=head1 NAME

protein module - part of the Wise2 package

=head1 SYNOPSIS

This module contains the following objects

=over

=item Protein


=back

=head1 DESCRIPTION

=head2 Object Protein

=over

=item baseseq

 Type [Sequence *] Scalar No documentation



=back

The protein object is a typed
example of a sequence object.

It does nothing more than a sequence
object but is typed



=head2 Member functions of Protein

=over

=item Protein_from_Sequence

&Wise2::Protein::Protein_from_Sequence(seq)

  makes a new protein from a Sequence. It 
  owns the Sequence memory, ie will attempt a /free_Sequence
  on the structure when /free_Protein is called

  If you want to give this protein this Sequence and
  forget about it, then just hand it this sequence and set
  seq to NULL (no need to free it). If you intend to use 
  the sequecne object elsewhere outside of the Protein datastructure
  then use Protein_from_Sequence(/hard_link_Sequence(seq))




  Argument seq          [OWNER] Sequence to make protein from [Sequence *]
  Return [UNKN ] Undocumented return value [Protein *]


=item hard_link_Protein

&Wise2::Protein::hard_link_Protein(obj)

  Bumps up the reference count of the object
  Meaning that multiple pointers can 'own' it



  Argument obj          [UNKN ] Object to be hard linked [Protein *]
  Return [UNKN ] Undocumented return value [Protein *]


=item alloc

&Wise2::Protein::alloc(void)

  Allocates structure: assigns defaults if given 



  Return [UNKN ] Undocumented return value [Protein *]


=item set_baseseq

&Wise2::Protein::set_baseseq(obj,baseseq)

  Replace member variable baseseq
  For use principly by API functions



  Argument obj          [UNKN ] Object holding the variable [Protein *]
  Argument baseseq      [OWNER] New value of the variable [Sequence *]
  Return [SOFT ] member variable baseseq [boolean]


=item baseseq

&Wise2::Protein::baseseq(obj)

  Access member variable baseseq
  For use principly by API functions



  Argument obj          [UNKN ] Object holding the variable [Protein *]
  Return [SOFT ] member variable baseseq [Sequence *]


=back