I would first off say sorry if the title is worded incorrectly.

Okay now let me give the scenario

I'm creating a 2 player fighting game, An average battle will include a Map (moving/still) and 2 characters (which are rendered by redrawing a varying amount of sprites one after the other).

Now at the moment I have a single game loop limiting me to a set number of frames per second (using Java):

Timer timer = new Timer(0, new AbstractAction() {

    @Override
    public void actionPerformed(ActionEvent e) {
        long beginTime; //The time when the cycle begun
        long timeDiff; //The time it took for the cycle to execute
        int sleepTime; //ms to sleep (< 0 if we're behind)
        int fps = 1000 / 40;

        beginTime = System.nanoTime() / 1000000;

        //execute loop to update check collisions and draw
        gameLoop();

        //Calculate how long did the cycle take
        timeDiff = System.nanoTime() / 1000000 - beginTime;

        //Calculate sleep time
        sleepTime = fps - (int) (timeDiff);

        if (sleepTime > 0) {//If sleepTime > 0 we're OK
                ((Timer)e.getSource()).setDelay(sleepTime);
        }
    }
});
timer.start();

in gameLoop() characters are drawn to the screen ( a character holds an array of images which consists of their current sprites) every gameLoop() call will change the characters current sprite to the next and loop if the end is reached.

But as you can imagine if a sprite is only 3 images in length than calling gameLoop() 40 times will cause the characters movement to be drawn 40/3=13 times. This causes a few minor anomilies in the sprited for some charcters

So my question is how would I go about delivering a set amount of frames per second in when I have 2 characters on screen with varying amount of sprites?