Commenting, some style fixes for output

.gitignore

@@ -1 +1,2 @@
 CryptoApplet.java
+cryptoworkbench.exe

affine.csharp

@@ -11,21 +11,33 @@ namespace AniNIX.Crypto {
         public override String Command() {return "affine";} 
         public Affine(Workbench w) : base (w) {}
 
+        /// <summary>
+        /// Encrypt a string with the Affine cipher
+        /// </summary>
+        /// <param name="workspace">A parameter for X</param>
+        /// <param name="inputText">A parameter for Y</param>
+        /// <param name="line">The line given by the user</param> 
+        /// <returns>The return value</returns>
         public override String Encrypt(String workSpace,String inputText,String[] line) {
+            // Affine requires two numbers
             if (line == null || line.Length != 4) { 
                 Console.Error.WriteLine("Malformed!");
                 return workSpace;
             }
             char[] changed = workSpace.ToCharArray();
             try { 
+                // Convert the first number to an int
                 int a = Int32.Parse(line[2]);
+                // Validate the first number is coprime to 26.
                 try { 
                     MultiplicativeInverse(a);
                 } catch (Exception e) {
                     Console.Error.WriteLine(String.Format("Value a <{0}> is not coprime to 26.\n{1}",a,e.Message));
                     return workSpace;
                 }
+                // Convert the second number to an int
                 int b = Int32.Parse(line[3]);
+                // For each letter in the workSpace, apply the forumula e(x) = (ax + b) mod m 
                 for (int i = 0; i <  changed.Length; i++) {
                     if (Char.IsLetter(changed[i])) {
                         int baseC = (Char.IsUpper(changed[i])) ? (int)'A' : (int)'a';
@@ -33,6 +45,7 @@ namespace AniNIX.Crypto {
                         changed[i] = (char)(((a*modC+b)%26)+baseC);
                     }
                 }
+            // If there's a problem solving, tell the user.
             } catch (Exception e) {
                 Console.Error.WriteLine(String.Format("Failed!\n{0}",e.Message));
                 return workSpace;
@@ -40,8 +53,14 @@ namespace AniNIX.Crypto {
             return new String(changed);
         }
 
-        public  int MultiplicativeInverse(int a) {
+        /// <summary>
+        /// Find the multiplicative inverse of a number. 
+        /// </summary>
+        /// <param name="a">A number</param>
+        /// <returns>The inverse</returns>
+        public int MultiplicativeInverse(int a) {
             for (int x=1; x < 27; x++) {
+                //Try to find a number where the input times that number mod 26 is 1. If we roll through 26 numbers and don't find it, there isn't one.
                 if ((a*x)%26 == 1) {
                     Console.WriteLine(String.Format("Found Multiplicative Inverse of {0}",x));
                     return x;
@@ -50,16 +69,27 @@ namespace AniNIX.Crypto {
             throw new Exception("A is not coprime.");
         }
 
+        /// <summary>
+        /// Decrypt a string with the cipher
+        /// </summary>
+        /// <param name="workSpace">A parameter for X</param>
+        /// <param name="inputText">A parameter for Y</param>
+        /// <param name="line">The user input</param>
+        /// <returns>The decrypted string</returns>
         public override String Decrypt(String workSpace,String inputText,String[] line) {
+            // Decryption requires two numbers.
             if (line == null || line.Length != 4) { 
                 Console.Error.WriteLine("Malformed!");
                 return workSpace;
             }
             char[] changed = workSpace.ToCharArray();
             try {
+                //Convert both numbers to ints
                 int a = Int32.Parse(line[2]); 
                 int b = Int32.Parse(line[3]);
+                //Find the multiplicative inverse of the first.
                 int multiinv = MultiplicativeInverse(a);
+                // For each character, decrypt with d(x) = a-1(x - b) mod m
                 for (int i = 0; i <  changed.Length; i++) {
                     if (Char.IsLetter(changed[i])) {
                         int baseC = (Char.IsUpper(changed[i])) ? (int)'A' : (int)'a';

analysis.csharp

@@ -8,11 +8,22 @@ using System.Collections.Generic;
 namespace AniNIX.Crypto {
     public class Analysis : Cipher {
 
+        private Substitution _sb;
         public override String Description() { return "Analysis tools"; }
         public override String Command() { return "analysis"; }
 
-        public Analysis(Workbench w) : base (w) {}
+        public Analysis(Workbench w) : base (w) {
+            //Analysis needs to be able to read the EngCommon array from the Substition class
+            this._sb = new Substitution(w);
+        }
 
+        /// <summary>
+        /// Decode the user's input and relate to an existing function.
+        /// </summary>
+        /// <param name="workSpace">The working copy of the cipher</param>
+        /// <param name="inputText">The original cipher</param>
+        /// <param name="line">The user input</param>
+        /// <returns>The modified workspace string</returns>
         public override String RunCommand(String workSpace, String inputText, String[] line) {
             if (workSpace == null || inputText == null || line == null || line.Length < 2) {
                 Console.Error.WriteLine("Malformed!");
@@ -41,28 +52,46 @@ namespace AniNIX.Crypto {
             return workSpace;
         }
 
+        /// <summary>
+        /// Show this help text
+        /// </summary>
         public override void GetHelp() {
             Console.WriteLine("Analysis tools help:\nfreq         -- Get frequency of characters.\nfreqinfo     -- Return the most common English frequencies.\none-to-one   -- See if there is a direct correspondence of characters between cipher and workspace.\ndiff a b     -- get the difference between two characters\ncharinfo     -- get the info about a character");
         }
 
