%{
#include "sequence.h"



%}

api
object cDNA
des free_cDNA
func truncate_cDNA
func read_fasta_file_cDNA
func cDNA_name
func cDNA_length
func cDNA_seqchar
func cDNA_from_Sequence
endobject
endapi


struct cDNA
Sequence * baseseq;


#SequenceErrorList * se // list of the sequence errors



%{
#include "cdna.h"



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

It does not alter cdna, rather it returns a new
sequence with that truncation
%arg
cdna r cDNA that is truncated
%%
cDNA * truncate_cDNA(cDNA * cdna,int start,int stop)
{
  return cDNA_from_Sequence(magic_trunc_Sequence(cdna->baseseq,start,stop));
}

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

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

  return cDNA_from_Sequence(seq);
}


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

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

  return cDNA_from_Sequence(seq);
}

%func
Reads a efetch specified query
Uses, of course /read_efetch_Sequence
%arg
estr r efetch string which is read
%%
cDNA * read_efetch_cDNA(char * estr)
{
  return cDNA_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
%%
cDNA * read_SRS_cDNA(char * srsquery)
{
  return cDNA_from_Sequence(read_SRS_Sequence(srsquery));
}


%func
Returns the name of the cDNA
%arg
%%
char * cDNA_name(cDNA * cdna)
{
  return cdna->baseseq->name;
}

%func
Returns the length of the cDNA
%arg
%%
int cDNA_length(cDNA * cdna)
{
  return cdna->baseseq->len;
}

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


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

If you want to give this cDNA 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 cDNA datastructure
then use cDNA_from_Sequence(/hard_link_Sequence(seq))

%arg
seq o Sequence to make cDNA from
%%
cDNA * cDNA_from_Sequence(Sequence * seq)
{
  cDNA * out;
  int conv;

  if( seq == NULL ) {
    warn("Trying to make a cdna sequence from a NULL baseseq.");
    return NULL;
  }

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

  uppercase_Sequence(seq);

  force_to_dna_Sequence(seq,1.0,&conv);
 
  if( conv != 0 ) {
    log_full_error(INFO,0,"In making %s a cdna sequence, converted %d bases (%2.1f%%) to N's from non ATGCN",seq->name,conv,(double)conv*100/(double)seq->len);
  }

  out = cDNA_alloc();

  out->baseseq = seq;

  return out;
}




%}