%{
#include "dyna.h"

%}

api
object Translation
func get_Protein_from_Translation
des  free_Translation
endobject
endapi

friend Transcript

struct Translation
int start
int end
Transcript * parent !link
Protein * protein
%info

Translation represents a single translation from
a cDNA. Although most cDNAs will have one translation, 
this does allow us to deal with alternative translation 
points etc.

As with Transcript and Gene before it, the 
translation does not necessarily have any
sequence in it. When sequence is asked for by
get_Protein_from_Translation() the cache is checked,
and if it is empty, then the transcript's DNA
is called for, and the converted into the translation
with appropiate start and stops.

Of course, get_Protein_from_Translation can
potentially trigger the construction of an entire
gene upstairs, but that need not worry you here
%%

%{
#include "translation.h"

%func
Makes a complete clean copy of the translation
%%
Translation * copy_Translation(Translation * t)
{
  Translation * out;
  out = Translation_alloc();
  out->start = t->start;
  out->end   = t->end;

  return out;

}

%func
Gets the protein
%arg
ts translation
ct codon table to use
return s Protein sequence
%%
Protein * get_Protein_from_Translation(Translation * ts,CodonTable * ct)
{
  cDNA * cd;
  int i,j;
  Sequence * seq;
  char buffer[64];

  if( ts->protein != NULL)
    return ts->protein;

  if( ts->parent == NULL ) {
    warn("Cannot get Protein from translation as no parent!");
    return NULL;
  }


  cd = get_cDNA_from_Transcript(ts->parent);

  if( cd == NULL ) {
    warn("Cannot make translation as can't get transcript!");
    return NULL;
  }

  if( cd->baseseq == NULL ) {
    warn("A bad error - a non NULL cDNA with a null sequence object. No translation here!");
    return NULL;
  }
  if( cd->baseseq->len == 0 ) {
    warn("Attempting to translate a zero length cDNA. Yikes!");
    return NULL;
  }

  if( cd->baseseq->len%3 != 0 ) {
    warn("Cannot make translation, cDNA is not mod3!");
  }

  seq = Sequence_alloc();
  sprintf(buffer,"%s.tr",cDNA_name(cd));
  seq->name = stringalloc(buffer);
  seq->seq = ckcalloc(cd->baseseq->len/3 + 1,sizeof(char));
  seq->type = SEQUENCE_PROTEIN;

  for(i=0,j=0;i<cd->baseseq->len;i+=3,j++) {
    if( is_stop_codon(codon_from_seq(cd->baseseq->seq+i),ct) == TRUE ) {
      if( i+3 >= cd->baseseq->len ) 
	break;
      else {
	warn("Got a stop codon in the middle of a translation at postion [%d]. Yuk!",i);
	seq->seq[j] = '*';
      }
    } else {
      seq->seq[j] = aminoacid_from_seq(ct,cd->baseseq->seq+i);
    }
  }
  seq->seq[j]='\0';
  make_len_type_Sequence(seq);

  /*write_fasta_Sequence(seq,stdout);*/
  seq->type = SEQUENCE_PROTEIN;
  ts->protein = Protein_from_Sequence(seq);

  return ts->protein;

}


%func
shows a translation in vaguely human form
%%
void show_Translation(Translation *ts,FILE * ofp)
{
  fprintf(ofp,"Translation %d - %d\n",ts->start,ts->end);
}


%}