code clear up, javadoc

src/gui/DisproHandler.java

@@ -6,7 +6,6 @@
 package gui;
 
 import java.io.IOException;
-import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -15,7 +14,6 @@ import java.util.Map;
 import java.util.Set;
 
 import org.fxmisc.richtext.CodeArea;
-import org.jgrapht.ext.JGraphModelAdapter.CellFactory;
 
 import edu.kit.joana.ifc.sdg.core.SecurityNode;
 import edu.kit.joana.ifc.sdg.core.violations.ClassifiedViolation;
@@ -37,7 +35,6 @@ import javafx.scene.layout.AnchorPane;
 import javafx.scene.paint.Color;
 import javafx.util.Callback;
 import joanakey.JoanaAndKeYCheckData;
-import joanakey.customlistener.SummaryEdgeAndMethodToCorresData;
 import joanakey.customlistener.ViolationsWrapperListener;
 import joanakey.errorhandling.ErrorLogger;
 import joanakey.persistence.DisprovingProject;
@@ -49,7 +46,7 @@ import keyjoana.settings.SettingsObserver;
 
 /**
  *
- * @author holger
+ * @author holger, joachim
  */
 public class DisproHandler implements ViolationsWrapperListener, SettingsObserver {
 
@@ -91,7 +88,6 @@ public class DisproHandler implements ViolationsWrapperListener, SettingsObserve
     private AnchorPane anchorPaneKeyContract;
 
     private Map<Integer, ViolationChop> itemIndexToViolation = new HashMap<>();
-    private Map<ViolationChop, Boolean> violationChecked = new HashMap<>();
     private Map<Integer, SDGEdge> itemIndexToSummaryEdge = new HashMap<>();
     private HashMap<Integer, SDGNodeTuple> currentIndexToNodeTuple = new HashMap<>();
     private Map<SDGEdge, StaticCGJavaMethod> summaryEdgesAndCorresJavaMethods;
@@ -103,7 +99,6 @@ public class DisproHandler implements ViolationsWrapperListener, SettingsObserve
     private SDGEdge currentSelectedEdge;
     private StaticCGJavaMethod currentSelectedMethod;
     private CurrentActionLogger currentActionLogger;
-    private boolean autoRunIsRunning = false;
     private boolean useSlicing = false;
     private boolean useLoopUnwinding = false;
     private boolean useMethodInlining = false;
@@ -204,6 +199,11 @@ public class DisproHandler implements ViolationsWrapperListener, SettingsObserve
         setSUViewListFactory();
     }
 
+    /**
+     * enable or disable all Buttons 
+     * (auto run, mark as disproven, reset loop invariant, save loop invariant, open selected in KeY and try Disprove)
+     * @param disable true to disable all {@link Button}s or false to enable all {@link Button}s.
+     */
     public void setAllButtonsDisable(boolean disable) {
         buttonRunAuto.setDisable(disable);
         buttonMarkAsDisproved.setDisable(disable);
@@ -213,6 +213,9 @@ public class DisproHandler implements ViolationsWrapperListener, SettingsObserve
         buttonTryDisprove.setDisable(disable);
     }
     
+    /**
+     * toggle availability of all Buttons except the Auto run button.
+     */
     private void toggleButtonsForAutoRun() {
     	buttonMarkAsDisproved.setDisable(!buttonMarkAsDisproved.isDisabled());
     	buttonResetLoopInvariant.setDisable(!buttonResetLoopInvariant.isDisabled());
@@ -342,6 +345,12 @@ public class DisproHandler implements ViolationsWrapperListener, SettingsObserve
         return disprovingProject;
     }
 
+
+    /**
+     * generate a new {@link DisprovingProject} with the given {@link JoanaAndKeYCheckData}. This method disable all Buttons while generating 
+     * the {@link DisprovingProject}.
+     * @param checkData 
+     */
     public void handleNewDispro(JoanaAndKeYCheckData checkData) {
         setAllButtonsDisable(true);
         backgroundDisproCreator.generateFromCheckData(checkData, (dispro, worked) -> {
@@ -769,7 +778,6 @@ public class DisproHandler implements ViolationsWrapperListener, SettingsObserve
 //            labelSomeOtherData.setText("All security violations have been disproved with KeY!");
             this.setSomeOtherMessageAndColor("All security violations have been disproved with KeY!", Color.GREEN);
             buttonRunAuto.setDisable(true);
-            //TODO: check this method !
             displayAllViolationChecked();
            // AutomationHelper.playSound(SOUND);
         });
@@ -822,7 +830,7 @@ public class DisproHandler implements ViolationsWrapperListener, SettingsObserve
 	}
 	
 	
-	//TODO:	 "CLOSED" check with datastructure
+	//TODO:	 "CLOSED" check with datastructure. Dont use the the list item name ?
 	private void displayAllViolationChecked() {
 //		for (int i : itemIndexToViolation.keySet()) {
 		for (int i = 0; i < listViewUncheckedChops.getItems().size(); i++) {
@@ -884,8 +892,6 @@ public class DisproHandler implements ViolationsWrapperListener, SettingsObserve
                             if (item.startsWith("CLOSED")) {
                                 setStyle("-fx-control-inner-background: " + HIGHLIGHTED_CONTROL_INNER_BACKGROUND + ";");
                                 
-                                
-                                //TODO: dont disable, so you can still see the disproven edges. But disable the buttons for closed summary edges !
 //                                setDisable(true);
                                 if(!violationsWrapper.allCheckedOrDisproved()) {
                                 	listViewUncheckedChops.getSelectionModel().select(0);
@@ -903,8 +909,8 @@ public class DisproHandler implements ViolationsWrapperListener, SettingsObserve
 	}
 	
