Added Javadoc comments to the classes

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

@@ -1,7 +1,23 @@
 //CipherStreamJava/src/main/java/com/mattrixwv/cipherstream/monosubstitution/Caesar.java
 //Matthew Ellison
 // 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;
 
 
@@ -11,19 +27,39 @@ import org.slf4j.LoggerFactory;
 import com.mattrixwv.cipherstream.exceptions.InvalidInputException;
 
 
+/**
+ * A class for encoding and decoding strings using the Caesar cipher.
+ *
+ * <p>
+ * The Caesar cipher is a substitution cipher where each letter in the
+ * plaintext is shifted a fixed number of places down or up the alphabet.
+ * This class allows you to encode and decode strings with options to preserve
+ * capitalization, whitespace, and symbols.
+ * </p>
+ */
 public class Caesar{
 	private static final Logger logger = LoggerFactory.getLogger(Caesar.class);
-	//Fields
-	protected String inputString;	//The string that needs encoded/decoded
-	protected String outputString;	//The encoded/decoded string
-	protected int shift;	//The amount that you need to shift each letter
-	//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
+	/** The string that needs encoded/decoded */
+	protected String inputString;
+	/** The encoded/decoded string */
+	protected String outputString;
+	/** The amount that you need to shift each letter */
+	protected int shift;
+	//?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;
 
 
-	//Sets shift and makes sure it is within the propper bounds
+	/**
+	 * Sets the shift amount and ensures it is within the proper bounds (0-25).
+	 *
+	 * @param shiftAmount the amount to shift each letter
+	 */
 	protected void setShift(int shiftAmount){
 		logger.debug("Setting shift {}", shiftAmount);
 
@@ -32,7 +68,13 @@ public class Caesar{
 
 		logger.debug("Cleaned shift {}", shift);
 	}
-	//Sets the input string
+	/**
+	 * Sets the input string for encoding or decoding, applying removal options
+	 * for case, whitespace, and symbols.
+	 *
+	 * @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");
@@ -63,7 +105,9 @@ public class Caesar{
 			throw new InvalidInputException("Input must contain at least 1 letter");
 		}
 	}
-	//Encodes the inputString and stores the result in outputString
+	/**
+	 * Encodes the input string by shifting letters according to the Caesar cipher.
+	 */
 	protected void encode(){
 		logger.debug("Encoding");
 
@@ -111,7 +155,9 @@ public class Caesar{
 		outputString = output.toString();
 		logger.debug("Saving encoded string '{}'", outputString);
 	}
-	//Decodes the inputString and stores the result in outputString
+	/**
+	 * Decodes the input string by reversing the shift applied during encoding.
+	 */
 	protected void decode(){
 		logger.debug("Decoding");
 
@@ -164,13 +210,23 @@ public class Caesar{
 		logger.debug("Saving decoded string '{}'", outputString);
 	}
 
-	//Constructor
+	//?Constructor
+	/**
+	 * Constructs a new {@code Caesar} instance with default settings.
+	 */
 	public Caesar(){
 		reset();
 		preserveCapitals = false;
 		preserveWhitespace = false;
 		preserveSymbols = false;
 	}
+	/**
+	 * Constructs a new {@code Caesar} instance with specified settings.
+	 *
+	 * @param preserveCapitals   whether to preserve capitalization in the output
+	 * @param preserveWhitespace whether to preserve whitespace in the output
+	 * @param preserveSymbols    whether to preserve symbols in the output
+	 */
 	public Caesar(boolean preserveCapitals, boolean preserveWhitespace, boolean preserveSymbols){
 		reset();
 		this.preserveCapitals = preserveCapitals;
@@ -178,7 +234,14 @@ public class Caesar{
 		this.preserveSymbols = preserveSymbols;
 	}
 
-	//Sets the shift and inputString and encodes the message
+	/**
+	 * Encodes the input string with the specified shift amount.
+	 *
+	 * @param shiftAmount the amount to shift each letter
+	 * @param inputString the string to be encoded
+	 * @return the encoded string
+	 * @throws InvalidInputException if the input string is invalid
+	 */
 	public String encode(int shiftAmount, String inputString) throws InvalidInputException{
 		reset();
 		setShift(shiftAmount);
@@ -186,7 +249,14 @@ public class Caesar{
 		encode();
 		return outputString;
 	}
-	//Sets the shift and inputString and decodes the message
+	/**
+	 * Decodes the input string with the specified shift amount.
+	 *
+	 * @param shiftAmount the amount to shift each letter
+	 * @param inputString the string to be decoded
+	 * @return the decoded string
+	 * @throws InvalidInputException if the input string is invalid
+	 */
 	public String decode(int shiftAmount, String inputString) throws InvalidInputException{
 		reset();
 		setShift(shiftAmount);
@@ -195,17 +265,34 @@ public class Caesar{
 		return outputString;
 	}
 
-	//Getters
+	//?Getters
+	/**
+	 * Gets the current input string.
+	 *
+	 * @return the input string
+	 */
 	public String getInputString(){
 		return inputString;
 	}
+	/**
+	 * Gets the current shift amount.
+	 *
+	 * @return the shift amount
+	 */
 	public int getShift(){
 		return shift;
 	}
+	/**
+	 * Gets the current output string.
+	 *
+	 * @return the output string
+	 */
 	public String getOutputString(){
 		return outputString;
 	}
-	//Makes sure all variables are empty
+	/**
+	 * Resets the internal fields to their default values.
+	 */
 	public void reset(){
 		logger.debug("Resetting fields");