Here is the code snippet.
read = new FileReader("trainfiles/"+filenames[i]);
                br = new BufferedReader(read);
                while((lines = br.readLine())!=null){
                    st = new StringTokenizer(lines);
                    while(st.hasMoreTokens()){
                        bw = new BufferedWriter(new FileWriter("files/file.txt"));
                        bw.write(st.nextToken());
                        bw.newLine();
                    }
                }
Edit: I am reading files from a directory. So, I need to open the reader in every loop. I have made some modification, but then also it is not writing to that file. Here is the code:
for(i=0;i==0;i++){
            if(filenames[i].matches(".*ham.*")){
                System.out.println("ham:"+filenames[i]);
                read = new FileReader("trainfiles/"+filenames[i]);
                br = new BufferedReader(read);
                while((lines = br.readLine())!=null){
                    st = new StringTokenizer(lines);
                    while(st.hasMoreTokens()){
                        System.out.println(st.nextToken());
                       bw.write(st.nextToken());
                    }
                }
                bw.close();
                br.close();
            }else{
                System.out.println("spam:"+filenames[i]);
            }
                        }
edit: I modified the code, but no success,
while((lines = br.readLine())!=null){
                    st = new StringTokenizer(lines);
                    bw = new BufferedWriter(new FileWriter("files/file.txt"));
                    while(st.hasMoreTokens()){
                        System.out.println(st.nextToken());
                       bw.write(st.nextToken());
                    }
                    bw.close();
                }
                br.close();
And i am getting this error: Exception in thread "main" java.util.NoSuchElementException
    at java.util.StringTokenizer.nextToken(StringTokenizer.java:332)
    at Test.main(Test.java:30)
edit: Thanks guys.. I figured it out. Actually I created an directory in eclipse and I did not refresh it to see the content. Its silly... anyways.thanks a lot