void print_lav_match
(FILE* f,
seq* seq1,
unspos pos1,
seq* seq2,
unspos pos2,
unspos length,
score s)
{
seqpartition* sp1 = &seq1->partition;
seqpartition* sp2 = &seq2->partition;
unspos end1 = pos1 + length;
unspos end2 = pos2 + length;
int pctId;
if ((sp1->p != NULL) || (sp2->p != NULL))
suicide ("lav format can't handle multi-sequences");
// compute percent identity
pctId = percent_identical (seq1, pos1, seq2, pos2, length);
// print it
fprintf (f, "a {\n");
fprintf (f, " s " scoreFmtSimple "\n", s);
fprintf (f, " b " unsposFmt " " unsposFmt "\n",
pos1+1, pos2+1);
fprintf (f, " e " unsposFmt " " unsposFmt "\n",
end1, end2);
fprintf (f, " l " unsposFmt " " unsposFmt
" " unsposFmt " " unsposFmt " %d\n",
pos1+1, pos2+1, end1, end2, pctId);
fprintf (f, "}\n");
}
static void print_match_composition
(FILE* f,
seq* seq1,
unspos pos1,
seq* seq2,
unspos pos2,
unspos length,
score s,
seed* hitSeed,
u32 step)
{
int pctId;
unspos count[4][4];
float p;
char pstr[6];
int ix, iy;
// compute percent identity, match compostion, and discovery probability
pctId = percent_identical (seq1, pos1, seq2, pos2, length);
match_composition (seq1, pos1, seq2, pos2, length, count);
p = discovery_probability (seq1, pos1+length, seq2, pos2+length, length,
hitSeed, step);
// convert discovery probability to a string
if (p < 0.0) p = 0.0;
else if (p > 1.0) p = 1.0;
snprintf (pstr, sizeof(pstr), "%.3f", p);
if (pstr[0] == '1') // (1.000 -> 1.00)
pstr[4] = 0;
else // (0.XXX -> .XXX)
{
pstr[0] = pstr[1];
pstr[1] = pstr[2];
pstr[2] = pstr[3];
pstr[3] = pstr[4];
pstr[4] = 0;
}
// print it
fprintf (f, "%d " scoreFmtSimple " " unsposSlashSFmt " " unsposFmt " %s",
pctId, s,
pos1+1, ((seq1->revCompFlags & rcf_rev) != 0)? "-" : "+",
pos2+1, ((seq2->revCompFlags & rcf_rev) != 0)? "-" : "+",
length, pstr);
for (ix=0 ; ix<4 ; ix++)
for (iy=0 ; iy<4 ; iy++)
fprintf (f, " " unsposFmt, count[ix][iy]);
fprintf (f, "\n");
}
