Add comments and clean some code.

# Conflicts:
#	src/main/java/org/nwapw/abacus/Abacus.java
#	src/main/java/org/nwapw/abacus/plugin/PluginManager.java

README.md

@@ -5,10 +5,10 @@ Summer project for NWAPW.
 Created by Arthur Drobot, Danila Fedorin and Riley Jones.
 
 ## Project Description
-Abacus is a calculator built with extensibility and usability in mind. It provides a plugin interface, via Java, as Lua provides too difficult to link up to the Java core. The description of the internals of the project can be found on the wiki page.
+Abacus is a calculator built with extensibility and usability in mind. It provides a plugin interface, via Java, as Lua proves too difficult to link up to the Java core. The description of the internals of the project can be found on the wiki page.
 
 ## Current State
-Abacus is being built for the Northwest Advanced Programming Workshop, a 3 week program in which students work in treams to complete a single project, following principles of agile development. Because of its short timeframe, Abacus is not even close to completed state. Below is a list of the current features and problems.
+Abacus is being built for the Northwest Advanced Programming Workshop, a 3 week program in which students work in teams to complete a single project, following principles of agile development. Because of its short timeframe, Abacus is not even close to completed state. Below is a list of the current features and problems.
 - [x] Basic number class
 - [x] Implementation of basic functions 
 - [x] Implementation of `exp`, `ln`, `sqrt` using the basic functions and Taylor Series

src/main/java/org/nwapw/abacus/Abacus.java

@@ -1,6 +1,7 @@
 package org.nwapw.abacus;
 
-import org.nwapw.abacus.config.ConfigurationObject;
+import org.nwapw.abacus.config.Configuration;
+import org.nwapw.abacus.fx.AbacusApplication;
 import org.nwapw.abacus.number.NumberInterface;
 import org.nwapw.abacus.parsing.LexerTokenizer;
 import org.nwapw.abacus.parsing.ShuntingYardParser;
@@ -11,9 +12,7 @@ import org.nwapw.abacus.plugin.PluginManager;
 import org.nwapw.abacus.plugin.StandardPlugin;
 import org.nwapw.abacus.tree.NumberReducer;
 import org.nwapw.abacus.tree.TreeNode;
-import org.nwapw.abacus.window.Window;
 
-import javax.swing.*;
 import java.io.File;
 import java.io.IOException;
 
@@ -43,7 +42,7 @@ public class Abacus {
     /**
      * The configuration loaded from a file.
      */
-    private ConfigurationObject configuration;
+    private Configuration configuration;
     /**
      * The tree builder used to construct a tree
      * from a string.
@@ -54,10 +53,10 @@ public class Abacus {
      * Creates a new instance of the Abacus calculator.
      */
     public Abacus() {
-        pluginManager = new PluginManager();
+        pluginManager = new PluginManager(this);
         numberReducer = new NumberReducer(this);
-        configuration = new ConfigurationObject(CONFIG_FILE);
-        configuration.save(CONFIG_FILE);
+        configuration = new Configuration(CONFIG_FILE);
+        configuration.saveTo(CONFIG_FILE);
         LexerTokenizer lexerTokenizer = new LexerTokenizer();
         ShuntingYardParser shuntingYardParser = new ShuntingYardParser(this);
         treeBuilder = new TreeBuilder<>(lexerTokenizer, shuntingYardParser);
@@ -75,13 +74,7 @@ public class Abacus {
     }
 
     public static void main(String[] args) {
-        try {
-            UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
-        } catch (ClassNotFoundException | InstantiationException | UnsupportedLookAndFeelException | IllegalAccessException e) {
-            e.printStackTrace();
-        }
-
-        new Window(new Abacus()).setVisible(true);
+        AbacusApplication.launch(AbacusApplication.class, args);
     }
 
     /**
@@ -117,7 +110,7 @@ public class Abacus {
      *
      * @return the configuration object.
      */
-    public ConfigurationObject getConfiguration() {
+    public Configuration getConfiguration() {
         return configuration;
     }
 

src/main/java/org/nwapw/abacus/config/Configuration.java

@@ -1,14 +1,108 @@
 package org.nwapw.abacus.config;
 
+import com.moandjiezana.toml.Toml;
+import com.moandjiezana.toml.TomlWriter;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.Set;
+
 /**
- * Serializable class that will be used to load TOML
- * configurations.
+ * The configuration object that stores
+ * options that the user can change.
  */
 public class Configuration {
 
