Ouput file problems

Question

Hi,
The attached code is supposed to read in a file and only print out to a file those lines that have CA and ARG. However, it is also printing out other rubbish: Please help, thanks
import java.io.*;
public class ForCampBell {
/** Creates a new instance of ForCampBell */
public ForCampBell(String inputFile, String outputFile) {
File input = new File(inputFile);
File output = new File(outputFile);
if (input.exists()){
BufferedReader oInput;
PrintWriter oOutput;
try {
oInput = new BufferedReader (new FileReader(input));
oOutput = new PrintWriter( new FileWriter(output), true);
String strLine = "";
while ((strLine = oInput.readLine ()) != null){
if (strLine.indexOf("CA") != -1){ // the line contains CA
int argLocation = strLine.indexOf("ARG");
oOutput.println( strLine.substring(0, argLocation + 3));
oOutput.close();
oInput.close();
catch (IOException err) {
System.out.println("IO Error while reading input file...");
else{
System.out.println("Input file specified not found...");
public static void main(String[] args) {
if (args.length != 2){
System.out.println("usage: java ForCampBell inputFile outputFile");
else{
new ForCampBell(args[0], args[1]);
input file:
ATOM 138 CA ASP 8 109.508 74.207 140.047
ATOM 150 CA LYS 9 108.132 70.857 141.312
ATOM 172 CA ARG 10 110.758 70.962 144.119 // only this line for example
outputfile:
AT
ATOM 172 CA ARG 10 110.758 70.962 144.119
AT

Answer 1

You have told it to print out all lines with CA in them, up to and including where it finds ARG (though if it doesn't find an ARG it will print out the first couple characters, I think) - did you mean to do that? Or did you mean something like:
if (strLine.indexOf("CA") != -1){ // the line contains CA
    int argLocation = strLine.indexOf("ARG");
    if (argLocation != -1) {
        // line also contains an ARG - dump it
         oOutput.println( strLine.substring(0, argLocation + 3));