Dp_Result * make_fast_dp_pair_wise (Alignment *A,int*ns, int **l_s, Constraint_list *CL,Dp_Model *M)
{
/*SIZE VARIABLES*/
int ndiag;
int l0, l1, len_al,len_diag;
static int max_len_al, max_len_diag;
static int mI, mJ;
/*EVALUATION*/
int **mat;
int a1, a2;
/*DP VARIABLES*/
static int *Mat, *LMat, *trace;
int a, i, j,l;
int state, cur_state, prev_state;
int pos_i, pos_j;
int last_i=0, last_j=0;
int prev_i, prev_j;
int len_i, len_j, len;
int t, e, em;
int prev_score;
int pc, best_pc;
int *prev;
int model_index;
/*TRACEBACK*/
Dp_Result *DPR;
int k=0, next_k;
int new_i, new_j;
ndiag=M->diag[0];
l0=strlen (A->seq_al[l_s[0][0]]);
l1=strlen (A->seq_al[l_s[1][0]]);
len_al =l0+l1+1;
len_diag=ndiag+4;
if ( (len_al>max_len_al || len_diag>max_len_diag))
{
vfree (Mat);
vfree (LMat);
vfree(trace);
max_len_diag=max_len_al=0;
}
if (max_len_al==0)
{
max_len_al=len_al;
max_len_diag=len_diag;
mI=max_len_al*max_len_diag;
mJ=max_len_diag;
Mat =vcalloc ( M->nstate*max_len_al*max_len_diag, sizeof (int));
LMat =vcalloc ( M->nstate*max_len_al*max_len_diag, sizeof (int));
trace=vcalloc ( M->nstate*max_len_al*max_len_diag, sizeof (int));
}
prev=vcalloc ( M->nstate, sizeof (int));
DPR=vcalloc ( 1, sizeof ( Dp_Result));
DPR->traceback=vcalloc (max_len_al, sizeof (int));
/*PREPARE THE EVALUATION*/
if (ns[0]+ns[1]>2)
{
fprintf ( stderr, "\nERROR: function make_fasta_cdna_pair_wise can only handle two sequences at a time [FATAL:%s]",PROGRAM);
crash ("");
}
mat=CL->M;
/*INITIALIZATION OF THE DP MATRICES*/
for (i=0; i<=l0;i++)
{
for (j=0; j<=ndiag;j++)
{
for ( state=0; state<M->nstate; state++)
{
Mat [state*mI+i*mJ+j]=UNDEFINED;
LMat [state*mI+i*mJ+j]=UNDEFINED;
trace [state*mI+i*mJ+j]=M->START;
}
}
}
M->diag[0]=0;
for (i=0; i<=l0; i++)
for ( j=0; j<=ndiag; j++)
{
pos_j=M->diag[j]-l0+i;
pos_i=i;
if (!(pos_j==0 || pos_i==0))continue;
if ( pos_j<0 || pos_i<0)continue;
if ( pos_i==0 && pos_j==0)
{
for ( a=0; a< M->nstate; a++)
{
Mat [a*mI+i*mJ+j]=0;
LMat [a*mI+i*mJ+j]=0;
trace[a*mI+i*mJ+j]=M->START;
}
}
else
{
l=MAX(pos_i,pos_j);
for ( state=0; state<M->START; state++)
{
if (pos_j==0 && M->model_properties[state][M->LEN_J])continue;
if (pos_i==0 && M->model_properties[state][M->LEN_I])continue;
t=M->model[M->START][state];
e=M->model_properties[state][M->TERM_EMISSION];
Mat [state*mI+i*mJ+j]=t+e*l;
LMat [state*mI+i*mJ+j]=l;
trace [state*mI+i*mJ+j]=M->START;
}
}
}
/*DYNAMIC PROGRAMMING: Forward Pass*/
for (i=1; i<=l0;i++)
{
for (j=1; j<=ndiag;j++)
{
pos_j=M->diag[j]-l0+i;
pos_i=i;
if (pos_j<=0 || pos_j>l1 )continue;
last_i=i;
last_j=j;
for (cur_state=0; cur_state<M->START; cur_state++)
{
if (M->model_properties[cur_state][M->DELTA_J])
{
prev_j=j+M->model_properties[cur_state][M->DELTA_J];
prev_i=i+M->model_properties[cur_state][M->DELTA_I]*FABS((M->diag[j]-M->diag[prev_j]));
}
else
{
prev_j=j;
prev_i=i+M->model_properties[cur_state][M->DELTA_I];
}
len_i=FABS((i-prev_i));
