use withXXX methods when building graphs with dependencies

[eparejatobes]

as was discussed in bio4j/bio4j#60

[eparejatobes]

OK some stuff to do:

1. [x] add withXXX methods for all possible extensions of a graph, some of them are missing
2. [x] init deps in constructors call withXXX(this); as a side-effect, this is a good way of checking that we do have all of the withXXX methods
3. [x] check that the naming conventions for withXXX are being adhered to
4. [x] do covariant overriding of all the methods returning extension graphs; fields should also have the right type

[eparejatobes]

review please @pablopareja

[pablopareja]

looks OK to me :+1:

[eparejatobes]

OK merging