Refactor data pipeline, add Caesar algorithm as IV

* Refactor data analysis pipeline to use DataFileReader as helper class
* Add CaesarDecryptionMethod enum and parameter for data analysis and Vigenere class (with Kerckhoff/Chi square as default/fallback)
* Remove cipher interface to simplify package
* Output folders now use the format "KEYLENGTHMETHOD_CAESARMETHOD"

src/main/java/dataanalysis/DataCollector.java

@@ -4,6 +4,7 @@
 import java.io.FileWriter;
 import java.io.IOException;
 
+import frequencyanalysissimulator.crypto.CaesarDecryptionMethod;
 import frequencyanalysissimulator.crypto.KeyLengthMethod;
 import frequencyanalysissimulator.crypto.Vigenere;
 
@@ -15,10 +16,11 @@ public class DataCollector {
      *            arg[0]: Input must be one line
      *            arg[1]: Trial Id for output file
      *            arg[2]: (Optional) key length calculation algorithm
-     *            arg[3]: (Optional): key
+     *            arg[3]: (Optional) Caesar decryption algorithm
+     *            arg[4]: (Optional): key
      */
     public static void main(String[] args) {
-        final String key = args.length > 3 ? args[3] : "DONQUIXOTECOYOTEWILL";
+        final String key = args.length > 4 ? args[4] : "DONQUIXOTECOYOTEWILL";
         String expectedText = args[0].toUpperCase();
         String output = String.format("Len,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,Avg(%s)\n", args[1]);
 
@@ -31,7 +33,7 @@ public static void main(String[] args) {
                 String ciphertext = Vigenere.encrypt(input, subKey);
                 Vigenere v = args[2] != null ? new Vigenere(ciphertext, KeyLengthMethod.valueOf(args[2].toUpperCase()))
                         : new Vigenere(ciphertext);
-                String decryptedText = v.decrypt();
+                String decryptedText = v.decrypt(CaesarDecryptionMethod.valueOf(args[3]));
                 double accuracy = percentageSimilarity(decryptedText, input);
 
                 output += Math.round(accuracy) + ",";
@@ -42,7 +44,8 @@ public static void main(String[] args) {
         }
 
         try (FileWriter writer = new FileWriter(
-                new File(String.format("data/outputs/%s/Trial %s.csv", args[2], args[1])))) {
+                new File(String.format("data/outputs/%s_%s/Trial %s.csv", args[2].toLowerCase(), args[3].toLowerCase(),
+                        args[1])))) {
             writer.append(output);
         } catch (IOException e) {
             e.printStackTrace();

src/main/java/dataanalysis/DataFileReader.java

@@ -5,19 +5,8 @@
 import java.nio.file.Path;
 
 public class DataFileReader {
-    /**
-     * Reads from data/inputs/arg[0].txt
-     * 
-     * @param args
-     *            arg[0] = trial id
-     */
-    public static void main(String... args) {
-        try {
-            String expectedText = Files.readString(Path.of(String.format("data/inputs/%s.txt", args[0])));
-            expectedText = expectedText.replace(System.getProperty("line.separator"), " ");
-            DataCollector.main(new String[] { expectedText, args[0], args[1] });
-        } catch (IOException e) {
-            e.printStackTrace();
-        }
+    static String readInput(String id) throws IOException {
+        String expectedText = Files.readString(Path.of(String.format("data/inputs/%s.txt", id)));
+        return expectedText.replace(System.getProperty("line.separator"), " ");
     }
 }

src/main/java/dataanalysis/DataPopulater.java

@@ -1,25 +1,32 @@
 package dataanalysis;
 
 import java.io.File;
+import java.io.IOException;
 
+import frequencyanalysissimulator.crypto.CaesarDecryptionMethod;
 import frequencyanalysissimulator.crypto.KeyLengthMethod;
 
 /**
  * Runs DataAnalysis without arguments, taking contents of every input file and feeding this to
  * DataFileWriter, which in return feeds the content to DataAnalysis
- * Used for populating all data, takes ~20 seconds to run and collects 5000 data points
+ * Used for populating all data, takes ~10 seconds to run and collects 5000 data points
  */
 public class DataPopulater {
-    DataPopulater(String method) {
+    DataPopulater(String keyLenAlg, String caesarAlg) {
         File inputFolder = new File("data/inputs");
         File[] allInputs = inputFolder.listFiles();
 
         for (int i = 0; i < allInputs.length; i++) {
             System.out.printf("Collecting data on %s...%-20s", allInputs[i].getName(), ' ');
 
