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AbstractFactory Vs Prototype

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I was reading the GoF book. There it was mentioned how the Prototype pattern can avoid the necessity of a parallel class hierarchy of Abstract and Concrete factories by sending the prototypical instance to the constructor of the only factory class required. Then he talks about how the new object gets created by cloning the prototype. The problems of objects being able to support the cloning effectively were also discussed.
My question is -
If prototype pattern is going to solve some of the cumbersome approaches of AbstractFactory, then when would people prefer to go for AbstractFactory against the choice of prototyping??
The reasons i can see are given below -
1) the problems with deep cloning, sharing common references to other objects, etc.
2) Abstract factory automatically enforces that all the objects being generated by a given factory belong to the same family, once the client creates the proper concrete factory. I guess this is not ensured in the prototype pattern wherein the client can give apples and oranges if they just conform to the interfaces supplied to the constructor of the concrete factory object.
Please let me know if any of the above observations are flawed and also there are some other pros and cons b/w choosing a pattern from the above two.
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The AbstractFactory is also more flexible in some regards - for example I could imagine a factory reading classnames from a configuration file or the like.
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