void __show_regs(struct pt_regs *regs)
{
int i, top_reg;
u64 lr, sp;
if (compat_user_mode(regs)) {
lr = regs->compat_lr;
sp = regs->compat_sp;
top_reg = 12;
} else {
lr = regs->regs[30];
sp = regs->sp;
top_reg = 29;
}
show_regs_print_info(KERN_DEFAULT);
print_pstate(regs);
if (!user_mode(regs)) {
printk("pc : %pS\n", (void *)regs->pc);
printk("lr : %pS\n", (void *)lr);
} else {
printk("pc : %016llx\n", regs->pc);
printk("lr : %016llx\n", lr);
}
printk("sp : %016llx\n", sp);
if (system_uses_irq_prio_masking())
printk("pmr_save: %08llx\n", regs->pmr_save);
i = top_reg;
while (i >= 0) {
printk("x%-2d: %016llx ", i, regs->regs[i]);
i--;
if (i % 2 == 0) {
pr_cont("x%-2d: %016llx ", i, regs->regs[i]);
i--;
}
pr_cont("\n");
}
}
static cell * pviterbi_propagate_step (pmodel *mo, psequence * X, psequence * Y,
cell * start, cell * stop,
double * log_p,
plocal_propagate_store_t * pv) {
#define CUR_PROC "pviterbi_step"
/* printf("---- propagate step -----\n"); */
int u, v, j, i;
double value, max_value, previous_prob;
/* int len_path = mo->N*len; the length of the path is not known apriori */
int start_x, start_y, stop_x, stop_y;
double log_b_i, log_in_a_ij;
cell * middle = NULL;
int middle_x;
double (*log_in_a)(plocal_propagate_store_t*, int, int, psequence*,
psequence*, int, int);
log_in_a = &sget_log_in_a_prop;
init_start_stop(start, stop, X, Y, &start_x, &start_y, &stop_x, &stop_y);
middle_x = start_x + (stop_x - start_x) / 2;
/* if (mo->model_type == kSilentStates && */
/* mo->silent != NULL && */
/* mo->topo_order == NULL) { */
/* model_topo_ordering( mo ); */
/* } */
init_phi_prop(pv, X, Y, start, stop);
#ifdef DEBUG
if (start != NULL && mo->s[start->state].offset_y == 0) {
for (u = 0; u<=mo->max_offset_x; u++) {
printf("row %i of phi\n", u);
for (v = start_y - 1; v < stop_y; v++) {
printf("phi(0, %i, %i): %f, ", v, start->state, get_phi_prop(pv, 0, v, 0, 0, start->state));
}
printf("\n\n");
}
}
#endif
/* u, v > 0 */
/** THIS IS THE MAIN RECURRENCE **/
/* printf("Main loop x from %i to %i and y from %i to %i\n",
start_x + mo->max_offset_x + 1, stop_x, start_y, stop_y);*/
for (u = start_x + mo->max_offset_x + 1; u < stop_x; u++) {
for (v = start_y - mo->max_offset_y; v < stop_y; v++) {
for (j = 0; j < mo->N; j++)
{
/** initialization of phi (lookback matrix) **/
set_phi_prop(pv, u, v, j, +1);
set_end_of_first(pv, 0, v, j, NULL);
}
for (i = 0; i < mo->N; i++) {
/* Determine the maximum */
/* max_phi = phi[i] + log_in_a[j][i] ... */
if ( mo->model_type != kSilentStates || !mo->silent[i] ) {
max_value = -DBL_MAX;
set_end_of_first(pv, 0, v, i, NULL);
for (j = 0; j < mo->s[i].in_states; j++) {
/* look back in the phi matrix at the offsets */
previous_prob = get_phi_prop(pv, u, v, mo->s[i].offset_x,
mo->s[i].offset_y, mo->s[i].in_id[j]);
log_in_a_ij = (*log_in_a)(pv, i, j, X, Y, u, v);
if ( previous_prob != +1 &&
log_in_a_ij != +1) {
value = previous_prob + log_in_a_ij;
if (value > max_value) {
max_value = value;
/* Critical point for the propagate algorithm if we are at the
middle point of sequence X store this at the end point of
the first alignment */
if (u - middle_x < mo->s[i].offset_x && u - middle_x >= 0) {
cell * end_of_first = init_cell(u - (mo->s[i].offset_x - 1),
v - (mo->s[i].offset_y - 1),