     /**
-     * The type of number this calculator should use.
+     * The defaults TOML string.
      */
-    public String numberType;
+    private static final String DEFAULT_CONFIG =
+            "numberImplementation = \"naive\"\n" +
+            "disabledPlugins = []";
+    /**
+     * The defaults TOML object, parsed from the string.
+     */
+    private static final Toml DEFAULT_TOML = new Toml().read(DEFAULT_CONFIG);
+    /**
+     * The TOML writer used to write this configuration to a file.
+     */
+    private static final TomlWriter TOML_WRITER = new TomlWriter();
+
+    /**
+     * The implementation of the number that should be used.
+     */
+    private String numberImplementation = "<default>";
+    /**
+     * The list of disabled plugins in this Configuration.
+     */
+    private Set<String> disabledPlugins = new HashSet<>();
+
+    /**
+     * Creates a new configuration with the given values.
+     * @param numberImplementation the number implementation, like "naive" or "precise"
+     * @param disabledPlugins the list of disabled plugins.
+     */
+    public Configuration(String numberImplementation, String[] disabledPlugins){
+        this.numberImplementation = numberImplementation;
+        this.disabledPlugins.addAll(Arrays.asList(disabledPlugins));
+    }
+
+    /**
+     * Loads a configuration from a given file, keeping non-specified fields default.
+     * @param fromFile the file to load from.
+     */
+    public Configuration(File fromFile){
+        if(!fromFile.exists()) return;
+        copyFrom(new Toml(DEFAULT_TOML).read(fromFile).to(Configuration.class));
+    }
+
+    /**
+     * Copies the values from the given configuration into this one.
+     * @param otherConfiguration the configuration to copy from.
+     */
+    public void copyFrom(Configuration otherConfiguration){
+        this.numberImplementation = otherConfiguration.numberImplementation;
+        this.disabledPlugins.addAll(otherConfiguration.disabledPlugins);
+    }
+
+    /**
+     * Saves this configuration to the given file, creating
+     * any directories that do not exist.
+     * @param file the file to save to.
+     */
+    public void saveTo(File file){
+        if(file.getParentFile() != null) file.getParentFile().mkdirs();
+        try {
+            TOML_WRITER.write(this, file);
+        } catch (IOException e) {
+            e.printStackTrace();
+        }
+    }
+
+    /**
+     * Gets the number implementation from this configuration.
+     * @return the number implementation.
+     */
+    public String getNumberImplementation() {
+        return numberImplementation;
+    }
+
+    /**
+     * Sets the number implementation for the configuration
+     * @param numberImplementation the number implementation.
+     */
+    public void setNumberImplementation(String numberImplementation) {
+        this.numberImplementation = numberImplementation;
+    }
+
+    /**
+     * Gets the list of disabled plugins.
+     * @return the list of disabled plugins.
+     */
+    public Set<String> getDisabledPlugins() {
+        return disabledPlugins;
+    }
 
 }

src/main/java/org/nwapw/abacus/config/ConfigurationObject.java

@@ -1,111 +0,0 @@
-package org.nwapw.abacus.config;
-
-import com.moandjiezana.toml.Toml;
-import com.moandjiezana.toml.TomlWriter;
-
-import java.io.File;
-import java.io.IOException;
-
-/**
- * A configuration object, which essentially
- * manages saving, loading, and getting values
- * from the configuration. While Configuration is
- * the data model, this is the interface with it.
- */
-public class ConfigurationObject {
-
-    /**
-     * The writer used to store the configuration.
-     */
-    private static final TomlWriter TOML_WRITER = new TomlWriter();
-    /**
-     * The configuration instance being modeled.
-     */
-    private Configuration configuration;
-
-    /**
-     * Creates a new configuration object with the given config.
-     *
-     * @param config the config to use.
-     */
-    public ConfigurationObject(Configuration config) {
-        setup(config);
-    }
-
-    /**
-     * Create a configuration object by attempting to
-     * load a config from the given path, using the
-     * default configuration otherwise.
-     *
-     * @param path the path to attempt to load.
-     */
-    public ConfigurationObject(File path) {
-        Configuration config;
-        if (!path.exists()) {
-            config = getDefaultConfig();
-        } else {
-            Toml parse = new Toml();
-            parse.read(path);
-            config = parse.to(Configuration.class);
-        }
-        setup(config);
-    }
-
-    /**
-     * Creates a new configuration object with the
-     * default configuration.
-     */
-    public ConfigurationObject() {
-        setup(getDefaultConfig());
-    }
-
-    /**
-     * Sets up the ConfigurationObject.
-     * different constructors do different things,
-     * but they all lead here.
-     *
-     * @param configuration the configuration to set up with.
-     */
-    private void setup(Configuration configuration) {
-        this.configuration = configuration;
-    }
-
-    /**
-     * Creates a default configuration.
-     *
-     * @return the newly created default configuration.
-     */
-    private Configuration getDefaultConfig() {
-        configuration = new Configuration();
-        configuration.numberType = "naive";
-        return configuration;
-    }
-
-    /**
-     * Returns the implementation the user has requested to
-     * represent their numbers.
-     *
-     * @return the implementation name.
-     */
-    public String getNumberImplementation() {
-        return configuration.numberType;
-    }
-
-    /**
-     * Saves the ConfigurationObject to the given file.
-     *
-     * @param toFile the file to save ot.
-     * @return true if the save succeed, false if otherwise.
-     */
-    public boolean save(File toFile) {
-        if (toFile.getParentFile() != null) toFile.getParentFile().mkdirs();
-        try {
-            TOML_WRITER.write(configuration, toFile);
-            return true;
-        } catch (IOException e) {
-            e.printStackTrace();
-        }
-        return false;
-    }
-
-}

src/main/java/org/nwapw/abacus/function/OperatorType.java

@@ -4,5 +4,5 @@ package org.nwapw.abacus.function;
  * The type of an operator, describing how it should behave.
  */
 public enum OperatorType {
-    BINARY_INFIX, UNARY_POSTFIX
+    BINARY_INFIX, UNARY_POSTFIX, UNARY_PREFIX
 }

