Fixed some SonarCloud issues from the complete code analysis

src/main/java/de/unijena/cheminf/mortar/controller/MainViewController.java

@@ -790,7 +790,7 @@ private void openGlobalSettingsView() {
                     ((GridTabForTableView) tmpTab).getPagination().setPageCount(tmpPageCount);
                     ((GridTabForTableView) tmpTab).getPagination().setCurrentPageIndex(tmpPageIndex);
                     ((GridTabForTableView) tmpTab).getTableView().refresh();
-                    GuiUtil.setImageStructureHeight(((GridTabForTableView) tmpTab).getTableView(), ((GridTabForTableView) tmpTab).getTableView().getHeight(), this.settingsContainer);
+                    GuiUtil.setImageStructureHeight(((GridTabForTableView) tmpTab).getTableView(), ((GridTabForTableView) tmpTab).getTableView().getHeight(), this.settingsContainer.getRowsPerPageSetting());
                     ((GridTabForTableView) tmpTab).getTableView().refresh();
                 }
             }

src/main/java/de/unijena/cheminf/mortar/controller/OverviewViewController.java

@@ -746,7 +746,7 @@ hold the pagination node (since the structureGridPane and pagination node size a
             //check if the limits for the image dimensions are being exceeded
             if ((tmpImageHeight >= OverviewViewController.OVERVIEW_VIEW_STRUCTURE_IMAGE_MIN_HEIGHT)
                     && (tmpImageWidth >= OverviewViewController.OVERVIEW_VIEW_STRUCTURE_IMAGE_MIN_WIDTH)) {
-                //optional setting for change in usage of shadow effect
+                //optional setting for change in usage of shadow effect - deprecated
                 boolean tmpDrawImagesWithShadow = true;
                 //main loop for generation of the page content
                 generationOfStructureImagesLoop:

