It's the same way in WLD. I had the same problem until I realized that I had to transform all of the vertices for the model before rendering it. The way to do it is to load the list of vertex-bone indices in advance. When you are ready to render the model, iterate through all of the vertices and go from un-transformed vertex to transformed vertex (basically keep them in two different arrays, so the original ones are never lost). Then just render all of the polygons, using the list of transformed vertices. It means that you can't get away with using the matrix stack to go from parent bone to child bone, but it will render the models properly (besides, OpenGL has pretty small limits on some stack depths).
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