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

@@ -0,0 +1,24 @@
+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 {
+
+    @Override
+    public void start(Stage primaryStage) throws Exception {
+        Parent parent = FXMLLoader.load(getClass().getResource("/abacus.fxml"));
+        Scene mainScene = new Scene(parent, 320, 480);
+        primaryStage.setScene(mainScene);
+        primaryStage.setTitle("Abacus");
+        primaryStage.show();
+    }
+
+}

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

@@ -0,0 +1,240 @@
+package org.nwapw.abacus.fx;
+
+import javafx.collections.FXCollections;
+import javafx.collections.ObservableList;
+import javafx.fxml.FXML;
+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.number.NumberInterface;
+import org.nwapw.abacus.plugin.PluginListener;
+import org.nwapw.abacus.plugin.PluginManager;
+import org.nwapw.abacus.tree.TreeNode;
+
+import java.util.Set;
+
+
+/**
+ * The controller for the abacus FX UI, responsible
+ * for all the user interaction.
+ */
+public class AbacusController implements PluginListener {
+
+    /**
+     * 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";
+
+    @FXML
+    private TabPane coreTabPane;
+    @FXML
+    private Tab calculateTab;
+    @FXML
+    private Tab settingsTab;
+    @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 ComboBox<String> numberImplementationBox;
+    @FXML
+    private ListView<ToggleablePlugin> enabledPluginView;
+
+    /**
+     * 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 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;
+
+    /**
+     * 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::enabledProperty, 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(true, string);
+                    }
+                });
+
+        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().inputProperty());
+        parsedColumn.setCellFactory(cellFactory);
+        parsedColumn.setCellValueFactory(cell -> cell.getValue().parsedProperty());
+        outputColumn.setCellFactory(cellFactory);
+        outputColumn.setCellValueFactory(cell -> cell.getValue().outputProperty());
+        coreTabPane.getSelectionModel().selectedItemProperty().addListener((observable, oldValue, newValue) -> {
+            if(oldValue.equals(settingsTab)) alertIfApplyNeeded(true);
+        });
+
+        abacus = new Abacus();
+        abacus.getPluginManager().addListener(this);
+        abacus.getPluginManager().reload();
+
+        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
+    private void performCalculation(){
+        inputButton.setDisable(true);
+        TreeNode constructedTree = abacus.parseString(inputField.getText());
+        if(constructedTree == null){
+            outputText.setText(ERR_SYNTAX);
+            inputButton.setDisable(false);
+            return;
+        }
+        NumberInterface evaluatedNumber = abacus.evaluateTree(constructedTree);
+        if(evaluatedNumber == null){
+            outputText.setText(ERR_EVAL);
+            inputButton.setDisable(false);
+            return;
+        }
+        outputText.setText(evaluatedNumber.toString());
+        historyData.add(new HistoryModel(inputField.getText(), constructedTree.toString(), evaluatedNumber.toString()));
+
+        inputButton.setDisable(false);
+        inputField.setText("");
+    }
+
+    @FXML
+    private void performSaveAndReload(){
+        performSave();
+        performReload();
+        changesMade = false;
+        reloadAlertShown = false;
+    }
+
+    @FXML
+    private void performReload(){
+        alertIfApplyNeeded(true);
+        abacus.getPluginManager().reload();
+    }
+
+    @FXML
+    private 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());
+        }
+        configuration.saveTo(Abacus.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(!disabledPlugins.contains(fullName), fullName);
+            plugin.enabledProperty().addListener(e -> changesMade = true);
+            enabledPlugins.add(plugin);
+        }
+    }
+
+    @Override
+    public void onUnload(PluginManager manager) {
+        enabledPlugins.clear();
+        numberImplementationOptions.clear();
+    }
+}

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

@@ -0,0 +1,35 @@
+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);
+    }
+}

