Split the project into separate modules.

fx/build.gradle

@@ -0,0 +1,7 @@
+apply plugin: 'application'
+
+dependencies {
+  compile project(':core')
+}
+
+mainClassName = 'org.nwapw.abacus.fx.AbacusApplication'

fx/src/main/java/org/nwapw/abacus/fx/AbacusApplication.java

@@ -0,0 +1,41 @@
+package org.nwapw.abacus.fx;
+
+import javafx.application.Application;
+import javafx.fxml.FXMLLoader;
+import javafx.scene.Parent;
+import javafx.scene.Scene;
+import javafx.stage.Stage;
+
+/**
+ * The main application class for JavaFX responsible for loading
+ * and displaying the fxml file.
+ */
+public class AbacusApplication extends Application {
+
+    /**
+     * The controller currently managing the application.
+     */
+    private AbacusController controller;
+
+    @Override
+    public void start(Stage primaryStage) throws Exception {
+        FXMLLoader loader = new FXMLLoader(getClass().getResource("/abacus.fxml"));
+        Parent parent = loader.load();
+        controller = loader.getController();
+        Scene mainScene = new Scene(parent, 320, 480);
+        primaryStage.setScene(mainScene);
+        primaryStage.setTitle("Abacus");
+        primaryStage.show();
+    }
+
+    @Override
+    public void stop() throws Exception {
+        super.stop();
+        controller.performStop();
+    }
+
+    public static void main(String[] args){
+        launch(args);
+    }
+
+}