src/main/java/de/unijena/cheminf/mortar/controller/ViewToolsManager.java

@@ -113,7 +113,7 @@ public ViewToolsManager(IConfiguration aConfiguration) {
         this.viewToolsArray[1] = this.overviewViewController;
         try {
             this.checkViewTools();
-        } catch (Exception anException) {
+        } catch (IOException anException) {
             ViewToolsManager.LOGGER.log(Level.SEVERE, anException.toString(), anException);
             GuiUtil.guiExceptionAlert(Message.get("Error.ExceptionAlert.Title"),
                     Message.get("Error.ExceptionAlert.Header"),
@@ -210,13 +210,14 @@ public void persistViewToolsSettings() {
                 PreferenceContainer tmpPrefContainer = PreferenceUtil.translateJavaFxPropertiesToPreferences(tmpSettings, tmpFilePath);
                 tmpPrefContainer.writeRepresentation();
             } catch (NullPointerException | IllegalArgumentException | IOException | SecurityException anException) {
-                ViewToolsManager.LOGGER.log(Level.WARNING, "View tools settings persistence went wrong, exception: "
-                        + anException.toString(), anException);
+                ViewToolsManager.LOGGER.log(Level.WARNING,
+                        String.format("View tools settings persistence went wrong, exception: %s", anException.toString()),
+                        anException);
                 GuiUtil.guiExceptionAlert(Message.get("Error.ExceptionAlert.Title"),
                         Message.get("Error.ExceptionAlert.Header"),
                         Message.get("ViewToolsManager.Error.settingsPersistence"),
                         anException);
-                continue;
+                //continue;
             }
         }
     }
@@ -236,14 +237,15 @@ public void reloadViewToolsSettings() {
                 try {
                     tmpContainer = new PreferenceContainer(tmpViewToolsSettingsFile);
                 } catch (IllegalArgumentException | IOException anException) {
-                    ViewToolsManager.LOGGER.log(Level.WARNING, "Unable to reload settings of view tool "
-                            + tmpClassName + " : " + anException.toString(), anException);
+                    ViewToolsManager.LOGGER.log(Level.WARNING,
+                            String.format("Unable to reload settings of view tool %s: %s", tmpClassName, anException.toString()),
+                            anException);
                     continue;
                 }
                 this.updatePropertiesFromPreferences(tmpViewTool.settingsProperties(), tmpContainer);
             } else {
                 //settings will remain in default
-                ViewToolsManager.LOGGER.log(Level.WARNING, "No persisted settings for " + tmpClassName + " available.");
+                ViewToolsManager.LOGGER.log(Level.WARNING, "No persisted settings for {0} available.", tmpClassName);
             }
         }
     }
@@ -274,32 +276,32 @@ private void updatePropertiesFromPreferences(List<Property> aPropertiesList, Pre
                         tmpSettingProperty.setValue(tmpStringPreference.getContent());
                     } else {
                         //setting will remain in default
-                        ViewToolsManager.LOGGER.log(Level.WARNING, "Setting " + tmpPropertyName + " is of unknown type.");
+                        ViewToolsManager.LOGGER.log(Level.WARNING, "Setting {0} is of unknown type.", tmpPropertyName);
                     }
                 } catch (ClassCastException | IllegalArgumentException anException) {
                     //setting will remain in default
                     ViewToolsManager.LOGGER.log(Level.WARNING, anException.toString(), anException);
                 }
             } else {
                 //setting will remain in default
-                ViewToolsManager.LOGGER.log(Level.WARNING, "No persisted settings for " + tmpPropertyName + " available.");
+                ViewToolsManager.LOGGER.log(Level.WARNING, "No persisted settings for {0} available.", tmpPropertyName);
             }
         }
     }
     /**
-     * Checks the available view tools and their settings for restrictions imposed by persistence. Throws an exception if
+     * Checks the available view tools and their settings for restrictions imposed by persistence. Throws an IOException if
