throw() instead of die()  if program can't be found ......

In translate():

  Allow for seq_region attributes 'complete5' and 'complete3' to be
  fetched and used.  These will be fetched from the slice and used in
  the call to Bio::PrimarySeqI::translate() (see the documentation for
  that BioPerl module).

  Formatting.

  Be explicit, using defined() and scalar().

  Use index() rather than more expensive regular expression match for
  fixed string matching.

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.