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

@@ -0,0 +1,87 @@
+package org.nwapw.abacus.fx;
+
+import javafx.beans.property.SimpleStringProperty;
+import javafx.beans.property.StringProperty;
+
+/**
+ * The data model used for storing history entries.
+ */
+public class HistoryModel {
+
+    /**
+     * The property used for displaying the column
+     * for the user input.
+     */
+    private final StringProperty input;
+    /**
+     * The property used for displaying the column
+     * that contains the parsed input.
+     */
+    private final StringProperty parsed;
+    /**
+     * The property used for displaying the column
+     * that contains the program output.
+     */
+    private final StringProperty output;
+
+    /**
+     * Creates a new history model with the given variables.
+     * @param input the user input
+     * @param parsed the parsed input
+     * @param output the program output.
+     */
+    public HistoryModel(String input, String parsed, String output){
+        this.input = new SimpleStringProperty();
+        this.parsed = new SimpleStringProperty();
+        this.output = new SimpleStringProperty();
+        this.input.setValue(input);
+        this.parsed.setValue(parsed);
+        this.output.setValue(output);
+    }
+
+    /**
+     * Gets the input property.
+     * @return the input property.
+     */
+    public StringProperty inputProperty() {
+        return input;
+    }
+    /**
+     * Gets the input.
+     * @return the input.
+     */
+    public String getInput() {
+        return input.get();
+    }
+
+    /**
+     * Gets the parsed input property.
+     * @return the parsed input property.
+     */
+    public StringProperty parsedProperty() {
+        return parsed;
+    }
+    /**
+     * Gets the parsed input.
+     * @return the parsed input.
+     */
+    public String getParsed() {
+        return parsed.get();
+    }
+
+    /**
+     * Gets the output property.
+     * @return the output property.
+     */
+    public StringProperty outputProperty() {
+        return output;
+    }
+    /**
+     * Gets the program output.
+     * @return the output.
+     */
+    public String getOutput() {
+        return output.get();
+    }
+
+}

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

@@ -0,0 +1,56 @@
+package org.nwapw.abacus.fx;
+
+import javafx.beans.property.BooleanProperty;
+import javafx.beans.property.SimpleBooleanProperty;
+
+/**
+ * Class that represents an entry in the plugin check box list.
+ * The changes from this property are written to the config on application.
+ */
+public class ToggleablePlugin {
+
+    /**
+     * The property that determines whether the plugin will be enabled.
+     */
+    private final BooleanProperty enabled;
+    /**
+     * The name of the class this entry toggles.
+     */
+    private final String className;
+
+    /**
+     * Creates a new toggleable plugin with the given properties.
+     * @param enabled the enabled / disabled state at the beginning.
+     * @param className the name of the class this plugin toggles.
+     */
+    public ToggleablePlugin(boolean enabled, String className){
+        this.enabled = new SimpleBooleanProperty();
+        this.enabled.setValue(enabled);
+        this.className = className;
+    }
+
+    /**
+     * Gets the enabled property of this plugin.
+     * @return the enabled property.
+     */
+    public BooleanProperty enabledProperty() {
+        return enabled;
+    }
+
+    /**
+     * Checks if this plugin entry should be enabled.
+     * @return whether this plugin will be enabled.
+     */
+    public boolean isEnabled() {
+        return enabled.get();
+    }
+
+    /**
+     * Gets the class name this plugin toggles.
+     * @return the class name that should be disabled.
+     */
+    public String getClassName() {
+        return className;
+    }
+
+}

src/main/java/org/nwapw/abacus/number/PreciseNumber.java

@@ -3,6 +3,10 @@ package org.nwapw.abacus.number;
 import java.math.BigDecimal;
 import java.math.RoundingMode;
 
+/**
+ * A number that uses a BigDecimal to store its value,
+ * leading to infinite possible precision.
+ */
 public class PreciseNumber implements NumberInterface {
 
     /**

src/main/java/org/nwapw/abacus/parsing/ShuntingYardParser.java

@@ -55,9 +55,12 @@ public class ShuntingYardParser implements Parser<Match<TokenType>>, PluginListe
     public List<Match<TokenType>> intoPostfix(List<Match<TokenType>> from) {
         ArrayList<Match<TokenType>> output = new ArrayList<>();
         Stack<Match<TokenType>> tokenStack = new Stack<>();
+        TokenType previousType;
+        TokenType matchType = null;
         while (!from.isEmpty()) {
             Match<TokenType> match = from.remove(0);
-            TokenType matchType = match.getType();
+            previousType = matchType;
+            matchType = match.getType();
             if (matchType == TokenType.NUM) {
                 output.add(match);
             } else if (matchType == TokenType.FUNCTION) {
@@ -74,13 +77,19 @@ public class ShuntingYardParser implements Parser<Match<TokenType>>, PluginListe
                     continue;
                 }
 
