What is the difference between JoinQueryOver and JoinAlias?

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Functionally they do the same thing, create a join to another entity. The only difference is what they return. JoinQueryOver returns a new QueryOver with the current entity being the entity joined, while JoinAlias returns the original QueryOver that has the current entity as the original root entity.

Whichever one you use is a matter of personal taste:
(from http://nhibernate.info/doc/nh/en/index.html#queryqueryover)

IQueryOver<Cat,Kitten> catQuery =
    session.QueryOver<Cat>()
        .JoinQueryOver<Kitten>(c => c.Kittens)
            .Where(k => k.Name == "Tiddles");

and

Cat catAlias = null;
Kitten kittenAlias = null;
IQueryOver<Cat,Cat> catQuery =
    session.QueryOver<Cat>(() => catAlias)
        .JoinAlias(() => catAlias.Kittens, () => kittenAlias)
        .Where(() => kittenAlias.Name == "Tiddles");

Are functionally the same. Note how the kittenAlias is expressly referenced in the second query.

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