fx/src/main/java/org/nwapw/abacus/fx/AbacusController.java

@@ -0,0 +1,376 @@
+package org.nwapw.abacus.fx;
+
+import javafx.application.Platform;
+import javafx.beans.value.ChangeListener;
+import javafx.beans.value.ObservableValue;
+import javafx.collections.FXCollections;
+import javafx.collections.ObservableList;
+import javafx.collections.transformation.FilteredList;
+import javafx.fxml.FXML;
+import javafx.scene.Node;
+import javafx.scene.control.*;
+import javafx.scene.control.cell.CheckBoxListCell;
+import javafx.scene.text.Text;
+import javafx.util.Callback;
+import javafx.util.StringConverter;
+import org.nwapw.abacus.Abacus;
+import org.nwapw.abacus.config.Configuration;
+import org.nwapw.abacus.function.Documentation;
+import org.nwapw.abacus.function.DocumentationType;
+import org.nwapw.abacus.number.ComputationInterruptedException;
+import org.nwapw.abacus.number.NumberInterface;
+import org.nwapw.abacus.plugin.ClassFinder;
+import org.nwapw.abacus.plugin.PluginListener;
+import org.nwapw.abacus.plugin.PluginManager;
+import org.nwapw.abacus.plugin.StandardPlugin;
+import org.nwapw.abacus.tree.TreeNode;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Comparator;
+import java.util.Set;
+import java.util.stream.Collectors;
+
+
+/**
+ * The controller for the abacus FX UI, responsible
+ * for all the user interaction.
+ */
+public class AbacusController implements PluginListener {
+
+    /**
+     * The file used for saving and loading configuration.
+     */
+    public static final File CONFIG_FILE = new File("config.toml");
+    /**
+     * The title for the apply alert dialog.
+     */
+    private static final String APPLY_MSG_TITLE = "\"Apply\" Needed";
+    /**
+     * The text for the header of the apply alert dialog.
+     */
+    private static final String APPLY_MSG_HEADER = "The settings have not been applied.";
+    /**
+     * The text for the dialog that is shown if settings haven't been applied.
+     */
+    private static final String APPLY_MSG_TEXT = "You have made changes to the configuration, however, you haven't pressed \"Apply\". " +
+            "The changes to the configuration will not be present in the calculator until \"Apply\" is pressed.";
+    /**
+     * Constant string that is displayed if the text could not be lexed or parsed.
+     */
+    private static final String ERR_SYNTAX = "Syntax Error";
+    /**
+     * Constant string that is displayed if the tree could not be reduced.
+     */
+    private static final String ERR_EVAL = "Evaluation Error";
+    /**
+     * Constant string that is displayed if the calculations are stopped before they are done.
+     */
+    private static final String ERR_STOP = "Stopped";
+    /**
+     * Constant string that is displayed if the calculations are interrupted by an exception.
+     */
+    private static final String ERR_EXCEPTION = "Exception Thrown";
+    @FXML
+    private TabPane coreTabPane;
+    @FXML
+    private Tab calculateTab;
+    @FXML
+    private Tab settingsTab;
+    @FXML
+    private Tab functionListTab;
+    @FXML
+    private TableView<HistoryModel> historyTable;
+    @FXML
+    private TableColumn<HistoryModel, String> inputColumn;
+    @FXML
+    private TableColumn<HistoryModel, String> parsedColumn;
+    @FXML
+    private TableColumn<HistoryModel, String> outputColumn;
+    @FXML
+    private Text outputText;
+    @FXML
+    private TextField inputField;
+    @FXML
+    private Button inputButton;
+    @FXML
+    private Button stopButton;
+    @FXML
+    private ComboBox<String> numberImplementationBox;
+    @FXML
+    private ListView<ToggleablePlugin> enabledPluginView;
+    @FXML
+    private TextField computationLimitField;
+    @FXML
+    private ListView<Documentation> functionListView;
+    @FXML
+    private TextField functionListSearchField;
+
+    /**
+     * The list of history entries, created by the users.
+     */
+    private ObservableList<HistoryModel> historyData;
+
+    /**
+     * The abacus instance used for calculations and all
+     * other main processing code.
+     */
+    private ObservableList<String> numberImplementationOptions;
+
+    /**
+     * The list of plugin objects that can be toggled on and off,
+     * and, when reloaded, get added to the plugin manager's black list.
+     */
+    private ObservableList<ToggleablePlugin> enabledPlugins;
+    /**
+     * The list of functions that are registered in the calculator.
+     */
+    private ObservableList<Documentation> functionList;
+    /**
+     * The filtered list displayed to the user.
+     */
+    private FilteredList<Documentation> functionFilter;
+
+    /**
+     * The abacus instance used for changing the plugin configuration.
+     */
+    private Abacus abacus;
+
+    /**
+     * Boolean which represents whether changes were made to the configuration.
+     */
+    private boolean changesMade;
+    /**
+     * Whether an alert about changes to the configuration was already shown.
