=head1 NAME

sequence_codon module - part of the Wise2 package

=head1 SYNOPSIS

This module contains helper functions for the Wise2 package

=head1 DESCRIPTION

=over

=item reverse_complement_Sequence

&Wise2::reverse_complement_Sequence(seq)

  This both complements and reverses a sequence,
  - a common wish!

  The start/end are correct with respect to the start/end
  of the sequence (ie start = end, end = start).



  Argument seq          [READ ] Sequence to that is used to reverse (makes a new Sequence) [Sequence *]
  Return [OWNER] new Sequence which is reversed [Sequence *]


=item magic_trunc_Sequence

&Wise2::magic_trunc_Sequence(seq,start,end)

  Clever function for dna sequences.

  When start < end, truncates normally

  when start > end, truncates end,start and then
  reverse complements.

  ie. If you have a coordinate system where reverse 
  sequences are labelled in reverse start/end way,
  then this routine produces the correct sequence.



  Argument seq          [READ ] sequence that is the source to be truncated [Sequence *]
  Argument start        [READ ] start point [int]
  Argument end          [READ ] end point [int]
  Return [OWNER] new Sequence which is truncated/reversed [Sequence *]


=item translate_Sequence

&Wise2::translate(dna,ct)

  This translates a DNA sequence to a protein.
  It assummes that it starts at first residue
  (use trunc_Sequence to chop a sequence up).



  Argument dna          [READ ] DNA sequence to be translated [Sequence *]
  Argument ct           [READ ] Codon table to do codon->aa mapping [CodonTable *]
  Return [OWNER] new protein sequence [Sequence *]


=back