i, mo->s[i].in_id[j],
previous_prob,
log_in_a_ij);
if (get_end_of_first(pv, u, v, 0, 0, i) != NULL) {
cell * old = get_end_of_first(pv, u, v, 0, 0, i);
m_free(old);
}
set_end_of_first(pv, u, v, i, end_of_first);
}
else {
/* at all other points simply propagate the values on */
set_end_of_first(pv, u, v, i, get_end_of_first(pv, u, v,
mo->s[i].offset_x,
mo->s[i].offset_y,
mo->s[i].in_id[j]));
}
}
}
else
{;} /* fprintf(stderr, " %d --> %d = %f, \n", i,i,v->log_in_a[i][i]); */
}
#ifdef DEBUG
int emission = pair(get_char_psequence(X, mo->s[i].alphabet, u),
get_char_psequence(Y, mo->s[i].alphabet, v),
mo->size_of_alphabet[mo->s[i].alphabet],
mo->s[i].offset_x, mo->s[i].offset_y);
if (emission > emission_table_size(mo, i)){
printf("State %i\n", i);
print_pstate(&(mo->s[i]));
printf("charX: %i charY: %i alphabet size: %i emission table: %i emission index: %i\n",
get_char_psequence(X, mo->s[i].alphabet, u),
get_char_psequence(Y, mo->s[i].alphabet, v),
mo->size_of_alphabet[mo->s[i].alphabet],
emission_table_size(mo, i), emission);
}
#endif
log_b_i = log_b_prop(pv, i, pair(get_char_psequence(X, mo->s[i].alphabet, u),
get_char_psequence(Y, mo->s[i].alphabet, v),
mo->size_of_alphabet[mo->s[i].alphabet],
mo->s[i].offset_x, mo->s[i].offset_y));
/* No maximum found (that is, state never reached)
or the output O[t] = 0.0: */
if (max_value == -DBL_MAX ||/* and then also: (v->psi[t][j] == -1) */
log_b_i == +1 ) {
set_phi_prop(pv, u, v, i, 1);
}
else
set_phi_prop(pv, u, v, i, max_value + log_b_i);
}
} /* complete time step for emitting states */
/* last_osc = osc; */ /* save last transition class */
/*if ( mo->model_type == kSilentStates ) {
p__viterbi_silent( mo, t, v );
}*/ /* complete time step for silent states */
/**************
for (j = 0; j < mo->N; j++)
{
printf("\npsi[%d],in:%d, phi=%f\n", t, v->psi[t][j], v->phi[j]);
}
for (i = 0; i < mo->N; i++){
printf("%d\t", former_matchcount[i]);
}
for (i = 0; i < mo->N; i++){
printf("%d\t", recent_matchcount[i]);
}
****************/
} /* End for v in Y */
/* Next character in X */
/* push back the old phi values */
push_back_phi_prop(pv, Y->length);
} /* End for u in X */
/* Termination */
max_value = -DBL_MAX;
/* for the last segment search for the maximum probability at the end of the
two sequences */
if (stop == NULL){
for (j = 0; j < mo->N; j++){
#ifdef DEBUG
/* printf("phi(len_x)(len_y)(%i)=%f\n", j, pv->phi[0][stop_y-1][j]);
print_cell(pv->end_of_first[0][stop_y - 1][j]); */
#endif
if ( get_phi_prop(pv, stop_x - 1, stop_y - 1, 0, 0, j) != +1 &&
get_phi_prop(pv, stop_x - 1, stop_y - 1, 0, 0, j) > max_value) {
max_value = get_phi_prop(pv, stop_x - 1, stop_y - 1, 0, 0, j);
middle = get_end_of_first(pv, stop_x - 1, stop_y - 1, 0, 0, j);
}
}
}
/* traceback for the interior segments have to start with the previous state
of the middle beacuse the path has to be connected */
else {
if ( get_phi_prop(pv, stop_x - 1, stop_y - 1, 0, 0, stop->previous_state) != +1 ) {
max_value = get_phi_prop(pv, stop_x - 1, stop_y - 1, 0, 0, stop->previous_state);
middle = get_end_of_first(pv, stop_x - 1, stop_y - 1, 0, 0, stop->previous_state);
}
}
if (max_value == -DBL_MAX) {
/* Sequence can't be generated from the model! */
*log_p = +1;
}
else {
*log_p = max_value;
