%{
#include "sequence.h"



%}

api
object Protein
des free_Protein
func Protein_from_Sequence
endobject
endapi

struct Protein
Sequence * baseseq;
%info
The protein object is a typed
example of a sequence object.

It does nothing more than a sequence
object but is typed
%%

# SequenceErrorList * se // list of the sequence errors



%{
#include "protein.h"



%func
Truncates a protein sequence. Basically uses
the /trunc_Sequence function (of course!)

It does not alter pro, rather it returns a new
sequence with that truncation
%arg
pro r Protein that is truncated
%%
Protein * truncate_Protein(Protein * pro,int start,int stop)
{
  return Protein_from_Sequence(trunc_Sequence(pro->baseseq,start,stop));
}

%func
Reads a fasta file assumming that it is protein. 
Will complain if it is not, and return NULL.
%arg
filename filename to be opened and read
%%
Protein * read_fasta_file_Protein (char * filename)
{
  Sequence * seq;

  seq = read_fasta_file_Sequence(filename);
  if( seq == NULL ) {
    return NULL;
  }

  return Protein_from_Sequence(seq);
}


%func
Reads a fasta file assumming that it is protein. 
Will complain if it is not, and return NULL.
%arg
ifp file point to be read from
%%
Protein * read_fasta_Protein (FILE * ifp)
{
  Sequence * seq;

  seq = read_fasta_Sequence(ifp);
  if( seq == NULL ) {
    return NULL;
  }

  return Protein_from_Sequence(seq);
}

%func
Reads a efetch specified query
Uses, of course /read_efetch_Sequence
%arg
estr r efetch string which is read
%%
Protein * read_efetch_Protein(char * estr)
{
  return Protein_from_Sequence(read_efetch_Sequence(estr));
}

%func
Reads a SRS sequence using srs4 syntax.
Uses, of course, /read_SRS_Sequence

%arg
srsquery r string query representing SRS name
%%
Protein * read_SRS_Protein(char * srsquery)
{
  return Protein_from_Sequence(read_SRS_Sequence(srsquery));
}


%func
Returns the name of the protein
%arg
%%
char * Protein_name (Protein * pr)
{
  return pr->baseseq->name;
}

%func
Returns the length of the protein
%arg
%%
int Protein_length (Protein * pr)
{
  return pr->baseseq->len;
}

%func
Returns sequence character at this position.
%arg
pr Protein
pos position in protein to get char
%%
char Protein_seqchar(Protein * pr,int pos)
{
  return pr->baseseq->seq[pos];
}


%func
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))

%arg
seq o Sequence to make protein from
%%
Protein * Protein_from_Sequence(Sequence * seq)
{
  Protein * out;


  if( seq == NULL ) {
    warn("Attempting to make a protein from a NULL sequence");
    return NULL;
  }

  if( is_protein_Sequence(seq) == FALSE ) {
    warn("Trying to make a protein sequence from a non protein base sequence [%s].",seq->name);
    return NULL;
  }

  out = Protein_alloc();

  out->baseseq = seq;

  return out;
}




%}