I think what you are looking for is this:
public class Ques2 {
/**
* @param args the command line arguments
*/
public static void main(String[] args) throws IOException {
BufferedReader br = new BufferedReader(new InputStreamReader(System.in));
String input = br.readLine().toLowerCase();
StringBuilder result = new StringBuilder();
char currentCharacter;
int count;
for (int i = 0; i < input.length(); i++) {
currentCharacter = input.charAt(i);
count = 1;
while (i < input.length() - 1 && input.charAt(i + 1) == currentCharacter) {
count++;
i++;
}
result.append(currentCharacter);
result.append(count);
}
System.out.println("" + result);
}
}