%{
#include "sequence.h"



%}


struct DNA
Sequence * baseseq;



%{
#include "dna.h"



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

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

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

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

  return DNA_from_Sequence(seq);
}


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

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

  return DNA_from_Sequence(seq);
}

%func
Reads a efetch specified query
Uses, of course /read_efetch_Sequence
%arg
estr r efetch string which is read
%%
DNA * read_efetch_DNA(char * estr)
{
  return DNA_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
%%
DNA * read_SRS_DNA(char * srsquery)
{
  return DNA_from_Sequence(read_SRS_Sequence(srsquery));
}


%func
Returns the name of the DNA
%arg
%%
char * DNA_name (DNA * dna)
{
  return dna->baseseq->name;
}

%func
Returns the length of the DNA
%arg
%%
int DNA_length (DNA * dna)
{
  return dna->baseseq->len;
}

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


%func
makes a new DNA from a Sequence. It 
owns the Sequence memory, ie will attempt a /free_Sequence
on the structure when /free_DNA is called

If you want to give this DNA 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 sequence object elsewhere outside of the DNA datastructure
then use DNA_from_Sequence(/hard_link_Sequence(seq))

%arg
seq Sequence to make DNA from
%%
DNA * DNA_from_Sequence(Sequence * seq)
{
  DNA * out;


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

  out = DNA_alloc();

  out->baseseq = seq;

  return out;
}




%}