int ghmm_dpmodel_emission_table_size(ghmm_dpmodel* mo, int state_index) {
/* the alphabet is over single sequences so get the maximal index for the
lookup of emission probabilities and use it to determine the size of
the lookup table */
int size = mo->size_of_alphabet[mo->s[state_index].alphabet];
return ghmm_dpmodel_pair(size - 1, size - 1, size, mo->s[state_index].offset_x, mo->s[state_index].offset_y) + 1;
}
/*============================================================================*/
static cell * pviterbi_propagate_step (ghmm_dpmodel *mo, ghmm_dpseq * X, ghmm_dpseq * 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, ghmm_dpseq*,
ghmm_dpseq*, 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) { */
/* ghmm_dmodel_topo_order( 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 & GHMM_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 = ghmm_dpmodel_pair(ghmm_dpseq_get_char(X, mo->s[i].alphabet, u),
ghmm_dpseq_get_char(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 > ghmm_dpmodel_emission_table_size(mo, i)){
printf("State %i\n", i);
ghmm_dpmodel_state_print(&(mo->s[i]));
printf("charX: %i charY: %i alphabet size: %i emission table: %i emission index: %i\n",
ghmm_dpseq_get_char(X, mo->s[i].alphabet, u),
ghmm_dpseq_get_char(Y, mo->s[i].alphabet, v),
mo->size_of_alphabet[mo->s[i].alphabet],
ghmm_dpmodel_emission_table_size(mo, i), emission);
}
#endif
log_b_i = log_b_prop(pv, i, ghmm_dpmodel_pair(ghmm_dpseq_get_char(X, mo->s[i].alphabet, u),
ghmm_dpseq_get_char(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]);
ghmm_dpmodel_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, ghmm_dpseq * X,
ghmm_dpseq * Y, cell * start, cell * stop) {
#define CUR_PROC "init_phi_prop"
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;
ghmm_dpmodel * mo = pv->mo;
double (*log_in_a)(plocal_propagate_store_t*, int, int, ghmm_dpseq*,
ghmm_dpseq*, 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 & GHMM_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 & GHMM_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 = ghmm_dpmodel_pair(ghmm_dpseq_get_char(X, mo->s[i].alphabet, u + start_x),
ghmm_dpseq_get_char(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 > ghmm_dpmodel_emission_table_size(mo, i)){
printf("State %i\n", i);
ghmm_dpmodel_state_print(&(mo->s[i]));
printf("charX: %i charY: %i alphabet size: %i emission table: %i emission index: %i\n",
ghmm_dpseq_get_char(X, mo->s[i].alphabet, u),
ghmm_dpseq_get_char(Y, mo->s[i].alphabet, v),
mo->size_of_alphabet[mo->s[i].alphabet],
ghmm_dpmodel_emission_table_size(mo, i), emission);
}
#endif
log_b_i = log_b_prop(pv, i, ghmm_dpmodel_pair(ghmm_dpseq_get_char(X,
mo->s[i].alphabet,
u + start_x),
ghmm_dpseq_get_char(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",
ghmm_dpseq_get_char(X, mo->s[i].alphabet, u + start_x),
ghmm_dpseq_get_char(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 */
#undef CUR_PROC
}
/*============================================================================*/
double ghmm_dpmodel_viterbi_logp(ghmm_dpmodel *mo, ghmm_dpseq * X, ghmm_dpseq * Y,
int *state_seq, int state_seq_len) {
#define CUR_PROC "ghmm_dpmodel_viterbi_logp"
