Added Javadoc comments to the classes

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

@@ -1,7 +1,23 @@
 //CipherStreamJava/src/main/java/com/mattrixwv/cipherstream/monosubstitution/Atbash.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;
 
 
@@ -11,18 +27,34 @@ import org.slf4j.LoggerFactory;
 import com.mattrixwv.cipherstream.exceptions.InvalidInputException;
 
 
+/**
+ * Implements the Atbash cipher, a simple substitution cipher where each letter of the alphabet is mapped to its reverse.
+ * For example, 'A' is mapped to 'Z', 'B' to 'Y', and so on.
+ * This class provides methods to encode and decode strings using the Atbash cipher.
+ *
+ * <p>
+ * The Atbash cipher is symmetric, meaning that encoding and decoding are the same operation.
+ * </p>
+ */
 public class Atbash{
 	private static final Logger logger = LoggerFactory.getLogger(Atbash.class);
-	//Fields
-	protected String inputString;		//Holds the string that needs encoded or decoded
-	protected String outputString;		//The encoded/decoded string
-	//Settings
-	protected boolean preserveCapitals;		//Persist capitals in the output string
-	protected boolean preserveWhitespace;	//Persist whitespace in the output string
-	protected boolean preserveSymbols;		//Persist symbols in the output string
+	//?Fields
+	/** Holds the string that needs encoded or decoded */
+	protected String inputString;
+	/** The encoded/decoded string */
+	protected String outputString;
+	//?Settings
+	/** Persist capitals in the output string */
+	protected boolean preserveCapitals;
+	/** Persist whitespace in the output string */
+	protected boolean preserveWhitespace;
+	/** Persist symbols in the output string */
+	protected boolean preserveSymbols;
 
 
-	//Encodes inputString and stores in outputString
+	/**
+	 * Encodes the input string using the Atbash cipher.
+	 */
 	protected void encode(){
 		logger.debug("Encoding");
 		StringBuilder output = new StringBuilder();
@@ -57,7 +89,12 @@ public class Atbash{
 		outputString = output.toString();
 		logger.debug("Saving output string '{}'", outputString);
 	}
-	//Removes all invalid characters and sets inputString
+	/**
+	 * Sets and sanitizes the input string according to the preservation settings.
+	 *
+	 * @param inputString the string to be processed
+	 * @throws InvalidInputException if the input string is null or blank after processing
+	 */
 	protected void setInputString(String inputString) throws InvalidInputException{
 		if(inputString == null){
 			throw new InvalidInputException("Input cannot be null");
@@ -95,13 +132,24 @@ public class Atbash{
 	}
 
 
-	//Constructor
+	//?Constructor
+	/**
+	 * Constructs a new {@code Atbash} instance with default settings:
+	 * capitals, symbols, and whitespace are not preserved.
+	 */
 	public Atbash(){
 		reset();
 		preserveCapitals = false;
 		preserveWhitespace = false;
 		preserveSymbols = false;
 	}
+	/**
+	 * Constructs a new {@code Atbash} 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 Atbash(boolean preserveCapitals, boolean preserveWhitespace, boolean preserveSymbols){
 		reset();
 		this.preserveCapitals = preserveCapitals;
@@ -109,7 +157,13 @@ public class Atbash{
 		this.preserveSymbols = preserveSymbols;
 	}
 
-	//Encodes inputString and returns the result
+	/**
+	 * Encodes the provided input string using the Atbash cipher and returns the encoded result.
+	 *
+	 * @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{
 		//Make sure everything is empty before you begin
 		reset();
@@ -117,19 +171,38 @@ public class Atbash{
 		encode();
 		return outputString;
 	}
-	//Decodes inputString and returns the result
+	/**
+	 * Decodes the provided input string using the Atbash cipher and returns the decoded result.
+	 * Since the Atbash cipher is symmetric, this method performs the same operation as encoding.
+	 *
+	 * @param inputString the string to be decoded
+	 * @return the decoded string
+	 * @throws InvalidInputException if the input string is invalid
+	 */
 	public String decode(String inputString) throws InvalidInputException{
 		return encode(inputString);
 	}
 
-	//Getters
+	//?Getters
+	/**
+	 * Returns the current input string.
+	 *
+	 * @return the input string
+	 */
 	public String getInputString(){
 		return inputString;
 	}
+	/**
+	 * Returns the current output string.
+	 *
+	 * @return the output string
+	 */
 	public String getOutputString(){
 		return outputString;
 	}
-	//Makes sure all variables are empty
+	/**
+	 * Resets all fields to their default values.
+	 */
 	public void reset(){
 		logger.debug("Resetting fields");