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".