      * anything does not meet the requirements.
      */
-    private void checkViewTools() throws Exception {
+    private void checkViewTools() throws IOException {
         HashSet<String> tmpViewToolNames = new HashSet<>((int)(this.viewToolsArray.length * 1.5), 0.75f);
         for (IViewToolController tmpViewTool : this.viewToolsArray) {
             //view tool name should be singleton and must be persistable
             String tmpViewToolName = tmpViewTool.getViewToolNameForDisplay();
             if (!PreferenceUtil.isValidName(tmpViewToolName) || !SingleTermPreference.isValidContent(tmpViewToolName)) {
-                throw new Exception("View tool name " + tmpViewToolName + " is invalid.");
+                throw new IOException(String.format("View tool name %s is invalid.", tmpViewToolName));
             }
             if (tmpViewToolNames.contains(tmpViewToolName)) {
-                throw new Exception("View tool name " + tmpViewToolName + " is used multiple times.");
+                throw new IOException(String.format("View tool name %s is used multiple times.", tmpViewToolName));
             } else {
                 tmpViewToolNames.add(tmpViewToolName);
             }
@@ -310,29 +312,29 @@ private void checkViewTools() throws Exception {
             HashSet<String> tmpSettingNames = new HashSet<>((int) (tmpSettingsList.size() * 1.5), 0.75f);
             for (Property tmpSetting : tmpSettingsList) {
                 if (!PreferenceUtil.isValidName(tmpSetting.getName())) {
-                    throw new Exception("Setting " + tmpSetting.getName() + " has an invalid name.");
+                    throw new IOException(String.format("Setting %s has an invalid name.", tmpSetting.getName()));
                 }
                 if (tmpSettingNames.contains(tmpSetting.getName())) {
-                    throw new Exception("Setting name " + tmpSetting.getName() + " is used multiple times.");
+                    throw new IOException(String.format("Setting name %s is used multiple times.", tmpSetting.getName()));
                 } else {
                     tmpSettingNames.add(tmpSetting.getName());
                 }
                 if (tmpSetting instanceof SimpleBooleanProperty) {
                     //nothing to do here, booleans cannot have invalid values
                 } else if (tmpSetting instanceof SimpleIntegerProperty) {
                     if (!SingleIntegerPreference.isValidContent(Integer.toString(((SimpleIntegerProperty) tmpSetting).get()))) {
-                        throw new Exception("Setting value " + ((SimpleIntegerProperty) tmpSetting).get() + " of setting name " + tmpSetting.getName() + " is invalid.");
+                        throw new IOException(String.format("Setting value %d of setting name %s is invalid.", ((SimpleIntegerProperty) tmpSetting).get(), tmpSetting.getName()));
                     }
                 } else if (tmpSetting instanceof SimpleDoubleProperty) {
                     if (!SingleNumberPreference.isValidContent(((SimpleDoubleProperty) tmpSetting).get())) {
-                        throw new Exception("Setting value " + ((SimpleDoubleProperty) tmpSetting).get() + " of setting name " + tmpSetting.getName() + " is invalid.");
+                        throw new IOException(String.format("Setting value %d of setting name %s is invalid.", ((SimpleDoubleProperty) tmpSetting).get(), tmpSetting.getName()));
                     }
                 } else if (tmpSetting instanceof SimpleEnumConstantNameProperty || tmpSetting instanceof SimpleStringProperty) {
                     if (!SingleTermPreference.isValidContent(((SimpleStringProperty) tmpSetting).get())) {
-                        throw new Exception("Setting value " + ((SimpleStringProperty) tmpSetting).get() + " of setting name " + tmpSetting.getName() + " is invalid.");
+                        throw new IOException(String.format("Setting value %s of setting name %s is invalid.", ((SimpleStringProperty) tmpSetting).get(), tmpSetting.getName()));
                     }
                 } else {
-                    throw new Exception("Setting " + tmpSetting.getName() + " is of an invalid type.");
+                    throw new IOException(String.format("Setting %s is of an invalid type.", tmpSetting.getName()));
                 }
             }
         }

