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In the authoring environment embedded HTML5 animations seem to play and or not play randomly in the Captivate timeline. I am trying to sync some audio with the html5 animations. I hand code my animations using Greensock, zip the html and dependencies up and embed using Media/HTML5 Animations. The animation plays perfectly when I publish the course but that does not help me sync to audio.
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You are going to be much better off if you include the audio in the animation. You can load the audio and attach an event listener to start the animation when it's ready.
With both audio and an animation in Captivate are completely separate, which ever one loads first will play and you'd more than likely have the timing be different depending on bandwidth.
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There is a possibility to exchange values of variables between HTML5 animation and Captivate, but I totally agree with TLCMediaDesign to include audio within the animation, instead of trying to synchronize. Animations are not 'totally' controlled by Captivate. Read about what happens when you have a pausing point on the slide (from interactive object):
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I spent some time trying to figure out the scope of the HTML5 code once on the stage as an web object. I tried targeting the iFrame that it sits in with JS in Captivate and no luck, I have dropped it for now. These would be short animations that would only need to sync to the audio in terms of when they start. Coded HTML5 animations are sooooo much smoother and dynamic. I am going to look at Adobe Animate as a last resort.