int ssec_pwaln_maln (Alignment *A, int *ns, int **ls, Constraint_list *CL)
{
static Dp_Model *M=NULL;
Dp_Result *R=NULL;
int a, ndiag;
int Sa,Sb,St, Da, Db, Dt, Ia, Ib, It;
int ala, alb, s,b;
a=0;
Sa=a++;Da=a++;Ia=a++;
Sb=a++;Db=a++;Ib=a++;
St=a++;Dt=a++;It=a++;
if ( strm (CL->matrices_list[0], "analyse"))
{
for ( a=0; a< CL->n_matrices; a++)
{
rescale_two_mat(CL->matrices_list[1],CL->matrices_list[2],1000, 100, AA_ALPHABET);
exit (0);
}
}
/*2 Prepare the Model*/
M=initialize_sseq_model(2,2,CL);
ndiag=strlen (A->seq_al[0])+strlen (A->seq_al[1])-1;
M->diag=vcalloc (ndiag+1, sizeof (int));
M->diag[0]=ndiag-1;
for ( a=1; a<=M->diag[0]; a++)M->diag[a]=a;
/*3 Prepare Sequence Presentation*/
R=make_fast_generic_dp_pair_wise(A, ns, ls, M);
ala=alb=0;
A=realloc_aln2(A,A->nseq, R->len+1);
for (b=1; b<R->len;b++)
{
if (R->traceback[b]==Sa || R->traceback[b]==Sb ||R->traceback[b]==St )
{
for (s=0; s<ns[0]; s++)
A->seq_al[ls[0][s]][b-1]=(CL->S)->seq[A->order[ls[0][s]][0]][ala];
ala++;
for (s=0; s<ns[1]; s++)
A->seq_al[ls[1][s]][b-1]=(CL->S)->seq[A->order[ls[1][s]][0]][alb];
alb++;
}
else if ( R->traceback[b]==Da || R->traceback[b]==Db ||R->traceback[b]==Dt )
{
for (s=0; s<ns[0]; s++)
A->seq_al[ls[0][s]][b-1]=(CL->S)->seq[A->order[ls[0][s]][0]][ala];
ala++;
for (s=0; s<ns[1]; s++)
A->seq_al[ls[1][s]][b-1]='-';
}
else if ( R->traceback[b]==Ia || R->traceback[b]==Ib ||R->traceback[b]==It )
{
for (s=0; s<ns[0]; s++)
A->seq_al[ls[0][s]][b-1]='-';
for (s=0; s<ns[1]; s++)
A->seq_al[ls[1][s]][b-1]=(CL->S)->seq[A->order[ls[1][s]][0]][alb];
alb++;
}
}
for (s=0; s<ns[0]; s++)
A->seq_al[ls[0][s]][b-1]='\0';
for (s=0; s<ns[1]; s++)
A->seq_al[ls[1][s]][b-1]='\0';
A->len_aln=strlen (A->seq_al[ls[0][0]]);
R->Dp_model=M;
A->Dp_result=R;
return A->score;
}
int make_fasta_gotoh_pair_wise (Alignment *A,int*ns, int **l_s,Constraint_list *CL, int *diag)
{
/*TREATMENT OF THE TERMINAL GAP PENALTIES*/
/*TG_MODE=0---> gop and gep*/
/*TG_MODE=1---> --- gep*/
/*TG_MODE=2---> --- ---*/
int TG_MODE, gop, l_gop, gep,l_gep, maximise;
/*VARIABLES FOR THE MULTIPLE SEQUENCE ALIGNMENT*/
int a, b,c,k, t;
int l1, l2,eg, ch, sub,score=0, last_i=0, last_j=0, i, delta_i, j, pos_j, ala, alb, LEN, n_diag, match1, match2;
int su, in, de, tr;
int **C, **D, **I, **trace, **pos0, **LD;
int lenal[2], len;
char *buffer, *char_buf;
char **aln, **al;
/********Prepare Penalties******/
gop=CL->gop*SCORE_K;
gep=CL->gep*SCORE_K;
TG_MODE=CL->TG_MODE;
maximise=CL->maximise;
/********************************/
n_diag=diag[0];
l1=lenal[0]=strlen (A->seq_al[l_s[0][0]]);
l2=lenal[1]=strlen (A->seq_al[l_s[1][0]]);
if ( getenv ("DEBUG_TCOFFEE"))fprintf ( stderr, "\n\tNdiag=%d%% ", (diag[0]*100)/(l1+l2));