-
+        /// <summary>
+        /// Return a dictionary of letters mapped to the number of letters found in the workSpace
+        /// </summary>
+        /// <param name="workSpace">the current workSpace</param>
+        /// <returns>The dictionary of frequencies</returns>
         public static Dictionary<String,int> FindFrequencies(String workSpace) { 
             Dictionary<String,int> frequencies = new Dictionary<String,int>();
+            // For each letter in the workSpace,...
             for (int i = 0; i < workSpace.Length; i++) {
                 if (!Char.IsLetter(workSpace[i])) { continue; }
                 String charStr = String.Format("{0}",workSpace[i]);
+                // If the letter already exists, increment its frequency.
                 if (frequencies.ContainsKey(charStr)) {
                     frequencies[charStr] = frequencies[charStr] + 1;
                 } else {
+                    // Otherwise add it with a frequency of one.
                     frequencies.Add(charStr,1);
                 }
             }
             return frequencies;
         }
 
+        /// <summary>
+        /// Return an ordered list of the most common letters in the workSpace
+        /// </summary>
+        /// <param name="workSpace">The user workSpace</param>
+        /// <returns>An ordered list</returns>
         public static List<String> GetMostCommonLetters(String workSpace) {
+            // Find the frequencies.
             List<KeyValuePair<String,int>> freqList = FindFrequencies(workSpace).ToList();
+            // Sort the frequencies
             freqList.Sort((firstPair,nextPair)=>nextPair.Value.CompareTo(firstPair.Value));
+            // Pull out the letters in sorted order and return.
             List<String> returnL = new List<String>();
             foreach (var item in freqList) {
                 returnL.Add(item.Key);
@@ -70,8 +99,12 @@ namespace AniNIX.Crypto {
             return returnL;
         }
 
+        /// <summary> Find the doubles in a string </summary>
+        /// <param name="workSpace"> the string to analyze </param>
+        /// <returns> a list of doubles</returns>
         public static List<String> GetDoubles(String workSpace) {
             List<String> theList = new List<String>();
+            // For each character in the input, if the previous character is the same, it's a double. Add it to the list.
             for (int i=1; i<workSpace.Length; i++) {
                 if (workSpace[i] == workSpace[i-1] && !theList.Contains(workSpace[i].ToString())) {
                     theList.Add(workSpace[i].ToString());
@@ -80,12 +113,23 @@ namespace AniNIX.Crypto {
             return theList;
         }
 
+        /// <summary>
+        /// Find the substrings of a given length in the workSpace.
+        /// </summary>
+        /// <param name="workSpace">the workSpace to analyze</param>
+        /// <param name="length"> the length of the substrings to look for</param>
+        /// <returns>the dictionary of substrings by frequency</returns>
         public static Dictionary<String,int> GetSubstrings(String workSpace, int length) {
             Dictionary<string,int> theList = new Dictionary<string,int>();
+            // Start at the beginning of the string, and advance the substring window by one until the substring segment would be outside the workSpace.
             for (int i=1; i<workSpace.Length-(length-1); i++) {
+                // Get the substring
                 String segment = workSpace.Substring(i,length);
+                // Remove whitespace
                 segment = Regex.Replace(segment, @"[^\w]", string.Empty);
+                // If the segment is no longer the length, bypass.
                 if (segment.Length != length) continue;
+                // Otherwise add or increment the segment's frequency.
                 if (theList.ContainsKey(segment)) {
                     theList[segment] += 1;
                 } else {
@@ -95,8 +139,16 @@ namespace AniNIX.Crypto {
             return theList;
         }
 
+        /// <summary>
+        /// find words of a given length. 
+        /// </summary> 
+        /// <param name="length"> The length to look for </length>
+        /// <param name="bySpace"> A string broken down by spaces</param>
+        /// <returns> the words of the length with frequencies </returns>
         public static Dictionary<String,int> FindWordsOfLength(int length,String[] bySpace) {
             Dictionary<String,int> wordsFreq = new Dictionary<String,int>();
+            // TODO Replace this with whitespace and punctuation removal
+            // If the word ends in punctuation and is longer than the length or is equal to the length, add it to the list and track frequency.
             for (int i = 0; i < bySpace.Length; i++) {
                 if (bySpace[i].Length == length || (bySpace[i].Length == length+1 && Char.IsPunctuation(bySpace[i][length]))) {
                     if (Char.IsPunctuation(bySpace[i][bySpace[i].Length-1])) {
@@ -112,6 +164,11 @@ namespace AniNIX.Crypto {
             return wordsFreq;
         }
 
+        /// <summary>
+        /// Get the top entries in a frequency map
+        /// </summary>
+        /// <param name="theList">Frequency map</param>
+        /// <returns>A list of a given length with the top entries</returns>
         public static List<String> Top(Dictionary<String,int> theList) {
             List<KeyValuePair<string,int>> freqList = theList.ToList();
             List<String> returnL = new List<String>();
@@ -122,7 +179,11 @@ namespace AniNIX.Crypto {
             return returnL;
         }
 
