Add numerous documentation fixes.

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

@@ -6,12 +6,16 @@ import org.nwapw.abacus.number.NumberInterface;
 import org.nwapw.abacus.parsing.LexerTokenizer;
 import org.nwapw.abacus.parsing.ShuntingYardParser;
 import org.nwapw.abacus.parsing.TreeBuilder;
+import org.nwapw.abacus.plugin.ClassFinder;
 import org.nwapw.abacus.plugin.NumberImplementation;
 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 java.io.File;
+import java.io.IOException;
+
 /**
  * The main calculator class. This is responsible
  * for piecing together all of the components, allowing
@@ -23,6 +27,10 @@ public class Abacus {
      * The default number implementation to be used if no other one is available / selected.
      */
     public static final NumberImplementation DEFAULT_IMPLEMENTATION = StandardPlugin.IMPLEMENTATION_NAIVE;
+    /**
+     * The file used for saving and loading configuration.
+     */
+    public static final File CONFIG_FILE = new File("config.toml");
 
     /**
      * The plugin manager responsible for
@@ -47,16 +55,25 @@ public class Abacus {
     /**
      * Creates a new instance of the Abacus calculator.
      */
-    public Abacus(Configuration configuration) {
+    public Abacus() {
         pluginManager = new PluginManager(this);
         numberReducer = new NumberReducer(this);
-        this.configuration = new Configuration(configuration);
+        configuration = new Configuration(CONFIG_FILE);
+        configuration.saveTo(CONFIG_FILE);
         LexerTokenizer lexerTokenizer = new LexerTokenizer();
         ShuntingYardParser shuntingYardParser = new ShuntingYardParser(this);
         treeBuilder = new TreeBuilder<>(lexerTokenizer, shuntingYardParser);
 
-        pluginManager.addListener(shuntingYardParser);
         pluginManager.addListener(lexerTokenizer);
+        pluginManager.addListener(shuntingYardParser);
+        pluginManager.addInstantiated(new StandardPlugin(pluginManager));
+        try {
+            ClassFinder.loadJars("plugins")
+                    .forEach(plugin -> pluginManager.addClass(plugin));
+        } catch (IOException | ClassNotFoundException e) {
+            e.printStackTrace();
+        }
+        pluginManager.load();
     }
 
     public static void main(String[] args) {

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

@@ -39,15 +39,6 @@ public class Configuration {
      */
     private Set<String> disabledPlugins = new HashSet<>();
 
-    /**
-     * Creates a new configuration form the given configuration.
-     *
-     * @param copyFrom the configuration to copy.
-     */
-    public Configuration(Configuration copyFrom){
-        copyFrom(copyFrom);
-    }
-
     /**
      * Creates a new configuration with the given values.
      *
@@ -94,15 +85,6 @@ public class Configuration {
         }
     }
 
-    /**
-     * Gets the value of this configuration as a string.
-     *
-     * @return the string that represents this configuration.
-     */
-    public String asTomlString(){
-        return TOML_WRITER.write(this);
-    }
-
     /**
      * Gets the number implementation from this configuration.
      *

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

@@ -26,6 +26,7 @@ public class Operator {
      * Creates a new operator with the given parameters.
      *
      * @param associativity the associativity of the operator.
+     * @param operatorType  the type of this operator, like binary infix or unary postfix.
      * @param precedence    the precedence of the operator.
      * @param function      the function that the operator calls.
      */

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

@@ -12,14 +12,10 @@ 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.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.Set;
 
 
@@ -29,10 +25,6 @@ import java.util.Set;
  */
 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.
      */
@@ -180,16 +172,9 @@ public class AbacusController implements PluginListener {
             if (oldValue.equals(settingsTab)) alertIfApplyNeeded(true);
         });
 
-        abacus = new Abacus(new Configuration(CONFIG_FILE));
+        abacus = new Abacus();
-        PluginManager abacusPluginManager = abacus.getPluginManager();
+        abacus.getPluginManager().addListener(this);
-        abacusPluginManager.addListener(this);
+        abacus.getPluginManager().reload();
-        abacusPluginManager.addInstantiated(new StandardPlugin(abacus.getPluginManager()));
-        try {
-            ClassFinder.loadJars("plugins").forEach(abacusPluginManager::addClass);
-        } catch (IOException | ClassNotFoundException e) {
-            e.printStackTrace();
-        }
-        abacusPluginManager.reload();
 
         changesMade = false;
         reloadAlertShown = false;
@@ -284,7 +269,7 @@ public class AbacusController implements PluginListener {
         for (ToggleablePlugin pluginEntry : enabledPlugins) {
             if (!pluginEntry.isEnabled()) disabledPlugins.add(pluginEntry.getClassName());
         }
-        configuration.saveTo(CONFIG_FILE);
+        configuration.saveTo(Abacus.CONFIG_FILE);
         changesMade = false;
         reloadAlertShown = false;
     }

src/main/java/org/nwapw/abacus/lexing/pattern/ValueNode.java

@@ -15,7 +15,7 @@ public class ValueNode<T> extends PatternNode<T> {
     /**
      * Creates a new node that matches the given character.
      *
-     * @param value
+     * @param value the character value of the node.
      */
     public ValueNode(char value) {
         this.value = value;

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

@@ -82,14 +82,14 @@ public interface NumberInterface {
     /**
      * Returns the least integer greater than or equal to the number.
      *
-     * @return the least integer >= the number, if int can hold the value.
+     * @return the least integer bigger or equal to the number, if int can hold the value.
      */
     NumberInterface ceiling();
 
     /**
      * Return the greatest integer less than or equal to the number.
      *
-     * @return the greatest int >= the number, if int can hold the value.
+     * @return the greatest integer smaller or equal the number, if int can hold the value.
      */
     NumberInterface floor();
 
