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Animation management

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Hi guys! After reading this article: http://www.gamasutra.com/view/feature/3456/animation_blending_achieving_.php I've found very interesting the idea of a tree used for animation blending. But here's the problem: acutally the structure of the animation and the skeletal represent a problem. Until now, I'm playing animations saved from 3d studio max with a custom exporter I wrote as a set of "tracks" divided per bone. The update of a model is done by simply call for every bone in the skeleton an update, that takes the track of the bone and interpolate using the time of the animation. In a case in which I want to blend two different animations, say one that runs and another that shoots, how can I handle the bones that are not AFFECTED by one of the animations? Also...how do you handle animations and skinning in your engines? Thanks!

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