-
+        /// <summary> 
+        /// Print an ordered list with the frequency
+        /// </summary>
+        /// <param name="theList"> the frequency map </param>
+        /// <param name="header"> String header </param>
         public static void PrintOrdered(Dictionary<String,int> theList,String header) {
             List<KeyValuePair<string,int>> freqList = theList.ToList();
             freqList.Sort((firstPair,nextPair)=>nextPair.Value.CompareTo(firstPair.Value));
@@ -133,6 +194,11 @@ namespace AniNIX.Crypto {
             Console.WriteLine("");
         }
 
+        /// <summary>
+        /// Print an ordered list
+        /// </summary>
+        /// <param name="theList"> the frequency map </param>
+        /// <param name="header"> String header </param>
         public static void PrintOrdered(List<String> theList,String header) {
             Console.Write(header);
             foreach (String str in theList) {
@@ -142,6 +208,10 @@ namespace AniNIX.Crypto {
             Console.WriteLine();
         }
 
+        ///<summary>
+        /// Analyze a workspace
+        /// <summary>
+        /// <param name="workSpace">workSpace to analyze</param>
         public void Frequency(String workSpace) {
             //Show the individual letter frequeuncy.
             Console.ForegroundColor = ConsoleColor.Cyan;
@@ -164,14 +234,21 @@ namespace AniNIX.Crypto {
             Console.ResetColor();
         }
 
+        /// <summary>
+        /// Show the statistical frequencies.
+        /// </summary>
         public void FrequencyInfo() {
             // Thanks to http://norvig.com/mayzner.html for this info.
             // By letter
             Console.ForegroundColor = ConsoleColor.Cyan;
             Console.WriteLine("Letters by frequency:");
-            Console.WriteLine("E T A O I N S R H L D C U M F P G W Y B V K X J Q Z");
+            for (int i=0; i < this._sb.EngCommon.Length; i++) {
+                Console.Write(this._sb.EngCommon[i]);
+                Console.Write(" ");
+            }
+            Console.Write('\n');
             Console.ForegroundColor = ConsoleColor.Green;
-            Console.WriteLine("Possible doubles: LL EE SS OO TT FF RR NN PP CC BB MM GG UU ZZ AA");
+            Console.WriteLine("Possible doubles: ll ee ss oo tt ff rr nn pp cc bb mm gg uu zz aa");
             // By Substring 2,3 characters in length
             Console.ForegroundColor = ConsoleColor.Red;
             Console.WriteLine("Top sequences of N characters where N=...");
@@ -191,8 +268,14 @@ namespace AniNIX.Crypto {
             Console.ResetColor();
         }
 
-        public static void OneToOneQuery(String workSpace, String inputText) {
+        /// <summary>
+        /// Find out if the workSpace has a one-to-one relationship with the input.
+        /// </summary> 
+        /// <param name="workSpace">the workSpace</param>
+        /// <param name="inputText">the user input</param>
+        public bool OneToOneQuery(String workSpace, String inputText) {
             Dictionary<char,char> relation = new Dictionary<char,char>();
+            //Seed the keys so that we print efficiently.
             StringBuilder subKey = new StringBuilder(); 
             StringBuilder encKey = new StringBuilder();
             subKey.Append("True. These are one-to-one.\n");
@@ -200,12 +283,15 @@ namespace AniNIX.Crypto {
             subKey.Append("sub decrypt ");
             encKey.Append("sub encrypt ");
             for (int i = 0; i < workSpace.Length; i++) {
+                // For each non-whitespace character, if the relation is  known, ... 
                 if (!Char.IsWhiteSpace(workSpace[i])) { 
                     if (relation.ContainsKey(workSpace[i])) {
+                        // if the relation doesn't match up, we found the mismatch and should return false.
                         if (relation[workSpace[i]] != inputText[i]) {
                             Console.Error.WriteLine(String.Format("Character {0} repeated. These are not one-to-one.",workSpace[i]));
-                            return;
+                            return false;
                         }
+                        // Otherwise add the new relation pairing.
                     } else {
                         relation.Add(workSpace[i],inputText[i]);
                         encKey.Append(String.Format("{0}={1} ",inputText[i],workSpace[i]));
@@ -213,28 +299,44 @@ namespace AniNIX.Crypto {
                     }
                 }
             }
+            // Print the keys and return true.
             subKey.Append("\nInput-to-final key:");
             Console.WriteLine(subKey.ToString());
             Console.WriteLine(encKey.ToString());
+            return true;
         }
 
-        public void Diff(String[] line) {
+        /// <summary>
+        /// Show the numeric difference between two characters -- useful for identifying Caesarian ciphers
+        /// </summary> 
+        /// <param name="line">The user's input</param>
+        /// <returns>-99 if malformated or the difference between characters.</returns>
+        public int Diff(String[] line) {
+            // If the number of arguments or format is wrong, return -99
             if (line.Length != 4 || line[2].Length != 1 || line[3].Length != 1) {
                 Console.Error.WriteLine("Bad formatting");
-                return;
+                return -99;
             }
+            //Otherwise return -99
             char first = line[2][0];
             char second = line[3][0];
             Console.WriteLine(String.Format("These are different by {0}.",first-second));
+            return (first-second);
         }
 