int s, t, i, j, u, v;
double log_p = 0.0;
double log_b_i = 1.0;
double log_in_a = 1.0;
plocal_store_t *pv;
/* Allocate the matrices log_in_a, log_b,Vektor phi, phi_new, Matrix psi */
pv = pviterbi_alloc(mo, 0, 0);
pviterbi_precompute(mo, pv);
/* initial state */
t = 0; u = -1; v = -1;
if (state_seq_len > t) {
i = state_seq[t];
/* initial state probability */
/* log_p += log(mo->s[i].pi); */
log_p += mo->s[i].log_pi;
if (log_p == 1.0) {
pviterbi_free(&pv, mo->N, 0, 0, mo->max_offset_x, mo->max_offset_y);
fprintf(stderr, "the initial probability of state %i is zero\n", i);
return 1.0;/* the initial prob is zero */
}
/* consume the first characters of the sequences */
u += mo->s[i].offset_x;
v += mo->s[i].offset_y;
/* get the emission probability */
log_b_i = log_b(pv, i, ghmm_dpmodel_pair(ghmm_dpseq_get_char(X, mo->s[i].alphabet, u),
ghmm_dpseq_get_char(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 (log_b_i == 1.0) { /* chars cant be emitted */
pviterbi_free(&pv, mo->N, 0, 0, mo->max_offset_x, mo->max_offset_y);
fprintf(stderr, "characters (%i, %i) at position (%i, %i) cannot be emitted by state %i (t=%i)\n",
ghmm_dpseq_get_char(X, mo->s[i].alphabet, u),
ghmm_dpseq_get_char(Y, mo->s[i].alphabet, v), u, v, i, t);
return 1.0;
}
log_p += log_b_i;
}
else { /* there is no path.. */
pviterbi_free(&pv, mo->N, 0, 0, mo->max_offset_x, mo->max_offset_y);
fprintf(stderr, "No path given!\n");
return 1.0;
}
/* rest of the sequence */
for (t=1; t<state_seq_len; t++) {
j = i; /* predecessor state */
i = state_seq[t]; /* current state */
/* consume the next characters */
u += mo->s[i].offset_x;
v += mo->s[i].offset_y;
if (u >= X->length || v >= Y->length) { /* path consumes too many chars */
pviterbi_free(&pv, mo->N, 0, 0, mo->max_offset_x, mo->max_offset_y);
fprintf(stderr, "path consumes too many chars\n");
return 1.0;
}
/* transition prob state j -> i*/
log_in_a = 1.0;
for (s=0; s<mo->s[i].in_states; s++) {
if (mo->s[i].in_id[s] == j) {
log_in_a = sget_log_in_a(pv, i, s, X, Y, u, v);
break;
}
}
if (log_in_a == 1.0) {
pviterbi_free(&pv, mo->N, 0, 0, mo->max_offset_x, mo->max_offset_y);
fprintf(stderr, "transition (%i -> %i) at t=%i not possible\n", j, i,t);
return 1.0; /* transition not possible */
}
/* emission probability */
log_b_i = log_b(pv, i, ghmm_dpmodel_pair(ghmm_dpseq_get_char(X, mo->s[i].alphabet, u),
ghmm_dpseq_get_char(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 (log_b_i == 1.0) {
pviterbi_free(&pv, mo->N, 0, 0, mo->max_offset_x, mo->max_offset_y);
fprintf(stderr, "characters (%i, %i) at position (%i, %i) cannot be emitted by state %i (t=%i)\n",
ghmm_dpseq_get_char(X, mo->s[i].alphabet, u),
ghmm_dpseq_get_char(Y, mo->s[i].alphabet, v), u, v, i, t);
return 1.0; /* characters cant be emitted */
}
log_p += log_in_a + log_b_i;
}
pviterbi_free(&pv, mo->N, 0, 0, mo->max_offset_x,
mo->max_offset_y);
/* check if all of the sequences has been consumed */
if (u != X->length - 1 && v != Y->length - 1) {
fprintf(stderr, "path consumes not all characters (%i of %i, %i of %i)\n",
u + 1, X->length, v + 1, Y->length);
return 1.0;
}
return log_p;
#undef CUR_PROC
} /* ghmm_dpmodel_viterbi_logp */
