UPDATE:

Here is a jsbin example demonstrating the problem.

UPDATE 2:

And here is the fixed version thanks to fudgey.

Basically, I have the following javascript which scrolls the window to an anchor on the page:

 // get anchors with href's that start with #

 $(a[href^=#]).live(click, function(){

     var target = $($(this).attr(href));

     // if the target exists: scroll to it...

     if(target[0]){

         // If the page isn't long enough to scroll to the target's position

         // we want to scroll as much as we can. This part prevents a sudden 

         // stop when window.scrollTop reaches its maximum.

         var y = Math.min(target.offset().top, $(document).height() - $(window).height());

         // also, don't try to scroll to a negative value...

         y=Math.max(y,0);

         // OK, you can scroll now...

         $(html,body).stop().animate({ scrollTop: y }, 1000);

     }

     return false;

 });

It works perfectly......until I manually try to scroll the window. When the scrollbar or mousewheel is scrolled I need to stop the current scroll animation...but I'm not sure how to do this.

This is probably my starting point...

$(window).scroll(e){

    if(IsManuallyScrolled(e)){

        $(html,body).stop();

    }

} 

...but I'm not sure how to code the IsManuallyScrolled function. I've checked out e (the event object) in Google Chrome's console and AFAIK there is not way to differentiate between a manual scroll and jQuery's animate() scroll.

How can I differentiate between a manual scroll and one called via jQuery's $.fn.animate function?