jQuery delay not working

.delay() is used for items that are part of a queue, like animations. A simple addClass is not queued.

You could use setTimeout.

var trans = $('.transparent').removeClass('transparent');
setTimeout(function() {
    trans.addClass('not_transparent');
}, 2000);

As an alternative, you could add the non-queued item to the queue using .queue(), though I think a setTimeout would be better.

$('.transparent').removeClass('transparent').delay(2000).queue(function(nxt) {
      $(this).addClass('not_transparent');
      nxt();
});