-                while (!tokenStack.empty()) {
+                if(tokenString.equals("-") && (previousType == null || previousType == TokenType.OP ||
+                        previousType == TokenType.OPEN_PARENTH)){
+                    from.add(0, new Match<>("`", TokenType.OP));
+                    continue;
+                }
+
+                while (!tokenStack.empty() && type == OperatorType.BINARY_INFIX) {
                     Match<TokenType> otherMatch = tokenStack.peek();
                     TokenType otherMatchType = otherMatch.getType();
                     if (!(otherMatchType == TokenType.OP || otherMatchType == TokenType.FUNCTION)) break;
 
                     if (otherMatchType == TokenType.OP) {
-                        int otherPrecedence = precedenceMap.get(match.getContent());
+                        int otherPrecedence = precedenceMap.get(otherMatch.getContent());
                         if (otherPrecedence < precedence ||
                                 (associativity == OperatorAssociativity.RIGHT && otherPrecedence == precedence)) {
                             break;
@@ -103,8 +112,8 @@ public class ShuntingYardParser implements Parser<Match<TokenType>>, PluginListe
         }
         while (!tokenStack.empty()) {
             Match<TokenType> match = tokenStack.peek();
-            TokenType matchType = match.getType();
-            if (!(matchType == TokenType.OP || matchType == TokenType.FUNCTION)) return null;
+            TokenType newMatchType = match.getType();
+            if (!(newMatchType == TokenType.OP || newMatchType == TokenType.FUNCTION)) return null;
             output.add(tokenStack.pop());
         }
         return output;
@@ -127,11 +136,11 @@ public class ShuntingYardParser implements Parser<Match<TokenType>>, PluginListe
                 TreeNode right = constructRecursive(matches);
                 TreeNode left = constructRecursive(matches);
                 if (left == null || right == null) return null;
-                else return new BinaryInfixNode(operator, left, right);
+                else return new BinaryNode(operator, left, right);
             } else {
                 TreeNode applyTo = constructRecursive(matches);
                 if (applyTo == null) return null;
-                else return new UnaryPrefixNode(operator, applyTo);
+                else return new UnaryNode(operator, applyTo);
             }
         } else if (matchType == TokenType.NUM) {
             return new NumberNode(abacus.numberFromString(match.getContent()));

src/main/java/org/nwapw/abacus/plugin/PluginManager.java

@@ -1,5 +1,6 @@
 package org.nwapw.abacus.plugin;
 
+import org.nwapw.abacus.Abacus;
 import org.nwapw.abacus.function.Function;
 import org.nwapw.abacus.function.Operator;
 import org.nwapw.abacus.number.NumberInterface;
@@ -61,11 +62,17 @@ public class PluginManager {
      * The list of plugin listeners attached to this instance.
      */
     private Set<PluginListener> listeners;
+    /**
+     * The abacus instance used to access other
+     * components of the application.
+     */
+    private Abacus abacus;
 
     /**
      * Creates a new plugin manager.
      */
-    public PluginManager() {
+    public PluginManager(Abacus abacus) {
+        this.abacus = abacus;
         loadedPluginClasses = new HashSet<>();
         plugins = new HashSet<>();
         cachedFunctions = new HashMap<>();
@@ -210,8 +217,13 @@ public class PluginManager {
      * Loads all the plugins in the PluginManager.
      */
     public void load() {
-        for (Plugin plugin : plugins) plugin.enable();
+        Set<String> disabledPlugins = abacus.getConfiguration().getDisabledPlugins();
         for (Plugin plugin : plugins) {
+            if(disabledPlugins.contains(plugin.getClass().getName())) continue;
+            plugin.enable();
+        }
+        for (Plugin plugin : plugins) {
+            if(disabledPlugins.contains(plugin.getClass().getName())) continue;
             allFunctions.addAll(plugin.providedFunctions());
             allOperators.addAll(plugin.providedOperators());
             allNumberImplementations.addAll(plugin.providedNumberImplementations());
@@ -223,7 +235,17 @@ public class PluginManager {
      * Unloads all the plugins in the PluginManager.
      */
     public void unload() {
-        for (Plugin plugin : plugins) plugin.disable();
+        listeners.forEach(e -> e.onUnload(this));
+        Set<String> disabledPlugins = abacus.getConfiguration().getDisabledPlugins();
+        for (Plugin plugin : plugins) {
+            if(disabledPlugins.contains(plugin.getClass().getName())) continue;
+            plugin.disable();
+        }
+        cachedFunctions.clear();
+        cachedOperators.clear();
+        cachedNumberImplementations.clear();
+        cachedInterfaceImplementations.clear();
+        cachedPi.clear();
         allFunctions.clear();
         allOperators.clear();
         allNumberImplementations.clear();
@@ -235,7 +257,7 @@ public class PluginManager {
      */
     public void reload() {
         unload();
-        reload();
+        load();
     }
 
     /**
@@ -283,4 +305,12 @@ public class PluginManager {
         listeners.remove(listener);
     }
 
+    /**
+     * Gets a list of all the plugin class files that have been
+     * added to the plugin manager.
+     * @return the list of all the added plugin classes.
+     */
+    public Set<Class<?>> getLoadedPluginClasses() {
+        return loadedPluginClasses;
+    }
 }

src/main/java/org/nwapw/abacus/plugin/StandardPlugin.java

@@ -18,7 +18,7 @@ import java.util.function.BiFunction;
  */
 public class StandardPlugin extends Plugin {
 