/*diag:
diag[1..n_diag]--> flaged diagonal in order;
diag[0]=0--> first diagonal;
diag[n_diag+1]=l1+l2-1;
*/
/*numeration of the diagonals strats from the bottom right [1...l1+l2-1]*/
/*sequence s1 is vertical and seq s2 is horizontal*/
/*D contains the best Deletion in S2==>comes from diagonal N+1*/
/*I contains the best insertion in S2=> comes from diagonal N-1*/
C=declare_int (lenal[0]+lenal[1]+1, n_diag+2);
D=declare_int (lenal[0]+lenal[1]+1, n_diag+2);
LD=declare_int (lenal[0]+lenal[1]+1, n_diag+2);
I=declare_int (lenal[0]+lenal[1]+1, n_diag+2);
trace=declare_int (lenal[0]+lenal[1]+1, n_diag+2);
al=declare_char (2,lenal[0]+lenal[1]+lenal[1]+1);
len= MAX(lenal[0],lenal[1])+1;
buffer=(char*)vcalloc ( 2*len, sizeof (char));
char_buf=(char*) vcalloc (2*len, sizeof (char));
pos0=aln2pos_simple ( A,-1, ns, l_s);
C[0][0]=0;
t=(TG_MODE==0)?gop:0;
for ( j=1; j<= n_diag; j++)
{
l_gop=(TG_MODE==0)?gop:0;
l_gep=(TG_MODE==2)?0:gep;
if ( (diag[j]-lenal[0])<0 )
{
trace[0][j]=UNDEFINED;
continue;
}
C[0][j]=(diag[j]-lenal[0])*l_gep +l_gop;
D[0][j]=(diag[j]-lenal[0])*l_gep +l_gop+gop;
}
D[0][j]=D[0][j-1]+gep;
t=(TG_MODE==0)?gop:0;
for ( i=1; i<=lenal[0]; i++)
{
l_gop=(TG_MODE==0)?gop:0;
l_gep=(TG_MODE==2)?0:gep;
C[i][0]=C[i][n_diag+1]=t=t+l_gep;
I[i][0]=D[i][n_diag+1]=t+ gop;
for ( j=1; j<=n_diag; j++)
{
C[i][j]=C[i][0];
D[i][j]=I[i][j]=I[i][0];
}
for (eg=0, j=1; j<=n_diag; j++)
{
pos_j=diag[j]-lenal[0]+i;
if (pos_j<=0 || pos_j>l2 )
{
trace[i][j]=UNDEFINED;
continue;
}
sub=(CL->get_dp_cost) ( A, pos0, ns[0], l_s[0], i-1, pos0, ns[1], l_s[1],pos_j-1, CL );
/*1 identify the best insertion in S2:*/
l_gop=(i==lenal[0])?((TG_MODE==0)?gop:0):gop;
l_gep=(i==lenal[0])?((TG_MODE==2)?0:gep):gep;
len=(j==1)?0:(diag[j]-diag[j-1]);
if ( a_better_than_b(I[i][j-1], C[i][j-1]+l_gop, maximise))eg++;
else eg=1;
I[i][j]=best_of_a_b (I[i][j-1], C[i][j-1]+l_gop, maximise)+len*l_gep;
/*2 Identify the best deletion in S2*/
l_gop=(pos_j==lenal[1])?((TG_MODE==0)?gop:0):gop;
l_gep=(pos_j==lenal[1])?((TG_MODE==2)?0:gep):gep;
len=(j==n_diag)?0:(diag[j+1]-diag[j]);
delta_i=((i-len)>0)?(i-len):0;
if ( a_better_than_b(D[delta_i][j+1],C[delta_i][j+1]+l_gop, maximise)){LD[i][j]=LD[delta_i][j+1]+1;}
else {LD[i][j]=1;}
D[i][j]=best_of_a_b (D[delta_i][j+1],C[delta_i][j+1]+l_gop, maximise)+len*l_gep;
/*Identify the best way*/
/*
score=C[i][j]=best_int ( 3, maximise, &fop, I[i][j], C[i-1][j]+sub, D[i][j]);
fop-=1;
if ( fop<0)trace[i][j]=fop*eg;
else if ( fop>0 ) {trace[i][j]=fop*LD[i][j];}
else if ( fop==0) trace[i][j]=0;
*/
su=C[i-1][j]+sub;
in=I[i][j];
de=D[i][j];
/*HERE ("%d %d %d", su, in, de);*/
if (su>=in && su>=de)
{
score=su;
tr=0;
}
else if (in>=de)
{
score=in;
