%{
#include "dyna.h"


%}

struct CodonMatrix
Probability prob[125][125]

struct CodonMatrixScore
Score  score[125][125]

%{
#include "codonmatrix.h"



%func
Combines CodonMatrixScore_from_CodonMatrix and naive_CodonMatrix
%%
CodonMatrixScore * naive_CodonMatrixScore_from_prob(CodonTable * ct,CompProb * cm)
{
  CodonMatrixScore * out;
  CodonMatrix * com;

  com = naive_CodonMatrix(ct,cm);

  out = CodonMatrixScore_from_CodonMatrix(com);

  free_CodonMatrix(com);

  return out;
}


%func
Makes a CodonMatrixScore from a CodonMatrix
%%
CodonMatrixScore * CodonMatrixScore_from_CodonMatrix(CodonMatrix * cm)
{
  int i,j;
  CodonMatrixScore * out;

  out = CodonMatrixScore_alloc();

  for(i=0;i<125;i++) 
    for(j=0;j<125;j++) 
      out->score[i][j] = Probability2Score(cm->prob[i][j]);
  
  return out;
}

%func
Builds a probability matrix
  No codon bias
  No errors
N codons score 1.0, stop codons probability 0.00001
%%
CodonMatrix * naive_CodonMatrix(CodonTable * ct,CompProb * comp)
{
  int i;
  int j;
  CodonMatrix * out;


  out = CodonMatrix_alloc();

  for(i=0;i<125;i++)
    for(j=i;j<125;j++) {

      if( has_random_bases(i) == TRUE || has_random_bases(j) == TRUE ) {
	out->prob[i][j] = out->prob[j][i] = 1.0;
      } else if ( is_stop_codon(i,ct) == TRUE || is_stop_codon(j,ct) == TRUE ) {	
	out->prob[i][j] = out->prob[j][i] = 0.00001;
      } else { 
	out->prob[i][j] = out->prob[j][i] = comp->comp[aminoacid_no_from_codon(ct,i)][aminoacid_no_from_codon(ct,j)];
      }
    }
    

  return out;
}


%func
Builds a codon matrix from CompMat which assummes:
  No codon Bias
  No errors
N codons score 0, stop codons score ??
%arg
ct CodonTable for codon->aa mapping
comp Comparison matrix for the score of the individual access
%%
CodonMatrixScore * naive_CodonMatrixScore(CodonTable * ct,CompMat * comp)
{
  int i;
  int j;
  CodonMatrixScore * out;


  out = CodonMatrixScore_alloc();

  for(i=0;i<125;i++)
    for(j=i;j<125;j++) {
      if( has_random_bases(i) == TRUE || has_random_bases(j) == TRUE ) 
	out->score[i][j] = out->score[j][i] = 0;
      else 
	out->score[i][j] = out->score[j][i] = fail_safe_CompMat_access(comp,aminoacid_no_from_codon(ct,i),aminoacid_no_from_codon(ct,j));
    }

  return out;
}


%func
Shows a codonmatrix
%%
void show_CodonMatrixScore(CodonMatrixScore * cms,CodonTable * ct,FILE * ofp)
{
  int i;
  int j;

  for(i=0;i<125;i++) 
    for(j=0;j<125;j++) {
      fprintf(ofp,"%5d %c :%5d %c Score %5d\n",i,aminoacid_from_codon(ct,i),j,aminoacid_from_codon(ct,j),cms->score[i][j]);
    }

}