mostly done

input.txt

@@ -1,3 +1,3 @@
 Hello World!
 This is a file, that
-Has words and stuff in it
+Has words and stuff in it

output.txt

@@ -0,0 +1,3 @@
+HELLO WORLD!
+THIS IS A FILE, THAT
+HAS WORDS AND STUFF IN IT

src/Main.java

@@ -4,21 +4,27 @@ import java.io.*;
 public class Main {
 
     // Read contents of inFile, convert it all to uppercase, write to outFile
-    // Do line-by-line
+    // Will save each line of inFile in a string, convert string to upper,
-
+    // then write it to outFile
     public static void upperCaseFileConverter(String inFile, String outFile) {
         try {
+            // Make the input and output reader, for inFile and outFile respectively
             BufferedReader in = new BufferedReader(new FileReader(inFile));
             BufferedWriter out = new BufferedWriter(new FileWriter(outFile));
 
-            String line;
+            String line; // String to store the line we will read and convert
 
-            while((line = in.readLine()) != null) {
+            // Read inFile until its null input
+            while ((line = in.readLine()) != null) {
+                // WRite out the string, converted to uppercase
                 out.write(line.toUpperCase());
-                //out.newLine();
+                out.newLine(); // This will ensure new lines come correctly, platform independent
             }
-
+            // Closing the writing streams
+            in.close();
+            out.close();
         }
+        // In case inFile doesnt exist, or program is unable to write outFile
         catch (IOException e) {
             System.out.println("File not found:");
             System.out.println(e.getMessage());
@@ -28,9 +34,6 @@ public class Main {
     public static void main(String[] args) {
 
 
-
-
-
         // Main for Q2
         // Create the array of 5 testScore objects to be serialized later
         TestScores[] testScoresArray = new TestScores[5];
@@ -40,46 +43,65 @@ public class Main {
         testScoresArray[3] = new TestScores(new int[]{72, 87, 92, 92, 96});
         testScoresArray[4] = new TestScores(new int[]{100,100,100,100,100,100,100});
 
+        // Print out the averages of each testScores so we can compare it after
         for(TestScores testScore : testScoresArray) {
             System.out.println(testScore.getAverage());
         }
         System.out.println("\n");
+
+        // File to store the serilized classes
         String filename = "testScores.txt";
         // Serialize array to file
-        try{
+        try {
+            // Create file output stream to write to file
             FileOutputStream fileOut = new FileOutputStream(filename);
+            // Create objectOutputStream to be able to write the class to file
             ObjectOutputStream out = new ObjectOutputStream(fileOut);
             out.writeObject(testScoresArray);
             System.out.println("Test Scores written to " + filename);
+            // Close the streams
+            fileOut.close();
+            out.close();
 
         } catch (IOException e) {
             System.out.println(e.getMessage());
         }
 
         // Deserialize objects from file
+        // Array to store deserialized files
         TestScores[] deserializedScores = null;
-
         try{
             FileInputStream fileIn = new FileInputStream(filename);
             ObjectInputStream in = new ObjectInputStream(fileIn);
             deserializedScores = (TestScores[]) in.readObject();
             System.out.println("Test Scores deserialized from " + filename);
+            // Close the streams
+            in.close();
+            fileIn.close();
         }
-        //TODO: FIX THESE CATCH CLAUSES
+        catch(FileNotFoundException e){
-        catch(IOException e){
             System.out.println(e.getMessage());
-        } catch (ClassNotFoundException e) {
+        } catch (IOException e) {
             throw new RuntimeException(e);
         }
-        try {
+        catch(ClassNotFoundException e){
-            for (TestScores testScore : deserializedScores) {
-                System.out.println(testScore.getAverage());
-            }
-        }
-        catch(NullPointerException e){
             System.out.println(e.getMessage());
         }
 
+        if(deserializedScores != null) {
+            try {
+                for (TestScores testScore : deserializedScores) {
+                    // Print out averages of deserialized class to compare to original values
+                    System.out.println(testScore.getAverage());
+                }
+            }
+            catch(NullPointerException e){
+                System.out.println(e.getMessage());
+            }
+        }
+
+
+        // Running function for Q3
         upperCaseFileConverter("input.txt", "output.txt");