point triangle::calc_center( triangle* t )
{
arma::vec Pa(3);
Pa(0) = (t->m_vertex_list[0].x);
Pa(1) = (t->m_vertex_list[0].y);
Pa(2) = 0;
arma::vec Pb(3);
Pb(0) = (t->m_vertex_list[1].x);
Pb(1) = (t->m_vertex_list[1].y);
Pb(2) = 0;
arma::vec Pc(3);
Pc(0) = (t->m_vertex_list[2].x);
Pc(1) = (t->m_vertex_list[2].y);
Pc(2) = 0;
arma::vec AB = Pb - Pa;
arma::vec AC = Pc - Pa;
arma::vec BC = Pc - Pb;
//circumcenter
// arma::vec N = arma::cross(AC,AB);
// arma::vec L1 = arma::cross(AB,N);
// arma::vec L2 = arma::cross(BC,N);
// arma::vec P21 = (Pc - Pa)/2;
// arma::vec P1 = (Pa + Pb)/2;
//incenter
arma::vec uab = AB / arma::norm(AB,1);
arma::vec uac = AC / arma::norm(AC,1);
arma::vec ubc = BC / arma::norm(BC,1);
arma::vec uba = -uab;
arma::vec L1 = uab + uac;
arma::vec L2 = uba + ubc;
arma::vec P21 = Pb-Pa;
arma::vec P1 = Pa;
arma::mat ML1(L1);
arma::mat ML2(L2);
arma::mat ML = arma::join_rows(ML1,-ML2);
arma::vec lambda = arma::solve(ML,P21);
arma::vec pos = P1+lambda(0)*L1;
point p;
p.x = pos(0);
p.y = pos(1);
return p;
}
this is unfinished crap
// The below is the main from writing unmatched regions
int
main(int argc, char *argv[]) {
FILE *Aoutput = 0L;
FILE *Boutput = 0L;
char *matchesFile = 0L;
int arg=1;
while (arg < argc) {
if (strcmp(argv[arg], "-a") == 0) {
errno = 0;
Aoutput = fopen(argv[++arg], "w");
if (errno)
fprintf(stderr, "Failed to open '%s': %s\n", argv[arg], strerror(errno)), exit(1);
} else if (strcmp(argv[arg], "-b") == 0) {
errno = 0;
Boutput = fopen(argv[++arg], "w");
if (errno)
fprintf(stderr, "Failed to open '%s': %s\n", argv[arg], strerror(errno)), exit(1);
} else if (strcmp(argv[arg], "-m") == 0) {
matchesFile = argv[++arg];
} else {
fprintf(stderr, "usage: %s -a Aunmatched.fasta -b B.unmatched.fasta < matches\n", argv[0]);
exit(1);
}
arg++;
}
if ((Aoutput == 0L) || (Boutput == 0L) || (matchesFile == 0L)) {
fprintf(stderr, "usage: %s -a Aunmatched.fasta -b B.unmatched.fasta < matches\n", argv[0]);
exit(1);
}
atacMatchList ML1(matchesFile, 'm', false);
atacMatchList ML2(matchesFile, 'm', false);
ML1.sort1(); // Sorted by first index
ML2.sort2(); // Sorted by second index
seqCache *W1 = ML1._seq1;
seqCache *W2 = ML1._seq2;
// For every match,
// find the match before and the match after, on both axes
//
// Extract unmapped in sequence 1
ML.sort1();
W = ML._seq1;
W->find(ML[0]->iid1);
S = W->getSequenceInCore();
for (uint32 i=1; i<ML.numMatches(); i++) {
atacMatch *l = ML[i-1];
atacMatch *r = ML[i];
if (l->iid1 != r->iid1)
continue;
if (l->iid1 != S->getIID()) {
delete S;
W->find(l->iid1);
S = W->getSequenceInCore();
}
// Extract from (l->pos1 + l->len1) to (r->pos1), if it's longer than 20bp
//
if (l->pos1 + l->len1 + 20 < r->pos1)
writeGaplessSequence(Aoutput,
S,
l->pos1 + l->len1,
r->pos1);
}
// Extract unmapped in sequence 2
ML.sort2();
W = ML._seq2;
W->find(ML[0]->iid2);
S = W->getSequenceInCore();
for (uint32 i=1; i<ML.numMatches(); i++) {
atacMatch *l = ML[i-1];
atacMatch *r = ML[i];
if (l->iid2 != r->iid2)
continue;
if (l->iid2 != S->getIID()) {
delete S;
W->find(l->iid2);
S = W->getSequenceInCore();
}
// Extract from (l->pos2 + l->len2) to (r->pos2), if it's longer than 20bp
//
if (l->pos2 + l->len2 + 20 < r->pos2)
writeGaplessSequence(Boutput,
S,
l->pos2 + l->len2,
r->pos2);
}
fclose(Aoutput);
fclose(Boutput);
return(0);
}