tr=-eg;
}
else
{
score=de;
tr=LD[i][j];
}
trace[i][j]=tr;
C[i][j]=score;
last_i=i;
last_j=j;
}
}
/*
[0][Positive]
^ ^
| /
| /
| /
| /
|/
[Neg]<-------[*]
*/
i=last_i;
j=last_j;
ala=alb=0;
match1=match2=0;
while (!(match1==l1 && match2==l2))
{
if ( match1==l1)
{
len=l2-match2;
for ( a=0; a< len; a++)
{
al[0][ala++]=0;
al[1][alb++]=1;
match2++;
}
k=0;
break;
/*k=-(j-1);*/
}
else if ( match2==l2)
{
len=l1-match1;
for ( a=0; a< len; a++)
{
al[0][ala++]=1;
al[1][alb++]=0;
match1++;
}
k=0;
break;
/*k= n_diag-j;*/
}
else
{
k=trace[i][j];
}
if ( k==0)
{
if ( match2==l2 || match1==l1);
else
{
al[0][ala++]=1;
al[1][alb++]=1;
i--;
match1++;
match2++;
}
}
else if ( k>0)
{
len=diag[j+k]-diag[j];
for ( a=0; a<len; a++)
{
if ( match1==l1)break;
al[0][ala++]=1;
al[1][alb++]=0;
match1++;
}
i-=len;
j+=k;
}
else if ( k<0)
{
k*=-1;
len=diag[j]-diag[j-k];
for ( a=0; a<len; a++)
{
if ( match2==l2)break;
al[0][ala++]=0;
al[1][alb++]=1;
match2++;
}
j-=k;
}
}
LEN=ala;
c=LEN-1;
invert_list_char ( al[0], LEN);
invert_list_char ( al[1], LEN);
if ( A->declared_len<=LEN)A=realloc_aln2 ( A,A->max_n_seq, 2*LEN);
aln=A->seq_al;
for ( c=0; c< 2; c++)
{
for ( a=0; a< ns[c]; a++)
{
ch=0;
for ( b=0; b< LEN; b++)
{
if (al[c][b]==1)
char_buf[b]=aln[l_s[c][a]][ch++];
else
char_buf[b]='-';
}
char_buf[b]='\0';
aln[l_s[c][a]]=csprintf (aln[l_s[c][a]],"%s", char_buf);
}
}
A->len_aln=LEN;
A->nseq=ns[0]+ns[1];
free_int (pos0, -1);
free_int (C, -1);
free_int (D, -1);
free_int (I, -1);
free_int (trace, -1);
free_int (LD, -1);
free_char ( al, -1);
vfree(buffer);
vfree(char_buf);
return score;
}
int make_fasta_cdna_pair_wise (Alignment *B,Alignment *A,int*in_ns, int **l_s,Constraint_list *CL, int *diag)
{
int a,c,p,k;
Dp_Result *DPR;
static Dp_Model *M;
int l0, l1;
int len_i, len_j;
int f0=0, f1=0;
int deltaf0, deltaf1, delta;
int nr1, nr2;
int ala, alb, aa0, aa1;
int type;
char **al;
int **tl_s;
int *tns;
/*DEBUG*/
int debug_cdna_fasta=0;
Alignment *DA;
int score;
int state,prev_state;
int t, e;
int a1, a2;
l0=strlen ( B->seq_al[l_s[0][0]]);
l1=strlen ( B->seq_al[l_s[1][0]]);
al=declare_char (2, l0+l1+1);
B=realloc_aln2 (B,B->nseq,l0+l1+1);
free_int (B->cdna_cache, -1);
B->cdna_cache=declare_int(1, l0+l1+1);
if ( !M)M=initialize_dna_dp_model (CL);
M->diag=diag;
tl_s=declare_int (2, 2);tns=vcalloc(2, sizeof(int));tl_s[0][0]=0;tl_s[1][0]=3;tns[0]=tns[1]=1;
DPR=make_fast_dp_pair_wise (A,tns, tl_s,CL,M);
vfree(tns);free_int(tl_s, -1);
/*new_trace_back*/
a=p=0;
aa0=aa1=ala=alb=0;
while ( (k=DPR->traceback[a++])!=M->START);
while ( (k=DPR->traceback[a++])!=M->END)
{
f0=M->model_properties[k][M->F0];
f1=M->model_properties[k][M->F1];
len_i=M->model_properties[k][M->LEN_I];
