unsigned vertex(double* x, double* y)
{
if (tolerance_ == 0.0)
return geom_.vertex(x, y);
if (status_ == initial)
init_vertices();
return output_vertex(x, y);
}
unsigned vertex(double * x, double * y)
{
if (offset_ == 0.0)
{
return geom_.vertex(x, y);
}
if (status_ == initial)
{
init_vertices();
}
if (pos_ >= vertices_.size())
{
return SEG_END;
}
pre_ = (pos_ ? cur_ : pre_first_);
cur_ = vertices_.at(pos_++);
if (pos_ == vertices_.size())
{
return output_vertex(x, y);
}
double const check_dist = offset_ * threshold_;
double const check_dist2 = check_dist * check_dist;
double t = 1.0;
double vt, ut;
for (size_t i = pos_; i+1 < vertices_.size(); ++i)
{
//break; // uncomment this to see all the curls
vertex2d const& u0 = vertices_[i];
vertex2d const& u1 = vertices_[i+1];
double const dx = u0.x - cur_.x;
double const dy = u0.y - cur_.y;
if (dx*dx + dy*dy > check_dist2)
{
break;
}
if (!intersection(pre_, cur_, &vt, u0, u1, &ut))
{
continue;
}
if (vt < 0.0 || vt > t || ut < 0.0 || ut > 1.0)
{
continue;
}
t = vt;
pos_ = i+1;
}
cur_.x = pre_.x + t * (cur_.x - pre_.x);
cur_.y = pre_.y + t * (cur_.y - pre_.y);
return output_vertex(x, y);
}
int call_pregraph ( int argc, char ** argv )
{
time_t start_t, stop_t, time_bef, time_aft;
time ( &start_t );
initenv ( argc, argv );
if ( overlaplen % 2 == 0 )
{
overlaplen++;
printf ( "K should be an odd number\n" );
}
if ( overlaplen < 13 )
{
overlaplen = 13;
printf ( "K should not be less than 13\n" );
}
else if ( overlaplen > 31 )
{
overlaplen = 31;
printf ( "K should not be greater than 31\n" );
}
time ( &time_bef );
prlRead2HashTable ( shortrdsfile, graphfile );
time ( &time_aft );
printf ( "time spent on pre-graph construction: %ds\n\n", ( int ) ( time_aft - time_bef ) );
printf ( "deLowKmer %d, deLowEdge %d\n", deLowKmer, deLowEdge );
//analyzeTips(hash_table, graphfile);
if ( !deLowKmer && cutTips )
{
time ( &time_bef );
removeSingleTips();
removeMinorTips();
time ( &time_aft );
printf ( "time spent on cutTipe: %ds\n\n", ( int ) ( time_aft - time_bef ) );
}
else
{
time ( &time_bef );
removeMinorTips();
time ( &time_aft );
printf ( "time spent on cutTipe: %ds\n\n", ( int ) ( time_aft - time_bef ) );
}
initKmerSetSize = 0;
//combine each linear part to an edge
time ( &time_bef );
kmer2edges ( graphfile );
time ( &time_aft );
printf ( "time spent on making edges: %ds\n\n", ( int ) ( time_aft - time_bef ) );
//map read to edge one by one
time ( &time_bef );
prlRead2edge ( shortrdsfile, graphfile );
time ( &time_aft );
printf ( "time spent on mapping reads: %ds\n\n", ( int ) ( time_aft - time_bef ) );
output_vertex ( graphfile );
free_Sets ( KmerSets, thrd_num );
free_Sets ( KmerSetsPatch, thrd_num );
time ( &stop_t );
printf ( "overall time for lightgraph: %dm\n\n", ( int ) ( stop_t - start_t ) / 60 );
return 0;
}