/*  Last edited: Mar  3 13:16 1997 (birney) */

%{
#include "wisebase.h"
#include "probability.h"
#include "geneparser21.h"

enum GeneParser4Type {
  GP4_INTRON2CDS = 0,
  GP4_INTRON2INTRON,
  GP4_DELETE_1_BASE,
  GP4_DELETE_2_BASE,
  GP4_INSERT_1_BASE,
  GP4_INSERT_2_BASE,
  GP4_LOOP2LOOP,
  GP4_LOOP2MODEL,
  GP4_TRANSITION_LEN };

%}


struct GeneParser4
Probability transition[GP4_TRANSITION_LEN]
Probability intron[5]

struct GeneParser4Score
Score transition[GP4_TRANSITION_LEN]
Score intron[5]

%{
#include "geneparser4.h"


GeneParser4Score * GeneParser4Score_from_GeneParser21Score(GeneParser21Score * gp21s)
{
  int i;
  GeneParser4Score * out;

  out = GeneParser4Score_alloc();

  out->transition[GP4_INTRON2CDS] = gp21s->transition[GP21_CENTRAL2PY] + gp21s->transition[GP21_PY2SPACER] + gp21s->transition[GP21_SPACER2CDS];

  out->transition[GP4_INTRON2INTRON]    = gp21s->transition[GP21_CENTRAL2CENTRAL];
  out->transition[GP4_DELETE_1_BASE]    = gp21s->transition[GP21_DELETE_1_BASE];
  out->transition[GP4_DELETE_2_BASE]    = gp21s->transition[GP21_DELETE_2_BASE];
  out->transition[GP4_INSERT_1_BASE]    = gp21s->transition[GP21_INSERT_1_BASE];
  out->transition[GP4_INSERT_2_BASE]    = gp21s->transition[GP21_INSERT_2_BASE];
  out->transition[GP4_LOOP2MODEL]       = gp21s->transition[GP21_RND2MODEL];
  /*  out->transition[GP4_LOOP2LOOP]        = gp21s->transition[GP21_RND2RND]; */
  out->transition[GP4_LOOP2LOOP]        = 0;
  /*  fprintf(stderr,"Loop score is %d\n",out->transition[GP4_LOOP2LOOP]); */


  for(i=0;i<5;i++)
    out->intron[i] = gp21s->central[i];

  return out;
}
  
  

GeneParser4Score * GeneParser4Score_from_GeneParser4(GeneParser4 * gp4)
{
  GeneParser4Score * out;

  out = GeneParser4Score_alloc();

  Probability2Score_move(gp4->transition,out->transition,GP4_TRANSITION_LEN);
  Probability2Score_move(gp4->intron,out->intron,5);

  return out;
}


%}