Description:

Print lists of predicted signals (motif, score, position) using the selected output format. There are some parts of the list which will be not output to avoid printing twice the same signal (overlapping of fragments implies repeated computing). Before printing, signal limits are modified to display the positions of the core (AG, GT, ATG or TGA|TAG|TAA) as pos1 and pos2. Motifs are always printed using the correct reading sense (+ or -) as positive.

Briefing:

void PrintSite(site* s, int type, char Name[], int Strand, char* seq, profile* p)

Processing information about a signal to print its motif but anchored at the core (ATG, AG, GT or TGA|TAA|TAG) by computing the values k and offset (see profiles), and taking into account the COFFSET: everything according to the signal type and format (gff/geneid). Output motif, score and position of the input site.

void PrintSites (site* s, long ns, int type, char Name[], int Strand, long l1, long l2, char* seq, profile *p)

Print a list of sites, but only the signals between "i" and "printPoint" which are values depending on the type of the signals. This is to avoid print the same signal twice in two different fragments due to the overlapping.

Enrique Blanco Garcia © 2001