+     */
+    private boolean reloadAlertShown;
+    /**
+     * The alert shown when a press to "apply" is needed.
+     */
+    private Alert reloadAlert;
+    /**
+     * The runnable that takes care of killing computations that take too long.
+     */
+    private final Runnable TIMER_RUNNABLE = () -> {
+        try {
+            Configuration abacusConfig = abacus.getConfiguration();
+            if(abacusConfig.getComputationDelay() == 0) return;
+            Thread.sleep((long) (abacusConfig.getComputationDelay() * 1000));
+            performStop();
+        } catch (InterruptedException e) { }
+    };
+    /**
+     * The runnable used to perform the calculation.
+     */
+    private final Runnable CALCULATION_RUNNABLE = new Runnable() {
+
+        private String attemptCalculation(){
+            try {
+                TreeNode constructedTree = abacus.parseString(inputField.getText());
+                if (constructedTree == null) {
+                    return ERR_SYNTAX;
+                }
+                NumberInterface evaluatedNumber = abacus.evaluateTree(constructedTree);
+                if (evaluatedNumber == null) {
+                    return ERR_EVAL;
+                }
+                String resultingString = evaluatedNumber.toString();
+                historyData.add(new HistoryModel(inputField.getText(), constructedTree.toString(), resultingString));
+                return resultingString;
+            } catch (ComputationInterruptedException exception) {
+                return ERR_STOP;
+            } catch (RuntimeException exception){
+                exception.printStackTrace();
+                return ERR_EXCEPTION;
+            }
+        }
+
+        @Override
+        public void run() {
+            String calculation = attemptCalculation();
+            Platform.runLater(() -> {
+                outputText.setText(calculation);
+                inputField.setText("");
+                inputButton.setDisable(false);
+                stopButton.setDisable(true);
+            });
+        }
+    };
+    /**
+     * The thread that is waiting to pause the calculation.
+     */
+    private Thread computationLimitThread;
+    /**
+     * The thread in which the computation runs.
+     */
+    private Thread calculationThread;
+
+    /**
+     * Alerts the user if the changes they made
+     * have not yet been applied.
+     */
+    private void alertIfApplyNeeded(boolean ignorePrevious) {
+        if (changesMade && (!reloadAlertShown || ignorePrevious)) {
+            reloadAlertShown = true;
+            reloadAlert.showAndWait();
+        }
+    }
+
+    @FXML
+    public void initialize() {
+        Callback<TableColumn<HistoryModel, String>, TableCell<HistoryModel, String>> cellFactory =
+                param -> new CopyableCell<>();
+        Callback<ListView<ToggleablePlugin>, ListCell<ToggleablePlugin>> pluginCellFactory =
+                param -> new CheckBoxListCell<>(ToggleablePlugin::getEnabledProperty, new StringConverter<ToggleablePlugin>() {
+                    @Override
+                    public String toString(ToggleablePlugin object) {
+                        return object.getClassName().substring(object.getClassName().lastIndexOf('.') + 1);
+                    }
+
+                    @Override
+                    public ToggleablePlugin fromString(String string) {
+                        return new ToggleablePlugin(string, true);
+                    }
+                });
+        functionList = FXCollections.observableArrayList();
+        functionFilter = new FilteredList<>(functionList, (s) -> true);
+        functionListView.setItems(functionFilter);
+        functionListSearchField.textProperty().addListener((observable, oldValue, newValue) ->
+                functionFilter.setPredicate((newValue.length() == 0) ? ((s) -> true) : ((s) -> s.matches(newValue))));
+        functionListView.setCellFactory(param -> new DocumentationCell());
+        historyData = FXCollections.observableArrayList();
+        historyTable.setItems(historyData);
+        numberImplementationOptions = FXCollections.observableArrayList();
+        numberImplementationBox.setItems(numberImplementationOptions);
+        numberImplementationBox.getSelectionModel().selectedIndexProperty().addListener(e -> changesMade = true);
+        historyTable.getSelectionModel().setCellSelectionEnabled(true);
+        enabledPlugins = FXCollections.observableArrayList();
+        enabledPluginView.setItems(enabledPlugins);
+        enabledPluginView.setCellFactory(pluginCellFactory);
+        inputColumn.setCellFactory(cellFactory);
+        inputColumn.setCellValueFactory(cell -> cell.getValue().getInputProperty());
+        parsedColumn.setCellFactory(cellFactory);
+        parsedColumn.setCellValueFactory(cell -> cell.getValue().getParsedProperty());
+        outputColumn.setCellFactory(cellFactory);
+        outputColumn.setCellValueFactory(cell -> cell.getValue().getOutputProperty());