+        /// <summary>
+        /// Printout the info of a character
+        /// </summary>
+        /// <param name="line">line to analyze</param>
         public void CharInfo(String[] line) {
             if (line == null || line.Length != 3 || line[2].Length != 1) { 
                 Console.Error.WriteLine("Malformed");
                 return;
             }
+            // Print the ascii value of a character.
             Console.WriteLine(String.Format("Character: {0}\nASCII Value: {1}",line[2][0],(int)line[2][0]));
             if (Char.IsLetter(line[2][0])) {
+                // If the character is a letter, include the alphabet index
                 Console.WriteLine(String.Format("Alphabet index: {0}",(Char.IsUpper(line[2][0])) ? (int)line[2][0] - (int)'A' : (int)line[2][0] - (int)'a'));
             }
         }

caesarian.csharp

@@ -7,12 +7,18 @@ using System.Collections.Generic;
 namespace AniNIX.Crypto {
     public class Caesarian : Cipher {
 
-       public override String Description() { return "Caesarian cipher suite\nKey format is a numeric shift."; }
+        public override String Description() { return "Caesarian cipher suite\nKey format is a numeric shift."; }
-       public override String Command() { return "caesar"; }
+        public override String Command() { return "caesar"; }
+        public Caesarian(Workbench w) : base (w) {}
 
-       public Caesarian(Workbench w) : base (w) {}
+        /// <summary>
-
+        /// Decode the user's input and relate to an existing function.
-       public override String RunCommand(String workSpace,String inputText,String[] line) {
+        /// </summary>
+        /// <param name="workSpace">The working copy of the cipher</param>
+        /// <param name="inputText">The original cipher</param>
+        /// <param name="line">The user input</param>
+        /// <returns>The modified workspace string</returns>
+        public override String RunCommand(String workSpace,String inputText,String[] line) {
             if (workSpace == null || line == null || line.Length < 2) {
                 Console.Error.WriteLine("Malformed request.");
                 return workSpace;
@@ -31,12 +37,24 @@ namespace AniNIX.Crypto {
             } 
         }
 
-         public override void GetHelp() {
+        /// <summary>
+        /// Show this help text
+        /// </summary>
+        public override void GetHelp() {
             Console.WriteLine(String.Format("Help for the {0} cipher suite.\n{1}\n",Command(),Description()));
             Console.WriteLine("encrypt key         -- encrypt with the key\ndecrypt key         -- decrypt with the key\nbrute               -- brute-force for keys\nhelp                -- show this helptext.");
         }
 
-         public override String Encrypt(String workSpace,String inputText,String[] line) {
+
+        /// <summary>
+        /// Encrypt a string with the cipher
+        /// </summary>
+        /// <param name="workSpace">The working copy of the cipher</param>
+        /// <param name="inputText">The original cipher</param>
+        /// <param name="line">The user input</param>
+        /// <returns>The encrypted string</returns>
+        public override String Encrypt(String workSpace,String inputText,String[] line) {
+            // Validate input
             if (line.Length != 3) {
                 Console.Error.WriteLine("Bad formatting");
                 return workSpace;
@@ -50,31 +68,35 @@ namespace AniNIX.Crypto {
                 return workSpace;
             }
             char[] modified = workSpace.ToCharArray(); 
+
+            //For each character in the workSpace, rotate it by the offset given.
             for (int i = 0; i < modified.Length; i++) { 
                 if (Char.IsLetter(modified[i])) {
-                   int baseC;
+                    int baseC;
-                   int modC;
+                    int modC;
-                   if (modified[i] < 'a') {
+                    // Have to account for case.
-                       baseC = (int)'A';
+                    if (modified[i] < 'a') {
-                       modC = (int)modified[i] - (int)'A';
+                        baseC = (int)'A';
-                   } else {
+                        modC = (int)modified[i] - (int)'A';
-                       baseC = (int)'a';
+                    } else {
-                       modC = (int)modified[i] - (int)'a';
+                        baseC = (int)'a';
-                   }
+                        modC = (int)modified[i] - (int)'a';
-                   modC = (modC + rotation)%26;
+                    }
-                   //Debugging
+                    modC = (modC + rotation)%26;
-                   //Console.Write(String.Format("Updating index {0} <{5}> val {1} base {2} mod {3} rotation {4} --to-- ",i,(int)modified[i],baseC,modC,rotation,modified[i]));
+                    modified[i] = (char)(baseC+modC);
-                   modified[i] = (char)(baseC+modC);
-                   //Console.WriteLine(String.Format("<{0}> val {1}",modified[i],baseC+modC));
                 }
             }
             return new String(modified);
         }
         
-       public override String Decrypt(String workSpace,String inputText,String[] line) {
+        // This is a dummy override.
-           return Encrypt(workSpace,inputText,line);
+        public override String Decrypt(String workSpace,String inputText,String[] line) {
-       }
+            return Encrypt(workSpace,inputText,line);
+        }
 
+        /// <summary>
+        /// Try rotating through all 26 possible combinations.
+        /// </summary>
         public  void BruteForce(String workSpace) {
             String[] line = new String[3];
             line[0] = "rot";

chargrid.csharp

@@ -24,6 +24,12 @@ namespace AniNIX.Crypto {
             return input+(new String(pad));
         }
 
+        /// <summary>
+        /// Create a grid from the input and  row length
+        /// </summary>
+        /// <param name="input">The string to make the grid from</param>
+        /// <param name="width">The width of a row</param>
+        /// <returns>a grid</returns>
         private char[][] MakeGrid(String input, int width) {
             int k=0;
             int y=(input.Length%width == 0) ? input.Length/width : input.Length/width+1;
@@ -39,6 +45,12 @@ namespace AniNIX.Crypto {
             return newGrid;
         }
 
