"Finish" phase 3 and project

README.md

@@ -1,8 +1,10 @@
 # Frequency Analysis Simulator
 
-The purpose of this project is to decrypt a monoalphabetic substitution cipher using frequency analysis and find the optimal algorithm and conditions of decrypting a Vigenere cipher. 
+The purpose of this project is to decrypt a monoalphabetic substitution cipher using frequency analysis and find the
+optimal algorithm and conditions of decrypting a Vigenere cipher.
 
 ## Methods of Cryptanalysis
+
 * Frequency Analysis
 * Kasiski Examination
 * Freidman Test
@@ -12,7 +14,7 @@ The purpose of this project is to decrypt a monoalphabetic substitution cipher u
 ## Usage
 
 1. Clone this repo with `git clone https://github.com/varunsingh87/Frequency-Analysis-Simulator`
-(for help see the [GitHub documentation](https://help.github.com/articles/cloning-a-repository/)).
+   (for help see the [GitHub documentation](https://help.github.com/articles/cloning-a-repository/)).
 2. Run `mvn package`
 2. Run the GUI with the following command:
 
@@ -28,7 +30,10 @@ Run the following command for data collection of a single input (~480 runs/data
 mvn compile exec:java -Dexec.mainClass="dataanalysis.DataCollector"
 ```
 
-Run the following command for data population of experiment data. To use a different key you will need to edit the default in DataCollector.java and make a new folder and subfolders of all the combinations of key length and caesar decryption algorithms in the following format:
+Run the following command for data population of experiment data. To use a different key you will need to edit the
+default in DataCollector.java and make a new folder and subfolders of all the combinations of key length and caesar
+decryption algorithms in the following format:
+
 ```
 outputs/
     [ioc, friedman]_[kasiski, kerckhoff]/
@@ -37,54 +42,60 @@ outputs/
 
 ### Generate executable file
 
-To create an executable file without the user needing the Java Runtime Environment on his or her computer, use the `jpackage` utility from the Java Development Kit:
+To create an executable file without the user needing the Java Runtime Environment on his or her computer, use
+the `jpackage` utility from the Java Development Kit:
 
-**Mac**: `jpackage --input target/ --name 'Frequency Analysis Simulation' --main-jar com.varunsingh.frequencyanalysissimulator-1.00.jar --main-class frequencyanalysissimulator.presentation.main.Main --type dmg --icon ./assets/icon.icns`
+**Mac
+**: `jpackage --input target/ --name 'Frequency Analysis Simulation' --main-jar com.varunsingh.frequencyanalysissimulator-1.00.jar --main-class frequencyanalysissimulator.presentation.main.Main --type dmg --icon ./assets/icon.icns`
 
-**Windows**: `jpackage --input target/ --name 'Frequency Analysis Simulation' --main-jar com.varunsingh.frequencyanalysissimulator-1.00.jar --main-class frequencyanalysissimulator.presentation.main.Main --type exe --icon ./assets/icon.ico` *Does not work on Mac*
+**Windows
+**: `jpackage --input target/ --name 'Frequency Analysis Simulation' --main-jar com.varunsingh.frequencyanalysissimulator-1.00.jar --main-class frequencyanalysissimulator.presentation.main.Main --type exe --icon ./assets/icon.ico`
+*Does not work on Mac*
 
-**Linux**: `jpackage --input target/ --name 'Frequency Analysis Simulation' --main-jar com.varunsingh.frequencyanalysissimulator-1.00.jar --main-class frequencyanalysissimulator.presentation.main.Main --type deb --icon ./assets/icon.ico` *Does not work on Mac*
+**Linux
+**: `jpackage --input target/ --name 'Frequency Analysis Simulation' --main-jar com.varunsingh.frequencyanalysissimulator-1.00.jar --main-class frequencyanalysissimulator.presentation.main.Main --type deb --icon ./assets/icon.ico`
+*Does not work on Mac*
 
 ## Process
 
-
 **Phase I: Monoalphabetic Ciphers**: July 22, 2019 - February 16, 2020
 
 **Phase II: Vigenere Ciphers**: September 26, 2022 - May 8, 2023
 
-**Phase III: Finishing Touches, Rewrites, Expansions**: July 22, 2023 - Present
+**Phase III: Graphics, Refactors, Variants**: July 22, 2023 - November 26, 2023
 
 ### Phase III
 
-- [] Rewrite of simple substitution cipher (efficient and accurate, no dictionary)
-- [] Visualization of data
-- [] Data collection GUI
-- [x] Variants of Vigenere cipher
+* Data GUI
+* Data collection GUI
+* Variants of Vigenere cipher
 
 ### Phase II
 
 * [Data from Phase II](https://docs.google.com/spreadsheets/d/e/2PACX-1vQIqW8qXtnbI1yTCQR_LcYpy6F7p6eZg5EP07no3c-lBoEkMUbpTPyxo_oa5mCCj7Gfk8LOTonOY-4a/pubhtml)
 * [Presentation](https://docs.google.com/presentation/d/e/2PACX-1vR5Vu_MXCbKyHm0vHaMW5Tn4qaJWVDV34Z_WX1WpHbejcwIzODNiuNKExOOTFTRUUDs7CPsYwz8PA1T/pub?start=false&loop=false&delayms=3000)
 