+        coreTabPane.getSelectionModel().selectedItemProperty().addListener((observable, oldValue, newValue) -> {
+            if (oldValue.equals(settingsTab)) alertIfApplyNeeded(true);
+        });
+
+        abacus = new Abacus(new Configuration(CONFIG_FILE));
+        PluginManager abacusPluginManager = abacus.getPluginManager();
+        abacusPluginManager.addListener(this);
+        performScan();
+
+        computationLimitField.setText(Double.toString(abacus.getConfiguration().getComputationDelay()));
+        computationLimitField.textProperty().addListener((observable, oldValue, newValue) -> {
+            if(!newValue.matches("(\\d+(\\.\\d*)?)?")) {
+                computationLimitField.setText(oldValue);
+            } else {
+                changesMade = true;
+            }
+        });
+
+        changesMade = false;
+        reloadAlertShown = false;
+
+        reloadAlert = new Alert(Alert.AlertType.WARNING);
+        reloadAlert.setTitle(APPLY_MSG_TITLE);
+        reloadAlert.setHeaderText(APPLY_MSG_HEADER);
+        reloadAlert.setContentText(APPLY_MSG_TEXT);
+    }
+
+    @FXML
+    public void performCalculation() {
+        inputButton.setDisable(true);
+        stopButton.setDisable(false);
+        calculationThread = new Thread(CALCULATION_RUNNABLE);
+        calculationThread.start();
+        computationLimitThread = new Thread(TIMER_RUNNABLE);
+        computationLimitThread.start();
+    }
+
+    @FXML
+    public void performStop(){
+        if(calculationThread != null) {
+            calculationThread.interrupt();
+            calculationThread = null;
+        }
+        if(computationLimitThread != null){
+            computationLimitThread.interrupt();
+            computationLimitThread = null;
+        }
+    }
+
+    @FXML
+    public void performSaveAndReload() {
+        performSave();
+        performReload();
+        changesMade = false;
+        reloadAlertShown = false;
+    }
+
+    @FXML
+    public void performScan(){
+        PluginManager abacusPluginManager = abacus.getPluginManager();
+        abacusPluginManager.removeAll();
+        abacusPluginManager.addInstantiated(new StandardPlugin(abacus.getPluginManager()));
+        try {
+            ClassFinder.loadJars("plugins").forEach(abacusPluginManager::addClass);
+        } catch (IOException | ClassNotFoundException e) {
+            e.printStackTrace();
+        }
+        abacusPluginManager.reload();
+    }
+
+    @FXML
+    public void performReload() {
+        alertIfApplyNeeded(true);
+        abacus.getPluginManager().reload();
+    }
+
+    @FXML
+    public void performSave() {
+        Configuration configuration = abacus.getConfiguration();
+        configuration.setNumberImplementation(numberImplementationBox.getSelectionModel().getSelectedItem());
+        Set<String> disabledPlugins = configuration.getDisabledPlugins();
+        disabledPlugins.clear();
+        for (ToggleablePlugin pluginEntry : enabledPlugins) {
+            if (!pluginEntry.isEnabled()) disabledPlugins.add(pluginEntry.getClassName());
+        }
+        if(computationLimitField.getText().matches("\\d*(\\.\\d+)?") && computationLimitField.getText().length() != 0)
+            configuration.setComputationDelay(Double.parseDouble(computationLimitField.getText()));
+        configuration.saveTo(CONFIG_FILE);
+        changesMade = false;
+        reloadAlertShown = false;
+    }
+
+    @Override
+    public void onLoad(PluginManager manager) {
+        Configuration configuration = abacus.getConfiguration();
+        Set<String> disabledPlugins = configuration.getDisabledPlugins();
+        numberImplementationOptions.addAll(abacus.getPluginManager().getAllNumberImplementations());
+        String actualImplementation = configuration.getNumberImplementation();
+        String toSelect = (numberImplementationOptions.contains(actualImplementation)) ? actualImplementation : "<default>";
+        numberImplementationBox.getSelectionModel().select(toSelect);
+        for (Class<?> pluginClass : abacus.getPluginManager().getLoadedPluginClasses()) {
+            String fullName = pluginClass.getName();
+            ToggleablePlugin plugin = new ToggleablePlugin(fullName, !disabledPlugins.contains(fullName));
+            plugin.getEnabledProperty().addListener(e -> changesMade = true);
+            enabledPlugins.add(plugin);
+        }
+        PluginManager pluginManager = abacus.getPluginManager();
+        functionList.addAll(manager.getAllFunctions().stream().map(name -> pluginManager.documentationFor(name, DocumentationType.FUNCTION))
+                .collect(Collectors.toCollection(ArrayList::new)));
+        functionList.sort(Comparator.comparing(Documentation::getCodeName));
+    }
+
+    @Override
+    public void onUnload(PluginManager manager) {
+        functionList.clear();
+        enabledPlugins.clear();
+        numberImplementationOptions.clear();
+    }
+
+}