+        /// <summary>
+        /// Create a grid from a width and length 
+        /// </summary>
+        /// <param name="length">The  length of a column </param>
+        /// <param name="width">The width of a row</param>
+        /// <returns>a grid</returns>
         private char[][] MakeVGrid(int length, int width) {
             int y = (length%width == 0) ? length/width : length/width+1;
             char[][] newGrid = new char[y][];
@@ -82,12 +94,19 @@ namespace AniNIX.Crypto {
 
         }
 
+        /// <summary>
+        /// Create a string representation
+        /// </summary>
+        /// <returns>representation</returns>
         public override String ToString() {
             StringBuilder sb = new StringBuilder();
+            // Include a line to indicate height vs. width
             sb.Append(String.Format("{0} {1} ------------->\n",theGrid.Length,theGrid[0].Length));
+            // Iterate through the arrays
             for (int j=0; j<theGrid.Length; j++) {
                 sb.Append("| ");
                 for (int i=0; i<theGrid[j].Length; i++) {
+                    // Print the letters as either letters or ASCII codes.
                     if (Char.IsLetter(theGrid[j][i])) {
                         sb.Append(String.Format("{0}     ",theGrid[j][i]));
                     } else {
@@ -100,6 +119,10 @@ namespace AniNIX.Crypto {
             return sb.ToString();
         }
 
+        /// <summary>
+        /// Return the array for manipulation
+        /// </summary>
+        /// <returns>the array</returns>
         public char[][] ToArray() {
             return theGrid;
         }

columntransposition.csharp

@@ -8,11 +8,15 @@ namespace AniNIX.Crypto {
 
         public override String Description() { return "Column Transposition cipher suite\nFormat is col <command> key1 [key2...]\nThe key format is any word to use for the transposition.\nThis cipher will use an irregular columnar transposition, without padding the input string.\n"; } 
          public override String Command() { return "col"; }
-
          public ColumnTransposition(Workbench w) : base (w) {}
          public ColumnTransposition() {}
 
+         /// <summary> 
+         /// Get the order of columns from a key
+         /// </summary>
+         /// <returns>an array of ints indicating order</returns>
         private int[] GetColumnOrder(String key) {
+            // Create an ordered list and sort from the key.
             List<char> orderList = new List<char>();
             for (int i = 0; i < key.Length; i++) {
                 orderList.Add(key[i]);
@@ -21,6 +25,7 @@ namespace AniNIX.Crypto {
             char[] charArr = orderList.ToArray();
             int[] returnOrderIndexes = new int[key.Length];
             Console.Write("Found key order: ");
+            // for each character in the key, find the index in tke sorted array
             for (int i = 0; i < key.Length; i++) {
                 for (int j = 0; j < charArr.Length; j++) {
                     if (key[i] == charArr[j]) {
@@ -34,18 +39,29 @@ namespace AniNIX.Crypto {
             return returnOrderIndexes;
         }
 
+        /// <summary>
+        /// Encrypt a string with the cipher. See https://en.wikipedia.org/wiki/Transposition_cipher#Columnar_transposition for an example of how this works.
+        /// </summary>
+        /// <param name="workSpace">The working copy of the cipher</param>
+        /// <param name="inputText">The original cipher</param>
+        /// <param name="line">The user input</param>
+        /// <returns>The encrypted string</returns>
         public override String Encrypt(String workSpace, String cipher, String[] line) {
             if (line.Length < 3) {
                 Console.Error.WriteLine("Bad formatting.");
                 return workSpace;
             }
+            //Remove newlines.
             String workSpaceNoNewline = workSpace.Replace("\n","");
             char[] changed = workSpaceNoNewline.ToCharArray();
+            // Create a grid from the key.
             CharGrid cg = new CharGrid(workSpaceNoNewline,line[2].Length,false);
             char[][] encryptionGrid = cg.ToArray();
+            //Get the key order. 
             int[] keyOrder = GetColumnOrder(line[2]);
             Console.Write(cg.ToString());
             int k = 0;
+            // Replace each character by the character in the right place in the character grid.
             for (int j = 0; j < encryptionGrid[0].Length; j++) {
                 for (int i = 0; i < encryptionGrid.Length; i++) {
                     if (i != (encryptionGrid.Length-1) || keyOrder[j] < encryptionGrid[i].Length) {
@@ -55,6 +71,7 @@ namespace AniNIX.Crypto {
                 }
             }
             String toReturn = new String(changed);
+            //Re-insert newlines.
             for (k = 0; k < workSpace.Length; k++) {
                 if (workSpace[k] == '\n') {
                     toReturn = toReturn.Insert(k,"\n");
@@ -63,22 +80,33 @@ namespace AniNIX.Crypto {
             return toReturn;
         }
 