/*============================================================================*/
int *ghmm_dpmodel_viterbi_variable_tb(ghmm_dpmodel *mo, ghmm_dpseq * X, ghmm_dpseq * Y,
double *log_p, int *path_length,
int start_traceback_with) {
#define CUR_PROC "ghmm_dpmodel_viterbi"
int u, v, j, i, off_x, off_y, current_state_index;
double value, max_value, previous_prob;
plocal_store_t *pv;
int *state_seq = NULL;
int emission;
double log_b_i, log_in_a_ij;
double (*log_in_a)(plocal_store_t*, int, int, ghmm_dpseq*, ghmm_dpseq*, int, int);
/* printf("---- viterbi -----\n"); */
i_list * state_list;
state_list = ighmm_list_init_list();
log_in_a = &sget_log_in_a;
/* int len_path = mo->N*len; the length of the path is not known apriori */
/* if (mo->model_type & kSilentStates && */
/* mo->silent != NULL && */
/* mo->topo_order == NULL) { */
/* ghmm_dmodel_topo_order( mo ); */
/* } */
/* Allocate the matrices log_in_a, log_b,Vektor phi, phi_new, Matrix psi */
pv = pviterbi_alloc(mo, X->length, Y->length);
if (!pv) { GHMM_LOG_QUEUED(LCONVERTED); goto STOP; }
/* Precomputing the log(a_ij) and log(bj(ot)) */
pviterbi_precompute(mo, pv);
/* Initialize the lookback matrix (for positions [-offsetX,0], [-1, len_y]*/
init_phi(pv, X, Y);
/* u > max_offset_x , v starts -1 to allow states with offset_x == 0
which corresponds to a series of gap states before reading the first
character of x at position x=0, y=v */
/** THIS IS THE MAIN RECURRENCE **/
for (u = mo->max_offset_x + 1; u < X->length; u++) {
for (v = -mo->max_offset_y; v < Y->length; v++) {
for (j = 0; j < mo->N; j++)
{
/** initialization of phi (lookback matrix), psi (traceback) **/
set_phi(pv, u, v, j, +1);
set_psi(pv, u, v, j, -1);
}
for (i = 0; i < mo->N; i++) {
/* Determine the maximum */
/* max_phi = phi[i] + log_in_a[j][i] ... */
if (!(mo->model_type & GHMM_kSilentStates) || !mo->silent[i] ) {
max_value = -DBL_MAX;
set_psi(pv, u, v, i, -1);
for (j = 0; j < mo->s[i].in_states; j++) {
/* look back in the phi matrix at the offsets */
previous_prob = get_phi(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;
set_psi(pv, u, v, i, mo->s[i].in_id[j]);
}
}
else
{;} /* fprintf(stderr, " %d --> %d = %f, \n", i,i,v->log_in_a[i][i]); */
}
emission = ghmm_dpmodel_pair(ghmm_dpseq_get_char(X, mo->s[i].alphabet, u),
ghmm_dpseq_get_char(Y, mo->s[i].alphabet, v),
mo->size_of_alphabet[mo->s[i].alphabet],
mo->s[i].offset_x, mo->s[i].offset_y);
#ifdef DEBUG
if (emission > ghmm_dpmodel_emission_table_size(mo, i)){
printf("State %i\n", i);
ghmm_dpmodel_state_print(&(mo->s[i]));
printf("charX: %i charY: %i alphabet size: %i emission table: %i emission index: %i\n",
ghmm_dpseq_get_char(X, mo->s[i].alphabet, u),
ghmm_dpseq_get_char(Y, mo->s[i].alphabet, v),
mo->size_of_alphabet[mo->s[i].alphabet],
ghmm_dpmodel_emission_table_size(mo, i), emission);
}
#endif
log_b_i = log_b(pv, i, ghmm_dpmodel_pair(ghmm_dpseq_get_char(X, mo->s[i].alphabet, u),
ghmm_dpseq_get_char(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(pv, u, v, i, +1);
}
else
set_phi(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_phi(pv, Y->length);
} /* End for u in X */
/* Termination */
max_value = -DBL_MAX;
ighmm_list_append(state_list, -1);
