Logical Debugging Help

Question

Help!
I've written an application that isn't working exactly like I think it should. The program is supposed to compare two files. If there is a string in file one that is not in file two, then it is supposed to write that string to a third file. To help clarify, the first file is a final list of students that are taking the class. The second file is a list of students that attended for that session (they will be registering electronically). Therefore, I need the program to exam the two lists and tell me who was absent. At the moment, it will work for the first absent person (ie. it writes the student information to the third file so I know they are absent) but it seems to just stop working after that. I'm sure there is a problem with the logic...but I can't figure out where. Below is the code that i'm using. I'd appreciate any assistance!
Thanks!
John
public void actionTaken(){
try {
//File with final registration list
classList = new BufferedReader(new FileReader("classList.txt"));
//File that has recorded attendance
studentInput = new BufferedReader(new FileReader("studentInput.txt"));
// String written to this file if they were absent.
absent = new BufferedWriter(new OutputStreamWriter(new FileOutputStream("Absent.txt", true)));
// First while loop examines every line that is in the classList.txt file. Should advance to the next line after the nested while loop executes.
while ((cLT = classList.readLine()) != null){
// Nested while loop examines every line in the studentInput.txt
while ((sIT = studentInput.readLine()) != null){     
//If statement checks to see if a student has logged in.
if (cLT.equals(sIT)){
countTemp++; //countTemp is tripped if the student has logged in.
studentInput.close(); //Closes file after the entire file has been examined.     
//If statement checks the countTemp to see if the student registered.
if (countTemp == 0){ //Writes to the absent file if this line is true.
absent.newLine();
absent.write(cLT);
absent.close();
countTemp = 0; //reinitialized to test next student name.
classList.close(); //Closes file after the entire file has been examined.
} catch (IOException x) {

Answer 1

You close the student attendance file (studentInput) after you read the first student name from the class list!!!
Unless the files are going to get really big, I wouldn't do it this way. I'd create a Map of students who attended. Then I'd go through the names list and see if the names are present in the map. That way you could re-use the map for every student name.
If you don't want to do it that way, you're going to have to make assumptions about the ordering of the two name lists, and whether one is necessarily a subset of the other.