-        // TODO 
+       /// <summary>
+       /// Decrypt a string with the cipher
+       /// </summary>
+       /// <param name="workSpace">The working copy of the cipher</param>
+       /// <param name="inputText">The original cipher</param>
+       /// <param name="line">The user input</param>
+       /// <returns>The decrypted string</returns> 
         public  override String Decrypt(String workSpace, String cipher, String[] line) {
             if (line.Length < 3) {
                 Console.Error.WriteLine("Bad formatting.");
                 return workSpace;
             }
+            // Remove newlines.
             String workSpaceNoNewline = workSpace.Replace("\n","");
+            // Find the key order.
             int[] keyOrder = GetColumnOrder(line[2]);
+            // Create a new chargrid to solve from.
             CharGrid cg = new CharGrid(workSpaceNoNewline,line[2].Length,keyOrder);
             Console.Write(cg.ToString());
             char[][] cgArray = cg.ToArray();
             StringBuilder sb = new StringBuilder();
+            // For each row, read the row and add to the solution.
             for (int i=0; i < cgArray.Length; i++) {
                 sb.Append(new String(cgArray[i]));
             }
             String toReturn = sb.ToString();
+            // Add back in the newlines.
             for (int i=0; i < workSpace.Length; i++) {
                 if (workSpace[i] == '\n') {
                     toReturn = toReturn.Insert(i,"\n");

cryptoworkbench.csharp

@@ -11,6 +11,7 @@ namespace AniNIX.Crypto {
         public string workSpace { get; private set; }
         public StringBuilder HelpText = new StringBuilder();
         public Dictionary<String,Cipher> SwitchCases = new Dictionary<String,Cipher>();
+        // The workbench needs to maintain an instance of each ciphersuite for operation. 
         private Substitution _sub;
         private Analysis _analysis;
         private Simple _simple;
@@ -19,19 +20,28 @@ namespace AniNIX.Crypto {
         private Vigenere _vig;
         private ColumnTransposition _col;
         private Ubchi _ubchi;
+        // If this is true, we will prevent prompt and filesystem access.
         private bool _isBlind = false;
 
+        /// <summary> 
+        /// Read in a cipher either from a filename or from stdin
+        /// <summary>
+        /// <param name="line">user input</param>
         private void ReadCipher(String[] line) {
+            // If a filename's not provided.
             if (line == null || line.Length !=2) {
                 Console.WriteLine("Please paste your ciphertext.");
                 string readLn = Console.ReadLine();
                 StringBuilder sb = new StringBuilder();
+                //Read lines from stdin until a blank line is given.
                 while (readLn != null && !String.IsNullOrWhiteSpace((readLn))) {
                     sb.AppendLine(readLn);
                     readLn=Console.ReadLine();
                 }
+                // The user's input is the trimmed sum of the lines.
                 inputText = sb.ToString().Trim();
             } else { 
+                // Try to read the file into the input.
                 try { 
                     StringBuilder sb = new StringBuilder();
                     StreamReader fileReader = new StreamReader(line[1]);
@@ -45,6 +55,7 @@ namespace AniNIX.Crypto {
                     inputText = sb.ToString().Trim();
                     Console.WriteLine(String.Format("Read {0}",line[1]));
                 }
+                // If there's a problem, input is null.
                 catch (Exception e) {
                     Console.Error.WriteLine(e.Message);
                     inputText = null;
@@ -55,24 +66,34 @@ namespace AniNIX.Crypto {
 
         }        
 
+        /// <summary>
+        /// Create a new workbench from input.
+        /// </summary> 
+        /// <param name="args">the arguments provided for execution</param>
         public Workbench(string[] args) {
+            // If args are null, read from STDIN.
             if (args.Length == 0) {
                 ReadCipher(null);
+                // If there's only one arg and that's --blind, set the blind option and read from stdin.
             } else if (args.Length == 1) {
                 if (args[0].Equals("--blind")) {
                     this._isBlind = true;
                     ReadCipher(null);
+                    // Otherwise, try to use the first argument as a filename.
                 } else {
                     String[] line = new String[2];
                     line[0] = "reread";
                     line[1] = args[0];
                     ReadCipher(line);            
                 }
+                // Otherwise, give some help and exit.
             } else {
                 Console.Error.WriteLine("The only argument allowed is a filename containing the ciphertext or --blind to block filesystem access.");
                 System.Environment.Exit(1);
             }
+            // Seed the helptext.
             HelpText.Append("You can get help on any command by running \"<command> help\".\nSuppress printing the cipher with a trailing ;.\nAvailable commands:\n");
+            // Don't tell users about things they can't use.
             if (!_isBlind) {
                 HelpText.Append("reread           -- Read in a new cipher\n");
                 HelpText.Append("write            -- write the workspace to a file\n");
@@ -81,8 +102,11 @@ namespace AniNIX.Crypto {
             HelpText.Append("reset            -- reset workspace to the ciphertext.\n");
             HelpText.Append("links            -- show some helpful links\n");
             HelpText.Append("help             -- show this HelpText\n");
+            HelpText.Append("print            -- show the current workspace\n");
+            HelpText.Append("display          -- alias of print\n");
             HelpText.Append("exit             -- exit and show the result.\n");
             HelpText.Append("quit             -- alias of exit.\n");
+            // Initialize the ciphersuites.
             _sub = new Substitution(this);
             _analysis = new Analysis(this);
             _simple = new Simple(this);
@@ -94,6 +118,9 @@ namespace AniNIX.Crypto {
 
         }
 
+        /// <summary> 
+        /// Convert this workbench into a readable string.
+        /// </summary>
         public override String ToString() {
             StringBuilder currentStatus = new StringBuilder();
             currentStatus.Append("Input:\n");
@@ -104,6 +131,9 @@ namespace AniNIX.Crypto {
             return currentStatus.ToString();
         }
 
+        /// <summary>
+        /// Display this workbench to stdout with colors.
+        /// </summary>
         public void Print() {
             Console.ForegroundColor = ConsoleColor.Red;
             Console.WriteLine("Input:");
@@ -136,6 +166,9 @@ namespace AniNIX.Crypto {
             Console.WriteLine(); 
         }
         