/* if start_traceback_with is -1 (it is by default) search for the most
likely state at the end of both sequences */
if (start_traceback_with == -1) {
for (j = 0; j < mo->N; j++){
#ifdef DEBUG
printf("phi(len_x)(len_y)(%i)=%f\n", j, get_phi(pv, u, Y->length-1, 0, 0, j));
#endif
if ( get_phi(pv, u, Y->length-1, 0, 0, j) != +1 &&
get_phi(pv, u, Y->length-1, 0, 0, j) > max_value) {
max_value = get_phi(pv, X->length-1, Y->length-1, 0, 0, j);
state_list->last->val = j;
}
}
}
/* this is the special traceback mode for the d & c algorithm that also
connects the traceback to the first state of the rest of the path */
else {
#ifdef DEBUG
printf("D & C traceback from state %i!\n", start_traceback_with);
printf("Last characters emitted X: %i, Y: %i\n",
ghmm_dpseq_get_char(X, mo->s[start_traceback_with].alphabet,
X->length-1),
ghmm_dpseq_get_char(Y, mo->s[start_traceback_with].alphabet,
Y->length-1));
for (j = 0; j < mo->N; j++){
printf("phi(len_x)(len_y)(%i)=%f\n", j, get_phi(pv, X->length-1, Y->length-1, 0, 0, j));
}
#endif
max_value = get_phi(pv, X->length-1, Y->length-1, 0, 0, start_traceback_with);
if (max_value != 1 && max_value > -DBL_MAX)
state_list->last->val = start_traceback_with;
}
if (max_value == -DBL_MAX) {
/* Sequence can't be generated from the model! */
*log_p = +1;
/* Backtracing doesn't work, because state_seq[*] allocated with -1 */
/* for (t = len - 2; t >= 0; t--)
state_list->last->val = -1; */
}
else {
/* Backtracing, should put DEL path nicely */
*log_p = max_value;
/* removed the handling of silent states here */
/* start trace back at the end of both sequences */
u = X->length - 1;
v = Y->length - 1;
current_state_index = state_list->first->val;
off_x = mo->s[current_state_index].offset_x;
off_y = mo->s[current_state_index].offset_y;
while (u - off_x >= -1 && v - off_y >= -1 && current_state_index != -1) {
/* while (u > 0 && v > 0) { */
/* look up the preceding state and save it in the first position of the
state list */
/* printf("Current state %i at (%i,%i) -> preceding state %i\n",
current_state_index, u, v, get_psi(pv, u, v, current_state_index)); */
/* update the current state */
current_state_index = get_psi(pv, u, v, current_state_index);
if (current_state_index != -1)
ighmm_list_insert(state_list, current_state_index);
/* move in the alignment matrix */
u -= off_x;
v -= off_y;
/* get the next offsets */
off_x = mo->s[current_state_index].offset_x;
off_y = mo->s[current_state_index].offset_y;
}
}
/* Free the memory space */
pviterbi_free(&pv, mo->N, X->length, Y->length, mo->max_offset_x ,
mo->max_offset_y);
/* printf("After traceback: last state = %i\n", state_list->last->val); */
state_seq = ighmm_list_to_array(state_list);
*path_length = state_list->length;
/* PRINT PATH */
/* fprintf(stderr, "Viterbi path: " ); */
/* int t; */
/* for(t=0; t < *path_length; t++) */
/* if (state_seq[t] >= 0) fprintf(stderr, " %d ", state_seq[t]); */
/* fprintf(stderr, "\n Freeing ... \n"); */
return (state_seq);
STOP: /* Label STOP from ARRAY_[CM]ALLOC */
/* Free the memory space */
pviterbi_free(&pv, mo->N, X->length, Y->length, mo->max_offset_x,
mo->max_offset_y);
m_free(state_seq);
ighmm_list_free(state_list);
