diff --git a/helperFunctions.hpp b/helperFunctions.hpp
index c1ce073..5582697 100644
--- a/helperFunctions.hpp
+++ b/helperFunctions.hpp
@@ -1,12 +1,11 @@
 //Ciphers/helperFunctions.hpp
 //Matthew Ellison
 // Created: 4-29-18
-//Modified: 5-2-18
+//Modified: 5-8-18
 //This file contains the driver function and the test functions for the Cipher program
 //This program will use some simple ciphers that are no longer widely used but still fun to play with
 
 
-
 #ifndef HELPER_FUNCTIONS_HPP
 #define HELPER_FUNCTIONS_HPP
 
@@ -33,6 +32,15 @@ typedef std::string (*Fn)(std::ifstream&, bool);
 
 
 
+/**
+ * @brief Takes all of the arguments that were given to the program and sets boolean flags inside the program that will change behavior
+ * 
+ * @param argc The number of arguments given
+ * @param argv The arguments given
+ * @param cipherFlags The array of booleans that represent the possible options passed in
+ * @param inputFileString The name of the input file, if given
+ * @param outputFileString The name of the output file if given
+ */
 void getFlags(int argc, char** argv, bool cipherFlags[], std::string& inputFileString, std::string& outputFileString){
 	//Cycle through every argument
 	bool valid = false;
@@ -67,6 +75,13 @@ void getFlags(int argc, char** argv, bool cipherFlags[], std::string& inputFileS
 	}
 }
 
+/**
+ * @brief Checks that the flags given are valid
+ * 
+ * @param flags All of the flags that the program can have
+ * @return true If valid options were chosen
+ * @return false If invalid options were chosen
+ */
 bool checkFlags(bool flags[]){
 	int counter = 0;
 	bool correct = false;
@@ -90,6 +105,10 @@ bool checkFlags(bool flags[]){
 	return correct;
 }
 
+/**
+ * @brief Set the array of strings that controls what each flag should look
+ * 
+ */
 void setFlagStrings(){
 	flagStrings[CAESAR] = "-c";
 	flagStrings[PLAYFAIR] = "-p";
@@ -103,6 +122,13 @@ void setFlagStrings(){
 	flagStrings[OUTPUT_FILE] = "-o";
 }
 
+/**
+ * @brief Run the appropriate commands to use a Caesar cipher
+ * 
+ * @param infile The input file if one was provided
+ * @param encode Whether the encoding flag was set. True if encoding, false if decoding
+ * @return The new message
+ */
 std::string runCaesar(std::ifstream& infile, bool encode){
 	std::string inputString, cipherString;
 	int offset;
@@ -140,6 +166,13 @@ std::string runCaesar(std::ifstream& infile, bool encode){
 	return cipherString;
 }
 
+/**
+ * @brief Run the appropriate commands to use a Playfair cipher
+ * 
+ * @param infile The input file if one was provided
+ * @param encode Whether the encoding flag was set. True if encoding, false if decoding
+ * @return The new message
+ */
 std::string runPlayfair(std::ifstream& infile, bool encode){
 	std::string keyword, inputString, cipherString;
 	Playfair cipher;
@@ -175,6 +208,13 @@ std::string runPlayfair(std::ifstream& infile, bool encode){
 	return cipherString;
 }
 
+/**
+ * @brief Run the appropriate commands to use a Vigenere cipher
+ * 
+ * @param infile The input file if one was provided
+ * @param encode Whether the encoding flag was set. True if encoding, false if decoding
+ * @return The new message
+ */
 std::string runVigenere(std::ifstream& infile, bool encode){
 	std::string keyword, inputString, cipherString;
 	Vigenere cipher;
@@ -210,6 +250,13 @@ std::string runVigenere(std::ifstream& infile, bool encode){
 	return cipherString;
 }
 
+/**
+ * @brief Run the appropriate commands to use an Atbash cipher
+ * 
+ * @param infile The input file if one was provided
+ * @param encode Whether the encoding flag was set. True if encoding, false if decoding
+ * @return The new message
+ */
 std::string runAtbash(std::ifstream& infile, bool encode){
 	std::string inputString, cipherString;
 	Atbash cipher;
@@ -242,6 +289,13 @@ std::string runAtbash(std::ifstream& infile, bool encode){
 	return cipherString;
 }
 
+/**
+ * @brief Run the appropriate commands to use Morse code
+ * 
+ * @param infile The input file if one was provided
+ * @param encode Whether the encoding flag was set. True if encoding, false if decoding
+ * @return The new message
+ */
 std::string runMorse(std::ifstream& infile, bool encode){
 	std::string inputString, cipherString;
 	Morse cipher;
@@ -274,6 +328,13 @@ std::string runMorse(std::ifstream& infile, bool encode){
 	return cipherString;
 }
 
