/*
* pops the top state off the stack
*/
static JSON_EN pop_state(LINKLST_T* stack) {
JSON_EN *allocated_state, state;
if (!linklst_size(stack)) return JSON_ERROR;
allocated_state = linklst_pop(stack);
state = *allocated_state;
free(allocated_state);
return state;
}
/**************************************************************************
* Outputs txt for the spacings
**************************************************************************/
void output_secondary_motif_txt(FILE *txt_output,
MOTIF_DB_T *primary_db, MOTIF_T *primary_motif,
SECONDARY_MOTIF_T *parent, SECONDARY_MOTIF_T *smotif,
int n_secondary_motifs, LINKLST_T *rmotifs) {
LINK_T *node;
SIGSPACE_T sig;
int i, quad;
char* orient_names[NORIENTS];
// this maintains the previous definition of orientation but actual names would be better
orient_names[LEFT | SAME] = "0";
orient_names[LEFT | OPPO] = "1";
orient_names[RIGHT | SAME] = "2";
orient_names[RIGHT | OPPO] = "3";
orient_names[UP_SEC_PAL] = "4";
orient_names[UP_PRI_PAL] = "5";
orient_names[DOWN_PRI_PAL] = "6";
orient_names[DOWN_SEC_PAL] = "7";
orient_names[BOTH_PAL] = "8";
for (i = 0; i < smotif->sig_count; ++i) {
sig = smotif->sigs[i];
// Output txt line.
fprintf(txt_output, "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\t%.2e\t%d\t%s\t%d\t%d\t%.2e\t%.2e\n",
primary_db->name,
get_motif_id(primary_motif),
strcmp(get_motif_id2(primary_motif), "") ? get_motif_id2(primary_motif) : ".",
get_motif_consensus(primary_motif),
smotif->db->name,
get_motif_id(smotif->motif),
strcmp(get_motif_id2(smotif->motif), "") ? get_motif_id2(smotif->motif) : ".",
get_motif_consensus(smotif->motif),
get_motif_trim_left(smotif->motif),
get_motif_trim_right(smotif->motif),
parent ? smotif->db->name : ".",
parent ? get_motif_id(parent->motif) : ".",
parent && strcmp(get_motif_id2(parent->motif), "") ? get_motif_id2(parent->motif) : ".",
smotif->min_pvalue * n_secondary_motifs, // E-value
sig.bin, // gap
orient_names[sig.orient], // orientation
smotif->spacings[sig.orient].count[sig.bin], // count
smotif->total_spacings, // total occurrences of secondary in margins
sig.pvalue < 1e-10 ? sig.pvalue/NORIENTS : 1-pow((1-sig.pvalue),1.0/NORIENTS),
sig.pvalue
);
}
if (rmotifs != NULL && linklst_size(rmotifs) > 0) {
for (node = linklst_first(rmotifs); node != NULL; node = linklst_next(node)) {
SECONDARY_MOTIF_T *rmotif = linklst_get(node);
output_secondary_motif_txt(txt_output, primary_db, primary_motif, smotif, rmotif, n_secondary_motifs, NULL);
}
}
}
short dxml_has_error(void *data) {
DXML_T *parser;
parser = (DXML_T*)data;
return linklst_size(parser->data->errors) > 0;
}
short dxml_has_motif(void *data) {
DXML_T *parser;
parser = (DXML_T*)data;
return linklst_size(parser->data->motif_queue) > 0;
}
/*****************************************************************************
* Check if the parser has found a problem with the file that has not already
* been returned.
****************************************************************************/
short mxml_has_warning(void *data) {
MXML_T *parser;
parser = (MXML_T*)data;
return linklst_size(parser->data->warnings) > 0;
}
