public class Server implements Runnable{
...
public void run(){
     long period = 45000L;
     long start = System.currentTimeMillis();
     while (System.currentTimeMillis() - start < period) {
         ...
         String input = readInput(); // - Execution gets "paused" since user is asked to enter input
         while (true){
             ...perform some other commands...
         }
     }