The vast majority of JS content works great on iBooks, including manipulating the DOM. However, with respect to the positions, the basic concept of positions is different in the e-book (although with the new iBooks 3.0 scrolling mode it looks more like a traditional web page), and you probably want to limit the position logic to determining whether something is happening or from the screen. If it is not on the screen, trying to scroll it by setting scollPos or something like that will not work well, if at all; instead, try navigating to the appropriate location with something like location.href="foo.xhtml#myanchor;
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