add upstream/downstream flanking 5kb around transcript when consider a variation is involved in the transcript

Use warning() from Bio::EnsEBML::Utils::Exception instead of warn() from Bio::EnsEMBL::Root.
Fix warning message in pop_stack()

fix for no species being specified and more than one core database bring called (connection was not dropped)

much code duplication removed by adding load_adaptors which other load methods call. load_adaptors is now also called if an unknown DBAdaptor is passed (which could happen with registry autoloading. Added a test for variation adaptor

Added $subname in the key of the DEPRECATED hash. Useful when calling several methods from the same line like when using the Bio::EnsEMBL::Test::TestUtils::test_getter_setter method.