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I'd like to get transparency of a layer , not of the whole surface of the layer , but only for a specific color of this layer . Is it possible ?
Best if you could provide an example image to get the best suggestion(s), but in the meantime you
could try Select>Color Range and then add a layer mask using the resulting selection.
My $0.02. In Layer Style dialogue, Blending Options tab you can use Blend If, advanced blending per channel if that can help something.