How to parse a big file with Regex/Patternthan

Question

I would parse a big file by using matcher/pattern so i have thought to use a BufferedReader.
The problem is that a BufferedReader constraints to read
the file line by line and my patterns are not only inside a line but also at the end and at the beginning of each one.
For example this class:
import java.util.regex.*;
import java.io.*;
public class Reg2 {
  public static void main (String [] args) throws IOException {
    File in = new File(args[1]);
    BufferedReader get = new BufferedReader(new FileReader( in ));
    Pattern hunter = Pattern.compile(args[0]);
    String line;
    int lines = 0;
    int matches = 0;
    System.out.print("Looking for "+args[0]);
    System.out.println(" in "+args[1]);
    while ((line = get.readLine()) != null) {
      lines++;
      Matcher fit = hunter.matcher(line);
      //if (fit.matches()) {
      if (fit.find()) {
     System.out.println ("" + lines +": "+line);
     matches++;
    if (matches == 0) {
      System.out.println("No matches in "+lines+" lines");
  }used with the pattern "ERTA" and this file (genomic sequence) :
AAAAAAAAAAAERTAAAAAAAAAERT [end of line]
ABBBBBBBBBBBBBBBBBBBBBBERT [end of line]
ACCCCCCCCCCCCCCCCCCCCCCERT [end of line]
returns it has found the pattern only in this line
"1: AAAAAAAAAAAERTAAAAAAAAAERT"
while my pattern is present 4 times.
Is really a good idea to use a BufferedReader ?
Has someone an idea ?
thanx
Edited by: jfact on Dec 21, 2007 4:39 PM
Edited by: jfact on Dec 21, 2007 4:43 PM

Answer 1

Quick and dirty demo:
import java.io.*;
import java.util.regex.*;
public class LineDemo {
    public static void main (String[] args) throws IOException {
        File in = new File("test.txt");
        BufferedReader get = new BufferedReader(new FileReader(in));
        int found = 0;
        String previous = "", next = "", lookingFor = "ERTA";
        Pattern p = Pattern.compile(lookingFor);
        while((next = get.readLine()) != null) {
            String toInspect = previous+next;
            Matcher m = p.matcher(toInspect);
            while(m.find()) found++;
            previous = next.substring(next.length()-lookingFor.length());
        System.out.println("Found '"+lookingFor+"' "+found+" times.");
/* test.txt contains these four lines:
AAAAAAAAAAAERTAAAAAAAAAERT
ABBBBBBBBBBBBBBBBBBBBBBERT
ACCCCCCCCCCCCCCCCCCCCCCERT
ACCCCCCCCCCCCCCCCCCCCCCBBB
*/