void Matcher::handle_token(Token& token)
{
if (LOG_WOULD_LOG(debug)) {
char utf8token[1024];
Fast_UnicodeUtil::utf8ncopy(utf8token, token.token, 1024,
(token.token != NULL ? token.curlen : 0));
LOG(debug, "handle_token(%s)", utf8token);
}
unsigned options = 0;
if (_mo->Match(_match_iter, token, options)) {
// Found a match. Record it with original pos and length
add_occurrence(token.bytepos, token.wordpos, token.bytelen);
}
// Keep track of end of the text
_endpos = token.bytepos + token.bytelen;
}
/***********************************************************************
* Record one motif occurrence.
***********************************************************************/
static void record_occurrence(
char* sequence_id,
char* motif_id,
double p_threshold,
double motif_p,
char* prev_motif,
int* prev_position,
int motif_position,
MATRIX_T* transp_freq,
MATRIX_T* spacer_ave,
ORDER_T* new_order,
int num_motifs,
MOTIF_T* motifs
) {
int prev_motif_location;
int motif_location;
/* Always include transitions to the end state. */
if (strcmp(motif_id, END_TRANSITION) == 0) {
}
/* Check to see if this motif was not given. */
else if (!have_motif(motif_id, num_motifs, motifs)) {
if (verbosity > NORMAL_VERBOSE) {
fprintf(stderr, "Skipping motif %s in sequence %s.\n", motif_id,
sequence_id);
}
return;
}
/* Check to see if the threshold was exceeded. */
else if ((p_threshold > 0.0) && (motif_p > p_threshold)) {
if (verbosity > NORMAL_VERBOSE) {
fprintf(stderr, "Skipping motif %s in sequence %s (%g > %g).\n",
motif_id, sequence_id, motif_p, p_threshold);
}
return;
}
if (verbosity > NORMAL_VERBOSE) {
if (strcmp(motif_id, END_TRANSITION) == 0) {
fprintf(stderr, "Adding transition to end in sequence %s.\n",
sequence_id);
} else {
fprintf(stderr, "Adding motif %s in sequence %s.\n", motif_id,
sequence_id);
}
}
// If we're at the end, store in the last column of the matrix.
if (strcmp(motif_id, END_TRANSITION) == 0) {
motif_location = num_motifs + 1;
} else {
// It's somewhat tricky to figure out where this motif goes in the matrix.
motif_location = find_matrix_location(motifs, motif_id, num_motifs);
}
prev_motif_location = find_matrix_location(motifs, prev_motif, num_motifs);
// Increment the transition count and spacer length matrices.
incr_matrix_cell(prev_motif_location, motif_location, 1, transp_freq);
incr_matrix_cell(prev_motif_location, motif_location,
motif_position - *prev_position, spacer_ave);
// Add the occurrence to the order list.
add_occurrence(motif_id, motif_position - *prev_position, new_order);
strcpy(prev_motif, motif_id);
}