+/**
+ * @brief Run the appropriate commands to use an Autokey cipher
+ * 
+ * @param infile The input file if one was provided
+ * @param encode Whether the encoding flag was set. True if encoding, false if decoding
+ * @return The new message
+ */
 std::string runAutokey(std::ifstream& infile, bool encode){
 	std::string keyword, inputString, cipherString;
 	Autokey cipher;
@@ -309,6 +370,12 @@ std::string runAutokey(std::ifstream& infile, bool encode){
 	return cipherString;
 }
 
+/**
+ * @brief Uses the flags to determine which cipher needs to be run
+ * 
+ * @param cipherFlags The possible flags given to the program
+ * @return The appropriate run___ function based on the flags
+ */
 //Returns the correct function for the flags that are set
 Fn getCipher(const bool cipherFlags[]){
 	if(cipherFlags[CAESAR]){
diff --git a/main.cpp b/main.cpp
index be8ad54..3f0e993 100644
--- a/main.cpp
+++ b/main.cpp
@@ -1,7 +1,7 @@
 //Ciphers/main.cpp
 //Matthew Ellison
 // Created: 4-25-18
-//Modified: 5-2-18
+//Modified: 5-8-18
 //This file contains the driver function and the test functions for the Cipher program
 //This program will use some simple ciphers that are no longer widely used but still fun to play with
 
diff --git a/testMain.hpp b/testMain.hpp
index 86a8ce0..8469ba2 100644
--- a/testMain.hpp
+++ b/testMain.hpp
@@ -1,7 +1,7 @@
 //Ciphers/testMain.hpp
 //Matthew Ellison
 // Created: 4-30-18
-//Modified: 4-30-18
+//Modified: 5-8-18
 //This file contains the driver function and the test functions for the Cipher program
 //This program will use some simple ciphers that are no longer widely used but still fun to play with
 
@@ -25,37 +25,92 @@
 #define ATBASH_TEST
 #define MORSE_TEST
 #define AUTOKEY_TEST
+/**
+ * @brief Helper for determining the state of a cipher when an error occured
+ * 
+ */
 enum codingState { ENCODE, DECODE };
+/**
+ * @brief Creates an error message
+ * 
+ * @param type Determines whether the cipher was encoding or decoding when an error occured
+ * @param input The string that was input into the cipher
+ * @param output The string that was the expected output of the cipher
+ * @param cipher The string that was the actual output of the cipher
+ * @return The appropriate error message
+ */
 std::string testingError(codingState type, const std::string& input, const std::string& output, const std::string& cipher);
 #endif //TEST_VERSION definition
 
 #ifdef CAESAR_TEST
+/**
+ * @brief Runs several tests on the Caesar cipher, checking if encoding and decoding are working propperly
+ * 
+ * @param errorString A string to store any error messages
+ * @return true If all tests completed successfully
+ * @return false If 1 or more tests failed
+ */
 bool caesarTest(std::string& errorString);
 #endif //CAESAR_TEST
 
 #ifdef PLAYFAIR_TEST
+/**
+ * @brief Runs several tests on the Playfair cipher, checking if encoding and decoding are working propperly
+ * 
+ * @param errorString A string to store any error messages
+ * @return true If all tests completed successfully
+ * @return false If 1 or more tests failed
+ */
 bool playfairTest(std::string& errorString);
 #endif //PLAYFAIR_TEST
 
 #ifdef VIGENERE_TEST
+/**
+ * @brief Runs several tests on the Vigenere cipher, checking if encoding and decoding are working propperly
+ * 
+ * @param errorString A string to store any error messages
+ * @return true If all tests completed successfully
+ * @return false If 1 or more tests failed
+ */
 bool vigenereTest(std::string& errorString);
 #endif //VIGENERE_TEST
 
 #ifdef ATBASH_TEST
+/**
+ * @brief Runs several tests on the Atbash cipher, checking if encoding and decoding are working propperly
+ * 
+ * @param errorString A string to store any error messages
+ * @return true If all tests completed successfully
+ * @return false If 1 or more tests failed
+ */
 bool atbashTest(std::string& errorString);
 #endif //ATBASH_TEST
 
 #ifdef MORSE_TEST
+/**
+ * @brief Runs several tests on Morse code, checking if encoding and decoding are working propperly
+ * 
+ * @param errorString A string to store any error messages
+ * @return true If all tests completed successfully
+ * @return false If 1 or more tests failed
+ */
 bool morseTest(std::string& errorString);
 #endif //MORSE_TEST
 
 #ifdef AUTOKEY_TEST
+/**
+ * @brief Runs several tests on the Autokey cipher, checking if encoding and decoding are working propperly
+ * 
+ * @param errorString A string to store any error messages
+ * @return true If all tests completed successfully
+ * @return false If 1 or more tests failed
+ */
 bool autokeyTest(std::string& errorString);
 #endif //AUTOKEY_TEST
 
 
 #ifdef TEST_VERSION
-
+//A different main function that facilitates all tests
 int main(int argc, char** argv){
 	bool testResult = false;
 	std::string resultString = "";