/*  Last edited: Jan 12 14:16 1997 (birney) */


%{
#include "dyna.h"
#include "randommodel.h"


#define SPLICESITEMODELER_TYPE 474


%}



struct SpliceSiteModel
int offset
int pre_splice_site
int post_splice_site
int start_random;
int stop_random;
ComplexConsensi     * cc;
RandomModelDNAScore * rmds;
Score error_pos;


%{
#include "splicesitemodeler.h"




int SpliceSiteModeler_ComplexSequence_eval_func(int type,void * data,char * seq)
{
  if( type != SPLICESITEMODELER_TYPE ) {
    warn("In evaluating a ComplexSequence Eval function using a SpliceSite modeler, the type was wrong. This is a bad bug, indicating a bad data problem which will probably repeat");
  }

  return SpliceSiteModel_score((SpliceSiteModel *) data,seq);
}


ComplexSequenceEval * ComplexSequenceEval_from_SpliceSiteModel(SpliceSiteModel * ssm)
{
  ComplexSequenceEval * out;

  out = ComplexSequenceEval_alloc();

  /* shouldn't really add ones, but this is ok anyway. 
     Yukky hack due to not understanding a bug in the window 
     determination
     */

  /*  out->left_window  = ssm->offset + ssm->pre_splice_site +1; */
  out->left_window  = 11;
  /*  out->right_window = ssm->offset + ssm->post_splice_site +1; */
  out->right_window = 8;
  out->outside_score= NEGI;
  out->data_type    = SPLICESITEMODELER_TYPE;
  out->data         = ssm;
  out->type         = SEQUENCE_GENOMIC;
  out->eval_func    = SpliceSiteModeler_ComplexSequence_eval_func;

  return out;
}



/***
  This *must* have been passed a *seq with
  appropiate lengths on the left and right
  otherwise there is going to be tears!

  Really this function is only to be called from
  trusted function, for example, SpliceSite_ComplexSequence_eval


***/
Score SpliceSiteModel_score(SpliceSiteModel * ssm,char * seq)
{
  int len;
  int i;
  int score;
  char * be = seq;
  base b;

  /* check I have enough sequence */

  /*  fprintf(stderr,"Being passed sequence %c%c%c\n",seq[0],seq[1],seq[2]); */

  /* first calculate the CC score */

  score = score_from_ComplexConsensi(seq- ssm->offset - ssm->pre_splice_site,ssm->cc);
  
  /* now move over the random score          */
  /* random score is subtracted - ie divided */
  /* out from the model                      */

  len = ssm->start_random - ssm->stop_random +1;

  for(i=0,seq = seq - ssm->start_random+1;i<len;i++,seq++) {

    if( *seq == '\0' ) {
      warn("You are attempting to score an impossible base (%d from SS) [%s] in a splice site",(int)(seq - be),be);
      return NEGI;
    }

    b = base_from_char(*seq);
    score -= ssm->rmds->base[b];
  }

  /* this is for the possibility of errors/non splice consensus etc */

  if( score < ssm->error_pos ) 
    score = ssm->error_pos;

  return score;
}

SpliceSiteModel * std_5SS_SpliceSiteModel(int offset,ComplexConsensi * cc,RandomModelDNAScore * rmds)
{
  return new_SpliceSiteModel(offset,3,7,7,0,cc,rmds,0.0000001);
}

SpliceSiteModel * std_3SS_SpliceSiteModel(int offset,ComplexConsensi * cc,RandomModelDNAScore * rmds)
{

  /** mystical -1 everywhere because naturally we call
    caGcag - G as being the 3' SS

    however, if you think about it, it is the

    cacCag which is really the 3'SS (the residue after the splice site).

    Rather than enforcing these rules in the calling function, we subtract one from the offset here

    **/

  return new_SpliceSiteModel(offset-1,3,3,offset+2,offset-1,cc,rmds,0.0000001);
}

SpliceSiteModel * new_SpliceSiteModel(int offset,int pre_length,int post_length,int start,int stop,ComplexConsensi * cc,RandomModelDNAScore * rmds,Probability error)
{
  SpliceSiteModel * out;

  out = SpliceSiteModel_alloc();
  if( out == NULL )
    return NULL;

  out->offset = offset;
  out->pre_splice_site = pre_length;
  out->post_splice_site = post_length;
  out->start_random = start;
  out->stop_random  = stop;
  out->cc  = hard_link_ComplexConsensi(cc);
  out->rmds = hard_link_RandomModelDNAScore(rmds);
  out->error_pos = Probability2Score(error);

  return out;
}

%}