len_j=M->model_properties[k][M->LEN_J];
type=M->model_properties[k][M->TYPE];
if (type==M->CODING0)
{
deltaf0=(aa0*3+f0)-ala;
deltaf1=(aa1*3+f1)-alb;
delta=MAX(deltaf0, deltaf1);
for (nr1=0, nr2=0,c=0; c<delta; c++, nr1++, nr2++,p++)
{
if (nr1<deltaf0 && ala<l0)al[0][p]=B->seq_al[l_s[0][0]][ala++];
else al[0][p]='-';
if (nr2<deltaf1 && alb<l1)al[1][p]=B->seq_al[l_s[1][0]][alb++];
else al[1][p]='-';
B->cdna_cache[0][p]=M->NON_CODING;
if ( is_gap(al[1][p]) && is_gap(al[0][p]))p--;
else if ( debug_cdna_fasta)fprintf (stderr, "\nUM: %c %c", al[0][p], al[1][p]);
}
for ( c=0; c< 3; c++, p++)
{
if ( c==0)B->cdna_cache[0][p]=M->CODING0;
else if ( c==1)B->cdna_cache[0][p]=M->CODING1;
else if ( c==2)B->cdna_cache[0][p]=M->CODING2;
if (ala<l0)al[0][p]=B->seq_al[l_s[0][0]][ala++];
else al[0][p]='-';
if (alb<l1)al[1][p]=B->seq_al[l_s[1][0]][alb++];
else al[1][p]='-';
if ( is_gap(al[1][p]) && is_gap(al[0][p]))p--;
else if ( debug_cdna_fasta)fprintf (stderr, "\n%d: %c %c",k, al[0][p], al[1][p]);
}
}
aa0+=len_i;
aa1+=len_j;
}
deltaf0=(aa0*3+f0)-ala;
deltaf1=(aa1*3+f1)-alb;
delta=MAX(deltaf0, deltaf1);
for (nr1=0, nr2=0,c=0; c<delta; c++, nr1++, nr2++,p++)
{
if (nr1<deltaf0 && ala<l0)al[0][p]=B->seq_al[l_s[0][0]][ala++];
else al[0][p]='-';
if (nr2<deltaf1 && alb<l1)al[1][p]=B->seq_al[l_s[1][0]][alb++];
else al[1][p]='-';
B->cdna_cache[0][p]=M->NON_CODING;
if ( is_gap(al[1][p]) && is_gap(al[0][p]))p--;
else if ( debug_cdna_fasta)fprintf (stderr, "\nUM: %c %c", al[0][p], al[1][p]);
}
/*End New traceback*/
al[0][p]='\0';
al[1][p]='\0';
sprintf( B->seq_al[l_s[0][0]], "%s", al[0]);
sprintf( B->seq_al[l_s[1][0]], "%s", al[1]);
B->len_aln=strlen (al[0]);
B->nseq=2;
if ( debug_cdna_fasta)
{
fprintf ( stderr, "\nA-A=%d, %d", CL->M['a'-'A']['a'-'A'], CL->M['a'-'A']['a'-'A'] *SCORE_K);
for ( a=1; a<diag[0]; a++)
{
fprintf ( stderr, "\nchosen diag: %d", diag[a]);
}
fprintf ( stderr, "\n GOP=%d GEP=%d TG_MODE=%d", M->gop, M->gep, M->TG_MODE);
fprintf ( stderr, "\nF_GOP=%d F_GEP=%d F_TG_MODE=%d", M->gop, M->gep, M->F_TG_MODE);
DA=copy_aln (B, NULL);
DA=realloc_aln2 (DA,6,(DA->len_aln+1));
for ( a=0; a<B->len_aln; a++)
{
fprintf ( stderr, "\n%d", DA->cdna_cache[0][a]);
if (DA->cdna_cache[0][a]>=M->CODING0)DA->seq_al[DA->nseq][a]=DA->cdna_cache[0][a]-M->nstate+'0';
else DA->seq_al[DA->nseq][a]=DA->cdna_cache[0][a]-M->nstate+'0';
if (DA->cdna_cache[0][a]==M->CODING0)
{
DA->seq_al[DA->nseq+1][a]=translate_dna_codon (DA->seq_al[0]+a,'*');
DA->seq_al[DA->nseq+2][a]=translate_dna_codon (DA->seq_al[1]+a,'*');
}
else
{
DA->seq_al[DA->nseq+1][a]='-';
DA->seq_al[DA->nseq+2][a]='-';
}
}
DA->nseq+=3;
print_aln (DA);
free_aln(DA);
score=0;
for (prev_state=M->START,a=0; a< DA->len_aln;)
