Added Javadoc comments to the classes

src/main/java/com/mattrixwv/cipherstream/polysubstitution/RailFence.java

@@ -1,7 +1,23 @@
 //CipherStreamJava/src/main/java/com/mattrixwv/cipherstream/polysubstitution/RailFence.java
 //Mattrixwv
 // Created: 03-21-22
-//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.polysubstitution;
 
 
@@ -14,19 +30,35 @@ import com.mattrixwv.cipherstream.exceptions.InvalidBaseException;
 import com.mattrixwv.cipherstream.exceptions.InvalidInputException;
 
 
+/**
+ * Represents the Rail Fence cipher encryption and decryption.
+ * The Rail Fence cipher is a form of transposition cipher that writes the message in a zigzag pattern
+ * across multiple "rails" and then reads it off row by row to encode or decode the message.
+ */
 public class RailFence{
 	private static final Logger logger = LoggerFactory.getLogger(RailFence.class);
-	//Fields
-	protected String inputString;		//The message that needs to be encoded/decoded
-	protected String outputString;		//The encoded/decoded message
-	protected StringBuilder[] fence;	//The fence used for encoding/decoding
-	//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 message that needs to be encoded/decoded */
+	protected String inputString;
+	/** The encoded/decoded message */
+	protected String outputString;
+	/** The fence used for encoding/decoding */
+	protected StringBuilder[] fence;
+	//?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;
 
 
-	//Strips invalid characters from the string that needs encoded/decoded
+	/**
+	 * Strips invalid characters from the string that needs to be encoded/decoded.
+	 *
+	 * @param inputString the input string to be cleaned
+	 * @throws InvalidInputException if the input string is null or invalid
+	 */
 	protected void setInputString(String inputString) throws InvalidInputException{
 		//Ensure the input string isn't null
 		if(inputString == null){
@@ -61,7 +93,12 @@ public class RailFence{
 			throw new InvalidInputException("Input must contain at least 1 letter");
 		}
 	}
-	//Ensures the number of rails is valid and sets up the fence
+	/**
+	 * Ensures the number of rails is valid and sets up the fence.
+	 *
+	 * @param numRails the number of rails to be used
+	 * @throws InvalidBaseException if the number of rails is less than 2
+	 */
 	protected void setNumRails(int numRails) throws InvalidBaseException{
 		if(numRails < 2){
 			throw new InvalidBaseException("You must use at least 2 rails");
@@ -74,13 +111,21 @@ public class RailFence{
 			fence[cnt] = new StringBuilder();
 		}
 	}
-	//Strip the inputString of all non-letter characters
+	/**
+	 * Strips the input string of all non-letter characters.
+	 *
+	 * @return the cleaned input string
+	 */
 	protected String getCleanInputString(){
 		logger.debug("Getting input string for encoding");
 
 		return inputString.replaceAll("[^a-zA-Z]", "");
 	}
-	//Ensures capitals, lowercase, and symbols are displayed in the output string
+	/**
+	 * Ensures capitals, lowercase, and symbols are displayed in the output string.
+	 *
+	 * @param outputString the encoded/decoded output string to be formatted
+	 */
 	protected void formatOutput(String outputString){
 		logger.debug("Formatting output string");
 
@@ -109,7 +154,11 @@ public class RailFence{
 		this.outputString = output.toString();
 		logger.debug("Formatted output '{}'", this.outputString);
 	}
-	//Returns the decoded string found in the fence after all characters are placed correctly
+	/**
+	 * Returns the decoded string found in the fence after all characters are placed correctly.
+	 *
+	 * @return the decoded string
+	 */
 	protected String getDecodedStringFromFence(){
 		logger.debug("Getting decoded string from the fence");
 
@@ -161,7 +210,9 @@ public class RailFence{
 		logger.debug("Fence output '{}'", output);
 		return output.toString();
 	}
-	//Encodes inputString using the RailFence cipher and stores the result in outputString
+	/**
+	 * Encodes the input string using the Rail Fence cipher and stores the result in the output string.
+	 */
 	protected void encode(){
 		logger.debug("Encoding");
 
@@ -204,7 +255,9 @@ public class RailFence{
 		//Format the output
 		formatOutput(output.toString());
 	}
-	//Decodes inputString using the RailFence cipher and stores the result in outputString
+	/**
+	 * Decodes the input string using the Rail Fence cipher and stores the result in the output string.
+	 */
 	protected void decode(){
 		logger.debug("Decoding");
 
@@ -256,13 +309,23 @@ public class RailFence{
 		formatOutput(output);
 	}
 
-	//Constructor
+	//?Constructor
+	/**
+	 * Constructs a RailFence cipher instance with default settings.
+	 */
 	public RailFence(){
 		preserveCapitals = false;
 		preserveWhitespace = false;
 		preserveSymbols = false;
 		reset();
 	}
+	/**
+	 * Constructs a RailFence cipher instance with specified settings.
+	 *
+	 * @param preserveCapitals whether to preserve uppercase letters
+	 * @param preserveWhitespace whether to preserve whitespace
+	 * @param preserveSymbols whether to preserve symbols
+	 */
 	public RailFence(boolean preserveCapitals, boolean preserveWhitespace, boolean preserveSymbols){
 		this.preserveCapitals = preserveCapitals;
 		this.preserveWhitespace = preserveWhitespace;
@@ -270,7 +333,15 @@ public class RailFence{
 		reset();
 	}
 
-	//Encodes inputString using a Rail Fence of length numRails and returns the result
+	/**
+	 * Encodes the input string using a Rail Fence of the specified number of rails and returns the result.
+	 *
+	 * @param numRails the number of rails to use
+	 * @param inputString the message to encode
+	 * @return the encoded message
+	 * @throws InvalidBaseException if the number of rails is invalid
+	 * @throws InvalidInputException if the input string is invalid
+	 */
 	public String encode(int numRails, String inputString) throws InvalidBaseException, InvalidInputException{
 		//Set the parameters
 		setNumRails(numRails);
@@ -280,7 +351,15 @@ public class RailFence{
 		encode();
 		return outputString;
 	}
-	//Decodes inputString using a Rail Fence of length numRails and returns the result
+	/**
+	 * Decodes the input string using a Rail Fence of the specified number of rails and returns the result.
+	 *
+	 * @param numRails the number of rails to use
+	 * @param inputString the encoded message to decode
+	 * @return the decoded message
+	 * @throws InvalidBaseException if the number of rails is invalid
+	 * @throws InvalidInputException if the input string is invalid
+	 */
 	public String decode(int numRails, String inputString) throws InvalidBaseException, InvalidInputException{
 		//Set the parameters
 		setNumRails(numRails);
@@ -291,7 +370,9 @@ public class RailFence{
 		return outputString;
 	}
 
-	//Makes sure all variables are empty
+	/**
+	 * Resets all variables to their default values.
+	 */
 	public void reset(){
 		logger.debug("Resetting fields");
 
@@ -300,13 +381,28 @@ public class RailFence{
 		fence = null;
 	}
 
-	//Getters
+	//?Getters
+	/**
+	 * Returns the input string that was set for encoding/decoding.
+	 *
+	 * @return the input string
+	 */
 	public String getInputString(){
 		return inputString;
 	}
+	/**
+	 * Returns the output string after encoding/decoding.
+	 *
+	 * @return the output string
+	 */
 	public String getOutputString(){
 		return outputString;
 	}
+	/**
+	 * Returns the number of rails used in the Rail Fence cipher.
+	 *
+	 * @return the number of rails
+	 */
 	public int getNumRails(){
 		return fence.length;
 	}