-            String fileNameWithoutExtension = allInputs[i].getName().substring(0,
-                    allInputs[i].getName().lastIndexOf("."));
-            DataFileReader.main(fileNameWithoutExtension, method);
+            try {
+                String fileNameWithoutExtension = allInputs[i].getName().substring(0,
+                        allInputs[i].getName().lastIndexOf("."));
+                String inputText = DataFileReader.readInput(fileNameWithoutExtension);
+                DataCollector.main(new String[] { inputText, fileNameWithoutExtension, keyLenAlg, caesarAlg });
+            } catch (IOException e) {
+                e.printStackTrace();
+            }
 
             System.out.print("\rData collection complete. Moving to next file...\n");
         }
@@ -29,15 +36,18 @@ public class DataPopulater {
      * 
      * @param args
      *            args[0]: key length calculation algorithm
+     *            args[1]: Caesar decryption algorithm
      * @throws InterruptedException
      */
     public static void main(String[] args) throws InterruptedException {
         if (args[0] == null || args[0].equals("all")) {
-            for (KeyLengthMethod method : KeyLengthMethod.values()) {
-                new DataPopulater(method.name());
+            for (KeyLengthMethod keyLenAlg : KeyLengthMethod.values()) {
+                for (CaesarDecryptionMethod keyAlg : CaesarDecryptionMethod.values()) {
+                    new DataPopulater(keyLenAlg.name(), keyAlg.name());
+                }
             }
         } else
-            new DataPopulater(args[0]);
+            new DataPopulater(args[0], args[1]);
 
         System.out.print("\rData population complete");
     }

src/main/java/frequencyanalysissimulator/crypto/Caesar.java

@@ -1,6 +1,6 @@
 package frequencyanalysissimulator.crypto;
 
-public class Caesar implements Cipher {
+public class Caesar {
     private String ciphertext;
     private int[] ciphertextAsNumbers;
 
@@ -9,6 +9,25 @@ public Caesar(String t) {
         ciphertextAsNumbers = new int[t.length()];
     }
 
+    /**
+     * Decrypts a Caesar cipher using the passed method of frequency analysis
+     * 
+     * @param m
+     *            The CaesarDecryptionMethod (enum)
+     * @return The decrypted text
+     */
+    public String decrypt(CaesarDecryptionMethod m) {
+        switch (m) {
+            case KASISKI:
+                return decryptByKasiski();
+            case KERCKHOFF:
+            default:
+                char keyLet = getKeyByChiSquare();
+                int keyLetAsNum = 27 - (keyLet - 64);
+                return Caesar.encrypt(ciphertext, keyLetAsNum);
+        }
+    }
+
     /**
      * Use most common occurence, assume it's e, and shift the rest using this (Kasiski's original
      * method of finding the key)
@@ -81,13 +100,6 @@ public char getKeyByChiSquare() {
         return letter;
     }
 
-    @Override
-    public String decrypt() {
-        char keyLet = getKeyByChiSquare();
-        int keyLetAsNum = 27 - (keyLet - 64);
-        return Caesar.encrypt(ciphertext, keyLetAsNum);
-    }
-
     /**
      * Encrypts a text with the key where A = key with Casar Shift
      * 

src/main/java/frequencyanalysissimulator/crypto/CaesarDecryptionMethod.java

@@ -0,0 +1,5 @@
+package frequencyanalysissimulator.crypto;
+
+public enum CaesarDecryptionMethod {
+    KERCKHOFF, KASISKI
+}

src/main/java/frequencyanalysissimulator/crypto/KeyLengthMethod.java

@@ -2,5 +2,5 @@
 
 public enum KeyLengthMethod {
     // KASISKI,
-    INDEX_OF_COINCIDENCE, FRIEDMAN
+    IOC, FRIEDMAN
 }

src/main/java/frequencyanalysissimulator/crypto/Possibility.java

@@ -0,0 +1,5 @@
+package frequencyanalysissimulator.crypto;
+
+class Possibility {
+
+}

src/main/java/frequencyanalysissimulator/crypto/SimpleSubstitutionCipher.java

@@ -5,11 +5,10 @@
  * 
  * @author Varun Singh on 2/20/2023
  */
-public class SimpleSubstitutionCipher implements Cipher {
+public class SimpleSubstitutionCipher {
     private String ciphertext;
     private double[] frequencies;
 