-
 ### Phase I
 
 * [Data from Phase I](https://docs.google.com/spreadsheets/d/130cqH1bGJPZ7mq2LrrTY6sMdm6E7qZP2Jea3s8cg3tA/edit#gid=0)
 * [Presentation](https://docs.google.com/presentation/d/e/2PACX-1vT29PD0nv69KI9cNDpZdsEA1p4eDg4P8V_XLVCWtpIFXDGnp_WmLrg-xiH120KWJkqppP9DZ-DlREr_/pub?start=false&loop=false&delayms=3000)
 
 ## Concepts Used
+
 * Advanced Data Structures - Java Collections API, including TreeSet, HashMap, ArrayList
-* Layered Architecture - separated into presentation code (Java Swing framework), business logic (pure Java), and data analysis module (pure Java I/O)
+* Layered Architecture - separated into presentation code (Java Swing framework), business logic (pure Java), and data
+  analysis module (pure Java I/O)
 * Recursion
 
 ## Built With
 
 * [Java](https://www.java.com/en/) - The programming language
-* [Maven](https://maven.apache.org/) - The dependency management system 
+* [Maven](https://maven.apache.org/) - The dependency management system
 * [JUnit](https://junit.org/junit5/) - The testing framework
 
 ## Sources of Research
 
 * Inspiration from _The Code Book_ by Simon Singh
 * _The Cryptanalyst_ by Helen Fouche Gaines
-* Michigan Technological University - explanations of the Kasiski Examination and index of coincidence with working examples
+* Michigan Technological University - explanations of the Kasiski Examination and index of coincidence with working
+  examples

src/main/java/dataanalysis/DataCollector.java

@@ -10,6 +10,11 @@
 import frequencyanalysissimulator.crypto.Vigenere;
 import frequencyanalysissimulator.crypto.VigenereDecryption;
 
+/**
+ * Outputs data table containing accuracy of the
+ * subsequences of a ciphertext encrypted from subsequences of a key of an input message
+ * to a CSV file in the outputs/ folder
+ */
 public class DataCollector {
 	private final static int PREFERRED_CIPHER_LENGTH = 1000;
 	private final static int PREFERRED_KEY_LENGTH = 20;

src/main/java/dataanalysis/DataFileReader.java

@@ -4,9 +4,12 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 
+/**
+ * Utility class for reading files as Strings
+ */
 public class DataFileReader {
-    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"), " ");
-    }
+	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/DataVisualizer.java

@@ -21,7 +21,17 @@ public DataVisualizer() {
 		DataPopulater.main(new String[]{"all"});
 		setCount = 1;
 		trialCount = 'A';
+
 		File dataFile = new File("data/outputs/HARSHTRAITSHINEIMPORT/ioc_kerckhoff/1A.csv");
+		GraphPanel g = new GraphPanel(findAverages(dataFile));
+		add(g, BorderLayout.CENTER);
+		add(dataGroupControls(), BorderLayout.NORTH);
+		trialIdLabel = new JLabel(setCount + "" + trialCount);
+		trialIdLabel.setHorizontalAlignment(SwingConstants.CENTER);
+		add(trialIdLabel, BorderLayout.SOUTH);
+	}
+
+	public static List<Double> findAverages(File dataFile) {
 		List<Double> averages = new ArrayList<>();
 		try (Scanner dataFileReader = new Scanner(dataFile)) {
 			dataFileReader.nextLine(); // Skip header
@@ -33,12 +43,7 @@ public DataVisualizer() {
 		} catch (IOException e) {
 			e.printStackTrace();
 		}
-		g = new GraphPanel(averages);
-		add(g, BorderLayout.CENTER);
-		add(dataGroupControls(), BorderLayout.NORTH);
-		trialIdLabel = new JLabel(setCount + "" + trialCount);
-		trialIdLabel.setHorizontalAlignment(SwingConstants.CENTER);
-		add(trialIdLabel, BorderLayout.SOUTH);
+		return averages;
 	}
 
 	private void updateTrialIdLabel() {

src/main/java/dataanalysis/presentation/VigenereTab.java

@@ -2,6 +2,7 @@
 
 import dataanalysis.DataCollector;
 import dataanalysis.DataFileReader;
+import dataanalysis.DataVisualizer;
 import frequencyanalysissimulator.crypto.CaesarDecryptionMethod;
 import frequencyanalysissimulator.crypto.KeyLengthMethod;
 import frequencyanalysissimulator.crypto.VigenereDecryption;
@@ -58,13 +59,15 @@ JComponent submission() {
 	private void collect(KeyLengthMethod keyLengthMethod, CaesarDecryptionMethod caesarDecryptionMethod) {
 		// Specific method for both steps (stopping case)
 		if (caesarDecryptionMethod != CaesarDecryptionMethod.ALL && keyLengthMethod != KeyLengthMethod.ALL) {
-			DataCollector.main(new String[]{
-					inputInfoMenu.getPlaintext(),
-					inputInfoMenu.getPlaintextId(),
-					keyLengthMethod.name(),
-					caesarDecryptionMethod.name(),
-					decryptParamsMenu.getKey()
-			});
+			new Thread(() -> {
+				DataCollector.main(new String[]{
+						inputInfoMenu.getPlaintext(),
+						inputInfoMenu.getPlaintextId(),
+						keyLengthMethod.name(),
+						caesarDecryptionMethod.name(),
+						decryptParamsMenu.getKey()
+				});
+			}).start();
 		} else if (keyLengthMethod == KeyLengthMethod.ALL) { // All key length methods
 			for (KeyLengthMethod method : KeyLengthMethod.values()) {
 				if (method != KeyLengthMethod.ALL) {