Fix file referencing, jar should work now

CryptoApp/src/main/java/crypto/cryptanalysis/AttackTranspositionCipher.java

@@ -30,7 +30,8 @@ public AttackTranspositionCipher() {
         this.combi = new Combinatorics();
         this.alphabet = "abcdefghijklmnopqrstuvwxyz";
         this.ciph = new TranspositionCipher();
-        this.quad = new Ngrams(4, "src/main/resources/english_quadgrams.txt");
+        this.quad = new Ngrams(4);
+        this.quad.readInputStream(getClass().getResourceAsStream("/english_quadgrams.txt"));
         this.hillClimber = new HillClimber(this.quad);
     }
 

CryptoApp/src/main/java/crypto/cryptanalysis/Ngrams.java

@@ -6,8 +6,12 @@
 package crypto.cryptanalysis;
 
 import crypto.datastructures.HashTable;
+import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
 import java.util.Scanner;
 
 /**
@@ -19,7 +23,6 @@
 public class Ngrams {
 
     private final int n;
-    private final String filename;
     private long sampleSize;
     private HashTable<String, Long> ngramStats;
 
@@ -28,35 +31,25 @@ public class Ngrams {
      * @param n The desired n-gram substring length i.e. monogram is 1-gram and
      * is related to frequencies of single letter in a text, bigram (2-gram) is
      * related to frequencies of letter pairs in a text etc.
-     * @param filename A text file which contains data related to the specified
-     * n-gram. For each row the file should have the n-gram string, then a
-     * single space and finally the count of said n-grams in sample text. If the
-     * file violates this rule, then the results most likely will not be
-     * accurate.
      */
-    public Ngrams(int n, String filename) {
+    public Ngrams(int n) {
         this.n = n;
-        this.filename = filename;
         this.sampleSize = 0;
         this.ngramStats = new HashTable<>();
-        readFile();
     }
 
     public int getN() {
         return n;
     }
 
-    /**
-     * Reads the n-gram statistical data from a text file and then stores it in
-     * a hash table. The text file is provided as a constructor parameter.
-     *
-     * @return The sample size of the statistical data contained in the text
-     * file
-     */
-    private long readFile() {
-        try (Scanner scanner = new Scanner(new File(this.filename))) {
-            while (scanner.hasNextLine()) {
-                String[] line = scanner.nextLine().split(" ");
+    public void readInputStream(InputStream stream) {
+        InputStreamReader isr = new InputStreamReader(stream);
+        BufferedReader br = new BufferedReader(isr);
+
+        try {
+            String lineString = br.readLine();
+            while (lineString != null) {
+                String[] line = lineString.split(" ");
                 if (line.length >= 2) {
                     long frequency = 0;
                     try {
@@ -67,12 +60,13 @@ private long readFile() {
                         System.err.println("The file is corrupted");
                     }
                 }
+
+                lineString = br.readLine();
             }
-        } catch (FileNotFoundException exc) {
+            System.out.println("File read successfully");
+        } catch (IOException exc) {
             System.err.println("File not found");
         }
-
-        return this.sampleSize;
     }
 
     /**

CryptoApp/src/main/java/crypto/cryptoapp/CryptoUserInterface.java

@@ -14,6 +14,9 @@
 import crypto.cryptanalysis.IndexOfCoincidence;
 import crypto.cryptanalysis.Ngrams;
 import crypto.helpers.CharacterValue;
+import java.io.BufferedReader;
+import java.io.InputStream;
+import java.io.InputStreamReader;
 import javafx.application.Application;
 import javafx.collections.FXCollections;
 import javafx.collections.ObservableList;
@@ -73,7 +76,9 @@ public void start(Stage stage) throws Exception {
         keyedVig = new KeyedVigenereCipher("");
         autokeyVig = new AutokeyVigenereCipher();
         transposition = new TranspositionCipher();
-        quadgrams = new Ngrams(4, "src/main/resources/english_quadgrams.txt");
+
+        quadgrams = new Ngrams(4);
+        quadgrams.readInputStream(getClass().getResourceAsStream("/english_quadgrams.txt"));
         hillClimber = new HillClimber(quadgrams);
         freq = new FrequencyAnalysis();
         ic = new IndexOfCoincidence(freq);

CryptoApp/src/test/java/crypto/cryptanalysis/HillClimberTest.java

@@ -22,7 +22,8 @@ public class HillClimberTest {
 
     @Before
     public void setUp() {
-        this.quad = new Ngrams(4, "src/main/resources/english_quadgrams.txt");
+        this.quad = new Ngrams(4);
+        this.quad.readInputStream(getClass().getResourceAsStream("/english_quadgrams.txt"));
         this.hc = new HillClimber(quad);
     }
 

CryptoApp/src/test/java/crypto/cryptanalysis/NgramsTest.java

@@ -5,16 +5,13 @@
  */
 package crypto.cryptanalysis;
 
+import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
-import java.io.File;
-import java.io.FileWriter;
 import java.io.PrintStream;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
 import static org.junit.Assert.*;
-import org.junit.Rule;
-import org.junit.rules.TemporaryFolder;
 