-    private static HashMap<Class<? extends NumberInterface>, ArrayList<NumberInterface>> factorialLists = new HashMap<Class<? extends NumberInterface>, ArrayList<NumberInterface>>();
+    private static final HashMap<Class<? extends NumberInterface>, ArrayList<NumberInterface>> FACTORIAL_LISTS = new HashMap<>();
 
     /**
      * The addition operator, +
@@ -52,6 +52,20 @@ public class StandardPlugin extends Plugin {
             return params[0].subtract(params[1]);
         }
     });
+    /**
+     * The negation operator, -
+     */
+    public static final Operator OP_NEGATE = new Operator(OperatorAssociativity.LEFT, OperatorType.UNARY_PREFIX, 0, new Function() {
+        @Override
+        protected boolean matchesParams(NumberInterface[] params) {
+            return params.length == 1;
+        }
+
+        @Override
+        protected NumberInterface applyInternal(NumberInterface[] params) {
+            return params[0].negate();
+        }
+    });
     /**
      * The multiplication operator, *
      */
@@ -76,16 +90,12 @@ public class StandardPlugin extends Plugin {
     public static final Operator OP_DIVIDE = new Operator(OperatorAssociativity.LEFT, OperatorType.BINARY_INFIX, 1, new Function() {
         @Override
         protected boolean matchesParams(NumberInterface[] params) {
-            return params.length >= 1;
+            return params.length == 2 && params[1].compareTo(NaiveNumber.ZERO.promoteTo(params[1].getClass())) != 0;
         }
 
         @Override
         protected NumberInterface applyInternal(NumberInterface[] params) {
-            NumberInterface product = params[0];
-            for (int i = 1; i < params.length; i++) {
-                product = product.multiply(params[i]);
-            }
-            return product;
+            return params[0].divide(params[1]);
         }
     });
     /**
@@ -95,7 +105,9 @@ public class StandardPlugin extends Plugin {
         //private HashMap<Class<? extends NumberInterface>, ArrayList<NumberInterface>> storedList = new HashMap<Class<? extends NumberInterface>, ArrayList<NumberInterface>>();
         @Override
         protected boolean matchesParams(NumberInterface[] params) {
-            return params.length == 1;
+            return params.length == 1
+                    && params[0].fractionalPart().compareTo(NaiveNumber.ZERO.promoteTo(params[0].getClass())) == 0
+                    && params[0].signum() >= 0;
         }
 
         @Override
@@ -194,7 +206,7 @@ public class StandardPlugin extends Plugin {
     public static final Function FUNCTION_LN = new Function() {
         @Override
         protected boolean matchesParams(NumberInterface[] params) {
-            return params.length == 1;
+            return params.length == 1 && params[0].compareTo(NaiveNumber.ZERO.promoteTo(params[0].getClass())) > 0;
         }
 
         @Override
@@ -212,7 +224,7 @@ public class StandardPlugin extends Plugin {
                 } else {
                     param = param.multiply(new NaiveNumber(2).promoteTo(param.getClass()));
                     powersOf2--;
-                    if (param.subtract(NaiveNumber.ONE.promoteTo(param.getClass())).signum() != 1) {
+                    if (param.subtract(NaiveNumber.ONE.promoteTo(param.getClass())).signum() != -1) {
                         break;
                         //No infinite loop for you.
                     }
@@ -306,6 +318,82 @@ public class StandardPlugin extends Plugin {
         }
     };
 
+    /**
+     * The cosine function (the argument is in radians).
+     */
+    public final Function functionCos = new Function() {
+        @Override
+        protected boolean matchesParams(NumberInterface[] params) {
+            return params.length == 1;
+        }
+
+        @Override
+        protected NumberInterface applyInternal(NumberInterface[] params) {
+            return functionSin.apply(getPi(params[0].getClass()).divide(new NaiveNumber(2).promoteTo(params[0].getClass()))
+                .subtract(params[0]));
+        }
+    };
+
+    /**
+     * The tangent function (the argument is in radians).
+     */
+    public final Function functionTan = new Function() {
+        @Override
+        protected boolean matchesParams(NumberInterface[] params) {
+            return params.length == 1;
+        }
+
+        @Override
+        protected NumberInterface applyInternal(NumberInterface[] params) {
+            return functionSin.apply(params[0]).divide(functionCos.apply(params[0]));
+        }
+    };
+
+    /**
+     * The secant function (the argument is in radians).
+     */
+    public final Function functionSec = new Function() {
+        @Override
+        protected boolean matchesParams(NumberInterface[] params) {
+            return params.length == 1;
+        }
+
+        @Override
+        protected NumberInterface applyInternal(NumberInterface[] params) {
+            return NaiveNumber.ONE.promoteTo(params[0].getClass()).divide(functionCos.apply(params[0]));
+        }
+    };
+
+    /**
+     * The cosecant function (the argument is in radians).
+     */
+    public final Function functionCsc = new Function() {
+        @Override
+        protected boolean matchesParams(NumberInterface[] params) {
+            return params.length == 1;
+        }
+
+        @Override
+        protected NumberInterface applyInternal(NumberInterface[] params) {
+            return NaiveNumber.ONE.promoteTo(params[0].getClass()).divide(functionSin.apply(params[0]));
+        }
+    };
+
+    /**
+     * The cotangent function (the argument is in radians).
+     */
+    public final Function functionCot = new Function() {
+        @Override
+        protected boolean matchesParams(NumberInterface[] params) {
+            return params.length == 1;
+        }
+
+        @Override
+        protected NumberInterface applyInternal(NumberInterface[] params) {
+            return functionCos.apply(params[0]).divide(functionCos.apply(params[0]));
+        }
+    };
+
     /**
      * The implementation for double-based naive numbers.
      */
@@ -395,6 +483,7 @@ public class StandardPlugin extends Plugin {
 
