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html - Pausing Javascript execution until button press

I'm creating a visualization of a Sudoku creator for my Algorithms class (in Javascript). The algorithm works great, but I'm having trouble finding a way to pause execution.

Currently, I'm using prompt() to pause, but that's bulky and annoying. Is there any way to pause until another function is run (via HTML button) other than a continuous while loop?

I can post code, but I don't think it's needed. I'm not currently using jQuery, but I can if needed.

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var flag = true;
function foo(){
    if (flag){
        // Do your magic here
        ...
        ...
        setTimeout(foo, 100);
    }
}

function stop(){
    flag = false;
}
<input type="button" onclick="stop();" value="stop it!!!" />

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