}
return middle;
#undef CUR_PROC
}
static void init_phi_prop (plocal_propagate_store_t * pv, psequence * X,
psequence * Y, cell * start, cell * stop) {
int u, v, j, i, off_x, y;
double value, max_value, previous_prob, log_b_i, log_in_a_ij ;
int start_x, start_y, stop_x, stop_y, middle_x;
pmodel * mo = pv->mo;
double (*log_in_a)(plocal_propagate_store_t*, int, int, psequence*,
psequence*, int, int);
log_in_a = &sget_log_in_a_prop;
init_start_stop(start, stop, X, Y, &start_x, &start_y, &stop_x, &stop_y);
pv->start_x = start_x;
pv->start_y = start_y;
middle_x = start_x + (stop_x - start_x) / 2;
/* to be sure that we do not look up something out of the bounds set the
whole matrix to 1 */
/* Initialize the lookback matrix (for positions [-offsetX,0], [0, len_y]*/
for (off_x=0; off_x<mo->max_offset_x + 1; off_x++)
for (y=0; y<Y->length + mo->max_offset_y + 1; y++)
for (j=0; j<mo->N; j++) {
pv->phi[off_x][y][j] = +1;
}
/* Inititalize the end_of_first matrix */
for (off_x=0; off_x<mo->max_offset_x + 1; off_x++)
for (y=0; y<Y->length + mo->max_offset_y + 1; y++)
for (j=0; j<mo->N; j++)
if (pv->end_of_first[off_x][y][j]) {
/* m_free(pv->end_of_first[off_x][y][j]); */
pv->end_of_first[off_x][y][j] = NULL;
}
if ( mo->model_type & kSilentStates ) { /* could go into silent state at t=0 */
/*p__viterbi_silent( mo, t=0, v);*/
}
/*for (j = 0; j < mo->N; j++)
{
printf("\npsi[%d],in:%d, phi=%f\n", t, v->psi[t][j], v->phi[j]);
}
for( i = 0; i < mo->N; i++){
printf("%d\t", former_matchcount[i]);
}
for (i = 0; i < mo->N; i++){
printf("%d\t", recent_matchcount[i]);
}*/
/* initialize for offsets > 1 (u < max_offset_x, v < max_offset_y) */
/* this is in principle the same as the main recurrence but adds initial
probabilities to states that cannot be inhabitated at u=0, v=0 because
of greater offsets than one */
/* u, v <= max offsets */
for (u = -1; u <= mo->max_offset_x; u++) {
for (v = start_y - mo->max_offset_y; v < stop_y; v++) {
for (j = 0; j < mo->N; j++)
{
/** initialization of phi (lookback matrix) **/
set_phi_prop(pv, u, v, j, 1);
/** traceback for the propagate algorithm **/
set_end_of_first(pv, u, v, j, NULL);
}
for (i = 0; i < mo->N; i++) {
/* Determine the maximum */
/* max_phi = phi[i] + log_in_a[j][i] ... */
if ( mo->model_type != kSilentStates || !mo->silent[i] ) {
max_value = -DBL_MAX;
set_end_of_first(pv, u, v, i, NULL);
for (j = 0; j < mo->s[i].in_states; j++) {
/* look back in the phi matrix at the offsets */
previous_prob = get_phi_prop(pv, u, v, mo->s[i].offset_x,
mo->s[i].offset_y, mo->s[i].in_id[j]);
log_in_a_ij = (*log_in_a)(pv, i, j, X, Y, u, v);
if ( previous_prob != +1 && log_in_a_ij != +1) {
value = previous_prob + log_in_a_ij;
if (value > max_value) {
max_value = value;
/* Critical point for the propagate algorithm if we are at the
middle point of sequence X store this at the end point of
the first alignment */
if (u - middle_x < mo->s[i].offset_x && u - middle_x >= 0) {
cell * end_of_first = init_cell(u - (mo->s[i].offset_x - 1),
v - (mo->s[i].offset_y - 1),
i, mo->s[i].in_id[j],
previous_prob,
log_in_a_ij);
if (get_end_of_first(pv, u, v, 0, 0, i) != NULL) {
cell * old = get_end_of_first(pv, u, v, 0, 0, i);
m_free(old);
}
set_end_of_first(pv, u, v, i, end_of_first);
}
else {
