(), Stubs.JRE_15);
             config.setComputeInterferences(true);
             config.setMhpType(MHPType.PRECISE);
             config.setPointsToPrecision(PointsToPrecision.INSTANCE_BASED);
             config.setExceptionAnalysis(ExceptionAnalysis.INTERPROC);
             config.setFieldPropagation(FieldPropagation.OBJ_GRAPH_NO_MERGE_AT_ALL);
-    
             // save intermediate results of SDG generation points to call graph
             config.setCGConsumer(stateSaverBuilder);
             // Schneidet beim SDG application edges raus, so besser sichtbar mit dem graphviewer
             config.setPruningPolicy(ApplicationLoaderPolicy.INSTANCE);
-    
-            System.out.println("File not found: "+ pathToSDG);
+            //System.out.println("File not found: "+ pathToSDG);
             program = SDGProgram.createSDGProgram(config, System.out,
                     new NullProgressMonitor());
         } else {
             program = SDGProgram.loadSDG(pathToSDG, MHPType.PRECISE);
-            System.out.println("SDG loaded from file "+ pathToSDG);
+            //System.out.println("SDG loaded from file "+ pathToSDG);
         }
-        //TODO check if overloading or overriding methods ?!
+        //TODO check if some methods should be overwritten ?!
         SDGAnalysis ana = new SDGAnalysis(program);
-        
         return ana;
-    
     }
     
     private static String concatenatePaths(String firstPart, String secondPart) {

src/joanakey/SDGAnalysis.java

-/**
- * This file is part of the Joana IFC project. It is developed at the
- * Programming Paradigms Group of the Karlsruhe Institute of Technology.
- *
- * For further details on licensing please read the information at
- * http://joana.ipd.kit.edu or contact the authors.
- */
 package joanakey;
 
 import java.util.Collection;
@@ -26,14 +19,10 @@ import joanakey.annotations.SDGNodeAnnotation;
 import joanakey.annotations.SDGNodeAnnotationManager;
 
 /**
+ * Subclass of {@link IFCAnalysis} which also allows to annotate {@link SDGNode}s instead of only {@link SDGProgramPart}s.
  * @author muessig.
  */
 public class SDGAnalysis extends IFCAnalysis {
-
-//	private SDGNodeAnnotationManager sdgAnnManager;
-//	private SDGProgram program;
-//    private IFC<String> ifc;
-//    private IStaticLattice<String> secLattice;
     
 	/**
 	 * @param program

src/joanakey/StateSaver.java

@@ -43,66 +43,7 @@ public class StateSaver {
     private HashMap<SDGNode, PersistentCGNode> formalInsToPersistentCGNodes = new HashMap<>();
     private TIntIntMap node2CG = null;
     private TIntIntMap node2SSA = null;
-
-//    @Override
-//    public void consume(CallGraph callGraph,
-//                        PointerAnalysis<? extends InstanceKey> pointerAnalyis) {
-//        this.callGraph = callGraph;
-//        this.pointerAnalyis = pointerAnalyis;
-//    }
-
-//    public static StateSaver generateFromJson(JSONObject jsonObj, SDG sdg)
-//            throws IOException {
-//        StateSaver stateSaver = new StateSaver();
-//
-//        JSONArray formalNodeToCGNodeArr = jsonObj.getJSONArray(FORMAL_INS_TO_PERS_CG);
-//        for (int i = 0; i < formalNodeToCGNodeArr.length(); ++i) {
-//            JSONObject currentPair = formalNodeToCGNodeArr.getJSONObject(i);
-//            int sdgIndex = currentPair.getInt(SDG_NODE);
-//            JSONObject persistentCGNode = currentPair.getJSONObject(CG_NODE);
-//            SDGNode node = sdg.getNode(sdgIndex);
-//            stateSaver.formalInsToPersistentCGNodes.put(node,
-//                                                        PersistentCGNode
-//                                                        .generateFromJsonObj(persistentCGNode));
-//        }
-//
-//        JSONArray cgNodeArr = jsonObj.getJSONArray(CG_NODE + "s");
-//        for (int i = 0; i < cgNodeArr.length(); ++i) {
-//            JSONObject currentCGNodeSaveObj = cgNodeArr.getJSONObject(i);
-//            PersistentCGNode currentPersistentCGNode =
-//                    PersistentCGNode.generateFromJsonObj(currentCGNodeSaveObj);
-//            stateSaver.persistentCGNodes.add(currentPersistentCGNode);
-//            stateSaver.cgNodeIdToPersistentCGNodes.put(currentPersistentCGNode.getCgNodeId(),
-//                                                       currentPersistentCGNode);
-//        }
-//
-//        JSONArray pointerKeyArr = jsonObj.getJSONArray(LOCAL_POINTER_KEYS);
-//        for (int i = 0; i < pointerKeyArr.length(); ++i) {
-//            JSONObject currentPointerKeyJsonObj = pointerKeyArr.getJSONObject(i);
-//            PersistentLocalPointerKey currentLocalPointerKey =
-//                    PersistentLocalPointerKey.generateFromJsonObj(currentPointerKeyJsonObj,
-//                                                                  stateSaver.persistentCGNodes);
-//            stateSaver.persistentLocalPointerKeys.add(currentLocalPointerKey);
-//        }
-//
-//        JSONArray disjunctPointstoArr = jsonObj.getJSONArray(DISJUNCT_POINTS_TO);
-//        for (int i = 0; i < disjunctPointstoArr.length(); ++i) {
-//            JSONObject currentDisjObj = disjunctPointstoArr.getJSONObject(i);
-//            int key = currentDisjObj.getInt(KEY);
-//            JSONArray values = currentDisjObj.getJSONArray(VALUES);
-//            List<PersistentLocalPointerKey> disPointers = new ArrayList<>();
-//            for (int j = 0; j < values.length(); ++j) {
-//                int currDisIndex = values.getInt(j);
-//                disPointers.add(stateSaver.persistentLocalPointerKeys.get(currDisIndex));
-//            }
-//            PersistentLocalPointerKey keyPointerKey =
-//                    stateSaver.persistentLocalPointerKeys.get(key);
-//            stateSaver.disjunctPointsToSets.put(keyPointerKey, disPointers);
-//        }
-//
-//        return stateSaver;
-//    }    
-    
+   
     public CallGraph getCallGraph() {
 		return callGraph;
 	}