len_j=FABS((M->diag[prev_j]-M->diag[j]));
len=MAX(len_i, len_j);
a1=A->seq_al[M->model_properties[cur_state][M->F0] ][pos_i-1];
a2=A->seq_al[M->model_properties[cur_state][M->F1]+3][pos_j-1];
if (M->model_properties[cur_state][M->TYPE]==M->CODING0)
{
if ( a1=='o' || a2=='o')em=-(mat['w'-'A']['w'-'A'])*SCORE_K;
else if (a1=='x' || a2=='x')em=UNDEFINED;
else if ( a1==0 || a2==0)exit (0);
else
{
em=(mat[a1-'A'][a2-'A'])*SCORE_K;
}
}
else
{
em=M->model_properties[cur_state][M->EMISSION];
}
for (pc=best_pc=UNDEFINED, model_index=1; model_index<=M->bounded_model[cur_state][0]; model_index++)
{
prev_state=M->bounded_model[cur_state][model_index];
if(prev_i<0 || prev_j<0 ||prev_i>l0 || prev_j>ndiag || len==UNDEFINED)prev_score=UNDEFINED;
else prev_score=Mat[prev_state*mI+prev_i*mJ+prev_j];
t=M->model[prev_state][cur_state];
e=em;
if (prev_score==UNDEFINED || len==UNDEFINED)e=UNDEFINED;
else if (len==0|| e==UNDEFINED)e=UNDEFINED;
else e=e*len;
if (is_defined_int(3,prev_score,e, t))
{
pc=prev_score+t+e;
}
else pc=UNDEFINED;
/*Identify the best previous score*/
if (best_pc==UNDEFINED || (pc>best_pc && pc!=UNDEFINED))
{
prev[cur_state]=prev_state;
best_pc=pc;
}
}
Mat[cur_state*mI+i*mJ+j]=best_pc;
if ( Mat[cur_state*mI+i*mJ+j]==UNDEFINED)
{
LMat[cur_state*mI+i*mJ+j]=UNDEFINED;
trace[cur_state*mI+i*mJ+j]=UNDEFINED;
continue;
}
else if ( prev[cur_state]==cur_state)
{
LMat [cur_state*mI+i*mJ+j]= LMat [cur_state*mI+prev_i*mJ+prev_j]+len;
trace[cur_state*mI+i*mJ+j]= trace[cur_state*mI+prev_i*mJ+prev_j];
}
else
{
LMat[cur_state*mI+i*mJ+j]=len;
trace[cur_state*mI+i*mJ+j]=prev[cur_state];
}
}
}
}
i=last_i;
j=last_j;
for (pc=best_pc=UNDEFINED, state=0; state<M->START; state++)
{
t=M->model[state][M->END];
e=M->model_properties[state][M->TERM_EMISSION];
l=LMat[state*mI+i*mJ+j];
if (!is_defined_int(4,t,e,Mat[state*mI+i*mJ+j],l))Mat[state*mI+i*mJ+j]=UNDEFINED;
else Mat[state*mI+i*mJ+j]+=t+e*(l);
pc=Mat[state*mI+i*mJ+j];
if (best_pc==UNDEFINED || (pc>best_pc && pc!=UNDEFINED))
{
k=state;
best_pc=pc;
}
}
DPR->score=best_pc;
/*TRACEBACK*/
e=0;
len=0;
while (k!=M->START)
{
next_k=trace[k*mI+i*mJ+j];
new_i=i;
new_j=j;
l=LMat[k*mI+i*mJ+j];
for (a=0; a< l; a++)
{
DPR->traceback[len++]=k;
}
new_i+=M->model_properties[k][M->DELTA_I]*l;
if ( M->model_properties[k][M->DELTA_J])
{
while ( next_k!=M->START && FABS((M->diag[j]-M->diag[new_j]))!=l)new_j+=M->model_properties[k][M->DELTA_J];
}
i=new_i;
j=new_j;
k=next_k;
}
DPR->len=len;
DPR->traceback[DPR->len++]=M->START;
invert_list_int (DPR->traceback,DPR->len);
DPR->traceback[DPR->len]=M->END;
vfree (prev);
return DPR;
}
Dp_Result * make_fast_generic_dp_pair_wise (Alignment *A, int*ns, int **l_s,Dp_Model *M)
{
/*SIZE VARIABLES*/
int ndiag;
int l0, l1, len_al,len_diag;
static int max_len_al, max_len_diag;
static int mI, mJ;
/*Evaluation*/
int **pos0;
/*DP VARIABLES*/
static int *Mat, *LMat, *trace;
