file!

get slice adaptor from the destination slice, rather then the current db - because userdata features are stored in a different db

of SQL.

  - Use defined() in if-statements.
  - Properly quote the $hit_name in the SQL.

argument $pid is not defined, even though it isn't and even though $pid
is optional.  Fixed.

that does not exist.  Fixed.

   Arg [1]    : Bio::EnsEMBL::Slice $slice
                The slice from which to obtain align features.
   Arg [2]    : String $external_db_name
                Name of the external DB to which the align features
                should be restricted.
   Arg [3]    : (optional) string $logic_name
                The logic name of the type of features to obtain.
   Example    : @feats =
                 $adaptor->fetch_all_by_Slice_and_external_db( $slice, 'EMBL' );
   Description: Returns a listref of features created from the
                database which are on the Slice $slice and associated
                with external DB $external_db_name.  If logic name
                is defined, only features with an analysis of type
                $logic_name will be returned.
   Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
                in Slice coordinates
   Exceptions : thrown if $external_db_name is not defined or if
                the subclass does not return a table alias for the
                external_db table from _tables()
   Caller     : general
   Status     : At Risk


Also change one occurance of the word "PepAlignFeatureAdaptor" to
"ProteinAlignFeatureAdaptor".

Formatting of method documentation.

modified to support schema changes in release 52 (new columns in external_db and dna_align_feature tables)

modified method get_species_and_object_type to retrieve ExonAdaptor as well and changed implementation to make it easier to maintain

changes introduced in release 52: new column description in external_db and new column in dna_align_feature