-    @Override
     public String decrypt() {
         return null;
     }

src/main/java/frequencyanalysissimulator/crypto/Vigenere.java

@@ -7,7 +7,7 @@
 import java.util.Map;
 import java.util.TreeMap;
 
-public class Vigenere implements Cipher {
+public class Vigenere {
     private String cipherText;
     private String letterOnlyCipherText;
     private int keylength;
@@ -17,22 +17,20 @@ public Vigenere(String cipher, KeyLengthMethod m) {
         cipherText = cipher.replaceAll("\\s+", " ");
         letterOnlyCipherText = removeNonLetters();
         method = m;
-        if (m.equals(KeyLengthMethod.INDEX_OF_COINCIDENCE)) {
+        if (m.equals(KeyLengthMethod.IOC)) {
             keylength = this.calculateKeyLengthByIndexOfCoincidence();
         } else if (m.equals(KeyLengthMethod.FRIEDMAN)) {
             keylength = this.calculateKeyLengthByFriedmanTest();
         }
     }
 
     public Vigenere(int keylen, String cipher) {
-        cipherText = cipher.replaceAll("\\s+", " ");
-        letterOnlyCipherText = removeNonLetters();
+        setCipherText(cipher);
         keylength = keylen;
     }
 
     public Vigenere(String cipher) {
-        cipherText = cipher.replaceAll("\\s+", " ");
-        letterOnlyCipherText = removeNonLetters();
+        setCipherText(cipher);
         keylength = this.calculateKeyLengthByIndexOfCoincidence();
     }
 
@@ -41,7 +39,7 @@ public String getCipherText() {
     }
 
     public void setCipherText(String newCipher) {
-        cipherText = newCipher;
+        cipherText = newCipher.replaceAll("\\s+", " ");
         letterOnlyCipherText = removeNonLetters();
     }
 
@@ -103,7 +101,7 @@ int calculateKeyLengthByIndexOfCoincidence() {
 
     }
 
-    int calculateKeylengthByKasiskiExamination() {
+    int calculateKeyLengthByKasiskiExamination() {
         Map<String, Integer> ngrams = new HashMap<>();
         Map<String, Integer> repeatedNGrams = new HashMap<>();
         Map<Integer, Integer> possibleKeyLengths = new TreeMap<>();
@@ -222,14 +220,13 @@ public String getKey() {
         return key.toString();
     }
 
-    @Override
-    public String decrypt() {
+    public String decrypt(CaesarDecryptionMethod keyAlg) {
         StringBuilder plaintext = new StringBuilder("");
         String[] cosets = this.distributeCiphertextIntoCosets();
 
         for (int i = 0; i < keylength; i++) {
             Caesar coset = new Caesar(cosets[i]);
-            cosets[i] = coset.decrypt();
+            cosets[i] = coset.decrypt(keyAlg);
         }
 
         for (int i = 0; i < letterOnlyCipherText.length(); i++) {
@@ -240,15 +237,16 @@ public String decrypt() {
 
         for (int i = 0; i < nonLetterLocations.size(); i++) {
             int index = nonLetterLocations.get(i);
-            // System.out.print("\r" + plaintext.toString());
-            // System.out.println("Inserting " + cipherText.charAt(index) + " at index " + index);
-            // System.out.println("New length of plaintext: " + plaintext.length());
             plaintext.insert(index, cipherText.charAt(index));
         }
 
         return plaintext.toString();
     }
 
+    public String decrypt() {
+        return decrypt(null);
+    }
+
     public static String encrypt(String plaintext, String key) {
         StringBuilder ciphertext = new StringBuilder("");
         ArrayList<Integer> nonLetters = new ArrayList<>();