+        /// <summary>
+        /// Show some helpful links.
+        /// </summary>
         public static void HelpfulLinks() {
             StringBuilder linksText = new StringBuilder();
             linksText.Append("http://www.visca.com/regexdict/ -- RegEx word dictionary\n");
@@ -144,42 +177,61 @@ namespace AniNIX.Crypto {
             Console.Write(linksText.ToString());
         }
 
+        /// <summary>
+        /// Save the workspace to a file
+        /// </summary>
+        /// <param name="workSpace"> what to write </param>
+        /// <param name="line"> user input, which should include a file</param>
         public void WriteWorkspace(String workSpace, String[] line) {
+            // Require a filename.
             if (line == null || line.Length != 2) {
                 Console.Error.WriteLine("Need a file.");
                 return;
             }
             try {
+                // If we are actually given a file, write the workspace to a file and close.
                 StreamWriter fileWriter = new StreamWriter(line[1],false);
                 fileWriter.WriteLine(workSpace);
                 fileWriter.Dispose();
                 fileWriter = null;
                 Console.WriteLine(String.Format("Wrote file {0}",line[1]));
             } catch (Exception e) {
+                // Let the user know the file's not writeable.
                 Console.WriteLine(String.Format("Couldn't write file.\n{0}",e.Message));
             }
         }
 
+        /// <summary>
+        /// Interact with the user.
+        /// </summary>
         public void Run() {
+            // Display the header.
             Console.ForegroundColor = ConsoleColor.Red;            
             Console.WriteLine("### Welcome to the AniNIX::CryptoWorkbench ###");
             Console.ResetColor();
             try { 
+                // Set the initial command to be show the helptext.
                 string command = "help";
                 string read = "help";
                 string[] line;
                 bool showCipher=true;
 
+                // Until the user exits...
                 while (command != "exit" && command != "quit") {
+                    // parse shell-type command unification with semicolons
                     foreach (String executable in read.Split(';')) {
+
+                        // If the command is only whitespace, continue and don't show the cipher.
                         if (String.IsNullOrWhiteSpace(executable)) {
-                            showCipher = false;
+                            showCipher = false; // if the last nonwhitespace character is a semicolon, we won't bother printing.
                             continue;
                         }
 
+                        // Otherwise we will show the cipehr.
                         showCipher = true;
                         line = executable.Trim().Split(' '); 
                         command = line[0];
+                        // Command is first space-delimited entry.
                         switch (command) {
                             case "reread":
                                 if (!_isBlind) ReadCipher(line);
@@ -211,6 +263,10 @@ namespace AniNIX.Crypto {
                             case "help":
                                 Console.WriteLine(HelpText.ToString());
                                 break;
+                            case "display":
+                            case "print":
+                                showCipher = true;
+                                break;
                             case "exit": 
                             case "quit":
                                 throw new Exception("");
@@ -223,7 +279,10 @@ namespace AniNIX.Crypto {
                                 break;
                         }
                     }
+
+                    // Show the cipher if the user asked.
                     if (showCipher) Print();
+                    // Display an AniNIX-standard prompt.
                     Console.Write("\nWhat command would you like to execute?\n");
                     Console.ForegroundColor = ConsoleColor.Red;
                     Console.Write("|");
@@ -231,16 +290,22 @@ namespace AniNIX.Crypto {
                     Console.Write("> ");
                     read = Console.ReadLine().Trim();
                 }
+                // If we run into trouble, tell the user.
             } catch (Exception e) {
                 Console.Error.WriteLine(e.Message);
             }
 
+            // When we exit, show the result to the user.
             finally { 
                 Console.WriteLine("\nFinal result:");
                 this.Print();
             }
         }
 
+
+        /// <summary> 
+        /// Create  and execute a workbench program.
+        /// </summary>
         public static void Main(string[] args) {
             Workbench cw = new Workbench(args);
             try {

substitution.csharp

@@ -49,6 +49,13 @@ namespace AniNIX.Crypto {
             Console.WriteLine("encrypt key[s]         -- encrypt with the key[s]\ndecrypt key[s]         -- decrypt with the key[s]\ntry-common          -- try common sub keys\nhelp                -- show this helptext.");
         }
 
+        /// <summary>
+        /// Encrypt a string with the cipher, replacing one character with another. 
+        /// </summary>
+        /// <param name="workSpace">The working copy of the cipher</param>
+        /// <param name="inputText">The original cipher</param>
+        /// <param name="line">The user input</param>
+        /// <returns>The encrypted string</returns>
         public override String Encrypt(String workSpace, String cipher, String[] line) {
             if (line.Length < 3) {
                 Console.Error.WriteLine("Bad formatting.");
@@ -58,17 +65,17 @@ namespace AniNIX.Crypto {
             for (int i=2; i<line.Length;i++) {
                 if (line[i].Length < 3 || line[i].Length%2 != 1 || line[i][line[i].Length/2] != '=') {
                     Console.Error.WriteLine("Bad substitution. Aborting.");
-                    /* Console.Error.WriteLine(String.Format("Line length: {0}",line[i].Length));
-                     * Console.Error.WriteLine(String.Format("Line mod 2:  {0}",line[i].Length%2));
-                     * Console.Error.WriteLine(String.Format("Line[length/2+1]: {0}",line[i][line[i].Length/2+1]));
-                     */
                     return workSpace;
                 }
+                // For each key-value pair...
                 for (int k = 0; k < line[i].Length/2; k++) {
                     char oldS = line[i].Substring(k,1)[0];
                     char newS = line[i].Substring(k+line[i].Length/2+1,1)[0];
                     Console.WriteLine(String.Format("Replacing cipher {0} to be workspace {1}",oldS,newS));
+                    // for each character in the workspace...
                     for (int j = 0; j < workSpace.Length; j++) {
+
+                        // replace the old character with the requested replacement.
                         if (cipher[j] == oldS) {
                             changed[j] = newS;
                         }
@@ -78,14 +85,24 @@ namespace AniNIX.Crypto {
             return new String(changed);
         }
 