 /**
  *
@@ -39,25 +36,14 @@ public void restoreStreams() {
         System.setErr(originalErr);
     }
 
-    @Rule
-    public TemporaryFolder testFolder = new TemporaryFolder();
-
-    private File testFile;
     private Ngrams ngrams;
 
     @Before
     public void setUp() throws Exception {
-        this.testFile = testFolder.newFile("test_ngram.txt");
-        try (FileWriter file = new FileWriter(this.testFile.getAbsolutePath())) {
-            file.write("THET 3597105\nHEIR 2630839\nTOBE 1850003\nTHRO 1239338");
-
-        }
-        this.ngrams = new Ngrams(4, this.testFile.getAbsolutePath());
-    }
-
-    @After
-    public void tearDown() {
-        testFile.delete();
+        String str = "THET 3597105\nHEIR 2630839\nTOBE 1850003\nTHRO 1239338";
+        byte[] bytes = str.getBytes("UTF-8");
+        this.ngrams = new Ngrams(4);
+        this.ngrams.readInputStream(new ByteArrayInputStream(bytes));
     }
 
     @Test
@@ -112,39 +98,32 @@ public void fitnessTest3() {
 
     @Test
     public void corruptedFileTest1() throws Exception {
-        File testFile2 = testFolder.newFile("test_2.txt");
-        try (FileWriter file = new FileWriter(testFile2.getAbsolutePath())) {
-            file.write("THET TEST\n");
-        }
+        String str = "THET TEST\n";
+        byte[] bytes = str.getBytes("UTF-8");
 
-        Ngrams ngrams2 = new Ngrams(4, testFile2.getAbsolutePath());
+        Ngrams ngrams2 = new Ngrams(4);
+        ngrams2.readInputStream(new ByteArrayInputStream(bytes));
         assertEquals("The file is corrupted\n", errContent.toString());
-        testFile2.delete();
     }
 
     @Test
     public void corruptedFileTest2() throws Exception {
-        File testFile2 = testFolder.newFile("test_2.txt");
-        try (FileWriter file = new FileWriter(testFile2.getAbsolutePath())) {
-            file.write("THET\n");
-        }
+        String str = "THET TEST\n";
+        byte[] bytes = str.getBytes("UTF-8");
 
-        Ngrams ngrams2 = new Ngrams(4, testFile2.getAbsolutePath());
+        Ngrams ngrams2 = new Ngrams(4);
+        ngrams2.readInputStream(new ByteArrayInputStream(bytes));
         assertEquals(0, ngrams2.getSampleSize());
-        testFile2.delete();
-    }
-
-    @Test
-    public void nonExistentFileTest() {
-        Ngrams ngrams2 = new Ngrams(4, "test3.txt");
-        assertEquals("File not found\n", errContent.toString());
     }
 
     @Test
     public void monoBiTrigramsTest1() {
-        Ngrams mono = new Ngrams(1, "src/main/resources/english_monograms.txt");
-        Ngrams bi = new Ngrams(2, "src/main/resources/english_bigrams.txt");
-        Ngrams tri = new Ngrams(3, "src/main/resources/english_trigrams.txt");
+        Ngrams mono = new Ngrams(1);
+        mono.readInputStream(getClass().getResourceAsStream("/english_monograms.txt"));
+        Ngrams bi = new Ngrams(2);
+        bi.readInputStream(getClass().getResourceAsStream("/english_bigrams.txt"));
+        Ngrams tri = new Ngrams(3);
+        tri.readInputStream(getClass().getResourceAsStream("/english_trigrams.txt"));
 
         assertEquals(1, mono.getN());
         assertEquals(2, bi.getN());

CryptoApp/src/test/java/crypto/cryptanalysis/TextProcessor.java

@@ -15,8 +15,6 @@
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Scanner;
-import javafx.application.Application;
-import javafx.geometry.Insets;
 import javafx.scene.Scene;
 import javafx.scene.control.Button;
 import javafx.scene.control.Label;
@@ -53,7 +51,8 @@ public static void main(String[] args) {
         int algoRuns = 10;
         int iterations = 500;
         System.out.println("Encryption done");
-        Ngrams ngrams = new Ngrams(4, "src/main/resources/english_quadgrams.txt");
+        Ngrams ngrams = new Ngrams(4);
+        ngrams.readInputStream(TextProcessor.class.getResourceAsStream("/english_quadgrams.txt"));
         HillClimber hill = new HillClimber(ngrams);
         ArrayList<String> foundKeys = cryptanalysisTransposition("src/main/resources/501_sample_ciphertexts.txt", key.length(), hill, algoRuns, iterations);
 
@@ -165,7 +164,7 @@ public static void main(String[] args) {
             } else {
 //                System.out.println("Len " + (i * 50 + 1) + "-" + ((i + 2) * 50) + " Correct: " + counts[i] + "/" + samples[i].size());
             }
-            
+
 //            System.out.println(counts[i] + " " + samples[i].size());
             System.out.println(counts[i]);
 //            System.out.printf("%.1f", avgs[i]);