@@ -104,7 +104,7 @@ public interface NumberInterface {
      * Returns the integer representation of this number, discarding any fractional part,
      * if int can hold the value.
      *
-     * @return
+     * @return the integer value of this number.
      */
     int intValue();
 

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

@@ -28,7 +28,7 @@ public abstract class NumberImplementation {
      * Creates a new number implementation with the given data.
      *
      * @param implementation the implementation class.
-     * @param priority       the priority, higher -> more likely to be converted into.
+     * @param priority       the priority, higher means more likely to be converted into.
      */
     public NumberImplementation(Class<? extends NumberInterface> implementation, int priority) {
         this.implementation = implementation;

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

@@ -70,6 +70,8 @@ public class PluginManager {
 
     /**
      * Creates a new plugin manager.
+     *
+     * @param abacus the abacus instance.
      */
     public PluginManager(Abacus abacus) {
         this.abacus = abacus;

src/test/java/org/nwapw/abacus/tests/CalculationTests.java

@@ -1,104 +0,0 @@
-package org.nwapw.abacus.tests;
-
-import org.junit.Assert;
-import org.junit.BeforeClass;
-import org.junit.Test;
-import org.nwapw.abacus.Abacus;
-import org.nwapw.abacus.config.Configuration;
-import org.nwapw.abacus.number.NumberInterface;
-import org.nwapw.abacus.plugin.StandardPlugin;
-import org.nwapw.abacus.tree.TreeNode;
-
-public class CalculationTests {
-
-    private static Abacus abacus = new Abacus(new Configuration("precise", new String[]{}));
-
-    @BeforeClass
-    public static void prepareTests(){
-        abacus.getPluginManager().addInstantiated(new StandardPlugin(abacus.getPluginManager()));
-        abacus.getPluginManager().load();
-    }
-
-    private void testOutput(String input, String parseOutput, String output){
-        TreeNode parsedTree = abacus.parseString(input);
-        Assert.assertNotNull(parsedTree);
-        Assert.assertEquals(parsedTree.toString(), parseOutput);
-        NumberInterface result = abacus.evaluateTree(parsedTree);
-        Assert.assertNotNull(result);
-        Assert.assertTrue(result.toString().startsWith(output));
-    }
-
-    private void testEvalError(String input, String parseOutput){
-        TreeNode parsedTree = abacus.parseString(input);
-        Assert.assertNotNull(parsedTree);
-        Assert.assertEquals(parsedTree.toString(), parseOutput);
-        Assert.assertNull(abacus.evaluateTree(parsedTree));
-    }
-
-    @Test
-    public void testAddition(){
-        testOutput("9.5+10", "(9.5+10)", "19.5");
-    }
-
-    @Test
-    public void testSubtraction(){
-        testOutput("9.5-10", "(9.5-10)", "-0.5");
-    }
-
-    @Test
-    public void testMultiplication(){
-        testOutput("9.5*10", "(9.5*10)", "95");
-    }
-
-    @Test
-    public void testDivision(){
-        testOutput("9.5/2", "(9.5/2)", "4.75");
-    }
-
-    @Test
-    public void testNegation(){
-        testOutput("-9.5", "(9.5)`", "-9.5");
-    }
-
-    @Test
-    public void testFactorial(){
-        testOutput("7!", "(7)!", "5040");
-    }
-
-    @Test
-    public void testAbs(){
-        testOutput("abs(-1)", "abs((1)`)", "1");
-        testOutput("abs(1)", "abs(1)", "1");
-    }
-
-    @Test
-    public void testLn(){
-        testEvalError("ln(-1)", "ln((1)`)");
-        testOutput("ln2", "ln(2)", "0.6931471805599453094172321214581765680755");
-    }
-
-    @Test
-    public void testSqrt(){
-        testOutput("sqrt0", "sqrt(0)", "0");
-        testOutput("sqrt4", "sqrt(4)", "2");
-        testOutput("sqrt2", "sqrt(2)", "1.4142135623730950488016887242096980785696");
-    }
-
-    @Test
-    public void testExp(){
-        testOutput("exp0", "exp(0)", "1");
-        testOutput("exp1", "exp(1)", "2.718281828459045235360287471352662497757247");
-        testOutput("exp300", "exp(300)", "19424263952412559365842088360176992193662086");
-        testOutput("exp300", "exp(300)", "19424263952412559365842088360176992193662086");
-    }
-
-    @Test
-    public void testPow(){
-        testOutput("0^2", "(0^2)", "0");
-        testOutput("2^0", "(2^0)", "1");
-        testOutput("2^1", "(2^1)", "2");
-        testOutput("2^-1", "(2^(1)`)", "0.5");
-        testOutput("2^50", "(2^50)", "112589990684262");
-    }
-
-}

src/test/java/org/nwapw/abacus/tests/TokenizerTests.java

@@ -4,7 +4,6 @@ import org.junit.Assert;
 import org.junit.BeforeClass;
 import org.junit.Test;
 import org.nwapw.abacus.Abacus;
-import org.nwapw.abacus.config.Configuration;
 import org.nwapw.abacus.function.Function;
 import org.nwapw.abacus.function.Operator;
 import org.nwapw.abacus.function.OperatorAssociativity;
@@ -19,7 +18,7 @@ import java.util.List;
 
 public class TokenizerTests {
 
-    private static Abacus abacus = new Abacus(new Configuration("precise", new String[]{}));
+    private static Abacus abacus = new Abacus();
     private static LexerTokenizer lexerTokenizer = new LexerTokenizer();
     private static Function subtractFunction = new Function() {
         @Override