+        
+        // This is a dummy for encrypt -- the functions are the same.
         public  override String Decrypt(String workSpace, String cipher, String[] line) {
             return Encrypt(workSpace, cipher, line);
         }
 
+        /// <summary> 
+        /// Perform a frequency analysis and see if ETAOIN substitution will solve the problem. TODO this should look at a dictionary for confirmation.
+        /// </summary>
+        /// <param name="workSpace"> the string to analyze and brute-force</param>
+        /// <returns> an attempted solution. </returns>
         public  String TryCommon(String workSpace) {
+            // Get the frequency analysis
             List<String> sortedChars = Analysis.GetMostCommonLetters(workSpace.ToLower());
+            // Strip to lower for now and replace. TODO ensure all manipulation is done in lower case and restored later.
             char[] modified = workSpace.ToLower().ToCharArray();
             char replaceChar;
+            // For each character in the string, replace with its frequency map equivalent.
             for (int i = 0; i < modified.Length; i++) { 
                 if (!Char.IsLetter(modified[i])) { continue; }
                 Console.WriteLine(String.Format("Character <{0}> occurs {1}st in frequency, corresponding with <{2}> -- replacing...",

ubchi.csharp

@@ -14,25 +14,42 @@ namespace AniNIX.Crypto {
 
         private ColumnTransposition col = new ColumnTransposition();
 
+        /// <summary>
+        /// Encrypt a string with the cipher
+        /// </summary>
+        /// <param name="workSpace">The working copy of the cipher</param>
+        /// <param name="inputText">The original cipher</param>
+        /// <param name="line">The user input</param>
+        /// <returns>The encrypted string</returns>
         public override String Encrypt(String workSpace,String inputText,String[] line) {
             if (line == null || line.Length != 3) { 
                 Console.Error.WriteLine("Malformed!");
                 return workSpace;
             }
+            // Pad the incoming workspace
             String changed = CharGrid.RandPad(workSpace,line[2].Length);
+            // Transpose twice.
             changed = col.Encrypt(changed,inputText,line);
             changed = col.Encrypt(changed,inputText,line);           
             return changed;
         }
 
+        /// <summary>
+        /// Decrypt a string with the cipher
+        /// </summary>
+        /// <param name="workSpace">The working copy of the cipher</param>
+        /// <param name="inputText">The original cipher</param>
+        /// <param name="line">The user input</param>
+        /// <returns>The encrypted string</returns>
         public override String Decrypt(String workSpace,String inputText,String[] line) {
             if (line == null || line.Length != 3) { 
                 Console.Error.WriteLine("Malformed!");
                 return workSpace;
             }
+            // De-transpose twice. Without encrypting a number, we don't have a way to programmatically trim.
             String changed = col.Decrypt(workSpace,inputText,line);
             changed = col.Decrypt(changed,inputText,line);
-            return changed; // TODO Remove padding
+            return changed;
         }
 
     }

vigenere.csharp

@@ -12,6 +12,13 @@ namespace AniNIX.Crypto {
 
         public Vigenere(Workbench w) : base (w) {}
 
+        /// <summary>
+        /// Encrypt a string with the cipher. Encryption and decryption work like a substitution but is rotated with a key.
+        /// </summary>
+        /// <param name="workSpace">The working copy of the cipher</param>
+        /// <param name="inputText">The original cipher</param>
+        /// <param name="line">The user input</param>
+        /// <returns>The encrypted string</returns>
         public override String Encrypt(String workSpace,String inputText,String[] line) {
             if (line == null || line.Length != 3) { 
                 Console.Error.WriteLine("Malformed!");
@@ -27,6 +34,7 @@ namespace AniNIX.Crypto {
                         return workSpace;
                     }
                 }
+                // For each letter in the workspace, substitute with an offset given by the key. Rotate which letter in the key is used.
                 for (int i = 0; i <  changed.Length; i++) {
                     if (Char.IsLetter(changed[i])) {
                         int baseC = (Char.IsUpper(changed[i])) ? (int)'A' : (int)'a';
@@ -44,6 +52,13 @@ namespace AniNIX.Crypto {
             return new String(changed);
         }
 
+        /// <summary>
+        /// Decrypt a string with the cipher. Like the encryption method, we decrypt by removing the offset as given by the key.
+        /// </summary>
+        /// <param name="workSpace">The working copy of the cipher</param>
+        /// <param name="inputText">The original cipher</param>
+        /// <param name="line">The user input</param>
+        /// <returns>The decrypted string</returns>
         public override String Decrypt(String workSpace,String inputText,String[] line) {
             if (line == null || line.Length != 3) { 
                 Console.Error.WriteLine("Malformed!");