Added Javadoc comments to the classes

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

@@ -1,7 +1,23 @@
 //CipherStreamJava/src/test/java/com/mattrixwv/CipherStreamJava/Baconian.java
 //Mattrixwv
 // Created: 01-12-22
-//Modified: 04-19-24
+//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;
 
 
@@ -16,20 +32,38 @@ import com.mattrixwv.cipherstream.exceptions.InvalidCharacterException;
 import com.mattrixwv.cipherstream.exceptions.InvalidInputException;
 
 
+/**
+ * Implements the Baconian cipher, a method of steganography where each letter of the alphabet is represented by a unique sequence of five characters ('a' or 'b').
+ * The Baconian cipher is a simple substitution cipher that can encode and decode text based on these sequences.
+ *
+ * <p>
+ * The cipher uses a predefined list of five-character strings to represent each letter of the alphabet (A-Z). The input string is converted to these sequences for encoding,
+ * and sequences are converted back to letters for decoding.
+ * </p>
+ */
 public class Baconian{
 	private static final Logger logger = LoggerFactory.getLogger(Baconian.class);
 
-	//Conversions
+	//?Conversions
+	/** Predefined code for Baconian cipher (5-character strings for A-Z) */
 	protected static final ArrayList<String> code = new ArrayList<>(Arrays.asList(
 		"aaaaa", "aaaab", "aaaba", "aaabb", "aabaa", "aabab", "aabba","aabbb", "abaaa", "abaaa", "abaab", "ababa", "ababb",	//A-M
 		"abbaa", "abbab", "abbba", "abbbb", "baaaa", "baaab", "baaba", "baabb", "baabb", "babaa", "babab", "babba", "babbb"		//N-Z
 	));
-	protected String inputString;		//The string that needs encoded/decoded
-	protected String outputString;		//The encoded/decoded string
-	protected boolean preserveCapitals;	//Persist capitals in the output string
+	/** The string that needs encoded/decoded */
+	protected String inputString;
+	/** The encoded/decoded string */
+	protected String outputString;
+	/** Persist capitals in the output string */
+	protected boolean preserveCapitals;
 
 
-	//Sets the input string
+	/**
+	 * Sets the input string for encoding, removing whitespace and symbols, and handling capitalization based on the flag.
+	 *
+	 * @param inputString the string to be encoded
+	 * @throws InvalidInputException if the input string is null, empty, or invalid
+	 */
 	protected void setInputStringEncode(String inputString) throws InvalidInputException{
 		if(inputString == null){
 			throw new InvalidInputException("Input cannot be null");
@@ -53,6 +87,13 @@ public class Baconian{
 			throw new InvalidInputException("Input must contain at least 1 letter");
 		}
 	}
+	/**
+	 * Sets the input string for decoding, ensuring it contains only valid Baconian characters (a's and b's) with a length of 5.
+	 *
+	 * @param inputString the string to be decoded
+	 * @throws InvalidCharacterException if the input string contains invalid Baconian characters
+	 * @throws InvalidInputException     if the input string is null or empty
+	 */
 	protected void setInputStringDecode(String inputString) throws InvalidCharacterException, InvalidInputException{
 		if(inputString == null){
 			throw new InvalidInputException("Input cannot be null");
@@ -91,7 +132,10 @@ public class Baconian{
 
 		logger.debug("Cleaned input string '{}'", inputString);
 	}
-	//Encodes the inputString and stores the result in outputString
+	/**
+	 * Encodes the input string using the Baconian cipher.
+	 * Each character in the input string is converted to its corresponding Baconian sequence.
+	 */
 	protected void encode(){
 		logger.debug("Encoding");
 		StringJoiner output = new StringJoiner(" ");
@@ -121,7 +165,10 @@ public class Baconian{
 		outputString = output.toString();
 		logger.debug("Saving output string '{}'", outputString);
 	}
-	//Decodes the inputString and stores the result in outputString
+	/**
+	 * Decodes the input string using the Baconian cipher.
+	 * Each Baconian sequence in the input string is converted back to its corresponding character.
+	 */
 	protected void decode(){
 		logger.debug("Decoding");
 
@@ -157,24 +204,45 @@ public class Baconian{
 		logger.debug("Saving output string '{}'", outputString);
 	}
 
-	//Constructor
+	//?Constructor
+	/**
+	 * Constructs a new {@code Baconian} instance with default settings for preserving capitals.
+	 */
 	public Baconian(){
 		reset();
 		preserveCapitals = false;
 	}
+	/**
+	 * Constructs a new {@code Baconian} instance with a specified setting for preserving capitals.
+	 *
+	 * @param preserveCapitals whether to preserve capital letters in the output
+	 */
 	public Baconian(boolean preserveCapitals){
 		reset();
 		this.preserveCapitals = preserveCapitals;
 	}
 
-	//Sets the inputString and encodes the message
+	/**
+	 * Encodes the input string using the Baconian cipher.
+	 *
+	 * @param inputString the string to be encoded
+	 * @return the encoded string
+	 * @throws InvalidInputException if the input string is invalid
+	 */
 	public String encode(String inputString) throws InvalidInputException{
 		reset();
 		setInputStringEncode(inputString);
 		encode();
 		return outputString;
 	}
-	//Sets the inputString and decodes the message
+	/**
+	 * Decodes the input string using the Baconian cipher.
+	 *
+	 * @param inputString the string to be decoded
+	 * @return the decoded string
+	 * @throws InvalidCharacterException if the input string contains invalid Baconian characters
+	 * @throws InvalidInputException     if the input string is invalid
+	 */
 	public String decode(String inputString) throws InvalidCharacterException, InvalidInputException{
 		reset();
 		setInputStringDecode(inputString);
@@ -182,14 +250,26 @@ public class Baconian{
 		return outputString;
 	}
 
-	//Getters
+	//?Getters
+	/**
+	 * Gets the current input string.
+	 *
+	 * @return the input string
+	 */
 	public String getInputString(){
 		return inputString;
 	}
+	/**
+	 * Gets the current output string.
+	 *
+	 * @return the output string
+	 */
 	public String getOutputString(){
 		return outputString;
 	}
-	//Makes sure all variables are empty
+	/**
+	 * Resets the input and output strings to empty.
+	 */
 	public void reset(){
 		logger.debug("Resetting fields");