bio.java

import java.util.*;
public class bio{
	public static void main(String[] args){
		char[] c = "aabc".toCharArray();
		//String s = "eabahgcabah";
		String s = "aaaaaaabc";
		int[] r = list(c,s);
		for(int i=0;i<r.length;i++){
			System.out.println(r[i]);
		}

	}
	public static int[] list(char[] c1, String s1){
		//Preparing the data
		char[] t = s1.toCharArray();
		int[] s = new int[t.length];
		int[] c = new int[c1.length];
		for(int i=0;i<s.length;i++){
			s[i] = (int) t[i];
		}
		for(int i=0;i<c.length;i++){
			c[i] = (int) c1[i];
		}
		int[] z = new int[256];
		for(int i=0;i<c.length;i++){
			z[c[i]]++;
		}
		for(int i=0;i<256;i++){
			if(z[i]==0){
				z[i] = -1;
			}
		}
		Queue<Integer> q = new LinkedList<Integer>();
		ArrayList<Integer> l = new ArrayList<Integer>();
		//The algorithm
		for(int i=0;i<s.length;i++){
			if(z[s[i]]<0){
				//pop the entire queue;
				while(q.size()!=0){
					z[q.remove()]++;
				}
			}else if(z[s[i]]==0){
				int o = q.remove();
				while(o!=s[i]){
					z[o]++;
					o = q.remove();
				}
				q.offer(s[i]);
			}else{
				z[s[i]]--;
				q.offer(s[i]);
			}
			if(q.size()==c.length){
				l.add(i+2-c.length);
			}
			//System.out.println(q);
		}
		int[] r = new int[l.size()];
		for(int i=0;i<l.size();i++){
			r[i] = l.get(i);
		}
		return r;
	}
}