src/main/java/de/unijena/cheminf/mortar/gui/controls/MainMenuBar.java

@@ -41,123 +41,121 @@
  * @version 1.0.0.0
  */
 public class MainMenuBar extends MenuBar {
-
-    //<editor-fold desc="private class variables" defaultstate="collapsed">
+    //<editor-fold desc="private final class constants" defaultstate="collapsed">
     /**
      * FileMenu
      */
-    private Menu fileMenu;
+    private final Menu fileMenu;
     /**
      * MenuItem to import molecules
      */
-    private MenuItem openMenuItem;
+    private final MenuItem openMenuItem;
     /**
      * MenuItem for export
      */
-    private Menu exportMenu;
+    private final Menu exportMenu;
     /**
      * Menu for fragments export
      */
-    private Menu fragmentsExportMenu;
+    private final Menu fragmentsExportMenu;
     /**
      * MenuItem to export fragments as csv file
      */
-    private MenuItem fragmentsExportToCSVMenuItem;
+    private final MenuItem fragmentsExportToCSVMenuItem;
     /**
      * MenuItem to export fragments as pdb file
      */
-    private MenuItem fragmentsExportToPDBMenuItem;
+    private final MenuItem fragmentsExportToPDBMenuItem;
     /**
      * MenuItem to export fragments as pdf file
      */
-    private MenuItem fragmentsExportToPDFMenuItem;
+    private final MenuItem fragmentsExportToPDFMenuItem;
     /**
      * Menu for fragments export as sdf
      */
-    private Menu fragmentsExportToSDFMenu;
+    private final Menu fragmentsExportToSDFMenu;
     /**
      * MenuItem to export fragments as sd file
      */
-    private MenuItem fragmentsExportToSingleSDFMenuItem;
+    private final MenuItem fragmentsExportToSingleSDFMenuItem;
     /**
      * MenuItem to export fragments as sd file separately
      */
-    private MenuItem fragmentsExportToSeparateSDFsMenuItem;
+    private final MenuItem fragmentsExportToSeparateSDFsMenuItem;
     /**
      * Menu for items export
      */
-    private Menu itemsExportMenu;
+    private final Menu itemsExportMenu;
     /**
      * MenuItem to export items as csv file
      */
-    private MenuItem itemsExportToCSVMenuItem;
+    private final MenuItem itemsExportToCSVMenuItem;
     /**
      * MenuItem to export fragments as pdf file
      */
-    private MenuItem itemsExportToPDFMenuItem;
+    private final MenuItem itemsExportToPDFMenuItem;
     /**
      * MenuItem to exit app
      */
-    private MenuItem exitMenuItem;
+    private final MenuItem exitMenuItem;
     /**
      * Menu for settings
      */
-    private Menu settingsMenu;
+    private final Menu settingsMenu;
     /**
      * Menu for pipeline
      */
-    private Menu pipelineMenu;
+    private final Menu pipelineMenu;
     /**
      * Menu for help
      */
-    private Menu helpMenu;
+    private final Menu helpMenu;
     /**
      * MenuItem to open fragmentation settings
      */
-    private MenuItem fragmentationSettingsMenuItem;
+    private final MenuItem fragmentationSettingsMenuItem;
     /**
      * MenuItem to open global settings
      */
-    private MenuItem globalSettingsMenuItem;
+    private final MenuItem globalSettingsMenuItem;
     /**
      * MenuItem to open pipeline settings
      */
-    private MenuItem pipelineSettingsMenuItem;
+    private final MenuItem pipelineSettingsMenuItem;
     /**
      * MenuItem to open AboutView
      */
-    private MenuItem aboutViewMenuItem;
+    private final MenuItem aboutViewMenuItem;
     /**
      * Menu to choose fragmentation algorithm
      */
-    private Menu fragmentationAlgorithmMenu;
+    private final Menu fragmentationAlgorithmMenu;
     /**
      * MenuItem to cancel molecule import, only visible if import is running
      */
-    private MenuItem cancelImportMenuItem;
+    private final MenuItem cancelImportMenuItem;
     /**
      * MenuItem to cancel export, only visible if import is running
      */
-    private MenuItem cancelExportMenuItem;
+    private final MenuItem cancelExportMenuItem;
     /**
      * Menu to open views
      */
-    private Menu viewsMenu;
+    private final Menu viewsMenu;
     /**
      * MenuItem to open the histogram
      */
-    private MenuItem histogramViewerMenuItem;
+    private final MenuItem histogramViewerMenuItem;
     /**
      * MenuItem to open the OverviewView
      */
-    private MenuItem overviewViewMenuItem;
+    private final MenuItem overviewViewMenuItem;
     //</editor-fold>
     //
     //<editor-fold desc="constructor" defaultstate="collapsed">
     /**
-     * Constructor
-     * It initialises the MainMenuBar's components, adds them to the MainMenuBar.
-     * No listeners were added here.
+     * Initialises the MainMenuBar's components and adds them to the MainMenuBar.
+     * No listeners are added here.
      */
     public MainMenuBar(){
         super();
@@ -275,7 +273,6 @@ private void addComponentsToExportMenu(){
         this.fragmentsExportMenu.getItems().add(this.fragmentsExportToSDFMenu);
         this.fragmentsExportToSDFMenu.getItems().add(this.fragmentsExportToSingleSDFMenuItem);
         this.fragmentsExportToSDFMenu.getItems().add(this.fragmentsExportToSeparateSDFsMenuItem);
-//        this.exportMenu.show();
         //</editor-fold>
         //<editor-fold desc="itemsExportMenu" defaultstate="collapsed">
         this.exportMenu.getItems().add(this.itemsExportMenu);

src/main/java/de/unijena/cheminf/mortar/gui/controls/StatusBar.java

@@ -41,20 +41,19 @@
  * @version 1.0.0.0
  */
 public class StatusBar extends FlowPane {
-
-    //<editor-fold desc="private class variables" defaultstate="collapsed">
+    //<editor-fold desc="private final class constants" defaultstate="collapsed">
     /**
      * Label to show status message
      */
-    private Label statusLabel;
+    private final Label statusLabel;
     /**
      * ProgressBar
      */
-    private ProgressBar progressBar;
+    private final ProgressBar progressBar;
     //</editor-fold>
     //
     /**
-     * Constructor
+     * Constructor.
      */
     public StatusBar(){
         super();
@@ -73,15 +72,15 @@ public StatusBar(){
     //
     //<editor-fold desc="properties" defaultstate="collapsed">
     /**
-     * Returns statusLabel
+     * Returns statusLabel.
      * @return Label
      */
     public Label getStatusLabel() {
         return this.statusLabel;
     }
     //
     /**
-     * Returns the progressBar
+     * Returns the progressBar.
      * @return ProgressBar
      */
     public ProgressBar getProgressBar() {