         registerOperator("+", OP_ADD);
         registerOperator("-", OP_SUBTRACT);
+        registerOperator("`", OP_NEGATE);
         registerOperator("*", OP_MULTIPLY);
         registerOperator("/", OP_DIVIDE);
         registerOperator("^", OP_CARET);
@@ -405,6 +494,11 @@ public class StandardPlugin extends Plugin {
         registerFunction("ln", FUNCTION_LN);
         registerFunction("sqrt", FUNCTION_SQRT);
         registerFunction("sin", functionSin);
+        registerFunction("cos", functionCos);
+        registerFunction("tan", functionTan);
+        registerFunction("sec", functionSec);
+        registerFunction("csc", functionCsc);
+        registerFunction("cot", functionCot);
     }
 
     @Override
@@ -420,12 +514,12 @@ public class StandardPlugin extends Plugin {
      * @return a number of numClass with value n factorial.
      */
     public static NumberInterface factorial(Class<? extends NumberInterface> numberClass, int n){
-        if(!factorialLists.containsKey(numberClass)){
-            factorialLists.put(numberClass, new ArrayList<NumberInterface>());
-            factorialLists.get(numberClass).add(NaiveNumber.ONE.promoteTo(numberClass));
-            factorialLists.get(numberClass).add(NaiveNumber.ONE.promoteTo(numberClass));
+        if(!FACTORIAL_LISTS.containsKey(numberClass)){
+            FACTORIAL_LISTS.put(numberClass, new ArrayList<>());
+            FACTORIAL_LISTS.get(numberClass).add(NaiveNumber.ONE.promoteTo(numberClass));
+            FACTORIAL_LISTS.get(numberClass).add(NaiveNumber.ONE.promoteTo(numberClass));
         }
-        ArrayList<NumberInterface> list = factorialLists.get(numberClass);
+        ArrayList<NumberInterface> list = FACTORIAL_LISTS.get(numberClass);
         if(n >= list.size()){
             while(list.size() < n + 16){
                 list.add(list.get(list.size()-1).multiply(new NaiveNumber(list.size()).promoteTo(numberClass)));

src/main/java/org/nwapw/abacus/tree/BinaryNode.java

@@ -3,7 +3,7 @@ package org.nwapw.abacus.tree;
 /**
  * A tree node that represents an operation being applied to two operands.
  */
-public class BinaryInfixNode extends TreeNode {
+public class BinaryNode extends TreeNode {
 
     /**
      * The operation being applied.
@@ -18,7 +18,7 @@ public class BinaryInfixNode extends TreeNode {
      */
     private TreeNode right;
 
-    private BinaryInfixNode() {
+    private BinaryNode() {
     }
 
     /**
@@ -27,7 +27,7 @@ public class BinaryInfixNode extends TreeNode {
      *
      * @param operation the operation.
      */
-    public BinaryInfixNode(String operation) {
+    public BinaryNode(String operation) {
         this(operation, null, null);
     }
 
@@ -39,7 +39,7 @@ public class BinaryInfixNode extends TreeNode {
      * @param left      the left node of the expression.
      * @param right     the right node of the expression.
      */
-    public BinaryInfixNode(String operation, TreeNode left, TreeNode right) {
+    public BinaryNode(String operation, TreeNode left, TreeNode right) {
         this.operation = operation;
         this.left = left;
         this.right = right;

