Added Javadoc comments to the classes

src/main/java/com/mattrixwv/cipherstream/monosubstitution/Autokey.java

@@ -1,7 +1,23 @@
 //CipherStreamJava/src/main/java/com/mattrixwv/CipherStreamJava/Autokey.java
 //Mattrixwv
 // Created: 07-25-21
-//Modified: 05-04-23
+//Modified: 08-11-24
+/*
+	Copyright (C) 2024  Mattrixwv
+
+	This program is free software: you can redistribute it and/or modify
+	it under the terms of the GNU Lesser General Public License as published by
+	the Free Software Foundation, either version 3 of the License, or
+	(at your option) any later version.
+
+	This program is distributed in the hope that it will be useful,
+	but WITHOUT ANY WARRANTY; without even the implied warranty of
+	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+	GNU Lesser General Public License for more details.
+
+	You should have received a copy of the GNU Lesser General Public License
+	along with this program.  If not, see <https://www.gnu.org/licenses/>.
+*/
 package com.mattrixwv.cipherstream.monosubstitution;
 
 
@@ -12,11 +28,28 @@ import com.mattrixwv.cipherstream.exceptions.InvalidInputException;
 import com.mattrixwv.cipherstream.exceptions.InvalidKeywordException;
 
 
+/**
+ * Implements the Autokey cipher, an extension of the Vigenère cipher that uses a keyword combined with the plaintext itself as the key.
+ * The Autokey cipher adds the plaintext to the end of the keyword to create a longer key, which helps to make the encryption stronger.
+ * This class inherits from the {@code Vigenere} class and overrides methods to handle encoding and decoding with the Autokey cipher.
+ *
+ * <p>
+ * The Autokey cipher is symmetric, meaning that encoding and decoding are essentially the same process, but with a different key setup for decoding.
+ * </p>
+ */
 public class Autokey extends Vigenere{
 	private static final Logger logger = LoggerFactory.getLogger(Autokey.class);
 
 
-	//Special rules for setting the strings for encoding
+	/**
+	 * Sets up the keyword and input string for encoding, generating a longer key that includes the plaintext.
+	 * This method is used internally to prepare the cipher for encoding.
+	 *
+	 * @param keyword      the keyword used for encoding
+	 * @param inputString  the string to be encoded
+	 * @throws InvalidKeywordException if the keyword is invalid
+	 * @throws InvalidInputException   if the input string is invalid
+	 */
 	protected void encodeSet(String keyword, String inputString) throws InvalidKeywordException, InvalidInputException{
 		logger.debug("Setting fields for encoding");
 
@@ -44,7 +77,15 @@ public class Autokey extends Vigenere{
 		offset.clear();
 		setOffset();
 	}
-	//Setting the strings for decoding
+	/**
+	 * Sets up the keyword and input string for decoding. The keyword is used to decode the input string.
+	 * This method is used internally to prepare the cipher for decoding.
+	 *
+	 * @param keyword      the keyword used for decoding
+	 * @param inputString  the string to be decoded
+	 * @throws InvalidKeywordException if the keyword is invalid
+	 * @throws InvalidInputException   if the input string is invalid
+	 */
 	protected void decodeSet(String keyword, String inputString) throws InvalidKeywordException, InvalidInputException{
 		logger.debug("Setting fields for decoding");
 
@@ -56,7 +97,10 @@ public class Autokey extends Vigenere{
 		logger.debug("Setting input string");
 		setInputString(inputString);
 	}
-	//Decodes the inputString
+	/**
+	 * Decodes the input string using the Autokey cipher.
+	 * This method is overridden to handle decoding with the Autokey cipher, which involves using the key and updating it with decoded characters.
+	 */
 	@Override
 	protected void decode(){
 		logger.debug("Decoding");
@@ -113,14 +157,32 @@ public class Autokey extends Vigenere{
 	}
 
 
-	//Constructor
+	//?Constructor
+	/**
+	 * Constructs a new {@code Autokey} instance with default settings for preserving capitals, whitespace, and symbols.
+	 */
 	public Autokey(){
 		super();
 	}
+	/**
+	 * Constructs a new {@code Autokey} instance with specified settings for preserving capitals, whitespace, and symbols.
+	 *
+	 * @param preserveCapitals     whether to preserve capital letters in the output
+	 * @param preserveWhitespace   whether to preserve whitespace in the output
+	 * @param preserveSymbols      whether to preserve symbols in the output
+	 */
 	public Autokey(boolean preserveCapitals, boolean preserveWhitespace, boolean preserveSymbols){
 		super(preserveCapitals, preserveWhitespace, preserveSymbols);
 	}
-	//Encodes inputString using the Autokey cipher
+	/**
+	 * Encodes the input string using the Autokey cipher with the provided keyword.
+	 *
+	 * @param keyword      the keyword used for encoding
+	 * @param inputString  the string to be encoded
+	 * @return the encoded string
+	 * @throws InvalidKeywordException if the keyword is invalid
+	 * @throws InvalidInputException   if the input string is invalid
+	 */
 	@Override
 	public String encode(String keyword, String inputString) throws InvalidKeywordException, InvalidInputException{
 		reset();
@@ -128,7 +190,15 @@ public class Autokey extends Vigenere{
 		encode();
 		return outputString;
 	}
-	//Decodes inputString using the Autokey cipher
+	/**
+	 * Decodes the input string using the Autokey cipher with the provided keyword.
+	 *
+	 * @param keyword      the keyword used for decoding
+	 * @param inputString  the string to be decoded
+	 * @return the decoded string
+	 * @throws InvalidKeywordException if the keyword is invalid
+	 * @throws InvalidInputException   if the input string is invalid
+	 */
 	@Override
 	public String decode(String keyword, String inputString) throws InvalidKeywordException, InvalidInputException{
 		reset();