fx/src/main/java/org/nwapw/abacus/fx/CopyableCell.java

@@ -0,0 +1,36 @@
+package org.nwapw.abacus.fx;
+
+import javafx.scene.control.TableCell;
+import javafx.scene.input.MouseEvent;
+
+import java.awt.*;
+import java.awt.datatransfer.StringSelection;
+
+/**
+ * A cell that copies its value to the clipboard
+ * when double clicked.
+ *
+ * @param <S> The type of the table view generic type.
+ * @param <T> The type of the value contained in the cell.
+ */
+public class CopyableCell<S, T> extends TableCell<S, T> {
+
+    /**
+     * Creates a new copyable cell.
+     */
+    public CopyableCell() {
+        addEventFilter(MouseEvent.MOUSE_CLICKED, event -> {
+            if (event.getClickCount() == 2) {
+                Toolkit.getDefaultToolkit().getSystemClipboard()
+                        .setContents(new StringSelection(getText()), null);
+            }
+        });
+    }
+
+    @Override
+    protected void updateItem(T item, boolean empty) {
+        super.updateItem(item, empty);
+        setText((empty || item == null) ? null : item.toString());
+        setGraphic(null);
+    }
+}

fx/src/main/java/org/nwapw/abacus/fx/DocumentationCell.java

@@ -0,0 +1,59 @@
+package org.nwapw.abacus.fx;
+
+import javafx.scene.control.Label;
+import javafx.scene.control.ListCell;
+import javafx.scene.control.TitledPane;
+import javafx.scene.layout.VBox;
+import org.nwapw.abacus.function.Documentation;
+
+public class DocumentationCell extends ListCell<Documentation> {
+
+    private Label codeNameLabel;
+    private Label nameLabel;
+    private Label description;
+    private Label longDescription;
+    private TitledPane titledPane;
+
+    public DocumentationCell(){
+        VBox vbox = new VBox();
+        vbox.setSpacing(10);
+        titledPane = new TitledPane();
+        codeNameLabel = new Label();
+        nameLabel = new Label();
+        description = new Label();
+        longDescription = new Label();
+        codeNameLabel.setWrapText(true);
+        nameLabel.setWrapText(true);
+        description.setWrapText(true);
+        longDescription.setWrapText(true);
+        vbox.getChildren().add(codeNameLabel);
+        vbox.getChildren().add(nameLabel);
+        vbox.getChildren().add(description);
+        vbox.getChildren().add(longDescription);
+        titledPane.textProperty().bindBidirectional(codeNameLabel.textProperty());
+        titledPane.setContent(vbox);
+        titledPane.setExpanded(false);
+        titledPane.prefWidthProperty().bind(widthProperty().subtract(32));
+
+        visibleProperty().addListener((a, b, c) -> titledPane.setExpanded(false));
+    }
+
+    @Override
+    protected void updateItem(Documentation item, boolean empty) {
+        super.updateItem(item, empty);
+        if(empty){
+            codeNameLabel.setText("");
+            nameLabel.setText("");
+            description.setText("");
+            longDescription.setText("");
+            setGraphic(null);
+        } else {
+            codeNameLabel.setText(item.getCodeName());
+            nameLabel.setText(item.getName());
+            description.setText(item.getDescription());
+            longDescription.setText(item.getLongDescription());
+            setGraphic(titledPane);
+        }
+        titledPane.setExpanded(false);
+    }
+}