 	/**
-	 * this method set the cell factory of the violation listView. 
-	 * Change the cells if the violation is closed/checked
+	 * this method set the cell factory of the summary edges listView. 
+	 * Change the cells occurrence if the summary edge is closed/checked
 	 */
 	private void setSUViewListFactory() {
 		listViewSummaryEdges.setCellFactory(new Callback<ListView<String>, ListCell<String>>() {
@@ -936,6 +942,11 @@ public class DisproHandler implements ViolationsWrapperListener, SettingsObserve
 	}
 
 	
+	/**
+	 * set the gui status 'other message' to the given message in the given color
+	 * @param message you want to print at the gui
+	 * @param color in which you would like to have the message 
+	 */
 	public void setSomeOtherMessageAndColor(String message, javafx.scene.paint.Color color) {
 		this.labelSomeOtherData.setText(message);
 		this.labelSomeOtherData.setTextFill(color);

src/gui/JoanaKeYInterfacer.java

@@ -8,6 +8,7 @@ package gui;
 import java.io.IOException;
 import java.util.ArrayList;
 
+import edu.kit.joana.ifc.sdg.graph.SDG;
 import edu.kit.joana.ifc.sdg.graph.SDGEdge;
 import edu.kit.joana.ifc.sdg.graph.SDGNodeTuple;
 import joanakey.AutomationHelper;
@@ -19,11 +20,10 @@ import joanakey.violations.ViolationChop;
 import joanakey.violations.ViolationsDisproverSemantic;
 import joanakey.violations.ViolationsDisproverSemantic.PO_TYPE;
 import joanakey.violations.ViolationsWrapper;
-import keyjoana.settings.SettingsObserver;
 
 /**
- *
- * @author holger
+ * this class can be used to start the disproving process with KeY (also with command line mode)
+ * @author holger, joachim
  */
 public class JoanaKeYInterfacer {
 
@@ -83,6 +83,14 @@ public class JoanaKeYInterfacer {
 		}
     }
 
+    /**
+     * try to disprove the given summary Edge with KeY in command line mode.
+     * @param e {@link SDGEdge} you want to disprove
+     * @param tuple 
+     * @param corresMethod
+     * @return true if successfully disproven. Otherwise return False.
+     * @throws IOException
+     */
     public boolean tryDisproveEdge(
             SDGEdge e,
             SDGNodeTuple tuple,
@@ -111,6 +119,11 @@ public class JoanaKeYInterfacer {
         return worked;
     }
 
+    /**
+     * mark the given {@link SDGEdge} as disproven and remove it from the {@link SDG} in {@link ViolationsWrapper}.
+     * @param currentSelectedEdge the {@link SDGEdge} you want to mark as disproven.
+     * @throws IllegalArgumentException
+     */
     public void markAsDisproved(SDGEdge currentSelectedEdge) throws IllegalArgumentException{
     	if(currentSelectedEdge == null) {
     		throw new IllegalArgumentException("No method selected!");
@@ -132,11 +145,19 @@ public class JoanaKeYInterfacer {
 		this.useSlicedFiles = selected;
 	}
 
+	/**
+	 * set method inlining option for the disproving process
+	 * @param selected true, if you want to use method inlining 
+	 */
 	public void setUseMethodInlining(boolean selected) {
 		this.useMethodInlining = selected;
 		javaForKeyCreator.setMethodInlining(selected);
 	}
-	
+
+	/**
+	 * set loop unwinding option for the disproving process
+	 * @param selected true, if you want to use loop unwinding 
+	 */
 	public void setUseLoopUnwinding(boolean selected) {
 		this.useLoopUnwinding = selected;
 		javaForKeyCreator.setUseLoopUnwinding(selected);

src/gui/MainWindowController.java

@@ -37,7 +37,7 @@ import keyjoana.util.FilesUtil;
 
 /**
  *
- * @author holger
+ * @author holger,joachim
  */
 public class MainWindowController implements Initializable, SettingsObserver {
 
@@ -282,6 +282,7 @@ public class MainWindowController implements Initializable, SettingsObserver {
 		});
 	}
 
+	@SuppressWarnings("unused")
 	@Deprecated
 	private void reloadLastFile() {
 		if (lastFileLoaded == null) {
@@ -340,9 +341,7 @@ public class MainWindowController implements Initializable, SettingsObserver {
 		keyJoanaSettings.addSettingObserver(settingsManager);
 		keyJoanaSettings.addSettingObserver(this);
 		settingsManager.loadSettings();
-		//TODO: load settings from file with settingsmanager
 		
-		//TODO: remove boolean settings (loopundwind, method expand, slicing, and use keyJoanaSettings instead
 		disproHandler = new DisproHandler(actionLogger, labelProjName, labelSummaryEdge, labelSomeOtherData,
 				menuBarMain, listViewUncheckedEdges, listViewUncheckedChops, listViewCalledMethodsOfSE,
 				listViewLoopsOfSE, listViewFormalInoutPairs, anchorPaneMethodCode, anchorPaneLoopInvariant,

src/gui/RecentlyUsedFilesManager.java

@@ -9,7 +9,7 @@ import java.util.ArrayList;
 
 /**
  * this class manages the recently loaded files 
- * @author joachim muessig
+ * @author joachim
  *
  */
 public class RecentlyUsedFilesManager {
@@ -93,7 +93,6 @@ public class RecentlyUsedFilesManager {
 		if (recentlyUsedFiles.size() > maxNumberOfSavedRecentlyLoadedFiles) {
 			recentlyUsedFiles.remove(recentlyUsedFiles.size()-1);
 		}
-		//TODO:Update list/stack/array for the recently loaded file
 		//Update mostRecentlyUsedFile
 		//store new content in the File for recently loaded files
 		try {