%{
#include "dyna.h"

typedef enum NMaskType {
  NMaskType_BASE,
  NMaskType_VARIABLE,
  NMaskType_EXCLUDED,
  NMaskType_BANNED
} NMaskType;

#define DnaMatrix_MATCH(mat,one,two) (mat->score[one][two])

%}

struct DnaProbMatrix
Probability prob[5][5]

struct DnaMatrix 
Score score[5][5]

api
object DnaMatrix
des free_DnaMatrix
endobject
object DnaProbMatrix
des free_DnaProbMatrix
func flat_null_DnaProbMatrix
endobject
func identity_DnaMatrix
func DnaProbMatrix_from_match
func DnaMatrix_from_DnaProbMatrix
endapi


%{
#include "dnamatrix.h"

%func
Makes a probability matrix from simple match/mismatch 
probabilities.

%%
DnaProbMatrix * DnaProbMatrix_from_match(Probability match,int nmask_type)
{
  int i,j;
  DnaProbMatrix * out;
  Probability factor;

  switch (nmask_type ) {
  case NMaskType_BASE :
    factor = ((1.0 - match)/4.0);
    break;
  case NMaskType_VARIABLE :
  case NMaskType_EXCLUDED :
  case NMaskType_BANNED :
    factor = ((1.0 - match)/3.0);
    break;
  default :
    warn("No valid mask type. Ugh!");
    return NULL;
  }

    

  out = DnaProbMatrix_alloc();
  
  for(i=0;i<4;i++) {
    for(j=0;j<4;j++) {
      if( i == j ) {
	out->prob[i][j]  = match;
      } else {
	out->prob[i][j] = factor;
      }
    }
  }

  for(i=0;i<5;i++) {
    switch (nmask_type ) {
    case NMaskType_BASE :
      if( i == BASE_N ) {
	out->prob[i][i]  = match;
      } else {
	out->prob[BASE_N][i] = out->prob[i][BASE_N] = factor;
      }
      break;
    case NMaskType_VARIABLE :
      if( i == BASE_N ) {
	out->prob[i][i]  = 0.25;
      } else {
	out->prob[BASE_N][i] = out->prob[i][BASE_N] = 0.25;
      }
      break;

    case NMaskType_EXCLUDED :
      if( i == BASE_N ) {
	out->prob[i][i]  = 1.0;
      } else {
	out->prob[BASE_N][i] = out->prob[i][BASE_N] = 0.0;
      }
      break;
    case NMaskType_BANNED :
      out->prob[BASE_N][i] = out->prob[i][BASE_N] = 0.0;      
      break;
    default :
      warn("No valid mask type. Ugh! Shouldn't be here. A BAD  BAD bug!!!");
    }

  }

  return out;

}

%func
makes a odds of dpm via a 0.25 factor 
into each base.
%%
void flat_null_DnaProbMatrix(DnaProbMatrix * dpm)
{
  int i,j;

  for(i=0;i<4;i++) {
    for(j=0;j<4;j++) {
      dpm->prob[i][j] = dpm->prob[i][j]/0.25;
    }
  }

  return;
}
  
    
%func
Maps probabilities to scores
%%
DnaMatrix * DnaMatrix_from_DnaProbMatrix(DnaProbMatrix * dpm)
{
  int i,j;
  DnaMatrix * out;
  
  out = DnaMatrix_alloc();
  for(i=0;i<5;i++) 
    for(j=0;j<5;j++) 
      out->score[i][j] = Probability2Score(dpm->prob[i][j]);

  return out;
}

%func
Simple view of DnaMatrix
%%
void show_DnaMatrix(DnaMatrix * dcm,FILE * ofp)
{
  int i,j;

  for(i=0;i<5;i++) {
    for(j=0;j<5;j++) {
      fprintf(ofp,"%c %c - %d\n",char_from_base(i),char_from_base(j),dcm->score[i][j]);
    }
  }
}

%func
Simple view of DnaProbMatrix
%%
void show_DnaProbMatrix(DnaProbMatrix * dpm,FILE * ofp)
{
  int i,j;

  for(i=0;i<5;i++) {
    for(j=0;j<5;j++) {
      fprintf(ofp,"%c %c - %g\n",char_from_base(i),char_from_base(j),dpm->prob[i][j]);
    }
  }
}


%func
Run-time checked that one and two are ok to pass
into dm as bases

%arg
dm DnaMatrix to get score from
one base of one sequence
two base of the other sequence
%%
Score fail_safe_DnaMatrix_access(DnaMatrix * dm,base one,base two)
{
  if( dm == NULL) {
    warn("Passing in a NULL dna matrix into fail_safe_DnaMatrix_access, can't get a score therefore");
    return 0;
  }

  if( one < 0 || one > 4 || two < 0 || two > 4 ) {
    warn("In fail safe DnaMatrix access, trying to access a position [%d][%d] where this is meant to be 0-4",one,two);
    return 0;
  }

  return dm->score[one][two];
}

%func 
makes an idenity matrix wth id_score on the leading
diagonal and mismatch elsewhere.

%arg
id_score score of idenities
mismatch score of mistmatches
%%
DnaMatrix * identity_DnaMatrix(Score id_score,Score mismatch)
{
  DnaMatrix * out;
  int i;
  int j;

  out = DnaMatrix_alloc();

  for(i=0;i<4;i++)
    for(j=i;j<4;j++) {
      if( i == j ) 
	out->score[i][j] = id_score;
      else 
	out->score[i][j] = out->score[j][i] = mismatch;
    }
  
  for(i=0;i<4;i++) {
    out->score[i][4] = out->score[4][i] = 0;
  }
  out->score[4][4] = 0;

  return out;
}

%}