[shanePreater]

Your problem is that you are creating an extra BufferedReader if you remove the creation of userInput and re-use the inputFile variable the bufferedReader should work better.

Also you want to add a finally block to ensure the readers are all closed at the end.

Here is one I have edited for you:

Code:

BufferedReader userInput = null;
		BufferedReader input = null;
		PrintWriter outputFile = null;
		try {
			System.out.print("Enter the input filename: ");// open file
			userInput = new BufferedReader(new InputStreamReader(System.in));
			String str = userInput.readLine();
			input = new BufferedReader(new FileReader(str));
			System.out.print("Enter the output filename: ");
			String str1 = userInput.readLine();
			outputFile = new PrintWriter(new FileOutputStream(str1));// create
			// output
			// file
			int numberOfSeries = Integer.parseInt(input.readLine());
			for (int i = 0; i < numberOfSeries; i = i + 1) {
				int maximum = 0, minimum = 99999;
				int numberOfValues = Integer.parseInt(input.readLine());
				int[] dataSpread = new int[numberOfValues];
				for (int t = 0; numberOfValues > t; numberOfValues = numberOfValues - 1) {
					int dataValue = Integer.parseInt(userInput.readLine());
					if (dataValue > maximum)
						dataValue = maximum;
					if (dataValue < minimum)
						dataValue = minimum;
					dataValue = dataSpread[numberOfValues - 1];
				}
			}
		} catch (IOException e) {
			System.out.println("Error occured, please restart application.");
		} finally {
			try {
				// close all the readers.
				input.close();
				userInput.close();
				outputFile.flush();
				outputFile.close();
			} catch (Exception e) {
				e.printStackTrace();
			}
		}

Hope this helps.