return NULL;
#undef CUR_PROC
} /* viterbi */
/*============================================================================*/
static void init_phi(plocal_store_t * pv, ghmm_dpseq * X, ghmm_dpseq * Y) {
#ifdef DEBUG
int emission;
#endif
int u, v, j, i, off_x, y;
double log_in_a_ij;
double value, max_value, previous_prob, log_b_i;
/* printf("ghmm_dpmodel_viterbi init\n"); */
ghmm_dpmodel * mo = pv->mo;
double (*log_in_a)(plocal_store_t*, int, int, ghmm_dpseq*, ghmm_dpseq*,
int, int);
log_in_a = &sget_log_in_a;
/* 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;
}
if ( mo->model_type & GHMM_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
iteration start is u=-1 v=-1 to allow states with offset_x == 0
which corresponds to a series of gap states before reading the first
character of x at position x=0, y=v or equally for offset_y == 0 */
/* u, v <= max offsets */
for (u = -1; u <= mo->max_offset_x; u++) {
for (v = -mo->max_offset_y; v < Y->length; v++) {
for (j = 0; j < mo->N; j++)
{
/** initialization of phi (lookback matrix), psi (traceback) **/
set_phi(pv, u, v, j, +1);
set_psi(pv, u, v, j, -1);
}
/* for each state i */
for (i = 0; i < mo->N; i++) {
/* Determine the maximum */
/* max_phi = phi[i] + log_in_a[j][i] ... */
if (!(mo->model_type & GHMM_kSilentStates) || !mo->silent[i] ) {
max_value = -DBL_MAX;
set_psi(pv, u, v, i, -1);
for (j = 0; j < mo->s[i].in_states; j++) {
/* look back in the phi matrix at the offsets */
previous_prob = get_phi(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;
set_psi(pv, u, v, i, mo->s[i].in_id[j]);
}
}
else
{;} /* fprintf(stderr, " %d --> %d = %f, \n", i,i,v->log_in_a[i][i]); */
}
#ifdef DEBUG
emission = ghmm_dpmodel_pair(ghmm_dpseq_get_char(X, mo->s[i].alphabet, u),
ghmm_dpseq_get_char(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 > ghmm_dpmodel_emission_table_size(mo, i)){
printf("State %i\n", i);
ghmm_dpmodel_state_print(&(mo->s[i]));
printf("charX: %i charY: %i alphabet size: %i emission table: %i emission index: %i\n",
ghmm_dpseq_get_char(X, mo->s[i].alphabet, u),
ghmm_dpseq_get_char(Y, mo->s[i].alphabet, v),
mo->size_of_alphabet[mo->s[i].alphabet],
ghmm_dpmodel_emission_table_size(mo, i), emission);
}
#endif
log_b_i = log_b(pv, i, ghmm_dpmodel_pair(ghmm_dpseq_get_char(X, mo->s[i].alphabet, u),
ghmm_dpseq_get_char(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(pv, u, v, i, +1);
}
else {
if (max_value == -DBL_MAX)
set_phi(pv, u, v, i, +1);
else
set_phi(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 == v) { */
if (mo->s[i].log_pi != 1 && mo->s[i].offset_x - 1 == u &&
mo->s[i].offset_y - 1 == v) {
set_phi(pv, u, v, i, mo->s[i].log_pi);
#ifdef DEBUG
printf("Initial log prob state %i at (%i, %i) = %f\n", i, u, v, get_phi(pv, u, v, 0, 0, i));
printf("Characters emitted X: %i, Y: %i\n",
ghmm_dpseq_get_char(X, mo->s[i].alphabet, u),
ghmm_dpseq_get_char(Y, mo->s[i].alphabet, v));
#endif
}
if (get_phi(pv, u, v, 0, 0, i) != 1)
set_phi(pv, u, v, i, get_phi(pv, u, v, 0, 0, i) + log_b_i);
}
}
/* if (v == 0) {
printf"(%i, %i, %i) preceding %i\n", u, v, i, pv->psi[u][v][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(pv, Y->length);
} /* End for u in X */
}
