now imports throw() method out of Bio::EnsEMBL::Utils::Exception to
properly compile after changes done on  29-Oct-08 r 1.27

  When removing the final stop codon from the mRNA (if present), use the
  codon table properly, i.e. do not assume we're using codon table 1.

  Format it.

  The method never actually throws an exception.

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.