{
state=DA->cdna_cache[0][a];
t=M->model[prev_state][state];
if ( DA->cdna_cache[0][a]==M->CODING0)
{
a1=translate_dna_codon (A->seq_al[0]+a,'x');
a2=translate_dna_codon (A->seq_al[1]+a,'x');
if ( a1!='x' && a2!='x')
{
e=CL->M[a1-'A'][a2-'A']*SCORE_K;
}
}
else if ( DA->cdna_cache[0][a]>M->CODING0);
else
{
e=M->model_properties[B->cdna_cache[0][a]][M->EMISSION];
}
if ( e==UNDEFINED || t==UNDEFINED) fprintf ( stderr, "\nPROBLEM %d\n", a);
fprintf ( stderr, "\n[%c..%c: %d(e)+%d(t)=%d]", A->seq_al[0][a], A->seq_al[1][a], e,t,e+t);
score+=e+t;
prev_state=state;
if (B->cdna_cache[0][a]==M->NON_CODING)a++;
else a+=3;
}
}
for ( a=0; a<B->len_aln; a++)
{
if ( B->cdna_cache[0][a]<M->CODING0)B->cdna_cache[0][a]=0;
else B->cdna_cache[0][a]=1;
}
free_char ( al, -1);
return DPR->score;
}
int myers_miller_pair_wise (Alignment *A,int *ns, int **ls,Constraint_list *CL )
{
int **pos;
int a,b, i, j, l,l1, l2, len;
int *S;
char ** char_buf;
int score;
/********Prepare Penalties******/
//ns2master_ns (ns,ls, &sns,&sls);
sns=ns;
sls=ls;
/********************************/
pos=aln2pos_simple ( A,-1, ns, ls);
l1=strlen (A->seq_al[ls[0][0]]);
l2=strlen (A->seq_al[ls[1][0]]);
S=(int*)vcalloc (l1+l2+1, sizeof (int));
last=0;
sapp=S;
score=diff (A,ns, ls, 0, l1, 0, l2, 0, 0, CL, pos);
diff (NULL,ns, ls, 0, l1, 0, l2, 0, 0, CL, pos);
i=0;
j=0;
sapp=S;
len=0;
while (!(i==l1 && j==l2))
{
if (*sapp==0) {
i++;
j++;
len++;
}
else if ( *sapp<0) {
i-=*sapp;
len-=*sapp;
}
else if ( *sapp>0) {
j+=*sapp;
len+=*sapp;
}
sapp++;
}
A=realloc_aln2 ( A,A->max_n_seq,len+1);
char_buf=declare_char (A->max_n_seq,len+1);
i=0;
j=0;
sapp=S;
len=0;
while (!(i==l1 && j==l2))
{
if (*sapp==0)
{
for (b=0; b< ns[0]; b++)
char_buf[ls[0][b]][len]=A->seq_al[ls[0][b]][i];
for (b=0; b< ns[1]; b++)
char_buf[ls[1][b]][len]=A->seq_al[ls[1][b]][j];
i++;
j++;
len++;
}
else if ( *sapp>0)
{
l=*sapp;
for ( a=0; a<l; a++, j++, len++)
{
for (b=0; b< ns[0]; b++)
char_buf[ls[0][b]][len]='-';
for (b=0; b< ns[1]; b++)
char_buf[ls[1][b]][len]=A->seq_al[ls[1][b]][j];
}
}
else if ( *sapp<0)
{
l=-*sapp;
for ( a=0; a<l; a++, i++, len++)
{
for (b=0; b< ns[0]; b++)
char_buf[ls[0][b]][len]=A->seq_al[ls[0][b]][i];;
for (b=0; b< ns[1]; b++)
char_buf[ls[1][b]][len]='-';
}
}
sapp++;
}
A->len_aln=len;
A->nseq=ns[0]+ns[1];
for ( a=0; a< ns[0]; a++) {
char_buf[ls[0][a]][len]='\0';
sprintf ( A->seq_al[ls[0][a]], "%s", char_buf[ls[0][a]]);
}
for ( a=0; a< ns[1]; a++) {
char_buf[ls[1][a]][len]='\0';
sprintf ( A->seq_al[ls[1][a]], "%s", char_buf[ls[1][a]]);
}
vfree (S);
free_char ( char_buf, -1);
l1=strlen (A->seq_al[ls[0][0]]);
l2=strlen (A->seq_al[ls[1][0]]);
if ( l1!=l2) exit(1);
free_int (pos, -1);
return score;
}