Completed RailFence cipher

src/main/java/com/mattrixwv/CipherStreamJava/polySubstitution/RailFence.java

@@ -1,7 +1,7 @@
 //CipherStreamJava/src/main/java/com/mattrixwv/CipherStreamJava/polySubstitution/RailFence.java
 //Mattrixwv
 // Created: 03-21-22
-//Modified: 03-21-22
+//Modified: 03-22-22
 package com.mattrixwv.CipherStreamJava.polySubstitution;
 
 
@@ -13,13 +13,14 @@ import com.mattrixwv.CipherStreamJava.exceptions.InvalidInputException;
 
 public class RailFence{
 	//Variables
-	private String inputString;
-	private String outputString;
-	private StringBuilder[] fence;
-	private boolean preserveCapitals;
-	private boolean preserveWhitespace;
-	private boolean preserveSymbols;
+	private String inputString;		//The message that needs to be encoded/decoded
+	private String outputString;	//The encoded/decoded message
+	private StringBuilder[] fence;	//The fence used for encoding/decoding
+	private boolean preserveCapitals;	//Persist capitals in the output string
+	private boolean preserveWhitespace;	//Persist whitespace in the output string
+	private boolean preserveSymbols;	//Persist symbols in the output string
 
+	//Strips invalid characters from the string that needs encoded/decoded
 	private void setInputString(String inputString) throws InvalidInputException{
 		//Ensure the input string isn't null
 		if(inputString == null){
@@ -45,9 +46,10 @@ 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
 	private void setNumRails(int numRails) throws InvalidBaseException{
-		if(numRails <= 0){
-			throw new InvalidBaseException();
+		if(numRails < 2){
+			throw new InvalidBaseException("You must use at least 2 rails");
 		}
 
 		fence = new StringBuilder[numRails];
@@ -55,9 +57,11 @@ public class RailFence{
 			fence[cnt] = new StringBuilder();
 		}
 	}
+	//Strip the inputString of all non-letter characters
 	private String getCleanInputString(){
 		return inputString.replaceAll("[^a-zA-Z]", "");
 	}
+	//Ensures capitals, lowercase, and symbols are displayed in the output string
 	private void formatOutput(String outputString){
 		StringBuilder output = new StringBuilder();
 		int outputLoc = 0;
@@ -75,6 +79,7 @@ public class RailFence{
 
 		this.outputString = output.toString();
 	}
+	//Returns the decoded string found in the fence after all characters are placed correctly
 	private String getDecodedStringFromFence(){
 		boolean down = true;
 		int rail = 0;
@@ -82,6 +87,7 @@ public class RailFence{
 		int insideCol = -1;
 		StringBuilder output = new StringBuilder();
 		while(true){
+			//Get the next character based on what rail you are currently usinig
 			if(rail == 0){
 				if(outsideCol >= fence[rail].length()){
 					break;
@@ -103,6 +109,7 @@ public class RailFence{
 				output.append(fence[rail].charAt(insideCol));
 			}
 
+			//Make sure you're still in bounds
 			if(down){
 				++rail;
 			}
@@ -121,6 +128,7 @@ public class RailFence{
 
 		return output.toString();
 	}
+	//Encodes inputString using the RailFence cipher and stores the result in outputString
 	private void encode(){
 		boolean up = true;
 		int rail = 0;
@@ -151,7 +159,9 @@ public class RailFence{
 
 		formatOutput(output.toString());
 	}
+	//Decodes inputString using the RailFence cipher and stores the result in outputString
 	private void decode(){
+		//Determine the number of characters on each rail
 		String cleanInputString = getCleanInputString();
 		int cycleLength = 2 * (fence.length - 1);
 		BigDecimal k = new BigDecimal(cleanInputString.length()).divide(new BigDecimal(cycleLength));
@@ -172,6 +182,7 @@ public class RailFence{
 			middleNum = (cycleLength - (k.remainder(BigDecimal.ONE).multiply(new BigDecimal(cycleLength))).intValue());
 		}
 
+		//Add the correct number of characters to each rail
 		fence[0].append(cleanInputString.substring(0, numInTopRail));
 		int start = numInTopRail;
 		int end = numInTopRail + numInMiddleRails;
@@ -183,8 +194,10 @@ public class RailFence{
 			start = end;
 			end += numInMiddleRails;
 		}
-		fence[fence.length - 1].append(cleanInputString.substring(start));
+		end = start + numInBottomRail;
+		fence[fence.length - 1].append(cleanInputString.substring(start, end));
 
+		//Get the decoded string from the constructed fence
 		String output = getDecodedStringFromFence();
 		formatOutput(output);
 	}