/* at all other points simply propagate the values on */
set_end_of_first(pv, u, v, i, get_end_of_first(pv, u, v,
mo->s[i].offset_x,
mo->s[i].offset_y,
mo->s[i].in_id[j]));
}
}
}
else
{;} /* fprintf(stderr, " %d --> %d = %f, \n", i,i,v->log_in_a[i][i]); */
}
#ifdef DEBUG
int emission = pair(get_char_psequence(X, mo->s[i].alphabet, u + start_x),
get_char_psequence(Y, mo->s[i].alphabet, v),
mo->size_of_alphabet[mo->s[i].alphabet],
mo->s[i].offset_x, mo->s[i].offset_y);
if (emission > emission_table_size(mo, i)){
printf("State %i\n", i);
print_pstate(&(mo->s[i]));
printf("charX: %i charY: %i alphabet size: %i emission table: %i emission index: %i\n",
get_char_psequence(X, mo->s[i].alphabet, u),
get_char_psequence(Y, mo->s[i].alphabet, v),
mo->size_of_alphabet[mo->s[i].alphabet],
emission_table_size(mo, i), emission);
}
#endif
log_b_i = log_b_prop(pv, i, pair(get_char_psequence(X,
mo->s[i].alphabet,
u + start_x),
get_char_psequence(Y,
mo->s[i].alphabet,
v),
mo->size_of_alphabet[mo->s[i].alphabet],
mo->s[i].offset_x, mo->s[i].offset_y));
/* this is the difference from the main loop:
check whether this state could be an initial state and add the
initial probability */
if (log_b_i == +1 ) {
set_phi_prop(pv, u, v, i, +1);
}
else {
if (max_value == -DBL_MAX)
set_phi_prop(pv, u, v, i, +1);
else
set_phi_prop(pv, u, v, i, max_value);
/* if (mo->s[i].pi != 0 && mo->s[i].offset_x - 1 == u &&
mo->s[i].offset_y - 1 + start_y == v) { */
if (mo->s[i].log_pi != 1 && mo->s[i].offset_x - 1 == u &&
mo->s[i].offset_y - 1 + start_y == v){
set_phi_prop(pv, u, v, i, mo->s[i].log_pi);
#ifdef DEBUG
printf("Initial log prob state %i at (%i, %i) = %f\n", i, start_x + u, v, get_phi_prop(pv, u, v, 0, 0, i));
printf("Characters emitted X: %i, Y: %i\n",
get_char_psequence(X, mo->s[i].alphabet, u + start_x),
get_char_psequence(Y, mo->s[i].alphabet, v));
#endif
}
if (get_phi_prop(pv, u, v, 0, 0, i) != 1) {
set_phi_prop(pv, u, v, i, get_phi_prop(pv, u, v, 0, 0, i) + log_b_i);
}
}
}
} /* complete time step for emitting states */
/* last_osc = osc; */ /* save last transition class */
/*if ( mo->model_type == kSilentStates ) {
p__viterbi_silent( mo, t, v );
}*/ /* complete time step for silent states */
/**************
for (j = 0; j < mo->N; j++)
{
printf("\npsi[%d],in:%d, phi=%f\n", t, v->psi[t][j], v->phi[j]);
}
for (i = 0; i < mo->N; i++){
printf("%d\t", former_matchcount[i]);
}
for (i = 0; i < mo->N; i++){
printf("%d\t", recent_matchcount[i]);
}
****************/
} /* End for v in Y */
/* Next character in X */
/* push back the old phi values */
push_back_phi_prop(pv, Y->length);
#ifdef DEBUG
if (start != NULL && mo->s[start->state].offset_y == 0) {
max_value = -DBL_MAX;
i = -1;
y = -1;
off_x = -1;
int x;
for (x = 0; x<=mo->max_offset_x; x++)
for (v = - mo->max_offset_y; v<Y->length; v++) {
for (j=0; j<mo->N; j++) {
if (get_phi_prop(pv, x, v, x, 0, j) >= max_value &&
get_phi_prop(pv, x, v, x, 0, j) < 1 - PROP_EPS) {
max_value = get_phi_prop(pv, x, v, x, 0, j);
i = j;
off_x = x;
y = v;
}
}
}
printf("u = %i start_x = %i off_x = %i ", u, start_x, off_x);
printf("max log prob state %i at (%i, %i) = %f after pushback\n",
i, start_x + u - (off_x - 1), y, get_phi_prop(pv, u, y, off_x, 0, i));
}
#endif
} /* End for u in X */
}