src/main/java/org/nwapw/abacus/tree/NumberReducer.java

@@ -28,15 +28,15 @@ public class NumberReducer implements Reducer<NumberInterface> {
     public NumberInterface reduceNode(TreeNode node, Object... children) {
         if (node instanceof NumberNode) {
             return ((NumberNode) node).getNumber();
-        } else if (node instanceof BinaryInfixNode) {
+        } else if (node instanceof BinaryNode) {
             NumberInterface left = (NumberInterface) children[0];
             NumberInterface right = (NumberInterface) children[1];
-            Function function = abacus.getPluginManager().operatorFor(((BinaryInfixNode) node).getOperation()).getFunction();
+            Function function = abacus.getPluginManager().operatorFor(((BinaryNode) node).getOperation()).getFunction();
             if (function == null) return null;
             return function.apply(left, right);
-        } else if (node instanceof UnaryPrefixNode) {
+        } else if (node instanceof UnaryNode) {
             NumberInterface child = (NumberInterface) children[0];
-            Function functionn = abacus.getPluginManager().operatorFor(((UnaryPrefixNode) node).getOperation()).getFunction();
+            Function functionn = abacus.getPluginManager().operatorFor(((UnaryNode) node).getOperation()).getFunction();
             if (functionn == null) return null;
             return functionn.apply(child);
         } else if (node instanceof FunctionNode) {

src/main/java/org/nwapw/abacus/tree/UnaryNode.java

@@ -1,6 +1,6 @@
 package org.nwapw.abacus.tree;
 
-public class UnaryPrefixNode extends TreeNode {
+public class UnaryNode extends TreeNode {
 
     /**
      * The operation this node will apply.
@@ -16,7 +16,7 @@ public class UnaryPrefixNode extends TreeNode {
      *
      * @param operation the operation for this node.
      */
-    public UnaryPrefixNode(String operation) {
+    public UnaryNode(String operation) {
         this(operation, null);
     }
 
@@ -26,7 +26,7 @@ public class UnaryPrefixNode extends TreeNode {
      * @param operation the operation for this node.
      * @param applyTo   the node to apply the function to.
      */
-    public UnaryPrefixNode(String operation, TreeNode applyTo) {
+    public UnaryNode(String operation, TreeNode applyTo) {
         this.operation = operation;
         this.applyTo = applyTo;
     }

src/main/resources/abacus.fxml

@@ -0,0 +1,63 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<?import javafx.geometry.Insets?>
+<?import javafx.scene.control.*?>
+<?import javafx.scene.layout.BorderPane?>
+<?import javafx.scene.layout.VBox?>
+<?import javafx.scene.text.Text?>
+<?import javafx.scene.layout.HBox?>
+<?import javafx.scene.layout.GridPane?>
+<?import javafx.scene.layout.FlowPane?>
+<BorderPane xmlns="http://javafx.com/javafx"
+            xmlns:fx="http://javafx.com/fxml"
+            fx:controller="org.nwapw.abacus.fx.AbacusController">
+    <center>
+        <TabPane fx:id="coreTabPane">
+            <Tab fx:id="calculateTab" text="Calculator" closable="false">
+                <BorderPane>
+                    <center>
+                        <TableView fx:id="historyTable">
+                            <columnResizePolicy>
+                                <TableView fx:constant="CONSTRAINED_RESIZE_POLICY"/>
+                            </columnResizePolicy>
+                            <columns>
+                                <TableColumn fx:id="inputColumn" text="Input" sortable="false"/>
+                                <TableColumn fx:id="parsedColumn" text="Parsed" sortable="false"/>
+                                <TableColumn fx:id="outputColumn" text="Output" sortable="false"/>
+                            </columns>
+                        </TableView>
+                    </center>
+                    <bottom>
+                        <VBox>
+                            <ScrollPane prefHeight="50" vbarPolicy="NEVER">
+                                <padding>
+                                    <Insets top="10" bottom="10" left="10" right="10"/>
+                                </padding>
+                                <Text fx:id="outputText"/>
+                            </ScrollPane>
+                            <TextField fx:id="inputField" onAction="#performCalculation"/>
+                            <Button fx:id="inputButton" text="Calculate" maxWidth="Infinity"
+                                    onAction="#performCalculation"/>
+                        </VBox>
+                    </bottom>
+                </BorderPane>
+            </Tab>
+            <Tab fx:id="settingsTab" text="Settings" closable="false">
+                <GridPane hgap="10" vgap="10">
+                    <padding><Insets left="10" right="10" top="10" bottom="10"/></padding>
+                    <Label text="Number Implementation" GridPane.columnIndex="0" GridPane.rowIndex="0"/>
+                    <ComboBox fx:id="numberImplementationBox" GridPane.columnIndex="1" GridPane.rowIndex="0"/>
+                    <ListView fx:id="enabledPluginView"
+                              GridPane.rowIndex="1" GridPane.columnIndex="0"
+                              GridPane.columnSpan="2" maxHeight="100"/>
+                    <FlowPane GridPane.columnIndex="0" GridPane.columnSpan="2" GridPane.rowIndex="2" hgap="10" vgap="10">
+                        <Button text="Apply" onAction="#performSave"/>
+                        <Button text="Reload Plugins" onAction="#performReload"/>
+                        <Button text="Apply and Reload" onAction="#performSaveAndReload"/>
+                    </FlowPane>
+                </GridPane>
+            </Tab>
+        </TabPane>
+    </center>
+
+</BorderPane>