What is the difference in use between "whole" and "all" ?

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I think the only difference is whether the described thing is countable or not. If there can be a discrete, countable number, one would use "all;" but if it is an uncountable substance or a mass-count noun, one would say "whole." For instance, you could not say how many waters are in a glass of water, so you would say "the whole glass of water" instead of "all the waters in the glass."