int a, i, j,l;
int state, cur_state, prev_state;
int pos_i=0, pos_j=0;
int last_i=0, last_j=0;
int prev_i, prev_j;
int len_i, len_j, len;
int t, e, em;
int prev_score;
int pc, best_pc;
int *prev;
int model_index;
/*TRACEBACK*/
Dp_Result *DPR;
int k=0, next_k;
int new_i, new_j;
/*Cleqanning CALL*/
if ( A==NULL)
{
max_len_al=0; max_len_diag=0;mI=0;mJ=0;
vfree (Mat); vfree(LMat);vfree(trace);
Mat=trace=LMat=NULL;
return NULL;
}
ndiag=M->diag[0];
l0=strlen (A->seq_al[l_s[0][0]]);
l1=strlen (A->seq_al[l_s[1][0]]);
len_al =l0+l1+1;
len_diag=ndiag+4;
if ( (len_al>max_len_al || len_diag>max_len_diag))
{
vfree (Mat);
vfree (LMat);
vfree(trace);
max_len_diag=max_len_al=0;
}
if (max_len_al==0)
{
max_len_al=len_al;
max_len_diag=len_diag;
mI=max_len_al*max_len_diag;
mJ=max_len_diag;
Mat =(int*)vcalloc ( M->nstate*max_len_al*max_len_diag, sizeof (int));
LMat =(int*)vcalloc ( M->nstate*max_len_al*max_len_diag, sizeof (int));
trace=(int*)vcalloc ( M->nstate*max_len_al*max_len_diag, sizeof (int));
}
prev=(int*)vcalloc ( M->nstate, sizeof (int));
DPR=( Dp_Result*)vcalloc ( 1, sizeof ( Dp_Result));
DPR->traceback=(int*)vcalloc (max_len_al, sizeof (int));
/*PREPARE THE EVALUATION*/
pos0=aln2pos_simple ( A,-1, ns, l_s);
/*INITIALIZATION OF THE DP MATRICES*/
for (i=0; i<=l0;i++)
{
for (j=0; j<=ndiag+1;j++)
{
for ( state=0; state<M->nstate; state++)
{
Mat [state*mI+i*mJ+j]=UNDEFINED;
LMat [state*mI+i*mJ+j]=UNDEFINED;
trace [state*mI+i*mJ+j]=M->START;
}
}
}
M->diag[0]=1;
M->diag[ndiag+1]=M->diag[ndiag];
for (i=0; i<=l0; i++)
for ( j=0; j<=ndiag+1; j++)
{
pos_j=M->diag[j]-l0+i;
pos_i=i;
if (!(pos_j==0 || pos_i==0))continue;
if ( pos_j<0 || pos_i<0)continue;
if ( pos_i==0 && pos_j==0)
{
for ( a=0; a< M->nstate; a++)
{
Mat [a*mI+i*mJ+j]=0;
LMat [a*mI+i*mJ+j]=0;
trace[a*mI+i*mJ+j]=M->START;
}
}
else
{
l=MAX(pos_i,pos_j);
for ( state=0; state<M->START; state++)
{
if (pos_j==0 && M->model_properties[state][M->LEN_J])continue;
if (pos_i==0 && M->model_properties[state][M->LEN_I])continue;
t=M->model[M->START][state];
e=((M->model_emission_function)[state][M->START_EMISSION])(A, pos0, ns[0], l_s[0], pos_i-1, pos0, ns[1], l_s[1],pos_j-1,M->CL);
/*e=((M->get_dp_cost_list)[M->model_properties[state][M->START_EMISSION]])(A, pos0, ns[0], l_s[0], pos_i-1, pos0, ns[1], l_s[1],pos_j-1,M->CL);*/
Mat [state*mI+i*mJ+j]=t+e*l;
LMat [state*mI+i*mJ+j]=l;
trace [state*mI+i*mJ+j]=M->START;
}
}
}
/*DYNAMIC PROGRAMMING: Forward Pass*/
/*Diagonals:
M->diag[0]=Number of diagonals being considered
M->diag[1]=First diagonal being considered
Diagonals are numbered 1...L0+l1-1
1 is the bottom-left diag
*/
for (i=1; i<=l0;i++)
{
for (j=1; j<=ndiag;j++)
{
pos_j=M->diag[j]-l0+i;
pos_i=i;
if (pos_j<=0 || pos_j>l1 )continue;
last_i=i;
last_j=j;
for (cur_state=0; cur_state<M->START; cur_state++)
{
if (M->model_properties[cur_state][M->DELTA_J])
{
prev_j=j+M->model_properties[cur_state][M->DELTA_J];
