There are a couple of ways to do this, but one of the
more flexible is to use two threads: One to do the repetitive
work, and one to wait for user input.  The repetitive thread
does its parcel of work and then waits for notification that
input has arrived, using the wait(long) method to specify a
timeout.  Upon awakening, it can check whether it's received
an input notice or has timed out.  (It may also awaken for no
good reason, so if there's no input you should probably check
System.currentTimeMillis() to see if enough time has passed.)

    Meanwhile, the input thread simply reads user input, taking
as long as it takes.  When something arrives, it sets the "input
is here" indicator and calls notify() or notifyAll() to awaken
the repeating thread.

    There are, as I say, other ways to do this.  Some of the
other ways may be better suited to your situation -- but you
haven't told us much about your situation, so I've described an
approach that should cover pretty much everything, although it
may be more involved than you need.