int cfasta_cdna_pair_wise (Alignment *A,int*ns, int **l_s,Constraint_list *CL)
{
/*TREATMENT OF THE TERMINAL GAP PENALTIES*/
/*TG_MODE=0---> gop and gep*/
/*TG_MODE=1---> --- gep*/
/*TG_MODE=2---> --- ---*/
int maximise;
/*VARIABLES FOR THE MULTIPLE SEQUENCE ALIGNMENT*/
int **tot_diag;
int *diag;
int ktup;
static int n_groups;
static char **group_list;
int score, new_score;
int n_chosen_diag=0;
int step;
int max_n_chosen_diag;
int l0, l1;
Alignment *B;
/********Prepare Penalties******/
maximise=CL->maximise;
ktup=CL->ktup;
/********************************/
if ( !group_list)
{
group_list=make_group_aa (&n_groups, CL->matrix_for_aa_group);
}
B=dna_aln2_3frame_cdna_aln(A, ns, l_s);
l0=strlen(B->seq_al[0]);
l1=strlen(B->seq_al[3]);
tot_diag=evaluate_diagonals_cdna ( B, ns, l_s, CL, maximise,n_groups,group_list, ktup);
max_n_chosen_diag=100;
n_chosen_diag=step=10 ;
n_chosen_diag=MIN(n_chosen_diag, max_n_chosen_diag);
diag=extract_N_diag (l0,l1, tot_diag, n_chosen_diag,2);
score =make_fasta_cdna_pair_wise ( A,B, ns, l_s, CL, diag);
new_score=0;
vfree ( diag);
while (new_score!=score && n_chosen_diag< max_n_chosen_diag )
{
score=new_score;
ungap_sub_aln ( A, ns[0], l_s[0]);
ungap_sub_aln ( A, ns[1], l_s[1]);
n_chosen_diag+=step;
n_chosen_diag=MIN(n_chosen_diag, max_n_chosen_diag);
diag =extract_N_diag (l0,l1, tot_diag, n_chosen_diag,3);
new_score=make_fasta_cdna_pair_wise ( A, B,ns, l_s, CL, diag);
vfree ( diag);
}
score=new_score;
free_int (tot_diag, -1);
free_aln(B);
return score;
}
int cfasta_gotoh_pair_wise (Alignment *A,int*ns, int **l_s,Constraint_list *CL)
{
/*TREATMENT OF THE TERMINAL GAP PENALTIES*/
/*TG_MODE=0---> gop and gep*/
/*TG_MODE=1---> --- gep*/
/*TG_MODE=2---> --- ---*/
int maximise;
/*VARIABLES FOR THE MULTIPLE SEQUENCE ALIGNMENT*/
int **tot_diag;
int *diag;
int ktup;
static int n_groups;
static char **group_list;
int score, new_score;
int n_chosen_diag=20;
int step;
int max_n_chosen_diag;
int l1, l2;
/********Prepare Penalties******/
maximise=CL->maximise;
ktup=CL->ktup;
/********************************/
if ( !group_list)
{
group_list=make_group_aa (&n_groups, CL->matrix_for_aa_group);
}
l1=strlen (A->seq_al[l_s[0][0]]);
l2=strlen (A->seq_al[l_s[1][0]]);
if ( !CL->fasta_step)
{
step=MIN(l1,l2);
step=(int) log ((double)MAX(step, 1));
step=MAX(step, 20);
}
else
{
step=CL->fasta_step;
}
tot_diag=evaluate_diagonals ( A, ns, l_s, CL, maximise,n_groups,group_list, ktup);
max_n_chosen_diag=strlen (A->seq_al[l_s[0][0]])+strlen (A->seq_al[l_s[1][0]])-1;
/*max_n_chosen_diag=(int)log10((double)(l1+l2))*10;*/
n_chosen_diag+=step;
n_chosen_diag=MIN(n_chosen_diag, max_n_chosen_diag);
diag=extract_N_diag (strlen (A->seq_al[l_s[0][0]]),strlen (A->seq_al[l_s[1][0]]), tot_diag, n_chosen_diag, 0);
score =make_fasta_gotoh_pair_wise ( A, ns, l_s, CL, diag);
new_score=0;
vfree ( diag);
while (new_score!=score && n_chosen_diag< max_n_chosen_diag )
{
score=new_score;
ungap_sub_aln ( A, ns[0], l_s[0]);
ungap_sub_aln ( A, ns[1], l_s[1]);
n_chosen_diag+=step;
n_chosen_diag=MIN(n_chosen_diag, max_n_chosen_diag);
diag =extract_N_diag (strlen (A->seq_al[l_s[0][0]]),strlen (A->seq_al[l_s[1][0]]), tot_diag, n_chosen_diag, 0);
new_score=make_fasta_gotoh_pair_wise ( A, ns, l_s, CL, diag);
vfree ( diag);
}
score=new_score;
free_int (tot_diag, -1);
return score;
}