prev_i=i+M->model_properties[cur_state][M->DELTA_I]*FABS((M->diag[j]-M->diag[prev_j]));
}
else
{
prev_j=j;
prev_i=i+M->model_properties[cur_state][M->DELTA_I];
}
len_i=FABS((i-prev_i));
len_j=FABS((M->diag[prev_j]-M->diag[j]));
len=MAX(len_i, len_j);
em=((M->model_emission_function[cur_state][M->EMISSION]))(A, pos0, ns[0], l_s[0], pos_i-1, pos0, ns[1], l_s[1],pos_j-1,M->CL);
/*em=((M->get_dp_cost_list)[M->model_properties[cur_state][M->EMISSION]])(A, pos0, ns[0], l_s[0], pos_i-1, pos0, ns[1], l_s[1],pos_j-1,M->CL);*/
for (pc=best_pc=UNDEFINED, model_index=1; model_index<=M->bounded_model[cur_state][0]; model_index++)
{
prev_state=M->bounded_model[cur_state][model_index];
if(prev_i<0 || prev_j<0 ||prev_i>l0 || prev_j>ndiag || len==UNDEFINED)prev_score=UNDEFINED;
else prev_score=Mat[prev_state*mI+prev_i*mJ+prev_j];
t=M->model[prev_state][cur_state];
e=em;
if (prev_score==UNDEFINED || len==UNDEFINED)e=UNDEFINED;
else if (len==0|| e==UNDEFINED)e=UNDEFINED;
else e=e*len;
if (is_defined_int(3,prev_score,e, t))
{
pc=prev_score+t+e;
}
else pc=UNDEFINED;
/*Identify the best previous score*/
if (best_pc==UNDEFINED || (pc>best_pc && pc!=UNDEFINED))
{
prev[cur_state]=prev_state;
best_pc=pc;
}
}
Mat[cur_state*mI+i*mJ+j]=best_pc;
if ( Mat[cur_state*mI+i*mJ+j]==UNDEFINED)
{
LMat[cur_state*mI+i*mJ+j]=UNDEFINED;
trace[cur_state*mI+i*mJ+j]=UNDEFINED;
continue;
}
else if ( prev[cur_state]==cur_state)
{
LMat [cur_state*mI+i*mJ+j]= LMat [cur_state*mI+prev_i*mJ+prev_j]+len;
trace[cur_state*mI+i*mJ+j]= trace[cur_state*mI+prev_i*mJ+prev_j];
}
else
{
LMat[cur_state*mI+i*mJ+j]=len;
trace[cur_state*mI+i*mJ+j]=prev[cur_state];
}
}
}
}
i=last_i;
j=last_j;
for (pc=best_pc=UNDEFINED, state=0; state<M->START; state++)
{
t=M->model[state][M->END];
e=( M->model_emission_function[state][M->TERM_EMISSION])(A, pos0, ns[0], l_s[0], pos_i-1, pos0, ns[1], l_s[1],pos_j-1,M->CL);
/*e=((M->get_dp_cost_list)[M->model_properties[state][M->TERM_EMISSION]])(A, pos0, ns[0], l_s[0], pos_i-1, pos0, ns[1], l_s[1],pos_j-1,M->CL);*/
l=LMat[state*mI+i*mJ+j];
if (!is_defined_int(4,t,e,Mat[state*mI+i*mJ+j],l))Mat[state*mI+i*mJ+j]=UNDEFINED;
else Mat[state*mI+i*mJ+j]+=t+e*(l);
pc=Mat[state*mI+i*mJ+j];
if (best_pc==UNDEFINED || (pc>best_pc && pc!=UNDEFINED))
{
k=state;
best_pc=pc;
}
}
DPR->score=best_pc;
/*TRACEBACK*/
e=0;
len=0;
while (k!=M->START)
{
next_k=trace[k*mI+i*mJ+j];
new_i=i;
new_j=j;
l=LMat[k*mI+i*mJ+j];
for (a=0; a< l; a++)
{
DPR->traceback[len++]=k;
}
new_i+=M->model_properties[k][M->DELTA_I]*l;
if ( M->model_properties[k][M->DELTA_J])
{
while ( next_k!=M->START && FABS((M->diag[j]-M->diag[new_j]))!=l)new_j+=M->model_properties[k][M->DELTA_J];
}
i=new_i;
j=new_j;
k=next_k;
}
DPR->len=len;
DPR->traceback[DPR->len++]=M->START;
invert_list_int (DPR->traceback,DPR->len);
DPR->traceback[DPR->len]=M->END;
vfree (prev);
free_int (pos0, -1);
return DPR;
}
